@article{fdcb6c23e34749f3a78f6db6f63e3359,
title = {Quantifying Synergistic Information Using Intermediate Stochastic Variables},
author = {Rick Quax and Omri Har-Shemesh and Peter M. A. Sloot},
year = {2017},
month = {2},
doi = {10.3390/e19020085},
volume = {19},
journal = {Entropy},
issn = {1099-4300},
number = {2},
eid = {85},
}
@article{Sloot2017a,
title={Big Nonsense: the end of scientific thinking is near' in 43 Visions for Complexity},
author={P.M.A. Sloot},
year={2017},
journal={Ed. S. Thurner, World Scientific Publishing Co. Pte. Ltd, ISBN 978-981-3206-84-7},
hash={390495691534335408222581000043928450588825580398728902260389482414996},
metis_id={542889},
refereed={Y}
}
@article{Traag2016a,
title={Modelling the distance impedance of protest attendance},
author={V.A. Traag and R. Quax and P.M.A. Sloot},
year={2016},
journal={Physica A: Statistical Mechanics and its Applications},
hash={117314568720361009731128747382088103842414945468662},
metis_id={544378},
url={http://dx.doi.org/10.1016/j.physa.2016.10.054},
refereed={Y}
}
@article{Simaitis2016a,
title={Smile and Default: The Role of Stochastic Volatility and Interest Rates in Counterparty Credit Risk},
author={S. Simaitis and C.S.L. de Graaf and N. Hari and B.D. Kandhai},
year={2016},
journal={Quantitative Finance},
hash={5225340641663152223764368684817468772553930016022301464528200731715013473377526226730435},
metis_id={528663},
url={http://dx.doi.org/http://authorservices.taylorandfrancis.com/wp-content/uploads/2015/07/guide-for-reusing-content.pdf},
refereed={Y}
}
@article{Yurkin2016a,
title={Corrigendum to “The discrete dipole approximation: An overview and recent developments” [J. Quant. Spectrosc. Radiat. Transfer 106 (2007) 558–589]},
author={M.A. Yurkin and A.G. Hoekstra},
year={2016},
journal={Journal of Quantitative Spectroscopy & Radiative Transfer},
hash={5535916730329388468888309251612766947500784552279288770937122989377440092774694749901811594902498735336563190437092596},
metis_id={542944},
url={http://dx.doi.org/10.1016/j.jqsrt.2015.11.025},
refereed={Y}
}
@article{Har_Shemesh2016a,
title={Information geometric analysis of phase transitions in complex patterns: the case of the Gray-Scott reaction-diffusion model},
author={O. Har Shemesh and R. Quax and A.G. Hoekstra and P.M.A. Sloot},
year={2016},
journal={Journal of Statistical Mechanics : Theory and Experiment},
hash={204957554073484776659349149024127734265500703766328175248771241500291249411241041570128670352737447943110453545},
metis_id={513622},
url={http://arxiv.org/abs/1512.02077},
refereed={Y}
}
@article{Mountrakis2016a,
title={Scaling of shear-induced diffusion and clustering in a blood-like suspension},
author={L. Mountrakis and E. Lorenz and A.G. Hoekstra},
year={2016},
journal={Europhysics Letters},
hash={81092668859570052111511895791893130805329329533541459772049525585952},
metis_id={542946},
url={http://dx.doi.org/10.1209/0295-5075/114/14002},
refereed={Y}
}
@article{Graaf2016a,
title={Efficient Estimation of Sensitivities for Counterparty Credit Risk with the Finite Difference Monte-Carlo Method},
author={C.S.L. de Graaf and B.D. Kandhai and P.M.A. Sloot},
year={2016},
journal={Journal of Computational Finance},
hash={466125079194035774145058442795169305873894372234087938702618922457527357500850751042406170742346990317},
metis_id={528662},
refereed={Y}
}
@article{Donald_Combs2016a,
title={Systems Biology and Health Systems Complexity in;},
author={C. Donald Combs and S.R. Barham and P.M.A. Sloot},
year={2016},
journal={The Digital Patient: Advancing Healthcare, Research, and Education},
hash={101289003781804251046989406312206025639971381},
metis_id={539232},
url={http://dx.doi.org/10.1002/9781118952788.ch7}
}
@Misc{Mizeranschi2016a,
title={Anatomy and Physiology of Multiscale Modeling and Simulation in Systems Medicine},
author={A. Mizeranschi and D.J. Groen and J. Borgdorff and A.G. Hoekstra and B. Chopard and W. Dubitzky},
year={2016},
hash={859486999399737028636160900624577215582010290902113149771564069163709741},
metis_id={512064},
publisher={Springer},
issn_isbn={},
url={http://dx.doi.org/10.1007/978-1-4939-3283-2_17},
refereed={Y}
}
@article{Har-Shemesh2016a,
title={Nonparametric estimation of Fisher information from real data},
author={O. Har-Shemesh and R. Quax and Borja Miñano and A.G. Hoekstra and P.M.A. Sloot},
year={2016},
journal={Physical Review E},
hash={224863838033729750844643595522438789824923100008308731142},
metis_id={513618},
url={http://dx.doi.org/http://dx.doi.org/10.1103/PhysRevE.93.023301},
refereed={Y}
}
@phdthesis{Javaheri2016a,
title={Biosilicification mechanisms: An investigation using computational modeling and experimentation},
author={N. Javaheri},
year={2016},
tutor={Promotor:prof.dr. P.M.A. Sloot, Co-promotor:dr. J.A. Kaandorp},
hash={61265755689957592540223812900704660321448807091645129437352583946451774768613624408489117},
metis_id={527001},
issn_isbn={978-94-028-0112-5}
}
@phdthesis{Botman2016a,
title={Spatial gene expression quantification in changing morphologies},
author={D. Botman},
year={2016},
tutor={Promotor:prof.dr. P.M.A. Sloot, Co-promotor:dr. J.A. Kaandorp},
hash={403004342665690987775355349754286475208253147744103281183163},
metis_id={533847},
issn_isbn={}
}
@inproceedings{Koziel2015a,
title={Computational Science at the Gates of Nature, preface for ICCS 2015},
author={S. Koziel and L. Leifsson and M. Lees and V.V. Krzhizhanovskaya and J. Dongarra and P.M.A. Sloot},
year={2015},
journal={Procedia Computer Science},
hash={1049381934847018051612398221161519319042958244705120050907},
metis_id={478297},
publisher={Elsevier},
issn_isbn={},
url={http://dx.doi.org/10.1016/j.procs.2015.05.177},
refereed={Y},
booktitle={International Conference On Computational Science, ICCS 2015: Computational Science at the Gates of Nature}
}
@article{Litescu2015a,
title={Information impact on transportation systems},
author={S. Litescu and V. Viswanathan and M.H. Lees and A. Knoll and H. Aydt},
year={2015},
journal={Journal of Computational Science},
hash={379967725529971484210207241767917604206395},
metis_id={487254},
url={http://dx.doi.org/http://dx.doi.org/10.1016/j.jocs.2015.04.019},
refereed={Y}
}
@article{Merelli2015a,
title={Topological Characterization of Complex Systems: Using Persistent Entropy},
author={E. Merelli and M. Rucco and P.M.A. Sloot and L. Tesei},
year={2015},
journal={Entropy},
hash={90977387017466239331214677516502386744474482450137721813088562278678},
metis_id={495884},
url={http://dx.doi.org/10.3390/e17106872},
refereed={Y}
}
@Misc{Jansson2015a,
title={Kilombo: a Kilobot simulator to enable effective research in swarm robotics},
author={F.R. Jansson and M. Hartley and M. Hinsch and I. Slavkov and N. Carranza and T.S.G Olsson and R.M. Dries and J. H. Grönqvist and A.F.M Marée and J Sharpe and J.A. Kaandorp and V. A. Grieneisen},
year={2015},
hash={4388831772011072831927705221672367484756744815318686044106745399556},
metis_id={494101},
publisher={Arxiv},
issn_isbn={},
url={http://arxiv.org/abs/1511.04285}
}
@phdthesis{Mountrakis2015b,
title={Transport of blood cells studied with fully resolved models},
author={L. Mountrakis},
year={2015},
tutor={Promotores:prof.dr. P.M.A. Sloot, prof.dr.ir. A.G. Hoekstra},
hash={241315129716132049319093901765007160459375552443432956},
metis_id={485135},
issn_isbn={978-94-6259-775-4}
}
@article{Mei2015a,
title={Complex agent networks: An emerging approach for modeling complex systems},
author={S. Mei and N. Zarrabi and M.H. Lees and P.M.A. Sloot},
year={2015},
journal={Applied Soft Computing},
hash={124672785798374668215417459705742135385239476330435301918746445134},
metis_id={487252},
url={http://dx.doi.org/10.1016/j.asoc.2015.08.010},
refereed={Y}
}
@inproceedings{Melnikov2015a,
title={Data-driven modeling of transportation systems and traffic data analysis during a major power outage in the Netherlands},
author={V.R. Melnikov and V.V. Krzhizhanovskaya and A.V. Boukhanovsky and P.M.A. Sloot},
year={2015},
journal={Procedia Computer Science},
hash={4786109964230215418584441852108604144910111171352224407201242866338704692712966526633188672403490119435047},
metis_id={487077},
publisher={Elsevier},
issn_isbn={},
url={http://dx.doi.org/10.1016/j.procs.2015.11.039},
refereed={Y},
booktitle={4th International Young Scientist Conference on Computational Science}
}
@article{Krishna2015a,
title={SIM-CITY: An e-Science Framework for Urban Assisted Decision Support},
author={H. Krishna and J. Borgdorff and M.H. Lees},
year={2015},
journal={Procedia Computer Science},
hash={391569646260851538753840381043512014955384125069817129676013},
metis_id={487257},
publisher={Elsevier},
issn_isbn={},
url={http://dx.doi.org/10.1016/j.procs.2015.05.399},
refereed={Y}
}
@article{Duijn2015a,
title={From Data to Disruption},
author={P.A.C. Duijn and P.M.A. Sloot},
year={2015},
journal={Digital Investigation},
hash={407954895198051379818},
metis_id={495883},
url={http://dx.doi.org/10.1016/j.diin.2015.09.005},
refereed={Y}
}
@article{Yurkin2015a,
title={Convergence of the discrete dipole approximation. I. Theoretical analysis: erratum},
author={M.A. Yurkin and V.P. Maltsev and A.G. Hoekstra},
year={2015},
journal={Journal of the Optical Society of America. A, Optics and Image Science},
hash={2438397802294490068168607245665861666717271388824226029504926161071727721},
metis_id={512028},
url={http://dx.doi.org/10.1364/JOSAA.32.002407},
refereed={Y}
}
@article{Mountrakis2015a,
title={Parallel performance of an IB-LBM suspension simulation framework},
author={L. Mountrakis and E. Lorenz and O. Malaspinas and S. Alowayyed and B. Chopard and A.G. Hoekstra},
year={2015},
journal={Journal of Computational Science},
hash={314886513540429343448412722477478080262706808261465528505292},
metis_id={477879},
url={http://dx.doi.org/10.1016/j.jocs.2015.04.006},
refereed={Y}
}
@inproceedings{Xu2015b,
title={How to Speed up Optimization? Opposite-Center Learning and Its Application to Differential Evolution},
author={H. Xu and C.D. Erdbrink and V.V. Krzhizhanovskaya},
year={2015},
journal={Procedia Computer Science},
hash={279419282615038448263559615483350590281750171086203238693500331926564660835160626071471588},
metis_id={478300},
publisher={Elsevier},
issn_isbn={},
url={http://dx.doi.org/10.1016/j.procs.2015.05.203},
refereed={Y},
booktitle={International Conference On Computational Science, ICCS 2015: Computational Science at the Gates of Nature}
}
@article{Melnikova2015b,
title={Numerical prediction of the IJkDijk trial embankment failure},
author={N. Melnikova and D. Jordan and V. Krzhizhanovskaya and P. Sloot},
year={2015},
journal={Proceedings of the Institution of Civil Engineers. Geotechnical Engineering},
hash={21195039240503822269972034387973469884289313151514468194},
metis_id={407880},
url={http://dx.doi.org/10.1680/geng.14.00040},
refereed={Y}
}
@article{Maslov2015a,
title={Quantum chemistry calculation of the electronic spectrum of graphene nanoribbons: emergence of abnormally high oscillator strength},
author={V.G. Maslov and A.I. Svitenkov and V.V. Krzhizhanovskaya},
year={2015},
journal={Nanoscale Research Letters},
hash={84822214938082224879004119675922617749398320599037173376556043581609242194255406960117600852931937166910800826355873551},
metis_id={487078},
url={http://link.springer.com/journal/11671},
refereed={Y}
}
@inproceedings{Svitenkov2015a,
title={Fluid Simulations with Atomistic Resolution: Multiscale Model with Account of Nonlocal Momentum Transfer},
author={A.I. Svitenkov and S.A. Chivilikin and A.G. Hoekstra and A.V. Boukhanovsky},
year={2015},
journal={Procedia Computer Science},
hash={32789965506253659289326686311120486702005161289528192233750736597244250568833612484835158190173},
metis_id={512020},
publisher={Elsevier},
issn_isbn={},
url={http://dx.doi.org/10.1016/j.procs.2015.05.279},
refereed={Y},
booktitle={International Conference On Computational Science, ICCS 2015: Computational Science at the Gates of Nature}
}
@inproceedings{Krzhizhanovskaya2015a,
title={Multiscale Modelling and Simulation Workshop: 12 Years of Inspiration},
author={V.V. Krzhizhanovskaya and D. Groen and B. Bosak and A.G. Hoekstra},
year={2015},
journal={Procedia Computer Science},
hash={156078806769698878511773278435878639131375654239065788599824441},
metis_id={478299},
publisher={Elsevier},
issn_isbn={},
url={http://dx.doi.org/10.1016/j.procs.2015.05.268},
refereed={Y},
booktitle={International Conference On Computational Science, ICCS 2015: Computational Science at the Gates of Nature}
}
@article{Krzhizhanovskaya2015b,
title={Russian-Dutch double-degree Master’s programme in computational science in the age of global education},
author={V.V. Krzhizhanovskaya and A.V. Dukhanov and A. Bilyatdinova and A.V. Boukhanovsky and P.M.A. Sloot},
year={2015},
journal={Journal of Computational Science},
hash={6887957618810618159268250458079032942562908767374255782459753524438491387764507845393097166},
metis_id={487075},
url={http://dx.doi.org/10.1016/j.jocs.2015.05.001},
refereed={Y}
}
@article{Hoekstra2015a,
title={On the Possible Interaction Mechanism between Collateral Vessels and Restenosis},
author={A.G. Hoekstra and Z. Zun},
year={2015},
journal={Procedia Computer Science},
hash={11016594871710729616438738936137130622724173125808489900962141490088081658},
metis_id={512039},
publisher={Elsevier},
issn_isbn={},
url={http://dx.doi.org/10.1016/j.procs.2015.11.047},
refereed={Y}
}
@article{Tahir2015a,
title={An in silico study on the role of smooth muscle cell migration in neointimal formation after coronary stenting},
author={H. Tahir and I. Niculescu and C. Bona-Casas and R.M.H. Merks and A.G. Hoekstra},
year={2015},
journal={Journal of the Royal Society Interface},
hash={809372008110810363797534021601611354005979629393963627779463139368125044285687382245218203411578},
metis_id={478181},
url={http://dx.doi.org/10.1098/rsif.2015.0358},
refereed={Y}
}
@inproceedings{Xu2015a,
title={An Asynchronous Synchronization Strategy for Parallel Large-scale Agent-based Traffic Simulations},
author={Y. Xu and W. Cai and H. Aydt and M.H. Lees and D. Zehe},
year={2015},
hash={39490749981382996426957498840988659680070895071959699737974865054701745970781374090937678},
metis_id={487255},
publisher={ACM},
issn_isbn={978-1-4503-3583-6},
url={http://dx.doi.org/10.1145/2769458.2769461},
refereed={Y},
booktitle={Proceedings of the 3rd ACM Conference on SIGSIM-Principles of Advanced Discrete Simulation}
}
@article{Melnikova2015a,
title={Experience of using FEM for real-time flood early warning systems: Monitoring and modeling Boston levee instability},
author={N.B. Melnikova and D. Jordan and V.V. Krzhizhanovskaya},
year={2015},
journal={Journal of Computational Science},
hash={643898855372016064760210026718845739707090128710919734483052490340140172777834147631557397265120633938},
metis_id={487074},
url={http://dx.doi.org/10.1016/j.jocs.2015.04.033},
refereed={Y}
}
@article{Abramson2015a,
title={Perspectives of the International Conference of Computational Science 2014},
author={D. Abramson and V.V. Krzhizhanovskaya and M. Lees},
year={2015},
journal={Journal of Computational Science},
hash={124796239698141340133960159425572310817482290493349569592598865743345},
metis_id={487076},
url={http://dx.doi.org/10.1016/j.jocs.2015.08.007},
refereed={Y}
}
@article{Erdbrink2015a,
title={Differential evolution for system identification of self-excited vibrations},
author={C.D. Erdbrink and V.V. Krzhizhanovskaya},
year={2015},
journal={Journal of Computational Science},
hash={2035041812066680440771764931647127368866955323386968510306385554154365},
metis_id={487073},
url={http://dx.doi.org/10.1016/j.jocs.2015.03.004},
refereed={Y}
}
@article{Konakov2015a,
title={A mathematical model and simulation results of plasma enhanced chemical vapor deposition of silicon nitride films},
author={S.A. Konakov and V.V. Krzhizhanovskaya},
year={2015},
journal={Journal of Physics. Conference Series},
hash={114478878922666878426712584037177477180369342286160738169927792456362020909883274264193342419547811733},
metis_id={437684},
url={http://dx.doi.org/10.1088/1742-6596/574/1/012144},
refereed={Y}
}
@article{Mei2015b,
title={Simulating city-level airborne infectious diseases},
author={S. Mei and B. Chen and Y. Zhu and M.H. Lees and A.V. Boukhanovsky and P.M.A. Sloot},
year={2015},
journal={Computers, Environment and Urban Systems},
hash={124856329951407736319168565103453629792562507697},
metis_id={444241},
url={http://dx.doi.org/10.1016/j.compenvurbsys.2014.12.002},
refereed={Y}
}
@article{Zhong2015a,
title={Density-based evolutionary framework for crowd model calibration},
author={J. Zhong and N. Hu and W. Cai and M. Lees and L. Luo},
year={2015},
journal={Journal of Computational Science},
hash={72481562910658914065795642928268965581941459963139691646862},
metis_id={443504},
url={http://dx.doi.org/10.1016/j.jocs.2014.09.002},
refereed={Y}
}
@article{Viswanathan2015a,
title={The influence of memory on indoor environment exploration: A numerical study},
author={V. Viswanathan and M. Lees and P.M.A. Sloot},
year={2015},
journal={Behavior Research Methods},
hash={87715545965047442762619129485944213686238159711452503600598101320155},
metis_id={487253},
url={http://dx.doi.org/10.3758/s13428-015-0604-1},
refereed={Y}
}
@inproceedings{Pyayt2015a,
title={Combining Data-driven Methods with Finite Element Analysis for Flood Early Warning Systems},
author={A.L. Pyayt and D.V. Shevchenko and A.P. Kozionov and I.I. Mokhov and B. Lang and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year={2015},
journal={Procedia Computer Science},
hash={519146255514933375413413595662853315348092701133149922534394961805176788947663495},
metis_id={478298},
publisher={Elsevier},
issn_isbn={},
url={http://dx.doi.org/10.1016/j.procs.2015.05.404},
refereed={Y},
booktitle={International Conference On Computational Science, ICCS 2015: Computational Science at the Gates of Nature}
}
@article{Wagner2015a,
title={Evolving agent-based models using self-adaptive complexification},
author={M. Wagner and W. Cai and M.H. Lees and H. Aydt},
year={2015},
journal={Journal of Computational Science},
hash={125497542945516286186851281689121887551752835104155021407669},
metis_id={487256},
url={http://dx.doi.org/http://dx.doi.org/10.1016/j.jocs.2015.03.005},
refereed={Y}
}
@article{Konakov2015b,
title={Modeling chemical vapor deposition of silicon dioxide in microreactors at atmospheric pressure},
author={S.A. Konakov and V.V. Krzhizhanovskaya},
year={2015},
journal={Journal of Physics. Conference Series},
hash={329682124644358248456458164061627807832032156373884890560754863343542801793578203765329},
metis_id={437683},
url={http://dx.doi.org/10.1088/1742-6596/574/1/012145},
refereed={Y}
}
@article{1742-5468-2014-12-P12020,
title = {Topology dependent epidemic spreading velocity in weighted networks},
author = {Wei Duan and Rick Quax and Michael Lees and Xiaogang Qiu and Peter M A Sloot},
year = {2014},
journal = {Journal of Statistical Mechanics: Theory and Experiment},
volume = {2014},
number = {12},
pages = {P12020},
url = {http://stacks.iop.org/1742-5468/2014/i=12/a=P12020},
abstract = {Many diffusive processes occur on structured networks with weighted links, such as disease spread by airplane transport or information diffusion in social networks or blogs. Understanding the impact of weight-connectivity correlations on epidemic spreading in weighted networks is crucial to support decision-making on disease control and other diffusive processes. However, a real understanding of epidemic spreading velocity in weighted networks is still lacking. Here we conduct a numerical study of the velocity of a ReedFrost epidemic spreading process in various weighted network topologies as a function of the correlations between edge weights and node degrees. We find that a positive weight-connectivity correlation leads to a faster epidemic spreading compared to an unweighted network. In contrast, we find that both uncorrelated and negatively correlated weight distributions lead to slower spreading processes. In the case of positive weight-connectivity correlations, the acceleration of spreading velocity is weak when the heterogeneity of weight distribution increases.}
}
@proceedings{Abramson2014a,
title = {Proceedings of the International Conference on Computational Science, ICCS 2014},
author = {D. Abramson and M.H. Lees and V.V. Krzhizhanovskaya and J.J. Dongarra and P.M.A. Sloot},
year = {2014},
journal = {Procedia Computer Science},
volume = {29},
url = {http://www.sciencedirect.com/science/journal/18770509/29},
numpages = {2520},
issn_isbn = {ISSN 1877-0509}
}
@article{Abramson2014b,
title = {Big Data Meets Computational Science, Preface for ICCS 2014},
author = {D. Abramson and M.H. Lees and V.V. Krzhizhanovskaya and J.J. Dongarra and P.M.A. Sloot},
year = {2014},
journal = {Procedia Computer Science},
volume = {29},
pages = {1 - 7},
url = {http://www.sciencedirect.com/science/article/pii/S187705091400177X},
note = {2014 International Conference on Computational Science},
doi = {10.1016/j.procs.2014.04.002},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2014},
issn_isbn = {ISSN 1877-0509}
}
@article{Amartruda2014a,
title = {From histology and imaging data to models for in-stent restenosis},
author = {C.M. Amartruda and C. Bona-Casas and B. Keller and H. Tahir and G. Dubini and A.G. Hoekstra and D.R. Hose and P.V. Lawford and F. Migliavacca and A. Narracott and J. Gunn},
year = {2014},
journal = {The international journal of artificial organs},
metis_id = {404396},
note = {submitted}
}
@phdthesis{Borgdorff2014a,
title = {Distributed multiscale computing},
author = {J. Borgdorff},
year = {2014},
url = {http://dare.uva.nl/en/record/480406},
month = {July},
numpages = {173},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, co-promotor: Dr. A.G. Hoekstra},
issn_isbn = {ISBN 9789462592353}
}
@article{Bui2014a,
title = {A novel feature-based approach to extract drug-drug interactions from biomedical text},
author = {Q.-C. Bui and P.M.A. Sloot and E.M. van Mulligen and J.A. Kors},
year = {2014},
journal = {Bioinformatics},
metis_id = {430448},
url = {http://bioinformatics.oxfordjournals.org/content/early/2014/08/19/bioinformatics.btu557.abstract},
doi = {10.1093/bioinformatics/btu557}
}
@article{Cheong2014a,
title = {Short-Term Forecasting of Taiwanese Earthquakes Using a Universal Model of Fusion-Fission Processes},
author = {S.A. Cheong and T.L. Tan and C.-C. Chen and W.-L. Chang and Z. Liu and L.Y. Chew and P.M.A. Sloot and N.F. Johnson},
year = {2014},
journal = {Sci. Rep.},
volume = {4},
pages = {3624},
metis_id = {404180},
url = {http://www.nature.com/srep/2014/140110/srep03624/full/srep03624.html},
numpages = {7},
publisher = {Nature Publishing Group/Macmillan},
doi = {10.1038/srep03624},
issn_isbn = {ISSN 2045-2322}
}
@mastersthesis{Chirkin2014a,
title = {Multi-objective optimization approach to infer Drosophila gene regulatory parameters},
author = {A. Chirkin},
year = {2014},
url = {http://dare.uva.nl/en/scriptie/496303},
month = {June},
category = {pwrs, mastersthesis},
numpages = {60},
school = {University of Amsterdam \& ITMO St. Petersburg},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: A.S.Z. Belloum, S. Kovalchuk}
}
@article{Duijn2014a,
title = {The Relative Ineffectiveness of Criminal Network Disruption},
author = {P.A.C. Duijn and V. Kashirin and P.M.A. Sloot},
year = {2014},
journal = {Sci. Rep.},
volume = {4},
pages = {4238},
metis_id = {415607},
url = {http://www.nature.com/srep/2014/140228/srep04238/abs/srep04238.html},
numpages = {15},
publisher = {Nature Publishing Group/Macmillan},
doi = {10.1038/srep04238},
issn_isbn = {ISSN 2045-2322}
}
@article{Dukhanov2014a,
title = {Double-degree Master's Program in Computational Science: Experiences of ITMO University and University of Amsterdam},
author = {A.V. Dukhanov and V.V. Krzhizhanovskaya and A. Bilyatdinova and A.V. Boukhanovsky and P.M.A. Sloot},
year = {2014},
journal = {Procedia Computer Science},
volume = {29},
pages = {1433 - 1445},
url = {http://www.sciencedirect.com/science/article/pii/S187705091400307X},
note = {2014 International Conference on Computational Science},
doi = {10.1016/j.procs.2014.05.130},
abstract = {Abstract We present a new double-degree graduate (Master's) programme developed together by the ITMO University, Russia and University of Amsterdam, The Netherlands. First, we look into the global aspects of integration of d ifferent educational systems and list some funding opportunities fro m European foundations. Then we describe our double-degree program curricu lu m, suggest the time line of enrollment and studies, and give some e xa mples of student research topics. Finally, we d iscuss the peculiarities of joint progra ms with Russia, re flect on the first lessons learnt, and share our thoughts and experiences that could be of interest to the international community e xpanding the educational ma rkets to the vast countries like Russia, Ch ina or India. The paper is written for education professionals and contains useful information for potential students.},
keywords = {funding opportunities},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2014},
issn_isbn = {ISSN 1877-0509}
}
@article{Erdbrink2014a,
title = {Reducing cross-flow vibrations of underflow gates: experiments and numerical studies},
author = {C.D. Erdbrink and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2014},
journal = {Journal of Fluids and Structures},
metis_id = {404436},
url = {http://arxiv.org/abs/1312.7868}
}
@phdthesis{Erdbrink2014b,
title = {Modelling flow-induced vibrations of gates in hydraulic structures},
author = {C.D. Erdbrink},
year = {2014},
url = {http://dare.uva.nl/en/record/497231},
month = {September},
numpages = {198},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, co-promotor: Dr. V.V. Krzhizhanovskaya},
issn_isbn = {ISBN 9789064648007}
}
@article{Erdbrink2014c,
title = {Evolutionary Design of Numerical Methods: Generating Finite Difference and Integration Schemes by Differential Evolution},
author = {C.D. Erdbrink and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2014},
journal = {IEEE Transactions on Evolutionary Computation},
metis_id = {404385},
url = {http://arxiv.org/abs/1312.7852}
}
@article{Erdbrink2014d,
title = {Identifying Self-excited Vibrations with Evolutionary Computing},
author = {C.D. Erdbrink and V.V. Krzhizhanovskaya},
year = {2014},
journal = {Procedia Computer Science},
volume = {29},
pages = {637 - 647},
url = {http://www.sciencedirect.com/science/article/pii/S1877050914002348},
note = {2014 International Conference on Computational Science},
doi = {10.1016/j.procs.2014.05.057},
abstract = {Abstract This study uses differential evolution to identify the coefficients of second-order differential equations of self-excited vibrations from a time signal. The motivation is found in the ample occurrence of this vibration type in engineering and physics, in particular in the real-life problem of vibrations of hydraulic structure gates. In the proposed method, an equation structure is assumed at the level of the ordinary differential equation and a population of candidate coefficient vectors undergoes evolutionary training. In this way the numerical constants of non-linear terms of various self-excited vibration types were recovered from the time signal and the velocity value only at the initial time. Comparisons are given regarding accuracy and computing time. Dependency of the test errors on the algorithm parameters is studied in a sensitivity analysis. The presented evolutionary method shows good promise for future application in engineering systems, in particular operational early-warning systems that recognise oscillations with negative damping before they can cause damage.},
keywords = {differential evolution},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2014},
issn_isbn = {ISSN 1877-0509}
}
@article{Graaf2014a,
title = {Efficient Computation of Exposure Profiles for Counterparty Credit Risk},
author = {C.S.L. de Graaf and Q. Feng and B.D. Kandhai and C.W. Oosterlee},
year = {2014},
journal = {International Journal of Theoretical and Applied Finance},
volume = {17},
number = {4},
url = {http://dx.doi.org/10.1142/S0219024914500241}
}
@mastersthesis{Klimkina2014a,
title = {Study of the news spread among social network user with respect to their stakeholdership},
author = {A. Klimkina},
year = {2014},
month = {June},
category = {pwrs, mastersthesis},
school = {University of Amsterdam \& ITMO St. Petersburg},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: R. Quax, A. Yakushev}
}
@inproceedings{Lees2014a,
title = {Automatic Rule Identification for Agent-Based Crowd Models Through Gene Expression Programming},
author = {M.H. Lees and L. Luo and J. Zhong and W. Cai},
year = {2014},
metis_id = {402420},
publisher = {Springer (accepted)},
booktitle = {13th International Conference on Autonomous Agents and Multiagent Systems (AAMAS2014 )}
}
@phdthesis{Mancini2014a,
title = {Agent based modeling of viral infections: an investigation across several spatio-temporal scales},
author = {E. Mancini},
year = {2014},
url = {http://dare.uva.nl/record/1/417748},
month = {June},
numpages = {122},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot}
}
@article{Melnikova2014a,
title = {Slope Instability of the Earthen Levee in Boston, UK: Numerical Simulation and Sensor Data Analysis},
author = {N.B. Melnikova and D. Jordan and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2014},
journal = {Computers and Geotechnics},
metis_id = {407787},
url = {http://arxiv.org/abs/1401.7631}
}
@article{Melnikova2014b,
title = {Experimental Collapse of the IJkDijk: Numerical Prediction of Failure Mode and Posterior Sensor Data Analysis},
author = {N.B. Melnikova and D. Jordan and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2014},
journal = {Canadian Geotechnical Journal},
metis_id = {407880}
}
@phdthesis{Melnikova2014c,
title = {Finite element analysis of levee stability for flood early warning systems},
author = {N.B. Melnikova},
year = {2014},
url = {http://dare.uva.nl/en/record/497194},
month = {September},
numpages = {101},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, co-promotor: Dr. V.V. Krzhizhanovskaya},
issn_isbn = {ISBN 9789064648069}
}
@mastersthesis{Mikailov2014a,
title = {The use of genetic algorithms to find an optimum MHD as an approximate description of holes},
author = {K. Mikhailov},
year = {2014},
month = {June},
category = {pwrs, mastersthesis},
school = {University of Amsterdam \& ITMO St. Petersburg},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: S. Markoff, A. Boukhanovsky}
}
@article{Mountrakis2014a,
title = {Validation of an efficient two-dimensional model for dense suspensions of red blood cells},
author = {L. Mountrakis and E. Lorenz and A.G. Hoekstra},
year = {2014},
journal = {International Journal of Modern Physics C},
metis_id = {416342}
}
@article{Pyayt2014a,
title = {Time-frequency Methods for Structural Health Monitoring},
author = {A.L. Pyayt and A.P. Kozionov and I.I. Mokhov and B. Lang and R.J. Meijer and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2014},
journal = {Sensors},
volume = {14},
number = {3},
pages = {5147--5173},
metis_id = {406823},
url = {http://www.mdpi.com/1424-8220/14/3/5147},
month = {March},
doi = {10.3390/s140305147},
issn_isbn = {ISSN 1424-8220}
}
@phdthesis{Pyayt2014b,
title = {Data-driven methods in application to flood defence systems monitoring and analysis},
author = {A.L. Pyayt},
year = {2014},
url = {http://dare.uva.nl/en/record/497165},
month = {September},
numpages = {127},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, co-promotor: Dr. V.V. Krzhizhanovskaya},
issn_isbn = {ISBN 9789064648052}
}
@article{Roy2014a,
title = {The emergence of slums: A contemporary view on simulation models},
author = {D. Roy and M.H. Lees and B. Palavalli and K. Pfeffer and P.M.A. Sloot},
year = {2014},
journal = {Environmental Modelling \& Software},
volume = {59},
number = {0},
pages = {76--90},
metis_id = {430447},
month = {9},
doi = {10.1016/j.envsoft.2014.05.004},
abstract = {The existence of slums or informal settlements is common to most cities of developing countries. Its role as single housing delivery mechanism has seriously challenged the popular notion held by policy makers, planners and architects. Today informality is a paradigm of city making and economic growth in Africa, Asia and Latin America. This paper discusses the role of computer simulation models to understand the emergence and growth of slums in developing countries. We have identified the key factors influencing the growth of slums and formulated a standardized set of criteria for evaluating slum models. The review of existing computer simulation models designed to understand slum formation and expansion enabled us to define model requirements and to identify new research questions with respect to exploring the dynamics of slums. url = http://www.sciencedirect.com/science/article/pii/S1364815214001352}
}
@inproceedings{Konakov2014a,
title={Компьютерное моделирование и экспериментальные исследования закономерностей плазмохимического осаждения тонких пленок нитрида кремния},
author={S.A. Konakov and V.V. Krzhizhanovskaya},
year={2014},
hash={0},
metis_id={487081},
publisher={Polytechnic University},
issn_isbn={},
url={http://week-science.spbstu.ru/upload/file/immt-p2.pdf},
refereed={Y},
booktitle={Science Week. Proceedings of the International conference}
}
@inproceedings{Tahir2014a,
title={A cellular Potts model of a stented arterial vessel to study the role of initial smooth muscle cells migration in neointimal development},
author={H. Tahir and I. Niculescu and R. Merks and A.G. Hoekstra},
year={2014},
hash={11723501443045348214589232992246905548017223730732428762400182312315458498934767655701049138140069903414894507107764512},
metis_id={440280},
issn_isbn={},
url={http://www.ntnu.edu/vph2014/eposters},
refereed={Y},
booktitle={Virtual Physiological Human 2014}
}
@article{Tamulonis2014a,
title={A model of filamentous cyanobacteria leading to reticulate pattern formation},
author={C. Tamulonis and J. Kaandorp},
year={2014},
journal={Life Sciences},
hash={652260112305978077933841835024001935892802179645227908888983026692212},
metis_id={439977},
url={http://dx.doi.org/10.3390/life4030433},
refereed={Y}
}
@article{Nenashev2014a,
title={Scaling description of positive magnetoresistivity in doped dilute magnetic semiconductors},
author={A.V. Nenashev and F. Jansson and S. Petznick and M. Wiemer and P.J. Klar and A.V. Dvurechenskii and F. Gebhard and S.D. Baranovskii},
year={2014},
journal={Journal of Magnetism and Magnetic Materials},
hash={3726186111401270516635603650911306813975088162308063016140461152297395400295201339880},
metis_id={439470},
url={http://dx.doi.org/10.1016/j.jmmm.2014.11.069},
refereed={Y}
}
@inproceedings{Bilyatdinova2014a,
title={Dutch-Russian Double Degree Master's Program Curricula in Computational Science and High Performance Computing},
author={A. Bilyatdinova and A.V. Dukhanov and K.O. Bochenina and V.V. Krzhizhanovskaya and A.V. Boukhanovsky and P.M.A. Sloot},
year={2014},
hash={4258918824815301912863446206309102299608206103694472062516064896824206086732624995812230711829184407},
metis_id={437685},
publisher={IEEE},
issn_isbn={},
url={http://dx.doi.org/10.1109/FIE.2014.7044195},
refereed={Y},
booktitle={Frontiers in Education Conference (FIE)}
}
@article{Hoekstra2014b,
title={Multiscale modelling and simulation: a position paper},
author={A. Hoekstra and B. Chopard and P. Coveney},
year={2014},
journal={Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences},
hash={1014928935271141402586951711154898081900003580066},
metis_id={440269},
url={http://dx.doi.org/10.1098/rsta.2013.0377},
refereed={Y}
}
@inproceedings{Mountrakis2014a,
title={Looking into the transport of blood cells in flows without walls},
author={L. Mountrakis and E. Lorenz and O. Malaspinas and B. Chopard and A.G. Hoekstra},
year={2014},
hash={193693027322664952679876652628824396024032272315716203692},
metis_id={440284},
issn_isbn={},
url={http://ccp2014.bu.edu/wp-content/uploads/2014/08/abstracts-parallel.pdf},
refereed={Y},
booktitle={CCP2014: XXVI IUPAP Conference on Computational Physics: August 11-14, Boston, USA: abstracts: parallel sessions}
}
@inproceedings{Zhong2014b,
title={EA-based evacuation planning using agent-based crowd simulation},
author={J. Zhong and W. Cai and L. Luo and M. Lees},
year={2014},
hash={689124135611758812058514130574086331617932828460303908344},
metis_id={443502},
publisher={IEEE},
issn_isbn={9781479974849},
url={http://dx.doi.org/10.1109/WSC.2014.7019906},
refereed={Y},
booktitle={Proceedings of the 2014 Winter Simulation Conference: exploring big data through simulation: December 7-10, 2014, Westin Savannah Harbor Resort, Savannah, GA}
}
@inproceedings{Bona-Casas2014a,
title={A 3D Multiscale In-Stent Restenosis Model: A Milestone For The Next Generation of In-stent Restenosis Modelling},
author={C. Bona-Casas and H. Tahir and J. Borgdorff and A.G. Hoekstra},
year={2014},
hash={197994146844456941926956931847729779332714574981427344467988874106566532751598694740444459085686},
metis_id={440281},
issn_isbn={},
url={http://www.ntnu.edu/documents/22292352/641373742/Programme+day+by+day+VPH/87896386-ff5b-4777-9c37-7955a7d23014},
refereed={Y},
booktitle={Virtual Physiological Human 2014}
}
@inproceedings{Mordvintsev2014a,
title={Simulation of City Evacuation Coupled to Flood Dynamics},
author={A.S. Mordvintsev and V.V. Krzhizhanovskaya and M.H. Lees and P.M.A. Sloot},
year={2014},
hash={166183775236587614305694821630114703865291446205595},
metis_id={355143},
publisher={Springer},
issn_isbn={978-3-319-02446-2},
url={http://dx.doi.org/10.1007/978-3-319-02447-9_40},
refereed={Y},
booktitle={Pedestrian and Evacuation Dynamics 2012}
}
@Misc{Hoekstra2014a,
title={Multi-Scale Modelling and Simulation},
author={A. Hoekstra and B. Chopard and P. Lawford},
year={2014},
hash={2672625095564839574859323539648196},
metis_id={440276},
publisher={Oxford University Press},
issn_isbn={978-0-19-965818-3},
url={https://global.oup.com/academic/product/computational-biomedicine-9780199658183},
refereed={Y}
}
@article{Botman2014a,
title={A computational approach towards a gene regulatory network for the developing Nematostella vectensis gut},
author={D. Botman and E. Röttinger and M.Q. Martindale and J. de Jong and J.A. Kaandorp},
year={2014},
journal={PLoS One},
hash={1634795597490761327273960299595540235413296526789946753472440855762629372393998086252684241800},
metis_id={438482},
url={http://dx.doi.org/10.1371/journal.pone.0103341},
refereed={Y}
}
@article{Ramos-Silva2014a,
title={The skeleton of the staghorn coral Acropora millepora: molecular and structural characterization},
author={P. Ramos-Silva and J. Kaandorp and F. Herbst and L. Plasseraud and G. Alcaraz and C. Stern and M. Corneillat and N. Guichard and C. Durlet and G. Luquet and F. Marin},
year={2014},
journal={PLoS One},
hash={5366593646734828516577176074377906835979127041327650641569589572892469737590238639765726},
metis_id={439973},
url={http://dx.doi.org/10.1371/journal.pone.0097454},
refereed={Y}
}
@article{Jung2014a,
title={Applying Information Theory to Neuronal Networks: From Theory to Experiments},
author={T.I. Jung and F. Vogiatzian and O. Har-Shemesh and C.P. Fitzsimons and R. Quax},
year={2014},
journal={Entropy},
hash={73436172322307734874432166905657144310025578869418936062121620177585},
metis_id={438406},
url={http://dx.doi.org/10.3390/e16115721},
refereed={Y}
}
@article{Oelerich2014a,
title={Energy position of the transport path in disordered organic semiconductors},
author={J.O. Oelerich and F. Jansson and A.V. Nenashev and F. Gebhard and S.D. Baranovskii},
year={2014},
journal={Journal of Physics-Condensed Matter},
hash={23306948281829290713693250026320351845253583771431043001544351536435},
metis_id={439867},
url={http://dx.doi.org/10.1088/0953-8984/26/25/255801},
refereed={Y}
}
@inproceedings{Xu2014a,
title={Efficient graph-based dynamic load-balancing for parallel large-scale agent-based traffic simulation},
author={Y. Xu and W. Cai and H. Aydt and M. Lees},
year={2014},
hash={1633739966798302946095939313147222817337633844938245199476086489306282241484616955610680288},
metis_id={443499},
publisher={IEEE},
issn_isbn={9781479974849},
url={http://dx.doi.org/10.1109/WSC.2014.7020180},
refereed={Y},
booktitle={Proceedings of the 2014 Winter Simulation Conference: exploring big data through simulation: December 7-10, 2014, Westin Savannah Harbor Resort, Savannah, GA}
}
@article{Chopard2014a,
title={A framework for multi-scale modelling},
author={B. Chopard and J. Borgdorff and A.G. Hoekstra},
year={2014},
journal={Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences},
hash={114378894212703989978914443863494},
metis_id={440273},
url={http://dx.doi.org/10.1098/rsta.2013.0378},
refereed={Y}
}
@inproceedings{Aydt2014a,
title={Toward Simulation-Based Egress Optimization in Smart Buildings Using Symbiotic Simulation},
author={H. Aydt and M.H. Lees and S.J. Turner and W. Cai},
year={2014},
hash={34629366682833062768586621991440762950225314697693155376201732818747209052665881005},
metis_id={443507},
publisher={Springer},
issn_isbn={978-3-319-02446-2},
url={http://dx.doi.org/10.1007/978-3-319-02447-9_82},
refereed={Y},
booktitle={Pedestrian and Evacuation Dynamics 2012}
}
@article{Savickas2014a,
title={Super Fast Greeks: An Application to Counterparty Valuation Adjustments},
author={V. Savickas and N. Hari and T. Wood and D. Kandhai},
year={2014},
journal={Wilmott},
hash={66806261494936533676601970737972673617013031070929455526827877691},
metis_id={386011},
url={http://dx.doi.org/10.1002/wilm.10291},
refereed={Y}
}
@inproceedings{Teo2014a,
title={Analysing the Effectiveness of Wearable Wireless Sensors in Controlling Crowd Disasters},
author={Y.H.A. Teo and V. Viswanathan and M. Lees and W. Cai},
year={2014},
journal={Procedia Computer Science},
hash={16674837652148787970236797308273330312809484634653671053936668923357578760874232},
metis_id={443481},
publisher={Elsevier},
issn_isbn={},
url={http://dx.doi.org/10.1016/j.procs.2014.05.144},
refereed={Y},
booktitle={2014 International Conference on Computational Science}
}
@article{Erdbrink2014b,
title={Free-surface flow simulations for discharge-based operation of hydraulic structure gates},
author={C.D. Erdbrink and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year={2014},
journal={Journal of Hydroinformatics},
hash={92100096269295668748079706160380295033919654147404595160453224765851792390832014},
metis_id={404377},
url={http://dx.doi.org/10.2166/hydro.2013.215},
refereed={Y}
}
@article{Javaheri2014a,
title={Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization},
author={N. Javaheri and R Dries and J. Kaandorp},
year={2014},
journal={PLoS Computational Biology},
hash={51004462755840574800733700711647460596193202255753883875451592986635148336785473421174156371597049769221697198177004752429531111077940336},
metis_id={439951},
url={http://dx.doi.org/10.1371/journal.pcbi.1003687},
refereed={Y}
}
@article{Borgdorff2014c,
title={Performance of distributed multiscale simulations},
author={J. Borgdorff and M. Ben Belgacem and C. Bona-Casas and L. Fazendeiro and D. Groen and O. Hoenen and A. Mizeranschi and J.L. Sutter and D. Coster and P.V. Coveney and W. Dubitzky and A.G. Hoekstra and P. Strand and B. Chopard},
year={2014},
journal={Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences},
hash={102768673411156973054403137647207518924584461298},
metis_id={440278},
url={http://dx.doi.org/10.1098/rsta.2013.0407},
refereed={Y}
}
@article{Borgdorff2014b,
title={Distributed multiscale computing with MUSCLE 2, the Multiscale Coupling Library and Environment},
author={J. Borgdorff and M. Mamonski and B. Bosak and K. Kurowski and M. Ben Belgacem and B. Chopard and D. Groen and P.V. Coveney and A.G. Hoekstra},
year={2014},
journal={Journal of Computational Science},
hash={61379714257053146678805517638588760044416868073630265723499280820750211680054727780767},
metis_id={439342},
url={http://dx.doi.org/10.1016/j.jocs.2014.04.004},
refereed={Y}
}
@article{Karabasov2014a,
title={Multiscale modelling: approaches and challenges},
author={S. Karabasov and D. Nerukh and A. Hoekstra and B. Chopard and P.V. Coveney},
year={2014},
journal={Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences},
hash={69321011902953445979597438284021015928340051},
metis_id={439442},
url={http://dx.doi.org/10.1098/rsta.2013.0390},
refereed={Y}
}
@article{Tahir2014a,
title = {Endothelial repair process and its relevance to longitudinal neointimal tissue patterns: Comparing histology with in-silico modelling},
author = {H. Tahir and C. Bona-Casas and A. Narracott and J. Iqbal and J. Gunn and P.V. Lawford and A.G. Hoekstra},
year = {2014},
journal = {Journal of the Royal Society Interface},
metis_id = {404390},
note = {submitted}
}
@mastersthesis{Ullrich2014a,
title = {Feed-forward neural networks for boundary detection in music structure analysis},
author = {K. Ullrich},
year = {2014},
month = {August},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: M. Welling, G. Widmer}
}
@article{Viswanthan2014a,
title = {Quantitative Comparison Between Crowd Models for Evacuation Planning and Evaluation},
author = {V. Viswanthan and C.E. Lee and M.H. Lees and S.A. Cheong and P.M.A. Sloot},
year = {2014},
journal = {The European Physical Journal B. Condensed Matter Physics},
volume = {87},
number = {2},
pages = {1--11},
metis_id = {402417},
url = {http://dx.doi.org/10.1140/epjb/e2014-40699-x}
}
@article{Wagner2014a,
title = {Evolving Agent-based Models Using Complexification Approach},
author = {M. Wagner and W. Cai and M.H. Lees and H. Aydt},
year = {2014},
journal = {Procedia Computer Science},
volume = {29},
pages = {310 - 321},
url = {http://www.sciencedirect.com/science/article/pii/S1877050914002051},
note = {2014 International Conference on Computational Science},
doi = {10.1016/j.procs.2014.05.028},
abstract = {Abstract This paper focuses on parameter search for multi-agent based models using evolutionary algorithms. Large numbers and variable dimensions of parameters require a search method which can efficiently handle a high dimensional search space. We are proposing the use of complexification as it emulates the natural way of evolution by starting with a small constrained search space and expanding it as the evolution progresses. We examined the effects of this method on an EA by evolving parameters for two multi-agent based models.},
keywords = {Artificial Life},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2014},
issn_isbn = {ISSN 1877-0509}
}
@mastersthesis{Abdol2013a,
title = {Multi-objective optimization approach to infer Drosophila gene regulatory parameters},
author = {A.M. Abdol},
year = {2013},
month = {December},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: J.A. Kaandorp, F.R. Jansson}
}
@article{Afanasieva2013a,
title = {Modelling processes in the shock tube experiments with ignition of combustible gas mixtures},
author = {A.S. Afanasieva and S.A. Ponyaev and V.V. Krzhizhanovskaya},
year = {2013},
journal = {Technical Physics Letters},
metis_id = {377349}
}
@proceedings{Alexandrov2013a,
title = {Proceedings of the International Conference on Computational Science, ICCS 2013},
author = {V. Alexandrov and M. Lees and V. Krzhizhanovskaya and J. Dongarra and P.M.A. Sloot},
year = {2013},
journal = {Procedia Computer Science},
volume = {18},
url = {http://www.sciencedirect.com/science/journal/18770509/18},
numpages = {2650},
issn_isbn = {ISSN 1877-0509}
}
@misc{Alexandrov2013b,
title = {Computation at the Frontiers of Science, Preface for ICCS 2013},
author = {V. Alexandrov and M. Lees and V. Krzhizhanovskaya and J. Dongarra and P.M.A. Sloot},
year = {2013},
journal = {Procedia Computer Science},
volume = {18},
pages = {1 - 9},
url = {http://www.sciencedirect.com/science/article/pii/S1877050913003062},
doi = {10.1016/j.procs.2013.05.163},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2013},
issn_isbn = {ISSN 1877-0509}
}
@article{Bartha2013a,
title = {Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort},
author = {I. Bartha and M. Assel and P.M.A. Sloot and M. Zazzi and C. Torti and E. Sch\"ulter and A. De Luca and A. S\"onnerborg and A.B. Abecasis and K. van Laethem and A. Rosi and J. Sv\"ard and R. Paredes and D.A. van de Vijver and A.-M. Vandamme and V. M\"uller},
year = {2013},
journal = {BMC Infectious Diseases},
volume = {13},
metis_id = {401863},
url = {http://dx.doi.org/10.1186/1471-2334-13-537}
}
@inproceedings{Belgacem2013a,
title = {Distributed Multiscale Computations using the MAPPER framework},
author = {M.B. Belgacem and B. Chopard and J. Borgdorff and M. Mamonski and K.J. Rycerz and D. Harezlak},
year = {2013},
journal = {Procedia Computer Science},
volume = {18},
pages = {1106--1115},
metis_id = {401040},
url = {http://www.sciencedirect.com/science/article/pii/S1877050913004195},
publisher = {Elsevier},
organization = {International Conference on Computational Science, ICCS 2013},
booktitle = {International Conference on Computational Science, ICCS 2013}
}
@inproceedings{Bona-Casas2013a,
title = {An off-lattice 3D model for in-stent restenosis},
author = {C. Bona-Casas and J. Borgdorff and H. Tahir and A.G. Hoekstra},
year = {2013},
address = {Rotterdam, Netherlands},
organization = {8th International Symposium on Biomechanics in Vascular Biology and Cardiovascular Disease}
}
@inproceedings{Bona-Casas2013b,
title = {First results on a 3D model for in-stent restenosis},
author = {C. Bona-Casas and J. Borgdorff and H. Tahir and A.G. Hoekstra},
year = {2013},
url = {http://www.esbiomech.org/papers/ESB_congress_2013/oral/S37.3-345.pdf},
address = {Patras, Greece},
organization = {19th Congress of the European Society of Biomechanics}
}
@article{Borgdorff2013a,
title = {Foundations of Distributed Multiscale Computing: Formalization, Specification, and Analysis},
author = {J. Borgdorff and J.-L. Falcone and E. Lorenz and C. Bona-Casas and B. Chopard and A.G. Hoekstra},
year = {2013},
journal = {Journal of Parallel and Distributed Computing},
volume = {73},
number = {4},
pages = {465--483},
metis_id = {378357},
url = {http://www.sciencedirect.com/science/article/pii/S0743731512002924#},
month = {April},
doi = {10.1016/j/jpdc.2012.12.011},
issn_isbn = {ISSN 0743-7315}
}
@inproceedings{Borgdorff2013b,
title = {Multiscale Computing with the Multiscale Modeling Library and Runtime Environment},
author = {J. Borgdorff and M. Mamonski and B. Bosak and D. Groen and M.B. Belgacem and K. Kurowski and A.G. Hoekstra},
year = {2013},
journal = {Procedia Computer Science},
volume = {18},
pages = {1097-1105},
url = {http://www.sciencedirect.com/science/article/pii/S1877050913004183},
doi = {10.1016/j.procs.2013.05.275},
editor = {V. Alexandrov and M. Lees and V. Krzhizhanovskaya and J. Dongarra and P.M.A. Sloot},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2013},
issn_isbn = {ISSN 1877-0509}
}
@misc{Borgdorff2013c,
title = {Adding MUSCLE to Multiscale Simulations},
author = {J. Borgdorff and D.J. Groen and M. Mamonski},
year = {2013},
metis_id = {404274},
url = {http://www.hpcwire.com/2013/12/11/adding-muscle-multiscale-simulations/},
booktitle = {HPCWire}
}
@article{Carey2013a,
title = {Promoter sequence determines the relationship between expression level and noise},
author = {L.B. Carey and D. van Dijk and P. M.A. Sloot and J. A Kaandorp and E. Segal},
year = {2013},
journal = {Plos Biol.},
volume = {11},
number = {4},
pages = {e1001528},
metis_id = {386374},
numpages = {15},
doi = {10.1371/journal.pbio.1001528}
}
@mastersthesis{Chen2013a,
title = {Explicit modelling of membrane-bound structures in the cellular Potts model},
author = {C. Chen},
year = {2013},
month = {March},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: R.M.H. Merks, J.A. Kaandorp}
}
@article{Chindapol2013a,
title = {Modelling Growth and Form of the Scleractinian Coral Pocillopora verrucosa and the Influence of Hydrodynamics},
author = {N. Chindapol and J.A. Kaandorp and C. Cronemberger and T. Mass and A. Genin},
year = {2013},
journal = {PLoS Comput Biol},
volume = {9},
number = {1},
pages = {e1002849},
url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1002849},
month = {January},
publisher = {Public Library of Science},
doi = {10.1371/journal.pcbi.1002849},
abstract = {Author SummaryA long-standing question in marine biology and coral biology is the morphological plasticity of corals, sponges and other marine sessile organisms and the influence of water movement. Usually branching species tend to develop symmetrical colonies where branches are being formed in all directions. There is a long standing discussion if this process in which colonies develop symmetrical colonies is controlled by genes or by the environment. In this work, we address this question for the scleractinian coral Pocillopora verrucosa. We first have acquired coral colonies from a controlled in-situ flow experiment where the coral was growing under uni-directional flow conditions. The corals colonies were scanned using a Computed Tomography (CT) technique used for medical imaging and industrial imaging. We have developed a simulation for the growth and form of corals and the influence of water movement. We have compared the simulated morphologies to the three dimensional images obtained with the CT scanner. We have found that coral's branches predominantly develop in the upstream part of the colony and an asymmetrical colony is being formed under uni-directional flow conditions. Our results confirm that growth of the coral is strongly influenced by the flow conditions.
}
}
@article{Czaplicka2013a,
title = {Noise enhances information transfer in hierarchical networks},
author = {A. Czaplicka. and J.A. Ho\lyst and P.M.A. Sloot},
year = {2013},
journal = {Nature Scientific Reports},
volume = {3},
metis_id = {384790},
url = {http://dx.doi.org/10.1038/srep01223},
doi = {10.1038/srep01223}
}
@article{Czaplicka2013b,
title = {Stochastic resonance for information flows on hierarchical networks},
author = {A. Czaplicka and J.A. Ho\lyst and P.M.A. Sloot},
year = {2013},
journal = {The European Physical Journal - Special Topics},
volume = {222},
number = {6},
pages = {1335--1345},
metis_id = {398222},
url = {http://dx.doi.org/10.1140/epjst/e2013-01929-5},
doi = {10.1140/epjst/e2013-01929-5}
}
@phdthesis{Dijk2013a,
title = {The symphony of gene regulation},
author = {D. van Dijk},
year = {2013},
url = {http://dare.uva.nl/en/record/452579},
month = {September},
numpages = {151},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, co-promotor: Dr. J.A. Kaandorp},
keywords = {gene regulation; gene expression; complex networks}
}
@article{Dijkstra2013a,
title = {Inference of the Russian drug community from one of the largest social networks in the Russian Federation},
author = {L.J. Dijkstra and A.V. Yakushev and P.A.C. Duijn and A.V. Boukhanovsky and P.M.A. Sloot},
year = {2013},
journal = {Quality \& Quantity, International Journal of Methodology},
pages = {1-17},
url = {http://dx.doi.org/10.1007/s11135-013-9921-6},
publisher = {Springer Netherlands},
doi = {10.1007/s11135-013-9921-6},
keywords = {Illicit drug use; Drug use; Social network; LiveJournal; Power-law; Russian Federation},
issn_isbn = {ISSN 0033-5177}
}
@mastersthesis{Dijkstra2013b,
title = {Essays in Computational Science},
author = {L.J. Dijkstra},
year = {2013},
month = {August},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: P.M.A. Sloot}
}
@inproceedings{Dugundji2013a,
title = {Understanding Emergence in a Fully-Specified Nested Logit Model},
author = {E.R. Dugundji and L. Guly\'as},
year = {2013},
metis_id = {402446},
publisher = {Virginia Tech},
editor = {A.G. Hobeika and H. Rakha},
organization = {Conference on Agent-Based Modeling in Transportation Planning and Operations},
address = {Blacksburg, VA, USA}
}
@article{Erdbrink2013a,
title = {Free-surface flow simulations for discharge-based operation of hydraulic structure gates},
author = {C.D. Erdbrink and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2013},
journal = {Journal of Hydroinformatics},
metis_id = {377339},
url = {http://arxiv.org/abs/1211.4464}
}
@mastersthesis{Geldermalsen2013a,
title = {FlowCL -- Declarative dataflow API for heterogeneous platform computing},
author = {S. van Geldermalsen},
year = {2013},
url = {http://dare.uva.nl/en/scriptie/453444},
month = {August},
category = {pwrs, mastersthesis},
numpages = {68},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: S. Olabarriaga, A.S.Z. Belloum and H. Marquering}
}
@article{Groen2013a,
title = {Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations},
author = {D.J. Groen and J. Borgdorff and C. Bona-Casas and J. Hetherington and R. Nash and S.J. Zasada and I. Saverchenko and M. Mamonski and K. Kurowski and M.O. Bernabeu and A.G. Hoekstra and P.V. Coveney},
year = {2013},
journal = {Interface Focus},
volume = {3},
number = {2},
metis_id = {405694}
}
@inproceedings{Hoenen2013a,
title = {Designing and running turbulence transport simulations using a distributed multiscale computing approach},
author = {O. Hoenen and L. Fazendeiro and B.D. Scott and J. Borgdorff and A.G. Hoekstra and P. Strand and D.P. Coster},
year = {2013},
metis_id = {401039},
url = {http://ocs.ciemat.es/EPS2013PAP/pdf/P4.155.pdf},
publisher = {European Physical Society},
booktitle = {EPS 2013, Europhysics Conference Abstracts, 37D},
organization = {40th EPS Conference on Plasma Physics}
}
@mastersthesis{Hofman2013a,
title = {SPVAs: Grid GPU Implementation \& Risk Assessment of Investment Strategies},
author = {J. Hofman},
year = {2013},
month = {July},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: B.D. Kandhai, D. Schrager, V. Sergeev}
}
@mastersthesis{Hofmann2013a,
title = {Heterogeneous Multiscale Simulations of Blood Flow},
author = {J. Hofmann},
year = {2013},
url = {Hofmann2013a.pdf},
month = {August},
category = {pwrs, mastersthesis},
numpages = {37},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: A.G. Hoekstra, E. Lorenz}
}
@article{Kaandorp2013a,
title = {Macroscopic Modelling of Environmental Influence on Growth and Form of Sponges and Corals Using the Accretive Growth Model},
author = {J.A. Kaandorp},
year = {2013},
journal = {ISRN Biomathematics},
volume = {2013},
pages = {159170},
numpages = {14},
doi = {10.1155/2013/159170},
issn_isbn = {ISSN: 2090-7702}
}
@book{Kozionov2013a,
title = {Intelligent signal processing for dike health monitoring},
author = {A.P. Kozionov and A.L. Pyayt and V.T. Kusherbaeva},
year = {2013},
metis_id = {406821},
publisher = {Proceedings of the International Conference of Young Scientists},
address = {St. Petersburg, Russia},
issn_isbn = {ISBN 978-5-7422-4164-5}
}
@inproceedings{Krzhizhanovskaya2013a,
title = {Distributed Simulation of City Inundation by Coupled Surface and Subsurface Porous Flow for Urban Flood Decision Support System},
author = {V.V. Krzhizhanovskaya and N.B. Melnikova and A.M. Chirkin and S.V. Ivanov and A.V. Boukhanovsky and P.M.A. Sloot},
year = {2013},
journal = {Procedia Computer Science},
volume = {18},
pages = {1046-1056},
url = {http://www.sciencedirect.com/science/article/pii/S1877050913004134},
doi = {10.1016/j.procs.2013.05.270},
editor = {V. Alexandrov and M.H. Lees and V. Krzhizhanovskaya and J. Dongarra and P.M.A. Sloot},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2013},
issn_isbn = {ISSN 1877-0509}
}
@article{Lebanin2013a,
title = {The dependence of the rate constant of the interaction between two excited particles on the excitation energy and temperature. Verification of the model with examples transfer of electronic excitation energy of the argon atom and the nitrogen molecule in the reaction of dissociation of nitrogen atom of argon},
author = {V.S. Lebanin and V.V. Krzhizhanovskaya and S.E. Alexandrov},
year = {2013},
journal = {Technical Physics Letters},
metis_id = {379174},
note = {In Russian, under review}
}
@article{Libin2013a,
title = {RegaDB: Community-driven data management and analysis for infectious diseases},
author = {P. Libin and G. Beheydt and K. Deforche and S. Imbrechts and F. Ferreira and K. van Laethem and K. Theys and A.P. Carvalho and J. Cavaco-Silva and G. Lapadula and C. Torti and M. Assel and S. Wesner and J. Snoeck and J. Ruelle and A. De Bel and P. Lacor and P. De Munter and E. van Wijngaerden and M. Zazzi and R. Kaiser and A. Ayouba and M. Peeters and T. de Oliveira and L.C. Alcantara, Jr. and Z. Grossman and P.M.A. Sloot and D. Otelea and S. Paraschiv and C.A.B. Boucher and R. Camacho and A.-M. Vandamme},
year = {2013},
journal = {Bioinformatics},
url = {http://bioinformatics.oxfordjournals.org/content/early/2013/04/17/bioinformatics.btst162.abstract},
month = {April},
numpages = {5},
doi = {10.1093/bioinformatics/btst162},
abstract = {Summary: RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyze patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface.Availability and implementation: Source code, binaries and documentation are available on http://regaweb.med.kuleuven.be/software/regadb/ RegaDB is written in the Java programming language, using a web-service oriented architecture.Contact: pieter.libin@rega.kuleuven.beSupplementary information: Supplementary material demonstrating the functionalities of the system is available at Bioinformatics online.}
}
@inproceedings{Lorenz2013a,
title = {Strong Anisotropy in Shear-induced RBC-enhanced Platelet Diffusion},
author = {E. Lorenz and L. Mountrakis and A.G. Hoekstra},
year = {2013},
metis_id = {405752},
url = {https://dsfd2013.aua.am/2013/03/20/strong-anisotropy-in-shear-induced-rbc-enhanced-platelet-diffusion/},
booktitle = {International Conference on the Discrete Simulation of Fluid Dynamics 2013},
organization = {22nd International Conference on the Discrete Simulation of Fluid Dynamics}
}
@article{Marie2013a,
title = {The shell-forming proteome of Lottia gigantea reveals both deep conservations and lineage-specific novelties},
author = {B. Marie and D.J. Jackson and P. Ramos-Silva and I. Zanella-Cl\'eon and N. Guichard and F. Marin},
year = {2013},
journal = {FEBS Journal},
volume = {280},
number = {1},
pages = {214--232},
metis_id = {380135},
url = {http://dx.doi.org/10.1111/febs.12062},
doi = {10.1111/febs.12062},
abstract = {Proteins that are occluded within the molluscan shell, the so-called shell matrix proteins (SMPs), are an assemblage of biomolecules attractive to study for several reasons. They increase the fracture resistance of the shell by several orders of magnitude, determine the polymorph of CaCO3 deposited, and regulate crystal nucleation, growth initiation and termination. In addition, they are thought to control the shell microstructures. Understanding how these proteins have evolved is also likely to provide deep insight into events that supported the diversification and expansion of metazoan life during the Cambrian radiation 543 million years ago. Here, we present an analysis of SMPs isolated form the CaCO3 shell of the limpet Lottia gigantea, a gastropod that constructs an aragonitic cross-lamellar shell. We identified 39 SMPs by combining proteomic analysis with genomic and transcriptomic database interrogations. Among these proteins are various low-complexity domain-containing proteins, enzymes such as peroxidases, carbonic anhydrases and chitinases, acidic calcium-binding proteins and protease inhibitors. This list is likely to contain the most abundant SMPs of the shell matrix. It reveals the presence of both highly conserved and lineage-specific biomineralizing proteins. This mosaic evolutionary pattern suggests that there may be an ancestral molluscan SMP set upon which different conchiferan lineages have elaborated to produce the diversity of shell microstructures we observe nowadays. Database Novel protein sequences reported in this article have been deposited in Swiss-Prot database under accession nos. B3A0P1-B3A0S4},
keywords = {biomineralization, evolution, mantle, mollusc shell matrix proteins, proteome},
issn_isbn = {ISSN 1742-4658}
}
@article{Mei2013a,
title = {Individual decision making can drive epidemics: a fuzzy cognitive map study},
author = {S. Mei and Y. Zhu and X. Qiu and Z. Zu and T. Zheng and A.V. Boukhanovsky and P.M.A. Sloot},
year = {2013},
journal = {IEEE Transactions on Fuzzy Systems},
volume = {21},
number = {6},
pages = {1--10},
metis_id = {384795},
url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6475999},
note = {On-line first},
doi = {10.1109/TFUZZ.2013.2251638},
issn_isbn = {ISSN 1063-6706}
}
@article{Melnikova2013a,
title = {Modeling earthen dikes using real-time sensor data},
author = {N.B. Melnikova and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2013},
journal = {Journal of Hydrology},
volume = {496},
pages = {154--165},
metis_id = {395499},
url = {http://www.sciencedirect.com/science/article/pii/S0022169413003983},
doi = {10.1016/j.jhydrol.2013.05.031}
}
@article{Melnikova2013b,
title = {Modeling Earthen Dike Stability: Sensitivity Analysis and Automatic Calibration of Diffusivities Based on Live Sensor Data},
author = {N.B. Melnikova and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2013},
journal = {Journal of Hydrology},
metis_id = {372355},
url = {http://arxiv.org/abs/1211.4218}
}
@inproceedings{Mordvintsev2013a,
title = {Simulation of City Evacuation Coupled to Flood Dynamics},
author = {A.A. Mordvintsev and V.V. Krzhizhanovskaya and M.H. Lees and P.M.A. Sloot},
year = {2013},
metis_id = {355143},
url = {Mordvintsev2012a.pdf},
publisher = {Spinger},
booktitle = {Pedestrian and Evacuation Dynamics},
note = {in press},
organization = {6th International Conference on Pedestrian and Evacuation Dynamics}
}
@article{Mountrakis2013a,
title = {Where do the platelets go? A simulation study of fully resolved blood flow through aneurysmal vessels},
author = {L. Mountrakis and E. Lorenz and A.G. Hoekstra},
year = {2013},
journal = {Interface Focus},
volume = {3},
pages = {20120089},
metis_id = {379247},
doi = {10.1098/rsfs.2012.0089}
}
@inproceedings{Mountrakis2013b,
title = {Shape memory and membrane fluctuations of an RBC in shear flow},
author = {L. Mountrakis and E. Lorenz and A.G. Hoekstra},
year = {2013},
metis_id = {405755},
url = {https://dsfd2013.aua.am/2013/03/20/shape-memory-and-membrane-fluctuations-of-an-rbc-in-shear-flow/},
booktitle = {International Conference on the Discrete Simulation of Fluid Dynamics 2013},
organization = {22nd International Conference on the Discrete Simulation of Fluid Dynamics}
}
@article{Nichols2013a,
title = {Cost-Effectiveness of Pre-Exposure Prophylaxis (PrEP) in Preventing HIV-1 Infections in Rural Zambia: A Modeling Study},
author = {B.E. Nichols and C.A.B. Boucher and J.H. van Dijk and P.E. Thuma and J.L. Nouwen and R. Baltussen and J. van de Wijgert and P.M.A. Sloot and D.A.M.C. van de Vijver},
year = {2013},
journal = {PLoS ONE},
volume = {8},
number = {3},
pages = {e59549},
metis_id = {392712},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0059549},
month = {March},
publisher = {Public Library of Science},
doi = {10.1371/journal.pone.0059549},
abstract = {BackgroundPre-exposure prophylaxis (PrEP) with tenofovir and emtricitabine effectively prevents new HIV infections. The optimal scenario for implementing PrEP where most infections are averted at the lowest cost is unknown. We determined the impact of different PrEP strategies on averting new infections, prevalence, drug resistance and cost-effectiveness in Macha, a rural setting in Zambia.
MethodsA deterministic mathematical model of HIV transmission was constructed using data from the Macha epidemic (antenatal prevalence 7.7%). Antiretroviral therapy is started at CD4\<350 cells/mm3. We compared the number of infections averted, cost-effectiveness, and potential emergence of drug resistance of two ends of the prioritization spectrum: prioritizing PrEP to half of the most sexually active individuals (5``15% of the total population), versus randomly putting 40``60% of the total population on PrEP.
ResultsPrioritizing PrEP to individuals with the highest sexual activity resulted in more infections averted than a non-prioritized strategy over ten years (31% and 23% reduction in new infections respectively), and also a lower HIV prevalence after ten years (5.7%, 6.4% respectively). The strategy was very cost-effective at $323 per quality adjusted life year gained and appeared to be both less costly and more effective than the non-prioritized strategy. The prevalence of drug resistance due to PrEP was as high as 11.6% when all assumed breakthrough infections resulted in resistance, and as low as 1.3% when 10% of breakthrough infections resulted in resistance in both our prioritized and non-prioritized scenarios.
ConclusionsEven in settings with low test rates and treatment retention, the use of PrEP can still be a useful strategy in averting infections. Our model has shown that PrEP is a cost-effective strategy for reducing HIV incidence, even when adherence is suboptimal and prioritization is imperfect.
}
}
@incollection{Pengel2013a,
title = {Flood early warning system: sensors and internet},
author = {B.E. Pengel and V.V. Krzhizhanovskaya and N.B. Melnikova and G.S. Shirshov and A.R. Koelewijn and A.L. Pyayt and I.I. Mokhov},
year = {2013},
pages = {445--453},
metis_id = {355141},
url = {http://iahs.info/redbooks/357.htm},
publisher = {IAHS Press},
series = {IAHS publication},
booktitle = {Floods: from risk to opportunity},
editor = {Chavoshian,A. and Takeuchi,K.},
address = {Wallingford}
}
@article{Pyayt2013a,
title = {Signal analysis and anomaly detection for flood early warning systems},
author = {A.L. Pyayt and A.P. Kozionov and V.T. Kusherbaeva and I.I. Mokhov and V.V. Krzhizhanovskaya and B.J. Broekhuijsen and R.J. Meijer and P.M.A. Sloot},
year = {2013},
journal = {Journal of Hydroinformatics},
metis_id = {377783},
url = {http://dare.uva.nl/cgi/arno/showmts.cgi?mid=377340}
}
@inproceedings{Pyayt2013b,
title = {An Approach for Real-time Levee Health Monitoring Using Signal Processing Methods},
author = {A.L. Pyayt and A.P. Kozionov and I.I. Mokhov and B. Lang and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2013},
journal = {Procedia Computer Science},
volume = {18},
pages = {2357-2366},
url = {http://www.sciencedirect.com/science/article/pii/S1877050913005504},
doi = {10.1016/j.procs.2013.05.407},
editor = {V. Alexandrov and M.H. Lees and V. Krzhizhanovskaya and J. Dongarra and P.M.A. Sloot},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2013},
issn_isbn = {ISSN 1877-0509}
}
@article{Pyayt2013c,
title = {Intelligent system for monitoring the state critical infrastructure},
author = {A.L. Pyayt and I.I. Mokhov and A.P. Kozionov},
year = {2013},
journal = {Integral},
volume = {4},
number = {72},
pages = {84--86},
metis_id = {408609}
}
@phdthesis{Quax2013a,
title = {Information processing in complex networks},
author = {R. Quax},
year = {2013},
url = {http://dare.uva.nl/en/record/440949},
month = {March},
numpages = {151},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot},
keywords = {complex networks; information theory; mutual information; time series analysis; dynamical systems; financial data analysis; HIV; parameter estimation; phylogenetic data}
}
@article{Quax2013b,
title = {Information dissipation as an early-warning signal for the Lehman Brothers collapse in financial time series},
author = {R. Quax and B.D. Kandhai and P.M.A. Sloot},
year = {2013},
journal = {Scientific Reports},
volume = {3},
metis_id = {395500},
url = {http://www.nature.com/srep/2013/130530/srep01898/full/srep01898.html},
doi = {10.1038/srep01898}
}
@article{Quax2013c,
title = {The diminishing role of hubs in dynamical processes on complex networks},
author = {R. Quax and Apolloni,A. and P.M.A. Sloot},
year = {2013},
journal = {Journal of the Royal Society Interface},
volume = {10},
number = {88},
metis_id = {398155},
doi = {10.1098/rsif.2013.0568},
issn_isbn = {ISSN: 1742-5662}
}
@article{Quax2013d,
title = {Inferring epidemiological parameters from phylogenetic information for the HIV-1 epidemic among MSM},
author = {R. Quax and D.A. van de Vijver and D. Frentz and P.M.A. Sloot},
year = {2013},
journal = {The European Physical Journal - Special Topics},
volume = {222},
number = {6},
pages = {1347-1358 metis_id = 398223},
metis_id = {398223},
url = {http://dx.doi.org/10.1140/epjst/e2013-01930-0},
doi = {10.1140/epjst/e2013-01930-0},
issn_isbn = {ISSN 1951-6355 and 1951-6401}
}
@article{Quax2013e,
title = {Towards understanding the behavior of physical systems using information theory},
author = {R. Quax and A. Apolloni and P.M.A. Sloot},
year = {2013},
journal = {The European Physical Journal - Special Topics},
volume = {222},
number = {6},
pages = {1389--1401},
metis_id = {398225},
url = {http://dx.doi.org/10.1140/epjst/e2013-01933-9},
issn_isbn = {ISSN 1951-6355 and 1951-6401}
}
@article{Savickas2013a,
title = {Super Fast Greeks},
author = {V. Savickas and N. Hari and T. Wood and B.D. Kandhai},
year = {2013},
journal = {Wilmott},
metis_id = {386011}
}
@phdthesis{Silva2013a,
title = {The biocalcification of mollusk shells and coral skeletons: Integrating molecular, proteomics and bioinformatics methods},
author = {P. Sequeira dos Ramos Silva},
year = {2013},
url = {http://dare.uva.nl/en/record/460866},
numpages = {iv + 214},
tutor = {Promotor: P.M.A. Sloot, Co-promotores: J.A. Kaandorp, F.G. Marin},
date = {19-12-2013},
issn_isbn = {ISBN 9789810785635}
}
@article{Sloot2013a,
title = {Advances in dynamic temporal networks: Understanding the temporal dynamics of complex adaptive networks},
author = {P.M.A. Sloot and G. Kampis and L. Guly\'as},
year = {2013},
journal = {The European Physical Journal - Special Topics},
volume = {222},
number = {6},
pages = {1287--1293},
metis_id = {398221},
url = {http://dx.doi.org/10.1140/epjst/e2013-01926-8},
issn_isbn = {ISSN 1951-6355 and 1951-6401}
}
@article{Tahir2013a,
title = {Modelling the Effect of a Functional Endothelium on the Development of In-Stent Restenosis},
author = {H. Tahir and C. Bona-Casas and A.G. Hoekstra},
year = {2013},
journal = {PLoS One},
volume = {8},
number = {6},
metis_id = {395116},
url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0066138?utm_source=feedburner\&utm_medium=feed\&utm_campaign=Feed%3A+plosone%2FPLoSONE+(PLOS+ONE+Alerts%3A+New+Articles)},
doi = {10.1371/journal.pone.0066138}
}
@phdthesis{Tahir2013b,
title = {Modelling and simulating the dynamics of in-stent restenosis in porcine coronary arteries},
author = {H. Tahir},
year = {2013},
metis_id = {399979},
url = {http://dare.uva.nl/record/1/399979},
numpages = {122},
tutor = {Promotor: P.M.A. Sloot, Co-promotor: A.G. Hoekstra},
date = {05-12-2013}
}
@inproceedings{Tahir2013c,
title = {Modelling in-stent restenosis: morphological differences in the tissue patterns based on the origin of endothelium recovery},
author = {H. Tahir and C. Bona-Casas and A.G. Hoekstra},
year = {2013},
metis_id = {404413},
organization = {8th International Symposium on Biomechanics in Vascular Biology and Cardiovascular Disease},
address = {Rotterdam, Netherlands}
}
@inproceedings{Tahir2013d,
title = {In-stent restenosis patterns based on the origin of endothelium recovery},
author = {H. Tahir and C. Bona-Casas and A.G. Hoekstra},
year = {2013},
metis_id = {404420},
url = {http://www.esbiomech.org/papers/ESB_congress_2013/oral/S37.2-164.pdf},
organization = {19th Congress of the European Society of Biomechanics},
address = {Patras, Greece}
}
@phdthesis{Tamulonis2013a,
title = {Cell-based models},
author = {C.V.T. Tamulonis},
year = {2013},
metis_id = {394902},
url = {http://dare.uva.nl/record/447639},
numpages = {xii+214},
school = {Universiteit van Amsterdam},
tutor = {P.M.A. Sloot and J.A. Kaandorp}
}
@phdthesis{Tanzil2013a,
title = {Environmental controls of coral growth: Data driven multi-scale analyses of rates and patterns of growth in massive Porites corals around the Thai-Malay Peninsula},
author = {J.T.I. Tanzil},
year = {2013},
metis_id = {399986},
url = {http://dare.uva.nl/en/record/459188},
numpages = {250},
school = {Universiteit van Amsterdam},
tutor = {Promotor: P.M.A. Sloot and Co-promotor: J.A. Kaandorp},
date = {09-12-2013}
}
@mastersthesis{Theiakos2013a,
title = {GPU-based hedging of a mortgage portfolio using Monte-Carlo and finite difference methods},
author = {A. Theiakos},
year = {2013},
url = {Theiakos2013a},
month = {July},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: B.D. Kandhai, J. Tas, H. van der Lem}
}
@article{Toth2013a,
title = {The importance of centralities in dark network value chains},
author = {N. Toth and L. Guly\'as and R.O. Legendi and P. Duijn and P.M.A. Sloot and G. Kampis},
year = {2013},
journal = {The European Physical Journal - Special Topics},
volume = {222},
number = {6},
pages = {1413--1439},
metis_id = {398226},
url = {http://dx.doi.org/10.1140/epjst/e2013-01935-7},
issn_isbn = {ISSN 1951-6355 and 1951-6401}
}
@mastersthesis{Tyree2013a,
title = {A Linear Boundary for the Heston Model With Parallel ADI Finite Differencing on GPUs},
author = {J. Tyree},
year = {2013},
url = {http://dare.uva.nl/en/scriptie/453443},
month = {August},
category = {pwrs, mastersthesis},
numpages = {89},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: B.D. Kandhai}
}
@article{Wang2013a,
title = {Genetic, biological and structural hierarchies during sponge spicule formation: From soft sol-gels to solid 3D silica composite structures},
author = {X. Wang and H.C. Schr\"oder and K. Wang and J.A. Kaandorp and W.E.G. M\"uller},
year = {2013},
journal = {Soft Matter},
note = {in press}
}
@article{Zarrabi2013a,
title = {Combining social and genetic networks to study HIV transmission in mixing risk groups},
author = {N. Zarrabi and M.C.F. Prosperi and R.G. Belleman and S. Di Giambenedetto and M. Fabbiani and A. De Luca and P.M.A. Sloot},
year = {2013},
journal = {The European Physical Journal - Special Topics},
volume = {222},
number = {6},
pages = {1377-1387},
metis_id = {398224},
url = {http://dx.doi.org/10.1140/epjst/e2013-01932-x}
}
@phdthesis{Zarrabi2013b,
title = {Complex networks and agent-based models of HIV epidemic},
author = {N. Zarrabi},
year = {2013},
url = {http://dare.uva.nl/en/record/454094},
month = {September},
numpages = {vii+142},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot},
keywords = {Complex networks, agent-based models, HIV}
}
@article{Adamatzky2012a,
title = {Bio-development of motorway networks in the Netherlands: A slime mould approach},
author = {A. Adamatzky and M.H. Lees and P.M.A. Sloot},
year = {2012},
journal = {Advances in Complex Systems},
volume = {15},
number = {4},
pages = {1250034},
numpages = {28},
doi = {10.1142/S0219525912500348},
issn_isbn = {ISSN: 0219-5259, 1793-6802}
}
@article{Adamatzky2012b,
title = {Are motorways rational from slime mould's point of view},
author = {A. Adamatzky and S. Akl and R. Alonso-Sanz and W. van Dessel and Z. Ibrahim and A. Ilachinski and J. Jones and A.V.D.M. Kayem and G.J. Mart\'{\i}nez and P. De Oliveira and M. Prokopenko and T. Schubert and P.M.A. Sloot and E. Strano and X.-S. Yang},
year = {2012},
journal = {International Journal of Parallel, Emergent and Distributed Systems},
metis_id = {369714},
url = {http://www.tandfonline.com/doi/full/10.1080/17445760.2012.685884},
doi = {10.1080/17445760.2012.685884},
note = {Available on-line June 21 2012}
}
@inbook{Adamatzky2012c,
title = {Physarum in the Netherlands: Responding to the Flood},
author = {A. Adamatzky and M.H. Lees and P.M.A. Sloot},
year = {2012},
pages = {1--380},
metis_id = {370235},
url = {http://www.worldscibooks.com/chaos/8482.html},
publisher = {World Scientific},
series = {Non Linear Science},
booktitle = {Bioevaluation of World Transport Networks},
editor = {A. Adamatzky},
issn_isbn = {ISBN: 978-981-4407-03-8}
}
@inbook{Adamatzky2012d,
title = {Biorationality of motorways},
author = {A. Adamatzky and S. Akl and R. Alonso-Sanz and W. van Dessel and Z. Ibrahim and A. Ilachinski and J. Jones and A.V.D.M. Kayem and G.J. Mart\'{\i}nez and P. De Oliveira and M. Prokopenko and T. Schubert and P.M.A. Sloot and E. Strano and X.-S. Yang},
year = {2012},
metis_id = {370835},
url = {http://www.worldscibooks.com/chaos/8482.html},
publisher = {World Scientific},
booktitle = {Bioevaluation of World Transport Networks},
editor = {A. Adamatzky},
issn_isbn = {ISBN: 978-981-4407-03-8}
}
@inproceedings{Afanasieva2012a,
title = {Numerical modelling of fullerene synthesis in arc discharge.},
author = {A.S. Afanasieva and S.A. Ponyaev and V.V. Krzhizhanovskaya},
year = {2012},
metis_id = {379175},
url = {http://mir.spbu.ru/index.php?option=com_k2\&view=item\&id=916:phisics_2012\&Itemid=244},
publisher = {PhysicA. St. Petersburg, Ioffe Physical Technical Institute of the Russian Academy of Sciences},
booktitle = {Proceedings of Russian Conference of Young Scientists on Physics and Astronomy},
organization = {Russian Conference of Young Scientists on Physics and Astronomy PhysicA. St. Petersburg},
address = {St. Petersburg}
}
@proceedings{Ali2012a,
title = {Proceedings of the International Conference on Computational Science, ICCS 2012},
author = {H. Ali and Y. Shi and D. Khazanchi and M.H. Lees and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2012},
journal = {Procedia Computer Science},
volume = {9},
number = {0},
url = {http://www.sciencedirect.com/science/journal/18770509/9},
numpages = {2024},
issn_isbn = {ISSN 1877-0509}
}
@misc{Ali2012b,
title = {Empowering Science through Computing, Preface for ICCS 2012},
author = {H. Ali and Y. Shi and D. Khazanchi and M.H. Lees and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2012},
journal = {Procedia Computer Science},
volume = {9},
number = {0},
pages = {1 - 6},
url = {http://www.sciencedirect.com/science/article/pii/S1877050912001226},
doi = {10.1016/j.procs.2012.04.001},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2012},
issn_isbn = {ISSN 1877-0509}
}
@article{Bankhead2012a,
title = {A simulation framework to investigate in vitro viral infection dynamics},
author = {A. Bankhead, III and E. Mancini and A.C. Sims and R.S. Baric and S.K. McWeeney and P.M.A. Sloot},
year = {2012},
journal = {Journal of Computational Science},
metis_id = {352784},
doi = {10.1016/j.jocs.2011.08.007},
note = {In press}
}
@inproceedings{Borgdorff2012a,
title = {A distributed multiscale computation of a tightly coupled model using the Multiscale Modeling Language.},
author = {J. Borgdorff and C. Bona-Casas and M. Mamonski and K. Kurowski and T. Piontek and B. Bosak and K.J. Rycerz and E. Ciepiela and T. Gubala and D. Harezlak and M.T. Bubak and E. Lorenz and A.G. Hoekstra},
year = {2012},
journal = {Procedia Computer Science},
volume = {9},
pages = {596--605},
metis_id = {371896},
url = {http://www.sciencedirect.com/science/article/pii/S1877050912001858},
publisher = {Elsevier},
doi = {10.1016/j.procs.2012.04.064},
keywords = {multiscale modeling, distributed multiscale computing, MML, multiscale modeling language, in-stent restenosis, MUSCLE, QCG-Broker, Gridspace},
organization = {International Conference on Computational Science 2012}
}
@article{Borgdorff2012b,
title = {Multiscale Simulations on Distributed European e-Infrastructures},
author = {J. Borgdorff and D.J. Groen and S. Ferlin and I. Saverchenko and J. Suter and A.G. Hoekstra and P.V. Coveney},
year = {2012},
journal = {Inside},
volume = {10},
number = {1},
pages = {72--77},
metis_id = {378360},
url = {http://inside.hlrs.de/pdfs/inSiDE_spring2012.pdf}
}
@article{Botman2012a,
title = {Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone Nematostella vectensis},
author = {D. Botman and J.A. Kaandorp},
year = {2012},
journal = {BMC Research Notes},
volume = {5},
pages = {555},
metis_id = {376646},
url = {http://www.biomedcentral.com/1756-0500/5/555},
numpages = {19},
doi = {10.1186/1756-0500-5-555}
}
@article{Bui2012a,
title = {A robust approach to extract biomedical events from literature},
author = {Q.C. Bui and P.M.A. Sloot},
year = {2012},
journal = {Bioinformatics},
volume = {28},
number = {20},
pages = {2654--2661},
month = {October},
publisher = {Oxford University Press},
doi = {10.1093/bioinformatics/bts487},
issn_isbn = {Online ISSN 1460-2059 - Print ISSN 1367-4803}
}
@phdthesis{Bui2012b,
title = {Relation extraction methods for biomedical literature},
author = {Q.C. Bui},
year = {2012},
url = {http://dare.uva.nl/record/424695},
month = {September},
numpages = {v + 103},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot},
keywords = {biomedical text mining, relation extraction},
issn_isbn = {978-90-6464-578-5}
}
@article{Chindapol2012a,
title = {Geometric Theory Predicts Bifurcations in Minimal Wiring Cost Trees in Biology Are Flat},
author = {Y. Kim and R. Sinclair and N. Chindapol and J.A. Kaandorp and E. De Schutter},
year = {2012},
journal = {PLoS Comput Biol},
volume = {8},
number = {4},
pages = {e1002474},
url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1002474},
month = {April},
publisher = {Public Library of Science},
doi = {10.1371/journal.pcbi.1002474},
abstract = {Author SummaryMorphology is constrained by function and vice-versa. Often, intricate morphology can be explained by optimization of a cost. However, in biology, the exact form of the cost function is seldom clear. Previously, for many different natural trees authors have reported that most bifurcations are planar and we confirm this here for branching corals and mammalian neurons. In a three-dimensional space, where bifurcations can have many shapes, it is not clear why they are mostly planar. We show, using a geometric proof, that bifurcations that are part of an optimal wiring cost tree should be planar. We demonstrate this by proving that a bifurcation that is not planar cannot be part of an optimal wiring cost tree, using a very general form of wiring cost which applies even when the exact form of the cost function is not known. We conclude that nature selects for developmental mechanisms which produce planar bifurcations.
}
}
@inproceedings{Chirkin2012a,
title = {Signal analysis of flood gate vibrations},
author = {A.M. Chirkin and C.D. Erdbrink and V.V. Krzhizhanovskaya},
year = {2012},
pages = {251--251},
metis_id = {377342},
url = {http://fppo.ifmo.ru/kmu/kmu9/edition_2/2_6.pdf},
publisher = {St. Petersburg NIU ITMO},
series = {2},
booktitle = {Abstracts of All-Russian Congress of Young Scientists, N 2},
note = {In Russian},
organization = {All-Russian Congress of Young Scientists},
address = {St. Petersburg, Russia}
}
@mastersthesis{Dries2012a,
title = {3D mass-spring model for studying early development of the starlet sea anemone nematostella vectensis},
author = {R. Dries},
year = {2012},
month = {July},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: C. Tamulonis, J.A. Kaandorp}
}
@inproceedings{Erdbrink2012a,
title = {Controlling flow-induced vibrations of flood barrier gates with data-driven an d finite-element modelling},
author = {C.D. Erdbrink and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2012},
pages = {102--103},
metis_id = {372368},
publisher = {Taylor \& Francis Group},
booktitle = {Comprehensive Flood Risk Management, Book of abstracts of the 2nd European Conference on FLOODrisk Management},
editor = {Klijn, and Schweckendiek,},
organization = {2nd European Conference on FLOODrisk Management},
address = {London}
}
@inproceedings{Erdbrink2012b,
title = {Controlling flow-induced vibrations of flood barrier gates with data-driven and finite-element modelling},
author = {C.D. Erdbrink and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2012},
pages = {425--434},
metis_id = {377149},
publisher = {Taylor \& Francis Group},
booktitle = {Comprehensive Flood Risk Management},
editor = {Klijn, and Schweckendiek,},
organization = {2nd European Conference on FLOODrisk Management},
address = {London}
}
@article{Erdbrink2012c,
title = {Free-surface flow simulations for discharge-based operation of hydraulic structure gates},
author = {C.D. Erdbrink and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2012},
journal = {Journal of Hydroinformatics},
metis_id = {377339},
url = {http://arxiv.org/abs/1211.4464}
}
@mastersthesis{Firmpas-Nisantzis2012a,
title = {Evolving collective and single cell motility in a computational model of tumor invasion},
author = {P. Firmpas Nisantzis},
year = {2012},
url = {http://dare.uva.nl/en/scriptie/435634},
month = {November},
category = {pwrs, mastersthesis},
numpages = {67},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: R.M.H. Merks, J.A. Kaandorp}
}
@inproceedings{Groen2012a,
title = {A Distributed Infrastructure for Multiscale Biomedical Simulations},
author = {D.J. Groen and J. Borgdorff and S.J. Zasada and C. Bona-Casas and J. Hetherington and R. Nash and A.G. Hoekstra and P.V. Coveney},
year = {2012},
metis_id = {379824},
booktitle = {VPH-2012},
address = {Londen}
}
@inproceedings{Kaandorp2012a,
title = {Multi-scale modeling of gene regulation of morphogenesis},
author = {J.A. Kaandorp and D. Botman and C. Tamulonis and R.M. Dries},
year = {2012},
number = {7318},
pages = {355-362},
url = {http://link.springer.com/chapter/10.1007/978-3-642-30870-3_36},
publisher = {Springer},
doi = {10.1007/978-3-642-30870-3_36},
series = {Lecture Notes in Computer Science},
booktitle = {How the world computes, Turing Centenary Conference and 8th Conference on Computability in Europe},
editor = {S.B. Cooper and A. Dawar and B. Lowe},
address = {Cambridge, UK},
issn_isbn = {ISBN 978-3-642-30869-7}
}
@inproceedings{Konakov2012a,
title = {Computer simulation of a dependency of silicon nitride film chemical composition on gas mixture flow rate in plasma chemical deposition technology (PECVD)},
author = {S.A. Konakov and V.V. Krzhizhanovskaya},
year = {2012},
pages = {95--97},
metis_id = {379173},
url = {http://www.spbforum2012.narod.ru/index.html},
publisher = {St. Petersburg State Polytechnic University},
booktitle = {Proceedings of the Sixth All-Russian National Forum of students, postgraduates and young scientists "Science and Innovation in Technical Universities"},
note = {In Russian},
organization = {Sixth All-Russian National Forum of students, postgraduates and young scientists "Science and Innovation in Technical Universities"},
address = {St. Petersburg}
}
@inproceedings{Konakov2012b,
title = {Simualtion of aminosilane radical formation mechanism in PECVD technology of silicon nitride deposition from nitrogen with a small silane admixture},
author = {S.A. Konakov and V.V. Krzhizhanovskaya},
year = {2012},
volume = {6},
pages = {132--135},
metis_id = {379172},
url = {http://week-science.spbstu.ru/conf2012/about/proceedings/6-FMST.pdf},
publisher = {St. Petersburg State Polytechnic University},
note = {In Russian},
booktitle = {Proceedings of the International conference "The 41st Science Week", V. 6},
organization = {International conference "The 41st Science Week"},
address = {St. Petersburg}
}
@mastersthesis{Kongsgard2012a,
title = {Expertise Modeling on cQA Sites -- News Feed Optimization},
author = {K.W. Kongsgrd},
year = {2012},
url = {http://dare.uva.nl/en/scriptie/440729},
month = {August},
category = {pwrs, mastersthesis},
numpages = {117},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: E. Meij}
}
@article{Koulouzis2012a,
title = {Enabling Web Services to Consume and Produce Large Datasets},
author = {S. Koulouzis and R.S. Cushing and K.A. Karasavvas and A.S.Z. Belloum and M.T. Bubak},
year = {2012},
journal = {IEEE Internet Computing},
volume = {16},
number = {1},
pages = {52--60},
metis_id = {355053},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6030867\&tag=1}
}
@inproceedings{Kozionov2012a,
title = {The research of the time-frequency analysis and classification of signals for detection of objects abnormal behavior},
author = {A.P. Kozionov and A. Pyayt and I.I. Mokhov},
year = {2012},
pages = {22--23},
metis_id = {380030},
booktitle = {Scientific session of the SUAI (St. Petersburg State University of Aerospace Instrumentation), part 1}
}
@inproceedings{Krzhizhanovskaya2012a,
title = {Computational models in flood early warning systems},
author = {V.V. Krzhizhanovskaya and N.B. Melnikova and G.S. Shirshov and F.I. Rusadi and R.G. Belleman and J. Lhomme and B.P. Gouldby and A. Topple and J. Simm},
year = {2012},
pages = {1533},
metis_id = {377151},
url = {http://dare.uva.nl/document/475427},
publisher = {CRC Press},
booktitle = {Comprehensive Flood Risk Management, Book of abstracts of the 2nd European Conference on FLOODrisk Management},
editor = {F. Klijn and T. Schweckendiek},
organization = {2nd European Conference on FLOODrisk Management},
address = {London}
}
@inproceedings{Krzhizhanovskaya2012b,
title = {Modeling Earthen Dikes: Sensitivity Analysis and Calibration of Soil Properties Based on Sensor Data},
author = {V.V. Krzhizhanovskaya and N.B. Melnikova},
year = {2012},
volume = {IV},
pages = {1414--1424},
metis_id = {372359},
publisher = {CMMSE},
booktitle = {Proceedings of the 12th International Conference on Mathematical Methods in Science and Engineering},
editor = {Vigo-Aguiar,J.},
organization = {12th International Conference on Mathematical Methods in Science and Engineering},
address = {Murcia, Spain}
}
@inproceedings{Krzhizhanovskaya2012c,
title = {Modelling Dikes and Floods on HPC Clouds},
author = {V.V. Krzhizhanovskaya},
year = {2012},
pages = {10--11},
metis_id = {377341},
url = {http://promo.escience.ifmo.ru/content/files/abs.pdf},
booktitle = {Book of abstracts of the International Young Scientists Conference on High Performance Computing and Simulation},
organization = {International Young Scientists Conference on High Performance Computing and Simulation, YSC 2012},
address = {Amsterdam}
}
@inproceedings{Krzhizhanovskaya2012d,
title = {Information Technologies and Software Packages for Education of Masters of Science in Materials Science},
author = {V.V. Krzhizhanovskaya and S.V. Ryaboshuk},
year = {2012},
pages = {87--89},
metis_id = {379176},
url = {http://www.diag.ru/dl_files/I2T_sbornik.pdf},
publisher = {MIEM},
booktitle = {Proceedings of the International Conference on Innovative Information Technologies (I2T)},
editor = {Uvaysov,S.U.},
organization = {International Conference on Innovative Information Technologies (I2T). Prague, Czech},
address = {Moscow}
}
@inproceedings{Lebanin2012a,
title = {A model of reaction kinetics for two neutral particles in gases and plasmas},
author = {V.S. Lebanin and V.V. Krzhizhanovskaya},
year = {2012},
volume = {6},
pages = {146--149},
metis_id = {377350},
url = {http://week-science.spbstu.ru/conf2012/about/proceedings/6-FMST.pdf},
publisher = {St. Petersburg State Polytechnic University},
note = {In Russian},
booktitle = {Proceedings of the International conference "The 41st Science Week", V. 6},
organization = {International conference "The 41st Science Week"},
address = {St. Petersburg}
}
@article{Mancini2012a,
title = {HIV Reservoirs and Immune Surveillance Evasion Cause the Failure of Structured Treatment Interruptions: A Computational Study},
author = {E. Mancini and F. Castiglione and M. Bernaschi and A. de Luca and P.M.A. Sloot},
year = {2012},
journal = {PLoS ONE},
volume = {7},
number = {4},
pages = {e36108},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0036108},
month = {April},
publisher = {Public Library of Science},
doi = {10.1371/journal.pone.0036108},
abstract = {Continuous antiretroviral therapy is currently the most effective way to treat HIV infection. Unstructured interruptions are quite common due to side effects and toxicity, among others, and cannot be prevented. Several attempts to structure these interruptions failed due to an increased morbidity compared to continuous treatment. The cause of this failure is poorly understood and often attributed to drug resistance. Here we show that structured treatment interruptions would fail regardless of the emergence of drug resistance. Our computational model of the HIV infection dynamics in lymphoid tissue inside lymph nodes, demonstrates that HIV reservoirs and evasion from immune surveillance themselves are sufficient to cause the failure of structured interruptions. We validate our model with data from a clinical trial and show that it is possible to optimize the schedule of interruptions to perform as well as the continuous treatment in the absence of drug resistance. Our methodology enables studying the problem of treatment optimization without having impact on human beings. We anticipate that it is feasible to steer new clinical trials using computational models.
}
}
@inproceedings{Mordvintsev2012a,
title = {Simulation of City Evacuation Coupled to Flood Dynamics},
author = {A. Mordvintsev and V.V. Krzhizhanovskaya and M.H. Lees and P.M.A. Sloot},
year = {2012},
pages = {156--158},
metis_id = {372362},
publisher = {ETH Zurich},
booktitle = {Proceedings of the 6th International Conference on Pedestrian and Evacuation Dynamics. Book of abstracts.},
organization = {6th International Conference on Pedestrian and Evacuation Dynamics},
address = {Zurich}
}
@inproceedings{Mountrakis2012a,
title = {Modelling the transport behaviour of platelets in intracranial aneurysms},
author = {Mountrakis,L. and E. Lorenz and A.G. Hoekstra},
year = {2012},
metis_id = {379819},
booktitle = {VPH-2012},
address = {Londen}
}
@article{Pengel2012a,
title = {Flood Early Warning System: Sensors and Internet},
author = {B. Pengel and G.S. Shirshov and V.V. Krzhizhanovskaya and N.B. Melnikova and A. Koelewijn and A.L. Pyayt and I.I. Mokhov},
year = {2012},
journal = {Journal of Flood Risk Management},
metis_id = {355141},
note = {Submitted to the Journal of Flood Risk Management.}
}
@inproceedings{Prosnikov2012a,
title = {A review of methods and software packages for simulation of nanosystems},
author = {Prosnikov,M.A. and V.V. Krzhizhanovskaya},
year = {2012},
volume = {6},
pages = {128--130},
metis_id = {379171},
url = {http://week-science.spbstu.ru/conf2012/about/proceedings/6-FMST.pdf},
publisher = {St. Petersburg State Polytechnic University},
note = {In Russian},
booktitle = {Proceedings of the International conference "The 41st Science Week", V. 6},
organization = {International conference "The 41st Science Week"},
address = {St. Petersburg}
}
@inproceedings{Pyayt2012a,
title = {Data-driven methods in UrbanFlood project for flood defence structure measurements analysis},
author = {A.L. Pyayt and I.I. Mokhov and A. Kozionov and V. Kusherbaeva},
year = {2012},
metis_id = {354320},
organization = {2nd European Conference on FLOODrisk Management}
}
@inproceedings{Pyayt2012b,
title = {Signal Processing Methods for Flood Early Warning Systems},
author = {A.L. Pyayt and I.I. Mokhov and A. Kozionov and V. Kusherbaeva and V.V. Krzhizhanovskaya and B.J. Broekhuijsen and R.J. Meijer},
year = {2012},
pages = {1--8},
metis_id = {372357},
booktitle = {Proceedings of the 10th International Conference on Hydroinformatics -- HIC 2012},
editor = {R. Hinkelmann and M.H. Nasermoaddeli and S.Y. Liong and D. Savic and P. Fr\"ohle and K.F. Daemrich},
organization = {Conference on Hydroinformatics -- HIC 2012}
}
@inproceedings{Pyayt2012c,
title = {Data-driven modelling for flood defence structure analysis},
author = {A.L. Pyayt and I.I. Mokhov and A. Kozionov and V. Kusherbaeva and B. Lang and V.V. Krzhizhanovskaya and R.J. Meijer},
year = {2012},
pages = {77--77},
metis_id = {372367},
publisher = {Taylor \& Francis Group},
booktitle = {Comprehensive Flood Risk Management, Book of abstracts of the 2nd European Conference on FLOODrisk Management},
editor = {Klijn, and Schweckendiek,},
organization = {2nd European Conference on FLOODrisk Management},
address = {London}
}
@inproceedings{Pyayt2012d,
title = {Data-driven modelling for flood defence structure analysis},
author = {A.L. Pyayt and I.I. Mokhov and A. Kozionov and V. Kusherbaeva and B. Lang and V.V. Krzhizhanovskaya and R.J. Meijer},
year = {2012},
pages = {301--306},
metis_id = {377155},
publisher = {Taylor \& Francis Group},
booktitle = {Comprehensive Flood Risk Management},
editor = {Klijn, and Schweckendiek,},
organization = {2nd European Conference on FLOODrisk Management},
address = {London}
}
@article{Qiu2012a,
title = {Understanding Complex Dynamics in Derivatives Finance: Why do Options Markets Smile?},
author = {G. Qiu and B.D. Kandhai and N.F. Johnson and P.M.A. Sloot},
year = {2012},
journal = {Advances in Complex Systems},
volume = {15},
number = {5},
pages = {1250050},
metis_id = {370074},
url = {http://www.worldscinet.com/acs/00/preserved-docs/0002/S0219525912500506.pdf},
numpages = {19},
doi = {10.1142/S0219525912500506}
}
@article{Quax2012a,
title = {Information processing reveals how microscopic components affect the macroscopic system-state in complex networks},
author = {R. Quax and A. Apolloni and P.M.A. Sloot},
year = {2012},
journal = {Scientific Reports},
metis_id = {352578},
url = {http://arxiv.org/abs/1111.5483}
}
@article{Ramos-Silva2012a,
title = {Novel molluskan biomineralization proteins retrieved from proteomics: a case study with Upsalin},
author = {P. Ramos-Silva and S. Benhamada and N. Le Roy and B. Marie and N. Guichard and I. Zannella-Cl\'eon and L. Plasseraud and M. Corneillat and G. Alcaraz and J.A. Kaandorp and F. Marin},
year = {2012},
journal = {ChemBioChem},
volume = {13},
number = {7},
pages = {1067--1078},
metis_id = {380123},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22474002}
}
@inproceedings{Simm2012a,
title = {Interpreting sensor measurements in dikes - experiences from UrbanFlood pilot sites},
author = {J. Simm and D. Jordan and A. Topple and I.I. Mokhov and A. Pyayt and T. Abdoun and V. Bennett and B.J. Broekhuijsen and R.J. Meijer},
year = {2012},
pages = {327--336},
metis_id = {354321},
publisher = {Taylor \& Francis Group},
booktitle = {Comprehensive Flood Risk Management},
editor = {Klijn, and Schweckendiek,},
organization = {2nd European Conference on FLOODrisk Management},
address = {London}
}
@inproceedings{Simm2012b,
title = {Interpreting sensor measurements in dikes - experiences from UrbanFlood pilot sites},
author = {J. Simm and D. Jordan and A. Topple and I.I. Mokhov and A. Pyayt and T. Abdoun and V. Bennett and B.J. Broekhuijsen and R.J. Meijer},
year = {2012},
pages = {81--82},
metis_id = {354320},
publisher = {Taylor \& Francis Group},
booktitle = {Comprehensive Flood Risk Management, Book of abstracts of the 2nd European Conference on FLOODrisk Management},
editor = {Klijn, and Schweckendiek,},
organization = {2nd European Conference on FLOODrisk Management},
address = {London}
}
@article{Sloot2012a,
title = {Information processing as a paradigm to model and simulate complex systems},
author = {P.M.A. Sloot and R. Quax},
year = {2012},
journal = {Journal of Computational Science},
pages = {247--249},
month = {September},
doi = {10.1016/j.jocs.2012.07.001},
note = {editorial},
issn_isbn = {ISSN: 1877-7503}
}
@inproceedings{Szepieniec2012a,
title = {On Importance of Service Level Management in Grids},
author = {T. Szepieniec and J. Kocot and T. Schaaf and O. Appleton and M. Heikkurinen and A.S.Z. Belloum and J. Serrat-Fernandez and M.L. Metzker},
year = {2012},
volume = {7156},
number = {7156},
pages = {64--75},
publisher = {Springer},
doi = {10.1007/978-3-642-29740-3_9},
series = {Lecture Notes in Computer Science},
booktitle = {Euro-Par 2011: Parallel Processing Workshops},
editor = {M. Alexander and P. D'Ambra and A.S.Z. Belloum and G. Bosilca and M. Cannataro and M. Danelutto and B. Martino and M. Gerndt and E. Jeannot and R. Namyst and J. Roman and S.L. Scott and J.L. Tr\"aff and G. Vall\'ee and J. Weidendorfer},
organization = {7th International European Conference on Parallel and Distributed Computing},
issn_isbn = {ISBN: 978-3-642-29739-7}
}
@inproceedings{Tahir2012a,
title = {Modelling the influence of re-endothelialization on in-stent restenosis},
author = {H. Tahir and C. Bona-Casas and A.G. Hoekstra},
year = {2012},
metis_id = {379821},
booktitle = {VPH-2012},
address = {Londen}
}
@inproceedings{Varma2012a,
title = {Embodying a Patient Avatar for Computational Workflows},
author = {S. Varma and C. Pedronaci and D. Kalra and M.C. Villa Uriol and P. Lamata and E. Schileo and B. \'O Nuall\'ain and N.S.H. Smith and S. Wood and D.R. Hose},
year = {2012},
metis_id = {385970},
booktitle = {VPH Conference 2012, London},
note = {varma2012embodying}
}
@inproceedings{Varma2012b,
title = {Patient-Centred Multi-scale Computational Workflows},
author = {S. Varma and M.C. Villa Uriol and P. Lamata and E. Schileo and B. \'O Nuall\'ain and J. Fenner and N.S.H. Smith and D.R. Hose},
year = {2012},
metis_id = {385969},
booktitle = {VPH Conference 2012, London},
note = {varma2012patient}
}
@article{Zarrabi2012a,
title = {Combining Epidemiological and Genetic Networks Signifies the Importance of Early Treatment in HIV-1 Transmission},
author = {N. Zarrabi and M.C.F. Prosperi and R.G. Belleman and M. Colafigli and A. De Luca and P.M.A. Sloot},
year = {2012},
journal = {PLoS One},
volume = {7},
number = {9},
pages = {e46156},
metis_id = {373816},
url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046156},
month = {September},
numpages = {15},
publisher = {Public Library of Science},
doi = {10.1371/journal.pone.0046156}
}
@inproceedings{Zasada2012a,
title = {Distributed Infrastructure for Multiscale Computing},
author = {S.J. Zasada and M. Mamonski and D.J. Groen and J. Borgdorff and I. Saverchenko and T. Piontek and K. Kurowski and P.V. Coveney},
year = {2012},
pages = {65--74},
metis_id = {378362},
url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6365101},
publisher = {IEEE Computer Society},
booktitle = {Distributed Simulation and Real Time Applications (DS-RT), 2012 IEEE/ACM 16th International Symposium on},
editor = {Boukerche,A. and Cahill,V. and El-Saddik,A. and Theodoropoulos,G. and Walshe,R.},
organization = {Distributed Simulation and Real Time Applications (DS-RT), 2012 IEEE/ACM 16th International Symposium on},
address = {Dublin, Ireland}
}
@inproceedings{Afanasieva2011a,
title = {Modelling the processes of fullerene synthesis in arc discharge technology},
author = {A.S. Afanasieva and V.V. Krzhizhanovskaya and Ponyaev,S.A.},
year = {2011},
volume = {6},
pages = {129--131},
metis_id = {379177},
url = {http://week-science.spbstu.ru/upload/xl/6-xl.pdf},
publisher = {St. Petersburg State Polytechnic University},
note = {In Russian},
booktitle = {Proceedings of the International conference "The 40th Science Week", V. 6},
organization = {International conference "The 40th Science Week"},
address = {St. Petersburg}
}
@phdthesis{Altintas2011a,
title = {Collaborative provenance for workflow-driven science and engineering},
author = {I. Altintas},
year = {2011},
url = {http://dare.uva.nl/en/record/365434},
month = {February},
numpages = {xiv+153},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot; co-promotor: Prof. Dr. B. Lud\"ascher},
keywords = {scientific workflows; provenance; collaborative eScience; querying provenance},
issn_isbn = {ISBN13: 978-90-9025979-6}
}
@article{Altintas2011b,
title = {A Data Model for Analyzing User Collaborations in Workflow-Driven eScience},
author = {I. Altintas and M.K. Anand and T. Vuong and S. Bowers and B. Lud\"ascher and P.M.A. Sloot},
year = {2011},
journal = {The International Journal of Computers and Their Applications (IJCA)},
volume = {18},
number = {3},
pages = {160--179},
url = {Altintas2011b.pdf},
month = {Dec.},
issn_isbn = {ISSN 1076-5204}
}
@inproceedings{Bankhead2011a,
title = {A Simulation Framework to Investigate in vitro Viral Infection Dynamics},
author = {A. Bankhead, III and E. Mancini and A.C. Sims and R.S. Baric and S.K. McWeeney and P.M.A. Sloot},
year = {2011},
volume = {4},
number = {1},
pages = {1798-1807},
metis_id = {346507},
url = {http://dx.doi.org/10.1016/j.procs.2011.04.195},
publisher = {Elsevier},
doi = {10.1016/j.procs.2011.04.195},
series = {Procedia Computer Science},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2011},
editor = {M. Sato and S. Matsuoka and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
keywords = {Virtual Dike; flow; porous media; structural dynamics; flood protection; early warning system; UrbanFlood},
issn_isbn = {ISSN 1877-0509}
}
@article{Belloum2011a,
title = {Collaborative e-Science and scientific workflows},
author = {A.S.Z. Belloum and M.A. Inda and D. Vasunin and V.V. Korkhov and Z. Zhao and H. Rauwerda and T.M. Breit and M.T. Bubak and L.O. Hertzberger},
year = {2011},
journal = {Internet Computing},
volume = {15},
number = {4},
pages = {39--47},
metis_id = {348587},
url = {http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=\&arnumber=5934851},
publisher = {IEEE},
doi = {10.1109/MIC.2011.87},
issn_isbn = {ISSN 1089-7801}
}
@inproceedings{Bernsdorf2011a,
title = {Towards Distributed Multiscale Simulation of Biological Processes},
author = {J.M. Bernsdorf and G. Berti and B. Chopard and J. Hegewald and M. Krafczyk and E. Lorenz and A.G. Hoekstra and D. Wang},
year = {2011},
pages = {89--96},
metis_id = {353913},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6130736},
publisher = {IEEE Computer Society Press},
doi = {10.1109/eScienceW.2011.19},
booktitle = {Proceedings of the 7th IEEE conference on e-Science},
organization = {e-Science Workshops (eScienceW), 2011 IEEE Seventh International Conference on},
issn_isbn = {ISBN: 978-1-4673-0026-1}
}
@inproceedings{Berretz2011a,
title = {Actor-driven workflow execution in distributed environments},
author = {F. Berretz and S. Skorupa and V. Sander and A.S.Z. Belloum and M.T. Bubak},
year = {2011},
volume = {6586},
pages = {287--294},
metis_id = {328942},
url = {http://dx.doi.org/10.1007/978-3-642-21878-1_36},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Euro-Par 2010 parallel processing workshops: HeteroPar, HPPC, HiBB, CoreGrid, UCHPC, HPCF, PROPER, CCPI, VHPC: Ischia, Italy, August 31-September 3, 2010: Revised selected papers},
editor = {M.R. Guarracino and F. Vivien and J.L. Tr\"aff and M. Cannataro and M. Danelutto and A. Hast and F. Perla and A. Kn\"upfer and B. Di Martino and M. Alexander},
organization = {CoreGRID/ERCIM Workshop on Grids, Clouds and P2P Computing, Ischia, Italy},
address = {Heidelberg}
}
@inproceedings{Borgdorff2011a,
title = {A principled approach to Distributed Multiscale Computing, from formalization to execution},
author = {J. Borgdorff and J.-L. Falcone and E. Lorenz and B. Chopard and A.G. Hoekstra},
year = {2011},
pages = {97--104},
metis_id = {351108},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6130737},
publisher = {IEEE Computer Society Press},
doi = {10.1109/eScienceW.2011.9},
booktitle = {Proceedings of the 7th IEEE conference on e-Science},
organization = {e-Science Workshops (eScienceW), 2011 IEEE Seventh International Conference on},
address = {Stockholm, Sweden},
issn_isbn = {ISBN: 978-1-4673-0026-1}
}
@inproceedings{Botman2011a,
title = {An integrated approach to infer the gene network in early development of the cnidarian Nematostella venctensis},
author = {D. Botman and J.A. Kaandorp and P.M.A. Sloot},
year = {2011},
pages = {101--101},
metis_id = {354845},
url = {http://www.hydra-meeting.de/docs/programm2011.pdf},
booktitle = {Searching for Eve: Basal metazoans and the evolution of multicellular complexity},
note = {abstract},
editor = {T.C.G. Bosch and T.W. Holstein},
organization = {International Workshop: Searching for Eve},
address = {Tutzing, Germany}
}
@inproceedings{Botman2011b,
title = {An integrated approach to infer the gene network in early development of the cnidarian Nematostella vectensis.},
author = {D. Botman and J.A. Kaandorp},
year = {2011},
metis_id = {354818},
url = {http://isnb.amc.uva.nl/isnb2011/abstracts1.html#Daniel%20Botman},
organization = {ISNB 2011: The 8th International Symposium on Networks in Bioinformatics},
address = {Amsterdam}
}
@article{Bui2011a,
title = {A hybrid approach to extract protein-protein interactions},
author = {Q.C. Bui and S. Katrenko and P.M.A. Sloot},
year = {2011},
journal = {Bioinformatics},
volume = {27},
number = {2},
pages = {259--265},
metis_id = {329797},
url = {http://bioinformatics.oxfordjournals.org/content/early/2010/11/08/bioinformatics.btq620.full.pdf+html},
numpages = {7},
doi = {10.1093/bioinformatics/btq620},
abstract = {Motivation: Protein-protein interactions (PPIs) play an important role in understanding biological processes. Although recent research in text mining has achieved a significant progress in automatic PPI extraction from literature, performance of existing systems still needs to be improved.Results: In this study, we propose a novel algorithm for extracting PPIs from literature which consists of two phases. First, we automatically categorize the data into subsets based on its semantic properties and extract candidate PPI pairs from these subsets. Second, we apply support vector machines (SVM) to classify candidate PPI pairs using features specific for each subset. We obtain promising results on five benchmark datasets: AIMed, BioInfer, HPRD50, IEPA, and LLL with F-scores ranging from 60% to 84%, which are comparable to the state-of-the-art PPI extraction systems. Furthermore, our system achieves the best performance on cross-corpora evaluation and comparative performance in terms of computational efficiency.Availability: The source code and scripts used in this paper are available for academic use at http://staff.science.uva.nl/~bui/PPIs.zipContact: bqchinh@gmail.com}
}
@inproceedings{Bui2011b,
title = {Extracting Biological Events from Text Using Simple Syntactic Patterns},
author = {Q.C. Bui and P.M.A. Sloot},
year = {2011},
pages = {143--146},
metis_id = {373815},
url = {http://www.aclweb.org/anthology/W11-18.pdf},
publisher = {Association for Computational Linguistics},
booktitle = {Proceedings of BioNLP Shared Task 2011 Workshop},
organization = {BioNLP Shared Task 2011 Workshop},
address = {Portland Oregon}
}
@article{Caiazzo2011a,
title = {A Complex Automata approach for in-stent restenosis: Two-dimensional multiscale modelling and simulations},
author = {A. Caiazzo and D.E. Evans and J.-L. Falcone and J. Hegewald and E. Lorenz and B. Stahl and D. Wang and J.M. Bernsdorf and B. Chopard and J. Gunn and D.R. Hose and M. Krafczyk and P.V. Lawford and R.H. Smallwood and D. Walker and A.G. Hoekstra},
year = {2011},
journal = {Journal of Computational Science},
volume = {2},
number = {1},
pages = {9--17},
metis_id = {353916},
url = {http://www.sciencedirect.com/science/article/pii/S1877750311000056}
}
@inproceedings{Chopard2011a,
title = {A Framework for Multiscale and Multiscience Modeling and Numerical Simulations},
author = {B. Chopard and J.-L. Falcone and A.G. Hoekstra and J. Borgdorff},
year = {2011},
journal = {Lecture Notes in Computer Science},
volume = {6714},
pages = {2--8},
metis_id = {372344},
publisher = {Springer},
editor = {Calude,C and Kari,J and Petre,I and Rozenberg,G},
booktitle = {Unconventional Computation}
}
@inproceedings{Cushing2011a,
title = {Service Level Management for Executable Papers},
author = {R.S. Cushing and S. Koulouzis and A.S.Z. Belloum and R.J. Strijkers and M.T. Bubak},
year = {2011},
metis_id = {349052},
url = {http://dx.doi.org/10.1007/978-3-642-23400-2},
doi = {10.1007/978-3-642-23397-5},
booktitle = {7th International European Conference on Parallel and Distributed Computing (Euro-Par 2011), workshop MDGS2011},
organization = {17th International Conference on Parallel and Distributed Computing}
}
@inproceedings{Cushing2011b,
title = {Prediction-based Auto-scaling of Scientific Workflows},
author = {R.S. Cushing and S. Koulouzis and A.S.Z. Belloum and M.T. Bubak},
year = {2011},
pages = {1--6},
metis_id = {349075},
booktitle = {9th International Workshop on Middleware for Grids, Clouds and e-Science - MG},
organization = {MGC workshop conjunction with ACM/IFIP/USENIX 12th International Middleware Conference 2011}
}
@inproceedings{Cushing2011c,
title = {Dynamic Handling for Cooperating Scientific Web Services},
author = {R.S. Cushing and S. Koulouzis and A.S.Z. Belloum and M.T. Bubak},
year = {2011},
pages = {232--239},
metis_id = {349045},
publisher = {IEEE},
booktitle = {The seventh e-Science conference},
organization = {The seventh e-Science conference}
}
@phdthesis{Ertaylan2011a,
title = {A multi-scale approach for deciphering HIV infection},
author = {G. Ertaylan},
year = {2011},
metis_id = {332917},
url = {http://dare.uva.nl/en/record/367568},
month = {February},
category = {Virolab},
numpages = {144},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot},
keywords = {modeling; HIV; infection; protein interaction; network},
issn_isbn = {ISBN13 978-90-9025974-10}
}
@inproceedings{Gerhards2011a,
title = {HisT/PLIER: A Two-Fold Provenance Approach for Grid-Enabled Scientific Workflows Using WS-VLAM},
author = {M. Gerhards and S. Skorupa and V. Sander and A.S.Z. Belloum and D. Vasunin and A. Benabdelkader},
year = {2011},
pages = {224 -225},
metis_id = {349076},
month = {Sept.},
doi = {10.1109/Grid.2011.39},
booktitle = {Grid Computing (GRID), 2011 12th IEEE/ACM International Conference on},
issn_isbn = {ISSN 1550-5510}
}
@article{Hammel2011a,
title = {The non-hierarchical, non-uniformly branching topology of a leuconoid sponge aquiferous system revealed by 3D reconstruction and morphometrics using corrosion casting and X-ray microtomography},
author = {J.U. Hammel and M.V. Filatov and J. Herzen and F. Beckmann and J.A. Kaandorp and M. Nickel},
year = {2011},
journal = {Acta Zoologica},
metis_id = {342734},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1463-6395.2010.00492.x/abstract},
numpages = {12},
doi = {10.1111/j.1463-6395.2010.00492.x},
note = {preview}
}
@inproceedings{Javaheri2011a,
title = {A Particle-Based Model for Aggregate Formation in Biomineralization},
author = {N. Javaheri and C. Mendes Cronemberger and J.A. Kaandorp},
year = {2011},
pages = {23--23},
metis_id = {341217},
url = {http://biomintec.ibim.cnr.it/images/stories/book_abstracts.pdf},
month = {February},
publisher = {IBIM institute},
booktitle = {Molecular Biomineralization in marine organisms: Nanobiotechnology and biomedical application},
note = {abstract},
editor = {V. Matranga},
organization = {Biomintec International Workshop},
address = {Palermo, Italy}
}
@mastersthesis{Jnes2011a,
title = {Efficient integration of multiscale N-body systems},
author = {J. J\"anes},
year = {2011},
url = {http://dare.uva.nl/en/scriptie/411597},
month = {July},
category = {pwrs, mastersthesis},
numpages = {55},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: F.I. Pelupessy and S.F. Portegies Zwart}
}
@inproceedings{Kaandorp2011a,
title = {A spatial model of calcification in scleractinian corals},
author = {J.A. Kaandorp and C. Mendes Cronemberger and L. Huisman},
year = {2011},
pages = {14--14},
metis_id = {351113},
url = {http://biomintec.ibim.cnr.it/images/stories/book_abstracts.pdf},
month = {February},
publisher = {IBIM institute},
booktitle = {Molecular Biomineralization in marine organisms: Nanobiotechnology and biomedical application},
note = {abstract},
editor = {V. Matranga},
organization = {Biomintec International Workshop},
address = {Palermo, Italy}
}
@inproceedings{Kaandorp2011b,
title = {Simulating and quantifying the environmental influence on coral growth and form},
author = {J.A. Kaandorp and M.V. Filatov and N. Chindapol},
year = {2011},
volume = {Part 3},
pages = {177--185},
metis_id = {332800},
publisher = {Springer-verlag},
doi = {10.1007/978-94-007-0114-4_11},
booktitle = {Coral Reefs: An Ecosystem in Transition},
editor = {Z. Dubinsky and N. Stambler},
address = {Heidelberg}
}
@inproceedings{Kiseleva2011a,
title = {Modelling argon plasma in plasma chemical deposition reactor by ESI CFD-ACE+ software package},
author = {I.S. Kiseleva and V.V. Krzhizhanovskaya},
year = {2011},
volume = {6},
pages = {126--128},
metis_id = {379349},
url = {http://week-science.spbstu.ru/upload/xl/6-xl.pdf},
publisher = {St. Petersburg State Polytechnic University},
note = {In Russian},
booktitle = {Proceedings of the International conference "The 40th Science Week", V. 6},
organization = {International conference "The 40th Science Week"},
address = {St. Petersburg}
}
@inproceedings{Konakov2011a,
title = {Comparison of two models of plasma chemical processes in silicon nitride deposition technology},
author = {S.A. Konakov and V.V. Krzhizhanovskaya},
year = {2011},
volume = {6},
pages = {132--134},
metis_id = {379178},
url = {http://week-science.spbstu.ru/upload/xl/6-xl.pdf},
publisher = {St. Petersburg State Polytechnic University},
note = {In Russian},
booktitle = {Proceedings of the International conference "The 40th Science Week", V. 6},
organization = {International conference "The 40th Science Week"},
address = {St. Petersburg}
}
@inproceedings{Konakov2011b,
title = {Modeling PECVD deposition process of multilayered structures based on silicon nitride},
author = {S.A. Konakov and V.V. Krzhizhanovskaya},
year = {2011},
volume = {6},
pages = {12--13},
metis_id = {379180},
publisher = {St. Petersburg State Polytechnic University},
note = {Best presentation award. In Russian},
booktitle = {Proceedings of the Fifth All-Russian Forum "Science and Innovation in Technical Universities"},
organization = {International conference "The 40th Science Week"},
address = {St. Petersburg}
}
@inproceedings{Krzhizhanovskaya2011a,
title = {Virtual Dike and Flood Simulator: Parallel distributed computing for flood early warning systems},
author = {V.V. Krzhizhanovskaya and N.B. Melnikova and G.S. Shirshov and N.N. Shabrov},
year = {2011},
pages = {365--373},
metis_id = {344525},
url = {http://omega.sp.susu.ac.ru/books/conference/PaVT2011/short/139.pdf},
publisher = {Publishing Centre of the South Ural State University},
booktitle = {Proceedings of the International Conference on Parallel Computational Technologies (PAVT-2011)},
organization = {International Conference on Parallel Computational Technologies (PAVT-2011)},
address = {Chelyabinsk}
}
@inproceedings{Krzhizhanovskaya2011b,
title = {Flood early warning system: design, implementation and computational modules},
author = {V.V. Krzhizhanovskaya and G.S. Shirshov and N.B. Melnikova and R.G. Belleman and F.I. Rusadi and B.J. Broekhuijsen and B.P. Gouldby and J. Lhomme and B. Bali\'s and M.T. Bubak and A.L. Pyayt and I.I. Mokhov and A.V. Ozhigin and B. Lang and R.J. Meijer},
year = {2011},
volume = {4},
number = {1},
pages = {106 - 115},
metis_id = {346508},
url = {http://www.sciencedirect.com/science/article/pii/S1877050911000706},
publisher = {Elsevier},
doi = {10.1016/j.procs.2011.04.012},
series = {Procedia Computer Science},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2011},
editor = {M. Sato and S. Matsuoka and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
keywords = {UrbanFlood; early warning system; flood; modeling; dike stability; Flood Simulator; Virtual Dike; artificial intelligence; neural clouds},
issn_isbn = {ISSN 1877-0509}
}
@inproceedings{Krzhizhanovskaya2011c,
title = {Challenges and Solutions in Simulation of Multiphysics Multiscale Systems},
author = {V.V. Krzhizhanovskaya},
year = {2011},
metis_id = {355138},
publisher = {ACEEE in association with IET-UK},
booktitle = {International Conference on Advances in Recent Technologies in Communication \& Computing -- ARTCom},
note = {abstract}
}
@inproceedings{Lebanin2011a,
title = {A review of plasma chemical methods of silicon nitride production},
author = {V.S. Lebanin and V.V. Krzhizhanovskaya},
year = {2011},
volume = {6},
pages = {131--132},
metis_id = {379179},
url = {http://week-science.spbstu.ru/upload/xl/6-xl.pdf},
publisher = {St. Petersburg State Polytechnic University},
note = {In Russian},
booktitle = {Proceedings of the International conference "The 40th Science Week", V. 6},
organization = {International conference "The 40th Science Week"},
address = {St. Petersburg}
}
@article{Leguy2011a,
title = {Global sensitivity analysis of a wave propagation model for arm arteries},
author = {C.A.D. Leguy and E.M.H. Bosboom and A.S.Z. Belloum and A.P. Hoek and F.N. van de Vosse},
year = {2011},
journal = {Medical Engineering \& Physics},
volume = {8},
number = {33},
pages = {1008--1016},
metis_id = {349043},
url = {http://dx.doi.org/10.1016/j.medengphy.2011.04.003}
}
@inproceedings{Lorenz2011a,
title = {Distributions of Cluster Sizes in Shear-Thickening, Suspensions derived from a Statistical Clustering Model},
author = {E. Lorenz and A.G. Hoekstra},
year = {2011},
journal = {Philosophical transactions of the Royal Society of London. Series A, mathematical, physical and engineering sciences},
metis_id = {327892},
url = {http://rsta.royalsocietypublishing.org/search},
booktitle = {DSFD 2010}
}
@article{Lorenz2011b,
title = {Heterogeneous Multiscale Simulations of Suspension Flow},
author = {E. Lorenz and A.G. Hoekstra},
year = {2011},
journal = {Multiscale Modeling \& Simulation : A SIAM Interdisciplinary Journal},
volume = {9},
number = {4},
pages = {1301--1326},
metis_id = {353911},
url = {http://epubs.siam.org/mms/resource/1/mmsubt/v9/i4/p1301_s1},
doi = {10.1137/100818522}
}
@article{Lorenz2011c,
title = {Heterogeneous multiscale simulations of suspension flow},
author = {E. Lorenz and A.G. Hoekstra},
year = {2011},
journal = {Multiscale Modeling \& Simulation : A SIAM Interdisciplinary Journal},
volume = {9},
number = {4},
pages = {1301--1326},
metis_id = {372337},
url = {http://dx.doi.org/10.1137/100818522}
}
@incollection{Maltsev2011a,
title = {Optics of White Blood Cells: optical models, simulations, and experiments},
author = {V.P. Maltsev and A.G. Hoekstra and M.A. Yurkin},
year = {2011},
metis_id = {372341},
publisher = {Wiley-VCH Verlag GmbH \& Co},
booktitle = {Advanced Optical Flow Cytometry: Methods and Disease Diagnoses, First Edition},
editor = {Tuchin,V.V}
}
@article{Mei2011a,
title = {Increasing risk behaviour can outweigh the benefits of antiretroviral drug treatment on the HIV incidence among men-having-sex-with-men in Amsterdam},
author = {S. Mei and R. Quax and D.A.M.C. van de Vijver and Y. Zhu and P.M.A. Sloot},
year = {2011},
journal = {BMC Infectious Diseases},
volume = {11},
number = {118},
url = {http://www.biomedcentral.com/1471-2334/11/118},
numpages = {17},
doi = {10.1186/1471-2334-11-118},
abstract = {Background: The transmission through contacts among MSM (men who have sex with men) is one of the dominating contributors to HIV prevalence in industrialized countries. In Amsterdam, the capital of the Netherlands, the MSM risk group has been traced for decades. This has motivated studies which provide detailed information about MSM's risk behavior statistically, psychologically and sociologically. Despite the era of potent antiretroviral therapy, the incidence of HIV among MSM increases. In the long term the contradictory effects of risk behavior and effective therapy are still poorly understood. Methods: Using a previously presented Complex Agent Network model, we describe steady and casual partnerships to predict the HIV spreading among MSM. Behavior-related parameters and values, inferred from studies on Amsterdam MSM, are fed into the model; we validate the model using historical yearly incidence data. Subsequently, we study scenarios to assess the contradictory effects of risk behavior and effective therapy, by varying corresponding values of parameters. Finally, we conduct quantitative analysis based on the resulting incidence data. Results: The simulated incidence reproduces the ACS historical incidence well and helps to predict the HIV epidemic among MSM in Amsterdam. Our results show that in the long run the positive influence of effective therapy can be outweighed by an increase in risk behavior of at least 30% for MSM. Conclusion: We recommend, based on the model predictions, that lowering risk behavior is the prominent control mechanism of HIV incidence even in the presence of effective therapy.}
}
@inproceedings{Melnikova2011a,
title = {Virtual Dike: multiscale simulation of dike stability},
author = {N.B. Melnikova and G.S. Shirshov and V.V. Krzhizhanovskaya},
year = {2011},
volume = {4},
number = {1},
pages = {791 - 800},
metis_id = {346509},
url = {http://www.sciencedirect.com/science/article/pii/S1877050911001426},
publisher = {Elsevier},
doi = {10.1016/j.procs.2011.04.084},
series = {Procedia Computer Science},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2011},
editor = {M. Sato and S. Matsuoka and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
keywords = {Virtual Dike; flow; porous media; structural dynamics; flood protection; early warning system; UrbanFlood},
issn_isbn = {ISSN 1877-0509}
}
@article{MoGcicki,
title = {Processing moldable tasks on the grid: Late job binding with lightweight user-level overlay},
author = {J.T. Mo\'scicki and M. Lamanna and M.T. Bubak and P.M.A. Sloot},
year = {2011},
journal = {Future Generation Computer Systems},
volume = {27},
number = {6},
pages = {725--736},
metis_id = {342778},
month = {June},
doi = {10.1016/j.future.2011.02.002},
keywords = {Grid computing; Quality of service; Moldable task processing; Late binding; Agent scheduling; Pilot jobs; Applications; Interoperability},
issn_isbn = {ISSN 0167-739X}
}
@phdthesis{MoGcicki,
title = {Understanding and mastering dynamics in computing grids: processing moldable tasks with user-level overlay},
author = {J.T. Mo\'scicki},
year = {2011},
metis_id = {333467},
url = {http://dare.uva.nl/en/record/373814},
month = {April},
numpages = {viii+178},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. M.T. Bubak; co-promotor: Prof. Dr. P.M.A. Sloot},
keywords = {grid computing; task scheduling; Quality of Service applications; interoperability}
}
@article{Murtaza2011a,
title = {Cellular Automata Simulations on a FPGA cluster},
author = {S. Murtaza and A.G. Hoekstra and P.M.A. Sloot},
year = {2011},
journal = {International Journal of High Performance Computing Applications},
volume = {25},
number = {2},
pages = {193--204},
metis_id = {346510},
url = {http://dx.doi.org/10.1177/1094342010383138},
doi = {10.1177/1094342010383138}
}
@phdthesis{Naumov2011a,
title = {Modelling with Cellular Automata: Problem Solving Environments and Multidimensional Applications},
author = {L.A. Naumov},
year = {2011},
metis_id = {343177},
url = {http://dare.uva.nl/en/record/377630},
month = {June},
numpages = {iv+136 issn_isbn = ISBN 978-90-5776-225-3},
school = {Universiteit van Amsterdam},
tutor = {Promotor: prof.dr. P.M.A. Sloot, co-promotor: dr.ir. A.G. Hoekstra},
keywords = {computational science; cellular automata; modelling; generalised coordinates; tumour growth}
}
@article{Naumov2011b,
title = {Cellular automata models of tumour natural shrinkage},
author = {L.A. Naumov and A.G. Hoekstra and P.M.A. Sloot},
year = {2011},
journal = {Physica A},
volume = {390},
number = {12},
pages = {2283--2290},
metis_id = {342779},
month = {June},
doi = {10.1016/j.physa.2011.02.006},
keywords = {Cellular automaton; Tumour; Cell; Shrinkage; Computational biology},
issn_isbn = {ISSN 0378-4371}
}
@mastersthesis{Niculescu2011a,
title = {Towards a cell-based model of Neointimal Hyperplasia with Cellular Potts Model},
author = {I. Niculescu},
year = {2011},
url = {Niculescu2011a.pdf},
month = {April},
category = {pwrs, mastersthesis},
numpages = {78},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: A.G. Hoekstra and R.M.H. Merks}
}
@inproceedings{Pengel2011a,
title = {Flood early warning system: sensors and internet},
author = {B. Pengel and G.S. Shirshov and V.V. Krzhizhanovskaya and A.R. Koelewijn and I.I. Mokhov and A.L. Pyayt and N.B. Melnikova},
year = {2011},
pages = {212--221},
metis_id = {354305},
url = {http://www.ifi-home.info/icfm-icharm/Proceedings.html},
publisher = {ICHARM},
booktitle = {Abstract proceedings: 5th International CConference on Flood Management (ICFM5): Floods: from Risk to Opportunity: 27 to 29 September 2011, Tokyo-Japan},
organization = {5th International Conference on Flood Management (ICFM5)}
}
@inproceedings{Pengel2011b,
title = {The urbanflood early warning system: sensors and coastal flood safety},
author = {B. Pengel and L.R. Wentholt and V.V. Krzhizhanovskaya and G.S. Shirshov and N.B. Melnikova and J. Simm and A. Koelewijn and A.L. Pyayt and I.I. Mokhov and N. Pals and R.J. Meijer},
year = {2011},
booktitle = {Proceedings of the CoastGIS Conference},
note = {accepted},
organization = {CoastGIS Conference},
address = {Oostende, Belgium}
}
@misc{Prosperi2011a,
title = {Correction: Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models},
author = {M.C.F. Prosperi and M. Rosen-Zvi and A. Altmann and M. Zazzi and S. Di Giambenedetto and R. Kaiser and E. Sch\"ulter and D. Struck and P.M.A. Sloot and D.A.M.C. van de Vijver and A.-M. Vandamme and A. S\"onnerborg and for the EuResist and Virolab study groups},
year = {2011},
journal = {PLoS ONE},
volume = {6},
number = {4},
month = {October},
numpages = {1},
publisher = {Public Library of Science},
note = {Erratum for PLoS One. 2010;5(10). doi:10.1371/journal.pone.0013753},
doi = {10.1371/annotation/d0254103-21b9-4078-836b-57ba5bd1c26a}
}
@inproceedings{Pyayt2011a,
title = {Machine Learning Methods for Environmental Monitoring and Flood Protection},
author = {A.L. Pyayt and I.I. Mokhov and B. Lang and V.V. Krzhizhanovskaya and R.J. Meijer},
year = {2011},
journal = {World Academy of Science, Engineering and Technology},
volume = {78},
pages = {118--123},
metis_id = {354302},
url = {http://www.waset.org/journals/waset/v78/v78-23.pdf},
organization = {International Conference on Artificial Intelligence and Neural Networks (ICAINN) 2011}
}
@inproceedings{Pyayt2011b,
title = {Artificial Intelligence and Finite Element Modelling for Monitoring Flood Defence Structures},
author = {A.L. Pyayt and I.I. Mokhov and A. Kozionov and V. Kusherbaeva and N.B. Melnikova and V.V. Krzhizhanovskaya and R.J. Meijer},
year = {2011},
metis_id = {354306},
url = {http://dx.doi.org/10.1109/EESMS.2011.6067047},
organization = {2011 IEEE Workshop on Environmental, Energy, and Structural Monitoring Systems (EESMS)}
}
@phdthesis{Qiu2011a,
title = {Understanding the complex dynamics of financial markets through microsimulation},
author = {G. Qiu},
year = {2011},
metis_id = {329507},
url = {http://dare.uva.nl/en/record/367230},
month = {February},
category = {ComputationalFinance},
numpages = {vi, 141},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. B.D. Kandhai},
keywords = {microsimulation, financial markets},
issn_isbn = {ISBN13 978-94-91211-01-0}
}
@article{Quax2011a,
title = {SEECN: SIMULATING COMPLEX SYSTEMS USING DYNAMIC COMPLEX NETWORKS},
author = {R. Quax and D.A. Bader and P.M.A. Sloot},
year = {2011},
journal = {International Journal for Multiscale Computational Engineering, Special Section},
volume = {9},
number = {2},
pages = {201--214},
metis_id = {352731},
url = {http://www.begellhouse.com/journals/61fd1b191cf7e96f,510397234a1cbb30,16e7b6d5061ecf29.html},
doi = {10.1615/IntJMultCompEng.v9.i2.50},
abstract = {Multiscale, multiphysics systems are too complex for traditional mathematical modeling and require numerical simulation, yet such systems arise everywhere from modeling the immune system and protein interaction to epidemic spread in a human population. Unfortunately, at present researchers create their own ad hoc programs for their particular study. To address this problem we present the simulator for efficient evolution on complex networks (SEECN), an expressive simulator of complex systems that optimizes for both single-core and parallel performance. In SEECN, a complex network represents the system where the nodes and edges have specified properties that dictate the dynamics of the network over time. Our application is a detailed model of HIV spread among men who have sex with men and serves to show the simulator's expressiveness and to evaluate its performance.}
}
@inproceedings{Ramos-Silva2011a,
title = {Finding patterns and differences on biomineralization-related proteins from Metazoans},
author = {P. Ramos-Silva and C. Combet and F. Marin and J.A. Kaandorp},
year = {2011},
pages = {21--21},
url = {http://biomintec.ibim.cnr.it/images/stories/book_abstracts.pdf},
month = {February},
publisher = {IBIM institute},
booktitle = {Molecular Biomineralization in marine organisms: Nanobiotechnology and biomedical application},
note = {abstract},
editor = {V. Matranga},
organization = {Biomintec International Workshop},
address = {Palermo, Italy}
}
@proceedings{Sato2011a,
title = {Proceedings of the International Conference on Computational Science, ICCS 2011},
year = {2011},
volume = {4},
number = {1},
url = {http://www.sciencedirect.com/science/publication?issn=18770509\&volume=4\&issue=1},
numpages = {2354},
publisher = {Elsevier},
series = {Procedia Computer Science},
editor = {M. Sato and S. Matsuoka and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
issn_isbn = {ISSN 1877-0509}
}
@misc{Sato2011b,
title = {Preface},
author = {M. Sato and S. Matsuoka and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2011},
volume = {4},
number = {1},
pages = {1 - 6},
url = {http://www.sciencedirect.com/science/article/pii/S1877050911000597},
publisher = {Elsevier},
doi = {10.1016/j.procs.2011.04.001},
series = {Procedia Computer Science},
booktitle = {Proceedings of the International Conference on Computational Science, ICCS 2011},
editor = {M. Sato and S. Matsuoka and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
issn_isbn = {ISSN 1877-0509}
}
@mastersthesis{Speelman2011a,
title = {Position-Based Quantum Cryptography and the Garden-Hose Game},
author = {F. Speelman},
year = {2011},
url = {http://dare.uva.nl/en/scriptie/397555},
month = {August},
category = {pwrs, mastersthesis},
numpages = {34},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: H. Buhrman, C. Schaffner}
}
@inproceedings{Strijkers2011a,
title = {Toward executable scientific publications},
author = {R.J. Strijkers and R.S. Cushing and D. Vasyunin and C.T.A.M. de Laat and A.S.Z. Belloum and R. Meijer},
year = {2011},
journal = {Procedia Computer Science},
volume = {4},
pages = {707--715},
metis_id = {349050},
url = {http://dx.doi.org/10.1016/j.procs.2011.04.074},
publisher = {Elsevier},
editor = {Sato,M. and Matsuoka,S. and Sloot,P.M. and van Albada,G.D. and Dongarra,J.},
organization = {International Conference on Computational Science (ICCS 2011), Singapore},
booktitle = {Proceedings of the International Conference on Computational Science (ICCS 2011)},
address = {Amsterdam}
}
@article{Tahir2011a,
title = {Multi-scale simulations of the dynamics of in-stent restenosis: impact of stent deployment and design},
author = {H. Tahir and A.G. Hoekstra and E. Lorenz and P.V. Lawford and D.R. Hose and J. Gunn and D.J.W. Evans},
year = {2011},
journal = {Interface Focus},
volume = {1},
number = {3},
pages = {365--373},
metis_id = {343614},
url = {http://rsfs.royalsocietypublishing.org/content/early/2011/03/24/rsfs.2010.0024.abstract},
publisher = {Royal Society},
doi = {10.1098/rsfs.2010.0024},
abstract = {Neointimal hyperplasia, a process of smooth muscle cell re-growth, is the result of a natural wound healing response of the injured artery after stent deployment. Excessive neointimal hyperplasia following coronary artery stenting results in in-stent restenosis (ISR). Regardless of recent developments in the field of coronary stent design, ISR remains a significant complication of this interventional therapy. The influence of stent design parameters such as strut thickness, shape and the depth of strut deployment within the vessel wall on the severity of restenosis has already been highlighted but the detail of this influence is unclear. These factors impact on local haemodynamics and vessel structure and affect the rate of neointima formation. This paper presents the first results of a multi-scale model of ISR. The development of the simulated restenosis as a function of stent deployment depth is compared with an in vivo porcine dataset. Moreover, the influence of strut size and shape is investigated, and the effect of a drug released at the site of injury, by means of a drug-eluting stent, is also examined. A strong correlation between strut thickness and the rate of smooth muscle cell proliferation has been observed. Simulation results also suggest that the growth of the restenotic lesion is strongly dependent on the stent strut cross-sectional profile.},
issn_isbn = {ISSN 2042-8901}
}
@article{Tamulonis2011a,
title = {A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering},
author = {C. Tamulonis and M. Postma and H.Q. Marlow and C.R. Magie and J. de Jong and J.A. Kaandorp},
year = {2011},
journal = {Developmental Biology},
volume = {351},
number = {1},
pages = {217--228},
metis_id = {332804},
url = {http://dx.doi.org/10.1016/j.ydbio.2010.10.017},
doi = {10.1016/j.ydbio.2010.10.017}
}
@article{Tamulonis2011b,
title = {Modeling Filamentous Cyanobacteria Reveals the Advantages of Long and Fast Trichomes for Optimizing Light Exposure},
author = {C.V.T. Tamulonis and M. Postma and J.A. Kaandorp},
year = {2011},
journal = {PLoS One},
volume = {6},
number = {7},
metis_id = {351118},
url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0022084}
}
@mastersthesis{Teunissen2011a,
title = {Particle based 3D modeling of positive streamer inception},
author = {J. Teunissen},
year = {2011},
url = {http://dare.uva.nl/en/scriptie/401596},
month = {November},
category = {pwrs, mastersthesis},
numpages = {26},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisor: U. Ebert}
}
@mastersthesis{Thorsdottir2011a,
title = {Conservation Properties of the Hamiltonian Particle-Mesh method for the Quasi-Geostrophic Equations on a sphere},
author = {H. orsdottir},
year = {2011},
url = {http://dare.uva.nl/en/scriptie/427273},
month = {November},
category = {pwrs, mastersthesis},
numpages = {39},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisor: J. Frank}
}
@article{Yurkin2011a,
title = {The discrete-dipole-approximation code ADDA: Capabilities and known limitations},
author = {M.A. Yurkin and A.G. Hoekstra},
year = {2011},
journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
volume = {112},
pages = {2234--2247},
metis_id = {372342}
}
@inproceedings{Zarrabi2011a,
title = {Inferring HIV transmission networks from epidemic and genetic information},
author = {N. Zarrabi and M.C.F. Prosperi and A. de Luca and P.M.A. Sloot},
year = {2011},
metis_id = {354806},
url = {www.eccs2011.eu/eccs11bookofabstracts.pdf},
booktitle = {European Conference on Complex Systems, ECCS'11}
}
@inproceedings{Afanasieva2010a,
title = {Advantages of the OpenFOAM open-source software package for numerical simulation of gas and plasma dynamics problems [In Russian]},
author = {A.S. Afanasieva and V.V. Krzhizhanovskaya},
year = {2010},
volume = {6},
pages = {114--116},
metis_id = {344522},
publisher = {St. Petersburg State Polytechnic University},
booktitle = {Proceedings of the International conference "The 39th Science Week". V. 6.},
organization = {International conference "The 39th Science Week"}
}
@article{Altintas2010a,
title = {Understanding Collaborative Studies through Interoperable Workflow Provenance},
author = {I. Altintas and M.K. Anand and D. Crawl and S. Bowers and A.S.Z. Belloum and P. Missier and B. Lud\"ascher and C.A. Goble and P.M.A. Sloot},
year = {2010},
journal = {Lecture Notes in Computer Science},
volume = {6378},
pages = {42--58},
metis_id = {328943},
url = {http://www.springerlink.com/content/2338355nj46j4547/},
publisher = {Springer},
doi = {10.1007/978-3-642-17819-1_6},
editor = {D.L. McGuinness, J.R. Michaelis and L. Moreau},
organization = {Provenance and annotation of data and processes: The 3rd International Provenance and Annotation Workshop (IPAW 2010), Troy, NY, USA},
booktitle = {Provenance and Annotation of Data and Processes}
}
@inproceedings{Bar2010a,
title = {Running parallel applications with topology-aware grid middleware},
author = {P. Bar and C. Coti and D.J. Groen and T. Herault and V. Kravtsov and A. Schuster and M. Swain},
year = {2010},
pages = {292--299},
url = {Bar2010a.pdf},
publisher = {IEEE Computer Society},
doi = {10.1109/e-Science.2009.48},
booktitle = {Proceedings of the 2009 Fifth IEEE International Conference on e-Science},
abstract = {The concept of topology-aware grid applications is derived from parallelized computational models of complex systems that are executed on heterogeneous resources, either because they require specialized hardware for certain calculations, or because their parallelization is flexible enough to exploit such resources. Here we describe two such applications, a multi-body simulation of stellar evolution, and an evolutionary algorithm that is used for reverse-engineering gene regulatory networks. We then describe the topology-aware middleware we have developed to facilitate the ``modeling-implementing-executing'' cycle of complex systems applications. The developed middleware allows topology-aware simulations to run on geographically distributed clusters with or without firewalls between them. Additionally, we describe advanced coallocation and scheduling techniques that take into account the applications topologies. Results are given based on running the topology-aware applications on the Grid'5000 infrastructure.},
address = {Piscataway, NJ},
issn_isbn = {ISBN:978-0-7695-3877-8}
}
@inproceedings{Baryshnikova2010a,
title = {Model development of a PECVD reactor for titanium dioxide film deposition [in Russian]},
author = {M.V. Baryshnikova and V.V. Krzhizhanovskaya},
year = {2010},
pages = {148--150},
metis_id = {344095},
publisher = {Saint Petersburg State Polytechnic University},
booktitle = {Best papers of the International Conference "38th Science Week"},
organization = {International Conference "38th Science Week", Saint Petersburg, Russia},
address = {Saint Petersburg, Russia}
}
@inproceedings{Baryshnikova2010b,
title = {Simulation of Complex Gas Feed Systems in PECVD Reactors for Synthesis of Titanium Dioxide and Nickel Thin Films},
author = {M.V. Baryshnikova and V.A. Zverev and I.S. Kiseleva and V.V. Krzhizhanovskaya},
year = {2010},
pages = {301--302},
metis_id = {344096},
publisher = {VVM Publishing Co},
booktitle = {Proceedings of The Sixth International Conference on Computational Fluid Dynamics},
address = {Saint Petersburg, Russia}
}
@proceedings{Bellavista2010a,
author = {P. Bellavista and R.-S. Chang and H.-C. Chao and S.-F. Lin and P.M.A. Sloot},
year = {2010},
volume = {6104},
url = {http://www.springer.com/computer/theoretical+computer+science/book/978-3-642-13066-3},
month = {May},
note = {5th International Conference, CPC 2010, Hualien, Taiwan, May 10-13, 2010, Proceedings},
doi = {10.1007/978-3-642-13067-0},
series = {Lecture Notes in Computer Science},
booktitle = {Advances in Grid and Pervasive Computing},
publisher = {Springer},
keywords = {ad-hoc networks, ambient intelligence, cloud computing, distributed algorithms, distributed computing, distributed processing, e-commerce, mobile agents, p2p, resource management, semantic grid, sensor networks},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13: 978-3-642-13066-3}
}
@proceedings{Bellavista2010b,
title = {Advances in Grid and Pervasive Computing: 5th International Conference, GPC 2010, Hualien, Taiwan, May 10-13, 2010: Proceedings},
author = {P. Bellavista and R.-S. Chang and H.-C. Chao and S.-F. Lin and P.M.A. Sloot},
year = {2010},
metis_id = {325517},
url = {http://dx.doi.org/10.1007/978-3-642-13067-0},
publisher = {Springer},
booktitle = {Advances in Grid and Pervasive Computing},
note = {Bellavista2010a 5th International Conference, CPC 2010, Hualien, Taiwan, May 10-13, 2010, Proceedings}
}
@inproceedings{Belleman2010a,
title = {Visualization in Computational Science},
author = {R.G. Belleman},
year = {2010},
volume = {1},
number = {1},
pages = {1689 - 1690},
metis_id = {325518},
url = {http://www.sciencedirect.com/science/article/B9865-506HM1Y-6P/2/b9a808d81c2ce182eb095eded81c3891},
month = {May},
note = {Proceedings of the $10^th$ International Conference on Computational Science, May 31 - June 2, Amsterdam},
doi = {10.1016/j.procs.2010.04.189},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
publisher = {Elsevier B.V.},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
abstract = {This section and the papers that follow relate to to the workshop on Visualization in Computational Science which is held at the Tenth International Conference on Computational Science (ICCS2010) in Amsterdam, the Netherlands. This workshop brings together experts from visualization research and end-users to illustrate the state of the art and advance potential areas of common interest.},
address = {Amsterdam},
issn_isbn = {ISSN: 1877-0509}
}
@inproceedings{Belleman2010b,
title = {Interactive flood simulation and visualisation on a multitouch table},
author = {R.G. Belleman and F.I. Rusadi and G.S. Shirshov and V.V. Krzhizhanovskaya and B. J Broekhuijzen},
year = {2010},
pages = {16--16},
metis_id = {344519},
booktitle = {Proceedings of the Joint UrbanFlood \& SSG4Env Workshop on Monitoring and Flood Safety},
organization = {Joint UrbanFlood \& SSG4Env Workshop on Monitoring and Flood Safety},
address = {Amsterdam, The Netherlands}
}
@inproceedings{Berretz2010a,
title = {Towards an actor-driven workflow management system for Grids},
author = {F. Berretz and S. Skorupa and V. Sander and A.S.Z. Belloum},
year = {2010},
pages = {611--616},
metis_id = {328944},
url = {http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=05478458},
doi = {10.1109/CTS.2010.5478458},
booktitle = {International Symposium on Collaborative Technologies and Systems (CTS 2010), Chicago, IL, USA},
organization = {International Symposium on Collaborative Technologies and Systems (CTS 2010), Chicago, IL, USA}
}
@inproceedings{Berretz2010b,
title = {A novel approach to Workflow Management in Grid Environments},
author = {F. Berretz and S. Skorupa and A.S.Z. Belloum and B. Schuller and V. Sander},
year = {2010},
pages = {99--100},
metis_id = {328946},
url = {http://indico.cern.ch/contributionDisplay.py?contribId=52\&sessionId=31\&confId=69338},
booktitle = {5th EGEE User Forum 2010/Book of Contributions.},
editor = {Floros,E.},
organization = {5th EGEE User Forum 2010},
address = {Upsala}
}
@inproceedings{Botman2010a,
title = {An integrated approach to infer and model the gene network in early development of the cnidarian Nematostella vectensis},
author = {D. Botman and J.A. Kaandorp},
year = {2010},
pages = {62--62},
metis_id = {332899},
url = {https://togather.eu/view-abstractbook?collection_id=76},
booktitle = {Euro ISRS symposium 2010: Reefs in a changing environment, book of abstracts},
note = {abstract},
editor = {Kaandorp,J.A. and Meesters,E. and Osinga,R. and Verreth,J.A.J. and Wijgerde,T.H.M.},
organization = {Euro ISRS symposium 2010}
}
@article{Bui2010a,
title = {Extracting causal relations on HIV drug resistance from literature},
author = {Q.C. Bui and B. \'O Nuall\'ain and C.A.B. Boucher and P.M.A. Sloot},
year = {2010},
journal = {BMC Bioinformatics},
volume = {11},
number = {1},
pages = {101},
url = {http://www.biomedcentral.com/1471-2105/11/101},
numpages = {11},
note = {PubMedID 20178611},
doi = {10.1186/1471-2105-11-101},
abstract = {BACKGROUND:In HIV treatment it is critical to have up-to-date resistance data of applicable drugs since HIV has a very high rate of mutation. These data are made available through scientific publications and must be extracted manually by experts in order to be used by virologists and medical doctors. Therefore there is an urgent need for a tool that partially automates this process and is able to retrieve relations between drugs and virus mutations from literature.RESULTS:In this work we present a novel method to extract and combine relationships between HIV drugs and mutations in viral genomes. Our extraction method is based on natural language processing (NLP) which produces grammatical relations and applies a set of rules to these relations. We applied our method to a relevant set of PubMed abstracts and obtained 2,434 extracted relations with an estimated performance of 84% for F-score. We then combined the extracted relations using logistic regression to generate resistance values for each pair. The results of this relation combination show more than 85% agreement with the Stanford HIVDB for the ten most frequently occurring mutations. The system is used in 5 hospitals from the Virolab project http://www.virolab.org to preselect the most relevant novel resistance data from literature and present those to virologists and medical doctors for further evaluation.CONCLUSIONS:The proposed relation extraction and combination method has a good performance on extracting HIV drug resistance data. It can be used in large-scale relation extraction experiments. The developed methods can also be applied to extract other type of relations such as gene-protein, gene-disease, and disease-mutation.},
issn_isbn = {ISSN 1471-2105}
}
@inbook{Cui2010a,
title = {Simulating Calcineurin-Centered Calcium Signaling Network in Cardiac Myocytes},
author = {J. Cui and J.A. Kaandorp and P.M.A. Sloot and P.S. Thiagarajan},
year = {2010},
pages = {111--127},
metis_id = {312413},
url = {https://www.novapublishers.com/catalog/product_info.php?products_id=11091},
publisher = {Nova Publishers},
series = {Cardiology Research and Clinical Developments},
booktitle = {Congestive Heart Failure: Symptoms, Causes and Treatment},
editor = {J.E. Garc\'{\i}a and V.R. Wright},
issn_isbn = {ISBN 978-1-60876-677-2}
}
@mastersthesis{Daub2010a,
title = {A cell-based model of extracellular-matrix-guided endothelial cell migration during angiogenesis},
author = {J. Daub},
year = {2010},
url = {http://oai.cwi.nl/oai/asset/17513/17513B.pdf},
month = {June},
category = {pwrs, mastersthesis},
numpages = {76},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: R.M.H. Merks, J.A. Kaandorp}
}
@inproceedings{Dijk2010a,
title = {Individual-based simulation of sexual selection: A quantitative genetic approach},
author = {D. van Dijk and P.M.A. Sloot and J.C. Tay and M.C. Schut},
year = {2010},
volume = {1},
number = {1},
pages = {2003 - 2011},
url = {http://www.sciencedirect.com/science/article/B9865-506HM1Y-7Y/2/cf445059be996607b2556bcc343b3ad3},
month = {May},
note = {Proceedings of the $10^th$ International Conference on Computational Science, May 31 - June 2, Amsterdam},
doi = {10.1016/j.procs.2010.04.224},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
publisher = {Elsevier B.V.},
abstract = {Sexual selection has been mathematically modeled using quantitative genetics as well as population genetics. Two-locus simulation models have been used to study the evolution of male display and female preference. We present an individual-based simulation model of sexual selection in a quantitative genetic context. We show that under certain conditions Fisherian self-reinforcing sexual selection takes effect, predicted by Lande's analytic model of female choice. We also show that the dynamics involved in the co-evolution of male display and female preference is much more complex than mathematics would predict. We therefore argue that the study of sexual selection through individual-based simulation could give new and more realistic insight into a world dominated by overly simplified equations.},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
keywords = {Sexual selection, Individual-based modeling, Agent-based modeling},
address = {Amsterdam},
issn_isbn = {ISSN: 1877-0509}
}
@article{Dijk2010b,
title = {Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks},
author = {D. van Dijk and G. Ertaylan and C.A.B. Boucher and P.M.A. Sloot},
year = {2010},
journal = {BMC Systems Biology},
volume = {4},
number = {1},
pages = {96},
url = {http://www.biomedcentral.com/1752-0509/4/96},
numpages = {17},
note = {PubMedID 20633292},
doi = {10.1186/1752-0509-4-96},
abstract = {Background The National Institute of Allergy and Infectious Diseases has launched the HIV-1 Human Protein Interaction Database in an effort to catalogue all published interactions between HIV-1 and human proteins. In order to systematically investigate these interactions functionally and dynamically, we have constructed an HIV-1 human protein interaction network. This network was analyzed for important proteins and processes that are specific for the HIV life-cycle. In order to expose viral strategies, network motif analysis was carried out showing reoccurring patterns in virus-host dynamics. Results Our analyses show that human proteins interacting with HIV form a densely connected and central sub-network within the total human protein interaction network. The evaluation of this sub-network for connectivity and centrality resulted in a set of proteins essential for the HIV life-cycle. Remarkably, we were able to associate proteins involved in RNA polymerase II transcription with hubs and proteasome formation with bottlenecks. Inferred network motifs show significant over-representation of positive and negative feedback patterns between virus and host. Strikingly, such patterns have never been reported in combined virus-host systems. Conclusions HIV infection results in a reprioritization of cellular processes reflected by an increase in the relative importance of transcriptional machinery and proteasome formation. We conclude that during the evolution of HIV, some patterns of interaction have been selected for resulting in a system where virus proteins preferably interact with central human proteins for direct control and with proteasomal proteins for indirect control over the cellular processes. Finally, the patterns described by network motifs illustrate how virus and host interact with one another.},
issn_isbn = {ISSN 1752-0509}
}
@inproceedings{Falcone2010a,
title = {MML: towards a Multiscale Modeling Language},
author = {J.-L. Falcone and B. Chopard and A.G. Hoekstra},
year = {2010},
volume = {1},
number = {1},
pages = {819 - 826},
metis_id = {325520},
url = {http://www.sciencedirect.com/science/article/B9865-506HM1Y-34/2/a6d0938aba23bd1fcc55b7e5831d0bf7},
month = {May},
note = {Proceedings of the $10^th$ International Conference on Computational Science, May 31 - June 2, Amsterdam},
doi = {10.1016/j.procs.2010.04.089},
abstract = {Recent multiscale applications require more and more often the coupling of many sub-models, usually originating form different fields of science. Therefore, it is increasingly important to propose an effective description language that can help scientists with different background to co-develop a multiscale application. We propose a Multiscale Modeling Language (MML) i.e. a description language aiming at specifying the architecture of a multiscale simulation program. We will illustrate this approach by proposing a MML description of a computer model for restenosis in a stented vessel.},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
publisher = {Elsevier B.V.},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
keywords = {Multiscale modeling, Description language, Cellular automata, Lattice Boltzmann method, Scale separation},
address = {Amsterdam},
issn_isbn = {ISSN: 1877-0509}
}
@article{Filatov2010a,
title = {A comparison between coral colonies of the genus Madracis and simulated forms},
author = {M.V. Filatov and J.A. Kaandorp and M. Postma and R. van Liere and K.J. Kruszynski and M.J.A. Vermeij and G.J. Streekstra and R.P.M. Bak},
year = {2010},
journal = {Proceedings of the Royal Society of London. Series B-Biological Sciences},
volume = {277},
number = {1700},
pages = {3555--3561},
metis_id = {332801},
doi = {10.1098/rspb.2010.0957}
}
@phdthesis{Fomekong-Nanfack2010a,
title = {Genetic regulatory networks inference : modeling, parameters estimation \& model validation},
author = {Y. Fomekong-Nanfack},
year = {2010},
url = {http://dare.uva.nl/en/record/335069},
month = {April},
numpages = {xiv + 212},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr.J.A. Kaandorp}
}
@article{Frade2010a,
title = {Semi-permeable species boundaries in the coral genus Madracis: Introgression in a brooding coral system},
author = {P.R. Frade and M.C. Reyes-Nivia and J. Faria and J.A. Kaandorp and P.C. Luttikhuizen and R.P.M. Bak},
year = {2010},
journal = {Molecular Phylogenetics and Evolution},
volume = {57},
number = {3},
pages = {1072--1090},
metis_id = {332802},
doi = {10.1016/j.ympev.2010.09.010}
}
@article{Frentz2010a,
title = {Comparison of HIV-1 Genotypic Resistance Test Interpretation Systems in Predicting Virological Outcomes Over Time},
author = {D. Frentz and C.A.B. Boucher and M. Assel and A. De Luca and M. Fabbiani and F. Incardona and P. Libin and N. Manca and V. M\"uller and B. \'O Nuall\'ain and R. Paredes and M.C.F. Prosperi and E. Quiros-Roldan and L. Ruiz and P.M.A. Sloot and C. Torti and A.-M. Vandamme and K. van Laethem and M. Zazzi and D.A.M.C. van de Vijver},
year = {2010},
journal = {PLoS ONE},
volume = {5},
number = {7},
pages = {e11505},
metis_id = {327398},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0011505},
month = {July},
numpages = {9},
publisher = {Public Library of Science},
doi = {10.1371/journal.pone.0011505},
abstract = {Background Several decision support systems have been developed to interpret HIV-1 drug resistance genotyping results. This study compares the ability of the most commonly used systems (ANRS, Rega, and Stanford's HIVdb) to predict virological outcome at 12, 24, and 48 weeks. Methodology/Principal Findings Included were 3763 treatment-change episodes (TCEs) for which a HIV-1 genotype was available at the time of changing treatment with at least one follow-up viral load measurement. Genotypic susceptibility scores for the active regimens were calculated using scores defined by each interpretation system. Using logistic regression, we determined the association between the genotypic susceptibility score and proportion of TCEs having an undetectable viral load (\<50 copies/ml) at 12 (8-16) weeks (2152 TCEs), 24 (16-32) weeks (2570 TCEs), and 48 (44-52) weeks (1083 TCEs). The Area under the ROC curve was calculated using a 10-fold cross-validation to compare the different interpretation systems regarding the sensitivity and specificity for predicting undetectable viral load. The mean genotypic susceptibility score of the systems was slightly smaller for HIVdb, with 1.92-1.17, compared to Rega and ANRS, with 2.22-1.09 and 2.23-1.05, respectively. However, similar odds ratio's were found for the association between each-unit increase in genotypic susceptibility score and undetectable viral load at week 12; 1.6 [95% confidence interval 1.5-1.7] for HIVdb, 1.7 [1.5-1.8] for ANRS, and 1.7 [1.9-1.6] for Rega. Odds ratio's increased over time, but remained comparable (odds ratio's ranging between 1.9-2.1 at 24 weeks and 1.9-2.2 at 48 weeks). The Area under the curve of the ROC did not differ between the systems at all time points; p?=?0.60 at week 12, p?=?0.71 at week 24, and p?=?0.97 at week 48. Conclusions/Significance Three commonly used HIV drug resistance interpretation systems ANRS, Rega and HIVdb predict virological response at 12, 24, and 48 weeks, after change of treatment to the same extent.}
}
@inproceedings{Gerhards2010a,
title = {A History-tracing XML-based Provenance Framework for Workflows},
author = {M. Gerhards and A.S.Z. Belloum and F. Berretz and V. Sander and S. Skorupa},
year = {2010},
pages = {1--10},
metis_id = {328941},
url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5671873},
doi = {10.1109/WORKS.2010.5671873},
booktitle = {5th Workshop on Workflows in Support of Large-Scale Science},
address = {New Orleans, USA},
issn_isbn = {ISBN 978-1-4244-8989-3}
}
@inproceedings{Gouldby2010a,
title = {Multiscale modelling in real-time flood forecasting systems: From sand grain to dike failure and inundation},
author = {B.P. Gouldby and V.V. Krzhizhanovskaya and J. Simm},
year = {2010},
volume = {1},
number = {1},
pages = {809 - 809},
url = {http://www.sciencedirect.com/science/article/B9865-506HM1Y-32/2/e25dd5b085af0d40ba86381dee79a20b},
month = {May},
note = {Proceedings of the $10^th$ International Conference on Computational Science, May 31 - June 2, Amsterdam},
doi = {10.1016/j.procs.2010.04.087},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
publisher = {Elsevier B.V.},
abstract = {Severe events around the globe have highlighted the threat to life, infrastructure and the environment posed by flooding. Flood forecasting systems are a vital component of broader flood risk management activities. These systems are becoming increasingly more sophisticated as their importance in reducing life loss and economic damages is realized. Part of this increase in complexity is focused on the ability to predict and warn of failures in dykes, levees and embankments. A new European ICT project, UrbanFlood for Environmental Services and Climate Change Adaptation, has recently been commissioned and is introduced in this presentation. The primary objective of the Urban Flood project is to develop early warning systems that will monitor flood protection systems in real-time, identify vulnerable locations, model the failure and predict dike collapse and subsequent inundation. In combination with the damage assessment, Urban Flood will serve as an advanced decision support system, mitigating the impact of seasonal and catastrophic floods. Modeling is one of the key tasks in the project. The models will be required to simulate the behavior of the material properties of the layered dikes (sand, clay, peat, grass or concrete cover, metal frame, dam gates, etc.), during extreme hydraulic loading events. In earthen dikes, extra challenge is posed by the non-linear elastic plastic properties of the deformable clay. A realistic simulation of the dike will model the free-surface water dynamics; convective and diffusive transfer of water inside the porous materials; dynamic response of clay to the water pressure; structural mechanics, deformation and actual dike breakdown and flood. The models shall cover a wide range of scales from a sand grain to a flooded city. The time scales will range from seconds (for water penetrating the soil) to hours (for dike collapse dynamics and ocean tides). Eventually, the models will predict the influence of seasonal and global changes on the stability of flood defense systems. Full 3D transient simulation of dike failure with subsequent inundation will require significant computing resources. The project started three months ago, and we will present the plan for developing the modeling cascade for the system. This work is supported by the UrbanFlood European Union project N 248767, theme ICT-2009.6.4},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
keywords = {Flood, Forecast, Modeling, Multiscale, Dike failure, Inundation, UrbanFlood},
address = {Amsterdam},
issn_isbn = {ISSN: 1877-0509}
}
@article{Groen2010a,
title = {The living application: A self-organizing system for complex grid tasks},
author = {D.J. Groen and S. Harfst and S.F. Portegies Zwart},
year = {2010},
journal = {International Journal of High Performance Computing Applications},
volume = {24},
number = {2},
pages = {185--193},
metis_id = {316667},
url = {http://dx.doi.org/10.1177/1094342009347891},
doi = {10.1177/1094342009347891},
issn_isbn = {ISSN 1741-2846}
}
@inproceedings{Groen2010b,
title = {A platform independent communication library for distributed computing},
author = {D.J. Groen and S. Rieder and P. Grosso and C.T.A.M. de Laat and S.F. Portegies Zwart},
year = {2010},
volume = {1},
number = {1},
pages = {2693 - 2700},
metis_id = {325489},
url = {http://www.sciencedirect.com/science/article/B9865-506HM1Y-BS/2/75576e501f3aae60e0e213cc195a6170},
month = {May},
note = {Proceedings of the $10^th$ International Conference on Computational Science, May 31 - June 2, Amsterdam},
doi = {10.1016/j.procs.2010.04.303},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
publisher = {Elsevier B.V.},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
abstract = {We present MPWide, a platform independent communication library for performing message passing between supercomputers. Our library couples several local MPI applications through a long distance network using, for example, optical links. The implementation is deliberately kept light-weight, platform independent and the library can be installed and used without administrative privileges. The only requirements are a C++ compiler and at least one open port to a wide area network on each site. In this paper we present the library, describe the user interface, present performance tests and apply MPWide in a large scale cosmological N-body simulation on a network of two computers, one in Amsterdam and the other in Tokyo.},
address = {Amsterdam},
issn_isbn = {ISSN: 1877-0509}
}
@phdthesis{Groen2010c,
title = {High performance N-body simulation on computational grids},
author = {D.J. Groen},
year = {2010},
metis_id = {337587},
url = {http://dare.uva.nl/en/record/361053},
month = {November},
numpages = {vi + 134},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. S.F. Portegies Zwart, Co-promotores: Prof. Dr. P.M.A. Sloot, Prof. Dr. E.P.J. van den Heuvel}
}
@phdthesis{Ham2010a,
title = {A Semantic Model for Complex Computer Networks: The Network Description Language},
author = {J.J. van der Ham},
year = {2010},
url = {http://dare.uva.nl/en/record/331711},
month = {April},
category = {ComputerNetworks},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. Ir. C.T.A.M. de Laat},
issn_isbn = {ISBN13 9789081416023}
}
@book{Hoekstra2010a,
title = {Simulating Complex Systems by Cellular Automata},
year = {2010},
metis_id = {325730},
url = {http://springer.com/978-3-642-12202-6},
numpages = {384},
publisher = {Springer},
series = {Understanding Complex Systems},
editor = {A.G. Hoekstra and J. Kroc and P.M.A. Sloot},
issn_isbn = {ISBN: 978-3-642-12202-6}
}
@incollection{Hoekstra2010b,
title = {Introduction to Modeling of Complex Systems Using Cellular Automata},
author = {A.G. Hoekstra and J. Kroc and P.M.A. Sloot},
year = {2010},
pages = {1--16},
metis_id = {327893},
url = {http://dx.doi.org/10.1007/978-3-642-12203-3_1},
publisher = {Springer},
booktitle = {Simulating Complex Systems by Cellular Automata},
editor = {Hoekstra,A.G. and Kroc,J. and Sloot,P.M.A.}
}
@incollection{Hoekstra2010c,
title = {Complex Automata: Multi-scale Modeling with Coupled Cellular Automata},
author = {A.G. Hoekstra and A. Caiazzo and E. Lorenz and J.-L. Falcone and B. Chopard},
year = {2010},
pages = {29--57},
metis_id = {325729},
url = {http://dx.doi.org/10.1007/978-3-642-12203-3_3},
publisher = {Springer},
series = {Understanding Complex Systems},
booktitle = {Simulating Complex Systems by Cellular Automata},
editor = {Hoekstra,A.G. and Kroc,J. and Sloot,P.M.A.}
}
@inproceedings{Hoekstra2010d,
title = {Multiscale Coupling of a Lattice Boltzmann Simulation of Blood Flow to Cell- and Tissue-Level Processes: the Case of In-Stent Restenosis},
author = {A.G. Hoekstra},
year = {2010},
metis_id = {325726},
url = {http://web.univ-ubs.fr/limatb/EG2M/Disc_Seminaire/ECCOMAS-CFD2010/papers/01547.pdf},
numpages = {8},
publisher = {ECCOMAS},
booktitle = {Proceedeings of the V European Conference on Computational Fluid Dynamics},
note = {on-line only},
editor = {J.C.F. Pereira and A. Sequeira},
organization = {V European Conference on Computational Fluid Dynamics: ECCOMAS CFD 2010},
address = {Lisbon, Portugal}
}
@inproceedings{Hoekstra2010e,
title = {Modelling and simulating in-stent restenosis with complex automata},
author = {A.G. Hoekstra and P.V. Lawford and D.R. Hose},
year = {2010},
pages = {222--224},
metis_id = {327894},
url = {http://www.vph-noe.eu/vph-repository/doc_download/204-book-of-abstracts-for-vph2010},
publisher = {VPH Network of Excellence},
booktitle = {Conference abstracts VPH 2010, 1st Virtual Physiological Human Conference},
organization = {1st Virtual Physiological Human Conference (VPH 2010), Brussels, Belgium}
}
@inproceedings{Hoekstra2010f,
title = {Towards distributed multiscale computing for the VPH},
author = {A.G. Hoekstra and P.V. Coveney},
year = {2010},
pages = {198--200},
metis_id = {327895},
url = {http://www.vph-noe.eu/vph-repository/doc_download/204-book-of-abstracts-for-vph2010},
publisher = {VPH Network of Excellence},
booktitle = {Conference abstracts VPH 2010, 1st Virtual Physiological Human Conference},
organization = {1st Virtual Physiological Human Conference (VPH 2010), Brussels, Belgium}
}
@inproceedings{Ivanov2010a,
title = {Computer simulation of laser annealing of a nanostructured surface},
author = {D.A. Ivanov and I. Marinov and Y.E. Gorbachev and A.S. Smirnov and V.V. Krzhizhanovskaya},
year = {2010},
pages = {1197--1198 (DETC2009-87087)},
metis_id = {312427},
url = {http://dx.doi.org/10.1115/DETC2009-87087},
publisher = {ASME},
booktitle = {Proceedings of the ASME 2009 International Design Engineering Technical Conferences \& Computers and Information in Engineering Conference (IDETC/CIE 2009), San Diego, CA, USA: Volume 2: 29th Computers and Information in Engineering Conference},
note = {Ivanov2009a},
organization = {29th Computers and Information in Engineering Conference (CIE 2009), San Diego, CA, USA},
address = {New York}
}
@article{Jaeger2010a,
title = {Inference of Surface Membrane Factors of HIV-1 Infection through Functional Interaction Networks},
author = {S. Jaeger and G. Ertaylan and D. van Dijk and U. Leser and P.M.A. Sloot},
year = {2010},
journal = {PLoS One},
volume = {5},
number = {10},
pages = {e13139},
metis_id = {327960},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0013139},
numpages = {12},
doi = {10.1371/journal.pone.0013139}
}
@book{Kaandorp2010a,
title = {Euro ISRS symposium 2010: reefs in a changing environment (book of abstracts)},
author = {J.A. Kaandorp and E. Meesters and R. Osinga and J. Verreth and T.H.M. Wijgerde},
year = {2010},
metis_id = {332803},
publisher = {Grafisch Service Center, Wageningen, the Netherlands},
address = {Wageningen, the Netherlands},
issn_isbn = {ISBN 978-90-8585-897-3}
}
@inproceedings{Kaandorp2010b,
title = {Modeling skeletal growth in sponges and absorption of silicic acid},
author = {J.A. Kaandorp and N. Javaheri},
year = {2010},
metis_id = {341216},
publisher = {European society for Evolutionary Developmental biology},
booktitle = {Euro Evo Devo 2010},
organization = {Euro Evo Devo},
address = {Paris}
}
@inproceedings{Kiseleva2010a,
title = {Developing a model of silicon nitride film deposition in a remote inductively coupled low-pressure RF plasma discharge [in Russian]},
author = {I.S. Kiseleva and V.V. Krzhizhanovskaya},
year = {2010},
volume = {6},
pages = {116--117},
metis_id = {344520},
publisher = {St. Petersburg State Polytechnic University},
booktitle = {Proceedings of the International conference "The 39th Science Week". V. 6.},
organization = {International conference "The 39th Science Week"}
}
@inproceedings{Klimovich2010a,
title = {Simulation of Surface Chemistry in CVD technologies: a Detailed Deposition Model with Surface Diffusion},
author = {S. Klimovich and Y.E. Gorbachev and V.V. Krzhizhanovskaya},
year = {2010},
metis_id = {344378},
series = {DETC2010-28455},
booktitle = {Proceedings of ASME 2010 Computers and Information in Engineering Conference IDETC/CIE 2010},
organization = {ASME 2010 Computers and Information in Engineering Conference IDETC/CIE 2010},
address = {Montreal, Quebec, Canada}
}
@inproceedings{Koulouzis2010a,
title = {Enabling Large Data Transfers Between Web Services},
author = {S. Koulouzis and E.J. Meij and A.S.Z. Belloum},
year = {2010},
pages = {153--154},
metis_id = {328945},
url = {http://indico.cern.ch/contributionDisplay.py?contribId=79\&sessionId=30\&confId=69338},
booktitle = {5th EGEE User Forum 2010.},
editor = {Floros,E.},
organization = {5th EGEE User Forum 2010.},
address = {Upsala}
}
@inproceedings{Koulouzis2010b,
title = {Data transport between visualization web services for medical image analysis},
author = {S. Koulouzis and E.V. Zudilova-Seinstra and A.S.Z. Belloum},
year = {2010},
volume = {1},
number = {1},
pages = {1721 - 1730},
metis_id = {325532},
url = {http://www.sciencedirect.com/science/article/B9865-506HM1Y-6W/2/d5abb5fbb000c1b290a3bb31950d60ad},
month = {May},
note = {Proceedings of the $10^th$ International Conference on Computational Science, May 31 - June 2, Amsterdam},
doi = {10.1016/j.procs.2010.04.194},
abstract = {With the rapid development of IT data driven experiments and simulations have become very advanced and complicated. The amount and complexity of scientific data increase exponentially. Nowadays the challenge is to efficiently support scientists who generate more data than they can possibly look at and understand. This requires not only high-performance visualization and feature extraction techniques but also efficient and intuitive management of available data and underlying computational resources. Consequently, Service Oriented Architectures and workflow management systems are becoming popular solutions for the deployment of e-Science Infrastructures aimed to assist in exploration and analysis of large scientific data. In this paper, we compare two transport models of workflow execution for data-intensive medical visualizations that rely on web services. The image-based analysis of vascular disorders served as a case study for this project. We applied a service oriented approach to construct distributed visualization pipelines, which allow visualization experts to develop visualizations to view and interact with large medical data sets. Moreover, end-users (i.e., medical specialists) can explore these visualizations irrespective of their geographical location and available computing resources. The paper reports on the current implementation status and presents our main findings.},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
publisher = {Elsevier B.V.},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
keywords = {Service-oriented visualization, Web services, Data transfers, Image-based medical analysis},
address = {Amsterdam},
issn_isbn = {ISSN: 1877-0509}
}
@inproceedings{Krzhizhanovskaya2010a,
title = {Simulation of multiphysics multiscale systems, 7th international workshop},
author = {V.V. Krzhizhanovskaya},
year = {2010},
volume = {1},
number = {1},
pages = {603 - 605},
metis_id = {325523},
url = {http://www.sciencedirect.com/science/article/B9865-506HM1Y-27/2/b89ff4d79277869a3da1821889ed6186},
month = {May},
note = {Proceedings of the $10^th$ International Conference on Computational Science, May 31 - June 2, Amsterdam},
doi = {10.1016/j.procs.2010.04.064},
abstract = {Modeling and Simulation of Multiphysics Multiscale Systems (SMMS) poses a grand challenge to computational science. To adequately simulate numerous intertwined processes characterized by different spatial and temporal scales spanning many orders of magnitude, sophisticated models and advanced computational techniques are required. The aim of the SMMS workshop is to encourage and review the progress in this multidisciplinary research field. This short paper describes the scope of the workshop and gives pointers to the papers reflecting the latest developments in the field.},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
publisher = {Elsevier B.V.},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
keywords = {Multiphysics, Multiscale, Complex systems, Modeling, Simulation},
address = {Amsterdam},
issn_isbn = {ISSN: 1877-0509}
}
@inproceedings{Krzhizhanovskaya2010b,
title = {A roadmap to multiscale modeling of flood defense systems: from sand grain to dike failure and inundation},
author = {V.V. Krzhizhanovskaya},
year = {2010},
metis_id = {344377},
booktitle = {Proceedings of ASME 2010 Computers and Information in Engineering Conference IDETC/CIE 2010},
organization = {ASME 2010 Computers and Information in Engineering Conference IDETC/CIE 2010},
address = {Montreal, Quebec, Canada}
}
@inproceedings{Krzhizhanovskaya2010c,
title = {The UrbanFlood multiscale modelling cascade and Virtual Dike for simulation of dike stability under dynamic hydraulic loading},
author = {V.V. Krzhizhanovskaya and N.B. Melnikova and B.P. Gouldby},
year = {2010},
pages = {12--13},
metis_id = {344518},
booktitle = {Proceedings of the Joint UrbanFlood \& SSG4Env Workshop on Monitoring and Flood Safety},
organization = {Joint UrbanFlood \& SSG4Env Workshop on Monitoring and Flood Safety},
address = {Amsterdam, The Netherlands}
}
@inproceedings{Krzhizhanovskaya2010d,
title = {Dynamic workload balancing with user-level scheduling for parallel applications on heterogeneous Grid resources},
author = {V.V. Krzhizhanovskaya and V.V. Korkhov and J.T. Moscicki and P.M.A. Sloot},
year = {2010},
metis_id = {344380},
booktitle = {Proceedings of HPC 2010 "High Performance Computing, GRIDS and clouds", An International Advanced Workshop},
organization = {HPC 2010, "High Performance Computing, GRIDS and clouds", An International Advanced Workshop},
address = {Cetraro, Italy}
}
@inproceedings{Krzhizhanovskaya2010e,
title = {Multiphysics multi-model simulation of large-area plasma chemical reactors},
author = {V.V. Krzhizhanovskaya and D.A. Ivanov and Y.E. Gorbachev and A.S. Smirnov},
year = {2010},
pages = {1195--1196 (DETC2009-87039)},
metis_id = {312428},
url = {http://dx.doi.org/10.1115/DETC2009-87039},
publisher = {ASME},
booktitle = {Proceedings of the ASME 2009 International Design Engineering Technical Conferences \& Computers and Information in Engineering Conference (IDETC/CIE 2009), San Diego, CA, USA: Volume 2: 29th Computers and Information in Engineering Conference},
note = {Krzhizhanovskaya2009e},
organization = {29th Computers and Information in Engineering Conference (CIE 2009), San Diego, CA, USA},
address = {New York}
}
@inproceedings{Lebanin2010a,
title = {Development of a software package for processing the photoemission spectra of high-frequency nitrogen discharge, obtained from the MDR-12 monochromator [in Russian]},
author = {V.S. Lebanin and V.V. Krzhizhanovskaya},
year = {2010},
volume = {6},
pages = {112--114},
metis_id = {344521},
publisher = {St. Petersburg State Polytechnic University},
booktitle = {Proceedings of the International conference "The 39th Science Week". V. 6.},
organization = {International conference "The 39th Science Week"}
}
@phdthesis{Lorenz2010a,
title = {Multi-scale simulations with complex automata: in-stent restenosis and suspension flow},
author = {E. Lorenz},
year = {2010},
url = {http://dare.uva.nl/en/record/358709},
month = {November},
numpages = {186},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot; co-promotor: Dr.Ir. A.G. Hoekstra},
keywords = {multi-scale modeling; multi-scale simulations; in-stent restenosis; suspension flow}
}
@inproceedings{Lunzer2010a,
title = {Validating the ACGT Oncosimulator with a Grid-Supported Visualisation Environment},
author = {A. Lunzer and R.G. Belleman and P. Melis and J. Pukacki and P. Spychala and G. Stamatakos},
year = {2010},
pages = {93--96},
metis_id = {327132},
url = {http://www.4th-iarwisoci.iccs.ntua.gr/proceedings.pdf},
booktitle = {4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation},
editor = {G. Stamatakos and D. Dionysiou},
organization = {ContraCancrum Workshop}
}
@inproceedings{Lunzer2010b,
title = {Preparing, exploring and comparing cancer simulation results within a large parameter space},
author = {A. Lunzer and R.G. Belleman and P. Melis and G. Stamatakos},
year = {2010},
pages = {258--264},
metis_id = {327131},
url = {http://dx.doi.org/10.1109/IV.2010.46},
publisher = {IEEE Computer Society},
doi = {10.1109/IV.2010.46},
booktitle = {14th International Conference Information Visualisation},
organization = {Information Visualization},
address = {Los Alamitos, CA, USA}
}
@inproceedings{Mei2010a,
title = {Quantitatively evaluating interventions in the influenza A (H1N1) epidemic on China campus grounded on individual-based simulations},
author = {S. Mei and D.A.M.C. van de Vijver and L. Xuan and Y. Zhu and P.M.A. Sloot},
year = {2010},
volume = {1},
number = {1},
pages = {1675--1682},
metis_id = {325524},
url = {http://www.sciencedirect.com/science/publication?issn=18770509\&volume=1\&issue=1},
month = {May},
note = {Proceedings of the $10^th$ International Conference on Computational Science, May 31 - June 2, Amsterdam},
doi = {10.1016/j.procs.2010.04.187},
abstract = {The novel Influenza A (H1N1) virus is attacking the world in 2009. Among others, campuses in China, particularly most university/college campuses for bachelor students, are at-risk areas where many susceptible youngsters live. They most likely interact with each other quite often in dormitories, classrooms and refectories. We model the pandemic influenza A (H1N1) transmission through campus contacts and then forecast the effectiveness of interventions, based on a previously presented Complex Agent Network model for simulating infectious diseases~. Our results suggest that pandemic influenza A (H1N1) on campus will die out even with no intervention taken; the most effective intervention is still quarantining confirmed cases as early as possible and, in addition, vaccinating susceptible people can further decrease the maximum daily number of the infected. This study can support quantitative experimentation and prediction of infectious diseases within predefined areas, and assessment of intervention strategies.},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
publisher = {Elsevier B.V.},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
keywords = {Influenza A (H1N1), Human swine influenza, Swine flu, Infectious diseases, Complex agent networks, Host agents, Complex networks, Social networks},
address = {Amsterdam},
issn_isbn = {ISSN: 1877-0509}
}
@article{Mei2010b,
title = {Complex Agent Networks explaining the HIV epidemic among homosexual men in Amsterdam},
author = {S. Mei and P.M.A. Sloot and R. Quax and Y. Zhu and W. Wang},
year = {2010},
journal = {Mathematics and Computers in Simulation},
volume = {80},
number = {5},
pages = {1018--1030},
metis_id = {307614},
url = {http://dx.doi.org/10.1016/j.matcom.2009.12.008},
month = {Jan},
doi = {10.1016/j.matcom.2009.12.008}
}
@inproceedings{Melnikova2010a,
title = {Transient simulation of stress-strain behaviour of an earthen sea dike under the forces of tidal water infiltration and under the flood conditions [in Russian]},
author = {N.B. Melnikova and V.V. Krzhizhanovskaya and N.N. Shabrov},
year = {2010},
volume = {21},
pages = {70--71},
metis_id = {344524},
publisher = {St. Petersburg State Polytechnic University},
booktitle = {Proceedings of the International conference "The 39th Science Week". V. 21.},
organization = {International conference "The 39th Science Week"}
}
@phdthesis{Murtaza2010a,
title = {High performance reconfigurable computing with cellular automata},
author = {S. Murtaza},
year = {2010},
url = {http://dare.uva.nl/en/record/339482},
month = {May},
category = {HPC, Reconfigureable, Computing},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. A.G. Hoekstra}
}
@inproceedings{Naumov2010a,
title = {The influence of mitoses rate on growth dynamics of a cellular automata model of tumour growth},
author = {L.A. Naumov and A.G. Hoekstra and P.M.A. Sloot},
year = {2010},
volume = {1},
number = {1},
pages = {971 - 978},
metis_id = {325525},
url = {http://www.sciencedirect.com/science/article/B9865-506HM1Y-3S/2/aa78580f5173e11e4de938fd1a029392},
month = {May},
publisher = {Elsevier B.V.},
doi = {10.1016/j.procs.2010.04.107},
abstract = {Mitosis inside a tumour can be prohibited for different reasons, such as overcrowding or physical pressure. At the same time, the rate of successful mitoses inside a tumour can hardly be measured in vivo or vitro, but is easily modeled in silico. In this paper we present a study of the influence of mitoses rate on the growth dynamics of a cellular automata model for growth.},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
keywords = {Tumour, Mitosis, Cellular automata},
address = {Amsterdam},
issn_isbn = {ISSN: 1877-0509}
}
@article{Pol2010a,
title = {Optical and non-optical methods for detection and characterization of microparticles and exosomes},
author = {E. van der Pol and A.G. Hoekstra and A. Sturk and C. Otto and T.G. van Leeuwen and R. Nieuwland},
year = {2010},
journal = {Journal of Thrombosis and Haemostasis},
volume = {8},
number = {12},
pages = {2596--2607},
doi = {10.1111/j.1538-7836.2010.04074.x}
}
@article{Portegies_Zwart2010a,
title = {Simulating the universe on an intercontinental grid},
author = {S.F. Portegies Zwart and T. Ishiyama and D.J. Groen and K. Nitadori and J. Makino and C.T.A.M. de Laat and S.L.W. McMillan and K. Hiraki and S. Harfst and P. Grosso},
year = {2010},
journal = {IEEE Computer},
volume = {43},
number = {8},
pages = {63--70},
url = {PortegiesZwart2010a.pdf},
month = {January},
doi = {10.1109/MC.2009.419},
keywords = {Astrophysics - Cosmology and Extragalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Distributed, Parallel, and Cluster Computing, Physics - Computational Physics},
issn_isbn = {ISSN 0018-9162}
}
@article{Prosperi2010a,
title = {Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models},
author = {M.C.F. Prosperi and M. Rosen-Zvi and A. Altmann and M. Zazzi and S. Di Giambenedetto and R. Kaiser and E. Sch\"ulter and D. Struck and P.M.A. Sloot and D.A.M.C. van de Vijver and A.-M. Vandamme and A. S\"onnerborg and for the EuResist and Virolab study groups},
year = {2010},
journal = {PLoS ONE},
volume = {5},
number = {10},
pages = {e13753},
metis_id = {328716},
url = {Prosperi2010a.pdf},
month = {October},
numpages = {8},
publisher = {Public Library of Science},
note = {Erratum in PLoS One. 2011;6(4). doi:10.1371/annotation/d0254103-21b9-4078-836b-57ba5bd1c26a},
doi = {10.1371/journal.pone.0013753}
}
@article{Qiu2010a,
title = {Modeling options markets by focusing on active traders},
author = {G. Qiu and B.D. Kandhai and P.M.A. Sloot},
year = {2010},
volume = {1},
number = {1},
pages = {2457 - 2462},
metis_id = {325526},
url = {http://www.sciencedirect.com/science/article/B9865-506HM1Y-9V/2/23311ef2fd936580838bf294aea72bc6},
month = {May},
note = {Proceedings of the $10^th$ International Conference on Computational Science, May 31 - June 2, Amsterdam},
doi = {10.1016/j.procs.2010.04.277},
abstract = {In this work, we study the complex behavior of options markets characterized by the volatility smile phenomenon, through microsimulation (MS). We adopt two types of active traders in our MS model: speculators and arbitrageurs, and call and put options on one underlying asset. Speculators make decisions based on their expectations of the asset price at the option expiration time. Arbitrageurs trade at dierent arbitrage opportunities such as violation of put-call parity. Dierence in liquidity among options is also included. Notwithstanding its simplicity, our model can generate implied volatility (IV) curves similar to empirical observations. Our results suggest that the volatility smile is related to the competing eect of heterogeneous trading behavior and the impact of dierential liquidity.},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
publisher = {Elsevier B.V.},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
keywords = {Options markets, Volatility smile, Microsimulation},
address = {Amsterdam},
issn_isbn = {ISSN: 1877-0509}
}
@article{Schwiegelshohn2010a,
title = {Perspectives on grid computing},
author = {U. Schwiegelshohn and R.M. Badia and M.T. Bubak and M. Danelutto and S. Dustdar and F. Gagliardi and A. Geiger and L. Hluchy and D. Kranzlm\"uller and E. Laure and T. Priol and A. Reinefeld and M. Resch and A. Reuter and O. Rienhoff and T. R\"uter and P.M.A. Sloot and D. Talia and K. Ullmann and R. Yahyapour and G. von Voigt},
year = {2010},
journal = {Future Generation Computer Systems},
volume = {26},
number = {8},
pages = {1104--1115},
metis_id = {329798},
url = {http://www.sciencedirect.com/science/article/B6V06-5046M26-9/2/48b1a0c4be91df6f89554f74e94ae792},
doi = {10.1016/j.future.2010.05.010},
abstract = {Grid computing has been the subject of many large national and international IT projects. However, not all goals of these projects have been achieved. In particular, the number of users lags behind the initial forecasts laid out by proponents of grid technologies. This underachievement may have led to claims that the grid concept as a whole is on its way to being replaced by Cloud computing and various X-as-a-Service approaches. In this paper, we try to analyze the current situation and to identify promising directions for future grid development. Although there are shortcomings in current grid systems, we are convinced that the concept as a whole remains valid and can benefit from new developments, including Cloud computing. Furthermore, we strongly believe that some future applications will require the grid approach and that, as a result, further research is required in order to turn this concept into reliable, efficient and user-friendly computing platforms.},
keywords = {Grid computing, Virtual research environment, Grid applications, Grid middleware, Cloud computing},
issn_isbn = {ISSN 0167-739X}
}
@inproceedings{Shirshov2010a,
title = {Modelling the inundation process for flood early warning systems [in Russian]},
author = {G.S. Shirshov and V.V. Krzhizhanovskaya},
year = {2010},
volume = {21},
pages = {140--141},
metis_id = {344523},
publisher = {St. Petersburg State Polytechnic University},
booktitle = {Proceedings of the International conference "The 39th Science Week". V. 21.},
organization = {International conference "The 39th Science Week"}
}
@inproceedings{Shirshov2010b,
title = {Simulation of Shock Wave Propagation in Turbulent Flow of Compressible Gas Mixture for Ignition Experiments in Shock Tubes},
author = {G.S. Shirshov and V.V. Krzhizhanovskaya},
year = {2010},
pages = {342--343},
metis_id = {344097},
publisher = {VVM Publishing Co},
booktitle = {Proceedings of The Sixth International Conference on Computational Fluid Dynamics},
address = {Saint Petersburg, Russia}
}
@proceedings{Sloot2010a,
year = {2010},
volume = {1},
number = {1},
metis_id = {325528},
url = {http://www.sciencedirect.com/science/publication?issn=18770509\&volume=1\&issue=1},
month = {May},
numpages = {2772},
note = {Proceedings of the $10^th$ International Conference on Computational Science, May 31 - June 2, Amsterdam},
publisher = {Elsevier B.V.},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
address = {Amsterdam},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
issn_isbn = {ISSN: 1877-0509}
}
@article{Sloot2010b,
title = {Multi-scale modelling in computational biomedicine},
author = {P.M.A. Sloot and A.G. Hoekstra},
year = {2010},
journal = {Brief in Bioinform},
volume = {11},
number = {1},
pages = {142--152},
metis_id = {312436},
url = {Sloot2010a.pdf},
publisher = {Oxford University Press},
doi = {10.1093/bib/bbp038},
keywords = {computational biology; multi-scale modelling; molecular dynamics; cellular automata; complex networks},
abstract = {The inherent complexity of biomedical systems is well recognized; they are multi-scale, multi-science systems, bridging a wide range of temporal and spatial scales. This article reviews the currently emerging field of multi-scale modelling in computational biomedicine. Many exciting multi-scale models exist or are under development. However, an underpinning multi-scale modelling methodology seems to be missing. We propose a direction that complements the classic dynamical systems approach and introduce two distinct case studies, transmission of resistance in human immunodeficiency virus spreading and in-stent restenosis in coronary artery disease.}
}
@misc{Sloot2010c,
title = {Preface},
author = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
year = {2010},
volume = {1},
number = {1},
pages = {1 -- 5},
metis_id = {325529},
url = {http://www.sciencedirect.com/science/article/B9865-506HM1Y-1/2/aa80e3490fdd30bd8971161e3618f2e5},
doi = {10.1016/j.procs.2010.04.002},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
issn_isbn = {ISSN: 1877-0509}
}
@article{Sloot2010d,
title = {Computational science: A kaleidoscopic view into science},
author = {P.M.A. Sloot},
year = {2010},
journal = {Journal of Computational Science},
volume = {1},
number = {4},
pages = {189--189},
metis_id = {329799},
month = {December},
note = {editorial},
doi = {10.1016/j.jocs.2010.11.001},
publisher = {Elsevier B.V.},
issn_isbn = {ISSN 1877-7503}
}
@article{Sottoriva2010a,
title = {Exploring Cancer Stem Cell Niche Directed Tumor Growth},
author = {A. Sottoriva and P.M.A. Sloot and J.P. Medema and L. Vermeulen},
year = {2010},
journal = {Cell Cycle},
volume = {9},
number = {8},
pages = {1472--1479},
metis_id = {312416},
url = {http://www.landesbioscience.com/journals/cc/article/11198},
publisher = {Landes Bioscience},
doi = {10.4161/cc.9.8.11198}
}
@article{Sottoriva2010b,
title = {Cancer Stem Cell Tumor Model Reveals Invasive Morphology and Increased Phenotypical Heterogeneity},
author = {A. Sottoriva and J.J.C. Verhoeff and T. Borovski and S.K. McWeeney and L.A. Naumov and J.P. Medema and P.M.A. Sloot and L. Vermeulen},
year = {2010},
journal = {Cancer Research},
volume = {70},
number = {1},
pages = {46--56},
metis_id = {312415},
url = {Sottoriva2010a.pdf},
publisher = {American Association for Cancer Research},
doi = {10.1158/0008-5472.CAN-09-3663},
issn_isbn = {Print ISSN: 0008-5472; Online ISSN: 1538-7445}
}
@inproceedings{Stamatakos2010a,
title = {The ACGT Oncosimulator: from Conceptualization to Development via Multiscale Cancer Modeling},
author = {G. Stamatakos and D. Dionysiou and E. Georgiadi and E. Kolokotroni and S. Giatili and A. Hoppe and C. Desmedt and A. Lunzer and M. Erdt and J. Jacques and J. Pukacki and R.G. Belleman and P. Melis and A. d'Onofrio and F.M. Buffa and B. Claerhout and S. R\"uping and K. Marias and M. Tsiknakis and N. Graf},
year = {2010},
pages = {54--57},
metis_id = {327732},
url = {http://www.4th-iarwisoci.iccs.ntua.gr/proceedings.pdf},
booktitle = {4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation},
editor = {G. Stamatakos and D. Dionysiou},
organization = {ContraCancrum Workshop}
}
@article{Streekstra2010a,
title = {Quantification of the fraction poorly deformable red blood cells using ektacytometry},
author = {G.J. Streekstra and J.G.G. Dobbe and A.G. Hoekstra},
year = {2010},
journal = {Optics Express},
volume = {18},
number = {13},
pages = {14173--14182},
metis_id = {325728},
url = {http://www.opticsinfobase.org/oe/abstract.cfm?URI=oe-18-13-14173},
doi = {10.1364/OE.18.014173}
}
@inproceedings{Wang2010a,
title = {Computer Simulation for Design and Optimization of Large-Area VHF PECVD Reactors: Two Novel Electrode Configurations Improving Deposition Uniformity},
author = {R. Wang and J. Ye and D.A. Ivanov and A.S. Smirnov and V.V. Krzhizhanovskaya},
year = {2010},
metis_id = {344379},
publisher = {Applied Materials},
booktitle = {Proceedings of ET Conference},
address = {Santa Clara, USA}
}
@mastersthesis{Wood2010a,
title = {Applications of GPUs in Computational Finance},
author = {T. Wood},
year = {2010},
url = {Wood2010a.pdf},
month = {October},
category = {pwrs, mastersthesis},
numpages = {98},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: R.G. Belleman and B.D. Kandhai}
}
@article{Yurkin2010a,
title = {Application of the discrete dipole approximation to very large refractive indices: Filtered coupled dipoles revived},
author = {M.A. Yurkin and M. Min and A.G. Hoekstra},
year = {2010},
journal = {Physical Review. E Statistical Nonlinear and Soft Matter Physics},
volume = {82},
number = {3},
pages = {036703},
metis_id = {327896},
url = {http://link.aps.org/doi/10.1103/PhysRevE.82.036703},
numpages = {12},
doi = {10.1103/PhysRevE.82.036703}
}
@article{Yurkin2010b,
title = {Accuracy of the discrete dipole approximation for simulation of optical properties of gold nanoparticles},
author = {M.A. Yurkin and D. de Kanter and A.G. Hoekstra},
year = {2010},
journal = {Journal of Nanophotonics},
volume = {4},
pages = {041585},
metis_id = {325643},
url = {http://link.aip.org/link/?JNP/4/041585/1},
numpages = {15},
publisher = {SPIE},
doi = {10.1117/1.3335329}
}
@inproceedings{Yurkin2010c,
title = {Accuracy of the discrete dipole approximation for gold nanoparticles},
author = {M.A. Yurkin and D. de Kanter and A.G. Hoekstra},
year = {2010},
pages = {118--118},
metis_id = {330012},
url = {Yurkin2010c.pdf},
month = {September},
publisher = {Nato},
booktitle = {NATO Advanced Study Institute on "Special Detection Technique (Polarimetry) and Remote Sensing"},
note = {Abstract},
editor = {M.I. Mishchenko and Y. Yatskiv and V.K. Rosenbush and G. Videen},
address = {Kyiv, Ukraine}
}
@inproceedings{Yurkin2010d,
title = {Features and capabilities of the discrete dipole approximation code ADDA},
author = {M.A. Yurkin and O.M. Yurkina and A.G. Hoekstra},
year = {2010},
pages = {119--119},
metis_id = {330013},
url = {Yurkin2010d.pdf},
month = {September},
publisher = {Nato},
booktitle = {NATO ASI on Special Detection Technique (Polarimetry) and Remote Sensing},
note = {abstract},
editor = {M.I. Mishchenko and Y. Yatskiv and V.K. Rosenbush and G. Videen}
}
@inproceedings{Zarrabi2010a,
title = {Modeling HIV-1 intracellular replication: two simulation approaches},
author = {N. Zarrabi and E. Mancini and J.C. Tay and S. Shahand and P.M.A. Sloot},
year = {2010},
volume = {1},
number = {1},
pages = {555--564},
metis_id = {325530},
url = {http://www.sciencedirect.com/science/article/B9865-506HM1Y-22/2/3140f96fca63008d40c867352be29383},
month = {May},
publisher = {Elsevier B.V.},
doi = {10.1016/j.procs.2010.04.059},
abstract = {Many mathematical and computational models have been developed to investigate the complexity of HIV dynamics, immune response and drug therapy. However, there are not many models which consider the dynamics of virus intracellular replication at a single level. We propose a model of HIV intracellular replication where infected cells undergo a single cycle of virus replication. A cell is modeled as an individual entity with certain states and properties. The model is stochastic and keeps track of the main viral proteins and genetic materials inside the cell. Two simulation approaches are used for implementing the model: rate-based and diffusion-based approaches. The results of the simulation are discussed based on the number of integrated viral cDNA and the number of viral mRNA transcribed after a single round of replication. The model is validated by comparing simulation results with available experimental data. Simulation results give insights about the details of HIV replication dynamics inside the cell at the protein level. Therefore the model can be used for future studies of HIV intracellular replication in vivo and drug treatment.},
series = {Procedia Computer Science},
booktitle = {ICCS 2010},
editor = {P.M.A. Sloot and G.D. van Albada and J. Dongarra},
keywords = {HIV-1 intracellular replication, Agent-based simulation},
address = {Amsterdam},
issn_isbn = {ISSN: 1877-0509}
}
@article{Zudilova-Seinstra2010a,
title = {Evaluation of 2D and 3D Glove Input Applied to Medical Image Analysis},
author = {E.V. Zudilova-Seinstra and P.J.H. de Koning and A. Suinesiaputra and B.W. van Schooten and R.J. van der Geest and J.H.C. Reiber and P.M.A. Sloot},
year = {2010},
journal = {International Journal of Human-Computer Studies},
volume = {68},
number = {6},
pages = {355--369},
url = {http://dx.doi.org/10.1016/j.ijhcs.2009.08.001},
doi = {10.1016/j.ijhcs.2009.08.001}
}
@article{Zudilova-Seinstra2010b,
title = {Exploring Individual User Differences in the 2D/3D Interaction with Medical Image Data},
author = {E.V. Zudilova-Seinstra and B.W. van Schooten and A. Suinesiaputra and R.J. van der Geest and E.M.A.G. van Dijk and J.H.C. Reiber and P.M.A. Sloot},
year = {2010},
journal = {Virtual Reality},
volume = {14},
number = {2},
pages = {105--118},
publisher = {Springer},
doi = {10.1007/s10055-009-0131-4},
abstract = {User-centered design is often performed without regard to individual user differences. In this paper, we report results of an empirical study aimed to evaluate whether computer experience and demographic user characteristics would have an effect on the way people interact with the visualized medical data in a 3D virtual environment using 2D and 3D input devices. We analyzed the interaction through performance data, questionnaires and observations. The results suggest that differences in gender, age and game experience have an effect on people's behavior and task performance, as well as on subjective user preferences.},
keywords = {2D/3D interaction, Medical segmentation, Virtual environments, Multimodal, User study},
issn_isbn = {ISSN 1359-4338 (Print) 1434-9957 (Online)}
}
@proceedings{Allen2009a,
author = {G. Allen and J. Nabrzyski and E. Seidel and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2009},
volume = {5544},
url = {http://www.springer.com/computer/foundations/book/978-3-642-01969-2},
month = {May},
publisher = {Springer},
doi = {10.1007/978-3-642-01970-8},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2009: 9th International Conference, Baton Rouge, LA, USA, Proceedings, Part I},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13: 978-3-642-01969-2}
}
@proceedings{Allen2009b,
author = {G. Allen and J. Nabrzyski and E. Seidel and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2009},
volume = {5545},
url = {http://www.springer.com/computer/foundations/book/978-3-642-01972-2},
month = {May},
publisher = {Springer},
doi = {10.1007/978-3-642-01973-9},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2009: 9th International Conference, Baton Rouge, LA, USA, Proceedings, Part II},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13: 978-3-642-01972-2}
}
@article{Allison2009a,
title = {Using the minimum spanning tree to trace mass segregation},
author = {R.J. Allison and S.P. Goodwin and R.J. Parker and S.F. Portegies Zwart and R. de Grijs and M.B.N. Kouwenhoven},
year = {2009},
journal = {Mon.Not.RAS},
volume = {395},
number = {3},
pages = {1449--1454},
metis_id = {307603},
url = {http://adsabs.harvard.edu/abs/2009arXiv0901.2047A},
month = {Apr},
doi = {10.1111/j.1365-2966.2009.14508.x},
keywords = {Astrophysics - Galactic Astrophysics}
}
@article{Ashyraliyev2009a,
title = {Systems biology: parameter estimation for biochemical models},
author = {M. Ashyraliyev and Y. Fomekong-Nanfack and J.A. Kaandorp and J.G. Blom},
year = {2009},
journal = {FEBS Journal},
volume = {276},
number = {4},
pages = {886--902},
metis_id = {312417},
month = {January},
publisher = {Wiley InterScience},
doi = {10.1111/j.1742-4658.2008.06844.x}
}
@inproceedings{Assel2009a,
title = {A Collaborative Environment Allowing Clinical Investigations on Integrated Biomedical Databases},
author = {M. Assel and D.A.M.C. van de Vijver and P. Liblin and K. Theys and D. Harezlak and B. \'O Nuall\'ain and P. Nowakowski and M.T. Bubak and A.-M. Vandamme and S. Imbrechts and R. Sangeda and T. Jiang and D. Frentz and P.M.A. Sloot},
year = {2009},
volume = {147},
pages = {51--61},
url = {Assel2009a.pdf},
month = {January},
publisher = {IOS Press},
doi = {10.3233/978-1-60750-027-8-51},
series = {Studies in Health Technology and Informatics},
booktitle = {Healthgrid research, innovation, and business case: Proceedings of HealthGrid 2009},
editor = {T. Solomonides and M. Hofmann-Apitius and M. Freudigmann and S. C. Semler and Y. Legr\'e and M. Kratz},
issn_isbn = {ISBN 978-1-60750-027-8}
}
@article{Axner2009a,
title = {Simulations of time harmonic blood flow in the Mesenteric artery: comparing finite element and lattice Boltzmann methods},
author = {L. Axner and A.G. Hoekstra and A. Jeays and P.V. Lawford and D.R. Hose and P.M.A. Sloot},
year = {2009},
journal = {BioMedical Engineering OnLine},
volume = {8},
number = {1},
pages = {23},
url = {Axner2009a.pdf},
month = {October},
numpages = {8},
note = {on-line only; PubMedID = 19799782},
doi = {10.1186/1475-925X-8-23},
abstract = {BACKGROUND:Systolic blood flow has been simulated in the abdominal aorta and the superior mesenteric artery. The simulations were carried out using two different computational hemodynamic methods: the finite element method to solve the Navier Stokes equations and the lattice Boltzmann method.RESULTS:We have validated the lattice Boltzmann method for systolic flows by comparing the velocity and pressure profiles of simulated blood flow between methods. We have also analyzed flow-specific characteristics such as the formation of a vortex at curvatures and traces of flow.CONCLUSION:The lattice Boltzmann Method is as accurate as a Navier Stokes solver for computing complex blood flows. As such it is a good alternative for computational hemodynamics, certainly in situation where coupling to other models is required.},
issn_isbn = {ISSN 1475-925X}
}
@inproceedings{Bartynski2009a,
title = {Environment for collaborative e-science applications: CGW08 tutorial},
author = {T. Bartynski and M.T. Bubak and T. Guba\la and D. Harezlak and M. Kasztelnik and J. Kocot and P. Nowakowski},
year = {2009},
pages = {58--60},
metis_id = {307639},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'08 Grid Workshop: October 13-15, 2008 Cracow, Poland: proceedings},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
issn_isbn = {ISBN 978-83-61433-00-2}
}
@inproceedings{Baryshnikova2009a,
title = {Model development of a PECVD reactor for titanium dioxide film deposition},
author = {M.V. Baryshnikova and V.V. Krzhizhanovskaya},
year = {2009},
volume = {6},
pages = {56--57},
metis_id = {312419},
month = {November 30 -- December 5},
category = {PECVDreactor, FilmDeposition, titaniumdioxide},
publisher = {St. Petersburg State Polytechnic University},
note = {In Russian},
booktitle = {International Conference "38th Science Week"},
address = {Saint Petersburg, Russia}
}
@article{Bossenbroek2009a,
title = {Grid Resource Allocation by Means of Option Contracts},
author = {A. Bossenbroek and A. Tirado Ramos and P.M.A. Sloot},
year = {2009},
journal = {IEEE Systems Journal},
volume = {3},
number = {1},
pages = {49--64},
metis_id = {307604},
url = {Bossenbroek2009a.pdf},
month = {March}
}
@mastersthesis{Bossenbroek2009b,
title = {A Numerical Approach to Bonus-Malus Executive Compensation Plans},
author = {A. Bossenbroek},
year = {2009},
url = {http://dare.uva.nl/en/scriptie/319649},
month = {May},
category = {pwrs, mastersthesis},
numpages = {98},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisors: B.D. Kandhai, D.R. Fokkema and B. Bosma}
}
@inproceedings{Bubak2009a,
title = {A platform for collaborative e-science applications},
author = {M.T. Bubak and T. Guba\la and M. Malawski and B. Bali\'s and W. Funika and T. Bartynski and E. Ciepiela and D. Harezlak and M. Kasztelnik and J. Kocot and D. Kr\'ol and P. Nowakowski and M. Pelczar and M. Assel},
year = {2009},
pages = {7--9},
metis_id = {307640},
publisher = {ACK Cyfronet AGH},
booktitle = {KU KDM 2009: druga konferencja uytkownikw komputerw duej mocy: Zakopane, March 1213, 2009: abstracts}
}
@proceedings{Bubak2009b,
author = {M.T. Bubak and M. Tura\la and K. Wiatr},
year = {2009},
metis_id = {307733},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'08 Grid Workshop: October 13-15, 2008 Cracow, Poland: proceedings},
issn_isbn = {ISBN 978-83-61433-00-2}
}
@inbook{Bubak2009c,
title = {Chapter XXVII: Virtual Laboratory for Collaborative Applications},
author = {M.T. Bubak and M. Malawski and T. Guba\la and M. Kasztelnik and P. Nowakowski and D. Harezlak and T. Bartynski and J. Kocot and E. Ciepiela and W. Funika and D. Kr\'ol and B. Bali\'s and M. Assel and A. Tirado Ramos},
year = {2009},
metis_id = {307719},
url = {http://www.igi-global.com/reference/details.asp?ID=34292\&v=tableOfContents},
month = {May},
publisher = {IGI Publishing, Medical Information Science Reference},
booktitle = {Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare},
editor = {M. Cannataro},
issn_isbn = {ISBN: 978-1-60566-374-6}
}
@inproceedings{Caiazzo2009a,
title = {Towards a Complex Automata Multiscale Model of In-Stent Restenosis},
author = {A. Caiazzo and D.E. Evans and J.-L. Falcone and J. Hegewald and E. Lorenz and B. Stahl and D. Wang and J.M. Bernsdorf and B. Chopard and J. Gunn and D.R. Hose and M. Krafczyk and P.V. Lawford and R.H. Smallwood and D. Walker and A.G. Hoekstra},
year = {2009},
volume = {5544},
pages = {705--714},
metis_id = {307642},
url = {Caiazzo2009b.pdf},
month = {May},
publisher = {Springer},
doi = {10.1007/978-3-642-01970-8_70},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2009: 9th International Conference, Baton Rouge, LA, USA, Proceedings, Part I},
editor = {G. Allen and J. Nabrzyski and E. Seidel and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2009 (ICCS 2009), Baton Rouge, LA, USA},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13: 978-3-642-01969-2}
}
@article{Caiazzo2009b,
title = {Asymptotic analysis of Complex Automata models for reaction-diffusion systems},
author = {A. Caiazzo and J.-L. Falcone and B. Chopard and A.G. Hoekstra},
year = {2009},
journal = {Applied Numerical Mathematics},
volume = {59},
number = {8},
pages = {2023--2034},
metis_id = {307605},
url = {http://www.sciencedirect.com/science/article/B6TYD-4W1SRK6-1/2/9121fbc386eddc7e56179da698fa203b},
doi = {10.1016/j.apnum.2009.04.001},
memo = {url = Caiazzo2009b.pdf},
keywords = {Complex Automata modeling; Reaction-diffusion; Lattice Boltzmann method; Asymptotic expansion},
issn_isbn = {ISSN 0168-9274}
}
@inproceedings{Caroprese2009a,
title = {A Logical Framework for Detecting Anomalies in Drug Resistance Algorithms},
author = {L. Caroprese and B. \'O Nuall\'ain and P.M.A. Sloot and E. Zumpano},
year = {2009},
pages = {23--30},
metis_id = {312420},
url = {Caroprese2009a.pdf},
month = {September},
publisher = {ACM},
series = {ACM International Conference Proceeding Series},
booktitle = {Thirteenth International Database Engineering \& Applications Symposium (IDEAS)},
abstract = {Virology research is nowadays a discipline involving a broad number of researchers gathered in different institutes and cooperating on defined issues. An example of such an endeavor is the research tackling anti-HIV treatment problems [7] conducted within the Virolab project. The main objective of the ViroLab project is to develop a Virtual Laboratory for Infectious Diseases that facilitates medical knowledge discovery and decision support for HIV drug resistance. Large, high quality in-vitro and clinical patient databases which can be used to relate genotype to drug-susceptibility phenotype have become available. The core of the ViroLab Virtual Laboratory is a rule-based ranking system. More specifically, using a Grid-based service oriented architecture, Virolab vertically integrates the biomedical information from viruses (proteins and mutations), patients and literature (drug resistance experiments), resulting in a rule-based decision support system for drug ranking. This paper is a contribution to virologists, epidemiologists and clinicians in medical knowledge discovery and decision support. The final aim is reasoning on the properties of algorithm modeling the interaction among drugs and HIV virus and detecting its anomalies such as rules that can never be satisfied and subset of rules that are in contradiction.},
editor = {B.C. Desai},
organization = {Thirteenth International Database Engineering \& Applications Symposium (IDEAS'09), Cetraro, Calabria, Italy},
address = {Cetraro - Calabria - Italy},
issn_isbn = {ISBN:978-1-60558-402-7}
}
@techreport{Cook2009a,
title = {The Cook Report on Internet Protocol on Interactive Networks (A User Interface for Appliction Owned Lightpath Networks)},
author = {G.S. Cook and R.G. Belleman and R.J. Strijkers and M.L. Cristea and R.J. Meijer and C.T.A.M. de Laat},
year = {2009},
metis_id = {325168},
institution = {COOK network consultants},
address = {431 Greenway Ave. Ewing, NJ}
}
@techreport{Cook2009b,
title = {The Cook Report on Internet Protocol on WiVR: a Window into Virtual Reality},
author = {G.S. Cook and R.G. Belleman and M. Scarpa and C.T.A.M. de Laat},
year = {2009},
metis_id = {325169},
institution = {COOK network consultants},
address = {431 Greenway Ave. Ewing, NJ}
}
@article{Cui2009a,
title = {Calcium Homeostasis and Signaling in Yeast Cells and Cardiac Myocytes},
author = {J. Cui and J.A. Kaandorp and P.M.A. Sloot and C.M. Lloyd and M.V. Filatov},
year = {2009},
journal = {FEMS Yeast Research},
volume = {9},
number = {8},
pages = {1137--1147},
metis_id = {307606},
url = {http://www3.interscience.wiley.com/journal/122514646/abstract},
month = {Aug},
publisher = {Wiley InterScience},
doi = {10.1111/j.1567-1364.2009.00552.x}
}
@phdthesis{Cui2009b,
title = {Mathematical Modeling of Metal Ion Homeostasis and Signaling Systems},
author = {J. Cui},
year = {2009},
metis_id = {292882},
url = {http://dare.uva.nl/en/record/296715},
month = {March},
category = {Bioinformatics},
numpages = {142},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. J.A. Kaandorp}
}
@article{Cui2009c,
title = {Simulating Calcium Influx and Free Calcium Concentrations in Yeast},
author = {J. Cui and J.A. Kaandorp and O.O. Ositelu and V. Beaudry and A. Knight and Y. Fomekong-Nanfack and K.W. Cunningham},
year = {2009},
journal = {Cell Calcium},
volume = {45},
number = {2},
pages = {123--132},
metis_id = {296216},
doi = {10.1016/j.ceca.2008.07.005}
}
@phdthesis{Dijkstra2009a,
title = {Framework for path finding in multi-layer transport networks},
author = {F. Dijkstra},
year = {2009},
url = {http://dare.uva.nl/record/305829},
month = {June},
category = {ComputerNetworks},
numpages = {X, 207},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. Ir. C.T.A.M. de Laat},
issn_isbn = {ISBN: 9789081416016}
}
@inproceedings{Evans2009a,
title = {COAST: Multi-scale Simulation of Restenosis},
author = {D.J.W. Evans and D. Walker and J. Gunn and M. Krafczyk and B. Chopard and J.M. Bernsdorf and A.G. Hoekstra and D.R. Hose and P.V. Lawford},
year = {2009},
pages = {122--122},
metis_id = {330021},
booktitle = {Bioengineering 2009},
note = {abstract},
organization = {Bioengineering 2009},
address = {Oxford}
}
@article{Fomekong-Nanfack2009a,
title = {Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis},
author = {Y. Fomekong-Nanfack and M. Postma and J.A. Kaandorp},
year = {2009},
journal = {BMC Systems Biology},
volume = {3},
number = {94},
month = {September},
publisher = {BioMed Central Ltd.},
doi = {10.1186/1752-0509-3-94}
}
@article{Fomekong-Nanfack2009b,
title = {Inferring Drosophila gap gene regulatory network: pattern analysis of simulated gene expression profiles and stability analysis},
author = {Y. Fomekong-Nanfack and M. Postma and J.A. Kaandorp},
year = {2009},
journal = {BMC Res Notes},
volume = {2},
number = {256},
month = {December},
publisher = {BioMed Central Ltd.},
doi = {10.1186/1756-0500-2-256}
}
@article{Gaburov2009a,
title = {SAPPORO: A way to turn your graphics cards into a GRAPE-6},
author = {E. Gaburov and S. Harfst and S.F. Portegies Zwart},
year = {2009},
journal = {New Astronomy},
volume = {14},
number = {7},
pages = {630--637},
metis_id = {307607},
url = {http://adsabs.harvard.edu/abs/2009arXiv0902.4463G},
month = {February},
doi = {10.1016/j.newast.2009.03.002},
keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Distributed, Parallel, and Cluster Computing}
}
@article{Geerdink2009a,
title = {Comparing entropic and multiple relaxation time lattice Boltzmann methods for blood flow simulations},
author = {J.B.W. Geerdink and A.G. Hoekstra},
year = {2009},
journal = {Int. J. Mod. Phys. C},
volume = {20},
number = {5},
pages = {721-733},
metis_id = {316666},
url = {http://dx.doi.org/10.1142/S0129183109013947},
doi = {10.1142/S0129183109013947}
}
@article{Glebbeek2009a,
title = {The evolution of runaway stellar collision products},
author = {E. Glebbeek and E. Gaburov and S.E. de Mink and O.R. Pols and S.F. Portegies Zwart},
year = {2009},
journal = {Astron.Astrophys.},
volume = {497},
number = {1},
pages = {255--264},
metis_id = {307608},
url = {http://adsabs.harvard.edu/abs/2009arXiv0902.1753G},
month = {February},
doi = {10.1051/0004-6361/200810425},
memo = {url = Glebbeek2009a.pdf},
keywords = {Astrophysics - Solar and Stellar Astrophysics}
}
@article{Graf2009a,
title = {"In Silico" Oncology for Clinical Decision Making in the Context of Nephroblastoma},
author = {N. Graf and A. Hoppe and E. Georgiadi and R.G. Belleman and C. Desmedt and D. Dionysiou and M. Erdt and J. Jacques and E. Kolokotroni and A. Lunzer and M. Tsiknakis and G. Stamatakos},
year = {2009},
journal = {Klinische P\"adiatrie},
volume = {221},
number = {3},
pages = {141--149},
metis_id = {312423},
publisher = {Georg Thieme Verlag KG},
doi = {10.1055/s-0029-1216368},
keywords = {`in silico' oncology, Oncosimulator, nephroblastoma, decision making}
}
@inproceedings{Groen2009a,
title = {On the Origin of Grid Species: The Living Application},
author = {D.J. Groen and S. Harfst and S.F. Portegies Zwart},
year = {2009},
volume = {5544},
pages = {205--212},
metis_id = {307643},
url = {Groen2009a.pdf},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2009: 9th International Conference, Baton Rouge, LA, USA, Proceedings, Part I},
editor = {G. Allen and J. Nabrzyski and E. Seidel and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2009 (ICCS 2009), Baton Rouge, LA, USA},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13: 978-3-642-01969-2}
}
@inbook{Gubala2009a,
title = {Chapter XXVI: Semantic Integration for Research Environments},
author = {T. Guba\la and M.T. Bubak and P.M.A. Sloot},
year = {2009},
metis_id = {307720},
url = {http://www.igi-global.com/reference/details.asp?ID=34292\&v=tableOfContents},
month = {May},
publisher = {IGI Publishing, Medical Information Science Reference},
booktitle = {Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare},
editor = {M. Cannataro},
issn_isbn = {ISBN: 978-1-60566-374-6}
}
@inproceedings{Ivanov2009a,
title = {Computer Simulation of Laser Annealing of a Nanostructured Surface},
author = {D.A. Ivanov and I. Marinov and Y.E. Gorbachev and A.S. Smirnov and V.V. Krzhizhanovskaya},
year = {2009},
pages = {DETC2009-87087},
month = {August 30 - September 2},
category = {LaserAnnealing, NanostructuredSurface},
booktitle = {Proceedings of the ASME IDETC/CIE-2009 conference},
note = {on CD},
address = {San Diego, CA, USA},
issn_isbn = {ISBN: 978-0-7918-3856-3}
}
@inproceedings{Kitowski2009a,
title = {Structure and status of National Grid Initiative in Poland},
author = {J. Kitowski and M. Tura\la and K. Wiatr and M.T. Bubak and A. Kusznir and J. Niwicki and T. Szepieniec and M. Radecki and A. Ozieblo and Z. Mosurska and A. Szyma\'nska and K. Krawentek and et al.},
year = {2009},
pages = {39--51},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'08 Grid Workshop: October 13-15, 2008 Cracow, Poland: proceedings},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
issn_isbn = {ISBN 978-83-61433-00-2}
}
@phdthesis{Korkhov2009a,
title = {Hierarchical resource management in grid computing},
author = {V.V. Korkhov},
year = {2009},
metis_id = {307729},
url = {http://dare.uva.nl/en/record/301138},
month = {April},
category = {GridComputing},
numpages = {122 + VI},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. A.S.Z. Belloum},
keywords = {Grid Computing; Resource Management; Load Balancing; Scheduling}
}
@article{Korkhov2009b,
title = {User-Level Scheduling of Divisible Load Parallel Applications with Resource Selection and Adaptive Workload Balancing on the Grid},
author = {V.V. Korkhov and J.T. Mo\'scicki and V.V. Krzhizhanovskaya},
year = {2009},
journal = {IEEE Systems Journal, Special Issue on Grid Resource Management},
volume = {3},
number = {1},
pages = {121--130},
metis_id = {312424},
url = {http://dx.doi.org/10.1109/JSYST.2008.2011301},
category = {Grid, User-LevelScheduling, AdaptiveLoadBalancing},
publisher = {IEEE},
doi = {10.1109/JSYST.2008.2011301}
}
@article{Kouwenhoven2009a,
title = {Exploring the consequences of pairing algorithms for binary stars},
author = {M.B.N. Kouwenhoven and A.G.A. Brown and S.P. Goodwin and S.F. Portegies Zwart and L. Kaper},
year = {2009},
journal = {Astron. Astrophys.},
volume = {493},
number = {3},
pages = {979--1016},
metis_id = {307610},
url = {http://adsabs.harvard.edu/abs/2008arXiv0811.2859K},
month = {Jan},
doi = {10.1051/0004-6361:200810234},
memo = {url = Kouwenhove2009a.pdf},
keywords = {Astrophysics}
}
@inbook{Kroc2009a,
title = {Complex Systems Modeling by Cellular Automata},
author = {J. Kroc and P.M.A. Sloot},
year = {2009},
pages = {353--360},
metis_id = {296450},
url = {Kroc2008a.pdf},
month = {May},
publisher = {Information Science Reference},
booktitle = {Encyclopedia of Artificial Intelligence},
memo = {url = http://www.igi-pub.com/reference/details.asp?id=7733},
editor = {J.R. Rabu{\tilde n}al Dopico and J. Dorado de la Calle and A. Pazos Sierra},
issn_isbn = {ISBN: 978-1-59904-849-9}
}
@inproceedings{Krzhizhanovskaya2009a,
title = {Multi-Model Multi-Scale Simulation of Complex Plasma Chemical Processes},
author = {V.V. Krzhizhanovskaya},
year = {2009},
metis_id = {312429},
month = {October 11-16},
category = {Multi-ScaleSimulation, Plasma, PECVD},
booktitle = {EUCASS Aerospace Thematic Workshop on Fundamentals of Aerodynamic-Flow and Combustion Control by Plasmas},
note = {Poster presentation},
organization = {EUCASS Aerospace Thematic Workshop on Fundamentals of Aerodynamic-Flow and Combustion Control by Plasmas, Les Houches, France},
address = {Les Houches, France}
}
@misc{Krzhizhanovskaya2009b,
title = {Simulation of Multiphysics Multiscale Systems: Going Nano},
author = {V.V. Krzhizhanovskaya},
year = {2009},
journal = {International Journal for Multiscale Computational Engineering},
volume = {7},
number = {1},
numpages = {76},
note = {Special Section, Guest editorship and Preface},
doi = {10.1615/IntJMultCompEng.v7.i1}
}
@inproceedings{Krzhizhanovskaya2009c,
title = {Simulation of Plasma Chemical Processes on Heterogeneous Grid Resourses with Adaptive Load Balancing for Parallel Solvers},
author = {V.V. Krzhizhanovskaya and V.V. Korkhov},
year = {2009},
pages = {351--352},
metis_id = {312431},
url = {http://agora.guru.ru/display.php?conf=abrau2009\&page=item003},
month = {September 21-26},
category = {Simulation, Plasma, Grid, AdaptiveLoadBalancing, ParallelSolvers},
publisher = {Moscow State University},
booktitle = {Proceedings of the All-Russian Supercomputer conference "Scientific services on the Internet: Scalability, Parallelism, Efficiency"},
note = {In Russian},
organization = {All-Russian supercomputer conference 'Scientific services on the Internet: Scalability, parallelism, efficiency'},
address = {Novorossiysk, Russia},
issn_isbn = {ISBN 978-5-211-05697-8}
}
@inproceedings{Krzhizhanovskaya2009d,
title = {Information Technologies and Software Packages for Education of Specialists in Materials Science},
author = {V.V. Krzhizhanovskaya and S.V. Ryaboshuk},
year = {2009},
number = {Part I},
pages = {285--287},
month = {29 June--3 July},
category = {Education, InformationTechnologies},
booktitle = {Proceedings of the Third International Conference on Information Technologies in Education, Science and Industry},
note = {In Russian},
address = {Serpuhov, Russia}
}
@inproceedings{Krzhizhanovskaya2009e,
title = {Multiphysics Multi-model Simulation of Large-Area Plasma Chemical Reactors},
author = {V.V. Krzhizhanovskaya and D.A. Ivanov and Y.E. Gorbachev and A.S. Smirnov},
year = {2009},
pages = {1195--1196 (DETC2009-87039)},
month = {August 30 - September 2},
category = {Multiphysics, Simulation, Plasma, Large-Area, PECVD},
publisher = {ASME},
doi = {10.1115/DETC2009-87039},
booktitle = {Proceedings of the ASME IDETC/CIE-2009 conference},
note = {on CD},
address = {San Diego, CA, USA},
issn_isbn = {ISBN: 978-0-7918-3856-3}
}
@inproceedings{Krzhizhanovskaya2009f,
title = {Challenges and Solutions in Simulation of Plasma Discharge in Reactive Flows},
author = {V.V. Krzhizhanovskaya},
year = {2009},
metis_id = {312430},
month = {October 11-16},
category = {Simulation, PlasmaDischarge, ReactiveFlow},
booktitle = {EUCASS Aerospace Thematic Workshop on Fundamentals of Aerodynamic-Flow and Combustion Control by Plasmas},
note = {Invited lecture},
organization = {EUCASS Aerospace Thematic Workshop on Fundamentals of Aerodynamic-Flow and Combustion Control by Plasmas, Les Houches, France},
address = {Les Houches, France}
}
@inproceedings{Krzhizhanovskaya2009g,
title = {Simulation of Multiphysics Multiscale Systems, 6th International Workshop},
author = {V.V. Krzhizhanovskaya},
year = {2009},
volume = {5544},
pages = {653--654},
metis_id = {307644},
url = {Krzhizhanovskaya2009a.pdf},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2009: 9th International Conference, Baton Rouge, LA, USA, Proceedings, Part I},
editor = {G. Allen and J. Nabrzyski and E. Seidel and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2009 (ICCS 2009), Baton Rouge, LA, USA},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13: 978-3-642-01969-2}
}
@misc{Krzhizhanovskaya2009h,
title = {Simulation of Multiphysics Multiscale Systems: Going Nano},
author = {V.V. Krzhizhanovskaya},
year = {2009},
journal = {International Journal for Multiscale Computational Engineering, Special Section},
volume = {7},
number = {1},
pages = {vii--viii},
url = {http://dx.doi.org/10.1615/IntJMultCompEng.v7.i1},
category = {MultiphysicsMultiscaleSystemSimulation},
publisher = {Begell House},
doi = {10.1615/IntJMultCompEng.v7.i1},
note = {Guest editorship and Preface},
editor = {V.V. Krzhizhanovskaya}
}
@inproceedings{Krzhizhanovskaya2009i,
title = {Computer Simulation for Improving Deposition Uniformity in Large-Area RF/VHF PECVD Reactors},
author = {V.V. Krzhizhanovskaya and A.S. Smirnov and Y.E. Gorbachev and D.A. Ivanov and E. Sheykin and R. Wang and T. Tanaka},
year = {2009},
metis_id = {312425},
month = {12 June},
category = {PECVD, VirtualReactors, Large-AreaDeposition, RF-VHF},
publisher = {Applied Materials},
booktitle = {Proceedings of ET Conference},
address = {Santa-Clara, USA}
}
@article{Lorenz2009a,
title = {Lees-Edwards boundary conditions for lattice Boltzmann suspension simulations},
author = {E. Lorenz and A.G. Hoekstra and A. Caiazzo},
year = {2009},
journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
volume = {79},
number = {3},
pages = {036706+},
metis_id = {316668},
url = {http://dx.doi.org/10.1103/PhysRevE.79.036706},
numpages = {8},
publisher = {APS},
doi = {10.1103/PhysRevE.79.036706},
abstract = {When sheared suspensions are simulated, Lees-Edwards boundary conditions allow more realistic computational setups as they remove the need of a domain bounded by shearing walls (as in Couette-type flow) which bias typical flow structures. Lees-Edwards boundary conditions therefore allow investigation of pure bulk properties in a quasi-infinite system. In addition, they improve the computational efficiency of the simulations as the whole domain can be used to calculate averages. We propose an implementation of Lees-Edwards boundary conditions for lattice Boltzmann simulations of particulate suspensions, combined with an accurate treatment of fluid-particle interactions. The algorithm is validated using a simple single-particle benchmark and further applied to a fully resolved suspension flow. Shear-thickening behavior, which is prolonged to higher shear rates as compared to Couette flow results, could be observed.}
}
@article{Lorenz2009b,
title = {Corrected momentum exchange method for lattice Boltzmann simulations of suspension flow},
author = {E. Lorenz and A. Caiazzo and A.G. Hoekstra},
year = {2009},
journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
volume = {79},
number = {3},
pages = {036705+},
metis_id = {316669},
url = {http://dx.doi.org/10.1103/PhysRevE.79.036705},
numpages = {9},
publisher = {APS},
doi = {10.1103/PhysRevE.79.036705},
abstract = {Standard methods for lattice Boltzmann simulations of suspended particles, based on the momentum exchange algorithm, might lack accuracy or violate Galilean invariance in some particular situations. Aiming at simulations of dense suspensions in high-shear flows, we motivate and investigate necessary correction terms. We propose an approach which, combining accurate treatments of fluid-structure interaction and moving boundaries, is able to preserve Galilean invariance in relevant orders and to improve the physical behavior of the system. We validate the approach in a comparison with standard methods in simple test problems.}
}
@inproceedings{Marchi2009a,
title = {Time Evolution of the Stellar Mass Function of Galactic Clusters},
author = {G. de Marchi and F. Paresce and S.F. Portegies Zwart},
year = {2009},
volume = {41},
pages = {320},
url = {http://adsabs.harvard.edu/abs/2009AAS...21344206D},
month = {January},
numpages = {1},
note = {abstract},
series = {American Astronomical Society Meeting Abstracts},
booktitle = {American Astronomical Society Meeting #213, #442.06 Abstracts}
}
@inproceedings{Meizner2009a,
title = {Threat model for MOCCA component environment},
author = {J. Meizner and M. Malawski and S. Naqvi and M.T. Bubak},
year = {2009},
pages = {94--102},
metis_id = {307645},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'08 Grid Workshop: October 13-15, 2008 Cracow, Poland: proceedings},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
issn_isbn = {ISBN 978-83-61433-00-2}
}
@article{Miller-Jones2009a,
title = {The formation of the black hole in the X-ray binary system V404 Cyg},
author = {J.C.A. Miller-Jones and P.G. Jonker and G.A. Nelemans and S.F. Portegies Zwart and V. Dhawan and W. Brisken and E. Gallo and M.P. Rupen},
year = {2009},
journal = {Mon.Not.RAS},
volume = {394},
number = {3},
pages = {1440--1448},
url = {http://adsabs.harvard.edu/abs/2008arXiv0812.3327M},
month = {February},
category = {Astrophysics},
doi = {10.1111/j.1365-2966.2009.14404.x},
memo = {url = Miller-Jones2009a.pdf},
keywords = {astrometry , stars: individual: V404 Cyg , stars: kinematics , stars: supernovae: general , radio continuum: stars , X-rays: binaries}
}
@phdthesis{Msanjila2009a,
title = {On inter-organizational trust engineering in networked collaborations: modeling and management of rational trust},
author = {S.S. Msanjila},
year = {2009},
url = {http://dare.uva.nl/record/314807},
month = {September},
category = {Databases},
numpages = {vi, 196},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. H. Afsarmanesh},
issn_isbn = {ISBN: 9789057761966}
}
@article{Murtaza2009a,
title = {Compute Bound and I/O Bound Cellular Automata Simulations on FPGA Logic},
author = {S. Murtaza and A.G. Hoekstra and P.M.A. Sloot},
year = {2009},
journal = {ACM Trans. Reconfigurable Technol. Syst.},
volume = {1},
number = {4},
pages = {23:1--23:21},
metis_id = {307612},
url = {http://doi.acm.org/10.1145/1462586.1462592},
month = {January},
publisher = {ACM},
doi = {10.1145/1462586.1462592},
address = {New York, NY, USA},
issn_isbn = {ISSN 1936-7406}
}
@article{Portegies_Zwart2009a,
title = {The lost siblings of the Sun},
author = {S.F. Portegies Zwart},
year = {2009},
journal = {Astrophys.J. Let.},
volume = {696},
number = {1},
pages = {L13--L16},
url = {http://adsabs.harvard.edu/abs/2009arXiv0903.0237P},
month = {March},
doi = {10.1088/0004-637X/696/1/L13}
}
@article{Portegies_Zwart2009b,
title = {A multiphysics and multiscale software environment for modeling astrophysical systems},
author = {S.F. Portegies Zwart and S.L.W. McMillan and S. Harfst and D.J. Groen and M. Fujii and B. \'O Nuall\'ain and E. Glebbeek and D.C. Heggie and J.C. Lombardi and P. Hut and V. Angelou and S. Banerjee and H. Belkus and T. Fragos and J.M. Fregeau and E. Gaburov and R. Izzard and M. Juric and S. Justham and A. Sottoriva and P.J. Teuben and J. van Bever and O. Yaron and M. Zemp},
year = {2009},
journal = {New Astronomy},
volume = {14},
pages = {369--378},
url = {http://adsabs.harvard.edu/abs/2008arXiv0807.1996P},
month = {May},
doi = {10.1016/j.newast.2008.10.006},
keywords = {Astrophysics}
}
@inbook{Postma2009a,
title = {Mathematics of experimentally generated chemoattractant gradients},
author = {M. Postma and P.J.M. van Haastert},
year = {2009},
volume = {571},
pages = {473--488},
metis_id = {312432},
month = {September},
chapter = {31},
publisher = {Humana Press},
doi = {10.1007/978-1-60761-198-1_31},
series = {Methods in Molecular Biology},
booktitle = {Chemotaxis},
editor = {T. Jin and D. Hereld},
issn_isbn = {ISBN 978-1-60761-197-4 (Print) 978-1-60761-198-1 (online)}
}
@inproceedings{Quax2009a,
title = {Simulating Individual-Based Models of Epidemics in Hierarchical Networks},
author = {R. Quax and D.A. Bader and P.M.A. Sloot},
year = {2009},
volume = {5544},
pages = {725--734},
metis_id = {307646},
url = {Quax2009a.pdf},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2009: 9th International Conference, Baton Rouge, LA, USA, Proceedings, Part I},
editor = {G. Allen and J. Nabrzyski and E. Seidel and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2009 (ICCS 2009), Baton Rouge, LA, USA},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13: 978-3-642-01969-2}
}
@phdthesis{Rodrguez2009a,
title = {Stochasticity in Signal Transduction Pathways},
author = {J. Vidal Rodr\'{\i}guez},
year = {2009},
url = {Rodriguez2009a.pdf},
month = {November},
numpages = {123},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. J.A. Kaandorp},
issn_isbn = {ISBN 978-90-9024739-7}
}
@mastersthesis{Rusadi2009a,
title = {Interactive Visualization of Graphs on Multiple Levels of Detail Using a Direct-Touch Interactive Graphics Device},
author = {F.I. Rusadi},
year = {2009},
url = {Rusadi2009a.pdf},
month = {August},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisor: R.G. Belleman}
}
@inproceedings{Rzasa2009a,
title = {Application of Petri nets to evaluation of Grid applications efficiency},
author = {W. Rzasa and M.T. Bubak},
year = {2009},
pages = {261--269},
metis_id = {307647},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'08 Grid Workshop: October 13-15, 2008 Cracow, Poland: proceedings},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
issn_isbn = {ISBN 978-83-61433-00-2}
}
@inproceedings{Schooten2009a,
title = {Evaluating Visualization and Navigation Techniques for Interpretation of MRA Data},
author = {B.W. van Schooten and E.M.A.G. van Dijk and E.V. Zudilova-Seinstra and P.J.H. de Koning and J.H.C. Reiber},
year = {2009},
pages = {405--408},
month = {February},
booktitle = {International Conference on Computer Graphics Theory and Applications (GRAPP 2009)},
organization = {International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications (VISIGRAPP 2009), Lisbon, Portugal},
address = {Lisbon, Portugal}
}
@inproceedings{Shirshov2009a,
title = {Developing a model of processes in a shock tube with ignition of combustible gas mixtures},
author = {G.S. Shirshov and V.V. Krzhizhanovskaya},
year = {2009},
volume = {6},
pages = {65--66},
metis_id = {312434},
month = {November 30 - December 5},
category = {Shocktube, Model},
publisher = {Saint Petersburg State Polytechnic University},
note = {In Russian},
booktitle = {International Conference "38th Science Week"},
address = {Saint Petersburg, Russia}
}
@article{Sloot2009a,
title = {HIV Decision Support: From Molecule to Man},
author = {P.M.A. Sloot and P.V. Coveney and G. Ertaylan and V. M\"uller and C.A.B. Boucher and M.T. Bubak},
year = {2009},
journal = {Phil . Trans. R. Soc. A},
volume = {367},
number = {1898},
pages = {2691--2703},
metis_id = {307615},
url = {Sloot2009a.pdf},
doi = {10.1098/rsta.2009.0043}
}
@article{Sloot2009b,
title = {Crisis Computing: beslissingsondersteuning in een complexe wereld},
author = {P.M.A. Sloot},
year = {2009},
journal = {Magazine Nationale Veiligheid en Crisisbeheersing},
volume = {7},
number = {8},
pages = {62--63},
metis_id = {312435},
url = {Sloot2009b.pdf},
month = {Nov.-Dec.},
publisher = {Ministerie van Binnenlandse Zaken en Koninkrijksrelaties},
note = {in Dutch}
}
@inproceedings{Strijkers2009a,
title = {Interactive Control over a Programmable Computer Network Using a Multi-touch Surface},
author = {R.J. Strijkers and L.Y.L. Muller and M.L. Cristea and R.G. Belleman and C.T.A.M. de Laat and P.M.A. Sloot and R.J. Meijer},
year = {2009},
volume = {5545},
pages = {719--728},
url = {Strijkers2009a.pdf},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2009: 9th International Conference, Baton Rouge, LA, USA, Proceedings, Part II},
editor = {G. Allen and J. Nabrzyski and E. Seidel and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13: 978-3-642-01972-2}
}
@article{Strokotov2009a,
title = {Is there a difference between T- and B-lymphocyte morphology?},
author = {D.I. Strokotov and M.A. Yurkin and K.V. Gilev and D.R. van Bockstaele and A.G. Hoekstra and N.B. Rubtsov and V.P. Maltsev},
year = {2009},
journal = {Journal of Biomedical Optics},
volume = {14},
number = {6},
pages = {064036},
metis_id = {312437},
url = {http://link.aip.org/link/?JBO/14/064036/1},
numpages = {12},
publisher = {SPIE},
doi = {10.1117/1.3275471},
keywords = {biological techniques; bio-optics; blood; cellular biophysics; diameter measurement; light scattering; optical microscopy; optimisation; refractive index}
}
@inproceedings{Suinesiaputra2009a,
title = {In vivo validations of 3D tubular NURBS fitting model applied on severe stenotic and high curvature MRA of carotid arteries},
author = {A. Suinesiaputra and P.J.H. de Koning and E.V. Zudilova-Seinstra and J.H.C. Reiber and R.J. van der Geest},
year = {2009},
metis_id = {312438},
url = {Suinesiaputra2009a.pdf},
month = {October},
numpages = {5},
booktitle = {ESMRMB Congress},
note = {Electronic poster},
address = {Antalya, Turkey}
}
@inproceedings{Suinesiaputra2009b,
title = {A 3D MRA Segmentation Method Based on Tubular NURBS Model},
author = {A. Suinesiaputra and P.J.H. de Koning and E.V. Zudilova-Seinstra and J.H.C. Reiber and R.J. van der Geest},
year = {2009},
pages = {3149--3149},
metis_id = {312439},
url = {Suinesiaputra2009b.pdf},
month = {April},
booktitle = {International Society for Magnetic Resonance in Medicine 2009},
note = {abstract, poster},
address = {Honolulu, Hawaii}
}
@inproceedings{Tirado-Ramos2009a,
title = {Third Workshop on Teaching Computational Science (WTCS 2009)},
author = {A. Tirado Ramos and A.B. Shiflet},
year = {2009},
volume = {5545},
pages = {3--4},
url = {TiradoRamos2009a.pdf},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2009: 9th International Conference, Baton Rouge, LA, USA, Proceedings, Part II},
editor = {G. Allen and J. Nabrzyski and E. Seidel and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2009 (ICCS 2009), Baton Rouge, LA, USA},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13: 978-3-642-01972-2}
}
@inproceedings{Verkerk2009a,
title = {Compensation of decreased ion energy by increased hydrogen dilution in plasma deposition of thin film silicon solar cells at low substrate temperatures},
author = {A.D. Verkerk and M.M. de Jong and J.K. Rath and M. Brinza and R.E.I. Schropp and W.J. Goedheer and V.V. Krzhizhanovskaya and Y.E. Gorbachev and K.E. Orlov and E.M. Khilkevitch and A.S. Smirnov},
year = {2009},
journal = {Materials Science and Engineering B-Advanced Functional Solid-State Materials},
volume = {159-160},
pages = {53--56},
metis_id = {312447},
url = {http://dx.doi.org/10.1016/j.mseb.2008.11.013},
publisher = {Elsevier},
note = {Verkerk2008a},
editor = {Pizzini,S. and Kissinger,G. and Tu,H. and Yamada-Kaneta,H.},
organization = {European Materials Research Society (EMRS) Spring Meeting, Symposium K: Advanced silicon materials research for electronic and photovoltaic applications, Strasbourg, France},
booktitle = {Proceedings of the European Materials Research Society Spring Meeting, Symposium K: Advanced silicon materials research for electronic and photovoltaic applications, Strasbourg, France},
address = {Lausanne}
}
@mastersthesis{Zarrabi2009a,
title = {Modeling and Simulation of HIV-1 Intracellular Replication},
author = {N. Zarrabi},
year = {2009},
url = {Zarrabi2009a.pdf},
month = {August},
category = {pwrs, mastersthesis, virolab},
school = {University of Amsterdam},
tutor = {Supervisor: P.M.A. Sloot},
address = {Amsterdam, the Netherlands}
}
@inproceedings{Zudilova-Seinstra2009a,
title = {Exploring 2D/3D Input Techniques for Medical Image Analysis},
author = {E.V. Zudilova-Seinstra and P.M.A. Sloot and P.J.H. de Koning and A. Suinesiaputra and R.J. van der Geest and J.H.C. Reiber},
year = {2009},
volume = {2},
pages = {147--152},
url = {Zudilova-Seinstra2009a.pdf},
month = {July},
publisher = {IEEE Computer Society},
doi = {10.1109/VIZ.2009.18},
booktitle = {International Conference on Information Visualisation, track Biomedical Visualization (MediViz09)},
address = {Barcelona, Spain}
}
@inproceedings{Zverev2009a,
title = {Developing a model of nickel film growth in a PECVD reactor},
author = {V.A. Zverev and I.S. Kiseleva and V.V. Krzhizhanovskaya},
year = {2009},
volume = {6},
pages = {59--60},
metis_id = {312443},
month = {November 30 - December 5},
category = {PECVDreactor, FilmDeposition, nickel},
publisher = {Saint Petersburg State Polytechnic University},
note = {In Russian},
booktitle = {International Conference "38th Science Week"},
address = {Saint Petersburg, Russia}
}
@mastersthesis{zsoy2009a,
title = {Interactive Visualization of Large Medical Datasets on the Grid},
author = {A.Z. \"Ozsoy},
year = {2009},
month = {April},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisor: R.G. Belleman}
}
@inproceedings{Assel2008a,
title = {Integrating and accessing medical data resources within the ViroLab Virtual Laboratory},
author = {M. Assel and P. Nowakowski and M.T. Bubak},
year = {2008},
volume = {5103},
pages = {90--99},
metis_id = {307650},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69388-8},
month = {June},
publisher = {Springer},
note = {Also on CD-ROM},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part III},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2008 (ICCS 2008), Krak\'ow, Poland},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13 978-3-540-69388-8}
}
@article{Axner2008a,
title = {Performance evaluation of a parallel sparse lattice Boltzmann solver},
author = {L. Axner and J.M. Bernsdorf and T. Zeiser and P. Lammers and J. Linxweiler and A.G. Hoekstra},
year = {2008},
journal = {Journal of Computational Physics},
volume = {227},
number = {10},
pages = {4895--4911},
metis_id = {285199},
url = {http://dx.doi.org/10.1016/j.jcp.2008.01.013},
month = {May},
category = {LBM},
doi = {10.1016/j.jcp.2008.01.013},
memo = {url = Axner2008a.pdf}
}
@inproceedings{Badia2008a,
title = {Performance monitoring of GRID superscalar with OCM-G/G-PM: integration issues},
author = {R.M. Badia and R. Sirvent and M.T. Bubak and W. Funika and P. Machner},
year = {2008},
pages = {193--205},
metis_id = {307651},
publisher = {Springer},
booktitle = {Achievements in European Reseach on Grid Systems. CoreGRID Integration Workshop 2006 (Selected Papers)},
note = {Also published as CoreGRID Technical Report TR-0108},
editor = {S. Gorlatch and M.T. Bubak and T. Priol},
keywords = {WP7},
organization = {CoreGRID Integration Workshop 2006 (CGIW'2006), Krakow, Poland}
}
@inproceedings{Badia2008b,
title = {Performance monitoring of Grid superscalar: visualization modes},
author = {R.M. Badia and R. Sirvent and M.T. Bubak and W. Funika and P. Machner},
year = {2008},
pages = {266--274},
metis_id = {307652},
publisher = {Crete University Press},
booktitle = {CoreGRID integration workshop 2008 -- Integrated Research in Grid Computing: April 24, Hersonissos, Crete, Greece},
editor = {S. Gorlatch and P. Fragopoulou and T. Priol},
address = {Heraklion},
issn_isbn = {ISBN 978-960-524-260-2}
}
@inproceedings{Bali,
title = {Provenance tracking and querying in ViroLab},
author = {B. Bali\'s and M.T. Bubak and M. Pelczar and J. Wach},
year = {2008},
pages = {71--76},
metis_id = {307657},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'07 Grid Workshop: October 15--17, 2007 Cracow, Poland},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@article{Bali,
title = {Monitoring of Grid scientific workflows},
author = {B. Bali\'s and M.T. Bubak and B. Labno},
year = {2008},
journal = {Scientific Programming},
volume = {16},
number = {2, 3},
pages = {205--216},
note = {In special issue: Large-scale programming tools and environments},
doi = {10.3233/SPR-2008-0257},
issn_isbn = {ISSN 1058-9244}
}
@inproceedings{Bali,
title = {Provenance tracking in the ViroLab Virtual Laboratory},
author = {B. Bali\'s and M.T. Bubak and J. Wach},
year = {2008},
number = {4967},
pages = {381--390},
publisher = {Springer-Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Parallel Processing and Applied Mathematics: 7th international conference, PPAM 2007: Gdask, Poland, September 9--12, 2007: revised selected papers},
editor = {R. Wyrzykowski and J.J. Dongarra and K. Karczewski and J. Wa\'sniewski},
address = {Berlin ; Heidelberg},
issn_isbn = {ISBN-10 3-540-68105-1, ISBN-13 978-3-540-68105-2}
}
@inproceedings{Bali,
title = {Provenance tracking and querying in the ViroLab Virtual Laboratory},
author = {B. Bali\'s and M.T. Bubak and M. Pelczar and J. Wach},
year = {2008},
pages = {675--680},
metis_id = {307656},
publisher = {CPS Conference Publishing Services, IEEE Computer Society},
booktitle = {CCGRID 2008: eighth IEEE international symposium on Cluster Computing and the Grid: 19--22 May 2008, Lyon, France},
editor = {T. Priol and L. Lefevre and R. Buyya},
organization = {8th IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2008), Lyon, France},
issn_isbn = {ISBN 978-0-7695-3156-4}
}
@inproceedings{Bali,
title = {Provenance querying for end-users: a drug resistance case study},
author = {B. Bali\'s and M.T. Bubak and M. Pelczar and J. Wach},
year = {2008},
volume = {5103},
pages = {80--89},
metis_id = {307655},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69388-8},
month = {June},
publisher = {Springer},
note = {Also on CD-ROM},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part III},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2008 (ICCS 2008), Krak\'ow, Poland},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13 978-3-540-69388-8}
}
@inproceedings{Bali,
title = {An ontology model for execution records of Grid scientific applications},
author = {B. Bali\'s and M.T. Bubak},
year = {2008},
pages = {34--41},
metis_id = {307654},
month = {December},
publisher = {IEEE},
doi = {10.1109/SKG.2008.100},
booktitle = {SKG2008: proceedings of the fourth international conference on Semantics, Knowledge, and Grid},
organization = {4th International Conference on Semantics, Knowledge and Grid (SKG2008), Beijing, China},
address = {Beijing, China},
issn_isbn = {ISBN 978-0-7695-3401-5}
}
@article{Bali,
title = {LGF: a flexible framework for exposing legacy codes as services},
author = {B. Bali\'s and M.T. Bubak and M. Wegiel},
year = {2008},
journal = {Future Generation Computer Systems},
volume = {24},
number = {7},
pages = {711--719},
metis_id = {307616},
doi = {10.1016/j.future.2007.12.001},
issn_isbn = {ISSN 0167-739X}
}
@inproceedings{Bartynski2008a,
title = {Invocation of Grid operations in the ViroLab Virtual Laboratory},
author = {T. Bartynski and M. Malawski and M.T. Bubak},
year = {2008},
pages = {59--64},
metis_id = {307659},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'07 Grid Workshop: October 15--17, 2007 Cracow, Poland},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
organization = {Cracow' 07 Grid Workshop (CGW'07), Cracow, Poland},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@inproceedings{Bartynski2008b,
title = {Universal Grid client: Grid Operation Invoker},
author = {T. Bartynski and M. Malawski and T. Guba\la and M.T. Bubak},
year = {2008},
number = {4967},
pages = {1068--1077},
publisher = {Springer-Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Parallel Processing and Applied Mathematics: 7th international conference, PPAM 2007: Gdask, Poland, September 9--12, 2007: revised selected papers},
editor = {R. Wyrzykowski and J.J. Dongarra and K. Karczewski and J. Wa\'sniewski},
address = {Berlin ; Heidelberg},
issn_isbn = {ISBN-10 3-540-68105-1, ISBN-13 978-3-540-68105-2}
}
@article{Belleman2008a,
title = {High performance direct gravitational N-body simulations on graphics processing units II: An implementation in CUDA},
author = {R.G. Belleman and J. B\'edorf and S.F. Portegies Zwart},
year = {2008},
journal = {New Astronomy},
volume = {13},
number = {2},
pages = {103-112},
metis_id = {276799},
url = {http://adsabs.harvard.edu/abs/2008NewA...13..103B},
month = {feb},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1016/j.newast.2007.07.004},
memo = {url = Belleman2008a.pdf}
}
@inproceedings{Belloum2008a,
title = {International workshop on Applications of Workflows in Computational Science (AWCS 08)},
author = {A.S.Z. Belloum and Z. Zhao and M.T. Bubak},
year = {2008},
volume = {5103},
pages = {459--462},
metis_id = {307660},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69388-8},
month = {June},
publisher = {Springer},
note = {Also on CD-ROM},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part III},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2008 (ICCS 2008), Krak\'ow, Poland},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13 978-3-540-69388-8}
}
@phdthesis{Bernsdorf2008a,
title = {Simulation of Complex Flows and Multi-Physics with the Lattice-Boltzmann Method},
author = {J.M. Bernsdorf},
year = {2008},
metis_id = {292023},
url = {Bernsdorf2008a.pdf},
month = {January},
category = {LBM},
numpages = {142},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. A.G. Hoekstra}
}
@inproceedings{Bubak2008a,
title = {Appea: a framework for the design and development of business applications on the Grid},
author = {M.T. Bubak and D. Harezlak and P. Nowakowski and T. Guba\la and M. Malawski},
year = {2008},
pages = {220--225},
metis_id = {307661},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'07 Grid Workshop: October 1517, 2007 Cracow, Poland},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@inproceedings{Bubak2008b,
title = {Virtual Laboratory for Development and Execution of Biomedical Collaborative Applications},
author = {M.T. Bubak and T. Guba\la and M. Malawski and B. Bali\'s and W. Funika and T. Bartynski and E. Ciepiela and D. Harezlak and M. Kasztelnik and J. Kocot and D. Kr\'ol and P. Nowakowski and M. Pelczar and J. Wach and M. Assel and A. Tirado Ramos},
year = {2008},
pages = {373--378},
month = {June},
publisher = {IEEE},
doi = {10.1109/CBMS.2008.47},
booktitle = {21th IEEE International Symposium on Computer-Based Medical Systems (CBMS 2008)},
abstract = {The ViroLab Virtual Laboratory is a collaborative platform for scientists representing multiple fields of expertise while working together on common scientific goals. This environment makes it possible to combine efforts of computer scientists, virology and epidemiology experts and experienced physicians to support future advances in HIV-related research and treatment. The paper explains the challenges involved in building a modern, inter-organizational platform to support science and gives an overview of solutions to these challenges. Examples of real-world problems applied in the presented environment are also described to prove the feasibility of the solution.},
address = {Jyv\"askyl\"a, Finland},
issn_isbn = {ISBN: 978-0-7695-3165-6}
}
@proceedings{Bubak2008c,
author = {M.T. Bubak and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2008},
volume = {5101},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69383-3},
month = {June},
numpages = {1051},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part I},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69383-3}
}
@proceedings{Bubak2008d,
author = {M.T. Bubak and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2008},
volume = {5102},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69386-4},
month = {June},
numpages = {745},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69386-4}
}
@proceedings{Bubak2008e,
author = {M.T. Bubak and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2008},
volume = {5103},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69388-8},
month = {June},
numpages = {751},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part III},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69388-8}
}
@proceedings{Bubak2008f,
author = {M.T. Bubak and M. Tura\la and K. Wiatr},
year = {2008},
metis_id = {307734},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'07 Grid Workshop: October 1517, 2007 Cracow, Poland: proceedings},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@inproceedings{Caiazzo2008a,
title = {Scale-Splitting Error in Complex Automata models for Reaction-Diffusion Systems},
author = {A. Caiazzo and J.-L. Falcone and B. Chopard and A.G. Hoekstra},
year = {2008},
volume = {5102},
pages = {291--300},
metis_id = {285203},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69386-4},
month = {June},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69386-4}
}
@inproceedings{Caiazzo2008b,
title = {Error Investigations in Complex Automata models for Reaction-Diffusion systems},
author = {A. Caiazzo and J.-L. Falcone and B. Chopard and A.G. Hoekstra},
year = {2008},
volume = {5191},
pages = {260--267},
metis_id = {296516},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Cellular Automata, 8th International Conference on Cellular Automata for Reseach and Industry, ACRI 2008},
editor = {H. Umeo and S. Morishita and K. Nishinari and T. Komatsuzaki and S. Bandini},
organization = {8th International Conference on Cellular Automata for Reseach and Industry (ACRI 2008), Yokohama, Japan},
issn_isbn = {ISBN 978-3-540-79991-7}
}
@article{Chernyshev2008a,
title = {Erythrocyte lysis in isotonic solution of ammonium chloride: Theoretical modelling and experimental verification},
author = {A.V. Chernyshev and P.A. Tarasov and K.A. Semianov and V.M. Nekrasov and A.G. Hoekstra and V.P. Maltsev},
year = {2008},
journal = {Journal of Theoretical Biology},
volume = {251},
number = {1},
pages = {93--107},
metis_id = {285204},
url = {Chernyshev2008a.pdf},
doi = {10.1016/j.jtbi.2007.10.016}
}
@inproceedings{Chopard2008a,
title = {On the collision-propagation and gather-update formulations of a Cellular Automata rule},
author = {B. Chopard and J.-L. Falcone and R. Razakarinina and A.G. Hoekstra and A. Caiazzo},
year = {2008},
volume = {5191},
pages = {144--151},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Cellular Automata, 8th International Conference on Cellular Automata for Reseach and Industry, ACRI 2008},
editor = {H. Umeo and S. Morishita and K. Nishinari and T. Komatsuzaki and S. Bandini},
issn_isbn = {ISBN 978-3-540-79991-7}
}
@mastersthesis{Chu2008a,
title = {A survey of classical simulation methods for quantum computation},
author = {D.M. Chu},
year = {2008},
url = {Chu2008a.pdf},
month = {June},
category = {pwrs, mastersthesis, Programming},
school = {University of Amsterdam},
tutor = {Supervisors: H. Buhrman and R. de Wolf},
address = {Amsterdam, the Netherlands}
}
@inproceedings{Ciepiela2008a,
title = {GridSpace Engine of the ViroLab Virtual Laboratory},
author = {E. Ciepiela and J. Kocot and T. Guba\la and M. Malawski and M. Kasztelnik and M.T. Bubak},
year = {2008},
pages = {53--58},
metis_id = {307662},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'07 Grid Workshop: October 15--17, 2007 Cracow, Poland},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
organization = {Cracow' 07 Grid Workshop (CGW'07), Cracow, Poland},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@article{Cui2008a,
title = {Simulating In Vitro Transcriptional Response of Zinc Homeostasis System in Escherichia coli},
author = {J. Cui and J.A. Kaandorp and C.M. Lloyd},
year = {2008},
journal = {BMC Systems Biology},
volume = {2},
pages = {89},
metis_id = {296221},
url = {Cui2008b.pdf},
numpages = {14},
doi = {10.1186/1752-0509-2-89}
}
@inproceedings{Cui2008b,
title = {Simulating Complex Calcium-Calcineurin Signaling Network},
author = {J. Cui and J.A. Kaandorp},
year = {2008},
volume = {5103},
pages = {110--119},
metis_id = {285205},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69388-8},
month = {June},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part III},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69388-8}
}
@inproceedings{Ertaylan2008a,
title = {A complex automata model of HIV-1 co-receptor tropism: mutation rate prediction},
author = {G. Ertaylan and P.M.A. Sloot},
year = {2008},
pages = {85--85},
metis_id = {285206},
url = {http://www.cyfronet.pl/cgw07/proc-contents.pdf},
month = {October},
category = {CellularAutomata},
booktitle = {CGW'07 proceedings},
note = {abstract},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
organization = {Cracow' 07 Grid Workshop (CGW'07), Cracow, Poland},
address = {Krakow, Poland},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@inproceedings{Evans2008a,
title = {Multiscale Modelling: Application of the Complex Automata Simulation Technique (COAST)},
author = {D.J.W. Evans and A.G. Hoekstra and J. Gunn and D. Walker and D.R. Hose and R.H. Smallwood and B. Chopard and M. Krafczyk and J.M. Bernsdorf and P.V. Lawford},
year = {2008},
metis_id = {296222},
booktitle = {Proceedings of the European Biomechanics Society conference 2008}
}
@article{Evans2008b,
title = {The Application of Multiscale Modelling to the Process of Development and Prevention of Stenosis in a Stented Coronary Artery},
author = {D.J.W. Evans and P.V. Lawford and J. Gunn and D. Walker and D.R. Hose and R.H. Smallwood and B. Chopard and M. Krafczyk and J.M. Bernsdorf and A.G. Hoekstra},
year = {2008},
journal = {Phil. Trans. Roy. Soc A},
volume = {366},
number = {1879},
pages = {3343--3360},
metis_id = {285207},
url = {http://rsta.royalsocietypublishing.org/content/366/1879/3343.abstract},
doi = {10.1098/rsta.2008.0081}
}
@article{Faber2008a,
title = {On time-dependent orbital complexity in gravitational N-body simulations},
author = {N.T. Faber and C.M. Boily and S.F. Portegies Zwart},
year = {2008},
journal = {Mon. Not. Royal Astr. Soc},
volume = {386},
number = {1},
pages = {425-439},
metis_id = {301837},
url = {http://adsabs.harvard.edu/abs/2008MNRAS.386..425F},
month = {may},
doi = {10.1111/j.1365-2966.2008.13041.x},
keywords = {methods: N-body simulations , methods: numerical , stars: kinematics}
}
@mastersthesis{Filatov2008a,
title = {A compression-based group similarity measure with applications in phylogeny. Automatic detection of viral RNA recombination.},
author = {M.V. Filatov},
year = {2008},
url = {Filatov2008a.pdf},
month = {April},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
tutor = {Advisor: B. \'O~Nuall\'ain},
address = {Amsterdam, the Netherlands}
}
@inproceedings{Funika2008a,
title = {User interfaces of the Virolab Virtual Laboratory},
author = {W. Funika and D. Harezlak and D. Kr\'ol and P. Pegiel and M.T. Bubak},
year = {2008},
pages = {47--52},
metis_id = {307665},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'07 Grid Workshop: October 15--17, 2007 Cracow, Poland},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@inproceedings{Funika2008b,
title = {OCM2PRV: performance visualization of Grid applications based on OCM-G and Paraver},
author = {W. Funika and M. Zientarski and R.M. Badia and J. Labarta and M.T. Bubak},
year = {2008},
pages = {87--98},
metis_id = {307664},
publisher = {Crete University Press},
booktitle = {CoreGRID integration workshop 2008 -- Integrated Research in Grid Computing: April 24, Hersonissos, Crete, Greece},
editor = {S. Gorlatch and P. Fragopoulou and T. Priol},
address = {Heraklion},
issn_isbn = {ISBN 978-960-524-260-2}
}
@inproceedings{Funika2008c,
title = {Environment for collaborative development and execution of Virtual Laboratory applications},
author = {W. Funika and D. Harezlak and D. Kr\'ol and M.T. Bubak},
year = {2008},
volume = {5103},
pages = {446--455},
metis_id = {307663},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69388-8},
month = {June},
publisher = {Springer},
note = {Also on CD-ROM},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part III},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2008 (ICCS 2008), Krak\'ow, Poland},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13 978-3-540-69388-8}
}
@phdthesis{Gaburov2008a,
title = {Stellar collisions in young star clusters},
author = {E. Gaburov},
year = {2008},
metis_id = {292227},
url = {Gaburov2008c.pdf},
month = {November},
category = {Astronomy},
numpages = {143},
school = {University of Amsterdam},
tutor = {promotores: R.A.J.M. Weijers and P.M.A. Sloot; copromotores: S.F. Portegies Zwart and O.R. Pols}
}
@article{Gaburov2008b,
title = {On the onset of runaway stellar collisions in dense star clusters: I. Dynamics of the first collision},
author = {E. Gaburov and A. Gualandris and S.F. Portegies Zwart},
year = {2008},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {384},
number = {1},
pages = {376-385},
metis_id = {285208},
url = {http://adsabs.harvard.edu/abs/2007arXiv0707.0406G},
month = {feb},
doi = {10.1111/j.1365-2966.2007.12731.x}
}
@article{Gaburov2008c,
title = {Mixing in massive stellar mergers},
author = {E. Gaburov and J.C. Lombardi and S.F. Portegies Zwart},
year = {2008},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {383},
number = {1},
pages = {L5-L9},
metis_id = {276801},
url = {http://adsabs.harvard.edu/abs/2008MNRAS.383L...5G},
month = {jan},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1111/j.1745-3933.2007.00399.x}
}
@mastersthesis{Geerdink2008a,
title = {Entropic and multiple relaxation time lattice Boltzmann methods compared for time harmonic flows},
author = {J.B.W. Geerdink},
year = {2008},
url = {Geerdink2008a.pdf},
month = {January},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
tutor = {Supervisor: A.G. Hoekstra},
address = {Amsterdam, the Netherlands}
}
@book{Gorlatch2008a,
year = {2008},
publisher = {Springer},
booktitle = {Achievements in European Research on Grid Systems},
note = {ISBN 978-0-387-72811-7},
editor = {S. Gorlatch and M.T. Bubak and T. Priol},
address = {USA},
keywords = {WP4}
}
@inproceedings{Groen2008a,
title = {Simulating N-Body Systems on the Grid Using Dedicated Hardware},
author = {D.J. Groen and S.F. Portegies Zwart and S.L.W. McMillan and J. Makino},
year = {2008},
volume = {5101},
pages = {86--95},
metis_id = {285210},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69383-3},
month = {June},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part I},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69383-3}
}
@article{Groen2008b,
title = {Distributed N-body Simulation on the Grid Using Dedicated Hardware},
author = {D.J. Groen and S.F. Portegies Zwart and S.L.W. McMillan and J. Makino},
year = {2008},
journal = {New Astronomy},
volume = {13},
number = {5},
pages = {348--358},
metis_id = {285209},
url = {http://adsabs.harvard.edu/abs/2008NewA...13..348G},
month = {July},
category = {Astronomy},
doi = {10.1016/j.newast.2007.11.004}
}
@article{Gualandris2008a,
title = {Evolution of stellar orbits in the Galactic centre},
author = {A. Gualandris and S. Harfst and D. Merritt and S. Mikkola},
year = {2008},
journal = {Astronomische Nachrichten},
volume = {329},
number = {9-10},
pages = {1008-1011},
metis_id = {296225},
url = {http://adsabs.harvard.edu/abs/2008AN....329.1008G},
doi = {10.1002/asna.200811048},
keywords = {celestial mechanics, stellar dynamics, Galaxy: center, methods: N-body simulations}
}
@inproceedings{Gubala2008a,
title = {ViroLab Virtual Laboratory},
author = {T. Guba\la and B. Bali\'s and M. Malawski and M. Kasztelnik and P. Nowakowski and M. Assel and D. Harezlak and T. Bartynski and J. Kocot and E. Ciepiela and D. Kr\'ol and J. Wach and M. Pelczar and W. Funika and M.T. Bubak},
year = {2008},
pages = {35--40},
metis_id = {307666},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'07 Grid Workshop: October 15--17, 2007 Cracow, Poland},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@inproceedings{Gubala2008b,
title = {Towards a System-Level Science Support},
author = {T. Guba\la and M. Kasztelnik and M. Malawski and M.T. Bubak},
year = {2008},
volume = {5101},
pages = {56--65},
metis_id = {285211},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69383-3},
month = {June},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part I},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69383-3}
}
@inproceedings{Guisado2008a,
title = {Parallel Cellular Automata-based Simulation of Laser Dynamics using Dynamic Load Balancing},
author = {J.L. Guisado and F. Fern\'andez de Vega and F. Jim\'enez Morales and K.A. Iskra and P.M.A. Sloot},
year = {2008},
pages = {49--55},
metis_id = {307667},
url = {Guisado2008a.pdf},
month = {October},
publisher = {Universidad Complutense de Madrid},
booktitle = {First International Workshop on Parallel Architectures and Bioinspired Algorithms},
editor = {\'O. Garnica},
organization = {First International Workshop on Parallel Architectures and Bioinspired Algorithms (WPABA), Toronto, Canada},
address = {Toronto, Canada},
issn_isbn = {ISBN: 978-84-691-6512-6}
}
@article{Guisado2008b,
title = {Using cellular automata for parallel simulation of laser dynamics with dynamic load balancing},
author = {J.L. Guisado and F. Fern\'andez de Vega and F. Jim\'enez Morales and K.A. Iskra and P.M.A. Sloot},
year = {2008},
journal = {Int. J. of High Performance Systems Architecture (IJHPSA)},
volume = {1},
number = {4},
pages = {251--259},
metis_id = {307609},
url = {Guisado2010a.pdf},
doi = {10.1504/IJHPSA.2008.024209},
issn_isbn = {ISSN 1751-6528}
}
@article{Guo2008a,
title = {A hybrid agent-based approach for modeling microbiological systems},
author = {Z. Guo and P.M.A. Sloot and J.C. Tay},
year = {2008},
journal = {J. of Theor. Biology},
volume = {255},
number = {2},
pages = {163--175},
metis_id = {296226},
url = {Guo2008a.pdf},
month = {Nov.},
doi = {10.1016/j.jtbi.2008.08.008}
}
@article{Gvaramadze2008a,
title = {Hyperfast pulsars as the remnants of massive stars ejected from young star clusters},
author = {V.V. Gvaramadze and A. Gualandris and S.F. Portegies Zwart},
year = {2008},
journal = {Mon. Not. Royal Astr. Soc},
volume = {385},
number = {2},
pages = {929--938},
metis_id = {276752},
url = {http://adsabs.harvard.edu/abs/2008MNRAS.385..929G},
month = {apr},
doi = {10.1111/j.1365-2966.2008.12884.x},
keywords = {stellar dynamics , methods: N-body simulations , stars: individual: RX J0822-4300 , stars: neutron , pulsars: general , pulsars: individual: B1508+55}
}
@inproceedings{Gvaramadze2008b,
title = {On the origin of hyperfast neutron stars},
author = {V.V. Gvaramadze and A. Gualandris and S.F. Portegies Zwart},
year = {2008},
pages = {365--366},
url = {http://adsabs.harvard.edu/abs/2007arXiv0712.4230G},
month = {dec},
publisher = {Cambridge University Press},
doi = {10.1017/S1743921308015962},
booktitle = {Dynamical Evolution of Dense Stellar Systems, Proceed. of the IAU Symp. 246 (Capri, Sept. 2007)},
editor = {E. Vesperini and M. Giersz, and A.I. Sills}
}
@article{Harfst2008a,
title = {A hybrid N-body code incorporating algorithmic regularization and post-Newtonian forces},
author = {S. Harfst and A. Gualandris and D. Merritt and S. Mikkola},
year = {2008},
journal = {Mon. Not. Royal Astr. Soc},
volume = {389},
number = {1},
pages = {2-12},
metis_id = {296228},
url = {http://adsabs.harvard.edu/abs/2008MNRAS.389....2H},
month = {sep},
doi = {10.1111/j.1365-2966.2008.13557.x},
keywords = {stellar dynamics , methods: N-body simulations , galaxy: centre}
}
@article{Harfst2008b,
title = {Status and future of MUSE},
author = {S. Harfst and S.F. Portegies Zwart and S.L.W. McMillan},
year = {2008},
journal = {Astronomische Nachrichten},
volume = {329},
number = {9-10},
pages = {885-891},
metis_id = {296227},
url = {http://adsabs.harvard.edu/abs/2008AN....329..885H},
doi = {10.1002/asna.200811058},
keywords = {gravitation, hydrodynamics, methods: N-body simulations, methods: numerical, radiative transfer, stars: evolution, stars: kinematics}
}
@inproceedings{Hegewald2008a,
title = {An Agent-Based Coupling Platform for Complex Automata},
author = {J. Hegewald and M. Krafczyk and J. T\"olke and A.G. Hoekstra and B. Chopard},
year = {2008},
volume = {5102},
pages = {227--233},
metis_id = {285212},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69386-4},
month = {June},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69386-4}
}
@misc{Hoekstra2008a,
title = {Book review: Optical Polarization in Biomedical Applications, V.V. Tuchin, L.V. Wang, D.A. Zimnyakov},
author = {A.G. Hoekstra},
year = {2008},
journal = {Journal of Quantitative Spectroscopy \& Radiative Transfer},
volume = {109},
pages = {531--531}
}
@inproceedings{Hoekstra2008b,
title = {Multi-scale Modeling with Cellular Automata: The Complex Automata Approach},
author = {A.G. Hoekstra and J.-L. Falcone and A. Caiazzo and B. Chopard},
year = {2008},
volume = {5191},
pages = {192--199},
metis_id = {296698},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Cellular Automata, 8th International Conference on Cellular Automata for Reseach and Industry, ACRI 2008},
editor = {H. Umeo and S. Morishita and K. Nishinari and T. Komatsuzaki and S. Bandini},
organization = {8th International Conference on Cellular Automata for Reseach and Industry (ACRI 2008), Yokohama, Japan},
issn_isbn = {ISBN 978-3-540-79991-7}
}
@inbook{Hoekstra2008c,
title = {Towards Distributed Petascale Computing},
author = {A.G. Hoekstra and S.F. Portegies Zwart and M.T. Bubak and P.M.A. Sloot},
year = {2008},
pages = {147--164},
url = {http://www.crcpress.com/shopping_cart/products/product_contents.asp?id=\&parent_id=\&sku=C9098\&isbn=9781584889090\&pc=},
month = {mar},
chapter = {8},
publisher = {Chapman \& Hall},
booktitle = {Petascale Computing: Algorithms and Applications},
editor = {D.A. Bader},
issn_isbn = {ISBN: 9781584889090, ISBN 10: 1584889098}
}
@article{Huang2008a,
title = {Introduction to the Special Section on BioGrid: Biomedical Computations on the Grid},
author = {C.-H. Huang and A. Konagaya and V. Lanza and P.M.A. Sloot},
year = {2008},
journal = {IEEE Trans. on Inf. Techn. in Biomedicine},
volume = {12},
number = {2},
pages = {133--137},
url = {Huang2008a.pdf},
month = {March},
note = {Guest Editorial},
doi = {10.1109/TITB.2008.918585}
}
@misc{Kaandorp2008a,
title = {Book review: P. Pelce, New visions on growth and form: fingering growth, dendrites, and flames},
author = {J.A. Kaandorp},
year = {2008},
journal = {Mathematical Biosciences},
volume = {in press}
}
@misc{Kaandorp2008b,
title = {Exploring Theoretical Morphospaces, Book review: The Geometry of Evolution: Adaptive Landscapes and Theoretical Morphospaces. George R. McGhee},
author = {J.A. Kaandorp},
year = {2008},
journal = {BioScience},
volume = {58},
pages = {271--273}
}
@article{Kaandorp2008c,
title = {Modelling genetic regulation of growth and form in a branching sponge},
author = {J.A. Kaandorp and J.G. Blom and J. Verhoef and M.V. Filatov and M. Postma and W.E.G. M\"uller},
year = {2008},
journal = {Proc. Roy. Soc. B},
volume = {275},
number = {1651},
pages = {2569--2575},
metis_id = {296230},
month = {November},
doi = {10.1098/rspb.2008.0746}
}
@inproceedings{Kasztelnik2008a,
title = {Development and execution of collaborative application on the ViroLab Virtual Laboratory},
author = {M. Kasztelnik and T. Guba\la and M. Malawski and M.T. Bubak},
year = {2008},
pages = {41--46},
metis_id = {307668},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'07 Grid Workshop: October 15--17, 2007 Cracow, Poland},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
organization = {Cracow' 07 Grid Workshop (CGW'07), Cracow, Poland},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@article{Korkhov2008a,
title = {A Grid-Based Virtual Reactor: Parallel performance and adaptive load balancing},
author = {V.V. Korkhov and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2008},
journal = {Journal of Parallel and Distributed Computing},
volume = {68},
number = {5},
pages = {596--608},
metis_id = {285216},
url = {Korkhov2008a.pdf},
category = {Grid, VirtualReactor, LoadBalancing},
publisher = {Elsevier},
doi = {10.1016/j.jpdc.2007.08.010}
}
@article{Kouwenhoven2008a,
title = {Pairing mechanisms for binary stars},
author = {M.B.N. Kouwenhoven and A.G.A. Brown and S.P. Goodwin and S.F. Portegies Zwart and L. Kaper},
year = {2008},
journal = {Astronomische Nachrichten},
volume = {329},
number = {9-10},
pages = {984-987},
metis_id = {296231},
url = {http://adsabs.harvard.edu/abs/2008AN....329..984K},
doi = {10.1002/asna.200811061},
keywords = {binaries: general, methods: N-body simulations, stars: formation}
}
@inproceedings{Kowalewski2008a,
title = {An event-based approach to reducing coupling in large-scale applications},
author = {B. Kowalewski and M.T. Bubak and B. Bali\'s},
year = {2008},
volume = {5103},
pages = {358--367},
metis_id = {307669},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69388-8},
month = {June},
publisher = {Springer},
note = {Also on CD-ROM},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part III},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2008 (ICCS 2008), Krak\'ow, Poland},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13 978-3-540-69388-8}
}
@inproceedings{Krzhizhanovskaya2008a,
title = {Parallel Distributed Computing in Modeling of the Nanomaterials Production Technologies},
author = {V.V. Krzhizhanovskaya and V.V. Korkhov and M.A. Zatevakhin and Y.E. Gorbachev},
year = {2008},
pages = {585--590},
metis_id = {312444},
url = {http://www.ict.edu.ru/vconf/index.php?a=vconf\&c=getForm\&r=thesisDesc\&id_sec=299\&id_vconf=54\&id_thesis=11551\&d=light},
month = {January - February},
publisher = {YUSU},
booktitle = {Proceedings of the International Conference on Parallel Computing Technologies (PaVT'2008), St. Petersburg, Russia},
note = {Krzhizhanovskaya2008d},
organization = {International Conference on Parallel Computing Technologies (PaVT'2008), St. Petersburg, Russia},
address = {Chelyabinsk},
issn_isbn = {ISBN 978-5-696-03720-2}
}
@inproceedings{Krzhizhanovskaya2008b,
title = {Simulation of Multiphysics Multiscale Systems, 5th International Workshop},
author = {V.V. Krzhizhanovskaya and A.G. Hoekstra},
year = {2008},
volume = {5102},
pages = {165--166},
metis_id = {285217},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69386-4},
month = {June},
note = {editorial},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II},
publisher = {Springer},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69386-4}
}
@phdthesis{Krzhizhanovskaya2008c,
title = {A Virtual Reactor for Simulation of Plasma Enhanced Chemical Vapor Deposition},
author = {V.V. Krzhizhanovskaya},
year = {2008},
metis_id = {292032},
url = {Krzhizhanovskaya2008a.pdf},
month = {June},
category = {ComputationalScience},
numpages = {116},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Prof. Dr. Y.E. Gorbachev}
}
@misc{Krzhizhanovskaya2008d,
title = {Special Issue on Simulation of Multiphysics Multiscale Systems},
author = {V.V. Krzhizhanovskaya and A.G. Hoekstra},
year = {2008},
journal = {International Journal for Multiscale Computational Engineering},
volume = {6},
number = {1},
url = {http://dx.doi.org/10.1615/IntJMultCompEng.v6.i1},
category = {Multiphysics, Multiscale},
publisher = {Begell House},
doi = {10.1615/IntJMultCompEng.v6.i1},
note = {Guest editorship and Preface},
editor = {V.V. Krzhizhanovskaya and A.G. Hoekstra},
issn_isbn = {ISSN 1543-1649}
}
@inproceedings{Labno2008a,
title = {A P2P approach to resource discovery in on-line monitoring of Grid workflows},
author = {B. Labno and M.T. Bubak and B. Bali\'s},
year = {2008},
volume = {5168},
pages = {37--46},
metis_id = {307670},
publisher = {Springer-Verlag},
doi = {10.1007/978-3-540-85451-7_5},
series = {Lecture Notes in Computer Science},
booktitle = {Euro-Par 2008: parallel processing: 14th international Euro-Par conference: Las Palmas de Gran Canaria, Spain, August 26--29, 2008},
editor = {E. Luque and T. Margalef and D. Ben\'{\i}tez},
organization = {14th International Conference on Parallel and Distributed Computing (Euro-Par 2008), Las Palmas de Gran Canaria, Spain},
address = {Berlin ; Heidelberg},
issn_isbn = {ISBN-10 3-540-85450-9 ; ISBN-13 978-3-540-85450-0}
}
@article{Liu2008a,
title = {Ca2+-dependent metarhodopsin inactivation mediated by calmodulin and NINAC myosin III},
author = {C.H. Liu and A.K. Satoh and M. Postma and J. Huang and D.F. Ready and R.C. Hardie},
year = {2008},
journal = {Neuron},
volume = {59},
number = {5},
pages = {778--789},
metis_id = {312445},
month = {September},
publisher = {Cell Press},
doi = {10.1016/j.neuron.2008.07.007}
}
@inproceedings{Malawski2008a,
title = {Optimization of application execution in the ViroLab Virtual Laboratory},
author = {M. Malawski and J. Kocot and E. Ciepiela and M.T. Bubak},
year = {2008},
pages = {65--70},
metis_id = {307674},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'07 Grid Workshop: October 15--17, 2007 Cracow, Poland},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
organization = {Cracow' 07 Grid Workshop (CGW'07), Cracow, Poland},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@techreport{Malawski2008b,
title = {Optimization of Application Execution in the GridSpace Environment},
author = {M. Malawski and J. Kocot and I. Ryszka and M.T. Bubak and M. Wieczorek and T. Fahringer},
year = {2008},
number = {TR-0131},
metis_id = {307723},
institution = {Institute on Resource Management and Scheduling, CoreGRID - Network of Excellence},
url = {http://www.coregrid.net/mambo/images/stories/TechnicalReports/tr-0131.pdf},
month = {March},
keywords = {WP6}
}
@inproceedings{Malawski2008c,
title = {High-level scripting approach for building component-based applications on the Grid},
author = {M. Malawski and T. Guba\la and M. Kasztelnik and T. Bartynski and M.T. Bubak},
year = {2008},
pages = {309--321},
metis_id = {307671},
publisher = {Springer Science+Business Media},
booktitle = {Making Grids Work: proceedings of the CoreGRID workshop on Programming models Grid and P2P system architecture Grid systems, tools and environments: 1213 June 2007, Heraklion, Crete, Greece},
editor = {M. Danelutto and P. Fragopoulou and V.S. Getov},
organization = {CoreGRID Workshop on Grid Programming Model, Grid and P2P Systems Architecture, Grid Systems, Tools and Environments, Heraklion, Crete, Greece},
issn_isbn = {ISBN-13 978-0-387-78447-2}
}
@inproceedings{Malawski2008d,
title = {A tool for building collaborative applications by invocation of Grid Operations},
author = {M. Malawski and T. Bartynski and M.T. Bubak},
year = {2008},
volume = {5103},
pages = {243--252},
metis_id = {307672},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69388-8},
month = {June},
publisher = {Springer},
note = {Also on CD-ROM},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part III},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2008 (ICCS 2008), Krak\'ow, Poland},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN-13 978-3-540-69388-8}
}
@inproceedings{Malawski2008e,
title = {Optimization of application execution in the GridSpace environment},
author = {M. Malawski and J. Kocot and I. Ryszka and M.T. Bubak and M. Wieczorek},
year = {2008},
pages = {395--405},
metis_id = {307673},
publisher = {Crete University Press},
booktitle = {CoreGRID integration workshop 2008 -- Integrated Research in Grid Computing: April 24, Hersonissos, Crete, Greece},
editor = {S. Gorlatch and P. Fragopoulou and T. Priol},
organization = {CoreGRID integration workshop 2008: Integrated Research in Grid Computing},
address = {Heraklion},
issn_isbn = {ISBN 978-960-524-260-2}
}
@inproceedings{Mamikonyan2008a,
title = {TKira - A Hybrid N-Body Code},
author = {E.N. Mamikonyan and S.L.W. McMillan and S.F. Portegies Zwart and E. Vesperini},
year = {2008},
volume = {246},
pages = {471-472},
url = {http://adsabs.harvard.edu/abs/2008IAUS..246..471M},
doi = {10.1017/S1743921308016190},
series = {IAU Symposium},
booktitle = {IAU Symposium},
editor = {E. Vesperini and M. Giersz and A. Sills},
keywords = {methods: n-body simulations, galaxies: star clusters, Galaxy: center, galaxies: interactions}
}
@article{Meel2008a,
title = {Harvesting graphics power for MD simulations},
author = {J.A. van Meel and A. Arnold and D. Frenkel and S.F. Portegies Zwart and R.G. Belleman},
year = {2008},
journal = {Molecular Simulation},
volume = {34},
number = {3},
pages = {259--266},
url = {http://arxiv.org/pdf/0709.3225},
month = {March},
category = {GPUcomputing},
publisher = {Taylor \& Francis}
}
@article{Moll2008a,
title = {Dynamical mass of a star cluster in M 83: a test of fibre-fed multi-object spectroscopy},
author = {S.L. Moll and R. de Grijs and P. Anders and P.A. Crowther and S.S. Larsen and L.J. Smith and S.F. Portegies Zwart},
year = {2008},
journal = {Astron. Astrophys.},
volume = {490},
number = {1},
pages = {125--133},
metis_id = {296234},
url = {http://adsabs.harvard.edu/abs/2008A%26A...490..125M},
month = {oct},
doi = {10.1051/0004-6361:200810163},
keywords = {galaxies: clusters: general, galaxies: individual: M 83, galaxies: spiral}
}
@mastersthesis{Muller2008a,
title = {Multi-touch displays: design, applications and performance evaluation},
author = {L.Y.L. Muller},
year = {2008},
url = {Muller2008a.pdf},
month = {June},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
tutor = {Supervisor: R.G. Belleman},
address = {Amsterdam, the Netherlands}
}
@inproceedings{Murtaza2008a,
title = {Floating point based Cellular Automata simulations using a dual FPGA-enabled system},
author = {S. Murtaza and A.G. Hoekstra and P.M.A. Sloot},
year = {2008},
pages = {1-8},
metis_id = {296235},
publisher = {IEEE},
doi = {10.1109/HPRCTA.2008.4745686},
booktitle = {Proceedings of the High Performance Reconfigurable Computing Technology and Applications},
issn_isbn = {ISBN 978-1-4244-2826-7}
}
@inproceedings{Nuallin2008a,
title = {Enhanced Decision Support for HIV Drug Resistance Interpretation},
author = {B. \'O Nuall\'ain and D.A.M.C. van de Vijver and C.A.B. Boucher and A. Tirado Ramos and P.M.A. Sloot},
year = {2008},
url = {ONuallain2008a.pdf},
month = {March},
booktitle = {Proceedings of the 6th European HIV Drug Resistance Workshop},
address = {Budapest},
note = {abstract, in press}
}
@article{Orlova2008a,
title = {Light scattering by neutrophils: model, simulation, and experiment},
author = {D.Y. Orlova and M.A. Yurkin and A.G. Hoekstra and V.P. Maltsev},
year = {2008},
journal = {Journal of Biomedical Optics},
volume = {13},
number = {5},
pages = {054057},
metis_id = {296236},
month = {September},
numpages = {7},
doi = {10.1117/1.2992140}
}
@inproceedings{Portegies_Zwart2008a,
title = {Reconstructing the Initial Relaxation Time of Young Star Clusters in the Large Magellanic Cloud},
author = {S.F. Portegies Zwart and H.C. Chen},
year = {2008},
volume = {388},
pages = {329--329},
url = {http://adsabs.harvard.edu/abs/2008ASPC..388..329P,},
month = {jun},
numpages = {1},
note = {abstract},
series = {Astronomical Society of the Pacific Conference Series},
booktitle = {Mass Loss from Stars and the Evolution of Stellar Clusters},
editor = {A. de Koter and L.J. Smith and L.B.F.M. Waters}
}
@inproceedings{Portegies_Zwart2008b,
title = {A multiphysics and multiscale software environment for modeling astrophysical systems},
author = {S.F. Portegies Zwart and S.L.W. McMillan and B. \'O Nuall\'ain and D.C. Heggie and J.C. Lombardi and P. Hut and S. Banerjee and H. Belkus and T. Fragos and J. Fregeau and M. Fuji and E. Gaburov and E. Glebbeek and D.J. Groen and S. Harfst and R. Izzard and M. Juric and S. Justham and P.J. Teuben and J. van Bever and O. Yaron and M. Zemp},
year = {2008},
volume = {5102},
pages = {207--216},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69386-4},
month = {June},
publisher = {Springer},
doi = {10.1007/978-3-540-69387-1_23},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {8th International Conference on Computational Science (ICCS 2008), Krak\'ow, Poland},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69386-4}
}
@article{Portegies_Zwart2008c,
title = {A parallel gravitational N-body kernel},
author = {S.F. Portegies Zwart and S.L.W. McMillan and D.J. Groen and A. Gualandris and M.S. Sipior and W. Vermin},
year = {2008},
journal = {New Atronomy},
volume = {13},
number = {5},
pages = {285-295},
url = {http://adsabs.harvard.edu/abs/2008NewA...13..285P},
month = {July},
category = {Astronomy},
doi = {10.1016/j.newast.2007.11.002}
}
@mastersthesis{Quax2008a,
title = {Modeling and Simulating the Propagation of Infectious Diseases Using Complex Networks},
author = {R. Quax},
year = {2008},
url = {Quax2008a.pdf},
month = {August},
category = {pwrs, mastersthesis, virolab},
school = {Georgia Institute of Technology},
tutor = {Supervisor: David Bader},
address = {Atlanta, GA, USA}
}
@inproceedings{Rath2008a,
title = {Gas phase considerations for the deposition of thin film silicon cells by VHF-PECVD at low substrate temperatures},
author = {J.K. Rath and A. Verkerk and M. Brinza and R.E.I. Schropp and W.J. Goedheer and V.V. Krzhizhanovskaya and Y.E. Gorbachev and K.E. Orlov and E.M. Khilkevitch and A.S. Smirnov},
year = {2008},
month = {May},
category = {PECVD, ThinFilm, SolarCell},
publisher = {Elsevier},
booktitle = {Proceedings of 33rd IEEE Photovoltaic Specialists Conference},
address = {San Diego, California}
}
@mastersthesis{Rexhepi2008a,
title = {The Volatility Smile Dynamics Implied by Smile-Consistent Option Pricing Models and Empirical Data},
author = {B. Rexhepi},
year = {2008},
url = {Rexhepi2008a.pdf},
month = {August},
category = {pwrs, mastersthesis, ComputationalFinance},
school = {University of Amsterdam},
tutor = {Supervisors: B.D. Kandhai and G.-Z. Qiu},
address = {Amsterdam, the Netherlands}
}
@inproceedings{Rycerz2008a,
title = {Dynamic Interactions in HLA Component Model for Multiscale Simulations},
author = {K.J. Rycerz and P.M.A. Sloot and M.T. Bubak},
year = {2008},
volume = {5102},
pages = {217--226},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69386-4},
month = {June},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69386-4}
}
@inproceedings{Rycerz2008b,
title = {Using HLA and Grid for Distributed Multiscale Simulations},
author = {K.J. Rycerz and M.T. Bubak and P.M.A. Sloot},
year = {2008},
volume = {4967},
pages = {780--787},
metis_id = {296238},
url = {Rycerz2008c.pdf},
month = {May},
publisher = {Springer},
doi = {10.1007/978-3-540-68111-3},
series = {Lecture Notes in Computer Science},
booktitle = {Parallel Processing and Applied Mathematics: 7th International Conference, PPAM 2007, Gdansk, Poland, September 9-12, 2007 Revised Selected Papers},
editor = {R. Wyrzykowski and K. Karczewski and J.J. Dongarra and J. Wa\'sniewski},
organization = {7th International Conference on Parallel Processing and Applied Mathematics (PPAM 2007), Gdańsk, Poland},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-68105-2}
}
@inproceedings{Rycerz2008c,
title = {Problem solving environment for distributed interactive applications},
author = {K.J. Rycerz and M.T. Bubak and P.M.A. Sloot and V.S. Getov},
year = {2008},
pages = {55--66},
metis_id = {276802},
url = {Rycerz2006c.pdf},
publisher = {Springer},
booktitle = {Achievements in European Research on Grid Systems -- CoreGRID Integration Workshop 2006 (Selected Papers)},
editor = {S. Gorlatch and M.T. Bubak and T. Priol},
organization = {CoreGRID Integration Workshop (CGIW'2006), Krakow, Poland},
issn_isbn = {ISBN-13 978-0-387-72811-7}
}
@inproceedings{Rycerz2008d,
title = {HLA component model on the example of multiscale simulation},
author = {K.J. Rycerz and M.T. Bubak and P.M.A. Sloot},
year = {2008},
pages = {272--275},
metis_id = {307675},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Proceedings of Cracow'07 Grid Workshop, Oct 15-17 2007, Cracow, Poland, ACC Cyfronet AGH},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
keywords = {WP7},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@inproceedings{Rycerz2008e,
title = {HLA component based environment for distributed multiscale simulations},
author = {K.J. Rycerz and M.T. Bubak and P.M.A. Sloot},
year = {2008},
pages = {229--239},
metis_id = {307676},
publisher = {Springer},
booktitle = {From Grids to service and pervasive computing, CoreGRID symposium},
editor = {T. Priol and M. Vanneschi},
organization = {CoreGRID Symposium 2008, Las Palmas de Gran Canaria, Spain},
issn_isbn = {ISBN-13 978-0-387-09454-0}
}
@techreport{Rycerz2008f,
title = {HLA Component Based Environment for Distributed Multiscale Simulations},
author = {K.J. Rycerz and M.T. Bubak and P.M.A. Sloot and V.S. Getov},
year = {2008},
number = {TR-0137},
metis_id = {307724},
institution = {Institute on Grid Systems, Tools, and Environments, CoreGRID - Network of Excellence},
url = {http://www.coregrid.net/mambo/images/stories/TechnicalReports/tr-0137.pdf},
month = {April},
keywords = {WP7}
}
@article{Sloot2008a,
title = {Stochastic simulation of HIV population dynamics through complex network modelling},
author = {P.M.A. Sloot and S.V. Ivanov and A.V. Boukhanovsky and D.A.M.C. van de Vijver and C.A.B. Boucher},
year = {2008},
journal = {International Journal of Computer Mathematics},
volume = {85},
number = {8},
pages = {1175--1187},
metis_id = {296240},
url = {Sloot2008d.pdf},
publisher = {Taylor \& Francis},
doi = {10.1080/00207160701750583},
memo = {url = http://dx.doi.org/10.1080/00207160701750583}
}
@inproceedings{Sloot2008b,
title = {VIROLAB: a Distributed Decision Support System for Viral Disease Treatment},
author = {P.M.A. Sloot and A. Tirado Ramos and G. Ertaylan and B. \'O Nuall\'ain and D.A.M.C. van de Vijver and C.A.B. Boucher and M.T. Bubak},
year = {2008},
pages = {33--34},
metis_id = {285223},
url = {Sloot2008a.pdf},
month = {October},
category = {CellularAutomata},
booktitle = {CGW'07 proceedings},
note = {extended abstract},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
organization = {Cracow' 07 Grid Workshop (CGW'07)},
address = {Krakow, Poland},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@article{Sloot2008c,
title = {VIROLAB: from the molecule to the man},
author = {P.M.A. Sloot},
year = {2008},
journal = {eStrategies Projects},
number = {4},
pages = {53--55},
metis_id = {285224},
url = {Sloot2008b.pdf},
publisher = {British Publishers Ltd}
}
@inproceedings{Sloot2008d,
title = {Multi-Science Decision Support for HIV Drug Resistance Treatment},
author = {P.M.A. Sloot and P.V. Coveney and M.T. Bubak and A.-M. Vandamme and B. \'O Nuall\'ain and D.A.M.C. van de Vijver and C.A.B. Boucher},
year = {2008},
volume = {138},
pages = {188--198},
url = {Sloot2008c.pdf},
publisher = {IOS Press},
series = {Studies in Health Technology and Informatics},
booktitle = {Global Healthgrid: e-Science Meets Biomedical Informatics - Proceedings of HealthGrid 2008},
editor = {T. Solomonides and J.C. Silverstein and J. Saltz and Y. Legr\'e and M. Kratz and I. Foster and V. Breton and J.R. Beck},
issn_isbn = {ISBN: 978-1-58603-874-8}
}
@article{Sloot2008e,
title = {Virolab: A Collaborative Decision Support System in Viral Disease Treatment},
author = {P.M.A. Sloot and P.V. Coveney and M.T. Bubak and A.-M. Vandamme and B. \'O Nuall\'ain and D.A.M.C. van de Vijver and C.A.B. Boucher},
year = {2008},
journal = {Reviews in Antiviral Therapy},
volume = {3},
pages = {4--7},
url = {Sloot2008e.pdf},
publisher = {Virology Education},
issn_isbn = {ISSN 1872-437X}
}
@mastersthesis{Sottoriva2008a,
title = {Mathematical Modeling of Tumour Growth and Invasion Using a Hybrid Cellular Automaton},
author = {A. Sottoriva},
year = {2008},
month = {August},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, the Netherlands},
tutor = {Supervisor: P.M.A. Sloot, Co-advisor L. Vermeulen}
}
@inproceedings{Szepieniec2008a,
title = {Investigation of the DAG eligible jobs maximization algorithm in a grid},
author = {T. Szepieniec and M.T. Bubak},
year = {2008},
pages = {340--345},
metis_id = {307678},
publisher = {IEEE},
booktitle = {The 9th IEEE/ACM international conference on Grid computing (Grid 2008)},
organization = {9th IEEE/ACM International Conference on Grid Computing (Grid 2008), Tsukuba, Japan},
address = {Tsukuba, Japan},
issn_isbn = {ISBN 978-1-4244-2579-2}
}
@inproceedings{Szepieniec2008b,
title = {Evaluation of eligible jobs maximization algorithm for DAG scheduling in grids},
author = {T. Szepieniec and M.T. Bubak},
year = {2008},
volume = {5101},
pages = {254--263},
metis_id = {307677},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69383-3},
month = {June},
publisher = {Springer},
note = {Also on CD-ROM},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part I},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
organization = {International Conference on Computational Science 2008 (ICCS 2008), Krak\'ow, Poland},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69383-3}
}
@inbook{Tirado-Ramos2008a,
title = {Grid-based Interactive Decision Support in BioMedicine},
author = {A. Tirado Ramos and P.M.A. Sloot and M.T. Bubak},
year = {2008},
pages = {225--246},
url = {Tirado-Ramos2007a.pdf},
month = {January},
publisher = {John Wiley and Sons, USA},
series = {Wiley series on bioinformatics : computational techniques and engineering},
booktitle = {Grids for Bioinformatics and Computational Biology},
editor = {T. El-Ghazali and A.Y. Zomaya},
issn_isbn = {ISBN: 978-0-471-78409-8}
}
@inproceedings{Tirado-Ramos2008b,
title = {Second Workshop on Teaching Computational Science WTCS 2008},
author = {A. Tirado Ramos and Q. Luo},
year = {2008},
volume = {5102},
pages = {657--658},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69386-4},
month = {June},
note = {editorial},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II},
publisher = {Springer},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69386-4}
}
@article{Wang2008a,
title = {Axial growth of hexactinellid spicules: formation of cone-like structural units in the giant basal spicules of the hexactinellid Monorhaphis},
author = {X. Wang and D. Brandt and H.C. Schr\"oder and J. Li and A. Boreiko and U. Schlossmacher and J.A. Kaandorp and H. Gotz and H. Duschner and W.E.G. M\"uller},
year = {2008},
journal = {J. of Structural Biology},
volume = {164},
pages = {270--280},
month = {December},
doi = {10.1016/j.jsb.2008.08.005}
}
@inproceedings{Wibisono2008a,
title = {Towards a Virtual Laboratory for interactive parameter Sweep applications on the Grid},
author = {A. Wibisono and Z. Zhao and A.S.Z. Belloum and M.T. Bubak},
year = {2008},
pages = {266--271},
metis_id = {307679},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'07 Grid Workshop: October 15--17, 2007 Cracow, Poland},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
issn_isbn = {ISBN 978-83-915141-9-1}
}
@inproceedings{Wibisono2008b,
title = {A Framework for Interactive Parameter Sweep Applications},
author = {A. Wibisono and Z. Zhao and A.S.Z. Belloum and M.T. Bubak},
year = {2008},
volume = {5103},
pages = {481--490},
metis_id = {285226},
url = {http://www.springer.com/computer/foundations/book/978-3-540-69388-8},
month = {June},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part III},
editor = {M.T. Bubak and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
address = {Berlin, Heidelberg},
issn_isbn = {978-3-540-69388-8}
}
@article{Wiens2008a,
title = {Regional and modular expression of morphogenetic factors in the demosponge Lubomirskia baicalensis},
author = {M. Wiens and S.I. Belikov and O.V. Kaluzhnaya and T. Adella and H.C. Schr\"oder and S. Perovic-Ottstadt and J.A. Kaandorp and W.E.G. M\"uller},
year = {2008},
journal = {Micron},
volume = {39},
number = {4},
pages = {447--460},
url = {http://dx.doi.org/10.1016/j.micron.2007.02.003},
doi = {10.1016/j.micron.2007.02.003}
}
@article{Yungelson2008a,
title = {On the evolution and fate of super-massive stars},
author = {L.R. Yungelson and E.P.J. van den Heuvel and J.S. Vink and S.F. Portegies Zwart and A. de Koter},
year = {2008},
journal = {Astron. Astrophys.},
volume = {477},
number = {1},
pages = {223-237},
metis_id = {276803},
url = {http://adsabs.harvard.edu/abs/2008A%26A...477..223Y},
month = {jan},
doi = {10.1051/0004-6361:20078345}
}
@inproceedings{Yurkin2008a,
title = {Application of the discrete dipole approximation to extreme refractive indices: filtered coupled dipoles revived},
author = {M.A. Yurkin and M. Min and A.G. Hoekstra},
year = {2008},
pages = {109--112},
metis_id = {296244},
url = {http://star.herts.ac.uk/els/AbstractsBook.pdf},
category = {ElastLightScat},
publisher = {University of Hertfordshire},
booktitle = {Proceedings of the 11th Conference on Electromagnetic and Light Scattering},
note = {extended abstract},
organization = {11th Electromagnetic \& Light Scattering Conference (els-XI), Hatfield, UK}
}
@inproceedings{Yurkin2008b,
title = {Study of light scattering by a granulated coated sphere -- a model of granulated blood cells},
author = {M.A. Yurkin and D. de Kanter and A.G. Hoekstra},
year = {2008},
pages = {299--302},
metis_id = {296245},
url = {http://star.herts.ac.uk/els/AbstractsBook.pdf},
category = {ElastLightScat},
publisher = {University of Hertfordshire},
booktitle = {Proceedings of the 11th Conference on Electromagnetic and Light Scattering},
note = {extended abstract},
organization = {11th Electromagnetic \& Light Scattering Conference (els-XI), Hatfield, UK}
}
@inproceedings{Zudilova-Seinstra2008a,
title = {Making Virtual Reality Usable for Medical Specialists},
author = {E.V. Zudilova-Seinstra},
year = {2008},
pages = {10--11},
month = {September},
publisher = {D-CIS LAB},
booktitle = {In Book of Abstracts, D-CIS Human Factors Day},
address = {Delft, The Netherlands}
}
@article{Zudilova-Seinstra2008b,
title = {Service-Oriented Visualization applied to Medical Data Analysis},
author = {E.V. Zudilova-Seinstra and N. Yang and L. Axner and A. Wibisono and V. Vasunin},
year = {2008},
journal = {Int. J. of Service Oriented Computing and Applications},
volume = {2},
number = {4},
pages = {187--201},
url = {http://www.springerlink.com/content/p765v9622437w757/fulltext.pdf},
month = {December},
category = {Visualisation},
publisher = {Spinger},
doi = {10.1007/s11761-008-0031-6}
}
@book{Zudilova-Seinstra2008c,
author = {E.V. Zudilova-Seinstra and T. Adriaansen and R. van Liere},
year = {2008},
url = {http://www.springer.com/computer/foundations/book/978-1-84800-268-5},
month = {December},
category = {Visualisation},
numpages = {385},
publisher = {Springer},
doi = {10.1007/978-1-84800-269-2},
series = {Advanced Information and Knowledge Processing},
booktitle = {Trends in Interactive Visualization, State-of-the-Art Survey},
issn_isbn = {ISBN 978-1-84800-268-5}
}
@inbook{Zudilova-Seinstra2008d,
title = {Overview of Interactive Visualization},
author = {E.V. Zudilova-Seinstra and T. Adriaansen and R. van Liere},
year = {2008},
pages = {3--15},
month = {December},
category = {Visualisation},
publisher = {Springer},
doi = {10.1007/978-1-84800-269-2_1},
series = {Advanced Information and Knowledge Processing},
booktitle = {Trends in Interactive Visualization, State-of-the-Art Survey},
editor = {E.V. Zudilova and T. Adriaansen and R. van Liere}
}
@inproceedings{Zudilova-Seinstra2008e,
title = {Visualizing Climate Data on a Tiled Panel Display: A User-Centered Approach},
author = {E.V. Zudilova-Seinstra and J. Adriaanse and A. Berg},
year = {2008},
pages = {197--202},
month = {July},
category = {Visualisation},
publisher = {IADIS},
booktitle = {IADIS Computer Graphics and Visualization 2008 Conference},
organization = {IADIS International Conference on Computer Graphics and Visualization 2008},
address = {Amsterdam, The Netherlands},
issn_isbn = {ISBN 978-972-8924-63-8}
}
@phdthesis{Axner2007a,
title = {High Performance Computational Hemodynamics with the Lattics Boltzmann Method},
author = {L. Axner},
year = {2007},
metis_id = {276737},
url = {Axner2007c.pdf},
month = {December},
category = {LBM},
numpages = {103},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. A.G. Hoekstra}
}
@article{Axner2007b,
title = {Simulating Time Harmonic Flows with the Lattice Boltzmann Method},
author = {L. Axner and A.G. Hoekstra and P.M.A. Sloot},
year = {2007},
journal = {Phys. Rev. E},
pages = {036709},
metis_id = {276736},
url = {Axner2007b.pdf},
category = {LBM},
numpages = {7}
}
@article{Axner2007c,
title = {Simulating Time Harmonic Flows with the Regularized L-BGK Method},
author = {L. Axner and J. L\"att and A.G. Hoekstra and B. Chopard and P.M.A. Sloot},
year = {2007},
journal = {Int. J. of Mod. Phys. C},
volume = {18},
number = {4},
pages = {661--666},
metis_id = {276735},
url = {Axner2007a.pdf},
category = {LBM}
}
@inproceedings{Badia2007a,
title = {Performance Monitoring of Grid Superscalar with OCM-G/G-PM: Tuning and Improvements},
author = {R.M. Badia and R. Sirvent and M.T. Bubak and W. Funika and P. Machner},
year = {2007},
metis_id = {307680},
booktitle = {CoreGRID Workshop on Grid Programming Model, Grid and P2P Systems Architecture, Grid Systems, Tools and Environments},
keywords = {WP7}
}
@techreport{Badia2007b,
title = {Performance monitoring of GRID superscalar with OCM-G/G-PM: integration issues},
author = {R.M. Badia and R. Sirvent and M.T. Bubak and W. Funika and P. Machner},
year = {2007},
number = {TR-0108},
metis_id = {307725},
institution = {Institute on Grid Systems, Tools and Environments},
url = {http://www.coregrid.net/mambo/images/stories/TechnicalReports/tr-0108.pdf},
month = {September},
keywords = {WP7}
}
@inproceedings{Bali,
title = {Provenance tracking in the Virolab Virtual Laboratory},
author = {B. Bali\'s and M.T. Bubak and J. Wach},
year = {2007},
pages = {50--50},
metis_id = {307684},
booktitle = {PPAM 2007: 7th international conference on Parallel Processing \& Applied Mathematics: Gdask, Poland, September 9--12, Book of abstracts},
note = {abstract}
}
@inproceedings{Bali,
title = {Efficient and Reliable Execution of Legacy Codes Exposed as Services},
author = {B. Bali\'s and M.T. Bubak and K. Sterna and A. Bemben},
year = {2007},
volume = {4487},
pages = {390--397},
metis_id = {307681},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {International Conference on Computational Science (1)},
editor = {Y. Shi and G.D. van Albada and J.J. Dongarra and P.M.A. Sloot},
keywords = {WP7}
}
@inproceedings{Bali,
title = {GEMINI: Generic Monitoring Infrastructure for Grid resources and applications},
author = {B. Bali\'s and M.T. Bubak and B. Labno},
year = {2007},
pages = {60--73},
metis_id = {307683},
publisher = {Academic Computer Centre CYFRONET AGH},
editor = {M.T. Bubak and S. Unger},
issn_isbn = {ISBN 978-83-915141-8-4}
}
@inproceedings{Bali,
title = {From monitoring data to experimental information monitoring of Grid scientific workflows},
author = {B. Bali\'s and M.T. Bubak and M. Pelczar},
year = {2007},
pages = {77--84},
metis_id = {307682},
publisher = {IEEE Computer Society},
booktitle = {Third IEEE international conference on e-Science and Grid computing: Bangalore, India, 10--13 December 2007},
editor = {G. Fox and K. Chiu and R. Buyya},
address = {Piscataway, NJ},
issn_isbn = {ISBN-10: 0-7695-3064-8}
}
@inproceedings{Bartynski2007a,
title = {Universal Grid client: Grid Operation Invoker},
author = {T. Bartynski and M. Malawski and T. Guba\la and M.T. Bubak},
year = {2007},
pages = {93--93},
metis_id = {307685},
booktitle = {PPAM 2007: 7th international conference on Parallel Processing \& Applied Mathematics: Gdask, Poland, September 9--12, Book of abstracts},
note = {abstract}
}
@article{Belleman2007a,
title = {Interactive Simulation and Visualization for Cancer Treatment Planning with Grid-based Technology},
author = {R.G. Belleman and M. Scarpa and B. Stolk},
year = {2007},
journal = {ERCIM News, special theme: The Digital Patient},
volume = {69},
pages = {22--23},
metis_id = {276739},
url = {http://ercim-news.ercim.org/content/view/161/309/}
}
@article{Berk2007a,
title = {The formation of higher order hierarchical systems in star clusters},
author = {J. van den Berk and S.F. Portegies Zwart and S.L.W. McMillan},
year = {2007},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {379},
pages = {111-122},
url = {http://adsabs.harvard.edu/abs/2007MNRAS.379..111V},
month = {jul},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1111/j.1365-2966.2007.11913.x}
}
@inproceedings{Brandl2007a,
title = {On the Origin of the Most Massive Stars Around R136},
author = {B.R. Brandl and S.F. Portegies Zwart and A.F.J. Moffat and D.F. Chernoff},
year = {2007},
volume = {367},
pages = {629-629},
metis_id = {276740},
url = {http://adsabs.harvard.edu/abs/2007ASPC..367..629B},
note = {abstract},
series = {Astronomical Society of the Pacific Conference Series},
booktitle = {Massive Stars in Interactive Binaries},
editor = {N. St.Louis and A.F.J. Moffat}
}
@inproceedings{Bubak2007a,
title = {Collaborative Virtual Laboratory for e-Health},
author = {M.T. Bubak and T. Guba\la and M. Kasztelnik and M. Malawski and P. Nowakowski and P.M.A. Sloot},
year = {2007},
pages = {537--544},
metis_id = {276741},
url = {Bubak2007a.pdf},
publisher = {IOS Press},
booktitle = {Expanding the Knowledge Economy: Issues, Applications, Case Studies, eChallenges e-2007 Conference Proceedings},
editor = {P. Cunningham and M. Cunningham},
address = {Amsterdam},
issn_isbn = {ISBN 978-1-58603-801-4 (paper), ISBN: 978-1-905824-05-2 (CD)}
}
@inproceedings{Bubak2007b,
title = {Appea: A Platform for Development and Execution of Grid Applications},
author = {M.T. Bubak and D. Harezlak and P. Nowakowski and T. Guba\la and M. Malawski},
year = {2007},
pages = {123--130},
metis_id = {307686},
publisher = {IOS Press},
booktitle = {Expanding the Knowledge Economy: Issues, Applications, Case Studies, eChallenges e-2007 Conference Proceedings},
note = {ISBN 978-1-58603-801-4},
editor = {P. Cunningham and M. Cunningham},
keywords = {WP7},
address = {Amsterdam}
}
@proceedings{Bubak2007c,
author = {M.T. Bubak and S. Unger},
year = {2007},
issn_isbn = {ISBN 978-83-915141-8-4},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'06 Grid Workshop, Vol 2: K-Wf Grid: the knowledge-based workflow system for Grid applications: October 15--18, 2006 Cracow, Poland}
}
@proceedings{Bubak2007d,
title = {Cracow'06 Grid Workshop, Vol 1: October 15--18, 2006 Cracow, Poland: proceedings},
author = {M.T. Bubak and M. Tura\la and K. Wiatr},
year = {2007},
metis_id = {307736},
publisher = {Academic Computer Centre CYFRONET AGH},
issn_isbn = {ISBN 83-915141-7-X}
}
@inproceedings{Bubak2007e,
title = {K-WfGrid knowledge-based workflow system for Grid applicatiobs},
author = {M.T. Bubak and P. Nowakowski and S. Unger},
year = {2007},
pages = {1--12},
metis_id = {307687},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'06 Grid Workshop, Vol 2: K-Wf Grid: the knowledge-based workflow system for Grid applications: October 15--18, 2006 Cracow, Poland},
editor = {M.T. Bubak and S. Unger},
issn_isbn = {ISBN 978-83-915141-8-4}
}
@inproceedings{Bubak2007f,
title = {Software engineering aspects of K-WfGrid},
author = {M.T. Bubak and M. Malawski and P. Nowakowski and S. Unger},
year = {2007},
pages = {162--169},
metis_id = {307688},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'06 Grid Workshop, Vol 2: K-Wf Grid: the knowledge-based workflow system for Grid applications: October 15--18, 2006 Cracow, Poland},
editor = {M.T. Bubak and S. Unger},
issn_isbn = {ISBN 978-83-915141-8-4}
}
@mastersthesis{Bdorf2007a,
title = {High Performance Direct Gravitational N-body Simulations on Graphics Processing Units -- An implementation in CUDA},
author = {J. B\'edorf},
year = {2007},
url = {Bedorf2007a.pdf},
month = {November},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
tutor = {Advisors: R.G. Belleman and S.F. Portegies Zwart},
address = {Amsterdam, the Netherlands}
}
@article{Dobrzyski,
title = {Computational methods for diffusion-influenced biochemical reactions},
author = {M. Dobrzy\'nski and J. Vidal Rodr\'{\i}guez and J.A. Kaandorp and J.G. Blom},
year = {2007},
journal = {Bioinformatics},
volume = {23},
number = {15},
pages = {1969--1977},
url = {Dobrzinsky2007a.pdf},
doi = {doi:10.1093/bioinformatics/btm278}
}
@proceedings{Dubizky2007a,
author = {W. Dubizky and A. Schuster and P.M.A. Sloot and M. Schroeder and M. Romberg},
year = {2007},
volume = {4360},
pages = {1--190},
url = {http://www.springer.com/3-540-69841-8},
month = {January},
note = {Sublibrary: Lecture Notes in Bioinformatics},
series = {Lecture Notes in Computer Science},
booktitle = {Distributed, High-Performance and Grid Computing in Computational Biology},
publisher = {Springer},
address = {Berlin, Heidelberg},
issn_isbn = {ISSN 0302-9743; ISBN-10 3-540-69841-8}
}
@inproceedings{Ertaylan2007a,
title = {A complex automata model of HIV-1 co-receptor tropism: Understanding mutation rate pressure},
author = {G. Ertaylan and P.M.A. Sloot},
year = {2007},
volume = {2},
metis_id = {296248},
url = {http://www.hivpresentation.com/index.cfm?vid=EDE8FB47-423A-F6F7-C0921A2B09F679C8},
month = {December},
category = {CellularAutomata},
booktitle = {Reviews in Antiretroviral Therapy},
address = {Washington D.C., USA}
}
@article{Feyen2007a,
title = {Parameter optimisation and uncertainty assessment for large-scale streamflow simulation with the LISFLOOD model},
author = {L. Feyen and J.A. Vrugt and B. \'O Nuall\'ain and J. van der Knijff and A. De Roo},
year = {2007},
journal = {Journal of Hydrology},
volume = {332},
number = {3--4},
pages = {276--289},
url = {Feyen2007a.pdf},
month = {January},
publisher = {Elsevier},
doi = {10.1016/j.jhydrol.2006.07.004}
}
@article{Fomekong-Nanfack2007a,
title = {Efficient parameter estimation for spatio-temporal models of pattern formation: Case study of Drosophila melanogaster},
author = {Y. Fomekong-Nanfack and J.A. Kaandorp and J.G. Blom},
year = {2007},
journal = {Bioinformatics},
volume = {23},
number = {24},
pages = {3356-3363},
doi = {doi:10.1093/bioinformatics/btm433}
}
@inproceedings{Fregeau2007a,
title = {Stellar Collisions During Binary Interactions and the Effect on Runaway Collisions},
author = {J.M. Fregeau and F.A. Rasio and P. Cheung and S.F. Portegies Zwart},
year = {2007},
volume = {367},
pages = {715-715},
metis_id = {276746},
url = {http://adsabs.harvard.edu/abs/2007ASPC..367..715F},
note = {abstract},
series = {Astronomical Society of the Pacific Conference Series},
booktitle = {Massive Stars in Interactive Binaries},
editor = {N. St.Louis and A.F.J. Moffat}
}
@mastersthesis{Geldof2007a,
title = {Generic Computing on a Graphics Processing Unit},
author = {P.M. Geldof},
year = {2007},
url = {Geldof2007a.pdf},
month = {May},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
tutor = {Advisor: R.G. Belleman},
address = {Amsterdam, the Netherlands}
}
@article{Gieles2007a,
title = {On the Interpretation of the Age Distribution of Star Clusters in the Small Magellanic Cloud},
author = {M. Gieles and H.J.G.L.M. Lamers and S.F. Portegies Zwart},
year = {2007},
journal = {The Astrophysical Journal},
volume = {668},
pages = {268-274},
metis_id = {276747},
url = {http://adsabs.harvard.edu/abs/2007ApJ...668..268G},
month = {oct},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1086/520795}
}
@article{Gieles2007b,
title = {The effect of spiral arm passages on the evolution of stellar clusters},
author = {M. Gieles and E. Athanassoula and S.F. Portegies Zwart},
year = {2007},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {376},
pages = {809-819},
metis_id = {276748},
url = {http://adsabs.harvard.edu/abs/2007MNRAS.376..809G},
month = {apr},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1111/j.1365-2966.2007.11477.x}
}
@inproceedings{Gorbachev2007a,
title = {Virtual Laboratories: Problem Solving Environments for Science and Education},
author = {Y.E. Gorbachev and V.V. Krzhizhanovskaya and M.V. Bogdanov and A.I. Zhmakin and A.V. Kulik and M.S. Ramm},
year = {2007},
pages = {108-109},
metis_id = {312449},
url = {http://tm.ifmo.ru/tm2007/db/doc/get_thes.php?id=290},
month = {June},
category = {VirtualLaboratories, Education, PSE},
publisher = {University Telecommunications},
booktitle = {Proceedings of the XIV All-Russian conference Telematika-2007},
note = {In Russian},
address = {St. Petersburg, Russia}
}
@article{Gorbachev2007b,
title = {Numerical modeling of heat and mass transfer processes in PECVD reactors for growing silicon films under the conditions of intense formation of higher silanes in the gas phase},
author = {Y.E. Gorbachev and M.A. Zatevakhin and A.A. Ignatiev and V.V. Krzhizhanovskaya},
year = {2007},
volume = {38},
number = {1},
pages = {71-84},
metis_id = {312448},
url = {http://dx.doi.org/10.1615/HeatTransRes.v38.i1.70},
category = {NumericalModeling, PECVD},
doi = {10.1615/HeatTransRes.v38.i1.70},
booktitle = {Heat Transfer Research},
issn_isbn = {ISSN: 1064-2285}
}
@article{Gualandris2007a,
title = {Performance analysis of direct N-body algorithms on highly distributed systems},
author = {A. Gualandris and S.F. Portegies Zwart and A. Tirado Ramos},
year = {2007},
journal = {Parallel Computing},
volume = {33},
pages = {159-173},
metis_id = {276750}
}
@article{Gualandris2007b,
title = {A hypervelocity star from the Large Magellanic Cloud},
author = {A. Gualandris and S.F. Portegies Zwart},
year = {2007},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {376},
pages = {L29-L33},
metis_id = {276749},
url = {http://adsabs.harvard.edu/abs/2007MNRAS.376L..29G},
month = {mar},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1111/j.1745-3933.2007.00280.x}
}
@inproceedings{Gubala2007a,
title = {Constructing abstract workflows of applications with workflow composition tool},
author = {T. Guba\la and D. Harezlak and M.T. Bubak and M. Malawski},
year = {2007},
pages = {25--30},
metis_id = {307689},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow'06 Grid Workshop, Vol 2: K-Wf Grid: the knowledge-based workflow system for Grid applications: October 15--18, 2006 Cracow, Poland},
editor = {M.T. Bubak and S. Unger},
address = {Cracow, Poland},
issn_isbn = {ISBN 978-83-915141-8-4}
}
@article{Haastert2007a,
title = {Biased Random Walk by Stochastic Fluctuations of Chemoattractant-Receptor Interactions at the Lower Limit of Detection},
author = {P.J.M. van Haastert and M. Postma},
year = {2007},
journal = {Biophys J.},
volume = {93},
pages = {1787--1796},
url = {http://www.biophysj.org/cgi/content/full/93/5/1787},
doi = {10.1529/biophysj.107.104356}
}
@article{Harfst2007a,
title = {Performance analysis of direct N-body algorithms on special-purpose supercomputers},
author = {S. Harfst and A. Gualandris and D. Merritt and R. Spurzem and S.F. Portegies Zwart and P. Berczik},
year = {2007},
journal = {New Astronomy},
volume = {12},
pages = {357-377},
metis_id = {276754},
url = {http://adsabs.harvard.edu/abs/2007NewA...12..357H},
month = {jul},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1016/j.newast.2006.11.003}
}
@book{Hoekstra2007a,
title = {Optics of Biological Particles},
author = {A.G. Hoekstra and V.P. Maltsev and G. Videen},
year = {2007},
metis_id = {276755},
url = {http://www.springer.com/east/home/generic/search/results?SGWID=5-40109-22-173681338-0},
publisher = {Springer},
address = {London},
issn_isbn = {ISBN 978-1-4020-5501-0}
}
@inproceedings{Hoekstra2007b,
title = {Towards a Complex Automata Framework for Multi-Scale Modeling: Formalism and the Scale Separation Map},
author = {A.G. Hoekstra and E. Lorenz and J.-L. Falcone and B. Chopard},
year = {2007},
volume = {4487},
pages = {922--930},
metis_id = {277674},
url = {http://www.springer.com/978-3-540-72583-1},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2007: 7th International Conference, Beijing, China, Proceedings, Part I},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN: 978-3-540-72583-1}
}
@inbook{Hoekstra2007c,
title = {Modelleren en Simuleren},
author = {A.G. Hoekstra and P.M.A. Sloot},
year = {2007},
pages = {239--255},
metis_id = {277675},
publisher = {Reed Business Information},
series = {PBNA Polyzakboekjes},
booktitle = {ICT-Zakboek, 3e druk},
note = {in Dutch},
editor = {T.M.A. Bemelmans and M. van Keulen and R.J. Kusters and M. Looijen},
address = {Den Haag},
issn_isbn = {ISBN 978-90-6228-671-3}
}
@article{Hoekstra2007d,
title = {Toward a Complex Automata Formalism for Multi-Scale Modeling},
author = {A.G. Hoekstra and E. Lorenz and J.-L. Falcone and B. Chopard},
year = {2007},
journal = {International Journal for Multiscale Computational Engineering},
volume = {5},
number = {6},
pages = {491--502},
metis_id = {277815},
url = {http://www.edata-center.com/journals/61fd1b191cf7e96f,120489656946d0de,256884b10087d5f8.html},
publisher = {Begell House},
issn_isbn = {ISSN 1543-1649}
}
@inbook{Kasztelnik2007a,
title = {Fault tolerant Grid registery},
author = {M. Kasztelnik and M.T. Bubak and C. G\'orka and M. Malawski and T. Guba\la},
year = {2007},
pages = {135--144},
metis_id = {307721},
publisher = {Springer Science+Business Media},
booktitle = {Distributed and parallel systems: from cluster to Grid computing},
editor = {P. Kacsuk and T. Fahringer and Z. N\'emeth},
address = {New York, NY, USA},
issn_isbn = {ISBN-13: 978-0-387-69857-1 ; e-ISBN-13: 978-0-387-69858-8}
}
@article{Kitowski2007a,
title = {Rozw\'oj srodk\'ow i narzedzi informatyki dla potrzeb symulacji i budowy aplikacji gridowych (Development of tools and environments for computer simulations and grid applications)},
author = {J. Kitowski and K. Boryczko and M.T. Bubak and W. Dzwinel and W. Funika and R. Slota},
year = {2007},
journal = {Pomiary, Automatyka, Kontrola},
volume = {53},
number = {3},
pages = {26--40},
metis_id = {307618},
publisher = {Stowarzyszenie Inynierw i Technikw Mechanikw Polskich. Sekcja Metrologii, Polskie Stowarzyszenie Pomiarw Automatyki i Robotyki POLSPAR},
abstract = {Some main results of the research recently obtained by Computer Systems Group of the Department of Computer Science are presented in the paper. They are supported by descriptions of future plans and further development. The achievements include architecture of grid middleware for high performance computing and business applications, tools for grid computing, parallel algorithms for mezoscopic simulations and clustering, ontological representation and management of knowledge as well as virtual organizations.},
issn_isbn = {ISSN 0032-4140}
}
@mastersthesis{Kler2007a,
title = {Integration of the ARToolKitPlus optical tracker into the Personal Space Station},
author = {T. de Kler},
year = {2007},
url = {deKler2007a.pdf},
month = {May},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
tutor = {Advisor: R.G. Belleman},
address = {Amsterdam, the Netherlands}
}
@article{Kouwenhoven2007a,
title = {The primordial binary population. II.. Recovering the binary population for intermediate mass stars in Scorpius OB2},
author = {M.B.N. Kouwenhoven and A.G.A. Brown and S.F. Portegies Zwart and L. Kaper},
year = {2007},
journal = {Astron. Astrophys.},
volume = {474},
pages = {77-104},
metis_id = {276756},
url = {http://adsabs.harvard.edu/abs/2007A%26A...474...77K},
month = {oct},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1051/0004-6361:20077719}
}
@article{Kruszynski2007a,
title = {A computational method for quantifying morphological variation in scleractinian corals},
author = {K.J. Kruszynski and J.A. Kaandorp and R. van Liere},
year = {2007},
journal = {Coral Reefs},
volume = {26},
number = {4},
pages = {831-840},
metis_id = {276757},
doi = {10.1007/s00338-007-0270-6}
}
@misc{Krzhizhanovskaya2007a,
title = {Special Issue on Simulation of Multiphysics Multiscale Systems},
author = {V.V. Krzhizhanovskaya},
year = {2007},
journal = {International Journal for Multiscale Computational Engineering},
volume = {5},
number = {1},
url = {http://dx.doi.org/10.1615/IntJMultCompEng.v5.i1},
category = {Multiphysics, Multiscale},
publisher = {Begell House},
doi = {10.1615/IntJMultCompEng.v5.i1},
note = {Guest editorship and Preface},
editor = {V.V. Krzhizhanovskaya},
issn_isbn = {ISSN 1543-1649}
}
@inproceedings{Krzhizhanovskaya2007b,
title = {Simulation of Multiphysics Multiscale Systems: Introduction to the ICCS-2007 Workshop},
author = {V.V. Krzhizhanovskaya and S. Sun},
year = {2007},
volume = {4487},
pages = {755--761},
metis_id = {312451},
url = {http://dx.doi.org/10.1007/978-3-540-72584-8_100},
month = {May},
category = {MultiphysicsMultiscaleSystemSimulation},
publisher = {Springer Berlin, Heidelberg},
doi = {10.1007/978-3-540-72584-8_100},
series = {Lecture Notes in Computer Science},
booktitle = {Proceedings of the 7th International Conference on Computational Science, Part I},
address = {Beijing, China},
issn_isbn = {ISSN 0302-9743 (Print), 1611-3349 (Online), ISBN 978-3-540-72583-1}
}
@inproceedings{Krzhizhanovskaya2007c,
title = {Dynamic Load Balancing of Black-Box Applications with a Resource Selection Mechanism on Heterogeneous Resources of the Grid},
author = {V.V. Krzhizhanovskaya and V.V. Korkhov},
year = {2007},
volume = {4671},
pages = {245--260},
metis_id = {312452},
url = {http://dx.doi.org/10.1007/978-3-540-73940-1},
month = {September},
category = {DynamicLoadBalancing, ResourceSelection, Grid},
publisher = {Springer-Verlag Berlin, Heidelberg},
doi = {10.1007/978-3-540-73940-1},
series = {Lecture Notes in Computer Science},
booktitle = {Proceedings of the Ninth International Conference on Parallel Computing Technologies},
address = {Pereslavl-Zalessky, Russia},
issn_isbn = {ISSN 0302-9743 (Print), 1611-3349 (Online)}
}
@inproceedings{Krzhizhanovskaya2007d,
title = {Virtual Reactor -- Computational Environment for Multidimensional Simulation of Plasma Chemical Processing},
author = {V.V. Krzhizhanovskaya and Y.E. Gorbachev and M.A. Zatevakhin and P.M.A. Sloot},
year = {2007},
metis_id = {312450},
month = {May},
publisher = {MAI},
booktitle = {Proceedings of the XV International Conference on Computational Mechanics and Modern Applied Software Systems},
address = {Alushta, Ukraine}
}
@mastersthesis{Lankamp2007a,
title = {Developing a reference implementation for a microgrid of microthreaded microprocessors},
author = {M. Lankamp},
year = {2007},
url = {Lankamp2007a.pdf},
month = {August},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
tutor = {Advisor: C.R. Jesshope},
address = {Amsterdam, the Netherlands}
}
@article{Liu2007a,
title = {In Vivo Identification and Manipulation of the Ca2+ Selectivity Filter in the Drosophila Transient Receptor Potential Channel},
author = {C.H. Liu and T. Wang and M. Postma and A.G. Obukhov and C. Montell and R.C. Hardie},
year = {2007},
journal = {J. of Neuroscience},
volume = {27},
number = {3},
pages = {604--615},
metis_id = {276758},
doi = {10.1523/JNEUROSCI.4099-06.2007}
}
@mastersthesis{Maheshwari2007a,
title = {Problem Solving Environment for Medical Image Analysis Application Development},
author = {K.C. Maheshwari},
year = {2007},
url = {Maheshwari2007a.pdf},
month = {September},
category = {pwrs, Grid, mastersthesis},
school = {University of Amsterdam},
tutor = {Advisor: S. Olabarriaga and A.S.Z. Belloum},
address = {Amsterdam, the Netherlands}
}
@inproceedings{Malawski2007a,
title = {A new approach to supporting component applications on Grid},
author = {M. Malawski and T. Bartynski and E. Ciepiela and J. Kocot and P. Pelczar and M.T. Bubak},
year = {2007},
pages = {328--336},
metis_id = {307692},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow '06 Grid Workshop, October 15-18, 2006},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
address = {Cracow, Poland},
issn_isbn = {ISBN 83-915141-7-X}
}
@inproceedings{Malawski2007b,
title = {Interoperability of grid component models: GCM and CCA case study},
author = {M. Malawski and M.T. Bubak and F. Baude and D. Caromel and L. Henrio and M. Morel},
year = {2007},
pages = {95--105},
metis_id = {307690},
month = {August},
category = {Grid},
publisher = {Springer Verlag},
series = {CoreGRID series},
booktitle = {Towards Next Generation Grids, proceedings of the CoreGRID Symposium in conjunction with Euro-Par 2007},
editor = {T. Priol and M. Vanneschi},
keywords = {WP3},
issn_isbn = {ISBN 978-0-387-72497-3}
}
@inproceedings{Malawski2007c,
title = {Towards A High-Level Scripting Approach for Building Component-Based Gridspace Applications},
author = {M. Malawski and T. Guba\la and M. Kasztelnik and T. Bartynski and M.T. Bubak},
year = {2007},
pages = {309--321},
metis_id = {307691},
publisher = {Springer},
booktitle = {CoreGRID Workshop on Grid Programming Model, Grid and P2P Systems Architecture, Grid Systems, Tools and Environments},
editor = {M. Danelutto and P. Fragopoulou and V.S. Getov},
keywords = {WP7},
issn_isbn = {ISBN-13 978-0-387-78447-2}
}
@article{McMillan2007a,
title = {A Dynamical Origin for Early Mass Segregation in Young Star Clusters},
author = {S.L.W. McMillan and E. Vesperini and S.F. Portegies Zwart},
year = {2007},
journal = {Astronomical Journal Let.},
volume = {655},
pages = {L45-L49},
metis_id = {265167},
url = {http://adsabs.harvard.edu/abs/2007ApJ...655L..45M},
month = {jan},
category = {Astronomy},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1086/511763}
}
@inproceedings{McMillan2007b,
title = {Stellar Collisions and Black-Hole Formation in Dense Star Clusters},
author = {S.L.W. McMillan and S.F. Portegies Zwart},
year = {2007},
volume = {367},
pages = {697-697},
metis_id = {276759},
url = {http://adsabs.harvard.edu/abs/2007ASPC..367..697M},
note = {abstract},
series = {Astronomical Society of the Pacific Conference Series},
booktitle = {Massive Stars in Interactive Binaries},
editor = {N. St.Louis and A.F.J. Moffat}
}
@inproceedings{MoGcicki,
title = {Quality of Service on the Grid with User Level Scheduling},
author = {J.T. Mo\'scicki and M.T. Bubak and H.C. Lee and A. Muraru and P.M.A. Sloot},
year = {2007},
pages = {119--129},
metis_id = {276760},
url = {Moscicki2007a.pdf},
month = {July},
category = {Grid},
booktitle = {CGW'06 Proceedings},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
address = {Cracow, Poland},
issn_isbn = {ISBN 83-915141-7-X}
}
@article{Muno2007a,
title = {Exciting the magnetosphere of the magnetar CXOU J164710.2-455216 in Westerlund 1},
author = {M.P. Muno and B.M. Gaensler and J.S. Clark and R. de Grijs and D. Pooley and I.R. Stevens and S.F. Portegies Zwart},
year = {2007},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {378},
pages = {L44-L48},
metis_id = {276762},
url = {http://adsabs.harvard.edu/abs/2007MNRAS.378L..44M},
month = {jun},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1111/j.1745-3933.2007.00317.x}
}
@inproceedings{Murtaza2007a,
title = {Performance evaluation of FPGA-based Cellular Automata accelerators},
author = {S. Murtaza and A.G. Hoekstra and P.M.A. Sloot},
year = {2007},
metis_id = {277677},
url = {http://rssi.ncsa.uiuc.edu/proceedings/papers/rssi07_01_paper.pdf},
numpages = {7},
publisher = {Reconfigurable Systems Summer Institute},
booktitle = {Proceedings of the Third Annual Reconfigurable Systems Summer Institute (RSSI'07)},
note = {on line proceedings},
address = {National Center for Supercomputing Applications, Urbana, Illinois}
}
@inproceedings{Murtaza2007b,
title = {Performance Modeling of 2D Cellular Automata on FPGA},
author = {S. Murtaza and A.G. Hoekstra and P.M.A. Sloot},
year = {2007},
pages = {74--78},
metis_id = {277676},
url = {http://www.ieeexplore.ieee.org/xpl/freeabs_all.jsp?isnumber=4380602\&arnumber=4380628\&count=173\&index=25},
month = {August},
publisher = {IEEE},
doi = {10.1109/FPL.2007.4380628},
booktitle = {International Conference on Field Programmable Logic and Applications, FPL 2007},
editor = {A. van Genderen},
address = {Amsterdam},
issn_isbn = {ISBN: 978-1-4244-1060-6}
}
@article{Mller2007a,
title = {Fractal-related assembly of the axial filament in the demosponge Suberites domuncula: relevance to biomineralization and the formation of biogenic silica,},
author = {W.E.G. M\"uller and A. Boreiko and U. Schlossmacher and X. Wang and M. Nawaz Tahir and W. Tremel and D. Brandt and J.A. Kaandorp and H.C. Schr\"oder},
year = {2007},
journal = {Biomaterials},
volume = {28},
pages = {4501-4511},
metis_id = {276761},
doi = {10.1016/j.biomaterials.2007.06.030}
}
@inproceedings{Naumov2007a,
title = {Conceptual Changes in Cellular Automata Development Library (CADLib) from Version 1.0 to Version 1.1},
author = {L.A. Naumov},
year = {2007},
volume = {2},
pages = {529--530},
metis_id = {276764},
url = {Naumov2007b.pdf},
publisher = {SPbSU ITMO},
note = {In Russian},
booktitle = {Proceedings of XIV All-Russian Guidance Conference "Telematics-2007"}
}
@article{Olabarriaga2007a,
title = {Integrated Support for Medical Image Analysis Methods: from Development to Clinical Application},
author = {S.D. Olabarriaga and J.G. Snel and C.P. Botha and R.G. Belleman},
year = {2007},
journal = {IEEE Transactions on Information Technology in Biomedicine},
volume = {11},
number = {1},
pages = {47--57},
url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?tp=\&arnumber=4049800\&isnumber=4049787},
month = {January},
doi = {10.1109/TITB.2006.874929},
issn_isbn = {ISSN 1089-7771}
}
@article{Penttil2007a,
title = {Comparison between discrete dipole implementations and exact techniques},
author = {A. Penttil\"a and E. Zubko and K. Lumme and K. Muinonen and M.A. Yurkin and B.T. Draine and J. Rahola and A.G. Hoekstra and Y. Shkuratov},
year = {2007},
journal = {J. Quant. Spectr. Rad. Transf.},
volume = {106},
pages = {417--436},
metis_id = {276766},
category = {Nato-sfp},
doi = {10.1016/j.jqsrt.2007.01.026}
}
@article{Portegies_Zwart2007a,
title = {The evolution of binary star clusters and the nature of NGC 2136/NGC 2137},
author = {S.F. Portegies Zwart and S.P. Rusli},
year = {2007},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {374},
pages = {931-940},
url = {http://adsabs.harvard.edu/abs/2007MNRAS.374..931P},
month = {jan},
category = {Astronomy},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1111/j.1365-2966.2006.11202.x}
}
@inproceedings{Portegies_Zwart2007b,
title = {Simulating Young Star-Clusters with Primordial Binaries},
author = {S.F. Portegies Zwart and S.L.W. McMillan},
year = {2007},
volume = {367},
pages = {597-597},
url = {http://adsabs.harvard.edu/abs/2007ASPC..367..597P},
note = {abstract},
series = {Astronomical Society of the Pacific Conference Series},
booktitle = {Massive Stars in Interactive Binaries},
editor = {N. St.Louis and A.F.J. Moffat}
}
@article{Portegies_Zwart2007c,
title = {High-performance direct gravitational N-body simulations on graphics processing units},
author = {S.F. Portegies Zwart and R.G. Belleman and P.M. Geldof},
year = {2007},
journal = {New Astronomy},
volume = {12},
pages = {641-650},
url = {http://adsabs.harvard.edu/abs/2007NewA...12..641P},
month = {nov},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1016/j.newast.2007.05.004}
}
@article{Portegies_Zwart2007d,
title = {The gravitational wave signature of young and dense star clusters},
author = {S.F. Portegies Zwart},
year = {2007},
journal = {Advances in Space Research},
volume = {39},
pages = {275-279},
url = {http://adsabs.harvard.edu/abs/2007AdSpR..39..275P},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1016/j.asr.2006.02.018}
}
@article{Portegies_Zwart2007e,
title = {Star cluster ecology - VII. The evolution of young dense star clusters containing primordial binaries},
author = {S.F. Portegies Zwart and S.L.W. McMillan and J. Makino},
year = {2007},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {374},
pages = {95-106},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2007MNRAS.374...95P\&db_key=AST},
month = {jan},
category = {Astronomy},
doi = {10.1111/j.1365-2966.2006.11142.x}
}
@article{Portegies_Zwart2007f,
title = {A runaway collision in a young star cluster as the origin of the brightest supernova},
author = {S.F. Portegies Zwart and E.P.J. van den Heuvel},
year = {2007},
journal = {Nature},
volume = {450},
pages = {388-389},
url = {http://adsabs.harvard.edu/abs/2007Natur.450..388P},
month = {nov},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1038/nature06276}
}
@article{Portegies_Zwart2007g,
title = {The present day mass function in the central region of the Arches cluster},
author = {S.F. Portegies Zwart and E. Gaburov and H.C. Chen and M.A. G\"urkan},
year = {2007},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {378},
pages = {L29-L33},
url = {http://adsabs.harvard.edu/abs/2007MNRAS.378L..29P},
month = {jun},
note = {Provided by the Smithsonian/NASA Astrophysics Data System},
doi = {10.1111/j.1745-3933.2007.00313.x}
}
@article{Qiu2007a,
title = {Understanding the complex dynamics of stock markets through cellular automata},
author = {G. Qiu and B.D. Kandhai and P.M.A. Sloot},
year = {2007},
journal = {Phys Rev E.},
volume = {75},
pages = {046116},
metis_id = {276773},
url = {Qiu2007a.pdf},
numpages = {11},
doi = {10.1103/PhysRevE.75.046116}
}
@mastersthesis{Rahhal2007a,
title = {Interactive Distributed Computing Middleware},
author = {Z.R. Rahhal},
year = {2007},
url = {Rahhal2007a.pdf},
month = {May},
category = {pwrs, Grid, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
tutor = {Advisor: R.G. Belleman},
address = {Amsterdam, the Netherlands}
}
@article{Rodrguez2007a,
title = {Inferring the distribution of Inter-Reaction Intervals for Diffusion-Limited Reactions on Lattices},
author = {J. Vidal Rodr\'{\i}guez and J.A. Kaandorp},
year = {2007},
journal = {Intl. J. Mod. Phys. C},
volume = {18},
number = {4},
pages = {749--757},
url = {Rodriguez2007a.pdf},
month = {April},
category = {bioinformatics},
doi = {10.1142/S0129183107011017}
}
@techreport{Rycerz2007a,
title = {Problem Solving Environment for Distributed Interactive Applications},
author = {K.J. Rycerz and M.T. Bubak and P.M.A. Sloot and V.S. Getov},
year = {2007},
number = {TR-0107},
institution = {Institute on Grid Systems, Tools and Environments},
url = {http://www.coregrid.net/mambo/images/stories/TechnicalReports/tr-0107.pdf},
month = {August},
keywords = {WP7}
}
@inproceedings{Rycerz2007b,
title = {Multiple HLA Federate Processes in Grid Environment},
author = {K.J. Rycerz and M.T. Bubak and M. Malawski and P.M.A. Sloot},
year = {2007},
pages = {293--294},
metis_id = {276776},
url = {Rycerz2007b.pdf},
month = {July},
category = {Grid},
booktitle = {CGW'06 Proceedings},
note = {abstract},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
address = {Cracow, Poland},
issn_isbn = {ISBN 83-915141-7-X}
}
@article{Rycerz2007c,
title = {Interactive N-Body Simulations On the Grid: HLA Versus MPI},
author = {K.J. Rycerz and A. Tirado Ramos and A. Gualandris and S.F. Portegies Zwart and M.T. Bubak and P.M.A. Sloot},
year = {2007},
journal = {International Journal of High Performance Computing Applications},
volume = {21},
number = {2},
pages = {210--221},
metis_id = {276775},
category = {Grid},
note = {Selected papers from EuroPVM/MPI 2005 conference, Sorrento, Italy, 18--21 September 2005},
publisher = {SAGE Publications},
keywords = {WP7},
issn_isbn = {ISSN 1094-3420}
}
@article{Rzasa2007a,
title = {Overhead verification for cryptographically secured transmission on the Grid},
author = {W. Rzasa and M.T. Bubak and B. Bali\'s and T. Szepieniec},
year = {2007},
journal = {Computing and Informatics},
volume = {26},
number = {1},
pages = {89--101},
metis_id = {307620},
publisher = {Slovak Academy of Sciences. Institute of Informatics},
issn_isbn = {ISSN 1335-9150}
}
@inproceedings{Scarpa2007a,
title = {An interaction framework for VR and AR applications},
author = {M. Scarpa and R.G. Belleman},
year = {2007},
pages = {430--437},
metis_id = {276777},
url = {Scarpa2007a.pdf},
publisher = {ASCI},
booktitle = {ASCI 2007, Proceedings of the 13th annual conference of the Advanced School for Computing and Imaging},
editor = {F.W. Jansen and G.E.O. Pierre and C.J. Veenman and J.W.J. Heijnsdijk},
address = {Delft}
}
@inbook{Semyanov2007a,
title = {Optics of leucocytes},
author = {K.A. Semyanov and A.E. Zharinov and P.A. Tarasov and M.A. Yurkin and I.G. Skribunov and D.R. van Bockstaele and A.G. Hoekstra and V.P. Maltsev},
year = {2007},
pages = {253--264},
url = {http://www.springer.com/east/home/generic/search/results?SGWID=5-40109-22-173681338-0},
category = {Nato-sfp},
publisher = {Springer},
booktitle = {Optics of Biological Particles},
editor = {A.G. Hoekstra and V.P. Maltsev and G. Videen},
address = {London},
issn_isbn = {ISBN 978-1-4020-5501-0}
}
@inproceedings{Semyanov2007b,
title = {Characterization of native red blood cell morphology by scanning flow cytometry},
author = {K.A. Semyanov and P.A. Tarasov and M.A. Yurkin and A.G. Hoekstra and V.P. Maltsev},
year = {2007},
pages = {56},
month = {July},
category = {ElastLightScat, Nato-sfp},
booktitle = {8th International Congress on Optical Particle Characterization},
address = {Graz, Austria}
}
@proceedings{Shi2007a,
author = {Y. Shi and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2007},
volume = {4489},
metis_id = {276781},
url = {http://www.springer.com/978-3-540-72587-9},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2007: 7th International Conference, Beijing, China, Proceedings, Part III},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN: 978-3-540-72587-9}
}
@proceedings{Shi2007b,
author = {Y. Shi and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2007},
volume = {4490},
metis_id = {276782},
url = {http://www.springer.com/978-3-540-72589-3},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2007: 7th International Conference, Beijing, China, Proceedings, Part IV},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN: 978-3-540-72589-3}
}
@proceedings{Shi2007c,
author = {Y. Shi and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2007},
volume = {4487},
metis_id = {276779},
url = {http://www.springer.com/978-3-540-72583-1},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2007: 7th International Conference, Beijing, China, Proceedings, Part I},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN: 978-3-540-72583-1}
}
@proceedings{Shi2007d,
author = {Y. Shi and G.D. van Albada and J. Dongarra and P.M.A. Sloot},
year = {2007},
volume = {4488},
metis_id = {276780},
url = {http://www.springer.com/978-3-540-72585-5},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2007: 7th International Conference, Beijing, China, Proceedings, Part II},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN: 978-3-540-72585-5}
}
@article{Sills2007a,
title = {Joint Discussion 14 Modeling dense stellar systems},
author = {A.I. Sills and L. Subr and S.F. Portegies Zwart},
year = {2007},
journal = {Highlights of Astronomy},
volume = {14},
pages = {421-421},
metis_id = {276783},
url = {http://adsabs.harvard.edu/abs/2007HiA....14..421S},
note = {abstract},
doi = {10.1017/S1743921307011179}
}
@inbook{Sloot2007a,
title = {Multi-Science Decision Support for HIV Drug Resistance Treatment},
author = {P.M.A. Sloot and A. Tirado Ramos and M.T. Bubak},
year = {2007},
pages = {597--606},
metis_id = {276785},
url = {Sloot2007d.pdf},
publisher = {IOS Press},
booktitle = {Expanding the Knowledge Economy: Issues, Applications, Case Studies, eChallenges e-2007 Conference Proceedings},
editor = {P. Cunningham and M. Cunningham},
address = {Amsterdam},
issn_isbn = {ISBN 978-1-58603-801-4 (paper), ISBN: 978-1-905824-05-2 (CD)}
}
@inbook{Sloot2007b,
title = {Modeling Dynamic Systems with Cellular Automata},
author = {P.M.A. Sloot and A.G. Hoekstra},
year = {2007},
pages = {1--20},
metis_id = {276784},
url = {Sloot2007b.pdf},
chapter = {21},
publisher = {Chapman \& Hall/CRC},
booktitle = {Handbook of Dynamic System Modeling},
editor = {P.A. Fishwick},
issn_isbn = {ISBN 1-58488-565-3}
}
@booklet{Sloot2007c,
title = {Computational e-Science: Studying complex systems in silico. A National Coordinated Initiative. White Paper.},
author = {P.M.A. Sloot and D. Frenkel and H.A. Van der Vorst and A. van Kampen and H.E. Bal and P. Klint and R.M.M. Mattheij and J. van Wijk and J. Schaye and H.-J. Langevelde and R.H. Bisseling and B. Smit and E. Valenteyn and H.J. Sips and J.B.T.M. Roerdink and K.G. Langedoen},
year = {2007},
url = {Sloot2007a.pdf},
month = {February}
}
@mastersthesis{Strijkers2007a,
title = {The Network is in the Computer},
author = {R.J. Strijkers},
year = {2007},
url = {Strijkers2007a.pdf},
month = {March},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
tutor = {R.J. Meijer},
address = {Amsterdam, the Netherlands}
}
@inbook{Tarasov2007a,
title = {Optics of erythrocytes},
author = {P.A. Tarasov and M.A. Yurkin and P.A. Avrorov and K.A. Semyanov and A.G. Hoekstra and V.P. Maltsev},
year = {2007},
pages = {231--246},
url = {http://www.springer.com/east/home/generic/search/results?SGWID=5-40109-22-173681338-0},
category = {Nato-sfp},
publisher = {Springer},
booktitle = {Optics of Biological Particles},
editor = {A.G. Hoekstra and V.P. Maltsev and G. Videen},
address = {London},
issn_isbn = {ISBN 978-1-4020-5501-0}
}
@phdthesis{Tirado-Ramos2007a,
title = {Collaborative Software Architectures for Interactive Biomedical Applications},
author = {A. Tirado Ramos},
year = {2007},
url = {Tirado-Ramos2007b.pdf},
month = {June},
category = {Grid},
numpages = {154},
school = {University of Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Prof. Dr. M.T. Bubak},
issn_isbn = {ISBN-13: 978-90-6464-143-5}
}
@inproceedings{Woudenberg2007a,
title = {Development of Tools for Performing Computations on FPGA Systems, Using CAME\&L Software},
author = {M. van Woudenberg and L.A. Naumov},
year = {2007},
volume = {2},
pages = {527--529},
url = {Woudenberg2007a.pdf},
publisher = {SPbSU ITMO},
note = {In Russian},
booktitle = {Proceedings of XIV All-Russian Guidance Conference "Telematics-2007"}
}
@inproceedings{Yurkin2007a,
title = {Light scattering by granulated spheres applied to discriminate subtypes of granulated blood cells},
author = {M.A. Yurkin and K.A. Semyanov and V.P. Maltsev and A.G. Hoekstra},
year = {2007},
pages = {TuL07-II-3},
metis_id = {276791},
month = {June},
category = {Nato-sfp},
booktitle = {International Conference on Laser Applications in Life Sciences 2007},
note = {abstract},
address = {Moscow, Russia}
}
@article{Yurkin2007b,
title = {Systematic comparison of the discrete dipole approximation and the finite difference time domain method for large dielectric scatterers},
author = {M.A. Yurkin and A.G. Hoekstra and R.S. Brock and J.Q. Lu},
year = {2007},
journal = {Optics Express},
volume = {15},
number = {26},
pages = {17902-17911},
metis_id = {276794},
url = {http://www.opticsexpress.org/abstract.cfm?id=148490},
month = {Dec},
category = {Nato-sfp}
}
@inproceedings{Yurkin2007c,
title = {Current capabilities of the discrete dipole approximation for very large particles: speed, accuracy, and computational tricks},
author = {M.A. Yurkin},
year = {2007},
pages = {31-33},
metis_id = {276795},
url = {http://diogenes.iwt.uni-bremen.de/vt/laser/papers/DDA-Workshop-final-proceedings.pdf},
month = {March},
category = {ElastLightScat, Nato-sfp},
booktitle = {Proceedings of the DDA - Workshop},
editor = {T. Wriedt and A.G. Hoekstra},
address = {Bremen, Germany}
}
@inproceedings{Yurkin2007d,
title = {The Amsterdam DDA (tutorial)},
author = {M.A. Yurkin},
year = {2007},
pages = {30},
url = {http://diogenes.iwt.uni-bremen.de/vt/laser/papers/DDA-Workshop-final-proceedings.pdf},
month = {March},
category = {ElastLightScat, Nato-sfp},
numpages = {1},
booktitle = {Proceedings of the DDA - Workshop},
editor = {T. Wriedt and A.G. Hoekstra},
address = {Bremen, Germany}
}
@inproceedings{Yurkin2007e,
title = {Systematic comparison of the discrete dipole approximation and the finite difference time domain method},
author = {M.A. Yurkin and A.G. Hoekstra and R.S. Brock and J.Q. Lu},
year = {2007},
pages = {249-252},
metis_id = {276797},
url = {http://www.giss.nasa.gov/\tildecrmim/publications/ELS_10_abstracts.pdf},
month = {June},
category = {ElastLightScat, Nato-sfp},
booktitle = {The 10th Conference on Electromagnetic and Light Scattering},
address = {Bodrum, Turkey}
}
@article{Yurkin2007f,
title = {Discrimination of granulocyte subtypes from light scattering: theoretical analysis using a granulated sphere model},
author = {M.A. Yurkin and K.A. Semyanov and V.P. Maltsev and A.G. Hoekstra},
year = {2007},
journal = {Optics Express},
volume = {15},
number = {25},
pages = {16561-16580},
metis_id = {276798},
url = {http://www.opticsexpress.org/abstract.cfm?id=148215},
category = {ElastLightScat, Nato-sfp}
}
@article{Yurkin2007g,
title = {The discrete dipole approximation for simulation of light scattering by particles much larger than the wavelength},
author = {M.A. Yurkin and V.P. Maltsev and A.G. Hoekstra},
year = {2007},
journal = {J. Quant. Spectr. Rad. Transf.},
volume = {106},
pages = {546--557},
metis_id = {276793},
url = {http://dx.doi.org/10.1016/j.jqsrt.2007.01.033},
category = {Nato-sfp}
}
@phdthesis{Yurkin2007h,
title = {Discrete dipole simulations of light scattering by blood cells},
author = {M.A. Yurkin},
year = {2007},
metis_id = {276792},
url = {Yurkin2007c.pdf},
month = {December},
category = {Nato-sfp, ElastLightScat},
numpages = {207},
school = {Universiteit van Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. A.G. Hoekstra}
}
@article{Yurkin2007i,
title = {The discrete dipole approximation: an overview and recent developments},
author = {M.A. Yurkin and A.G. Hoekstra},
year = {2007},
journal = {J. Quant. Spectr. Rad. Transf.},
volume = {106},
pages = {558--589},
metis_id = {276790},
url = {http://dx.doi.org/10.1016/j.jqsrt.2007.01.034},
category = {Nato-sfp}
}
@article{Zudilova2007a,
title = {On the Role of Individual Human Abilities in the Design of Adaptive User Interfaces for Scientific Problem Solving Environments},
author = {E.V. Zudilova},
year = {2007},
journal = {Knowledge and Information Systems},
volume = {13},
number = {2},
pages = {243--270},
url = {http://www.springerlink.com/content/g328g34m0001v275/},
month = {February},
category = {Visualisation},
publisher = {Springer},
doi = {10.1007/s10115-006-0061-3}
}
@article{Zudilova2007b,
title = {Visualisation and interaction for scientific exploration and knowledge discovery},
author = {E.V. Zudilova and T. Adriaansen},
year = {2007},
journal = {Knowledge and Information Systems},
volume = {13},
number = {2},
pages = {115--117},
url = {http://www.springerlink.com/content/g328g34m0001v275/},
month = {February},
category = {Visualisation},
note = {Editorial},
doi = {10.1007/s10115-007-0098-y},
publisher = {Springer}
}
@inproceedings{Abrahamyan2006a,
title = {Choosing Optimal L-BGK Simulation Parameters for Time Harmonic Flows},
author = {L. Abrahamyan and A.G. Hoekstra and P.M.A. Sloot},
year = {2006},
metis_id = {264513},
url = {Abrahamyan2006b.pdf},
booktitle = {Proceedings Discrete Simulation of Fluid Dynamics DSFD2006, Geneva, Switserland},
note = {abstract}
}
@inproceedings{Abrahamyan2006b,
title = {MPI parallelization and performance aspects of a graph based LB flow solver},
author = {L. Abrahamyan and J.M. Bernsdorf and T. Zeiser and P. Lammers and A.G. Hoekstra and P.M.A. Sloot},
year = {2006},
metis_id = {264512},
url = {Abrahamyan2006a.pdf},
booktitle = {Proceedings Discrete Simulation of Fluid Dynamics DSFD2006, Geneva, Switserland},
note = {abstract}
}
@proceedings{Alexandrov2006a,
author = {V.N. Alexandrov and G.D. van Albada and P.M.A. Sloot and J. Dongarra},
year = {2006},
volume = {3993},
metis_id = {264562},
url = {http://www.springer.com/uk/home/computer/foundations?SGWID=3-156-22-173660150-0},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Proceedings, Part III},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-34383-3}
}
@proceedings{Alexandrov2006b,
author = {V.N. Alexandrov and G.D. van Albada and P.M.A. Sloot and J. Dongarra},
year = {2006},
volume = {3994},
metis_id = {264563},
url = {http://www.springer.com/uk/home/computer/foundations?SGWID=3-156-22-173660151-0},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Proceedings, Part IV},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-34385-7}
}
@proceedings{Alexandrov2006c,
author = {V.N. Alexandrov and G.D. van Albada and P.M.A. Sloot and J. Dongarra},
year = {2006},
volume = {3992},
metis_id = {264561},
url = {http://www.springer.com/uk/home/computer/foundations?SGWID=3-156-22-173660149-0},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Proceedings, Part II},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-34381-4}
}
@proceedings{Alexandrov2006d,
author = {V.N. Alexandrov and G.D. van Albada and P.M.A. Sloot and J. Dongarra},
year = {2006},
volume = {3991},
metis_id = {264560},
url = {http://www.springer.com/uk/home/computer/foundations?SGWID=3-156-22-173660148-0},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Proceedings, Part I},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-34379-2}
}
@article{Artoli2006a,
title = {Mesoscopic simulations of systolic flow in the Human abdominal aorta},
author = {A.M.M. Artoli and A.G. Hoekstra and P.M.A. Sloot},
year = {2006},
journal = {Journal of Biomechanics},
volume = {39},
number = {5},
pages = {873--884},
metis_id = {264514},
url = {Artoli2006a.pdf},
category = {LBM},
doi = {10.1016/j.jbiomech.2005.01.033}
}
@article{Artoli2006b,
title = {Optimizing lattice Boltzmann simulations for unsteady flows},
author = {A.M.M. Artoli and A.G. Hoekstra and P.M.A. Sloot},
year = {2006},
journal = {Computers \& Fluids},
volume = {35},
number = {2},
pages = {227--240},
metis_id = {264515},
url = {Artoli2006b.pdf},
month = {February},
category = {LBM},
doi = {10.1016/j.compfluid.2004.12.002}
}
@inproceedings{Badia2006a,
title = {Performance Monitoring of Grid Superscalar with OCM-G/G-PM: Integration Issues},
author = {R.M. Badia and R. Sirvent and M.T. Bubak and W. Funika and C. Klus and P. Machner and M. Smetek},
year = {2006},
pages = {321--331},
metis_id = {307694},
month = {October},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Proc. of the CoreGRID Integration Workshop, Oct 19-20, 2005, Krakow, Poland},
editor = {S. Gorlatch and M.T. Bubak and T. Priol},
keywords = {WP7},
address = {Krakow, Poland}
}
@techreport{Badia2006b,
title = {Lightweight Grid Platform: Design Methodology},
author = {R.M. Badia and O. Beckmann and S. Panagiotidi and M.T. Bubak and M. Malawski and D. Caromel and L. Henrio and N. Parlavantzas and V.S. Getov and S. Isaiadis and J. Thiyagalingam and V. Lazarov},
year = {2006},
number = {TR-0020},
metis_id = {307726},
institution = {Institute on Problem Solving Environment, Tools and Grid Systems, CoreGRID - Network of Excellence},
url = {http://www.coregrid.net/mambo/images/stories/TechnicalReports/tr-0020.pdf},
month = {January},
keywords = {WP7}
}
@inproceedings{Badia2006c,
title = {Integrating of the OCM-G Monitoring System into the GRID Superscalar},
author = {R.M. Badia and W. Funika and M. Smetek and M.T. Bubak},
year = {2006},
pages = {124--130},
metis_id = {307693},
month = {November},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Proceedings of Cracow Grid Workshop - CGW'05, November 20-23 2005},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
keywords = {WP7},
address = {Cracow, Poland}
}
@inproceedings{Bali,
title = {Fine-grained instrumentation and monitoring of legacy applications in a service-oriented environment},
author = {B. Bali\'s and M.T. Bubak and K. Guzy},
year = {2006},
volume = {3992},
pages = {542--548},
metis_id = {307696},
url = {http://www.springer.com/uk/home/computer/foundations?SGWID=3-156-22-173660149-0},
month = {May},
publisher = {Springer},
note = {Also on CD},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Proceedings, Part II},
editor = {V.N. Alexandrov and G.D. van Albada and P.M.A. Sloot and J.J. Dongarra},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-34381-4}
}
@inproceedings{Bali,
title = {Fine-grained instrumentation and monitoring of legacy applications in a service-oriented environment},
author = {B. Bali\'s and M.T. Bubak and K. Guzy},
year = {2006},
pages = {158--159},
metis_id = {307697},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow '05 Grid Workshop, November 20--23 2005},
note = {abstract},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
address = {Cracow, Poland}
}
@inproceedings{Bali,
title = {Towards a Generic P2P Monitoring Infrastructure for Grid Resources and Applications},
author = {B. Bali\'s and M.T. Bubak and J. Dziwisz and K. Rozkwitalski},
year = {2006},
pages = {17++},
metis_id = {307695},
month = {January},
booktitle = {Proc. 2nd CoreGRID Workshop on GRID and Peer to Peer Systems Architecture},
note = {CD-ROM},
keywords = {WP7},
address = {Paris, France}
}
@inproceedings{Bali,
title = {GEMINI -- a universal monitoring framework: concept, design, and first prototype: [abstract]},
author = {B. Bali\'s and M.T. Bubak and J. Dziwisz and K. Rozkwitalski and S. Hurnik},
year = {2006},
pages = {122--123},
metis_id = {307698},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow '05 Grid Workshop, November 20--23 2005},
note = {abstract},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
address = {Cracow, Poland}
}
@inproceedings{Bali,
title = {An Instrumentation Infrastructure for Grid Workflow Applications},
author = {B. Bali\'s and H.-L. Truong and M.T. Bubak and T. Fahringer and K. Guzy and K. Rozkwitalski},
year = {2006},
volume = {4276},
pages = {1305--1314},
url = {http://www.dps.uibk.ac.at/~truong/publications/kwfinst.pdf},
month = {November},
publisher = {Springer Verlag},
series = {Lecture Notes on Computer Science},
booktitle = {International Symposium on Grid Computing, High-Performance and Distributed Applications},
editor = {R. Meersman and et al.},
keywords = {WP5},
address = {Montpellier, France}
}
@article{Baumgardt2006a,
title = {Tidal capture of stars by intermediate-mass black holes},
author = {H. Baumgardt and C. Hopman and S.F. Portegies Zwart and J. Makino},
year = {2006},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {372},
pages = {467-478},
metis_id = {265171},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006MNRAS.372..467B\&db_key=AST},
month = {oct},
category = {Astronomy},
doi = {10.1111/j.1365-2966.2006.10885.x}
}
@article{Baumgardt2006b,
title = {Ejection of hypervelocity stars from the Galactic Centre by intermediate-mass black holes},
author = {H. Baumgardt and A. Gualandris and S.F. Portegies Zwart},
year = {2006},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {372},
pages = {174--182},
metis_id = {264518},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006MNRAS.372..174B\&db_key=AST},
month = {October},
doi = {10.1111/j.1365-2966.2006.10818.x}
}
@article{Baumgardt2006c,
title = {Ejection of Hyper-Velocity Stars by Intermediate-Mass Black Holes},
author = {H. Baumgardt and A. Gualandris and S.F. Portegies Zwart},
year = {2006},
journal = {Journal of Physics Conference Series},
volume = {54},
pages = {301-305},
metis_id = {265169},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006JPhCS..54..301B\&db_key=AST},
month = {dec},
category = {Astronomy},
doi = {10.1088/1742-6596/54/1/047}
}
@book{Bogdanov2006a,
author = {M.V. Bogdanov and Y.E. Gorbachev and V.V. Krzhizhanovskaya and A.V. Kulik and M.S. Ramm and D.H. Ofengeim and D.E. Tarakanov and A.V. Tsyrulnikov},
year = {2006},
metis_id = {312456},
category = {PECVD, CVD, VirtualReactor},
numpages = {68},
publisher = {St.Petersburg State Polytechnic University},
booktitle = {The processes of heat and mass transfer in modern semiconductor materials technology. Textbook for practical lessons in modeling and simulation},
address = {St. Petersburg, Russia},
note = {In Russian}
}
@inproceedings{Bubak2006a,
title = {Performance visualization in real time monitoring of Web service application},
author = {M.T. Bubak and W. Funika and D. Dziok and M. Koch and A.D. Malony and M. Smetek and R. Wism\"uller},
year = {2006},
pages = {160--166},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow '05 Grid Workshop, November 20--23 2005},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
address = {Cracow, Poland}
}
@inproceedings{Bubak2006b,
title = {Fault tolerance and data synchronization in Grid registry for workflow applications},
author = {M.T. Bubak and M. Kasztelnik and C. G\'orka and M. Malawski and T. Guba\la},
year = {2006},
pages = {57},
metis_id = {307701},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow '05 Grid Workshop, November 20--23 2005},
note = {abstract},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
address = {Cracow, Poland}
}
@inproceedings{Bubak2006c,
title = {Experiments with distributed training of neural networks on the Grid},
author = {M.T. Bubak and M. Malawski and E. Richter-Was and G. Sala and T. Szymocha},
year = {2006},
pages = {375},
metis_id = {307700},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow '05 Grid Workshop, November 20--23 2005},
note = {abstract},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
address = {Cracow, Poland}
}
@proceedings{Bubak2006d,
author = {M.T. Bubak and M. Tura\la and K. Wiatr},
year = {2006},
metis_id = {307737},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow '05 Grid Workshop, November 20--23 2005},
address = {Cracow, Poland}
}
@inproceedings{Bubak2006e,
title = {Using MOCCA Component Environment for Simulation of Gold Clusters},
author = {M.T. Bubak and M. Malawski and M. Placek},
year = {2006},
pages = {295--299},
metis_id = {307699},
publisher = {ACC-Cyfronet AGH},
booktitle = {Proceedings of Cracow Grid Workshop - CGW'05, November 20-23 2005},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
keywords = {WP7},
address = {Krakow, Poland}
}
@article{Cui2006a,
title = {Mathematical modeling of calcium homeostasis in yeast cells},
author = {J. Cui and J.A. Kaandorp},
year = {2006},
journal = {Cell Calcium},
volume = {39},
number = {4},
pages = {337--348},
metis_id = {264516},
url = {http://www.sciencedirect.com/science?_ob=ArticleURL\&_udi=B6WCC-4J5564H-2\&_coverDate=04%2F30%2F2006\&_alid=446774783\&_rdoc=1\&_fmt=\&_orig=search\&_qd=1\&_cdi=6735\&_sort=d\&view=c\&_acct=C000024218\&_version=1\&_urlVersion=0\&_userid=496085\&md5=e1ca4ee33e2b4d8968204e7ea2b0c7bc},
month = {April},
category = {bioinformatics},
publisher = {Elsevier Science},
doi = {doi:10.1016/j.ceca.2005.12.001}
}
@article{Davies2006a,
title = {The MODEST questions: Challenges and future directions in stellar cluster research},
author = {M.B. Davies and P. Amaro-Seoane and C. Bassa and J. Dale and F. de Angeli and M. Freitag and P. Kroupa and D. Mackey and M.C. Miller and S.F. Portegies Zwart},
year = {2006},
journal = {New Astronomy},
volume = {12},
pages = {201-214},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006NewA...12..201D\&db_key=AST},
month = {dec},
category = {Astronomy},
doi = {10.1016/j.newast.2006.09.004}
}
@inproceedings{Funika2006a,
title = {Towards user-defined performance monitoring of distributed Java applications},
author = {W. Funika and P. Godowski and P. Pegiel and M.T. Bubak},
year = {2006},
pages = {54},
metis_id = {307703},
numpages = {7},
publisher = {IEEE},
doi = {10.1109/E-SCIENCE.2006.144},
booktitle = {2nd IEEE International Conference on e-Science and Grid Computing},
note = {Full paper on CD ROM},
editor = {P.M.A. Sloot and G.D. van Albada and M.T. Bubak and A. Trefethen},
issn_isbn = {ISBN 0-7695-2734-5}
}
@article{Gieles2006a,
title = {The Oort problem solved},
author = {M. Gieles and H.J.G.L.M. Lamers and S.F. Portegies Zwart},
year = {2006},
journal = {Modelling Dense Stellar Systems, 26th meeting of the IAU, Joint Discussion 14, 22-23 August 2006, Prague, Czech Republic, JD14, \\#20},
volume = {14},
metis_id = {265177},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006IAUJD..14E..20G\&db_key=AST},
month = {aug},
category = {Astronomy}
}
@article{Gieles2006b,
title = {Star cluster disruption by giant molecular clouds},
author = {M. Gieles and S.F. Portegies Zwart and H. Baumgardt and E. Athanassoula and H.J.G.L.M. Lamers and M.S. Sipior and J. Leenaarts},
year = {2006},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {371},
pages = {793-804},
metis_id = {265173},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006MNRAS.371..793G\&db_key=AST},
month = {sep},
category = {Astronomy},
doi = {10.1111/j.1365-2966.2006.10711.x}
}
@article{Gorbachev2006a,
title = {From Electronic Textbooks to Virtual Laboratories},
author = {Y.E. Gorbachev and A.I. Zhmakin and M.A. Zatevakhin and V.V. Krzhizhanovskaya and M.V. Bogdanov and A.V. Kulik and D.H. Ofengeim and M.S. Ramm},
year = {2006},
journal = {Telecommunications and Informatization in Education},
number = {5(36)},
url = {http://www.edit.muh.ru/content/mags_telecom.htm},
category = {PECVD, VirtualReactor},
publisher = {SGU, Moscow},
note = {In Russian}
}
@proceedings{Gorlatch2006a,
title = {CoreGRID Integration Workshop 2006: CGIW'2006: integrated research in Grid computing},
author = {S. Gorlatch and M.T. Bubak and T. Priol},
year = {2006},
metis_id = {307738},
month = {October},
publisher = {Academic Computer Centre CYFRONET AGH},
address = {Krak\'ow, Poland}
}
@article{Grindlay2006a,
title = {Short gamma-ray bursts from binary neutron star mergers in globular clusters},
author = {J. Grindlay and S.F. Portegies Zwart and S.L.W. McMillan},
year = {2006},
journal = {Nature Physics},
volume = {2},
pages = {116-119},
metis_id = {265182},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006NatPh...2..116G\&db_key=AST},
month = {feb},
category = {Astronomy},
doi = {10.1038/nphys214}
}
@mastersthesis{Groen2006a,
title = {Reliability Analysis of Grid Resources: A User Perspective},
author = {D.J. Groen},
year = {2006},
url = {Groen2006a.pdf},
month = {August},
category = {pwrs, Grid, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
tutor = {G.D. van Albada and J. Templon, and D.L. Groep and A. Tirado-Ramos},
address = {Amsterdam, the Netherlands}
}
@phdthesis{Gualandris2006a,
title = {Simulating self-gravitating systems on parallel computers},
author = {A. Gualandris},
year = {2006},
metis_id = {263809},
url = {Gualandris2006a.pdf},
month = {September},
category = {Astronomy, pwrs, phdthesis},
numpages = {154},
school = {University of Amsterdam},
tutor = {Promotores: Prof. Dr. E.P.J. van den Heuvel and Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. S.F. Portegies Zwart},
issn_isbn = {ISBN-10: 9064640246 ISBN-13: 9789064640247}
}
@inproceedings{Gubala2006a,
title = {Support for automatic workflow composition based on ontologies in semantic Grid environment},
author = {T. Guba\la and M.T. Bubak and M. Malawski},
year = {2006},
pages = {34--40},
metis_id = {307705},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow '05 Grid Workshop, November 20--23 2005},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
address = {Cracow, Poland}
}
@inproceedings{Gubala2006b,
title = {Semantic composition of scientific workflows based on the Petri nets formalism},
author = {T. Guba\la and D. Harezlak and M.T. Bubak and M. Malawski},
year = {2006},
pages = {12},
metis_id = {307704},
numpages = {8 issn_isbn = ISBN 0-7695-2734-5},
publisher = {IEEE},
doi = {10.1109/E-SCIENCE.2006.127},
booktitle = {2nd IEEE International Conference on e-Science and Grid Computing},
note = {Full paper on CD ROM},
editor = {P.M.A. Sloot and G.D. van Albada and M.T. Bubak and A. Trefethen}
}
@article{Heggie2006a,
title = {McScatter: A simple three-body scattering package with stellar evolution},
author = {D.C. Heggie and S.F. Portegies Zwart and J.R. Hurley},
year = {2006},
journal = {New Astronomy},
volume = {12},
pages = {20-28},
metis_id = {265170},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006NewA...12...20H\&db_key=AST},
month = {oct},
category = {Astronomy},
doi = {10.1016/j.newast.2006.04.005}
}
@article{Hoekstra2006a,
title = {Preface to special issue dedicated to the Optical Properties of Biological Cells},
author = {A.G. Hoekstra and V.P. Maltsev and G. Videen},
year = {2006},
journal = {J. Quant. Sectr. Rad. Transf.},
volume = {102},
number = {1},
pages = {1--2},
metis_id = {264519},
month = {Nov.},
category = {ElastLightScat}
}
@inproceedings{Hoekstra2006b,
title = {Introducing Complex Automata for Modelling Multi-Scale Complex Systems},
author = {A.G. Hoekstra and B. Chopard and P.V. Lawford and D.R. Hose and M. Krafczyk and J.M. Bernsdorf},
year = {2006},
metis_id = {264520},
url = {Hoekstra2006b.pdf},
month = {September},
publisher = {European Complex Systems Society},
booktitle = {proceedings European Complex Systems Conference 2006},
note = {CD},
address = {Oxford, UK},
issn_isbn = {ISBN 0-9554123-0-7}
}
@article{Hopman2006a,
title = {The Redshift Distribution of Short Gamma-Ray Bursts from Dynamically Formed Neutron Star Binaries},
author = {C. Hopman and D. Guetta and E. Waxman and S.F. Portegies Zwart},
year = {2006},
journal = {Astronomical Journal Let.},
volume = {643},
pages = {L91-L94},
metis_id = {265180},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006ApJ...643L..91H\&db_key=AST},
month = {jun},
category = {Astronomy},
doi = {10.1086/505141}
}
@article{Kaandorp2006a,
title = {Groei en vorm van koralen \& de invloed van atmosferische CO2 en stijgende zeetemperaturen},
author = {J.A. Kaandorp},
year = {2006},
journal = {Ecologie \& Ontwikkeling},
volume = {71},
pages = {13--15},
metis_id = {264521},
note = {in Dutch}
}
@techreport{Kirchev2006a,
title = {Security Models for Lightweight Grid Architectures},
author = {L. Kirchev and M. Blyantov and V. Georgiev and K. Boyanov and M. Malawski and M.T. Bubak and S. Isaiadis and V.S. Getov},
year = {2006},
number = {TR-0023},
metis_id = {307727},
institution = {Institute on Grid Systems, Tools and Environments, CoreGRID - Network of Excellence},
url = {http://www.coregrid.net/mambo/images/stories/TechnicalReports/tr-0023.pdf},
month = {January},
keywords = {WP7}
}
@article{Kolesnikova2006a,
title = {Determination of volume, shape and refractive index of individual blood platelets},
author = {I.V. Kolesnikova and S.V. Potapov and M.A. Yurkin and A.G. Hoekstra and V.P. Maltsev and K.A. Semyanov},
year = {2006},
journal = {J. Quant. Spectr. Rad. Transf.},
volume = {102},
number = {1},
pages = {37--45},
metis_id = {264524},
url = {http://dx.doi.org/10.1016/j.jqsrt.2006.02.050},
month = {Nov.},
category = {Nato-sfp, ElastLightScat}
}
@inproceedings{Korkhov2006a,
title = {Workload Balancing in Heterogeneous Grid Environment: A Virtual Reactor Case Study},
author = {V.V. Korkhov and V.V. Krzhizhanovskaya},
year = {2006},
pages = {93},
metis_id = {263666},
url = {http://grid2006.jinr.ru/programme29.asp},
category = {PSE, Grid, VirtualReactor, LoadBalancing},
publisher = {JINR},
booktitle = {Book of abstracts of the Second International Conference on Distributed Computing and Grid Technologies in Science and Education},
address = {Dubna, Russia},
issn_isbn = {ISBN 5-9530-0117-7}
}
@inproceedings{Korkhov2006b,
title = {Benchmarking and Adaptive Load Balancing of the Virtual Reactor Application on the Russian-Dutch Grid},
author = {V.V. Korkhov and V.V. Krzhizhanovskaya},
year = {2006},
volume = {3991},
pages = {530--538},
metis_id = {264522},
url = {http://dx.doi.org/10.1007/11758501_72},
category = {PECVD, PSE, Grid, VirtualReactor, LoadBalancing},
publisher = {Springer Berlin, Heidelberg},
doi = {10.1007/11758501},
series = {Lecture Notes in Computer Science},
booktitle = {Proceedings of the 6th International Conference on Computational Science},
address = {Reading, UK},
issn_isbn = {ISBN: 3-540-34379-2}
}
@inproceedings{Korkhov2006c,
title = {Workload Balancing in Heterogeneous Grid Environment: A Virtual Reactor Case Study},
author = {V.V. Korkhov and V.V. Krzhizhanovskaya},
year = {2006},
volume = {D11-2006-167},
pages = {103-113},
category = {Grid, VirtualReactor, LoadBalancing},
publisher = {JINR},
booktitle = {Second International Conference on Distributed Computing and Grid Technologies in Science and Education},
address = {Dubna, Russia}
}
@inproceedings{Kouwenhoven2006a,
title = {Finding the Primordial Binary Population in Sco OB2: on the interpretation of binary star observations},
author = {M.B.N. Kouwenhoven and A.G.A. Brown and S.F. Portegies Zwart and L. Kaper},
year = {2006},
pages = {388-388},
url = {http://adsabs.harvard.edu/abs/2007IAUS..240..388K},
month = {aug},
category = {Astronomy},
booktitle = {IAU Symposium 240},
address = {Prague, Czech Republic}
}
@article{Kromkamp2006a,
title = {Lattice Boltzmann simulation of 2D and 3D non-Brownian suspensions in Couette flow},
author = {J. Kromkamp and D. van den Ende and B.D. Kandhai and R.G.M. Sman and R.M. Boom},
year = {2006},
journal = {Chem. Eng. Sc},
volume = {61},
number = {2},
pages = {858-873},
metis_id = {265087},
url = {http://dx.doi.org/10.1016/j.ces.2005.08.011},
month = {January},
doi = {10.1016/j.ces.2005.08.011}
}
@inproceedings{Kruszynski2006a,
title = {An Interactive Visualization System for Quantifying Coral Structures},
author = {K.J. Kruszynski and R. van Liere and J.A. Kaandorp},
year = {2006},
pages = {1--8},
metis_id = {264525},
url = {Kruszynski2006a.pdf},
month = {January},
category = {Visualisation},
booktitle = {Eurographics/ IEEE-VGTC Symposium on Visualization},
editor = {T. Ertl and K. Joy and B. Santos},
address = {Benidorm, Spain}
}
@inproceedings{Krzhizhanovskaya2006a,
title = {Modeling of Plasma Chemical Deposition and Degradation of Silicon Thin Films},
author = {V.V. Krzhizhanovskaya and P.M.A. Sloot and Y.E. Gorbachev},
year = {2006},
pages = {1347--1348},
metis_id = {264526},
url = {Krzhizhanovskaya2006a.pdf},
category = {PECVD, PSE, Grid},
publisher = {Springer},
booktitle = {Proceedings of the 16th European Conference of Fracture, Alexandroupolis, Greece, July 3-7, 2006},
note = {abstract},
editor = {E.E. Gdoutos},
address = {Alexandroupolis, Greece},
issn_isbn = {ISBN-10 1-4020-4971-4}
}
@inproceedings{Krzhizhanovskaya2006b,
title = {Computational Engineering on the Grid: Crafting a Distributed Virtual Reactor},
author = {V.V. Krzhizhanovskaya and V.V. Korkhov and A. Tirado Ramos and D.J. Groen and I.V. Shoshmina and I.A. Valuev and I.V. Morozov and N.V. Malyshkin and Y.E. Gorbachev and P.M.A. Sloot},
year = {2006},
pages = {101},
metis_id = {263663},
url = {http://doi.ieeecomputersociety.org/10.1109/E-SCIENCE.2006.42},
month = {December},
category = {Grid, PECVD, PSE, Grid, VirtualReactor},
publisher = {IEEE},
doi = {10.1109/E-SCIENCE.2006.42},
booktitle = {2nd IEEE International Conference on e-Science and Grid Computing},
note = {full paper on CD},
editor = {P.M.A. Sloot and G.D. van Albada and M.T. Bubak and A. Trefethen},
address = {Amsterdam, The Netherlands}
}
@article{Krzhizhanovskaya2006c,
title = {Simulation of Multiphysics Multiscale Systems},
author = {V.V. Krzhizhanovskaya and B. Chopard and Y.E. Gorbachev},
year = {2006},
journal = {International Journal for Multiscale Computational Engineering},
volume = {4},
number = {2},
pages = {207},
url = {http://dx.doi.org/10.1615/IntJMultCompEng.v4.i2},
category = {MultiphysicsMultiscaleSystemSimulation},
publisher = {Begell House},
doi = {10.1615/IntJMultCompEng.v4.i2},
note = {Guest editorship and Preface for special issue},
editor = {V.V. Krzhizhanovskaya and B. Chopard and Y.E. Gorbachev},
issn_isbn = {ISSN 1543-1649}
}
@inproceedings{Krzhizhanovskaya2006d,
title = {Virtual Reactor: a distributed computing environment for simulation of plasma chemical processes on heterogeneous resources of the Grid},
author = {V.V. Krzhizhanovskaya and V.V. Korkhov and P.M.A. Sloot},
year = {2006},
metis_id = {264528},
month = {September},
category = {PECVD, PSE, Grid, VirtualReactor},
booktitle = {All-Russian conference "Scientific services on the Internet: Parallel Programming Technologies"},
address = {Novorossiysk, Russia}
}
@inproceedings{Krzhizhanovskaya2006e,
title = {Problem-Solving Environments for Simulation and Optimization on Heterogeneous Distributed Computational Resources of the Grid},
author = {V.V. Krzhizhanovskaya and V.V. Korkhov},
year = {2006},
pages = {917-932},
metis_id = {263664},
url = {http://www.paco.sicpro.org/paco2006/code/e06_01.htm},
month = {October},
category = {PECVD, PSE, Grid, VirtualReactor},
publisher = {V.A. Trapeznikov Institute of Control Sciences RAS, Moscow},
booktitle = {Third International Conference on Parallel Computations and Control Problems PACO},
address = {Moscow, Russia},
issn_isbn = {ISBN 5-201-14990-1}
}
@article{Krzhizhanovskaya2006f,
title = {Simulation of Multiphysics Multiscale Systems},
author = {V.V. Krzhizhanovskaya and B. Chopard and Y.E. Gorbachev},
year = {2006},
journal = {Special Issue of International Journal for Multiscale Computational Engineering},
volume = {4},
number = {3},
pages = {305--306},
metis_id = {276734},
url = {http://dx.doi.org/10.1615/IntJMultCompEng.v4.i3},
category = {MultiphysicsMultiscaleSystemSimulation},
publisher = {Begell House},
doi = {10.1615/IntJMultCompEng.v4.i3},
note = {Guest editorship and Preface},
editor = {V.V. Krzhizhanovskaya and B. Chopard and Y.E. Gorbachev},
issn_isbn = {ISSN 1543-1649}
}
@inproceedings{Krzhizhanovskaya2006g,
title = {Software Environment for Simulation of Plasma-Chemical Deposition Reactors on Heterogeneous Computational Resources of the Grid},
author = {V.V. Krzhizhanovskaya},
year = {2006},
pages = {81--82},
metis_id = {264529},
month = {December},
category = {PECVD, PSE, Grid, VirtualReactor},
publisher = {St. Petersburg State Polytechnic University},
booktitle = {Conference on Computer Technologies in Modern Researches, Polytechnic Symposium "Young Scientists to the industry of Northwest Russia"},
note = {Best presentation award},
address = {St.Petersburg, Russia},
issn_isbn = {ISBN 5-7422-1365-4}
}
@proceedings{Lee2006a,
title = {IEEE Proceedings of the 2006 International Conference on Hybrid Information Technology},
author = {G. Lee and D. Slezak and T.H. Kim and P.M.A. Sloot and H.-K. Kim and I.S. Ko and M. Szczuka},
year = {2006},
metis_id = {264530},
month = {November},
publisher = {IEEE},
note = {IEEE Computer Society Order Number P2674},
issn_isbn = {ISBN 13:978-0-7695-2674-4, ISBN 10: 0-769-2674-8}
}
@inproceedings{Malawski2006a,
title = {An ADL-based Support for CCA Components on the Grid},
author = {M. Malawski and T. Bartynski and E. Ciepiela and J. Kocot and P. Pelczar and M.T. Bubak},
year = {2006},
metis_id = {307706},
month = {December},
booktitle = {CoreGRID Workshop on Grid Systems, Tools and Environments in Conjunction with GRIDS@work: CoreGRID Conference, Grid Plugtests and Contest},
keywords = {WP7},
address = {Sophia-Antipolis, France}
}
@inproceedings{Malawski2006b,
title = {Experiments with distributed component computing across Grid boundaries},
author = {M. Malawski and M.T. Bubak and M. Placek and D. Kurzyniec and V.S. Sunderam},
year = {2006},
pages = {109--116},
metis_id = {307707},
month = {June},
publisher = {IEEE},
booktitle = {Proceedings of the HPC-GECO/CompFrame workshop in conjunction with HPDC 2006},
keywords = {WP7},
address = {Paris, France}
}
@inproceedings{Malawski2006c,
title = {Towards Multiprotocol and Multilanguage Interoperability: Experiments with Babel and RMIX},
author = {M. Malawski and D. Harezlak and M.T. Bubak},
year = {2006},
pages = {266--278},
metis_id = {307708},
publisher = {ACC-Cyfronet AGH},
booktitle = {Proceedings of Cracow Grid Workshop - CGW'05, November 20-23 2005},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
keywords = {WP7},
address = {Krakow, Poland}
}
@article{Merks2006a,
title = {Problem-Solving Environments for Biological Morphogenesis},
author = {R.M.H. Merks and A.G. Hoekstra and J.A. Kaandorp and P.M.A. Sloot and P. Hogeweg},
year = {2006},
journal = {Comput. Sci. Eng},
volume = {8},
number = {1},
pages = {61--72},
metis_id = {264531},
url = {http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/mags/cs/\&toc=comp/mags/cs/2006/01/c1toc.xml\&DOI=10.1109/MCSE.2006.11},
category = {PSE},
doi = {10.1109/MCSE.2006.11},
abstract = {Simulation is becoming an important tool to understand developmental mechanisms. In this article we discuss two prototypical problem solving environments (PSEs) for biological development. The first PSE implements a three-dimensional model of coral growth and enables marine biologists to construct and analyze simulations with high-level concepts. The second PSE helps explore the interplay between genetic information and physical mechanisms during embryonic development of multicellular organisms and its evolution. The two PSEs have contrasting demands. A single simulation of a coral and its environment is very expensive. Thus the PSE manages single simulation set-ups and streamlines analysis of single simulations. The study of biological evolution requires high simulation throughput, and for this reason we use a simple, efficient two-dimensional model of biological development. The modular architecture of the PSEs gives advanced users full control, while keeping them accessible to the computationally unskilled.}
}
@article{Min2006a,
title = {Absorption and scattering properties of arbitrarily shaped particles in the Rayleigh domain: A rapid computational method and a theoretical foundation for the statistical approach},
author = {M. Min and J.W. Hovenier and C. Dominik and A. de Koter and M.A. Yurkin},
year = {2006},
journal = {J. Quant. Spectr. Rad. Transf.},
volume = {97},
number = {2},
pages = {161-180},
metis_id = {264532},
url = {http://dx.doi.org/10.1016/j.jqsrt.2005.05.059},
category = {Nato-sfp, ElastLightScat},
doi = {10.1016/j.jqsrt.2005.05.059}
}
@article{Muno2006a,
title = {A Neutron Star with a Massive Progenitor in Westerlund 1},
author = {M.P. Muno and J.S. Clark and P.A. Crowther and S.M. Dougherty and R. de Grijs and C. Law and S.L.W. McMillan and M.R. Morris and I. Negueruela and D. Pooley and S.F. Portegies Zwart and F. Yusef-Zadeh},
year = {2006},
journal = {Astrophys. J. Let.},
volume = {636},
pages = {L41-L44},
metis_id = {264534},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006ApJ...636L..41M\&db_key=AST},
month = {jan},
category = {astronomy},
doi = {10.1086/499776}
}
@article{Muno2006b,
title = {XMM Observations of AXP CXO J167410.2-455216 Four Days Prior to Outburst},
author = {M.P. Muno and B.M. Gaensler and J.S. Clark and S.F. Portegies Zwart and D. Pooley and R. de Grijs and I.R. Stevens and I. Negueruela},
year = {2006},
journal = {The Astronomer's Telegram},
volume = {902},
pages = {1-+},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006ATel..902....1M\&db_key=AST},
month = {sep},
category = {Astronomy}
}
@article{Muno2006c,
title = {Diffuse, Nonthermal X-Ray Emission from the Galactic Star Cluster Westerlund 1},
author = {M.P. Muno and C. Law and J.S. Clark and S.M. Dougherty and R. de Grijs and S.F. Portegies Zwart and F. Yusef-Zadeh},
year = {2006},
journal = {Astronomical Journal},
volume = {650},
pages = {203-211},
metis_id = {265172},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006ApJ...650..203M\&db_key=AST},
month = {oct},
category = {Astronomy},
doi = {10.1086/507175}
}
@article{Mller2006a,
title = {Magnetic resonance imaging of the siliceous skeleton of the demosponge Lubomirskia baicalensis},
author = {W.E.G. M\"uller and O.V. Kaluzhnaya and S.I. Belikov and M. Rothenberger and H.C. Schr\"oder and A. Reiber and J.A. Kaandorp and B. Manz and D. Mietchen and F. Volke},
year = {2006},
journal = {Journal of Structural Biology},
volume = {153},
number = {1},
pages = {31--41},
url = {Mueller2006a.pdf},
doi = {10.1016/j.jsb.2005.09.008}
}
@inproceedings{Naumov2006a,
title = {Comparision of Specialized Netwoking Protocols CTP (Commands Transfer Protocol) and IL (Internet Link)},
author = {L.A. Naumov},
year = {2006},
volume = {1},
pages = {266-267},
metis_id = {264535},
note = {in Russian},
booktitle = {Proceedings of XIII All-Russian Guidance Conference "Telematics-2006"},
publisher = {SPbSU ITMO},
address = {Saint-Petersburg},
issn_isbn = {ISBN 5-7577-0192-7}
}
@article{Naumov2006b,
title = {An Overview of Cellular Automata Modeling Software},
author = {L.A. Naumov},
year = {2006},
journal = {Telecommunications and Informatization of Education},
volume = {33},
number = {2},
pages = {114-125},
metis_id = {264536},
url = {http://camellab.spb.ru/utils/dl.jsp?tgt=/pubs/2006/SurveySoft.pdf},
note = {in Russian},
issn_isbn = {ISSN: 1609-4670}
}
@inproceedings{Olabarriaga2006a,
title = {A Virtual Laboratory for fMRI Data Management and Analysis},
author = {S.D. Olabarriaga and A.J. Nederveen and J.G. Snel and R.G. Belleman},
year = {2006},
month = {June},
booktitle = {Human Brain Mapping 2006},
address = {Florence}
}
@inproceedings{Olabarriaga2006b,
title = {Towards a Virtual Laboratory for fMRI Data Management and Analysis},
author = {S.D. Olabarriaga and A.J. Nederveen and J.G. Snel and R.G. Belleman},
year = {2006},
month = {June},
booktitle = {HealthGrid 2006},
address = {Valencia}
}
@article{Patruno2006a,
title = {The ultraluminous X-ray source in M82: an intermediate-mass black hole with a giant companion},
author = {A. Patruno and S.F. Portegies Zwart and J.D.M. Dewi and C. Hopman},
year = {2006},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {370},
pages = {L6-L9},
metis_id = {265179},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006MNRAS.370L...6P\&db_key=AST},
month = {jul},
category = {Astronomy},
doi = {10.1111/j.1745-3933.2006.00176.x}
}
@inproceedings{Penttil2006a,
title = {Comparison between discrete dipole and exact techniques},
author = {A. Penttil\"a and E. Zubko and K. Lumme and K. Muinonen and M.A. Yurkin and Y. Shkuratov and A.G. Hoekstra},
year = {2006},
pages = {227--230},
metis_id = {264539},
url = {http://www.astro.spbu.ru/ELS9/ELS9-22.pdf},
month = {June},
category = {Nato-sfp, ElastLightScat},
booktitle = {Proceedings of the 9th Conference on Electromagnetic and Light Scattering by Nonspherical Particles: Theory, Measurement and Applications},
address = {St.Petersburg,Russia},
issn_isbn = {ISBN 5-9651-0210-0}
}
@article{Portegies_Zwart2006a,
title = {The Ecology of Star Clusters and Intermediate-Mass Black Holes in the Galactic Bulge},
author = {S.F. Portegies Zwart and H. Baumgardt and S.L.W. McMillan and J. Makino and P. Hut and T. Ebisuzaki},
year = {2006},
journal = {Astronomical Journal},
volume = {641},
pages = {319-326},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006ApJ...641..319P\&db_key=AST},
month = {apr},
category = {Astronomy},
doi = {10.1086/500361}
}
@article{Rodrguez2006a,
title = {Spatial Stochastic Modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli},
author = {J. Vidal Rodr\'{\i}guez and J.A. Kaandorp and M. Dobrzy\'nski and J.G. Blom},
year = {2006},
journal = {Bioinformatics},
volume = {22},
number = {15},
pages = {1895--1901},
url = {Rodriguez2006a.pdf},
doi = {10.1093/bioinformatics/btl271}
}
@inproceedings{Rycerz2006a,
title = {A Grid Service for Management of Multiple HLA Federate Processes},
author = {K.J. Rycerz and M.T. Bubak and M. Malawski and P.M.A. Sloot},
year = {2006},
volume = {3911},
pages = {699--706},
metis_id = {264541},
url = {Rycerz2006a.pdf},
publisher = {Springer},
doi = {10.1007/11752578_84},
series = {Lecture Notes in Computer Science},
booktitle = {Parallel Processing and Applied Mathematics: 6th International Conference (PPAM) 2005, Revised selected papers},
editor = {R. Wyrzykowski and J.J. Dongarra and N. Meyer and J. Wa\'sniewski},
issn_isbn = {ISBN: 3-540-34141-2}
}
@phdthesis{Rycerz2006b,
title = {Grid-based HLA Simulation Support},
author = {K.J. Rycerz},
year = {2006},
metis_id = {264050},
url = {http://dare.uva.nl/en/record/192213},
month = {June},
category = {HLA, Grid, pwrs, phdthesis},
numpages = {225},
school = {University of Amsterdam},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. M.T. Bubak}
}
@inproceedings{Rycerz2006c,
title = {Problem solving environment for distributed interactive applications},
author = {K.J. Rycerz and M.T. Bubak and P.M.A. Sloot and V.S. Getov},
year = {2006},
pages = {129--140},
metis_id = {264542},
url = {Rycerz2006c.pdf},
month = {October},
publisher = {Academic Computing Centre CYFRONET AGH},
booktitle = {Integrated Research in Grid Computing, Integration Workshop},
editor = {S. Gorlatch and M.T. Bubak and T. Priol},
address = {Krakow, Poland},
issn_isbn = {ISBN 83-915141-6-1}
}
@inproceedings{Rycerz2006d,
title = {Grid support for HLA-based collaborative environment for vascular reconstruction},
author = {K.J. Rycerz and M.T. Bubak and M. Malawski and P.M.A. Sloot},
year = {2006},
pages = {48},
metis_id = {307709},
numpages = {8},
publisher = {IEEE},
doi = {10.1109/E-SCIENCE.2006.77},
booktitle = {2nd IEEE International Conference on e-Science and Grid Computing},
note = {Full paper on CD ROM},
editor = {P.M.A. Sloot and G.D. van Albada and M.T. Bubak and A. Trefethen},
issn_isbn = {ISBN 0-7695-2734-5}
}
@inproceedings{Rzasa2006a,
title = {Simulation method for estimation of security overhead of Grid applications},
author = {W. Rzasa and M.T. Bubak and B. Bali\'s and T. Szepieniec},
year = {2006},
pages = {300--307},
metis_id = {307710},
publisher = {Academic Computer Centre CYFRONET AGH},
booktitle = {Cracow '05 Grid Workshop, November 20--23 2005},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
address = {Cracow, Poland}
}
@article{Scarpa2006a,
title = {Highly interactive distributed visualization},
author = {M. Scarpa and R.G. Belleman and P.M.A. Sloot and C.T.A.M. de Laat},
year = {2006},
journal = {Future Generation Computer Systems},
volume = {22},
number = {8},
pages = {896--900},
metis_id = {263505},
url = {Scarpa2006a.pdf},
month = {May},
doi = {10.1016/j.future.2006.03.004}
}
@article{Sloot2006a,
title = {From Molecule to Man: Decision Support in Individualized E-Health},
author = {P.M.A. Sloot and A. Tirado Ramos and I. Altintas and M.T. Bubak and C.A.B. Boucher},
year = {2006},
journal = {IEEE Computer},
volume = {39},
number = {11},
pages = {40--46},
metis_id = {264545},
url = {Sloot2006b.pdf},
month = {November},
note = {Cover feature}
}
@misc{Sloot2006b,
title = {Handling Complexity},
author = {P.M.A. Sloot},
year = {2006},
metis_id = {264544},
url = {http://www.hoise.com/primeur/06/articles/weekly/AE-PR-02-06-29.html},
note = {Laudation for Carl Kesselman, dr. hc.}
}
@proceedings{Sloot2006c,
title = {2nd IEEE International Conference on e-Science and Grid Computing},
author = {P.M.A. Sloot and G.D. van Albada and M.T. Bubak and A. Trefethen},
year = {2006},
metis_id = {264546},
url = {http://doi.ieeecomputersociety.org/10.1109/E-SCIENCE.2006.125},
month = {12},
publisher = {IEEE},
note = {CD Only},
organization = {IEEE},
issn_isbn = {ISBN 0-7695-2734-5}
}
@mastersthesis{Sluijs2006a,
title = {Simulating Flow around a Complex Geometry},
author = {N. Sluijs},
year = {2006},
url = {Sluijs2006a.pdf},
month = {June},
category = {pwrs, LBM, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
tutor = {Advisor: J.G. Blom and J.A. Kaandorp},
address = {Amsterdam, the Netherlands}
}
@inproceedings{Snel2006a,
title = {A Distributed Workflow Management System for Automated Medical Image Analysis and Logistics},
author = {J.G. Snel and S.D. Olabarriaga and J. Alkemade and H.G. van Andel and A.J. Nederveen and C.B. Majoie and G.J. den Heeten and M. van Straten and R.G. Belleman},
year = {2006},
metis_id = {264548},
month = {June},
booktitle = {IEEE CMBS, special track on Grids for Biomedical Informatics},
address = {Salt Lake City}
}
@inproceedings{Tirado-Ramos2006a,
title = {A Conceptual Grid Architecture for Interactive Biomedical Applications},
author = {A. Tirado Ramos and P.M.A. Sloot},
year = {2006},
pages = {762--767},
url = {Tirado-Ramos2006a.pdf},
publisher = {IEEE},
booktitle = {19th IEEE International Symposium on Computer-Based Medical Systems (CBMS'06)},
address = {Salt Lake City, USA},
issn_isbn = {ISBN 0-7695-2517-1}
}
@inproceedings{Truong2006a,
title = {K-WfGrid Distributed Monitoring and Performance Analysis Services for Workflows in the Grid},
author = {H.-L. Truong and P. Brunner and T. Fahringer and F. Nerieri and R. Samborski and B. Bali\'s and M.T. Bubak and K. Rozkwitalski},
year = {2006},
metis_id = {307711},
url = {http://www.dps.uibk.ac.at/~truong/publications/kwfpma-submission.pdf},
month = {December},
publisher = {IEEE Computer Society Press},
doi = {10.1109/E-SCIENCE.2006.95},
booktitle = {International Conference on e-Science and Grid Computing},
keywords = {WP5},
address = {Amsterdam, The Netherlands}
}
@incollection{Truong2006b,
title = {Towards Distributed Monitoring and Performance Analysis Services in the K-WfGrid Project},
author = {H.-L. Truong and B. Bali\'s and M.T. Bubak and J. Dziwisz and T. Fahringer and A. Hoheisel},
year = {2006},
volume = {3911},
pages = {156--163},
publisher = {Springer-Verlag Berlin Heidelberg},
series = {Lecture Notes on Computer Science},
booktitle = {Parallel Processing and Applied Mathematics : 6th international conference, PPAM 2005: revised selected papers},
editor = {R. Wyrzykowski and et al.},
keywords = {WP5}
}
@article{Vesperini2006a,
title = {Mass segregation in young star clusters},
author = {E. Vesperini and S.L.W. McMillan and S.F. Portegies Zwart},
year = {2006},
journal = {Modelling Dense Stellar Systems, 26th meeting of the IAU, Joint Discussion 14, 22-23 August 2006, Prague, Czech Republic, JD14, \\#36},
volume = {14},
metis_id = {265176},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006IAUJD..14E..36V\&db_key=AST},
month = {aug},
category = {Astronomy}
}
@article{Vrugt2006a,
title = {Application of parallel computing to stochastic parameter estimation in environmental models},
author = {J.A. Vrugt and B. \'O Nuall\'ain and B.A. Robinson and W. Bouten and S.C. Dekker and P.M.A. Sloot},
year = {2006},
journal = {Computers \& Geosciences},
volume = {32},
number = {8},
pages = {1139--1155},
metis_id = {264552},
url = {Vrugt2006b.pdf},
month = {January},
doi = {10.1016/j.cageo.2005.10.015}
}
@article{Vrugt2006b,
title = {Real-time data assimilation for operational ensemble streamflow forecasting},
author = {J.A. Vrugt and H.V. Gupta and B. \'O Nuall\'ain and W. Bouten},
year = {2006},
journal = {Journal of Hydrometeorology},
volume = {7},
number = {3},
pages = {548--565},
metis_id = {264551},
url = {http://ams.allenpress.com/perlserv/?request=get-abstract\&doi=10%2E1175%2FJHM504%2E1},
month = {June},
doi = {10.1175/JHM504.1}
}
@inproceedings{Wegiel2006a,
title = {Fine-Grain Interoperability with Legacy Libraries Virtualized as Web Services},
author = {M. Wegiel and M.T. Bubak and B. Bali\'s},
year = {2006},
pages = {27--34},
metis_id = {307712},
month = {June},
booktitle = {Proc. Grid-Enabling Legacy Applications and Supporting End Users Workshop within the framework 15th IEEE International Symposium on High Performance Distributed Computing (HPDC.15)},
keywords = {WP7},
address = {Paris, France}
}
@article{Wiersma2006a,
title = {The Effect of Pre-Main-Sequence Stars on Star Cluster Dynamics},
author = {R. Wiersma and A.I. Sills and S.F. Portegies Zwart},
year = {2006},
journal = {Astrophys. J.},
volume = {637},
pages = {838--849},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006ApJ...637..838W\&db_key=AST},
month = {Feb},
category = {astronomy},
doi = {10.1086/498562}
}
@mastersthesis{Woudenberg2006a,
title = {Using FPGAs to Speed Up Cellular Automata Computations},
author = {M. van Woudenberg},
year = {2006},
url = {Woudenberg2006a.pdf},
month = {August},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
tutor = {Advisor: A.G. Hoekstra},
address = {Amsterdam, the Netherlands}
}
@mastersthesis{Wu2006a,
title = {Implementing microthreaded microprocessors in VHDL},
author = {J. Wu},
year = {2006},
url = {Wu2006a.pdf},
month = {August},
category = {csa, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: C.R. Jesshope}
}
@mastersthesis{Yang2006a,
title = {A Service-Oriented Visualization of Medical Data},
author = {N. Yang},
year = {2006},
url = {Yang2006a.pdf},
month = {August},
category = {csa, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: E.V. Zudilova-Seinstra}
}
@article{Yungelson2006a,
title = {The origin and fate of short-period low-mass black-hole binaries},
author = {L.R. Yungelson and J.-P. Lasota and G.A. Nelemans and G. Dubus and E.P.J. van den Heuvel and J.D.M. Dewi and S.F. Portegies Zwart},
year = {2006},
journal = {Astron. Astrophys.},
volume = {454},
pages = {559-569},
metis_id = {265178},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006A%26A...454..559Y\&db_key=AST},
month = {aug},
category = {Astronomy},
doi = {10.1051/0004-6361:20064984}
}
@article{Yurkin2006a,
title = {Convergence of the discrete dipole approximation. I. Theoretical analysis},
author = {M.A. Yurkin and V.P. Maltsev and A.G. Hoekstra},
year = {2006},
journal = {Journal of Optical Society of America A},
volume = {23},
number = {10},
pages = {2578-2591},
metis_id = {264554},
url = {http://josaa.osa.org/abstract.cfm?id=103799},
category = {Nato-sfp}
}
@article{Yurkin2006b,
title = {Convergence of the discrete dipole approximation. II. An extrapolation technique to increase the accuracy},
author = {M.A. Yurkin and V.P. Maltsev and A.G. Hoekstra},
year = {2006},
journal = {Journal of Optical Society of America A},
volume = {23},
number = {10},
pages = {2592-2601},
metis_id = {264555},
url = {http://josaa.osa.org/abstract.cfm?id=103800},
category = {Nato-sfp}
}
@inproceedings{Yurkin2006c,
title = {Can the Discrete Dipole Approximation Simulate Scattering of Particles with Size Parameter equal to 100?},
author = {M.A. Yurkin and V.P. Maltsev and A.G. Hoekstra},
year = {2006},
pages = {279--282},
metis_id = {264556},
url = {http://www.astro.spbu.ru/ELS9/ELS9-22.pdf},
month = {June},
category = {Nato-sfp, ElastLightScat},
booktitle = {Proceedings of 9th International Conference on Electromagnetic and Light Scattering by Non-Spherical Particles},
address = {Saint Peterburg, Russia},
issn_isbn = {ISBN 5-9651-0210-0}
}
@inproceedings{Yurkin2006d,
title = {An Extrapolation Technique to Increase the Accuracy of The Discrete Dipole Approximation},
author = {M.A. Yurkin and A.G. Hoekstra},
year = {2006},
pages = {283--286},
metis_id = {259756},
url = {http://www.astro.spbu.ru/ELS9/ELS9-22.pdf},
month = {June},
category = {Nato-sfp, ElastLightScat},
booktitle = {Proceedings of 9th International Conference on Electromagnetic and Light Scattering by Non-Spherical Particles},
address = {Saint Peterburg, Russia},
issn_isbn = {ISBN 5-9651-0210-0}
}
@article{Zudilova-Seinstra2006a,
title = {Ondersteuning van wetenschappelijk onderzoek},
author = {E.V. Zudilova-Seinstra},
year = {2006},
journal = {IT Monitor},
volume = {2},
pages = {4--6},
month = {February},
category = {Visualisation},
publisher = {Sdu uitgevers},
note = {in Dutch},
issn_isbn = {ISSN 1386-2871}
}
@inproceedings{Zudilova-Seinstra2006b,
title = {Combining Visualisation and Interaction to Facilitate Scientific Exploration and Discovery},
author = {E.V. Zudilova-Seinstra and T. Adriaansen},
year = {2006},
pages = {260-263},
month = {September},
category = {Visualisation},
booktitle = {Proc. of the 20th BCS HCI Group conference in co-operation with ACM "HCI 2006: Engage!"},
address = {London, UK},
issn_isbn = {ISSN 1470-5559}
}
@article{Zudilova-Seinstra2006c,
title = {Combining desktop and virtual realities. Addressing demands of real life clinical environments},
author = {E.V. Zudilova-Seinstra},
year = {2006},
journal = {Interfaces},
volume = {67},
pages = {11-13},
category = {Visualisation},
publisher = {British HCI Group},
issn_isbn = {ISSN 1351-119X}
}
@inproceedings{Abrahamyan2005a,
title = {A Problem Solving Environment for Image-Based Computational Hemodynamics},
author = {L. Abrahamyan and J.A. Schaap and A.G. Hoekstra and D.P. Shamonin and F.M.A. Box and R.J. van der Geest and J.H.C. Reiber and P.M.A. Sloot},
year = {2005},
volume = {3514},
pages = {287--294},
metis_id = {244235},
url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/11428831_36},
month = {May},
category = {LBM},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2005: 5th International Conference, Atlanta, GA, USA, Proceedings, Part I},
editor = {V.S. Sunderam and G.D. van Albada and P.M.A. Sloot and J.J. Dongarra},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-26032-3}
}
@inproceedings{Abramson2005a,
title = {Flexible IO services in the Kepler Grid Workflow System},
author = {D. Abramson and J. Kommineni and I. Altintas},
year = {2005},
metis_id = {252441},
month = {December},
booktitle = {Proceedings of the 1st E-Science Conference},
organization = {E-Science Conference, Melbourne, Australia},
abstract = {Existing Grid workflow tools assume that individual components either communicate by passing files from one application to another, or are explicitly linked using interprocess communication pipes. When files are used it is usually difficult to overlap reader and write execution. On the other hand, interprocess communication primitives are invasive and require substantial modification to existing code. We have built a library, called GriddLeS, that combines the advantages of both approaches without any changes to the application code. GriddLeS overloads conventional file IO operations, and supports either local, remote or replicated file access, or direct communication over pipes. In this paper we discuss how GriddLeS can be combined with workflow packages and show how flexible and powerful virtual applications can be constructed rapidly. A large atmospheric science case study is discussed.},
address = {Melbourne, Australia}
}
@inproceedings{Altintas2005a,
title = {A Framework for the Design and Reuse of Grid Workflows},
author = {I. Altintas and A. Birnbaum and K.K. Baldridge and W. Sudholt and M. Miller and C. Amoreira and Y. Potier and B. Lud\"ascher},
year = {2005},
number = {3},
pages = {119-132},
url = {http://www.springerlink.com/(mct5q5nzppet5j45vhsrctyz)/app/home/contribution.asp?referrer=parent\&backto=issue,11,18;journal,352,2319;linkingpublicationresults,1:105633,1},
publisher = {Springer-Verlag GmbH},
series = {Lecture Notes in Computer Science},
booktitle = {Scientific Applications of Grid Computing: First International Workshop, SAG 2004, Beijing, China, September 20-24, 2004, Revised Selected and Invited},
abstract = {Grid workflows can be seen as special scientific workflows involving high performance and/or high throughput computational tasks. Much work in grid workflows has focused on improving application performance through schedulers that optimize the use of computational resources and bandwidth. As high-end computing resources are becoming more of a commodity that is available to new scientific communities, there is an increasing need to also improve the design and reusability =93performance=94 of scientific workflow systems. To this end, we are developing a framework that supports the design and reuse of grid workflows. Individual workflow components (e.g., for data movement, database querying, job scheduling, remote execution etc.) are abstracted into a set of generic, reusable tasks. Instantiations of these common tasks can be functionally equivalent atomic components (called actors) or composite components (so-called composite actors or subworkflows). In this way, a grid workflow designer does not have to commit to a particular Grid technology when developing a scientific workflow; instead different technologies (e.g. GridFTP, SRB, and scp) can be used interchangeably and in concert. We illustrate the application of our framework using two real-world Grid workflows from different scientific domains, i.e., cheminformatics and bioinformatics, respectively.},
editor = {P. Herrero and M.S. P\'erez and V. Robles},
issn_isbn = {ISBN 3-540-25810-8}
}
@inproceedings{Badia2005a,
title = {Lightweight Grid Platform: Design Methodology},
author = {R.M. Badia and O. Beckmann and M.T. Bubak and D. Caromel and V.S. Getov and S. Isaiadis and V. Lazarov and M. Malawski and S. Panagiotidi and J. Thiyagalingam},
year = {2005},
metis_id = {307713},
booktitle = {CoreGRID Integration WorkShop 2005},
note = {Also published as CoreGRID Technical Report TR-0020},
keywords = {WP7}
}
@inproceedings{Badia2005b,
title = {Performance monitoring of GRID superscalar applications with OCM-G},
author = {R.M. Badia and M.T. Bubak and W. Funika and M. Smetek},
year = {2005},
pages = {229--236},
metis_id = {307714},
publisher = {Universit\'a di Pisa. Dipartimento di Informatica},
booktitle = {CoreGRID Integration WorkShop 2005},
editor = {S. Gorlatch and M. Danelutto},
keywords = {WP7}
}
@article{Baldridge2005a,
title = {The Computational Chemistry Prototyping Environment},
author = {K.K. Baldridge and J.P. Greenberg and W. Sudholt and S. Mock and I. Altintas and C. Amoreira and Y. Potier and A. Birnbaum and K. Bhatia and M. Taufer},
year = {2005},
journal = {Proceedings of the IEEE},
volume = {93},
number = {3},
pages = {510-521},
url = {http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1398007},
month = {March},
publisher = {John Wiley \& Sons},
abstract = {Evolving technologies, as exemplified by computational grids and Web services, have made it possible to solve new scientific problems that would not have been feasible previously. In order to make such advances available to the community in general and to be able to solve new problems, not necessarily from the same discipline, it is imperative to build tools that provide a common user interface in order that application programmers and users do not have to be concerned with particulars of Web services and their underlying code, computational platforms, or with data file formats. We will describe our efforts in creating a computational chemistry environment that encompasses a general scientific workflow environment, a domain specific example for quantum chemistry, our ongoing design of a workflow user interface, and our efforts at database integration.},
editor = {A.Y. Zomaya (Ed.)}
}
@misc{Belleman2005a,
title = {Simulation, visualisation, interaction and mixed reality: views of the University of Amsterdam and SARA},
author = {R.G. Belleman and P.M.A. Sloot and E.V. Zudilova-Seinstra and A. Osseyran},
year = {2005},
metis_id = {253635},
category = {Visualisation},
note = {Position paper at the EU workshop on Simulation, Visualisation, Interaction and Mixed Reality}
}
@incollection{Bucur2005a,
title = {A Grid Architecture for Medical Applications},
author = {A. Bucur and R. Kootstra and R.G. Belleman},
year = {2005},
volume = {112},
pages = {127-137},
metis_id = {296251},
url = {Bucur2005a.pdf},
publisher = {IOS Press},
booktitle = {From Grid to Healthgrid: Proceedings of Healthgrid 2005},
issn_isbn = {ISBN 1-58603-510-X}
}
@inproceedings{Gomes2005a,
title = {Experience with the International Testbed in the CrossGrid Project},
author = {J. Gomes and M. David and J. Martins and L. Bernardo and A. Garc\'{\i}a and M. Hardt and H. Kornmayer and J. Marco and R. Marco and D. Rodr\'{\i}guez and I. Diaz and D. Cano and J. Salt and S. Gonzalez and J. S\'anchez and F. Fassi and V. Lara and P. Nyczyk and P. Lason and A. Ozieblo and P. Wolniewicz and M. Bluj and K. Nawrocki and A. Padee and W. Wislicki and C. Fern\'andez and J. Font\'an and Y. Cotronis and E. Floros and G. Tsouloupas and W. Xing and M.D. Dikaiakos and J. Astalos and B. Coghlan and E. Heymann and M. Senar and C. Kanellopoulos and A. Tirado Ramos and D.J. Groen},
year = {2005},
volume = {3470},
pages = {98--110},
metis_id = {244237},
month = {February 14-16},
category = {LBM},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Advances in Grid Computing - EGC 2005},
editor = {P.M.A. Sloot and A.G. Hoekstra and T. Priol and A. Reinefeld and M.T. Bubak},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-26918-5}
}
@inproceedings{Gomes2005b,
title = {Organization of the International Testbed of the CrossGrid Project},
author = {J. Gomes and M. David and J. Martins and L. Bernardo and A. Garc\'{\i}a and M. Hardt and H. Kornmayer and J. Marco and R. Marco and D. Rodr\'{\i}guez and I. Diaz and D. Cano and J. Salt and S. Gonzalez and J. S\'anchez and F. Fassi and V. Lara and P. Nyczyk and P. Lason and A. Ozieblo and P. Wolniewicz and M. Bluj and K. Nawrocki and A. Padee and W. Wislicki and C. Fern\'andez and J. Font\'an and Y. Cotronis and E. Floros and G. Tsouloupas and W. Xing and M.D. Dikaiakos and J. Astalos and B. Coghlan and E. Heymann and M. Senar and C. Kanellopoulos and D.J. Groen and A. Tirado Ramos},
year = {2005},
metis_id = {252840},
month = {November},
category = {Grid},
booktitle = {Cracow Grid Workshop 2005},
editor = {Sloot,P.M.A. and Hoekstra,A.G. and Priol,T. and Reinefeld,A. and Bubak,M.},
address = {Cracow, Poland}
}
@article{Gualandris2005a,
title = {Has the Black Hole in XTE J1118+480 Experienced an Asymmetric Natal Kick?},
author = {A. Gualandris and M. Colpi and S.F. Portegies Zwart and A. Possenti},
year = {2005},
journal = {Astrophys. J.},
volume = {618},
number = {2},
pages = {845-851},
metis_id = {242512},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2005ApJ...618..845G\&db_key=AST},
month = {jan},
category = {astronomy}
}
@article{Gualandris2005b,
title = {Three-body encounters in the Galactic Centre: the origin of the hypervelocity star SDSS J090745.0+024507},
author = {A. Gualandris and S.F. Portegies Zwart and M.S. Sipior},
year = {2005},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {363},
pages = {223--228},
metis_id = {242511},
url = {http://cdsads.u-strasbg.fr/cgi-bin/nph-bib_query?bibcode=2005MNRAS.363..223G\&db_key=AST},
month = {October},
note = {doi: 10.1111/j.1365-2966.2005.09433.x}
}
@inproceedings{Hoekstra2005a,
title = {Introducing Grid Speedup Gamma: A Scalability Metric for Parallel Applications on the Grid},
author = {A.G. Hoekstra and P.M.A. Sloot},
year = {2005},
volume = {3470},
pages = {245--249},
url = {Hoekstra2005a.pdf},
month = {February 14-16},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Advances in Grid Computing - EGC 2005},
editor = {P.M.A. Sloot and A.G. Hoekstra and T. Priol and A. Reinefeld and M.T. Bubak},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-26918-5}
}
@inproceedings{Hoekstra2005b,
title = {Image-based computational hemodynamics with the Lattice Boltzmann Method},
author = {A.G. Hoekstra},
year = {2005},
pages = {672-675},
metis_id = {244230},
category = {LBM},
publisher = {Elsevier Ltd},
booktitle = {Computational Fluid and Solid Mechanics 2005},
editor = {K.J. Bathe}
}
@article{Hopman2005a,
title = {Gravitational waves from remnants of ultraluminous X-ray sources},
author = {C. Hopman and S.F. Portegies Zwart},
year = {2005},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {363},
pages = {L56-L60},
metis_id = {242706},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2005MNRAS.363L..56H\&db_key=AST},
month = {Oct},
category = {astronomy},
doi = {10.1111/j.1745-3933.2005.00083.x}
}
@mastersthesis{Huo2005a,
title = {A Projection and Its Implementation of a Ruby Subset to Program Algebra},
author = {R. Huo and Q. He},
year = {2005},
url = {Huo2005a.pdf},
month = {August},
category = {prg, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisors: I. Bethke and A. Ponse}
}
@article{Iskra2005a,
title = {Towards Grid-Aware Time Warp},
author = {K.A. Iskra and G.D. van Albada and P.M.A. Sloot},
year = {2005},
journal = {Simulation: Transactions of The Society for Modeling and Simulation International},
volume = {81},
number = {4},
pages = {293--306},
metis_id = {244229},
url = {http://sim.sagepub.com/cgi/content/abstract/81/4/293},
month = {April},
category = {TimeWarp}
}
@phdthesis{Iskra2005b,
title = {Time Warp -- from Cluster to Grid},
author = {K.A. Iskra},
year = {2005},
metis_id = {244228},
url = {Iskra2005b.pdf},
month = {June},
category = {Dynamite, TimeWarp, pwrs, phdthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. G.D. van Albada}
}
@inproceedings{Jaeger-Frank2005a,
title = {Integrating Seismic Events Focal Mechanisms with Image Services in Kepler},
author = {E. Jaeger-Frank and A. Memon and I. Altintas and G. Memon and D. Seber and B. Lud\"ascher and C. Baru},
year = {2005},
month = {July},
booktitle = {Proceedings of the Twenty-fifth Annual ESRI International User Conference},
abstract = {Geosciences Network (GEON) is a grand-challenge project to prototype cyberinfrastructure for the Earth Sciences. GEON is building a mechanism for integration and visualization of seismic events and their related fault orientations--referred by seismologists as focal mechanisms (or "beach balls") with other image (map) services using a service oriented architecture (SOA). The Kepler scientific workflow system provides capabilities to harvest and query datasets and services and process data using local and remote services. Using a workflow, we can combine the harvested datasets (such as seismic event locations) or map services of various formats with matching beach ball symbols, retrieved from a beach ball images database, for seismic events. The result is processed into a new dataset, using an ASCII to shapefile service, and integrated and visualized with other image services using ArcIMS. The new dataset can also be registered and searched within the GEONsearch registry.},
address = {San Diego, CA}
}
@inproceedings{Jaeger2005a,
title = {A Scientific Workflow Approach to Distributed Geospatial Data Processing using Web Services},
author = {E. Jaeger and I. Altintas and J. Zhang and B. Lud\"ascher and D. Pennington and W. Michener},
year = {2005},
metis_id = {252848 abstract = Geospatial analyses of distributed data from surveys and sensors are often stored and managed in diverse regional, national and global repositories. The nature of scientific processes require composition of these resources in a meaningful order to solve a specific geoscience problem. These tasks can be viewed as scientific workflows. Web based interfaces allow access to remote data and tools, and enable running computational experiments using different online resources. However, it requires manual processing to combine multiple resources in pipelines and scientists still need IT experts to automate their large-scale scientific workflows. The challenging problem is how to enable the scientists to harvest online data and models for designing and executing their experiments in a seamless manner. A solution becomes feasible by the introduction of Web and Grid Services in a variety of scientific domains. These services can be discovered and composed through generic visual interfaces and scientific workflow tools. For this purpose, we present a complete framework for creating, registering, discovering, composing and executing Web Services to support online science.},
month = {June},
booktitle = {Proceedings of the 17th Intl. Conference on Scientific and Statistical Database Management(SSDBM)},
address = {Santa Barbara, CA}
}
@article{Kaandorp2005a,
title = {Morphogenesis of the branching reef coral Madracis mirabilis},
author = {J.A. Kaandorp and P.M.A. Sloot and R.M.H. Merks and R.P.M. Bak and M.J.A. Vermeij and C. Maier},
year = {2005},
journal = {Proc. Roy. Soc. B},
volume = {272},
number = {1559},
pages = {127--133},
metis_id = {234030},
url = {http://www.journals.royalsoc.ac.uk/openurl.asp?genre=article\&id=doi:10.1098/rspb.2004.2934},
month = {January},
category = {bioinformatics}
}
@misc{Kaandorp2005b,
title = {'De witte dood': about coral bleaching and simulation models},
author = {J.A. Kaandorp},
year = {2005}
}
@article{Kaluzhnaya2005a,
title = {Dynamics of skeletal formation in the Lake Baikal sponge \em Lubomirskia baicalensis\/. Part I biological and biochemical studies},
author = {O.V. Kaluzhnaya and S.I. Belikov and H.C. Schr\"oder and S. Zapf and A. Borejko and J.A. Kaandorp and A. Krasko and I.M. M\"uller and W.E.G. M\"uller},
year = {2005},
journal = {Naturwissenschaften},
volume = {92},
pages = {128--133},
metis_id = {245631},
url = {http://www.springerlink.com/index/10.1007/s00114-004-0599-4},
category = {bioinformatics}
}
@inproceedings{Korneev2005a,
title = {Methods of Object-Oriented Reactive Agents Implementation on the Basis of Finite Automata},
author = {G. Korneev and L.A. Naumov and A.A. Shalyto},
year = {2005},
pages = {460--465},
metis_id = {252858},
category = {Automata},
publisher = {IEEE},
booktitle = {Proceedings of 2005 International Conference on "Integration of Knowledge Intensive Multiagent Systems. KIMAS'05: Modeling, Exploration, and Engineering"},
organization = {IEEE, Boston},
address = {Boston}
}
@article{Kouwenhoven2005a,
title = {The primordial binary population. I. A near-infrared adaptive optics search for close visual companions to A star members of Scorpius OB2},
author = {M.B.N. Kouwenhoven and A.G.A. Brown and H. Zinnecker and L. Kaper and S.F. Portegies Zwart},
year = {2005},
journal = {Astron. Astrophys.},
volume = {430},
pages = {137--154},
metis_id = {244227},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2005A%26A...430..137K\&db_key=AST},
month = {jan},
category = {astronomy}
}
@inbook{Kouwenhoven2005b,
title = {A search for close companions in Sco OB2},
author = {M.B.N. Kouwenhoven and A.G.A. Brown and H. Zinnecker and L. Kaper and S.F. Portegies Zwart and A. Gualandris},
year = {2005},
pages = {203--205},
metis_id = {276730},
category = {astronomy},
publisher = {Springer},
doi = {10.1007/10828557_33},
booktitle = {Science with Adaptive Optics}
}
@article{Kromkamp2005a,
title = {Shear-induced self-diffusion and microstructure in non-Brownian suspensions at non-zero Reynolds numbers},
author = {J. Kromkamp and D. van den Ende and B.D. Kandhai and R.G.M. Sman and R.M. Boom},
year = {2005},
journal = {J. Fluid Mech},
volume = {529},
pages = {253-278},
metis_id = {265088},
url = {http://journals.cambridge.org/action/displayAbstract?fromPage=online\&aid=292782},
month = {April},
doi = {doi:10.1017/S0022112005003551}
}
@inproceedings{Kruszynski2005a,
title = {Quantifying performance of 3D skeletonization algorithms},
author = {K.J. Kruszynski and R. van Liere and J.A. Kaandorp},
year = {2005},
metis_id = {252861},
url = {http://homepages.cwi.nl/~robertl/papers/2005/viip2/paper.pdf},
month = {September},
category = {Visualisation},
booktitle = {IASTED International Conference on Visualization, Imaging, and Image Processing (VIIP 2005)},
organization = {VIIP 2005, Benidorm, Spain},
address = {Benidorm, Spain}
}
@article{Krzhizhanovskaya2005a,
title = {Grid-based Simulation of Industrial Thin Film Production},
author = {V.V. Krzhizhanovskaya and P.M.A. Sloot and Y.E. Gorbachev},
year = {2005},
journal = {Simulation: Transactions of the Society for Modeling and Simulation International},
volume = {81},
number = {1},
pages = {77--85},
metis_id = {222843},
url = {http://sim.sagepub.com/cgi/content/abstract/81/1/77},
month = {January},
category = {PECVD, PSE, Grid, HLA},
note = {Special Issue on Applications of Parallel and Distributed Simulation},
doi = {10.1177/0037549705051972},
issn_isbn = {ISSN 0037-5497}
}
@inproceedings{Kvaly2005a,
title = {Automatic Composition and Selection of Semantic Web Services},
author = {T.A. Kval\oy and E. Rongen and A. Tirado Ramos and P.M.A. Sloot},
year = {2005},
volume = {3470},
pages = {184--192},
metis_id = {245638},
month = {February 14-16},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Advances in Grid Computing - EGC 2005},
editor = {P.M.A. Sloot and A.G. Hoekstra and T. Priol and A. Reinefeld and M.T. Bubak},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-26918-5}
}
@article{Lamers2005a,
title = {Disruption time scales of star clusters in different galaxies},
author = {H.J.G.L.M. Lamers and M. Gieles and S.F. Portegies Zwart},
year = {2005},
journal = {Astron. Astrophys.},
volume = {429},
pages = {173--179},
metis_id = {242711},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2005A%26A...429..173L\&db_key=AST},
month = {Jan},
category = {astronomy},
doi = {10.1051/0004-6361:20041476}
}
@mastersthesis{Leskes2005a,
title = {The Value of Agreement - a new boosting algorithm},
author = {B. Leskes},
year = {2005},
url = {Leskes2005a.pdf},
month = {February},
category = {pwrs, mastersthesis, ComputationalScience, Logic},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisors: L. Torenvliet and P. Grunwald and P. Adriaans and P. van Emde Boas}
}
@article{Lommen2005a,
title = {Cygnus X-3 and the problem of the missing Wolf-Rayet X-ray binaries},
author = {D. Lommen and L.R. Yungelson and E.P.J. van den Heuvel and G.A. Nelemans and S.F. Portegies Zwart},
year = {2005},
journal = {Astron. Astrophys.},
volume = {443},
pages = {231--241},
metis_id = {244453},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2005A%26A...443..231L\&db_key=AST},
month = {Nov},
category = {astronomy},
doi = {10.1051/0004-6361:20052824}
}
@article{Ludscher2005a,
title = {Scientific Workflow Management and the Kepler System},
author = {B. Lud\"ascher and I. Altintas and C. Berkley and D. Higgins and E. Jaeger-Frank and M. Jones and E. Lee and J. Tao and Y. Zhao},
year = {2005},
journal = {Concurrency and Computation: Practice \& Experience},
volume = {Special Issue on Scientific Workflows},
metis_id = {252398},
abstract = {A system paper on Kepler. Explains the requirements for such a system, capabilities and research issues.}
}
@mastersthesis{Manchego2005a,
title = {Methodologies of Retrieval, Management and Mediation of Sensor Data},
author = {P.J. Manchego},
year = {2005},
url = {Manchego2005a.pdf},
month = {November},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisors: R.J. Meijer and G.D. van Albada}
}
@article{McMillan2005a,
title = {Stellar Collisions in Young Star Clusters},
author = {S.L.W. McMillan and S.F. Portegies Zwart},
year = {2005},
journal = {AAS/Division of Dynamical Astronomy Meeting},
volume = {36},
metis_id = {242708},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2005DDA....36.0513M\&db_key=AST},
month = {may},
category = {astronomy},
note = {abstract}
}
@article{Merks2005a,
title = {Droogzwemmen in het koraalrif. Computersimulaties verklaren koraalgroei},
author = {R.M.H. Merks},
year = {2005},
journal = {Nederlands Tijdschrift voor Natuurkunde},
volume = {71},
number = {10},
pages = {314--317},
metis_id = {276731},
note = {in Dutch}
}
@article{Muno2005a,
title = {A Neutron Star with a Massive Progenitor in the Star Cluster Westerlund 1},
author = {M.P. Muno and J.S. Clark and P.A. Crowther and S.M. Dougherty and R. de Grijs and C. Law and S.L.W. McMillan and M.R. Morris and I. Negueruela and D. Pooley and S.F. Portegies Zwart and F. Yusef-Zadeh},
year = {2005},
journal = {American Astronomical Society Meeting Abstracts},
volume = {207},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2005AAS...207.9103M\&db_key=AST},
month = {dec},
category = {astronomy},
note = {abstract}
}
@inproceedings{Naumov2005a,
title = {New Version of the Networking Protocol for High-Performance Computations CTP (Commands Transfer Protocol) v. 1.2},
author = {L.A. Naumov},
year = {2005},
volume = {1},
pages = {92--93},
metis_id = {252873},
url = {http://www.camellab.spb.ru/utils/dl.jsp?tgt=/pubs/2005/CTP12.TM.pdf},
category = {ClusterNetworking},
publisher = {SPbSU ITMO},
note = {in Russian},
booktitle = {Proceedings of X All-Russian Guidance Conference "Telematics'2005"},
address = {Saint-Petersburg}
}
@inproceedings{Naumov2005b,
title = {Advantages of Using Generalized Coordinates for Multidimensional Cellular Automata Grids},
author = {L.A. Naumov},
year = {2005},
volume = {1},
pages = {93--95},
metis_id = {296252},
url = {http://www.camellab.spb.ru/utils/dl.jsp?tgt=/pubs/2005/AdvGen.TM.pdf},
category = {CA},
publisher = {SPbSU ITMO},
note = {in Russian},
booktitle = {Proceedings of X All-Russian Guidance Conference "Telematics'2005"},
address = {Saint-Petersburg}
}
@article{Naumov2005c,
title = {Classification of Structures Generated by One-Dimensional Binary Cellular Automata from a Point Embryo},
author = {L.A. Naumov and A.A. Shalyto},
year = {2005},
journal = {Journal of Computer and Systems Sciences International},
volume = {44},
number = {5},
pages = {800--807},
metis_id = {252402},
url = {http://www.camellab.spb.ru/utils/dl.jsp?tgt=/pubs/2005/Class.en.pdf},
category = {CA},
address = {Moscow}
}
@article{Naumov2005d,
title = {Solving Tasks with Cellular Automata using CAMEL Software. Part 1},
author = {L.A. Naumov},
year = {2005},
journal = {Informational Control Systems},
volume = {2005},
number = {5},
pages = {22--30},
metis_id = {252413},
url = {http://www.camellab.spb.ru/utils/dl.jsp?tgt=/pubs/2005/Solving1.pdf},
category = {CA},
note = {in Russian},
address = {Saint-Petersburg}
}
@article{Naumov2005e,
title = {Solving Tasks with Cellular Automata using CAMEL Software. Part 2},
author = {L.A. Naumov},
year = {2005},
journal = {Informational Control Systems},
volume = {2005},
number = {6},
pages = {30--38},
metis_id = {252414},
url = {http://www.camellab.spb.ru/utils/dl.jsp?tgt=/pubs/2005/Solving2.pdf},
category = {CA},
note = {in Russian},
address = {Saint-Petersburg}
}
@mastersthesis{Nguyen2005a,
title = {Robust tracking of input props with webcams},
author = {D.Q.A. Nguyen},
year = {2005},
url = {Nguyen2005a.pdf},
month = {July},
category = {csp, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: R. van Liere}
}
@misc{Portegies_Zwart2005a,
title = {Explanation for the existance of a planet in a triple star system},
author = {S.F. Portegies Zwart},
year = {2005}
}
@article{Portegies_Zwart2005b,
title = {Erratum: Intermediate mass black holes in accreting binaries: formation, evolution and observational appearance},
author = {S.F. Portegies Zwart and J.D.M. Dewi and T.J. Maccarone},
year = {2005},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {357},
pages = {1104--1104},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2005MNRAS.357.1104P\&db_key=AST},
month = {Mar},
category = {astronomy},
doi = {10.1111/j.1365-2966.2004.08550.x}
}
@article{Porubov2005a,
title = {On some localized waves described by the extended KdV equation},
author = {A.V. Porubov and G.A. Maugin and V.V. Gursky and V.V. Krzhizhanovskaya},
year = {2005},
journal = {Comptes Rendus M\'ecanique},
volume = {333},
number = {7},
pages = {528--533},
metis_id = {252416},
url = {http://dx.doi.org/10.1016/j.crme.2005.06.003},
month = {July},
category = {Soliton},
doi = {10.1016/j.crme.2005.06.003}
}
@article{Rohde2005a,
title = {A generic, mass conservative local grid refinement technique for lattice-Boltzmann schemes},
author = {M. Rohde and B.D. Kandhai and J.J. Derksen and H.E.A. van den Akker},
year = {2005},
journal = {Int. J. Num. Meth. Fluids},
volume = {51},
pages = {439-468},
url = {http://www3.interscience.wiley.com/cgi-bin/fulltext/112210359/PDFSTART},
month = {December},
doi = {10.1002/fld.1140}
}
@article{Rycerz2005a,
title = {A Framework for HLA-Based Interactive Simulations on the Grid},
author = {K.J. Rycerz and M.T. Bubak and M. Malawski and P.M.A. Sloot},
year = {2005},
journal = {Simulation: Transactions of The Society for Modeling and Simulation International},
volume = {81},
number = {1},
pages = {67--76},
metis_id = {245633},
url = {http://sim.sagepub.com/cgi/content/abstract/81/1/67},
month = {April},
category = {Grid, HLA, OGSA},
note = {Special Issue on Applications of Parallel and Distributed Simulation}
}
@inproceedings{Rycerz2005b,
title = {HLA Grid based support for simulation of vascular reconstruction},
author = {K.J. Rycerz and M.T. Bubak and M. Malawski and P.M.A. Sloot},
year = {2005},
pages = {165--174},
metis_id = {252878},
url = {Rycerz2005b.pdf},
month = {November},
publisher = {University of Pisa, Computer Science Department},
booktitle = {TR-05-22, Proceedings of the CoreGRID Workshop "Integrated Research in Grid Computing"},
editor = {S. Gorlatch and M. Danelutto},
address = {Pisa}
}
@misc{Sloot2005a,
title = {Preface},
author = {P.M.A. Sloot},
year = {2005},
journal = {Future Generation Computer Systems},
volume = {21},
number = {1},
pages = {1--2},
url = {http://dx.doi.org/10.1016/j.future.2004.09.015},
month = {January},
category = {editorial}
}
@misc{Sloot2005b,
title = {Research on Cellular Automata},
author = {P.M.A. Sloot},
year = {2005},
url = {http://www.science.uva.nl/research/scs/oud/News/salto.avi},
note = {20 minute documentary}
}
@inproceedings{Sloot2005c,
title = {VIROLAB - A Virtual Laboratory for Decision Support in Viral Diseases Treatment},
author = {P.M.A. Sloot and C.A.B. Boucher and M.T. Bubak and A.G. Hoekstra and P. Plaszczak and A. Posthumus and D.A.M.C. van de Vijver and S. Wesner and A. Tirado Ramos},
year = {2005},
pages = {33},
url = {Sloot2005e.pdf},
month = {November},
category = {Virolab},
numpages = {1},
booktitle = {Cracow Grid Workshop 2005},
note = {best poster award},
address = {Cracow, Poland}
}
@inproceedings{Sloot2005d,
title = {A Grid-based HIV Expert System},
author = {P.M.A. Sloot and A.V. Boukhanovsky and W. Keulen and C.A.B. Boucher},
year = {2005},
metis_id = {245634},
url = {http://shop.ieee.org/ieeestore/Product.aspx?product_no=EX1055C},
month = {May},
category = {Grid, HIV, bioinformatics},
publisher = {IEEE},
booktitle = {Proceedings of the 5th International Symposium on Cluster Computing and Grid, CCGrid},
note = {IEEE product number: EX1055C},
address = {Cardiff, Wales, UK},
issn_isbn = {ISBN: 0-7803-9075-X}
}
@article{Sloot2005e,
title = {A Grid-based HIV Expert System},
author = {P.M.A. Sloot and A.V. Boukhanovsky and W. Keulen and A. Tirado Ramos and C.A.B. Boucher},
year = {2005},
journal = {Journal of Clinical Monitoring and Computing},
volume = {19},
number = {4--5},
url = {Sloot2005c.pdf},
month = {October},
category = {Grid, HIV, bioinformatics},
issn_isbn = {ISSN: 11387-1307}
}
@proceedings{Sloot2005f,
author = {P.M.A. Sloot and A.G. Hoekstra and T. Priol and A. Reinefeld and M.T. Bubak},
year = {2005},
volume = {3470},
metis_id = {244224},
month = {February 14-16},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Advances in Grid Computing - EGC 2005},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-26918-5}
}
@article{Sloot2005g,
title = {Towards Virtual Physiological Human: Multilevel Modelling and Simulation of the Human Anatomy and Phsyiology},
author = {P.M.A. Sloot and J.A. Kaandorp and A.G. Hoekstra},
year = {2005},
url = {2005_VPH_white_paper.pdf},
month = {November}
}
@inproceedings{Strokotov2005a,
title = {Identification of blood cells subpopulations from angle resolved light scattering},
author = {D.I. Strokotov and I.G. Skribunov and M.A. Yurkin and D.R. van Bockstaele and M. Lenjou and K.A. Semyanov},
year = {2005},
pages = {48-49},
metis_id = {296253},
url = {http://cyto.kinetics.nsc.ru/OBP/abstracts.pdf},
month = {October},
category = {ElastLightScat, Nato-sfp},
booktitle = {Proceedings of the NATO Advanced Research Workshop: Optics of Biological Particles},
address = {Novosibirsk,Russia}
}
@proceedings{Sunderam2005a,
author = {V.S. Sunderam and G.D. van Albada and P.M.A. Sloot and J. Dongarra},
year = {2005},
volume = {3516},
url = {http://www.springerlink.com/openurl.asp?genre=volume\&id=doi:10.1007/b136575},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2005: 5th International Conference, Atlanta, GA, USA, Proceedings, Part III},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-26044-7}
}
@proceedings{Sunderam2005b,
author = {V.S. Sunderam and G.D. van Albada and P.M.A. Sloot and J. Dongarra},
year = {2005},
volume = {3515},
url = {http://www.springerlink.com/openurl.asp?genre=volume\&id=doi:10.1007/b136571},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2005: 5th International Conference, Atlanta, GA, USA, Proceedings, Part II},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-26043-9}
}
@proceedings{Sunderam2005c,
author = {V.S. Sunderam and G.D. van Albada and P.M.A. Sloot and J. Dongarra},
year = {2005},
volume = {3514},
url = {http://www.springerlink.com/openurl.asp?genre=volume\&id=doi:10.1007/b136570},
month = {May},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2005: 5th International Conference, Atlanta, GA, USA, Proceedings, Part I},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-26032-3}
}
@inproceedings{Tirado-Ramos2005a,
title = {Performance of a Parallel Astrophysical N-body Solver on pan-European Computational Grids},
author = {A. Tirado Ramos and A. Gualandris and S.F. Portegies Zwart},
year = {2005},
volume = {3470},
pages = {534--543},
month = {February 14-16},
category = {Grid, astronomy},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Advances in Grid Computing - EGC 2005},
editor = {P.M.A. Sloot and A.G. Hoekstra and T. Priol and A. Reinefeld and M.T. Bubak},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-26918-5}
}
@inproceedings{Tirado-Ramos2005b,
title = {On-line Application Performance Monitoring of Blood Flow Simulation in Computational Grid Architectures},
author = {A. Tirado Ramos and D.J. Groen and P.M.A. Sloot},
year = {2005},
pages = {511--516},
month = {June 23-24},
category = {Grid, LBM},
booktitle = {The 18th IEEE Symposium on Computer-Based Medical Systems, special track Grids for Biomedicine and Bioinformatics},
address = {Trinity College Dublin, Ireland},
issn_isbn = {ISBN 0769523552}
}
@inproceedings{Tirado-Ramos2005c,
title = {Grid Resource Selection by Application Benchmarking: a Computational Haemodynamics Case Study},
author = {A. Tirado Ramos and G. Tsouloupas and M.D. Dikaiakos and P.M.A. Sloot},
year = {2005},
volume = {3514},
pages = {534--543},
url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/11428831_66},
month = {May},
category = {LBM},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2005: 5th International Conference, Atlanta, GA, USA, Proceedings, Part I},
editor = {V.S. Sunderam and G.D. van Albada and P.M.A. Sloot and J.J. Dongarra},
address = {Berlin, Heidelberg},
issn_isbn = {ISBN 3-540-26032-3}
}
@inbook{Tirado-Ramos2005d,
title = {Interactive Problem Solving Environments on the Grid for Image-based Computational Haemodynamics},
author = {A. Tirado Ramos and D.P. Shamonin and R.M. Shulakov and D.J. Groen and A.G. Hoekstra and G.D. van Albada and E.V. Zudilova and P.M.A. Sloot},
year = {2005},
category = {GrossGrid, Grid, PSE, LBM},
booktitle = {The CrossGrid Book},
note = {accepted 15 January 2004},
organization = {The European CrossGrid Consortium}
}
@inproceedings{Tirado-Ramos2005e,
title = {Exploring OGSA Interoperability with LCG-based Production Grids for Biomedical Applications},
author = {A. Tirado Ramos and D.J. Groen and P.M.A. Sloot},
year = {2005},
pages = {367--374},
url = {Tirado-Ramos2005e.pdf},
month = {November},
category = {Grid},
publisher = {Ekodruk},
booktitle = {Cracow Grid Workshop 2005},
editor = {M.T. Bubak and M. Turala and K. Wiatr},
address = {Cracow, Poland}
}
@mastersthesis{Vankov2005a,
title = {Relational Approach to Program Slicing},
author = {I. Vankov},
year = {2005},
url = {Vankov2005a.pdf},
month = {August},
category = {prg, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: P. Klint}
}
@article{Voogd2005a,
title = {Equilibrium spherically curved two-dimensional Lennard-Jones systems},
author = {J.M. Voogd and P.M.A. Sloot and R. van Dantzig},
year = {2005},
journal = {J. Chem. Phys.},
volume = {123},
number = {084105},
pages = {1--5},
metis_id = {244087},
url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=JCPSA6000123000008084105000001\&idtype=cvips\&gifs=Yes},
doi = {10.1063/1.2007707}
}
@mastersthesis{Vu2005a,
title = {IMEX/Finite Volume for chemical reactions in fluid flow},
author = {V.T. Vu},
year = {2005},
url = {Vu2005a.pdf},
month = {November},
category = {prg, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisors: J.G. Blom and J.A. Kaandorp}
}
@mastersthesis{Wang2005a,
title = {Microsimulation of Financial Markets},
author = {Z.-D. Wang},
year = {2005},
url = {Wang2005a.pdf},
month = {November},
category = {prg, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisors: B.D. Kandhai and G. Qiu and P.M.A. Sloot}
}
@inproceedings{Yurkin2005a,
title = {Applicability of effective medium approximation to light scattering by granulated biological cells - first results},
author = {M.A. Yurkin and D. de Kanter and A.G. Hoekstra},
year = {2005},
pages = {46-47},
url = {http://cyto.kinetics.nsc.ru/OBP/abstracts.pdf},
month = {October},
category = {Nato-sfp, ElastLightScat},
booktitle = {Proceedings of the NATO Advanced Research Workshop: Optics of Biological Particles},
address = {Novosibirsk,Russia},
issn_isbn = {ISBN 5-98901-002-8}
}
@inproceedings{Yurkin2005b,
title = {Experimental and Theoretical Study of Light Scattering by Individual Mature Red Blood Cells with Scanning Flow Cytometry and Discrete Dipole Approximation},
author = {M.A. Yurkin and K.A. Semyanov and A.G. Hoekstra and V.P. Maltsev},
year = {2005},
pages = {333--336},
metis_id = {243294},
url = {http://www.iaa.es/\tildeconfels8/8thBook.pdf},
month = {May},
category = {ElastLightScat, Nato-sfp},
booktitle = {Proceedings of the 8th Conference on Electromagnetic and Light Scattering by Nonspherical Particles: Theory, Measurement and Applications},
address = {Salobrena, Spain}
}
@article{Yurkin2005c,
title = {Experimental and theoretical study of light scattering by individual mature red blood cells with scanning flow cytometry and discrete dipole approximation},
author = {M.A. Yurkin and K.A. Semyanov and P.A. Tarasov and A.V. Chernyshev and A.G. Hoekstra and V.P. Maltsev},
year = {2005},
journal = {Applied Optics},
volume = {44},
number = {25},
pages = {5249-5256},
url = {http://ao.osa.org/abstract.cfm?id=84971},
category = {Nato-sfp, ElastLightScat}
}
@inproceedings{Yurkin2005d,
title = {Capabilities of the discrete dipole approximation for simulation light scattering by biological cells},
author = {M.A. Yurkin and A.G. Hoekstra},
year = {2005},
pages = {19-20},
metis_id = {253147},
url = {http://cyto.kinetics.nsc.ru/OBP/abstracts.pdf},
month = {October},
category = {Nato-sfp, ElastLightScat},
booktitle = {Proceedings of the NATO Advanced Research Workshop: Optics of Biological Particles},
organization = {Novosibirsk, Russia},
address = {Novosibirsk,Russia},
issn_isbn = {ISBN 5-98901-002-8}
}
@mastersthesis{Zhang2005a,
title = {Experimental Validation of the Grid Speedup Theory},
author = {Y.-G. Zhang},
year = {2005},
url = {Zhang2005a.pdf},
month = {July},
category = {csp, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: A.G. Hoekstra}
}
@inproceedings{Zhao2005a,
title = {Agent technology and scientific workflow management in an e-Science environment},
author = {Z. Zhao and A.S.Z. Belloum and P.M.A. Sloot and L.O. Hertzberger},
year = {2005},
pages = {19--23},
metis_id = {253169},
url = {http://csdl.computer.org/dl/proceedings/ictai/2005/2488/00/24880019.pdf},
month = {November 14th-16th},
publisher = {IEEE Computer Society Press},
booktitle = {Proceedings of the 17th IEEE International conference on Tools with Artificial Intelligence (ICTAI05)},
organization = {ICTAI '05},
address = {Hongkong, China}
}
@inproceedings{Zhao2005b,
title = {Scientific workflow management: between generality and applicability},
author = {Z. Zhao and A.S.Z. Belloum and A. Wibisono and F. Terpstra and P.T. de Boer and P.M.A. Sloot and L.O. Hertzberger},
year = {2005},
pages = {357--364},
url = {http://csdl.computer.org/dl/proceedings/qsic/2005/2472/00/24720357.pdf},
month = {September 19th-21st},
publisher = {IEEE Computer Society Press},
booktitle = {Proceedings of the International Workshop on Grid and Peer-to-Peer based Workflows in conjunction with the 5th International Conference on Quality Software},
address = {Melbourne, Australia}
}
@inproceedings{Zhao2005c,
title = {Dynamic Workflow in a Grid Enabled Problem Solving Environment},
author = {Z. Zhao and A.S.Z. Belloum and H.H. Yakali and P.M.A. Sloot and L.O. Hertzberger},
year = {2005},
pages = {339-345},
url = {http://csdl.computer.org/dl/proceedings/cit/2005/2432/00/24320339.pdf},
month = {September},
publisher = {IEEE Computer Society Press},
booktitle = {Proceedings of the 5th International Conference on Computer and Information Technology (CIT2005)},
address = {Shanghai, China}
}
@article{Zhao2005d,
title = {Agent-based flow control for HLA components},
author = {Z. Zhao and G.D. van Albada and P.M.A. Sloot},
year = {2005},
journal = {International journal of simulation transaction, special issue Agent Directed Simulation},
volume = {81},
number = {7},
pages = {487-501},
metis_id = {252422},
url = {http://sim.sagepub.com/cgi/content/abstract/81/7/487},
category = {agents, workflow}
}
@inproceedings{Zhao2005e,
title = {Rapid Prototyping of Complex Interactive Simulation Systems},
author = {Z. Zhao and G.D. van Albada and P.M.A. Sloot},
year = {2005},
pages = {366-375},
metis_id = {243292},
month = {June},
publisher = {IEEE Computer Society Press},
booktitle = {Proceedings of the 10th IEEE International Conference on Engineering of Complex Computer Systems (ICECCS'05)},
address = {Shanghai, China}
}
@inproceedings{Zhao2005f,
title = {Agent Technology and Generic Workflow Management in an e-Science Environment},
author = {Z. Zhao and A.S.Z. Belloum and P.M.A. Sloot and L.O. Hertzberger},
year = {2005},
volume = {3795},
pages = {480--485},
metis_id = {253168},
url = {http://www.springerlink.com/openurl.asp?genre=article\&id=doi:10.1007/11590354_61},
month = {November},
publisher = {Springer},
doi = {10.1007/11590354_61},
series = {Lecture Notes in Computer Science},
booktitle = {Grid and Cooperative Computing - GCC 2005: 4th International Conference, Beijing, China},
editor = {Hai Zhuge and G.C. Fox},
issn_isbn = {ISBN 3-540-30510-6}
}
@inproceedings{Zudilova-Seinstra2005a,
title = {Towards Service-based Interactive Visualisation},
author = {E.V. Zudilova-Seinstra and N. Yang},
year = {2005},
pages = {15--25},
category = {computer, science},
booktitle = {Proc. of the Second Int. Symposium on Ambient Intelligence and Life, July 21-22, 2005, San Sebastian, Spain},
editor = {B. Siera and E. Lazkano},
issn_isbn = {ISBN 84-609-6632-1}
}
@article{Zudilova2005a,
title = {Bringing Combined Interaction to a Problem Solving Environment for Vascular Reconstruction},
author = {E.V. Zudilova and P.M.A. Sloot},
year = {2005},
journal = {Int. J. Future Generation Computer Systems},
volume = {21},
number = {7},
pages = {1167--1176},
category = {Visualisation, CrossGrid, LBM},
publisher = {Elsevier Science Publishers B. V.},
doi = {10.1016/j.future.2004.04.004},
address = {Amsterdam, The Netherlands, The Netherlands}
}
@inproceedings{Zudilova2005b,
title = {Multi-modal Interaction in Biomedicine},
author = {E.V. Zudilova and P.M.A. Sloot},
year = {2005},
volume = {3345},
pages = {184--201},
url = {Zudilova2004a-pre.pdf},
category = {LBM, Visualisation, CrossGrid},
publisher = {Springer-Verlag},
series = {Lecture Notes in Artificial Intelligence},
booktitle = {Ambient Intelligence for Scientific Discovery},
editor = {Y. Cai},
address = {Heidelberg}
}
@proceedings{Zudilova2005c,
author = {E.V. Zudilova and T. Adriaansen},
year = {2005},
month = {October},
category = {Visualisation},
publisher = {ITC-irst Press},
booktitle = {Multimodal Interaction for the Visualization and Exploration of Scientific Data, Proc. of the ICMI'05 Workshop},
address = {Trento, Italy}
}
@misc{Zudilova2005d,
title = {Special Issue on Interaction and Visualization Techniques for Problem Solving Environments},
author = {E.V. Zudilova and T. Adriaansen and B. Pham},
year = {2005},
journal = {Future Generation Computer Systems},
volume = {21},
number = {7},
month = {June},
category = {Visualisation},
note = {Guest Editorship}
}
@inproceedings{Altintas2004a,
title = {A Web Service Composition and Deployment Framework for Scientific Workflows},
author = {I. Altintas and E. Jaeger and K. Lin and B. Lud\"ascher and A. Memon},
year = {2004},
pages = {814--816},
metis_id = {276713},
url = {http://doi.ieeecomputersociety.org/10.1109/ICWS.2004.1314956},
month = {July},
doi = {10.1109/ICWS.2004.1314956},
booktitle = {Proceedings of the 2nd Intl. Conference on Web Services(ICWS)},
abstract = {We present the Kepler system for modeling and enacting scientific workflows. Kepler is unique in that it seamlessly combines high-level workflow design with execution and runtime interaction, access to local and remote data, and local and remote service invocation. We give an overview of the system, highlight some specific features, outline the planned (hands-on) demonstration, and report on the implementation status and next steps.},
address = {San Diego, California}
}
@inproceedings{Altintas2004b,
title = {Kepler: An Extensible System for Design and Execution of Scientific Workflows},
author = {I. Altintas and C. Berkley and E. Jaeger and M. Jones and B. Lud\"ascher and S. Mock},
year = {2004},
pages = {423--424},
metis_id = {276714},
url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=1311241},
month = {June},
doi = {10.1109/SSDM.2004.1311241},
booktitle = {Proceedings of the 16th Intl. Conference on Scientific and Statistical Database Management(SSDBM)},
abstract = {We present the Kepler system for modeling and enacting scientific workflows. Kepler is unique in that it seamlessly combines high-level workflow design with execution and runtime interaction, access to local and remote data, and local and remote service invocation. We give an overview of the system, highlight some specific features, outline the planned (hands-on) demonstration, and report on the implementation status and next steps.},
address = {Santorini Island, Greece}
}
@inproceedings{Altintas2004c,
title = {Kepler: Towards a Grid-Enabled System for Scientific Workflows},
author = {I. Altintas and C. Berkley and E. Jaeger and M. Jones and B. Lud\"ascher and S. Mock},
year = {2004},
metis_id = {276715},
url = {http://www.extreme.indiana.edu/groc/ggf10-ww/kepler_towards_grid-enabled_system_for_scientific_workflows__bertram_ludaescher},
month = {March},
numpages = {5},
booktitle = {Proceedings of the Workflow in Grid Systems Workshop in GGF10 - The Tenth Global Grid Forum},
note = {on-line proceedings},
abstract = {We present the Kepler system for modeling and enacting scientific workflows. Kepler is unique in that it seamlessly combines high-level workflow design with execution and runtime interaction, access to local and remote data, and local and remote service invocation. We give an overview of the system, highlight some specific features, outline the planned (hands-on) demonstration, and report on the implementation status and next steps.},
address = {Berlin, Germany}
}
@inproceedings{Artoli2004a,
title = {Accuracy versus Performance in Lattice Boltzmann BGK Simulations of Systolic Flows},
author = {A.M.M. Artoli and L. Abrahamyan and A.G. Hoekstra},
year = {2004},
volume = {3039},
pages = {548--555},
metis_id = {240483},
url = {http://www.springerlink.com/openurl.asp?genre=issue\&issn=0302-9743\&volume=3039\&issue=preprint},
month = {June},
category = {LBM},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2004: 4th International Conference, Krak\'ow, Poland, June 6-9, 2004, Proceedings, Part IV},
editor = {M.T. Bubak and G.D. van Albada and P.M.A. Sloot and J.J. Dongarra},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-22129-8}
}
@article{Artoli2004b,
title = {Lattice BGK simulations of flow in a symmetric bifurcation},
author = {A.M.M. Artoli and B.D. Kandhai and H.C.J. Hoefsloot and A.G. Hoekstra and P.M.A. Sloot},
year = {2004},
journal = {Future Generation Computer Systems},
volume = {20},
number = {6},
pages = {909--916},
metis_id = {222757},
category = {LBM},
annote = {Artoli2004c.pdf}
}
@mastersthesis{Ashyraliyev2004a,
title = {Implicit Schemes for the Lattice Boltzmann Equation},
author = {M. Ashyraliyev},
year = {2004},
url = {Ashyraliyev2004a.pdf},
month = {August},
category = {LBM, pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: A.G. Hoekstra}
}
@article{Baldridge2004a,
title = {Cluster and Grid Infrastructure for Computational Chemistry and Biochemistry},
author = {K.K. Baldridge and W. Sudholt and J.P. Greenberg and C. Amoreira and Y. Potier and I. Altintas and A. Birnbaum and D. Abramson and C. Enticott and S. Garic},
year = {2004},
journal = {Parallel Computing for Bioinformatics},
volume = {20},
number = {S2},
metis_id = {276716},
publisher = {John Wiley \& Sons},
editor = {A.Y. Zomaya (Ed.)}
}
@proceedings{Bubak2004a,
title = {Computational Science - ICCS 2004: 4th International Conference, Krak\'ow, Poland, June 6-9, 2004, Proceedings, Part II},
author = {M.T. Bubak and G.D. van Albada and P.M.A. Sloot and J. Dongarra},
year = {2004},
volume = {3037},
url = {http://www.springerlink.com/openurl.asp?genre=volume\&id=doi:10.1007/b97988},
month = {June},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-22115-8}
}
@proceedings{Bubak2004b,
title = {Computational Science - ICCS 2004: 4th International Conference, Krak\'ow, Poland, June 6-9, 2004, Proceedings, Part I},
author = {M.T. Bubak and G.D. van Albada and P.M.A. Sloot and J. Dongarra},
year = {2004},
volume = {3036},
url = {http://www.springerlink.com/openurl.asp?genre=volume\&id=doi:10.1007/b97987},
month = {June},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-22114-X}
}
@proceedings{Bubak2004c,
title = {Computational Science - ICCS 2004: 4th International Conference, Krak\'ow, Poland, June 6-9, 2004, Proceedings, Part IV},
author = {M.T. Bubak and G.D. van Albada and P.M.A. Sloot and J. Dongarra},
year = {2004},
volume = {3039},
url = {http://www.springerlink.com/openurl.asp?genre=volume\&id=doi:10.1007/b98005},
month = {June},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-22129-8}
}
@proceedings{Bubak2004d,
title = {Computational Science - ICCS 2004: 4th International Conference, Krak\'ow, Poland, June 6-9, 2004, Proceedings, Part III},
author = {M.T. Bubak and G.D. van Albada and P.M.A. Sloot and J. Dongarra},
year = {2004},
volume = {3038},
url = {http://www.springerlink.com/openurl.asp?genre=volume\&id=doi:10.1007/b97989},
month = {June},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-22116-6}
}
@mastersthesis{Bui2004a,
title = {The Network as a Data Transporting and Data Storing Application},
author = {H.V. Bui},
year = {2004},
url = {Bui2004a.pdf},
month = {August},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: R.J. Meijer}
}
@article{Chakrabarty2004a,
title = {An Inverse-Problem Approach to Cluster Dynamics},
author = {D. Chakrabarty and S.F. Portegies Zwart},
year = {2004},
journal = {Astronomical Journal},
volume = {128},
pages = {1046--1057},
metis_id = {228318},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004AJ....128.1046C\&db_key=AST},
month = {sep},
category = {Astrophysics}
}
@misc{Chopard2004a,
title = {Special Issue: Computational Science of Lattice Boltzmann Modelling (Editorial)},
author = {B. Chopard and A.G. Hoekstra},
year = {2004},
journal = {Future Generation Computer Systems},
volume = {20},
number = {6},
pages = {907--1095},
metis_id = {276718},
month = {August},
category = {LBM, pwrs, misc}
}
@article{Chopard2004b,
title = {Guest Editorial, Computational science of lattice Boltzmann modelling},
author = {B. Chopard and A.G. Hoekstra},
year = {2004},
journal = {Future Generation Computer Systems},
volume = {20},
number = {6},
pages = {907--908},
metis_id = {276717},
month = {August},
category = {LBM, pwrs, article}
}
@mastersthesis{Cramer2004a,
title = {Usability Evaluation And Context Analysis To Aid The Development Of Virtual Reality Applications applied to the Virtual Radiology Explorer},
author = {H.S.M. Cramer},
year = {2004},
url = {Cramer2004c.pdf},
month = {November},
category = {pwrs, mastersthesis, Visualisation, SocialScienceInformatics},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisors: V. Evers and E.V. Zudilova}
}
@article{Cramer2004b,
title = {Context analysis to support development of virtual reality applications},
author = {H.S.M. Cramer and V. Evers and E.V. Zudilova and P.M.A. Sloot},
year = {2004},
journal = {International Journal of Virtual Reality},
volume = {7},
number = {3},
pages = {177--186},
category = {Visualisation},
annote = {Cramer2004a.pdf}
}
@inproceedings{Cramer2004c,
title = {Usability Evaluation of a Simulated Vascular Reconstruction System},
author = {H.S.M. Cramer and V. Evers and E.V. Zudilova and P.M.A. Sloot},
year = {2004},
month = {January},
category = {Visualisation},
booktitle = {Proceedings of the VIRART Virtual Reality Design and Evaluation Workshop 2004},
note = {CD-ROM, Panel VI (Design methods/process and evaluation)},
annote = {Cramer2004b.pdf},
address = {University of Nottingham, United Kingdom},
issn_isbn = {ISBN 0 85358 123 1}
}
@inproceedings{Cui2004a,
title = {Mathematical modelling of calcium homeostasis in yeast cells},
author = {J. Cui and J.A. Kaandorp},
year = {2004},
pages = {215},
metis_id = {240482},
month = {July},
category = {bioinformatics},
booktitle = {Proceedings of the 12th International Conference on Intelligent Systems for Molecular Biology and 3rd European Conference on Computational Biology (ISMB/ECCB)},
note = {abstract},
address = {Glasgow, Scotland, UK}
}
@article{Fregeau2004a,
title = {Stellar collisions during binary-binary and binary-single star interactions},
author = {J.M. Fregeau and P. Cheung and S.F. Portegies Zwart and F.A. Rasio},
year = {2004},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {352},
pages = {1-19},
metis_id = {228320},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004MNRAS.352....1F\&db_key=AST},
month = {jul},
category = {astronomy}
}
@inproceedings{Gavidia_Simonetti2004a,
title = {A Client-Server Engine for Parallel Computation of High-Resolution Planes},
author = {D.P. Gavidia Simonetti and E.V. Zudilova and P.M.A. Sloot},
year = {2004},
volume = {3038},
pages = {970--977},
url = {http://www.springerlink.com/openurl.asp?genre=issue\&issn=0302-9743\&volume=3038\&issue=preprint},
month = {June},
category = {Visualisation},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2004: 4th International Conference, Krak\'ow, Poland, June 6-9, 2004, Proceedings, Part III},
editor = {M.T. Bubak and G.D. van Albada and P.M.A. Sloot and J.J. Dongarra},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-22116-6}
}
@article{Gieles2004a,
title = {The Effect of Spiral Arms on Star Cluster Evolution},
author = {M. Gieles and E. Athanassoula and S.F. Portegies Zwart},
year = {2004},
journal = {AAS/Division of Dynamical Astronomy Meeting},
volume = {35},
number = {3},
metis_id = {231924},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004DDA....35.0302G\&db_key=AST},
month = {may},
category = {astronomy}
}
@inproceedings{Gorbachev2004a,
title = {Virtual Laboratory for Research and Education},
author = {Y.E. Gorbachev and M.A. Zatevakhin and A.A. Ignatiev and V.V. Krzhizhanovskaya},
year = {2004},
pages = {59--60},
month = {February},
category = {PSE},
publisher = {SPbSPU},
booktitle = {XI International Conference on High Technologies and Quality of Education and Science},
address = {St. Petersburg Polytechnic University}
}
@inproceedings{Gorbachev2004b,
title = {Using GRID technologies for simulation of complex physical-chemical systems},
author = {Y.E. Gorbachev and V.V. Krzhizhanovskaya and P.M.A. Sloot},
year = {2004},
volume = {1},
pages = {165--167},
metis_id = {222842},
url = {http://tm.ifmo.ru/tm2004/db/doc/get_thes.php?id=392},
month = {June},
category = {PECVD, Grid, PSE},
publisher = {SPbSU ITMO"Informika", Moscow},
note = {In Russian},
booktitle = {Proceedings of the XI All-Russian conference Telematika'2004},
organization = {XI All-Russian conference Telematika'2004, St. Petersburg, Russia},
address = {St. Petersburg, Russia}
}
@inproceedings{Gorbachev2004c,
title = {Simulation of heat and mass transfer processes in PECVD reactors for silicon films growth under the conditions of intense formation of higher silanes in the gas phase},
author = {Y.E. Gorbachev and M.A. Zatevakhin and A.A. Ignatiev and V.V. Krzhizhanovskaya},
year = {2004},
volume = {1},
pages = {301--302},
metis_id = {240485},
url = {http://relay.itmo.by/forum/mif5/S04/4-08.PDF},
month = {May},
category = {PECVD},
publisher = {SPbSU ITMO"Informika", Moscow},
note = {abstract, in Russian; full paper at url and on CD},
booktitle = {5th Minsk International Heat and Mass Transfer Forum, MIF-2004},
address = {Minsk, Belarus}
}
@article{Gualandris2004a,
title = {N-body simulations of stars escaping from the Orion nebula},
author = {A. Gualandris and S.F. Portegies Zwart and P.-P. Eggleton},
year = {2004},
journal = {Mon.Not.Royal Astron. Soc.},
volume = {350},
pages = {615-626},
metis_id = {228261},
url = {http://cdsads.u-strasbg.fr/cgi-bin/nph-bib_query?bibcode=2004MNRAS.350..615G\&db_key=AST},
month = {May}
}
@article{Hlushkou2004a,
title = {Coupled lattice-Boltzmann method and finite-difference simulations of electroosmosis in microfluidic channels},
author = {D. Hlushkou and B.D. Kandhai and A. Seidel-Morgenstern and U. Tallarek},
year = {2004},
journal = {Int. J. Num. Meth. Fluid},
volume = {46},
pages = {507-532},
metis_id = {265090},
url = {http://www3.interscience.wiley.com/cgi-bin/fulltext/112210359/PDFSTART},
doi = {10.1002/fld.765}
}
@article{Hoekstra2004a,
title = {Unsteady flow in a 2D elastic tube with the LBGK method},
author = {A.G. Hoekstra and J. van 't Hoff and A.M.M. Artoli and P.M.A. Sloot},
year = {2004},
journal = {Future Generation Computer Systems},
volume = {20},
number = {6},
pages = {917--924},
metis_id = {222758},
category = {LBM},
doi = {10.1016/j.future.2003.12.003},
annote = {Hoekstra2004a.pdf}
}
@article{Hopman2004a,
title = {Ultraluminous X-Ray Sources as Intermediate-Mass Black Holes Fed by Tidally Captured Stars},
author = {C. Hopman and S.F. Portegies Zwart and T. Alexander},
year = {2004},
journal = {Astrophys. J. Let.},
volume = {604},
pages = {L101-L104},
metis_id = {231926},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004ApJ...604L.101H\&db_key=AST},
month = {apr},
category = {astronomy}
}
@inproceedings{Iskra2004a,
title = {Towards Grid-aware Time Warp},
author = {K.A. Iskra and G.D. van Albada and P.M.A. Sloot},
year = {2004},
pages = {63-70},
metis_id = {240489},
url = {http://csdl.computer.org/comp/proceedings/pads/2004/2111/00/21110063abs.htm},
month = {May},
category = {TimeWarp},
publisher = {IEEE Computer Society},
booktitle = {Proceedings of the 18th Workshop on Parallel and Distributed Simulation},
address = {Kufstein, Austria},
issn_isbn = {ISBN 0-7695-2111-8}
}
@incollection{Kaandorp2004a,
title = {Morphological analysis of two- and three-dimensional images of branching sponges and corals},
author = {J.A. Kaandorp and R.A. Garc\'{\i}a Leiva},
year = {2004},
pages = {83--94},
metis_id = {240396},
publisher = {Springer-Verlag},
booktitle = {Morphometrics - Applications in Biology and Paleontology},
editor = {A.M.T. Elewa},
issn_isbn = {ISBN 3-540-21429-1}
}
@mastersthesis{Korjoukov2004a,
title = {A Cognitive Model of Human Drawing},
author = {I.V. Korjoukov},
year = {2004},
url = {Korjoukov2004a.pdf},
month = {August},
category = {pwrs, mastersthesis, Cognition, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: E.V. Zudilova}
}
@inproceedings{Kouwenhoven2004a,
title = {The Primordial Binary Population in OB Associations},
author = {M.B.N. Kouwenhoven and A.G.A. Brown and A. Gualandris and L. Kaper and S.F. Portegies Zwart and H. Zinnecker},
year = {2004},
volume = {21},
pages = {139-140},
metis_id = {228259},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004RMxAC..21..139K\&db_key=AST},
month = {aug},
category = {astronomy},
booktitle = {Revista Mexicana de Astronomia y Astrofisica Conference Series},
editor = {Allen,C. and Scarfe,C.},
organization = {IAU Colloquium 191 held in Merida, Yucatan, Mexico}
}
@article{Kouwenhoven2004b,
title = {Recovering the primordial binary population using simulating observations of simulations},
author = {M.B.N. Kouwenhoven and S.F. Portegies Zwart and A. Gualandris and A.G.A. Brown and L. Kaper and H. Zinnecker},
year = {2004},
journal = {Astronomische Nachrichten Supplement},
volume = {325},
pages = {101+},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004ANS...325a.101K\&db_key=AST},
category = {astronomy},
note = {abstract}
}
@inproceedings{Krzhizhanovskaya2004a,
title = {A Grid-Based Problem-Solving Environment for Simulation of Plasma Enhanced Chemical Vapor Deposition},
author = {V.V. Krzhizhanovskaya and Y.E. Gorbachev and P.M.A. Sloot},
year = {2004},
pages = {262--271},
metis_id = {222840},
month = {June--July},
category = {PECVD, PSE, Grid},
publisher = {JINR Dubna},
booktitle = {Proceedings of the International Conference "Distributed Computing and Grid Technologies in Science and Education"},
address = {Dubna, Russia},
issn_isbn = {ISBN 5-9530-0052-9}
}
@inproceedings{Krzhizhanovskaya2004b,
title = {A Grid-Based Problem-Solving Environment for Simulation of Plasma Enhanced Chemical Vapor Deposition},
author = {V.V. Krzhizhanovskaya and Y.E. Gorbachev and P.M.A. Sloot},
year = {2004},
pages = {89--90},
metis_id = {222841},
month = {June--July},
category = {PECVD, PSE, Grid},
publisher = {JINR Dubna},
booktitle = {Book of abstracts of the International Conference "Distributed Computing and Grid Technologies in Science and Education"},
note = {abstract},
address = {Dubna, Russia},
issn_isbn = {ISBN 5-9530-0052-9}
}
@inproceedings{Krzhizhanovskaya2004c,
title = {A 3D Virtual Reactor for Simulation of Silicon-Based Film Production},
author = {V.V. Krzhizhanovskaya and M.A. Zatevakhin and A.A. Ignatiev and Y.E. Gorbachev and W.J. Goedheer and P.M.A. Sloot},
year = {2004},
volume = {491},
number = {2},
pages = {59--68},
month = {July},
category = {PECVD, PSE, Visualisation, VirtualReactor},
series = {ASME PVP},
booktitle = {5th International Bi-Annual Symposium on Computational Technologies for Fluid / Thermal / Chemical Systems with Industrial Applications, held in conjunction with the ASME/JSME PVP Conference},
address = {San Diego / La Jolla, California USA},
issn_isbn = {ISBN 0-7918-4686-5}
}
@mastersthesis{Kvaly2004a,
title = {Semantic Web Services Automated Matching, Composition and Selection},
author = {T.A. Kval\oy},
year = {2004},
url = {Kvaloy2004a.pdf},
month = {October},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisors: E. Rongen and A. Tirado-Ramos and P.M.A. Sloot}
}
@inproceedings{Leskes2004a,
title = {Unlearning Phenomena in Co-evolution of Non-uniform Cellular Automata},
author = {B. Leskes and P.M.A. Sloot},
year = {2004},
volume = {3305},
pages = {172--181},
metis_id = {240528},
url = {http://www.springerlink.com/app/home/contribution.asp?wasp=320ltvqxrj1wkx1jxdf1\&referrer=parent\&backto=issue,18,90;journal,12,1775;linkingpublicationresults,1:105633,1},
month = {October},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Cellular Automata: 6th International Conference on Cellular Automata for Research and Industry, ACRI 2004, Amsterdam, The Netherlands, October 25-28, 2004},
editor = {P.M.A. Sloot and B. Chopard and A.G. Hoekstra},
address = {Heidelberg},
issn_isbn = {ISBN: 3-540-23596-5}
}
@mastersthesis{Meijer2004a,
title = {Scheduling parallel processes using Genetic Algorithms},
author = {M. Meijer},
year = {2004},
url = {Meijer2004a.pdf},
month = {February},
category = {pwrs, mastersthesis, Dynamite, Scheduling, AI},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: G.D. van Albada}
}
@article{Merks2004a,
title = {Polyp oriented modelling of coral growth},
author = {R.M.H. Merks and A.G. Hoekstra and J.A. Kaandorp and P.M.A. Sloot},
year = {2004},
journal = {Journal of Theoretical Biology},
volume = {228},
number = {4},
pages = {559--576},
metis_id = {240369},
url = {http://dx.doi.org/10.1016/j.jtbi.2004.02.020},
category = {BioInformatics, LBM}
}
@article{Merritt2004a,
title = {Core Formation by a Population of Massive Remnants},
author = {D. Merritt and S. Piatek and S.F. Portegies Zwart and M. Hemsendorf},
year = {2004},
journal = {Astrophys. J. Let.},
volume = {608},
pages = {L25-L28},
metis_id = {228322},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004ApJ...608L..25M\&db_key=AST},
month = {jun},
category = {astronomy}
}
@article{Naumov2004a,
title = {"Colorful" Cellular Automata},
author = {L.A. Naumov and A.A. Shalyto},
year = {2004},
journal = {World of PC},
volume = {2004},
number = {5},
pages = {64-71},
metis_id = {276720},
url = {http://www.camellab.spb.ru/utils/dl.jsp?tgt=/pubs/2004/CA2.WPC.pdf},
category = {CA},
note = {in Russian},
address = {Moscow}
}
@inproceedings{Naumov2004b,
title = {Automata Implementation in Object-Oriented Programs},
author = {L.A. Naumov and A.A. Shalyto},
year = {2004},
volume = {1},
pages = {332--334},
metis_id = {276721},
category = {Automata},
publisher = {SPbSU ITMO},
note = {in Russian},
booktitle = {Proceedings of XI All-Russian Guidance Conference "Telematics'2004"},
address = {Saint-Petersburg}
}
@inproceedings{Naumov2004c,
title = {CAMEL - Cellular Automata Modeling Environment \& Library},
author = {L.A. Naumov},
year = {2004},
volume = {1},
pages = {184--186},
metis_id = {276722},
url = {http://www.camellab.spb.ru/utils/dl.jsp?tgt=/pubs/2004/CAMEL.TM.pdf},
category = {CA},
publisher = {SPbSU ITMO},
note = {in Russian},
booktitle = {Proceedings of XI All-Russian Guidance Conference "Telematics'2004"},
address = {Saint-Petersburg}
}
@inproceedings{Naumov2004d,
title = {CAMEL - Cellular Automata Modeling Environment \& Library},
author = {L.A. Naumov},
year = {2004},
volume = {3305},
pages = {735--744},
metis_id = {276724},
month = {October},
category = {CA},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Cellular Automata: 6th International Conference on Cellular Automata for Research and Industry, ACRI 2004, Amsterdam, The Netherlands, October 25-28, 2004},
editor = {P.M.A. Sloot and B. Chopard and A.G. Hoekstra},
address = {Heidelberg},
issn_isbn = {ISBN: 3-540-23596-5}
}
@inproceedings{Naumov2004e,
title = {Methods of Object-Oriented Agents Implementation, Basing on Finite Automata},
author = {L.A. Naumov and A.A. Shalyto},
year = {2004},
volume = {1},
pages = {279--284},
metis_id = {276725},
category = {Automata},
note = {in Russian},
booktitle = {Artificial Intelligence. Intellectual and Multiprocessor Systems. Proceedings of International Scientific and Technical Conference},
address = {Taganrog-Donetsk}
}
@article{Naumov2004f,
title = {Methods of Object-Oriented Agents Implementation, Basing on Finite Automata},
author = {L.A. Naumov and A.A. Shalyto},
year = {2004},
journal = {Artificial Intelligence},
volume = {2004},
number = {4},
pages = {756--762},
metis_id = {276726},
category = {Automata},
note = {in Russian}
}
@inproceedings{Naumov2004g,
title = {CTP (Commands Transfer Protocol) - Networking Protocol for High-Performance Computations},
author = {L.A. Naumov},
year = {2004},
volume = {1},
pages = {188--189},
metis_id = {276723},
url = {http://www.camellab.spb.ru/utils/dl.jsp?tgt=/pubs/2004/CTP10.TM.pdf},
category = {ClusterNetworking},
publisher = {SPbSU ITMO},
note = {in Russian},
booktitle = {Proceedings of XI All-Russian Guidance Conference "Telematics'2004"},
address = {Saint-Petersburg}
}
@article{Nelemans2004a,
title = {Short-period AM CVn systems as optical, X-ray and gravitational-wave sources},
author = {G.A. Nelemans and L.R. Yungelson and S.F. Portegies Zwart},
year = {2004},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {349},
pages = {181-192},
metis_id = {228326},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004MNRAS.349..181N\&db_key=AST},
month = {mar},
category = {astronomy}
}
@inproceedings{Nuallin2004a,
title = {Online Suffix Trees with Counts},
author = {B. \'O Nuall\'ain and S. de Rooij},
year = {2004},
pages = {555},
url = {http://csdl.computer.org/comp/proceedings/dcc/2004/2082/00/20820555.pdf},
category = {DataCompression},
publisher = {IEEE Computer Society Press},
booktitle = {Proceedings of the Data Compression Conference 2004},
note = {abstract},
issn_isbn = {ISBN 0-7695-2082-0}
}
@mastersthesis{Patrick2004a,
title = {Data Comunnication Infrastructure for Distributed Real-Time Simulation},
author = {M.J. Patrick},
year = {2004},
url = {Patrick2004a.pdf},
month = {August},
category = {pwrs, mastersthesis, DataCom, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: A. Tirado-Ramos and P.M.A. Sloot}
}
@article{Portegies_Zwart2004a,
title = {Star cluster ecology - V. Dissection of an open star cluster: spectroscopy},
author = {S.F. Portegies Zwart and P. Hut and S.L.W. McMillan and J. Makino},
year = {2004},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {351},
pages = {473-486},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004MNRAS.351..473P\&db_key=AST},
month = {jun},
category = {astronomy}
}
@article{Portegies_Zwart2004b,
title = {Formation of massive black holes through runaway collisions in dense young star clusters},
author = {S.F. Portegies Zwart and H. Baumgardt and P. Hut and J. Makino and S.L.W. McMillan},
year = {2004},
journal = {Nature},
volume = {428},
pages = {724-726},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004Natur.428..724P\&db_key=AST},
month = {apr},
category = {astronomy}
}
@article{Portegies_Zwart2004c,
title = {Intermediate mass black holes in accreting binaries: formation, evolution and observational appearance},
author = {S.F. Portegies Zwart and J.D.M. Dewi and T.J. Maccarone},
year = {2004},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {355},
pages = {413-423},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004MNRAS.355..413P\&db_key=AST},
month = {dec},
category = {astronomy}
}
@mastersthesis{Ridder2004a,
title = {Collaboration in the Virtual Laboratory for e-Science},
author = {A. de Ridder},
year = {2004},
month = {October},
category = {mastersthesis, ComputerScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: A.S.Z. Belloum}
}
@mastersthesis{Rodrguez2004a,
title = {Mesoscopic Stochastic Modelling for Biochemical Networks with Membrane-bound Molecules},
author = {J. Vidal Rodr\'{\i}guez},
year = {2004},
url = {Rodriguez2004a.pdf},
month = {August},
category = {pwrs, mastersthesis, BioInformatics, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: J.A. Kaandorp}
}
@inproceedings{Rycerz2004a,
title = {Support for Effective and Fault Tolerant Execution of HLA-Based Applications in the OGSA Framework},
author = {K.J. Rycerz and M.T. Bubak and M. Malawski and P.M.A. Sloot},
year = {2004},
volume = {3038},
pages = {848--855},
metis_id = {240531},
url = {http://www.springerlink.com/openurl.asp?genre=issue\&issn=0302-9743\&volume=3038\&issue=preprint},
month = {June},
category = {CrossGrid, HLA},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2004: 4th International Conference, Krak\'ow, Poland, June 6-9, 2004, Proceedings, Part III},
editor = {M.T. Bubak and G.D. van Albada and P.M.A. Sloot and J.J. Dongarra},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-22116-6}
}
@inproceedings{Rycerz2004b,
title = {Monitoring of HLA Grid Application Federates with OCM-G},
author = {K.J. Rycerz and B. Bali\'s and R. Szymacha and M.T. Bubak and P.M.A. Sloot},
year = {2004},
pages = {125--132},
metis_id = {240532},
url = {http://csdl.computer.org/comp/proceedings/ds-rt/2004/2232/00/22320125abs.htm},
month = {October},
category = {CrossGrid, HLA},
publisher = {IEEE},
booktitle = {Eighth IEEE International Symposium on Distributed Simulation and Real-Time Applications (DS-RT'04)},
editor = {S.J. Turner and D. Roberts and L. Wilson},
address = {Budapest, Hungary},
issn_isbn = {ISBN 3-540-22116-6}
}
@article{Rycerz2004c,
title = {Interactive Grid Computing: Adapting High Level Architecture-based Applications to the Grid},
author = {K.J. Rycerz and M.T. Bubak and M. Malawski and P.M.A. Sloot},
year = {2004},
journal = {TASK Quarterly, Scientific Bulletin of the Academic Centre of Gdansk},
volume = {8},
pages = {549--559},
metis_id = {276728},
url = {Rycerz2004c.pdf},
publisher = {TASK Publishing},
editor = {P. Doerffer and J. Rybicki}
}
@article{Salzberg2004a,
title = {Evolutionary dynamics of cellular automata-based self-replicators in hostile environments},
author = {C.P. Salzberg and A.T. Antony and H. Sayama},
year = {2004},
journal = {BioSystems},
volume = {78},
number = {1--3},
pages = {119--134},
url = {http://dx.doi.org/10.1016/j.biosystems.2004.07.004}
}
@article{Semyanov2004a,
title = {Single-Particle Sizing from Light Scattering by Spectral Decomposition},
author = {K.A. Semyanov and P.A. Tarasov and A.E. Zharinov and A.V. Chernyshev and A.G. Hoekstra and V.P. Maltsev},
year = {2004},
journal = {Applied Optics},
volume = {43},
number = {26},
pages = {5110-5115},
metis_id = {240385},
url = {http://www.opticsinfobase.org/abstract.cfm?id=81111},
month = {September},
category = {ElastLightScat, Cytometry},
abstract = {A Fourier transform was applied to size an individual spherical particle from an angular light-scattering pattern. The position of the peak in the amplitude spectrum has a strong correlation with the particle size. A linear equation retrieved from regression analysis of theoretically simulated patterns provides a relation between the particle size and the location of the amplitude spectrum's peak. The equation can be successfully applied to characterize particles of size parameters that range from 8 to 180 (corresponding to particle sizes that range from 1.2 to 27.2 \\mum at a wavelength of 0.633 \\mum). The precision of particle sizing depends on the refractive index and reaches a value of 60 nm within refractive-index region from 1.35 to 1.70. We have analyzed four samples of polystyrene microspheres with mean diameters of 1.9, 2.6, 3.0, and 4.2 \\mum and a sample of isovolumetrically sphered erythrocytes with a scanning flow cytometer to compare the accuracy of our new method with that of others. (c) 2004 Optical Society of America}
}
@article{Sipior2004a,
title = {Recycled pulsars with black hole companions: the high-mass analogues of PSR B2303+46},
author = {M.S. Sipior and S.F. Portegies Zwart and G.A. Nelemans},
year = {2004},
journal = {Mon. Not. Royal Astr. Soc.},
volume = {354},
pages = {L49-L53},
metis_id = {228317},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004MNRAS.354L..49S\&db_key=AST},
month = {nov},
category = {astronomy}
}
@misc{Sloot2004a,
title = {Virtual Vascular Surgery on the Grid},
author = {P.M.A. Sloot and A.G. Hoekstra},
year = {2004},
journal = {ERCIM news},
number = {59},
url = {Sloot2004b.pdf},
month = {October},
category = {LBM, CrossGrid, Visualisation}
}
@inproceedings{Sloot2004b,
title = {An Interactive Grid Environment for Non-Invasive Vascular Reconstruction},
author = {P.M.A. Sloot and A. Tirado Ramos and A.G. Hoekstra and M.T. Bubak},
year = {2004},
metis_id = {240533},
url = {Sloot2004a.pdf},
month = {April},
category = {LBM, CrossGrid, PSE},
publisher = {IEEE},
booktitle = {2nd International Workshop on Biomedical Computations on the Grid (BioGrid'04), in conjunction with Fourth IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid2004)},
note = {CD-ROM IEEE Catalog # 04EX836C},
address = {Chicago, Illinois, USA},
issn_isbn = {ISBN 0-7803-8431-8}
}
@proceedings{Sloot2004c,
title = {Cellular Automata: 6th International Conference on Cellular Automata for Research and Industry, ACRI 2004, Amsterdam, The Netherlands, October 25-28, 2004},
author = {P.M.A. Sloot and B. Chopard and A.G. Hoekstra},
year = {2004},
volume = {3305},
url = {http://www.springerlink.com/openurl.asp?genre=volume\&id=doi:10.1007/b102055},
month = {October},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
address = {Heidelberg},
issn_isbn = {ISBN: 3-540-23596-5}
}
@article{Spinnato2004a,
title = {Performance Modeling of Distributed Hybrid Architectures},
author = {P.F. Spinnato and G.D. van Albada and P.M.A. Sloot},
year = {2004},
journal = {IEEE Transactions on Parallel and Distributed Systems},
volume = {15},
number = {1},
pages = {81--92},
metis_id = {240302},
url = {http://csdl.computer.org/dl/trans/td/2004/01/l0081.pdf},
month = {January},
category = {PerfModelling}
}
@inproceedings{Tirado-Ramos2004a,
title = {Integration of Blood Flow Visualization on the Grid: the FlowFish/GVK Approach},
author = {A. Tirado Ramos and J.M. Ragas and D.P. Shamonin and H. Rosmanith and D. Kranzlm\"uller},
year = {2004},
volume = {3165},
pages = {77--79},
url = {http://springer.lib.tsinghua.edu.cn/app/home/issue.asp?wasp=p621amxuuj5tpby3rpfm\&referrer=parent\&backto=journal,135,1828;searchpublicationsresults,1,1;},
month = {January 28--30},
category = {LBM, CrossGrid, Visualisation},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Grid Computing: Proceedings of the 2nd European AcrossGrids Conference, Nicosia, Cyprus},
editor = {M.D. Dikaiakos},
address = {Nicosia, Cyprus},
issn_isbn = {ISBN: 30540-22888-8}
}
@article{Tirado-Ramos2004b,
title = {An Integrative Approach to High-Performance Biomedical Problem Solving Environments on the Grid},
author = {A. Tirado Ramos and P.M.A. Sloot and A.G. Hoekstra and M.T. Bubak},
year = {2004},
journal = {Parallel Computing},
volume = {30},
number = {9--10},
pages = {1037--1055},
url = {http://dx.doi.org/10.1016/j.parco.2004.07.010},
category = {LBM, CrossGrid, BioMed},
note = {special issue on High-Performance Parallel Bio-computing},
editor = {C.-H. Huang and S. Rajasekaran}
}
@article{Tirado-Ramos2004c,
title = {An Integrative Approach to High-Performance Biomedical Problem Solving Environments on the Grid},
author = {A. Tirado Ramos and P.M.A. Sloot and A.G. Hoekstra and M.T. Bubak},
year = {2004},
journal = {Parallel Computing},
volume = {30},
number = {9--10},
pages = {1037--1055},
url = {http://dx.doi.org/10.1016/j.parco.2004.07.010},
category = {LBM, CrossGrid, BioMed},
note = {special issue on High-Performance Parallel Bio-computing},
editor = {C.-H. Huang and S. Rajasekaran}
}
@mastersthesis{Vismans2004a,
title = {Enabling Intelligent Interaction in Virtual Environments -- A Generic Architecture},
author = {D.F.A. Vismans},
year = {2004},
month = {May},
category = {pwrs, mastersthesis, AI},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: J.A. Kaandorp}
}
@article{Wageningen2004a,
title = {Dynamic flow in a Kenics static mixer: An assessment of various CFD methods},
author = {W.F.C. van Wageningen and B.D. Kandhai and R.F. Mudde and H.E.A. van den Akker},
year = {2004},
journal = {AIChE J},
volume = {50},
number = {8},
pages = {1684-1696},
url = {http://www3.interscience.wiley.com/cgi-bin/fulltext/109086872/PDFSTART},
month = {July},
doi = {10.1002/aic.10178}
}
@mastersthesis{Wu2004a,
title = {A Probabilistic Multimedia Retrieval Model},
author = {F. Wu},
year = {2004},
url = {Wu2004a.pdf},
month = {August},
category = {pwrs, mastersthesis, multimedia, ComputerScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisors: A.P. de Vries and J.A. Kaandorp}
}
@inproceedings{Yungelson2004a,
title = {AM CVn systems as optical, X-ray and GWR sources},
author = {L.R. Yungelson and G.A. Nelemans and S.F. Portegies Zwart},
year = {2004},
pages = {117-119},
metis_id = {276729},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2004RMxAC..20..117Y\&db_key=AST},
month = {jul},
category = {astronomy},
booktitle = {Revista Mexicana de Astronomia y Astrofisica Conference Series}
}
@inproceedings{Zajac2004a,
title = {Execution and Migration Management of HLA-Based Interactive Simulations on the Grid},
author = {K.J. Zajac and M.T. Bubak and M. Malawski and P.M.A. Sloot},
year = {2004},
volume = {3019},
pages = {872--879},
metis_id = {240584},
url = {http://www.springerlink.com/openurl.asp?genre=article\&issn=0302-9743\&volume=3019\&spage=872},
category = {CrossGrid, HLA},
publisher = {Springer-Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Parallel Processing and Applied Mathematics: 5th International Conference, PPAM 2003, Czestochowa, Poland, September 7-10, 2003. Revised Papers},
editor = {R. Wyrzykowski and J.J. Dongarra and M. Paprzycki and J. Wa\'sniewski},
abstract = {This paper presents the design of a system that supports execution of a HLA distributed interactive simulations in an unreliable Grid environment. The design of the architecture is based on the OGSA concept that allows for modularity and compatibility with Grid Services already being developed. First of all, we focus on the part of the system that is responsible for migration of a HLA-connected component or components of the distributed application in the Grid environment. We present a runtime support library for easily plugging HLA simulations into the Grid Services Framework. We also present the impact of execution management (namely migration) on overall system performance. This research is partly funded by the European Commission IST-2001-32243 Project CrossGrid.},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-21946-3}
}
@phdthesis{Zhao2004a,
title = {An agent based architecture for constructing Interactive Simulation Systems},
author = {Z. Zhao},
year = {2004},
metis_id = {236254},
url = {Zhao2004a.pdf},
month = {December},
category = {CrossGrid, PSE, pwrs, phdthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. G.D. van Albada}
}
@inproceedings{Altintas2003a,
title = {A Modeling and Execution Environment for Distributed Scientific Workflows},
author = {I. Altintas and S. Bhagwanani and D. Buttler and S. Chandra and Z. Cheng and M. Coleman and T. Critchlow and A. Gupta and W. Han and L. Liu and B. Lud\"ascher and C. Pu and R. Moore and A. Shoshani and M. Vouk},
year = {2003},
pages = {247--250},
metis_id = {276696},
url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=1214989},
month = {June},
booktitle = {Proceedings of the 15th Intl. Conference on Scientific and Statistical Database Management(SSDBM)},
abstract = {The Scientific Data Management Center project (short: SDM) is part of a large research program sponsored by the US Department of Energy (DOE) to enable Scientific Discovery through Advanced Computing [SDM02, Sci]. SDM brings together research teams from DOE labs and universities to address and resolve novel data management challenges that arise due to the new data and information centric ways in which science is conducted today. This demonstration illustrates how a domain scientist can perform a complex scientific task by interleaving data access, querying, and manipulation, as well as analytical steps and computations in complex, problem specific ways. We show how our system is used by a geneticist for solving the problem of discovering so-called =93co-regulated=94 genes by interlinking data and computation from several web sites, local computations, as well as local and remote databases. The main distinctive features of our system (compared, e.g., to the ZOO environment) include (i) executable workflows run as web services, (ii) abstract workflows employ concept names and semantic types that are higher-level (and thus more =93scientist friendly=94) than executable workflows, and (iii) our system supports automatic translation of the latter into the former.},
address = {Boston, Massachussets},
issn_isbn = {ISBN: 0-7695-1964-4}
}
@article{Artoli2003a,
title = {Accelerated Lattice BGK method for unsteady simulations through Mach number annealing},
author = {A.M.M. Artoli and A.G. Hoekstra and P.M.A. Sloot},
year = {2003},
journal = {International Journal of Modern Physics C},
volume = {14},
number = {6},
pages = {835--847},
metis_id = {213718},
url = {Artoli2003c.pdf},
category = {LBM}
}
@article{Artoli2003b,
title = {Simulation of a Systolic Cycle in a Realistic Artery with the Lattice Boltzmann BGK Method},
author = {A.M.M. Artoli and A.G. Hoekstra and P.M.A. Sloot},
year = {2003},
journal = {International Journal of Modern Physics B},
volume = {17},
number = {1\&2},
pages = {95--98},
url = {http://ejournals.wspc.com.sg/ijmpb/17/1701n02/S0217979203017138.html},
month = {January},
category = {LBM},
publisher = {World Scientific Publishing Company},
abstract = {We present an analysis of the accuracy of the lattice Boltzmann BGK (LBGK) method in simulating pulsatile blood flow in a model of the Human Abdominal Aorta. The flow is driven by a systolic pressure cycle. As a benchmark, we consider fully developed pulsatile flow in a straight tube. We compare velocity profiles and shear stress to the analytical Womersley solutions. The accuracy of the bounce-back on the links and a curved boundary condition is compared at different Mach numbers. Preliminary results of systolic flow in the human abdominal aorta are presented.}
}
@inproceedings{Artoli2003c,
title = {Lattice Boltzmann, a Robust and Accurate Solver for Interactive Computational Hemodynamics},
author = {A.M.M. Artoli and B.D. Kandhai and H.C.J. Hoefsloot and A.G. Hoekstra and P.M.A. Sloot},
year = {2003},
volume = {2657},
pages = {1034--1043},
metis_id = {213715},
month = {June},
category = {LBM, PSE},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part I},
editor = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J.J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
issn_isbn = {ISBN 3-540-40194-6}
}
@phdthesis{Artoli2003d,
title = {Mesoscopic Computational Haemodynamics},
author = {A.M.M. Artoli},
year = {2003},
metis_id = {213057},
url = {Artoli2003e.pdf},
month = {October},
category = {LBM, pwrs, phdthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. Ir. A.G. Hoekstra}
}
@article{Baumgardt2003a,
title = {On the Central Structure of M15},
author = {H. Baumgardt and P. Hut and J. Makino and S.L.W. McMillan and S.F. Portegies Zwart},
year = {2003},
journal = {Astrophys. J. Let.},
volume = {582},
number = {1},
pages = {L21--L24},
metis_id = {213231},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2003ApJ...582L..21B\&db_key=AST},
month = {January},
category = {astronomy}
}
@article{Baumgardt2003b,
title = {A Dynamical Model for the Globular Cluster G1},
author = {H. Baumgardt and J. Makino and P. Hut and S.L.W. McMillan and S.F. Portegies Zwart},
year = {2003},
journal = {Astrophys. J. Let.},
volume = {589},
number = {1},
pages = {L25--L28},
metis_id = {213229},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2003ApJ...589L..25B\&db_key=AST},
month = {May},
category = {astronomy}
}
@phdthesis{Belleman2003a,
title = {Interactive Exploration in Virtual Environments},
author = {R.G. Belleman},
year = {2003},
metis_id = {213062},
url = {Belleman2003a.pdf},
month = {April},
category = {Visualisation, pwrs, phdthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot}
}
@proceedings{Boily2003a,
title = {Galactic and Stellar Dynamics, Proceedings of JENAM 2002, held in Porto, Portugal, 3-6 September, 2002},
author = {C.M. Boily and P. Pastsis and S.F. Portegies Zwart and R. Spurzem and C. Theis},
year = {2003},
volume = {10},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2003EAS....10.....B\&db_key=AST},
category = {astronomy},
series = {EAS Publications Series}
}
@inbook{Brown2003a,
title = {Evolution of Neutron Star, Carbon-Oxygen White Dwarf Binaries},
author = {G.E. Brown and C.-H. Lee and S.F. Portegies Zwart and H.A. Bethe},
year = {2003},
volume = {33},
pages = {345-354},
publisher = {World Scientific},
series = {World Scientific series in 20th century physics},
booktitle = {Formation and evolution of black holes in the Galaxy: selected papers with commentary},
editor = {H.A. Bethe and G.E. Brown and C.-H. Lee},
address = {Singapore}
}
@mastersthesis{Cui2003a,
title = {Mathematical Modelling of Calcium homeostasis in Yeast Cells},
author = {J. Cui},
year = {2003},
month = {August},
category = {pwrs, mastersthesis, bioinformatics, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: J.A. Kaandorp}
}
@mastersthesis{Cui2003b,
title = {Pricing Interest Rate Guarantees embedded in Life Insurance Contracts by Monte Carlo Simulation},
author = {Jiajia Cui},
year = {2003},
month = {August},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: B.D. Kandhai}
}
@mastersthesis{Gavidia_Simonetti2003a,
title = {Interactive Visualization of Biomedical Data},
author = {D.P. Gavidia Simonetti},
year = {2003},
url = {Gavidia-Simonetti2003a.pdf},
month = {August},
category = {LBM, Visualisation, pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: E.V. Zudilova}
}
@inproceedings{Gorbachev2003a,
title = {A Software-Hardware System for Simulation of Technological Devices on Distributed Computer Clusters},
author = {Y.E. Gorbachev and M.A. Zatevakhin and V.V. Krzhizhanovskaya and A.A. Ignatiev},
year = {2003},
volume = {1},
pages = {165--167},
metis_id = {276697},
url = {http://tm.ifmo.ru/tm2003/db/doc/get_thes.php?id=353},
month = {April},
category = {PECVD, PSE},
publisher = {SPbSU ITMO"Informika", Moscow},
note = {In Russian},
booktitle = {Proceedings of the X All-Russian conference Telematika'2003},
address = {St. Petersburg, Russia}
}
@inproceedings{Hoekstra2003a,
title = {Accuracy of internal fields inside spheroids in DDA-simulations of light scattering},
author = {A.G. Hoekstra and V.A. Babenko},
year = {2003},
pages = {123--126},
metis_id = {213738},
category = {ElastLightScat},
booktitle = {Electromagnetic and Light Scattering Theory and Applications VII},
editor = {T. Wriedt},
address = {Bremen},
issn_isbn = {ISBN 3-88722-579-1}
}
@inproceedings{Hoekstra2003b,
title = {Lattice BGK Simulations of Unsteady Flow in a 2D Elastic Tube},
author = {A.G. Hoekstra and J. van 't Hoff and A.M.M. Artoli and P.M.A. Sloot},
year = {2003},
volume = {2657},
pages = {997--1006},
metis_id = {213737},
month = {June},
category = {LBM, PSE},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part I},
editor = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J.J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
issn_isbn = {ISBN 3-540-40194-6}
}
@inproceedings{Iskra2003a,
title = {Time Warp Cancellation Optimisations on High Latency Networks},
author = {K.A. Iskra and G.D. van Albada and P.M.A. Sloot},
year = {2003},
pages = {128--135},
metis_id = {213739},
url = {http://csdl.computer.org/comp/proceedings/ds-rt/2003/2036/00/20360128abs.htm},
month = {October},
publisher = {IEEE Computer Society},
booktitle = {Proceedings Seventh IEEE International Symposium on Distributed Simulation and Real Time Applications (DS-RT 2003)},
editor = {S.J. Turner and S.J.E. Taylor},
address = {Delft, The Netherlands}
}
@article{Kaandorp2003a,
title = {Simulation and analysis of flow patterns around the scleractinian coral Madracis mirabilis (Duchassaing and Michelotti)},
author = {J.A. Kaandorp and E.A. Koopman and P.M.A. Sloot and R.P.M. Bak and M.J.A. Vermeij and L.E.H. Lampmann},
year = {2003},
journal = {Phil. Trans. R. Soc. Lond. B},
volume = {358 (1437)},
pages = {1551 -- 1557},
category = {LBM}
}
@inproceedings{Kaandorp2003b,
title = {Modelling growth and form of stony corals and the influence of hydrodynamics on suspension feeding},
author = {J.A. Kaandorp},
year = {2003},
volume = {I},
pages = {541-547},
category = {LBM},
booktitle = {Proceedings 9th International Coral Reef Symposium},
address = {Bali, Indonesia}
}
@article{Kandhai2003a,
title = {Interphase drag coefficients in gas-solid flows},
author = {B.D. Kandhai and J.J. Derksen and H.E.A. van den Akker},
year = {2003},
journal = {AIChE J.},
volume = {49},
pages = {1060--1065},
url = {http://www3.interscience.wiley.com/cgi-bin/fulltext/108065798/PDFSTART},
month = {April}
}
@inproceedings{Kiryukhin2003a,
title = {Stochastic Modeling of Temporal Variability of HIV-1 Population},
author = {I. Kiryukhin and K. Saskov and A.V. Boukhanovsky and W. Keulen and C.A.B. Boucher and P.M.A. Sloot},
year = {2003},
volume = {2657},
pages = {125--135},
metis_id = {213858},
month = {June},
category = {PSE},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part I},
editor = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J.J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
organization = {ICCS 2003},
issn_isbn = {ISBN 3-540-40194-6}
}
@inproceedings{Kouwenhoven2003a,
title = {The Primordial Binary Population in OB Associations},
author = {M.B.N. Kouwenhoven and A.G.A. Brown and A. Gualandris and L. Kaper and S.F. Portegies Zwart and H. Zinnecker},
year = {2003},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2003IAUS..221P..49K\&db_key=AST\&data_type=HTML\&format=\&high=41245ce60120906},
category = {astronomy},
booktitle = {IAU Symposium 221},
note = {abstract}
}
@inproceedings{Kranzlmller2003a,
title = {DeWiz - A Modular tool Architecture for Parallel Program Analysis},
author = {D. Kranzlm\"uller and M. Scarpa and J. Volkert},
year = {2003},
volume = {2790},
pages = {74--80},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
booktitle = {Euro-Par 2003. Parallel Processing, 9th International Euro-Par Conference, Klagenfurt, Austria, August 26-29, 2003. Proceedings},
editor = {H. Kosch and L. B\"osz\"orm\'enyi and H. Hellwagner},
issn_isbn = {ISBN 3-540-40788-X}
}
@inproceedings{Krul2003a,
title = {Modelling Developmental Regulatory Networks},
author = {T. Krul and J.A. Kaandorp and J.G. Blom},
year = {2003},
volume = {2660},
pages = {688--697},
metis_id = {213860},
month = {June},
category = {PSE},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part I},
editor = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J.J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
organization = {ICCS 2003},
issn_isbn = {ISBN 3-540-40194-6}
}
@mastersthesis{Krul2003b,
title = {Modelling and Inferring Developmental Networks},
author = {T. Krul},
year = {2003},
month = {July},
category = {pwrs, mastersthesis, bioinformatics, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: J.A. Kaandorp}
}
@mastersthesis{Kulk2003a,
title = {On the Computational Complexity of Lattice Gas Automata},
author = {N. Kulk},
year = {2003},
month = {June},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: A.G. Hoekstra}
}
@inproceedings{Ludscher2003a,
title = {Compiling Abstract Scientific Workflows into Web Service Workflows},
author = {B. Lud\"ascher and I. Altintas and A. Gupta},
year = {2003},
metis_id = {276698},
month = {July},
booktitle = {Proceedings of the 15th Intl. Conference on Scientific and Statistical Database Management(SSDBM)},
abstract = {On a method to convert abstract conceptual workflows into concrete executable workflows.},
address = {Boston, Massachussets}
}
@inproceedings{Marchi2003a,
title = {The Mass Function of Galactic Clusters and its Evolution},
author = {G. de Marchi and F. Paresce and S.F. Portegies Zwart},
year = {2003},
volume = {11},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2003IAUJD..11E..32D\&db_key=AST},
month = {July},
category = {astronomy},
note = {abstract},
booktitle = {Dynamics and Evolution of Dense Stellar Systems, 25th meeting of the IAU, Joint Discussion 11},
address = {Sydney, Australia}
}
@inproceedings{McMillan2003a,
title = {Evolution of Dense Star Clusters Near the Galactic Center},
author = {S.L.W. McMillan and S.F. Portegies Zwart},
year = {2003},
volume = {11},
metis_id = {213246},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2003IAUJD..11E..47M\&db_key=AST},
month = {July},
category = {astronomy},
note = {abstract},
booktitle = {Dynamics and Evolution of Dense Stellar Systems, 25th meeting of the IAU, Joint Discussion 11},
organization = {25th meeting of the IAU, Joint Discussion 11, Sydney, Australia},
address = {Sydney, Australia}
}
@article{McMillan2003b,
title = {The Fate of Star Clusters near the Galactic Center. I. Analytic Considerations},
author = {S.L.W. McMillan and S.F. Portegies Zwart},
year = {2003},
journal = {Astrophys. J.},
volume = {596},
number = {1},
pages = {314-322},
metis_id = {213222},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2003ApJ...596..314M\&db_key=AST},
month = {October},
category = {astronomy}
}
@inproceedings{Merks2003a,
title = {Problem Solving Environment for Modelling Stony Coral Morphogenesis},
author = {R.M.H. Merks and A.G. Hoekstra and J.A. Kaandorp and P.M.A. Sloot},
year = {2003},
volume = {2657},
pages = {639--648},
metis_id = {213883},
month = {June},
category = {LBM, PSE},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part I},
editor = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J.J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
organization = {ICCS 2003},
issn_isbn = {ISBN 3-540-40194-6}
}
@phdthesis{Merks2003b,
title = {Branching Growth in Stony Corals - a Modelling Approach},
author = {R.M.H. Merks},
year = {2003},
url = {Merks2003b.pdf},
month = {May},
category = {LBM, pwrs, phdthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotores: Dr. Ir. A.G. Hoekstra; Dr. J.A. Kaandorp}
}
@article{Merks2003c,
title = {Models of coral growth: Spontaneous branching, compactification and the Laplacian growth assumption},
author = {R.M.H. Merks and A.G. Hoekstra and J.A. Kaandorp and P.M.A. Sloot},
year = {2003},
journal = {Journal of Theoretical Biology},
volume = {224/2},
pages = {153--166},
url = {http://www.sciencedirect.com/science/article/B6WMD-498TR0W-3/1/6d27d133a4713c21b525160decc7c1cf},
month = {September},
category = {LBM}
}
@inproceedings{Merks2003d,
title = {Branching and compactification in a model of coral growth: a critical reinvestigation of the effect of hydrodynamics},
author = {R.M.H. Merks and A.G. Hoekstra and J.A. Kaandorp and P.M.A. Sloot},
year = {2003},
pages = {539--544},
metis_id = {213887},
category = {LBM, PSE},
publisher = {MIRIAM (Milan Research Centre for Industrial and Applied Mathematics)},
booktitle = {Mathematical modelling \& Computing in Biology and Medicine; 5th ESMTB Conference 2002},
editor = {V. Capasso}
}
@article{Merks2003e,
title = {Diffusion Limited Growth In Laminar Flows},
author = {R.M.H. Merks and A.G. Hoekstra and J.A. Kaandorp and P.M.A. Sloot},
year = {2003},
journal = {International Journal of Modern Physics C},
volume = {14},
number = {9},
pages = {1171--1182},
metis_id = {276699},
category = {LBM},
abstract = {In the diffusion-limited aggregation (DLA) model, pioneered by Witten and Sander (Phys. Rev. Lett. 47), 1400 (1981)) diffusing particles i rreversibly attach to a growing cluster which is initiated with a single solid seed. This process generates clusters with a branched morphology. Advection-diffusion-limited aggregation (ADLA) is a straightforward extension to this model, where the transport of the aggregating particles not only depends on diffusion , but also on a fluid flow. Authors studying two-dimensional and three-dimensional ADLA in laminar flows, reported clusters preferentially growing against the flow direction. The internal structure of the clusters was mostly reported to remain unaffected, except by Kaandorp et al. (Phys. Rev. Lett. 77, 2328 (1996)) who found compact clusters ``as flow becomes more important''. In the present paper we present three-dimensional simulations of ADLA. We did not find significant effects of low Reynolds-number advection on the cluster structure. We discuss the causes of the contradicting results by Kaandorp et al. (1996)}
}
@inproceedings{Naumov2003a,
title = {Generalized Coordinates for Cellular Automata Grids},
author = {L.A. Naumov},
year = {2003},
volume = {2658},
pages = {869-878},
metis_id = {276701},
url = {http://www.camellab.spb.ru/utils/dl.jsp?tgt=/pubs/2003/GenCoord.ICCS.pdf},
month = {June},
category = {CA, metrics},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part II},
editor = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J.J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
issn_isbn = {ISBN 3-540-40195-4}
}
@inproceedings{Naumov2003b,
title = {Automata Theory for Multi-Agent Systems Implementation},
author = {L.A. Naumov and A.A. Shalyto},
year = {2003},
pages = {65-71},
metis_id = {276702},
category = {Automata},
publisher = {IEEE},
booktitle = {Proceedings of International Conference Integration of Knowledge Intensive Multi-Systems: Modeling, Exploration and Engineering (KIMAS-03)},
address = {Boston}
}
@inproceedings{Naumov2003c,
title = {Automata Programming as a Sort of Synchronous Programming},
author = {L.A. Naumov and A.A. Shalyto},
year = {2003},
pages = {140-143},
metis_id = {276703},
category = {Automata},
publisher = {Kharkov National University of Radio Electronics},
booktitle = {Proceedings of East-West Design \& Test Conference (EWDTC 2003)}
}
@article{Naumov2003d,
title = {Cellular Automata. Realization and Experiments},
author = {L.A. Naumov and A.A. Shalyto},
year = {2003},
journal = {World of PC},
number = {8},
pages = {71--77},
url = {http://www.camellab.spb.ru/utils/dl.jsp?tgt=/pubs/2003/CA1.WPC.pdf},
category = {CA},
note = {in Russian},
address = {Moscow}
}
@inproceedings{Naumov2003e,
title = {Automata Theory for Applied Programming},
author = {L.A. Naumov and A.A. Shalyto},
year = {2003},
volume = {2},
pages = {86-92},
metis_id = {276704},
category = {Automata},
booktitle = {Second International Conference on the Problems of Controlling. Chosen Papers in Two Volumes}
}
@article{Naumov2003f,
title = {The Art of Lift Programming. Object-Oriented Programming with Explicit States Separation},
author = {L.A. Naumov and A.A. Shalyto},
year = {2003},
journal = {Informational Control Systems},
volume = {2003},
number = {6},
pages = {38-49},
metis_id = {276705},
category = {Automata},
note = {in Russian}
}
@inbook{Naumov2003g,
title = {Tasks Solving for the Correspondence School of Modern Programming. Lesson 9: Codes and Data Compression. Part 1.},
author = {L.A. Naumov},
year = {2003},
pages = {1--36},
metis_id = {276706},
publisher = {Informatization in Education},
note = {in Russian},
address = {Saint-Petersburg}
}
@book{Naumov2003h,
title = {Dynamic Programming},
author = {L.A. Naumov},
year = {2003},
pages = {1--32},
metis_id = {276707},
category = {DynamicProgramming},
publisher = {Informatization in Education},
address = {Saint-Petersburg},
issn_isbn = {ISBN 5-89733-047-6}
}
@article{Pooley2003a,
title = {Dynamical Formation of Close Binary Systems in Globular Clusters},
author = {D. Pooley and W.H.G. Lewin and S.F. Anderson and H. Baumgardt and A.V. Filippenko and B.M. Gaensler and L. Homer and P. Hut and V.M. Kaspi and J. Makino and B. Margon and S.L.W. McMillan and S.F. Portegies Zwart and M. van der Klis and F. Verbunt},
year = {2003},
journal = {Astrophys. J. Let.},
volume = {591},
number = {2},
pages = {L131--L134},
metis_id = {212999},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2003ApJ...591L.131P\&db_key=AST},
month = {July}
}
@article{Portegies_Zwart2003a,
title = {The Origin of IRS 16: Dynamically Driven In-Spiral of a Dense Star Cluster to the Galactic Center?},
author = {S.F. Portegies Zwart and S.L.W. McMillan and O. Gerhard},
year = {2003},
journal = {Astrophysical J.},
volume = {593},
number = {1},
pages = {352--357},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2003ApJ...593..352P\&db_key=AST},
month = {August},
category = {astronomy}
}
@inproceedings{Porubov2003a,
title = {Localized nonlinear strain waves in complex dispersive-dissipative solids},
author = {A.V. Porubov and G.A. Maugin and V.V. Gursky and V.V. Krzhizhanovskaya and D.V. Shevchenko},
year = {2003},
pages = {270--279},
metis_id = {276708},
category = {Soliton},
publisher = {Publ.: RAS IPM GAMM, St. Petersburg, Russia},
booktitle = {Proceedings of the XXXI International Conference "Advanced Problems in Mechanics", St. Petersburg, Russia, June 22-July 2, 2003}
}
@article{Rohde2003a,
title = {Improved bounce-back methods for no-slip walls in lattice-Boltzmann schemes: Theory and simulations},
author = {M. Rohde and B.D. Kandhai and J.J. Derksen and H.E.A. van den Akker},
year = {2003},
journal = {Phys. Rev. E},
volume = {67},
number = {6},
pages = {066703},
month = {Jun},
numpages = {10},
publisher = {American Physical Society},
doi = {10.1103/PhysRevE.67.066703}
}
@mastersthesis{Sakkos2003a,
title = {Physical Properties of Dendritic Structures under a constant Electric Field},
author = {K. Sakkos},
year = {2003},
month = {June},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands}
}
@inproceedings{Salzberg2003a,
title = {Visualizing evolutionary dynamics of self-replicators using graph-based genealogy},
author = {C.P. Salzberg and A.T. Antony and H. Sayama},
year = {2003},
pages = {387-394},
category = {Visualisation},
publisher = {Springer-Verlag},
booktitle = {Proceedings of the Seventh European Conference on Artificial Life (ECAL 2003)},
editor = {W. Banzhaf and T. Christaller and P. Dittrich and J.T. Kim and J. Ziegler},
address = {Dortmund, Germany}
}
@mastersthesis{Salzberg2003b,
title = {Emergent Evolutionary Dynamics of Self-Reproducing Cellular Automata},
author = {C.P. Salzberg},
year = {2003},
url = {Salzberg2003a.pdf},
month = {August},
category = {pwrs, mastersthesis, ComputationalScience},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Advisor: Hiroki Sayama, University of Electro-Communications, Chofugaoka, Chofu, Tokyo}
}
@article{Salzberg2003c,
title = {Genetic diversification and complex genealogy of self-replicators discovered in simple cellular automata: A preliminary report},
author = {C.P. Salzberg and A.T. Antony and H. Sayama},
year = {2003},
journal = {Journal of Three-dimensional Images},
volume = {17},
number = {4},
pages = {103--109}
}
@inproceedings{Salzberg2003d,
title = {Genetic diversification and adaptation of self-replicators discovered in simple cellular automata},
author = {C.P. Salzberg and A.T. Antony and H. Sayama},
year = {2003},
pages = {194-199},
booktitle = {Proceedings of the Sixth International Conference on Humans and Computers (HC-2003)},
address = {University of Aizu, Japan}
}
@mastersthesis{Shen2003a,
title = {Effectiveness of Approximation Models for Multi-Disciplinary Design Optimization},
author = {C. Shen},
year = {2003},
month = {August},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands}
}
@article{Sills2003a,
title = {MODEST-2: a summary},
author = {A.I. Sills and S. Deiters and P.-P. Eggleton and M. Freitag and M. Giersz and D.C. Heggie and J.R. Hurley and P. Hut and N. Ivanova and R.S. Klessen and P. Kroupa and J.C. Lombardi and S.L.W. McMillan and S.F. Portegies Zwart and H. Zinnecker},
year = {2003},
journal = {New Astronomy},
volume = {8},
pages = {605-628},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2003NewA....8..605S\&db_key=AST},
month = {aug},
category = {astronomy}
}
@inproceedings{Sloot2003a,
title = {Grid-based Interactive Visualisation of Medical Images},
author = {P.M.A. Sloot and G.D. van Albada and E.V. Zudilova and P. Heinzlreiter and D. Kranzlm\"uller and H. Rosmanith and J. Volkert},
year = {2003},
pages = {57 -- 66},
category = {Visualisation},
publisher = {Commission of the European Communities, Information Society Directorate-General},
booktitle = {Proceedings of the First European HealthGrid Conference, January, 16th-17th, 2003},
editor = {S. N\orager},
address = {Brussels, Belgium}
}
@proceedings{Sloot2003b,
title = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part I},
author = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
year = {2003},
volume = {2657},
url = {http://www.springerlink.com/openurl.asp?genre=issue\&issn=0302-9743\&volume=2657},
month = {June},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-40194-6}
}
@proceedings{Sloot2003c,
title = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part II},
author = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
year = {2003},
volume = {2658},
url = {http://www.springerlink.com/openurl.asp?genre=issue\&issn=0302-9743\&volume=2658},
month = {June},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-40195-4}
}
@proceedings{Sloot2003d,
title = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part III},
author = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
year = {2003},
volume = {2659},
url = {http://www.springerlink.com/openurl.asp?genre=issue\&issn=0302-9743\&volume=2659},
month = {June},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-40196-2}
}
@inproceedings{Sloot2003e,
title = {A grid-based problem-solving environment for biomedicine},
author = {P.M.A. Sloot and C.A.B. Boucher and I. Kiryukhin and K. Saskov and A.V. Boukhanovsky},
year = {2003},
pages = {300 -- 323},
metis_id = {214054},
publisher = {Commission of the European Communities, Information Society Directorate-General},
booktitle = {Proceedings of the First European HealthGrid Conference, January, 16th-17th, 2003},
editor = {S. N\orager},
address = {Brussels, Belgium}
}
@proceedings{Sloot2003f,
title = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part IV},
author = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
year = {2003},
volume = {2660},
url = {http://www.springerlink.com/openurl.asp?genre=issue\&issn=0302-9743\&volume=2660},
month = {June},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-40197-0}
}
@article{Spinnato2003a,
title = {The efficiency of the spiral-in of a black hole to the Galactic centre},
author = {P.F. Spinnato and M. Fellhauer and S.F. Portegies Zwart},
year = {2003},
journal = {Monthly Notices of the Royal Astronomical Society},
volume = {344},
number = {1},
pages = {22-33},
metis_id = {213223},
url = {http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-8711.2003.06782.x/abs/},
month = {September},
category = {ComputAstrophysics}
}
@inproceedings{Spinnato2003b,
title = {Tools and Techniques for N-body Simulations},
author = {P.F. Spinnato and S.F. Portegies Zwart and M. Fellhauer and G.D. van Albada and P.M.A. Sloot},
year = {2003},
volume = {1},
pages = {54--65},
metis_id = {213237},
category = {ComputAstrophysics},
publisher = {SAIt},
booktitle = {Proceedings of the 1st workshop on Computational Astrophysics in Italy: Methods and Tools, MemSAIt Suppl. Series},
editor = {R. Capuzzo Dolcetta}
}
@phdthesis{Spinnato2003c,
title = {Hybrid Systems for N-body Simulations},
author = {P.F. Spinnato},
year = {2003},
metis_id = {213063},
url = {Spinnato2003d.pdf},
month = {September},
category = {ComputAstrophysics, pwrs, phdthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands},
tutor = {Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. G.D. van Albada}
}
@article{Surovtsev2003a,
title = {Kinetics of the initial stage of immunoagglutionation studied with the scanning flow cytometer},
author = {I.V. Surovtsev and M.A. Yurkin and A.N. Shvalov and V.M. Nekrasov and G.F. Sivolobova and A.A. Grajdantseva and V.P. Maltsev and A.V. Chernyshev},
year = {2003},
journal = {Colloids and Surfaces B: Biointerfaces},
volume = {32},
number = {3},
pages = {245-255},
metis_id = {276710},
url = {http://dx.doi.org/10.1016/S0927-7765(03)00177-2},
category = {Nato-sfp},
doi = {10.1016/S0927-7765(03)00177-2}
}
@inproceedings{Surovtsev2003b,
title = {Kinetics of the initial stage of immunoagglutionation studied with the scanning flow cytometer},
author = {I.V. Surovtsev and M.A. Yurkin and A.N. Shvalov and G.F. Sivolobova},
year = {2003},
metis_id = {276712},
month = {January},
category = {Nato-sfp},
booktitle = {Proceedings of the Photonic West 2003, Manipulation and Analysis of Biomolecules, Cells and Tissues},
address = {San Jose, California, USA}
}
@article{Surovtsev2003c,
title = {Kinetics of the initial stage of immunoagglutionation studied with the scanning flow cytometer},
author = {I.V. Surovtsev and M.A. Yurkin and A.N. Shvalov and G.F. Sivolobova},
year = {2003},
journal = {SPIE Proceedings},
volume = {4962},
pages = {354-363},
metis_id = {276711},
url = {http://bookstore.spie.org/index.cfm?fuseaction=DetailPaper\&ProductId=477906\&coden=},
category = {Nato-sfp}
}
@inproceedings{Tirado-Ramos2003a,
title = {Experimental Grid Access for Dynamic Discovery and Data Transfer in Distributed Interactive Simulation Systems},
author = {A. Tirado Ramos and K.J. Zajac and Z. Zhao and P.M.A. Sloot and G.D. van Albada and M.T. Bubak},
year = {2003},
volume = {2657},
pages = {284--292},
month = {June},
category = {Grid},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part I},
editor = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J.J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
issn_isbn = {ISBN 3-540-40194-6}
}
@mastersthesis{Xiao2003a,
title = {A High Performance Distributed Computing Architecture for Molecular Image-Guided Local Drug Delivery -- An exercise in scenario based architecture design using the AFCR model},
author = {J. Xiao},
year = {2003},
url = {Xiao2003a.pdf},
month = {August},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands}
}
@inproceedings{Zajac2003a,
title = {Grid Services for HLA-based Distributed Simulation Frameworks},
author = {K.J. Zajac and A. Tirado Ramos and Z. Zhao and P.M.A. Sloot and M.T. Bubak},
year = {2003},
pages = {147--154},
metis_id = {214064},
month = {February},
category = {Grid},
publisher = {Springer-Verlag},
booktitle = {First European Across Grids Conference, Santiago de Compostela, Spain},
editor = {F. Fern\'andez Rivera and M.T. Bubak and A. G\'omez Tato and R. Doallo},
address = {Heidelberg},
issn_isbn = {ISBN 3-540-21048-2}
}
@inproceedings{Zajac2003b,
title = {Towards a Grid Management System for HLA-Based Interactive Simulations},
author = {K.J. Zajac and M.T. Bubak and M. Malawski and P.M.A. Sloot},
year = {2003},
pages = {4--11},
metis_id = {214075},
month = {October},
publisher = {IEEE Computer Society},
booktitle = {Proceedings Seventh IEEE International Symposium on Distributed Simulation and Real Time Applications (DS-RT 2003)},
editor = {S.J. Turner and S.J.E. Taylor},
address = {Delft, The Netherlands}
}
@inproceedings{Zhao2003a,
title = {Interaction Scenario: Orchestrating Agents in a multi-agent System},
author = {Z. Zhao and G.D. van Albada and P.M.A. Sloot},
year = {2003},
pages = {155--160},
metis_id = {214084},
month = {April},
category = {PSE},
booktitle = {Proceedings of the 4th workshop on Agent-Based Simulation},
editor = {J.-P. Muller and M.-M. Seidel},
address = {Montpellier, France},
issn_isbn = {ISBN 3-936-150-25-7}
}
@inproceedings{Zhao2003b,
title = {ISS-Studio: a prototype for a user-friendly tool for designing interactive experiments in Problem Solving Environments},
author = {Z. Zhao and G.D. van Albada and A. Tirado Ramos and K.J. Zajac and P.M.A. Sloot},
year = {2003},
volume = {2657},
pages = {679--688},
metis_id = {214079},
month = {June},
category = {LBM, PSE},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part I},
editor = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J.J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
issn_isbn = {ISBN 3-540-40194-6}
}
@inproceedings{Zudilova2003a,
title = {Virtual Reality and Desktop as a Combined Interaction-Visualisation Medium for a Problem-Solving Environment},
author = {E.V. Zudilova and P.M.A. Sloot},
year = {2003},
volume = {2659},
pages = {1025--1034},
month = {June},
category = {LBM, Visualisation, PSE},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2003, Melbourne, Australia and St. Petersburg, Russia, Proceedings Part III},
editor = {P.M.A. Sloot and D. Abramson and A.V. Bogdanov and J.J. Dongarra and A.Y. Zomaya and Y.E. Gorbachev},
issn_isbn = {ISBN 3-540-40196-2}
}
@article{Adams2002a,
title = {Structure of the Praesepe Star Cluster},
author = {J.D. Adams and J.R. Stauffer and M.F. Skrutskie and D.G. Monet and S.F. Portegies Zwart and K.A. Janes and C.A. Beichman},
year = {2002},
journal = {Astronomical Journal},
volume = {124},
number = {3},
pages = {1570-1584},
metis_id = {197887},
url = {http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2002AJ....124.1570A\&db_key=AST},
month = {September},
category = {astronomy}
}
@article{Afsarmanesh2002a,
title = {VLAM-G: A Grid-based virtual laboratory},
author = {H. Afsarmanesh and R.G. Belleman and A.S.Z. Belloum and A. Benabdelkader and J.F.J. van den Brand and G.B. Eijkel and A. Frenkel and C. Garita and D.L. Groep and R.M.A. Heeren and Z.W. Hendrikse and L.O. Hertzberger and J.A. Kaandorp and E.C. Kaletas and V.V. Korkhov and C.T.A.M. de Laat and P.M.A. Sloot and D. Vasunin and A. Visser and H.H. Yakali},
year = {2002},
journal = {Scientific Programming},
volume = {10},
number = {2},
pages = {173-181},
metis_id = {203318},
category = {Visualisation},
note = {Special issue on Grid Computing},
publisher = {IOS Press},
editor = {R.H. Perrott and B.K. Szymanski},
issn_isbn = {ISSN 1058-9244}
}
@inproceedings{Albada2002a,
title = {Surfing the Grid - Dynamic Task Migration in the Polder Metacomputer Project},
author = {G.D. van Albada and P.M.A. Sloot},
year = {2002},
pages = {4--5},
publisher = {Springer-Verlag},
booktitle = {Proceedings of the 9th European PVM/MPI Users' Group Meeting on Recent Advances in Parallel Virtual Machine and Message Passing Interface},
address = {London, UK},
issn_isbn = {3-540-44296-0}
}
@mastersthesis{Alimadhi2002a,
title = {Mobile Internet: Wireless access to Web-based interfaces of legacy simulations},
author = {F. Alimadhi},
year = {2002},
url = {Alimadhi2002a.pdf},
month = {September},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
abstract = {The work presented here focuses on the encounter between the WWW and mobile Internet. It is specifically focused on the need to provide gateways between Web resources and mobile technology. A prototype is designed and implemented to study the possibilities of making existing Web resources available to mobile devices. In the design phase, special considerations are made of the constraints inherent in mobile Internet and special emphasis is placed on overcoming these constraints in tractable ways. In order to achieve this goal, two methods are applied. In the first method an HTTP Proxy server is used between the mobile device and origin Web server. Proxy fetches Web pages on the client's behalf, extracts the most useful information from them and uses this information to construct new pages, which are delivered to the mobile device in an appropriate format. In the second method the advantages of Java technology are taken into account and specifically J2ME networking capabilities. By using these capabilities, the J2ME enabled device directly fetches the Web pages from the origin Web server. The processing power capabilities of today's mobile devices are used to extract and display the most useful information. A comparative analysis between the two methods is provided.},
address = {Amsterdam, The Netherlands}
}
@article{Artoli2002a,
title = {3D Pulsatile flow with the Lattice Boltzmann BGK Method},
author = {A.M.M. Artoli and A.G. Hoekstra and P.M.A. Sloot},
year = {2002},
journal = {International Journal of Modern Physics C},
volume = {13},
number = {8},
pages = {1119--1134},
metis_id = {201503},
month = {October}
}
@inproceedings{Artoli2002b,
title = {Accuracy of 2D pulsatile flow in the lattice Boltzmann BGK method},
author = {A.M.M. Artoli and A.G. Hoekstra and P.M.A. Sloot},
year = {2002},
volume = {2329},
pages = {361--370},
metis_id = {201502},
month = {April},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2002, Proceedings Part I},
editor = {P.M.A. Sloot and C.J.K. Tan and J.J. Dongarra and A.G. Hoekstra},
issn_isbn = {ISBN 3-54043591-3}
}
@inproceedings{Belleman2002a,
title = {High performance distributed simulation for interactive simulated vascular reconstruction},
author = {R.G. Belleman and R.M. Shulakov},
year = {2002},
volume = {2331},
pages = {265--274},
metis_id = {201507},
url = {Belleman2002b.pdf},
month = {April},
category = {Visualisation},
publisher = {Springer Verlag},
series = {Lecture Notes in Computer Science},
booktitle = {Computational Science - ICCS 2002, Proceedings Part III},
editor = {P.M.A. Sloot and C.J.K. Tan and J.J. Dongarra and A.G. Hoekstra},
issn_isbn = {ISBN 3-54043594-8}
}
@incollection{Belleman2002b,
title = {Dynamic Exploration Environments},
author = {R.G. Belleman and P.M.A. Sloot},
year = {2002},
pages = {771-787},
metis_id = {201506},
url = {Belleman2002a.pdf},
category = {Visualisation},
publisher = {STT/Beweton},
booktitle = {Dealing with the data flood (mining data, text and multimedia) (STT 65)},
editor = {J. Meij},
address = {The Hague, the Netherlands},
issn_isbn = {ISBN 90-804496-6-0}
}
@article{Bubak2002a,
title = {Portable Library of Migratable Sockets},
author = {M.T. Bubak and D. Zbik and G.D. van Albada and K.A. Iskra and P.M.A. Sloot},
year = {2002},
journal = {Scientific Programming},
volume = {9},
number = {apr-01},
pages = {211--222},
metis_id = {276686},
url = {http://iospress.metapress.com/openurl.asp?genre=issue\&issn=1058-9244\&volume=9\&issue=4},
category = {Dynamite, DPVM},
publisher = {IOS Press},
address = {Amsterdam, The Netherlands},
issn_isbn = {ISSN 1058-9244}
}
@mastersthesis{Caarls2002a,
title = {Genetic Alorithms Visualisation},
author = {W. Caarls},
year = {2002},
url = {Caarls2002a.pdf},
month = {April},
category = {Visualisation, pwrs, mastersthesis},
school = {University of Amsterdam},
address = {Amsterdam, The Netherlands}
}
@mastersthesis{Chen2002a,
title = {Model of Drug Therapy for HIV Infection using Non-uniform Cellular Automata},
author = {F. Chen},
year = {2002},
url = {Chen2002a.pdf},
month = {August},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
abstract = {In this study, we employ non-uniform Cellular Automata (CA) to simulate drug treatment of HIV infection, where each computational domain may contain different CA rules, in contrast to normal uniform CA models. Ordinary (or partial) differential equation models are insufficient to describe the two extreme time scales involved in HIV infection (days and decades), as well as the implicit spatial heterogeneity (Fischl, M.A. et al., 1990; Hershberg, U. et al., 2001; Kirschner D.E. and Webb, G.F., 1997a). Zorzenon dos Santose R.M. (2001) reported a cellular automata approach to simulate three-phase patterns of human immunodeficiency virus (HIV) infection consisting of primary response, clinical latency and onset of acquired immunodeficiency syndrome (AIDS), Here we report a related model. We developed a non-uniform CA model to study the dynamics of drug therapy of HIV infection, which simulates four-phases (acute, chronic, drug treatment responds and onset of AIDS). The results of our basic drug therapy of HIV infection model indicate that both simulations (with and without treatments) evolve to the relatively same steady state (characteristic of Wolfram's class II behavior). The results of our advanced drug therapy of HIV infection model, including lymphocytes mobility and threshold concept for Pinfect and Prepl, indicate that the healthy cells can evolve into undetected level. Three different drug therapies (monotherapy, combined drug therapy and highly active antiretroviral therapy HAART) can also be simulated in our model. Our model for prediction of the temporal behavior of the immune system to drug therapy qualitatively corresponds to clinical data.},
address = {Amsterdam, The Netherlands}
}
@mastersthesis{Dam2002a,
title = {Multi-disciplinair ontwerp en multi-objective optimalisatie van een blended-wing-body vliegtuigconfiguratie met behulp van benaderingsmodellen},
author = {M. ten Dam},
year = {2002},
url = {Dam2002a.pdf},
month = {February},
category = {pwrs, mastersthesis},
school = {University of Amsterdam},
abstract = {In multi-disciplinary aircraft design, numerical simulations of typically the aerodynamic behaviour and structural deformation of the aircraft, using Computational Fluid Dynamics (CFD) and Computational Structural Mechanics (CSM) analyses, are usually performed. Such analyses are computationally very expensive, and are normally executed many times, especially if design optimisations are performed. Therefore there is a need for approximation models that can represent the key characteristics of the design and are computationally much cheaper. In this study, Artificial Neural Networks (ANN) are used to make approximation models of some key design characteristics of the blended-wing-body (BWB) aircraft configuration. First, an approximation model is made of some properties of the 2-D airfoil of the BWB. This model is used to do a multi-discipline and multi-objective design optimisation study. In a similar way an approximation model is made and an optimisation study is done for some properties of the 3-D BWB configuration.},
address = {Amsterdam, The Netherlands},
note = {in Dutch}
}
@article{Ghulghazaryan2002a,
title = {Yang-Lee zeros of the Q-state Potts model on recursive lattices},
author = {R.G. Ghulghazaryan and N.S. Ananikian and P.M.A. Sloot},
year = {2002},
journal = {Physical Review E},
volume = {66},
number = {46110},
pages = {1-9},
metis_id = {276687},
url = {http://prola.aps.org/abstract/PRE/v66/i4/e046110},
doi = {10.1103/PhysRevE.66.046110},
abstract = {The Yang-Lee zeros of the Q-state Potts model on recursive lattices are studied for noninteger values of Q. Considering one-dimensional (1D) lattice as a Bethe lattice with coordination number equal to 2, the location of Yang-Lee zeros of 1D ferromagnetic and antiferromagnetic Potts models is completely analyzed in terms of neutral periodical points. Three different regimes for Yang-Lee zeros are found for Q>1 and 01. Complex magnetic field metastability regions are studied for the Q>1 and 0