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| I. Altintas: Collaborative provenance for workflow-driven science and engineering, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot; co-promotor: Prof. Dr. B. Ludäscher) February 2011. ISBN13: 978-90-9025979-6.
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| G. Ertaylan: A multi-scale approach for deciphering HIV infection, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot) February 2011. ISBN13 978-90-9025974-10.
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| J.T. Mościcki: Understanding and mastering dynamics in computing grids: processing moldable tasks with user-level overlay, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. M.T. Bubak; co-promotor: Prof. Dr. P.M.A. Sloot) April 2011.
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| L.A. Naumov: Modelling with Cellular Automata: Problem Solving Environments and Multidimensional Applications, PhD thesis, Universiteit van Amsterdam, (Promotor: prof.dr. P.M.A. Sloot, co-promotor: dr.ir. A.G. Hoekstra) June 2011.
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| 5
| G. Qiu: Understanding the complex dynamics of financial markets through microsimulation, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. B.D. Kandhai) February 2011. ISBN13 978-94-91211-01-0.
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| Y. Fomekong-Nanfack: Genetic regulatory networks inference : modeling, parameters estimation & model validation, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr.J.A. Kaandorp) April 2010.
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| D.J. Groen: High performance N-body simulation on computational grids, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. S.F. Portegies Zwart, Co-promotores: Prof. Dr. P.M.A. Sloot, Prof. Dr. E.P.J. van den Heuvel) November 2010.
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| J.J. van der Ham: A Semantic Model for Complex Computer Networks: The Network Description Language, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. Ir. C.T.A.M. de Laat) April 2010. ISBN13 9789081416023.
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| E. Lorenz: Multi-scale simulations with complex automata: in-stent restenosis and suspension flow, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot; co-promotor: Dr.Ir. A.G. Hoekstra) November 2010.
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| S. Murtaza: High performance reconfigurable computing with cellular automata, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. A.G. Hoekstra) May 2010.
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| 11
| J. Cui: Mathematical Modeling of Metal Ion Homeostasis and Signaling Systems, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. J.A. Kaandorp) March 2009.
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| F. Dijkstra: Framework for path finding in multi-layer transport networks, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. Ir. C.T.A.M. de Laat) June 2009. ISBN: 9789081416016.
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| V.V. Korkhov: Hierarchical resource management in grid computing, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. A.S.Z. Belloum) April 2009.
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| 14
| S.S. Msanjila: On inter-organizational trust engineering in networked collaborations: modeling and management of rational trust, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. H. Afsarmanesh) September 2009. ISBN: 9789057761966.
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| 15
| J. Vidal Rodríguez: Stochasticity in Signal Transduction Pathways, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. J.A. Kaandorp) November 2009. ISBN 978-90-9024739-7.
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| J.M. Bernsdorf: Simulation of Complex Flows and Multi-Physics with the Lattice-Boltzmann Method, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. A.G. Hoekstra) January 2008.
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| 17
| E. Gaburov: Stellar collisions in young star clusters, PhD thesis, University of Amsterdam, (promotores: R.A.J.M. Weijers and P.M.A. Sloot; copromotores: S.F. Portegies Zwart and O.R. Pols) November 2008.
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| 18
| V.V. Krzhizhanovskaya: A Virtual Reactor for Simulation of Plasma Enhanced Chemical Vapor Deposition, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Prof. Dr. Y.E. Gorbachev) June 2008.
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| 19
| L. Axner: High Performance Computational Hemodynamics with the Lattics Boltzmann Method, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. A.G. Hoekstra) December 2007.
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| 20
| A. Tirado Ramos: Collaborative Software Architectures for Interactive Biomedical Applications, PhD thesis, University of Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Prof. Dr. M.T. Bubak) June 2007. ISBN-13: 978-90-6464-143-5.
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| 21
| M.A. Yurkin: Discrete dipole simulations of light scattering by blood cells, PhD thesis, Universiteit van Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. A.G. Hoekstra) December 2007.
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| A. Gualandris: Simulating self-gravitating systems on parallel computers, PhD thesis, University of Amsterdam, (Promotores: Prof. Dr. E.P.J. van den Heuvel and Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. S.F. Portegies Zwart) September 2006. ISBN-10: 9064640246 ISBN-13: 9789064640247.
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| 23
| K.J. Rycerz: Grid-based HLA Simulation Support, PhD thesis, University of Amsterdam, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. M.T. Bubak) June 2006.
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| 24
| K.A. Iskra: Time Warp - from Cluster to Grid, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. G.D. van Albada) June 2005.
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| 25
| Z. Zhao: An agent based architecture for constructing Interactive Simulation Systems, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. G.D. van Albada) December 2004.
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| 26
| A.M.M. Artoli: Mesoscopic Computational Haemodynamics, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. Ir. A.G. Hoekstra) October 2003.
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| 27
| R.G. Belleman: Interactive Exploration in Virtual Environments, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot) April 2003.
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| 28
| R.M.H. Merks: Branching Growth in Stony Corals - a Modelling Approach, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotores: Dr. Ir. A.G. Hoekstra; Dr. J.A. Kaandorp) May 2003.
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| 29
| P.F. Spinnato: Hybrid Systems for N-body Simulations, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. G.D. van Albada) September 2003.
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| 30
| B.J. Overeinder: Distributed Event-driven Simulation - Scheduling Strategies and Resource Management, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Prof. Dr. M. Livny) November 2000.
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| 31
| B.D. Kandhai: Large Scale Lattice-Boltzmann Simulations: Computational Methods and Applications, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot, co-promotor: Dr. Ir. A.G. Hoekstra) 1999.
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| A. Schoneveld: Parallel Complex Systems Simulation, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot) 1999.
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| 33
| J.F. de Ronde: Mapping in High Performance Computing - A Case Study in Finite Element Simulation, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot, co-promotor: Prof. Dr. L.O. Hertzberger) 1998.
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| 34
| J.M. Voogd: Crystallisation on a Sphere - Computational Studies of two-dimensional Lennard-Jones Systems, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot, co-promotor: Dr. R. van Dantzig) 1998.
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| 35
| A.G. Hoekstra: Computer Simulations of Elastic Light Scattering, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. L.O. Hertzberger, co-promotor: Dr. P.M.A. Sloot) February 1994.
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| J.A. Kaandorp: Modelling growth forms of biological objects using fractals, PhD thesis, University of Amsterdam, (Promotor: Prof. Dr. Ir. F.C.A. Groen, 2nd promotor: Dr. J.H. Stock, co-promotor: Dr. E.H. Dooijes, 2nd co-promotor: Prof. Dr. H.A. Lauwerier) 1992.
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| P.M.A. Sloot: Elastic light scattering from leukocytes, in the development of computer assisted cell separation, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. dr. L.O. Hertzberger, co-promotor: Prof.dr. C.G. Figdor) 1988.
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| 38
| G.D. van Albada: The peculiar spiral galaxy NGC 4258 - high resolution radio observations and their interpretation, PhD thesis, Leiden Observatory, University of Leiden, Leiden, The Netherlands, (Promotor: Prof. Dr. H. van der Laan, co-referent: Dr. W.W. Shane) September 1978.
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