Publications of the CSL group

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2007

Proceedings

M. T. Bubak, P. Nowakowski, and S. Unger. K-WfGrid knowledge-based workflow system for Grid applicatiobs. In: Cracow'06 Grid Workshop, Vol 2: K-Wf Grid: the knowledge-based workflow system for Grid applications: October 15--18, 2006 Cracow, Poland. pp. 1-12.

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Article

A. I. Sills, L. Subr, and S. F. Portegies Zwart. Joint Discussion 14 Modeling dense stellar systems. Highlights of Astronomy 14, pp. 421-421.

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Proceedings

M. Malawski, M. T. Bubak, F. Baude, D. Caromel, L. Henrio, and M. Morel. Interoperability of grid component models: GCM and CCA case study. In: Towards Next Generation Grids, proceedings of the CoreGRID Symposium in conjunction with Euro-Par 2007. pp. 95-105.

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Book

P. M. A. Sloot. International Conference on Computational Science series.

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Article

R. G. Belleman, M. Scarpa, and B. Stolk. Interactive Simulation and Visualization for Cancer Treatment Planning with Grid-based Technology. ERCIM News 69, pp. 22-23.

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Article

K. J. Rycerz, A. Tirado Ramos, A. Gualandris, S. F. Portegies Zwart, M. T. Bubak, and P. M. A. Sloot. Interactive N-Body simulations on the Grid: HLA versus MPI. International Journal of High Performance Computing Applications 21, pp. 210-221.

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MSc Thesis

Z. R. Rahhal. Interactive Distributed Computing Middleware. Supervised by R. G. Belleman.

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MSc Thesis

T. de Kler. Integration of the ARToolKitPlus optical tracker into the Personal Space Station. Supervised by R. G. Belleman.

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Article

S. D. Olabarriaga, J. G. Snel, C. P. Botha, and R. G. Belleman. Integrated Support for Medical Image Analysis Methods: from Development to Clinical Application. IEEE Transactions on Information Technology in Biomedicine 11(1), pp. 47-57.

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Article

J. Vidal Rodríguez and J. A. Kaandorp. Inferring the distribution of Inter-Reaction Intervals for Diffusion-Limited Reactions on Lattices. International Journal of Modern Physics C 18, pp. 749-757.

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Article

C. H. Liu, T. Wang, M. Postma, A. G. Obukhov, C. Montell, and R. C. Hardie. In Vivo Identification and Manipulation of the Ca2+ Selectivity Filter in the Drosophila Transient Receptor Potential Channel. The Journal of Neuroscience 27(3), pp. 604-615.

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Article

S. F. Portegies Zwart, R. G. Belleman, and P. M. Geldof. High-performance direct gravitational N-body simulations on graphics processing units. New Astronomy 12, pp. 641-650.

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PhD Thesis

L. Axner. High performance computational hemodynamics with the Lattice Boltzmann method. ISBN 9789057761706. Supervised by P. M. A. Sloot and A. G. Hoekstra.

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MSc Thesis

J. Bédorf. High Performance Direct Gravitational N-body Simulations on Graphics Processing Units -- An implementation in CUDA. Supervised by R. G. Belleman and S. F. Portegies Zwart.

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Book

A. G. Hoekstra. Guest Editor Special Issue ‘Simulating Multiphysics Multiscale Systems’ of the International Journal for Multiscale Computational Engineering.

Citation
MSc Thesis

P. M. Geldof. Generic Computing on a Graphics Processing Unit. Supervised by R. G. Belleman.

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PhD Thesis

L. A. Naumov. Generalized Coordinates Introduction Method and a Tool for Computational Experiments' Software Design Automation, Basing on Cellular Automata. Supervised by A. A. Shalyto.

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Proceedings

B. Bali\'s, M. T. Bubak, and B. Labno. GEMINI: Generic Monitoring Infrastructure for Grid resources and applications. ISBN 978-83-915141-8-4. pp. 60-73.

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Proceedings

B. Baliś, M. T. Bubak, and M. Pelczar. From monitoring data to experimental information monitoring of Grid scientific workflows. In: Third IEEE international conference on e-Science and Grid computing: Bangalore, India, 10--13 December 2007. pp. 77-84.

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Article

W. E. G. Müller, A. Boreiko, U. Schloemacher, X. Wang, M. Nawaz Tahir, W. Tremel, D. Brandt, J. A. Kaandorp, and H. C. Schroeder. Fractal-related assembly of the axial filament in the demosponge Suberites domuncula: relevance to biomineralization and the formation of biogenic silica,. Biomaterials 28, pp. 4501-4511.

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Proceedings

M. B. N. Kouwenhoven, A. G. A. Brown, S. F. Portegies Zwart, and L. Kaper. Finding the Primordial Binary Population in Sco OB2: on the interpretation of binary star observations. In: IAU Symposium.

Citation
Chapter

M. Kasztelnik, M. T. Bubak, C. Górka, M. Malawski, and T. Gubala. Fault tolerant Grid registery. In: Distributed and parallel systems: from cluster to Grid computing. pp. 135-144.

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Article

M. P. Muno, B. M. Gaensler, J. S. Clark, R. de Grijs, D. Pooley, I. R. Stevens, and S. F. Portegies Zwart. Exciting the magnetosphere of the magnetar CXOU J164710.2-455216 in Westerlund 1. Monthly Notices of the Royal Astronomical Society 378, pp. L44-L48.

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Article

Y. Fomekong Nanfack, J. A. Kaandorp, and J. G. Blom. Efficient parameter estimation for spatio-temporal models of pattern formation: Case study of Drosophila melanogaster. Bioinformatics 23, pp. 3356-3363.

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Proceedings

B. Baliś, M. T. Bubak, K. Sterna, and A. Bemben. Efficient and Reliable Execution of Legacy Codes Exposed as Services. In: International Conference on Computational Science (1). 4487, pp. 390-397.

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Proceedings

V. V. Krzhizhanovskaya and V. V. Korkhov. Dynamic Load Balancing of Black-Box Applications with a Resource Selection Mechanism on Heterogeneous Resources of the Grid. In: Proceedings of the Ninth International Conference on Parallel Computing Technologies. pp. 245-260.

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Book

W. Dubizky, A Schuster, P. M. A. Sloot, M. Schroeder, and M. Romberg. Distributed, High-Performance and Grid Computing in Computational Biology.

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Article

M. A. Yurkin, K. A. Semyanov, V. P. Maltsev, and A. G. Hoekstra. Discrimination of granulocyte subtypes from light scattering: theoretical analysis using a granulated sphere model. Optics Express 15, pp. 16561-16580.

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PhD Thesis

M. A. Yurkin. Discrete dipole simulations of light scattering by blood cells. ISBN 9057761696, 9789057761690. Supervised by P. M. A. Sloot and A. G. Hoekstra.

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Proceedings

M. van Woudenberg and L. A. Naumov. Development of Tools for Performing Computations on FPGA Systems, Using CAME&L Software. In: Proceedings of XIV All-Russian Guidance Conference "Telematics-2007". 2, pp. 527-529.

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MSc Thesis

M. Lankamp. Developing a reference implementation for a microgrid of microthreaded microprocessors. Supervised by C. R. Jesshope.

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Proceedings

M. A. Yurkin. Current capabilities of the discrete dipole approximation for very large particles: speed, accuracy, and computational tricks. In: Proceedings of the DDA - Workshop. pp. 31-33.

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Book

M. Bubak, M. Turała, and K. Wiatr. Cracow '06 Grid Workshop, October 15-18, 2006 Cracow, Poland: proceedings. ISBN 9788391514177.

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Proceedings

T. Gubala, D. Harezlak, M. T. Bubak, and M. Malawski. Constructing abstract workflows of applications with workflow composition tool. In: Cracow'06 Grid Workshop, Vol 2: K-Wf Grid: the knowledge-based workflow system for Grid applications: October 15--18, 2006 Cracow, Poland. pp. 25-30.

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Proceedings

L. A. Naumov. Conceptual Changes in Cellular Automata Development Library (CADLib) from Version 1.0 to Version 1.1. In: Proceedings of XIV All-Russian Guidance Conference "Telematics-2007". 2, pp. 529-530.

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Article

M. Dobrzyński, J. Vidal Rodríguez, J. A. Kaandorp, and J. G. Blom. Computational methods for diffusion-influenced biochemical reactions. Bioinformatics 23, pp. 1969-1977.

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Book

P. M. A. Sloot, D. Frenkel, H. A. van der Vorst, A. van Kampen, H. Bal, P. Klint, R. M. M. Mattheij, J. van Wijk, J. Schaye, H.-J. Langevelde, R. H. Bisseling, B. de Smit, E. Valenteyn, H. Sips, J. B. T. M. Roerdink, and K. G. Langedoen. Computational e-Science: Studying complex systems in silico. A National Coordinated Initiative. White Paper..

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Book

Y. Shi, G. D. van Albada, J. J. Dongarra, and P. M. A. Sloot. Computational Science - ICCS 2007: 7th International Conference, Beijing, China, Proceedings, Part IV.

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Book

Y. Shi, G. D. van Albada, J. J. Dongarra, and P. M. A. Sloot. Computational Science - ICCS 2007: 7th International Conference, Beijing, China, Proceedings, Part III.

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Book

Y. Shi, G. D. van Albada, J. J. Dongarra, and P. M. A. Sloot. Computational Science - ICCS 2007: 7th International Conference, Beijing, China, Proceedings, Part II.

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Book

Y. Shi, G. D. van Albada, J. J. Dongarra, and P. M. A. Sloot. Computational Science - ICCS 2007: 7th International Conference, Beijing, China, Proceedings, Part I.

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Article

A. Penttilä, E. Zubko, K. Lumme, K. Muinonen, M. A. Yurkin, B. T. Draine, J. Rahola, A. G. Hoekstra, and Y. Shkuratov. Comparison between discrete dipole implementations and exact techniques. Journal of Quantitative Spectroscopy & Radiative Transfer 106, pp. 417-436.

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PhD Thesis

A. Tirado Ramos. Collaborative software architectures for interactive biomedical applications. ISBN 9789064641435. Supervised by P. M. A. Sloot and M. T. Bubak.

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Proceedings

M. T. Bubak, T. Gubala, M. Kasztelnik, M. Malawski, P. Nowakowski, and P. M. A. Sloot. Collaborative Virtual Laboratory for e-Health. In: Expanding the Knowledge Economy: Issues, Applications, Case Studies, eChallenges e-2007 Conference Proceedings. pp. 537-544.

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Proceedings

K. A. Semyanov, P. A. Tarasov, M. A. Yurkin, A. G. Hoekstra, and V. P. Maltsev. Characterization of native red blood cell morphology by scanning flow cytometry. In: 8th International Congress on Optical Particle Characterization. p. 56.

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Article

P. J. M. van Haastert and M. Postma. Biased Random Walk by Stochastic Fluctuations of Chemoattractant-Receptor Interactions at the Lower Limit of Detection. Biophysical Journal 93, pp. 1787-1796.

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Proceedings

M. T. Bubak, D. Harezlak, P. Nowakowski, T. Gubala, and M. Malawski. Appea: A Platform for Development and Execution of Grid Applications. In: Expanding the Knowledge Economy: Issues, Applications, Case Studies, eChallenges e-2007 Conference Proceedings. pp. 123-130.

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Proceedings

M. Scarpa and R. G. Belleman. An interaction framework for VR and AR applications. In: ASCI 2007, Proceedings of the 13th annual conference of the Advanced School for Computing and Imaging. pp. 430-437.

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Article

S. F. Portegies Zwart and E. P. J. van den Heuvel. A runaway collision in a young star cluster as the origin of the brightest supernova. Nature 450, pp. 388-389.

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Proceedings

M. Malawski, T. Bartynski, E. Ciepiela, J. Kocot, P. Pelczar, and M. T. Bubak. A new approach to supporting component applications on Grid. In: Cracow '06 Grid Workshop, October 15-18, 2006. pp. 328-336.

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Article

A. Gualandris and S. F. Portegies Zwart. A hypervelocity star from the Large Magellanic Cloud. Monthly Notices of the Royal Astronomical Society 376, pp. L29-L33.

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Article

K. Kruszynski, J. A. Kaandorp, and R. van Liere. A computational method for quantifying morphological variation in scleractinian corals. Coral reefs 26, pp. 831-840.

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Proceedings

G. Ertaylan and P. M. A. Sloot. A complex automata model of HIV-1 co-receptor tropism: Understanding mutation rate pressure. In: Reviews in Antiretroviral Therapy. 2.

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Article

S. L. W. McMillan, E. Vesperini, and S. F. Portegies Zwart. A Dynamical Origin for Early Mass Segregation in Young Star Clusters. Astrophysical Journal Letters 655, pp. L45-L49.

Citation
Proceedings

M. T. Bubak and S. Unger. In: Cracow'06 Grid Workshop, Vol 2: K-Wf Grid: the knowledge-based workflow system for Grid applications: October 15--18, 2006 Cracow, Poland. ISBN 978-83-915141-8-4.

Citation
Proceedings

W. Dubizky, A. Schuster, P. M. A. Sloot, M. Schroeder, and M. Romberg. In: Distributed, High-Performance and Grid Computing in Computational Biology. ISBN 978-3-540-69841-8. Lecture Notes in Computer Science 4360, pp. 1-190.

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2006

Book

P. M. A. Sloot. eScience 2006, Amsterdam, Proceedings published by IEEE.

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Article

M. P. Muno, B. Gaensler, J. S. Clark, S. F. Portegies Zwart, D. Pooley, R. de Grijs, I. Stevens, and I. Negueruela. XMM Observations of AXP CXO J167410.2-455216 Four Days Prior to Outburst. The astronomer's telegram p. #902.

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Proceedings

V. Korkhov and V. V. Krzhizhanovskaya. Workload Balancing in Heterogeneous Grid Environment: A Virtual Reactor Case Study. In: Distributed computing and grid-technologies in science and education = Raspredelennye vyčislenija i grid-technologii v nauke i obrazovanii. ISBN 595300138X, 9785953001380. pp. 103-113.

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Proceedings

V. Korkhov and V. V. Krzhizhanovskaya. Workload Balancing in Heterogeneous Grid Environment: A Virtual Reactor Case Study. In: Distributed computing and grid-technologies in science and education = Raspredelennye vyčislenija i grid-technologii v nauke i obrazovanii. ISBN 5953001177, 9785953001175. p. 93.

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Proceedings

V. V. Krzhizhanovskaya, V. Korkhov, and P. M. A. Sloot. Virtual Reactor: a distributed computing environment for simulation of plasma chemical processes on heterogeneous resources of the Grid. In: All-Russian conference "Scientific services on the Internet: Parallel Programming Technologies".

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Proceedings

M. T. Bubak, M. Malawski, and M. Placek. Using MOCCA Component Environment for Simulation of Gold Clusters. In: Proceedings of Cracow Grid Workshop - CGW'05, November 20-23 2005. pp. 295-299.

Citation
MSc Thesis

M. van Woudenberg. Using FPGAs to Speed Up Cellular Automata Computations. Supervised by A. G. Hoekstra.

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Proceedings

W. Funika, P. Godowski, P. Pegiel, and M. T. Bubak. Towards user-defined performance monitoring of distributed Java applications. In: 2nd IEEE International Conference on e-Science and Grid Computing. p. 54.

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Proceedings

S. D. Olabarriaga, A. Nederveen, J. G. Snel, and R. G. Belleman. Towards a Virtual Laboratory for fMRI Data Management and Analysis. In: HealthGrid 2006.

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Proceedings

B. Baliś, M. T. Bubak, J. Dziwisz, and K. Rozkwitalski. Towards a Generic P2P Monitoring Infrastructure for Grid Resources and Applications. In: Proc. 2nd CoreGRID Workshop on GRID and Peer to Peer Systems Architecture. p. 17++.

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Proceedings

M. Malawski, D. Harezlak, and M. T. Bubak. Towards Multiprotocol and Multilanguage Interoperability: Experiments with Babel and RMIX. In: Proceedings of Cracow Grid Workshop - CGW'05, November 20-23 2005. pp. 266-278.

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Other: incollection

H.-L. Truong, B. Bali\'s, M. T. Bubak, J. Dziwisz, T. Fahringer, and A. Hoheisel. Towards Distributed Monitoring and Performance Analysis Services in the K-WfGrid Project. In: Parallel Processing and Applied Mathematics : 6th international conference, PPAM 2005: revised selected papers. Lecture Notes on Computer Science 3911, pp. 156-163.

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Article

H. Baumgardt, C. Hopman, S. F. Portegies Zwart, and J. Makino. Tidal capture of stars by intermediate-mass black holes. Monthly Notices of the Royal Astronomical Society 372, pp. 467-478.

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Article

A. Patruno, S. Portegies Zwart, J. Dewi, and C. Hopman. The ultraluminous X-ray source in M82: an intermediate-mass black hole with a giant companion. Monthly Notices of the Royal Astronomical Society 370, pp. L6-L9.

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Book

M. V. Bogdanov, Y. E. Gorbachev, V. V. Krzhizhanovskaya, A. V. Kulik, M. S. Ramm, D. H. Ofengeim, D. E. Tarakanov, and A. V. Tsyrulnikov. The processes of heat and mass transfer in modern semiconductor materials technology. Textbook for practical lessons in modeling and simulation.

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Article

L. R. Yungelson, J.-P. Lasota, G. Nelemans, G. Dubus, E. P. J. van den Heuvel, J. Dewi, and S. Portegies Zwart. The origin and fate of short-period low-mass black-hole binaries. Astronomy & Astrophysics 454(2), pp. 559-569.

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Article

C. Hopman, D. Guetta, E. Waxman, and S. Portegies Zwart. The Redshift Distribution of Short Gamma-Ray Bursts from Dynamically Formed Neutron Star Binaries. Astrophysical Journal Letters 643, pp. L91-L94.

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Proceedings

M. Gieles, H. J. G. L. M. Lamers, and S. Portegies Zwart. The Oort problem solved. In: Modelling Dense Stellar Systems, 26th meeting of the IAU. Joint Discussion 14-20.

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Article

M. B. Davies, P. Amaro-Seoane, C. Bassa, J. Dale, F. De Angeli, M. Freitag, P. Kroupa, D. Mackey, M. C. Miller, and S. Portegies Zwart. The MODEST questions: Challenges and future directions in stellar cluster research. New Astronomy 12, pp. 201-214.

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Article

R. Wiersma, A. Sills, and S. F. Portegies Zwart. The Effect of Pre-Main-Sequence Stars on Star Cluster Dynamics. Astrophysical Journal 637, pp. 838-849.

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Article

S. F. Portegies Zwart, H. Baumgardt, S. L. W. McMillan, J. Makino, P. Hut, and T. Ebisuzaki. The Ecology of Star Clusters and Intermediate-Mass Black Holes in the Galactic Bulge. Astrophysical Journal 641, pp. 319-326.

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Proceedings

T. Gubala, M. T. Bubak, and M. Malawski. Support for automatic workflow composition based on ontologies in semantic Grid environment. In: Cracow '05 Grid Workshop, November 20--23 2005. pp. 34-40.

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Article

S. F. Portegies Zwart. Sterrenhopen in een Supercomputer. Natuurkunde.nl .

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Article

M. Gieles, S. F. Portegies Zwart, H. Baumgardt, E. Athanassoula, H. J. G. L. M. Lamers, M. Sipior, and J. Leenaarts. Star cluster disruption by giant molecular clouds. Monthly Notices of the Royal Astronomical Society 371, pp. 793-804.

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Book

A. G. Hoekstra. Special Issue ‘Optics of Biological Particles’ of J. Quant. Specrt. Rad. Transf. Volume 102, number 1, November 2006.

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Article

J. Vidal Rodríguez, J. A. Kaandorp, M. Dobrzyński, and J. G. Blom. Spatial Stochastic Modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli. Bioinformatics 22, pp. 1895-1901.

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Proceedings

V. V. Krzhizhanovskaya. Software Environment for Simulation of Plasma-Chemical Deposition Reactors on Heterogeneous Computational Resources of the Grid. In: Conference on Computer Technologies in Modern Researches, Polytechnic Symposium "Young Scientists to the industry of Northwest Russia". pp. 81-82.

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Article

V. V. Krzhizhanovskaya, B. Chopard, and Y. E. Gorbachev. Simulation of Multiphysics Multiscale Systems. International Journal for Multiscale Computational Engineering 4, p. 207.

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Article

V. V. Krzhizhanovskaya, B. Chopard, and Y. E. Gorbachev. Simulation of Multiphysics Multiscale Systems. International Journal for Multiscale Computational Engineering 4, pp. 305-306.

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Proceedings

W. Rzasa, M. T. Bubak, B. Baliś, and T. Szepieniec. Simulation method for estimation of security overhead of Grid applications. In: Cracow '05 Grid Workshop, November 20--23 2005. pp. 300-307.

Citation
PhD Thesis

A. Gualandris. Simulating self-gravitating systems on parallel computers. ISBN 9064640246, 9789064640247. Supervised by E. P. J. van den Heuvel, P. M. A. Sloot, and S. F. Portegies Zwart.

Citation
MSc Thesis

N. Sluijs. Simulating Flow around a Complex Geometry. Supervised by J. G. Blom and J. A. Kaandorp.

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Article

J. Grindlay, S. Portegies Zwart, and S. L. W. McMillan. Short gamma-ray bursts from binary neutron star mergers in globular clusters. Nature Physics 2, pp. 116-119.

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Proceedings

T. Gubala, D. Harezlak, M. T. Bubak, and M. Malawski. Semantic composition of scientific workflows based on the Petri nets formalism. In: 2nd IEEE International Conference on e-Science and Grid Computing. p. 12.

Citation
Report

L. Kirchev, M. Blyantov, V. Georgiev, K. Boyanov, M. Malawski, M. T. Bubak, S. Isaiadis, and V. S. Getov. Security Models for Lightweight Grid Architectures.

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MSc Thesis

D. J. Groen. Reliability Analysis of Grid Resources: A User Perspective. Supervised by G. D. van Albada, J. Templon, D. L. Groep, and A. Tirado-Ramos.

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Article

J. A. Vrugt, H. V. Gupta, B. S. Ó Nualláin, and W. Bouten. Real-time data assimilation for operational ensemble streamflow forecasting. Journal of hydrometeorology 7, pp. 548-565.

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Proceedings

V. V. Krzhizhanovskaya and V. Korkhov. Problem-Solving Environments for Simulation and Optimization on Heterogeneous Distributed Computational Resources of the Grid. In: Trudy III Meždunarodnoj Konferencii "Parallelʹnye Vyčislenija i Zadači Upravlenija", Moskva, 2-4 oktjabrja 2006, Institut Problem Upravlenija Im. V. A. Trapeznikova RAN = Proceedings of the III International Conference "Parallel Computations and control Problems", V. A. Trapezniko Institute of Control Sciences, Moscow, October 2-4, 2006. ISBN 5201149901, 9785201149901. pp. 917-932.

Citation
Article

R. M. H. Merks, A. G. Hoekstra, J. A. Kaandorp, P. M. A. Sloot, and P. Hogeweg. Problem-Solving Environments for Biological Morphogenesis. IEEE Computational Science and Engineering 8, pp. 61-72.

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Proceedings

K. J. Rycerz, M. T. Bubak, P. M. A. Sloot, and V. S. Getov. Problem solving environment for distributed interactive applications. In: Integrated Research in Grid Computing, Integration Workshop. pp. 129-140.

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Article

A. G. Hoekstra, V. P. Maltsev, and G. Videen. Preface to special issue dedicated to the Optical Properties of Biological Cells. Journal of Quantitative Spectroscopy & Radiative Transfer 102, pp. 1-2.

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Article

V. V. Krzhizhanovskaya, B. Chopard, and Y. E. Gorbachev. Preface. International Journal for Multiscale Computational Engineering 4(3), pp. 305-306.

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Proceedings

M. T. Bubak, W. Funika, D. Dziok, M. Koch, A. D. Malony, M. Smetek, and R. Wism\\""uller. Performance visualization in real time monitoring of Web service application. In: Cracow '05 Grid Workshop, November 20--23 2005. pp. 160-166.

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Proceedings

R. M. Badia, R. Sirvent, M. T. Bubak, W. Funika, C. Klus, P. Machner, and M. Smetek. Performance Monitoring of Grid Superscalar with OCM-G/G-PM: Integration Issues. In: Proc. of the CoreGRID Integration Workshop, Oct 19-20, 2005, Krakow, Poland. pp. 321-331.

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