-
Article
C. H. Liu, A. K. Satoh, M. Postma, J. Huang, D. F. Ready, and R. C. Hardie.
Ca2+-dependent metarhodopsin inactivation mediated by calmodulin and NINAC myosin III.
Neuron
59(5), pp. 778-789.
-
Other: misc
J. A. Kaandorp.
Book review: P. Pelce, New visions on growth and form: fingering growth, dendrites, and flames.
Mathematical Biosciences
in press.
-
Other: misc
A. G. Hoekstra.
Book review: Optical Polarization in Biomedical Applications, V.V. Tuchin, L.V. Wang, D.A. Zimnyakov.
Journal of Quantitative Spectroscopy \& Radiative Transfer
109, pp. 531-531.
-
Article
X. Wang, A. Boreiko, U. Schloßmacher, D. Brandt, H. C. Schröder, J. Li, J. A. Kaandorp, H. Götz, H. Duschner, and W. E. G. Müller.
Axial growth of hexactinellid spicules: Formation of cone-like structural units in the giant basal spicules of the hexactinellid Monorhaphis.
Journal of Structural Biology
164(3), pp. 270-280.
-
Proceedings
M. A. Yurkin, M. Min, and A. G. Hoekstra.
Application of the discrete dipole approximation to extreme refractive indices: Filtered coupled dipoles revived.
In:
11th Electromagnetic & Light Scattering Conference: Extended abstracts: 7-12 September 2008, de Havilland Campus, University of Hertfordshire.
pp. 109-112.
-
Proceedings
M. Bubak, D. Harezlak, P. Nowakowski, T. Gubala, and M. Malawski.
Appea: a framework for the design and development of business applications on the Grid.
In: Cracow'07 Grid Workshop: October 15-17, 2007 Cracow, Poland: proceedings.
ISBN 9788391514191.
pp. 220-225.
-
Proceedings
B. Baliś and M. Bubak.
An ontology model for execution records of Grid scientific applications.
In: Proceedings of the Fourth International Conference on Semantics, Knowledge and Grid: December 3-5, 2008, Beijing, China.
ISBN 9780769534015.
pp. 34-41.
-
Article
B. Kowalewski, M. Bubak, and B. Baliś.
An event-based approach to reducing coupling in large-scale applications.
Lecture Notes in Computer Science
5103, pp. 358-367.
-
Article
J. Hegewald, M. Krafczyk, J. Tölke, A. Hoekstra, and B. Chopard.
An agent-based coupling platform for complex automata.
Lecture Notes in Computer Science
5102, pp. 227-233.
-
Book
S. Gorlatch, M. Bubak, and T. Priol.
Achievements in European research on Grid systems: CoreGRID Integration Workshop 2006 (selected papers), October 19-20, Krakow, Poland.
ISBN 9780387728117.
-
PhD Thesis
-
Article
M. Malawski, T. Bartyński, and M. Bubak.
A tool for building collaborative applications by invocation of Grid Operations.
Lecture Notes in Computer Science
5103, pp. 243-252.
-
MSc Thesis
D. M. Chu.
A survey of classical simulation methods for quantum computation.
Supervised by H. Buhrman and R. de Wolf.
-
Article
S. Portegies Zwart, S. McMillan, D. Groen, A. Gualandris, M. Sipior, and W. Vermin.
A parallel gravitational N-body kernel.
New Astronomy
13(5), pp. 285-295.
-
Article
S. Portegies Zwart, S. McMillan, B. Ó Nualláin, D. Heggie, J. Lombardi, P. Hut, S. Banerjee, H. Belkus, T. Fragos, J. Fregeau, M. Fuji, E. Gaburov, E. Glebbeek, D. Groen, S. Harfst, R. Izzard, M. Jurić, S. Justham, P. Teuben, J. van Bever, O. Yaron, and M. Zemp.
A multiphysics and multiscale software environment for modeling astrophysical systems.
Lecture Notes in Computer Science
5102, pp. 207-216.
-
Article
Z. Guo, P. M. A. Sloot, and J. C. Tay.
A hybrid agent-based approach for modeling microbiological systems.
Journal of Theoretical Biology
255(2), pp. 163-175.
-
Article
S. Harfst, A. Gualandris, D. Merritt, and S. Mikkola.
A hybrid N-body code incorporating algorithmic regularization and post-Newtonian forces.
Monthly Notices of the Royal Astronomical Society
389(1), pp. 2-12.
-
Article
V. V. Korkhov, V. V. Krzhizhanovskaya, and P. M. A. Sloot.
A grid-based virtual reactor: Parallel performance and adaptive load balancing.
Journal of Parallel and Distributed Computing
68(5), pp. 596-608.
-
Article
A. Wibisono, Z. Zhao, A. Belloum, and M. Bubak.
A framework for interactive parameter sweep applications.
Lecture Notes in Computer Science
5103, pp. 481-490.
-
MSc Thesis
M. V. Filatov.
A compression-based group similarity measure with applications in phylogeny. Automatic detection of viral RNA recombination..
Supervised by B. Ó Nualláin.
-
Proceedings
G. Ertaylan and P. M. A. Sloot.
A complex automata model of HIV-1 co-receptor tropism: Mutation rate prediction.
In:
Cracow'07 Grid Workshop: October 15-17, 2007 Cracow, Poland: proceedings.
ISBN
9788391514191.
p. 85.
-
Article
B. Łabno, M. Bubak, and B. Baliś.
A P2P approach to resource discovery in on-line monitoring of Grid workflows.
Lecture Notes in Computer Science
5168, pp. 37-46.
-
Proceedings
M. T. Bubak, G. D. van Albada, J. Dongarra, and P. M. A. Sloot.
In:
Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part I.
ISBN
978-3-540-69383-3.
Lecture Notes in Computer Science
5101.
-
Proceedings
M. T. Bubak, G. D. van Albada, J. Dongarra, and P. M. A. Sloot.
In:
Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II.
ISBN
978-3-540-69386-4.
Lecture Notes in Computer Science
5102.
-
Proceedings
M. T. Bubak, G. D. van Albada, J. Dongarra, and P. M. A. Sloot.
In:
Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part III.
ISBN
978-3-540-69388-8.
Lecture Notes in Computer Science
5103.
-
Article
E. V. Zudilova-Seinstra and T. Adriaansen.
Visualisation and interaction for scientific exploration and knowledge discovery.
Knowledge and Information Systems
13, pp. 115-117.
-
Proceedings
V. V. Krzhizhanovskaya, Y. E. Gorbachev, M. A. Zatevakhin, and P. M. A. Sloot.
Virtual Reactor -- Computational Environment for Multidimensional Simulation of Plasma Chemical Processing.
In:
Proceedings of the XV International Conference on Computational Mechanics and Modern Applied Software Systems.
-
Proceedings
Y. E. Gorbachev, V. V. Krzhizhanovskaya, M. V. Bogdanov, A. I. Zhmakin, A. V. Kulik, and M. S. Ramm.
Virtual Laboratories: Problem Solving Environments for Science and Education.
In:
Proceedings of the XIV All-Russian conference Telematika-2007.
pp. 108-109.
-
Proceedings
T. Bartynski, M. Malawski, T. Gubala, and M. T. Bubak.
Universal Grid client: Grid Operation Invoker.
In: PPAM 2007: 7th international conference on Parallel Processing \& Applied Mathematics: Gdask, Poland, September 9--12, Book of abstracts.
p. 93.
-
Article
G. Qiu, B. D. Kandhai, and P. M. A. Sloot.
Understanding the complex dynamics of stock markets through cellular automata.
Physical Review E
75, p. 046116.
-
Proceedings
M. A. Yurkin.
Tutorial for "Amsterdam DDA".
In: Proceedings of the DDA - Workshop.
p. 30.
-
Chapter
A. G. Hoekstra, S. Portegies Zwart, M. Bubak, and P. M. A. Sloot.
Towards distributed petascale computing.
In:
Petascale computing: Algorithms and applications.
ISBN
9781584889090.
pp. 147-164.
-
Proceedings
A. G. Hoekstra, E. Lorenz, J.-L. Falcone, and B. Chopard.
Towards a Complex Automata Framework for Multi-Scale Modeling: Formalism and the Scale Separation Map.
In:
Computational Science - ICCS 2007: 7th International Conference, Beijing, China, Proceedings, Part I.
4487, pp. 922-930.
-
Proceedings
M. Malawski, T. Gubala, M. Kasztelnik, T. Bartynski, and M. T. Bubak.
Towards A High-Level Scripting Approach for Building Component-Based Gridspace Applications.
In: CoreGRID Workshop on Grid Programming Model, Grid and P2P Systems Architecture, Grid Systems, Tools and Environments.
pp. 309-321.
-
Article
A. G. Hoekstra, E. Lorenz, J.-L. Falcone, and B. Chopard.
Toward a Complex Automata Formalism for Multi-Scale Modeling.
International Journal for Multiscale Computational Engineering
5, pp. 491-502.
-
Article
M. B. N. Kouwenhoven, A. G. A. Brown, S. F. Portegies Zwart, and L. Kaper.
The primordial binary population. II.. Recovering the binary population for intermediate mass stars in Scorpius OB2.
Astronomy & Astrophysics
474, pp. 77-104.
-
Article
S. F. Portegies Zwart, E. Gaburov, H.-C. Chen, and M. A. Gürkan.
The present day mass function in the central region of the Arches cluster.
Monthly Notices of the Royal Astronomical Society
378, pp. L29-L33.
-
Book
M. Bubak and S. Unger.
The knowledge-based workflow system for grid applications: Cracow grid workshop '06 K-wf grid: October 15-18, 2006 Cracow, Poland: proceedings.
ISBN 9788391514184.
-
Article
S. F. Portegies Zwart.
The gravitational wave signature of young and dense star clusters.
Advances in Space Research
39, pp. 275-279.
-
Article
J. van den Berk, S. F. Portegies Zwart, and S. L. W. McMillan.
The formation of higher order hierarchical systems in star clusters.
Monthly Notices of the Royal Astronomical Society
379, pp. 111-122.
-
Article
S. F. Portegies Zwart and S. P. Rusli.
The evolution of binary star clusters and the nature of NGC 2136/NGC 2137.
Monthly Notices of the Royal Astronomical Society
374, pp. 931-940.
-
Article
M. Gieles, E. Athanassoula, and S. F. Portegies Zwart.
The effect of spiral arm passages on the evolution of stellar clusters.
Monthly Notices of the Royal Astronomical Society
376, pp. 809-819.
-
Article
M. A. Yurkin and A. G. Hoekstra.
The discrete dipole approximation: an overview and recent developments.
Journal of Quantitative Spectroscopy & Radiative Transfer
106, pp. 558-589.
-
Article
M. A. Yurkin, V. P. Maltsev, and A. G. Hoekstra.
The discrete dipole approximation for simulation of light scattering by particles much larger than the wavelength.
Journal of Quantitative Spectroscopy & Radiative Transfer
106, pp. 546-557.
-
MSc Thesis
R. J. Strijkers.
The Network is in the Computer.
Supervised by R. J. Meijer.
-
Proceedings
M. A. Yurkin.
The Amsterdam DDA (tutorial).
In: Proceedings of the DDA - Workshop.
p. 30.
-
Article
E. N. Mamikonyan, S. L. W. McMillan, S. F. Portegies Zwart, and E. Vesperini.
TKira—A hybrid N-body code.
Proceedings of the International Astronomical Union
246, pp. 471-472.
-
Article
M. A. Yurkin, A. G. Hoekstra, R. S. Brock, and J. Q. Lu.
Systematic comparison of the discrete dipole approximation and the finite difference time domain method for large dielectric scatterers.
Optics Express
15, pp. 17902-17911.
-
Proceedings
M. A. Yurkin, A. G. Hoekstra, R. S. Brock, and J. Q. Lu.
Systematic comparison of the discrete dipole approximation and the finite difference time domain method.
In:
The 10th Conference on Electromagnetic and Light Scattering.
pp. 249-252.
-
Proceedings
S. L. W. McMillan and S. F. Portegies Zwart.
Stellar Collisions and Black-Hole Formation in Dense Star Clusters.
In: Massive Stars in Interactive Binaries.
367, pp. 697-697.
-
Proceedings
J. M. Fregeau, F. A. Rasio, P. Cheung, and S. F. Portegies Zwart.
Stellar Collisions During Binary Interactions and the Effect on Runaway Collisions.
In: Massive Stars in Interactive Binaries.
367, pp. 715-715.
-
Article
S. F. Portegies Zwart, S. L. W. McMillan, and J. Makino.
Star cluster ecology - VII. The evolution of young dense star clusters containing primordial binaries.
Monthly Notices of the Royal Astronomical Society
374, pp. 95-106.
-
Other: misc
V. V. Krzhizhanovskaya.
Special Issue on Simulation of Multiphysics Multiscale Systems.
International Journal for Multiscale Computational Engineering
5(1).
-
Proceedings
M. T. Bubak, M. Malawski, P. Nowakowski, and S. Unger.
Software engineering aspects of K-WfGrid.
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. 162-169.
-
Proceedings
V. V. Krzhizhanovskaya and S. Sun.
Simulation of Multiphysics Multiscale Systems: Introduction to the ICCS-2007 Workshop.
In:
Proceedings of the 7th International Conference on Computational Science, Part I.
4487, pp. 755-761.
-
Proceedings
S. F. Portegies Zwart and S. L. W. McMillan.
Simulating Young Star-Clusters with Primordial Binaries.
In: Massive Stars in Interactive Binaries.
367, pp. 597-597.
-
Article
L. Axner, J. Lätt, A. G. Hoekstra, B. Chopard, and P. M. A. Sloot.
Simulating Time Harmonic Flows with the Regularized L-BGK Method.
International Journal of Modern Physics C
18, pp. 661-666.
-
Article
L. Axner, A. G. Hoekstra, and P. M. A. Sloot.
Simulating Time Harmonic Flows with the Lattice Boltzmann Method.
Physical Review E
p. 036709.
-
Article
J. Kitowski, K. Boryczko, M. T. Bubak, W. Dzwinel, W. Funika, and R. Slota.
Rozwój srodków i narzedzi informatyki dla potrzeb symulacji i budowy aplikacji gridowych (Development of tools and environments for computer simulations and grid applications).
Pomiary, Automatyka, Kontrola
53(3), pp. 26-40.
-
Proceedings
J. Mo'scicki, M. T. Bubak, H. C. Lee, A. Muraru, and P. M. A. Sloot.
Quality of Service on the Grid with User Level Scheduling.
In:
CGW'06 Proceedings.
pp. 119-129.
-
Proceedings
B. Baliś, M. T. Bubak, and J. Wach.
Provenance tracking in the Virolab Virtual Laboratory.
In: PPAM 2007: 7th international conference on Parallel Processing \& Applied Mathematics: Gdask, Poland, September 9--12, Book of abstracts.
pp. 50-50.
-
MSc Thesis
K. C. Maheshwari.
Problem Solving Environment for Medical Image Analysis Application Development.
Supervised by S. Olabarriaga and A. S. Z. Belloum.
-
Report
K. J. Rycerz, M. T. Bubak, P. M. A. Sloot, and V. S. Getov.
Problem Solving Environment for Distributed Interactive Applications.
.
-
Report
R. M. Badia, R. Sirvent, M. T. Bubak, W. Funika, and P. Machner.
Performance monitoring of GRID superscalar with OCM-G/G-PM: integration issues.
-
Proceedings
S. Murtaza, A. G. Hoekstra, and P. M. A. Sloot.
Performance evaluation of FPGA-based Cellular Automata accelerators.
In:
Proceedings of the Third Annual Reconfigurable Systems Summer Institute (RSSI'07).
-
Article
S. Harfst, A. Gualandris, D. Merritt, R. Spurzem, S. F. Portegies Zwart, and P. Berczik.
Performance analysis of direct N-body algorithms on special-purpose supercomputers.
New Astronomy
12, pp. 357-377.
-
Article
A. Gualandris, S. F. Portegies Zwart, and A. Tirado Ramos.
Performance analysis of direct N-body algorithms on highly distributed systems.
Parallel Computing
33, pp. 159-173.
-
Proceedings
R. M. Badia, R. Sirvent, M. T. Bubak, W. Funika, and P. Machner.
Performance Monitoring of Grid Superscalar with OCM-G/G-PM: Tuning and Improvements.
In: CoreGRID Workshop on Grid Programming Model, Grid and P2P Systems Architecture, Grid Systems, Tools and Environments.
-
Proceedings
S. Murtaza, A. G. Hoekstra, and P. M. A. Sloot.
Performance Modeling of 2D Cellular Automata on FPGA.
In:
International Conference on Field Programmable Logic and Applications, FPL 2007.
pp. 74-78.
-
Article
L. Feyen, J. A. Vrugt, B. S. Ó Nualláin, J. Knijff, and A. De Roo.
Parameter optimisation and uncertainty assessment for large-scale streamflow simulation with the LISFLOOD model.
Journal of Hydrology
332, pp. 276-289.
-
Proceedings
S. D. Olabarriaga, A. J. Nederveen, and B. Ó Nualláin.
Parameter Sweeps for Functional MRI Research in the ``Virtual Laboratory for e-Science'' Project.
In: CCGRID 2007. Seventh IEEE International Symposium on Cluster Computing and the Grid, 2007..
pp. 685-690.
-
Article
W. Rzasa, M. T. Bubak, B. Baliś, and T. Szepieniec.
Overhead verification for cryptographically secured transmission on the Grid.
Computing and Informatics
26(1), pp. 89-101.
-
Book
A. G. Hoekstra, V. P. Maltsev, and G. Videen.
Optics of Biological Particles.
-
Article
E. V. Zudilova-Seinstra.
On the role of individual human abilities in the design of adaptive user interfaces for scientific problem solving environments.
Knowledge and Information Systems
13(2), pp. 243-270.
-
Article
V. V. Gvaramadze, A. Gualandris, and S. Portegies Zwart.
On the origin of hyperfast neutron stars.
Proceedings of the International Astronomical Union
3, pp. 365-366.
-
Proceedings
B. R. Brandl, S. F. Portegies Zwart, A. F. J. Moffat, and D. F. Chernoff.
On the Origin of the Most Massive Stars Around R136.
In: Massive Stars in Interactive Binaries.
367, pp. 629-629.
-
Article
M. Gieles, H. J. G. L. M. Lamers, and S. F. Portegies Zwart.
On the Interpretation of the Age Distribution of Star Clusters in the Small Magellanic Cloud.
Astrophysical Journal
668, pp. 268-274.
-
Article
Y. E. Gorbachev, M. A. Zatevakhin, A. A. Ignatiev, and V. V. Krzhizhanovskaya.
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.
HEAT TRANSFER RESEARCH
38(1), pp. 71-84.
-
Proceedings
K. J. Rycerz, M. T. Bubak, M. Malawski, and P. M. A. Sloot.
Multiple HLA Federate Processes in Grid Environment.
In:
CGW'06 Proceedings.
pp. 293-294.
-
Chapter
P. M. A. Sloot, A. Tirado Ramos, and M. T. Bubak.
Multi-Science Decision Support for HIV Drug Resistance Treatment.
In:
Expanding the Knowledge Economy: Issues, Applications, Case Studies, eChallenges e-2007 Conference Proceedings.
pp. 597-606.
-
Chapter
-
Chapter
-
Proceedings
M. A. Yurkin, K. A. Semyanov, V. P. Maltsev, and A. G. Hoekstra.
Light scattering by granulated spheres applied to discriminate subtypes of granulated blood cells.
In:
International Conference on Laser Applications in Life Sciences 2007.
pp. TuL07-II3.
-
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.
-
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.
-
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.
-
Book
P. M. A. Sloot.
International Conference on Computational Science series.
-
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.
-
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.
-
MSc Thesis
Z. R. Rahhal.
Interactive Distributed Computing Middleware.
Supervised by R. G. Belleman.
-
MSc Thesis
T. de Kler.
Integration of the ARToolKitPlus optical tracker into the Personal Space Station.
Supervised by R. G. Belleman.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
Book
A. G. Hoekstra.
Guest Editor Special Issue ‘Simulating Multiphysics Multiscale Systems’ of the International Journal for Multiscale Computational Engineering.
-
MSc Thesis
P. M. Geldof.
Generic Computing on a Graphics Processing Unit.
Supervised by R. G. Belleman.
-
PhD Thesis
L. A. Naumov.
Generalized Coordinates Introduction Method and a Tool for Computational Experiments' Software Design Automation, Basing on Cellular Automata.
Supervised by Prof. Dr. A. A. Shalyto.
Publications of the CSL group