-
PhD Thesis
J. T. Mościcki.
Understanding and mastering dynamics in computing grids: processing moldable tasks with user-level overlay.
Supervised by
M. T. Bubak and P. M. A. Sloot.
-
Proceedings
J. Bernsdorf, G. Berti, B. Chopard, J. Hegewald, M. Krafczyk, D. Wang, E. Lorenz, and A. Hoekstra.
Towards distributed multiscale simulation of biological processes.
In:
The Seventh IEEE International Conference on e-Science. Workshops: eScienceW 2011: proceedings: Stockholm, Sweden, 5-8 December 2011.
ISBN
9781467300261.
pp. 89-96.
-
MSc Thesis
I. Niculescu.
Towards a cell-based model of Neointimal Hyperplasia with Cellular Potts Model.
Supervised by
A. G. Hoekstra and R. M. H. Merks.
-
Article
R. Strijkers, R. Cushing, D. Vasyunin, C. de Laat, A. S. Z. Belloum, and R. Meijer.
Toward executable scientific publications.
Procedia Computer Science
4, pp. 707-715.
-
Proceedings
B. Pengel, L. Wentholt, V. V. Krzhizhanovskaya, G. Shirshov, N. Melnikova, B. Gouldby, A. Koelewijn, A. Pyayt, I. Mokhov, N. Pals, R. Meijer, and J. Broekhuijsen.
The urbanflood early warning system: sensors and coastal flood safety.
In:
Proceedings of the CoastGIS 2011 Conference.
ISBN
9788889405246.
4, pp. 20-27.
-
Article
M. A. Yurkin and A. G. Hoekstra.
The discrete-dipole-approximation code ADDA: capabilities and known limitations.
Journal of Quantitative Spectroscopy & Radiative Transfer
112(13), pp. 2234-2247.
-
Chapter
J. A. Kaandorp, M. Filatov, and N. Chindapol.
Simulating and quantifying the environmental influence on coral colony growth and form.
In:
Coral reefs: An ecosystem in transition.
ISBN
9789400701137.
pp. 177-185.
-
Proceedings
R. S. Cushing, S. Koulouzis, A. S. Z. Belloum, R. J. Strijkers, and M. T. Bubak.
Service Level Management for Executable Papers.
In: 7th International European Conference on Parallel and Distributed Computing (Euro-Par 2011), workshop MDGS2011.
-
Article
R. Quax, D. A. Bader, and P. M. A. Sloot.
SEECN: simulating complex systems using dynamic complex networks.
International Journal for Multiscale Computational Engineering
9(2), pp. 201-214.
-
Article
J. T. Mościcki, M. Lamanna, M. Bubak, and P. M. A. Sloot.
Processing moldable tasks on the grid: late job binding with lightweight user-level overlay.
Future Generation Computer Systems
27(6), pp. 725-736.
-
Book
M. Sato, S. Matsuoka, P. M. A. Sloot, G. D. van Albada, and J. Dongarra.
Proceedings of the International Conference on Computational Science, ICCS 2011.
-
Article
M. Sato, S. Matsuoka, G. D. van Albada, J. Dongarra, and P. M. A. Sloot.
Preface.
Procedia Computer Science
4, pp. 1-6.
-
Proceedings
R. Cushing, S. Koulouzis, A. S. Z. Belloum, and M. Bubak.
Prediction-based auto-scaling of scientific workflows.
In: Proceedings of the 9th International Workshop on Middleware for Grids, Clouds and e-Science: MGC 2011, co-located with ACM/IFIP/USENIX 12th International Middleware Conference, December 12-16, 2011, Lisbon, Portugal.
ISBN 9781450310680.
p. 1.
-
MSc Thesis
F. Speelman.
Position-Based Quantum Cryptography and the Garden-Hose Game.
Supervised by H. Buhrman and C. Schaffner.
-
MSc Thesis
J. Teunissen.
Particle based 3D modeling of positive streamer inception.
Supervised by U. Ebert.
-
Article
V. V. Krzhizhanovskaya.
Overstromingsrisico's in Kaart Brenger met de HPC Cloud.
"High Performance Computing E-Science Support", SARA Jaarverslag 2010
pp. 38-38.
-
Chapter
V. P. Maltsev, A. G. Hoekstra, and M. A. Yurkin.
Optics of white blood cells: optical models, simulations, and experiments.
In:
Advanced optical flow cytometry: methods and disease diagnoses.
ISBN
9783527409341.
pp. 63-93.
-
Article
H. Tahir, A. G. Hoekstra, E. Lorenz, P. V. Lawford, D. R. Hose, J. Gunn, and D. J. W. Evans.
Multi-scale simulations of the dynamics of in-stent restenosis: impact of stent deployment and design.
Interface Focus
1(3), pp. 365-373.
-
PhD Thesis
L. A. Naumov.
Modelling with cellular automata: problem solving environments and multidimensional applications.
ISBN
9789057762253.
Supervised by
P. M. A. Sloot and A. G. Hoekstra.
-
Proceedings
A. S. Afanasieva, V. V. Krzhizhanovskaya, and S. A. Ponyaev.
Modelling the processes of fullerene synthesis in arc discharge technology.
In:
Proceedings of the International conference "The 40th Science Week", V. 6.
6, pp. 129-131.
-
Proceedings
I. S. Kiseleva and V. V. Krzhizhanovskaya.
Modelling argon plasma in plasma chemical deposition reactor by ESI CFD-ACE+ software package.
In:
Proceedings of the International conference "The 40th Science Week".
6, pp. 126-128.
-
Article
C. Tamulonis, M. Postma, and J. Kaandorp.
Modeling filamentous cyanobacteria reveals the advantages of long and fast trichomes for optimizing light exposure.
PLoS ONE
6(7).
-
Proceedings
S. A. Konakov and V. V. Krzhizhanovskaya.
Modeling PECVD deposition process of multilayered structures based on silicon nitride.
In:
Proceedings of the Fifth All-Russian Forum "Science and Innovation in Technical Universities".
6, pp. 12-13.
-
Article
A. L. Pyayt, I. I. Mokhov, B. Lang, V. V. Krzhizhanovskaya, and R. J. Meijer.
Machine learning methods for environmental monitoring and flood protection.
World Academy of Science, Engineering and Technology. Proceedings
78, pp. 118-123.
-
Proceedings
A. L. Pyayt, I. I. Mokhov, B. Lang, V. V. Krzhizhanovskaya, and R. J. Meijer.
Machine Learning Methods for Environmental Monitoring and Flood Protection.
World Academy of Science, Engineering and Technology
78, pp. 118-123.
-
Proceedings
N. Zarrabi, M. Prosperi, A. de Luca, and P. M. A. Sloot.
Inferring HIV transmission networks from epidemic and genetic information.
In:
European Conference on Complex Systems, ECCS'11.
p. 138.
-
Article
A. Mei Shan, R. Quax, D. van de Vijver, Y. Zhu, and P. M. A. Sloot.
Increasing risk behaviour can outweigh the benefits of antiretroviral drug treatment on the HIV incidence among men-having-sex-with-men in Amsterdam.
BMC Infectious Diseases
11(118).
-
Proceedings
M. Gerhards, V. Sander, A. Belloum, D. Vasunin, and A. Benabdelkader.
HisT/PLIER: A two-fold Provenance Approach for Grid-enabled Scientific Workflows using WS-VLAM.
In: 2011 12th IEEE/ACM International Conference on Grid Computing : Grid 2011.
ISBN 9780769545721, 9780769545726.
pp. 224-225.
-
Article
E. Lorenz and A. G. Hoekstra.
Heterogeneous multiscale simulations of suspension flow.
Multiscale Modeling & Simulation
9(4), pp. 1301-1326.
-
Article
C. A. D. Leguy, E. M. H. Bosboom, A. S. Z. Belloum, A. P. G. Hoeks, and F. N. van de Vosse.
Global sensitivity analysis of a wave propagation model for arm arteries.
Medical Engineering & Physics
33(8), pp. 1008-1016.
-
Proceedings
B. Pengel, G. S. Shirshov, V. V. Krzhizhanovskaya, A. R. Koelewijn, I. I. Mokhov, A. L. Pyayt, and N. B. Melnikova.
Flood early warning system: sensors and internet.
In:
Abstract proceedings: 5th International CConference on Flood Management (ICFM5): Floods: from Risk to Opportunity: 27 to 29 September 2011, Tokyo-Japan.
pp. 212-221.
-
Article
V. V. Krzhizhanovskaya, G. S. Shirshov, N. B. Melnikova, R. G. Belleman, F. I. Rusadi, B. J. Broekhuijsen, B. P. Gouldby, J. Lhomme, B. Balis, M. Bubak, A. L. Pyayt, I. I. Mokhov, A. V. Ozhigin, B. Lang, and R. J. Meijer.
Flood early warning system: design, implementation and computational modules.
Procedia Computer Science
4, pp. 106-115.
-
Proceedings
P. Ramos-Silva, C. Combet, F. Marin, and J. A. Kaandorp.
Finding patterns and differences on biomineralization-related proteins from Metazoans.
In:
Molecular Biomineralization in marine organisms: Nanobiotechnology and biomedical application.
p. 21.
-
Proceedings
Q. C. Bui and P. M. A. Sloot.
Extracting biological events from text using simple syntactic patterns.
In:
Proceedings of BioNLP Shared Task 2011 Workshop: Portland, Oregon, USA, 24 June, 2011.
ISBN
9781937284091.
pp. 143-146.
-
MSc Thesis
J. Jänes.
Efficient integration of multiscale N-body systems.
Supervised by F. I. Pelupessy and S. F. Portegies Zwart.
-
Proceedings
R. Cushing, S. Koulouzis, A. Belloum, and M. Bubak.
Dynamic handling for cooperating scientific web services.
In: Proceedings 2011 IEEE Seventh International Conference on eScience: 5-8 December 2011, Stockholm, Sweden.
ISBN 9780769545974.
pp. 232-239.
-
Other: misc
M. C. F. Prosperi, M. Rosen-Zvi, A. Altmann, M. Zazzi, S. Di Giambenedetto, R. Kaiser, E. Schülter, D. Struck, P. M. A. Sloot, D. A. M. C. van de Vijver, A.-M. Vandamme, and A. Sönnerborg.
Correction: Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models.
PLoS ONE
6(4).
-
Article
M. C. F. Prosperi, M. Rosen-Zvi, A. Altmann, M. Zazzi, S. Di Giambenedetto, R. Kaiser, E. Schülter, D. Struck, P. Sloot, D. A. van de Vijver, A.-M. Vandamme, and A. Sönnerborg.
Correction: Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models.
PLoS ONE
6(4).
-
MSc Thesis
H. Þorsdottir.
Conservation Properties of the Hamiltonian Particle-Mesh method for the Quasi-Geostrophic Equations on a sphere.
Supervised by J. Frank.
-
Proceedings
S. A. Konakov and V. V. Krzhizhanovskaya.
Comparison of two models of plasma chemical processes in silicon nitride deposition technology.
In:
Proceedings of the International conference "The 40th Science Week".
6, pp. 132-134.
-
PhD Thesis
İ. Altıntaş.
Collaborative provenance for workflow-driven science and engineering.
ISBN
9789090259796.
Supervised by
P. M. A. Sloot and B. Ludäscher.
-
Article
A. Belloum, M. A. Inda, D. Vasunin, V. Korkhov, Z. Zhao, H. Rauwerda, T. M. Breit, M. Bubak, and L. O. Hertzberger.
Collaborative e-Science Experiments and Scientific Workflows.
IEEE Internet Computing
15(4), pp. 39-47.
-
Article
S. Murtaza, A. G. Hoekstra, and P. M. A. Sloot.
Cellular automata simulations on a FPGA cluster.
International Journal of High Performance Computing Applications
25(2), pp. 193-204.
-
Article
L. Naumov, A. Hoekstra, and P. Sloot.
Cellular automata models of tumour natural shrinkage.
Physica A : Statistical Mechanics and its Applications
390(12), pp. 2283-2290.
-
Article
V. V. Krzhizhanovskaya.
Better Flood Protection thanks to SARA's HPC Cloud.
"High Performance Computing E-Science Support", SARA Annual Report 2010
pp. 39-39.
-
Proceedings
A. L. Pyayt, I. I. Mokhov, A. Kozionov, V. Kusherbaeva, N. B. Melnikova, V. V. Krzhizhanovskaya, and R. J. Meijer.
Artificial intelligence and finite element modelling for monitoring flood defence structures.
In:
EESMS 2011 proceedings.
ISBN
9781457706080.
-
Proceedings
A. L. Pyayt, I. I. Mokhov, A. Kozionov, V. Kusherbaeva, N. B. Melnikova, V. V. Krzhizhanovskaya, and R. J. Meijer.
Artificial Intelligence and Finite Element Modelling for Monitoring Flood Defence Structures.
-
Proceedings
D. Botman and J. A. Kaandorp.
An integrated approach to infer the gene network in early development of the cnidarian Nematostella vectensis..
-
Proceedings
F. Berretz, S. Skorupa, V. Sander, A. Belloum, and M. Bubak.
Actor-driven workflow execution in distributed environments.
In: Euro-Par 2010 Parallel Processing Workshops.
ISBN 9783642218781.
pp. 287-294.
-
Proceedings
J. A. Kaandorp, C. Cronemberger, and L. Huisman.
A spatial model of calcification in scleractinian corals.
In:
Molecular iomineralization in marine organisms: Nanobiotechnology and biomedical application.
ISBN
9788890580505.
p. 14.
-
Article
A. Bankhead, E. Mancini, A. C. Sims, R. S. Baric, S. McWeeney, and P. M. A. Sloot.
A simulation framework to investigate in vitro viral infection dynamics.
Procedia Computer Science
4, pp. 1798-1807.
-
Proceedings
V. S. Lebanin and V. V. Krzhizhanovskaya.
A review of plasma chemical methods of silicon nitride production.
In:
Proceedings of the International conference "The 40th Science Week".
6, pp. 131-132.
-
Proceedings
J. Borgdorff, J.-L. Falcone, E. Lorenz, B. Chopard, and A. G. Hoekstra.
A principled approach to distributed multiscale computing, from formalization to execution.
In:
Workshop Proceedings, 7th IEEE International Conference on eScience.
ISBN
9781467300261.
pp. 97-104.
-
PhD Thesis
G. Ertaylan.
A multi-scale approach for deciphering HIV infection.
Supervised by
P. M. A. Sloot.
-
Article
Q. C. Bui, S. Katrenko, and P. M. A. Sloot.
A hybrid approach to extract protein-protein interactions.
Bioinformatics
27(2), pp. 259-265.
-
Proceedings
B. Chopard, J.-L. Falcone, A. G. Hoekstra, and J. Borgdorff.
A framework for multiscale and multiscience modeling and numerical simulations.
In:
Unconventional Computation.
ISBN
9783642213410.
pp. 2-8.
-
Article
I. Altintas, M. K. Anand, T. N. Vuong, S. Bowers, B. Ludäscher, and P. M. A. Sloot.
A data model for analyzing user collaborations in workflow-driven e-Science.
The International Journal of Computers and Their Applications (IJCA)
18(3), pp. 160-179.
-
Article
C. Tamulonis, M. Postma, H. Q. Marlow, C. R. Magie, J. de Jong, and J. Kaandorp.
A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering.
Developmental Biology
351(1), pp. 217-228.
-
Proceedings
N. Javaheri, C. M. Cronemberger, and J. Kaandorp.
A Particle-Based Model for Aggregate Formation in Biomineralization.
In:
Molecular Biomineralization in marine organisms: Nanobiotechnology and biomedical application.
ISBN
9788890580505.
p. 23.
-
Article
I. Altintas, M. K. Anand, T. Vuong, S. Bowers, B. Ludäscher, and P. M. A. Sloot.
A Data Model for Analyzing User Collaborations in Workflow-Driven eScience.
The International Journal of Computers and Their Applications (IJCA)
18(3), pp. 160-179.
-
Article
A. Caiazzo, D. Evans, J.-L. Falcone, J. Hegewald, E. Lorenz, B. Stahl, D. Wang, J. Bernsdorf, B. Chopard, J. Gunn, R. Hose, M. Krafczyk, P. Lawford, R. Smallwood, D. Walker, and A. Hoekstra.
A Complex Automata approach for in-stent restenosis: two-dimensional multiscale modelling and simulations.
Journal of Computational Science
2(1), pp. 9-17.
Publications of the CSL group