-
Proceedings
S. A. Konakov and V. V. Krzhizhanovskaya.
Компьютерное моделирование и экспериментальные исследования закономерностей плазмохимического осаждения тонких пленок нитрида кремния.
In:
Science Week. Proceedings of the International conference.
pp. 31-33.
-
Article
L. Mountrakis, E. Lorenz, and A. G. Hoekstra.
Validation of an efficient two-dimensional model for dense suspensions of red blood cells.
International Journal of Modern Physics C
25(12), 1441005.
-
Article
N. Javaheri, R Dries, and J. Kaandorp.
Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization.
PLoS Computational Biology
10(6), e1003687.
-
Proceedings
H. Aydt, M. H. Lees, S. J. Turner, and W. Cai.
Toward Simulation-Based Egress Optimization in Smart Buildings Using Symbiotic Simulation.
In:
Pedestrian and Evacuation Dynamics 2012.
ISBN
9783319024462.
pp. 987-999.
-
Article
W. Duan, R. Quax, M. Lees, X. Qiu, and P. M. A. Sloot.
Topology dependent epidemic spreading velocity in weighted networks.
Journal of Statistical Mechanics : Theory and Experiment
2014(12), P12020.
-
Article
A. L. Pyayt, A. P. Kozionov, I. I. Mokhov, B. Lang, R. J. Meijer, V. V. Krzhizhanovskaya, and P. M. A. Sloot.
Time-frequency Methods for Structural Health Monitoring.
Sensors
14(3), pp. 5147-5173.
-
MSc Thesis
K. Mikhailov.
The use of genetic algorithms to find an optimum MHD as an approximate description of holes.
Supervised by S. Markoff and A. Boukhanovsky.
-
Article
P. Ramos-Silva, J. Kaandorp, F. Herbst, L. Plasseraud, G. Alcaraz, C. Stern, M. Corneillat, N. Guichard, C. Durlet, G. Luquet, and F. Marin.
The skeleton of the staghorn coral Acropora millepora: molecular and structural characterization.
PLoS One
9(6), e97454.
-
Article
D. Roy, M. H. Lees, B. Palavalli, K. Pfeffer, and P. M. A. Sloot.
The emergence of slums: A contemporary view on simulation models.
Environmental Modelling & Software
59, pp. 76-90.
-
Article
P. A. C. Duijn, V. Kashirin, and P. M. A. Sloot.
The Relative Ineffectiveness of Criminal Network Disruption.
Scientific Reports
4, 4238.
-
Article
V. Savickas, N. Hari, T. Wood, and D. Kandhai.
Super Fast Greeks: An Application to Counterparty Valuation Adjustments.
Wilmott
69, pp. 76-80.
-
MSc Thesis
A. Klimkina.
Study of the news spread among social network user with respect to their stakeholdership.
Supervised by
R. Quax and A. Yakushev.
-
Report
-
Proceedings
-
Article
A. L. Pyayt, A. P. Kozionov, V. T. Kusherbaeva, I. I. Mokhov, V. V. Krzhizhanovskaya, B. J. Broekhuijsen, R. J. Meijer, and P. M. A. Sloot.
Signal analysis and anomaly detection for flood early warning systems.
Journal of Hydroinformatics
16(5), pp. 1025-1043.
-
Article
S. A. Cheong, T. L. Tan, C.-C. Chen, W.-L. Chang, Z. Liu, L. Y. Chew, P. M. A. Sloot, and N. F. Johnson.
Short-Term Forecasting of Taiwanese Earthquakes Using a Universal Model of Fusion-Fission Processes.
Scientific Reports
4, 3624.
-
Article
C. D. Erdbrink, V. V. Krzhizhanovskaya, and P. M. A. Sloot.
Reducing cross-flow vibrations of underflow gates: experiments and numerical studies.
Journal of Fluids and Structures
50, pp. 25-48.
-
Article
V. Viswanathan, C. E. Lee, M. H. Lees, S. A. Cheong, and P. M. A. Sloot.
Quantitative Comparison Between Crowd Models for Evacuation Planning and Evaluation.
The European Physical Journal B. Condensed Matter Physics
87(2), 27.
-
Proceedings
-
Article
J. Borgdorff, M. Ben Belgacem, C. Bona-Casas, L. Fazendeiro, D. Groen, O. Hoenen, A. Mizeranschi, J. L. Sutter, D. Coster, P. V. Coveney, W. Dubitzky, A. G. Hoekstra, P. Strand, and B. Chopard.
Performance of distributed multiscale simulations.
Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences
372(2021), 20130407.
-
Article
S. Karabasov, D. Nerukh, A. Hoekstra, B. Chopard, and P. V. Coveney.
Multiscale modelling: approaches and challenges.
Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences
372(2021), 20130390.
-
Article
A. Hoekstra, B. Chopard, and P. Coveney.
Multiscale modelling and simulation: a position paper.
Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences
372(2021), 20130377.
-
MSc Thesis
A. Chirkin.
Multi-objective optimization approach to infer Drosophila gene regulatory parameters.
Supervised by A. S. Z. Belloum and S. Kovalchuk.
-
Chapter
A. Hoekstra, B. Chopard, and P. Lawford.
Multi-Scale Modelling and Simulation.
In:
Computational biomedicine: modelling the human body.
ISBN
9780199658183.
pp. 138-160.
-
PhD Thesis
-
Article
R. Strijkers, M. X. Makkes, C. de Laat, and R. Meijer.
Internet factories: Creating application-specific networks on-demand.
Computer Networks
68, pp. 187-198.
-
Article
L. J. Dijkstra, A. V. Yakushev, P. A. C. Duijn, A. V. Boukhanovsky, and P. M. A. Sloot.
Inference of the Russian drug community from one of the largest social networks in the Russian Federation.
Quality and Quantity
48(5), pp. 2739-2755.
-
Article
S. Mei, Y. Zhu, X. Qiu, X. Zhou, Z. Zu, A. V. Boukhanovsky, and P. M. A. Sloot.
Individual decision making can drive epidemics: a fuzzy cognitive map study.
IEEE Transactions on Fuzzy Systems
22(2), pp. 264-273.
-
Article
C. D. Erdbrink and V. V. Krzhizhanovskaya.
Identifying Self-excited Vibrations with Evolutionary Computing.
Procedia Computer Science
29, pp. 637-647.
-
Article
C. M. Amatruda, C. Bona Casas, B. K. Keller, H. Tahir, G. Dubini, A. Hoekstra, D. R. Hose, P. Lawford, F. Migliavacca, A. J. Narracott, and J. Gunn.
From histology and imaging data to models for in-stent restenosis.
The international journal of artificial organs
37(10), pp. 786-800.
-
Article
C. D. Erdbrink, V. V. Krzhizhanovskaya, and P. M. A. Sloot.
Free-surface flow simulations for discharge-based operation of hydraulic structure gates.
Journal of Hydroinformatics
16(1), pp. 189-206.
-
PhD Thesis
-
MSc Thesis
K. Ullrich.
Feed-forward neural networks for boundary detection in music structure analysis.
Supervised by M. Welling and G. Widmer.
-
Article
N. B. Melnikova, D. Jordan, V. V. Krzhizhanovskaya, and P. M. A. Sloot.
Experimental Collapse of the IJkDijk: Numerical Prediction of Failure Mode and Posterior Sensor Data Analysis.
Canadian Geotechnical Journal
.
-
Article
M. Wagner, W. Cai, M. H. Lees, and H. Aydt.
Evolving Agent-based Models Using Complexification Approach.
Procedia Computer Science
29, pp. 310-321.
-
Article
J. O. Oelerich, F. Jansson, A. V. Nenashev, F. Gebhard, and S. D. Baranovskii.
Energy position of the transport path in disordered organic semiconductors.
Journal of Physics-Condensed Matter
26(25), 255801.
-
Article
H. Tahir, C. Bona-Casas, A. J. Narracott, J. Iqbal, J. Gunn, P. Lawford, and A. G. Hoekstra.
Endothelial repair process and its relevance to longitudinal neointimal tissue patterns: Comparing histology with in silico modelling.
Journal of the Royal Society Interface
11(94), 20140022.
-
Proceedings
Y. Xu, W. Cai, H. Aydt, and M. Lees.
Efficient graph-based dynamic load-balancing for parallel large-scale agent-based traffic simulation.
In:
Proceedings of the 2014 Winter Simulation Conference: exploring big data through simulation: December 7-10, 2014, Westin Savannah Harbor Resort, Savannah, GA.
ISBN
9781479974849.
pp. 3483-3494.
-
Article
C. S. L. de Graaf, Q. Feng, D. Kandhai, and C. W. Oosterlee.
Efficient Computation of Exposure Profiles for Counterparty Credit Risk.
International Journal of Theoretical and Applied Finance
17(4), 1450024.
-
Proceedings
J. Zhong, W. Cai, L. Luo, and M. Lees.
EA-based evacuation planning using agent-based crowd simulation.
In:
Proceedings of the 2014 Winter Simulation Conference: exploring big data through simulation: December 7-10, 2014, Westin Savannah Harbor Resort, Savannah, GA.
ISBN
9781479974849.
pp. 395-406.
-
Proceedings
A. Bilyatdinova, A. Dukhanov, K. Bochenina, A. V. Boukhanovsky, V. V. Krzhizhanovskaya, and P. M. A. Sloot.
Dutch-Russian Double Degree Master's Program Curricula in Computational Science and High Performance Computing.
In:
2014 IEEE Frontiers in Education Conference.
ISBN
9781479939237.
-
Article
A. V. Dukhanov, V. V. Krzhizhanovskaya, A. Bilyatdinova, A. V. Boukhanovsky, and P. M. A. Sloot.
Double-degree Master's Program in Computational Science: Experiences of ITMO University and University of Amsterdam.
Procedia Computer Science
29, pp. 1433-1445.
-
Article
J. Borgdorff, M. Mamonski, B. Bosak, K. Kurowski, M. Ben Belgacem, B. Chopard, D. Groen, P. V. Coveney, and A. G. Hoekstra.
Distributed multiscale computing with MUSCLE 2, the Multiscale Coupling Library and Environment.
Journal of Computational Science
5(5), pp. 719-731.
-
PhD Thesis
-
PhD Thesis
-
Article
-
Proceedings
J. Zhong, L. Luo, W. Cai, and M. Lees.
Automatic Rule Identification for Agent-Based Crowd Models Through Gene Expression Programming.
In:
AAMAS '14: proceedings of the 2014 International Conference on Autonomous Agents & Multiagent Systems: May 5-9, 2014, Paris, France.
ISBN
9781450327381.
pp. 1125-1132.
-
Article
T. I. Jung, F. Vogiatzian, O. Har-Shemesh, C. P. Fitzsimons, and R. Quax.
Applying Information Theory to Neuronal Networks: From Theory to Experiments.
Entropy
16(11), pp. 5721-5737.
-
Article
Y. H. A. Teo, V. Viswanathan, M. Lees, and W. Cai.
Analysing the Effectiveness of Wearable Wireless Sensors in Controlling Crowd Disasters.
Procedia Computer Science
29, pp. 1590-1599.
-
Proceedings
S. Madougou, A. L. Varbanescu, C. de Laat, and R. van Nieuwpoort.
An empirical evaluation of GPGPU performance models.
In: Euro-Par 2014: Parallel Processing Workshops.
ISBN 9783319143248.
1, pp. 165-176.
-
PhD Thesis
E. Mancini.
Agent based modeling of viral infections: an investigation across several spatio-temporal scales.
Supervised by
P. M. A. Sloot.
-
Article
Q. C. Bui, P. M. A. Sloot, E. M. van Mulligen, and J. A. Kors.
A novel feature-based approach to extract drug-drug interactions from biomedical text.
Bioinformatics
30(23), pp. 3365-3371.
-
Article
C. Tamulonis and J. Kaandorp.
A model of filamentous cyanobacteria leading to reticulate pattern formation.
Life (Basel)
4(3), pp. 433-456.
-
Article
B. Chopard, J. Borgdorff, and A. G. Hoekstra.
A framework for multi-scale modelling.
Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences
372(2021), 2013037813.
-
Article
D. Botman, E. Röttinger, M. Q. Martindale, J. de Jong, and J. A. Kaandorp.
A computational approach towards a gene regulatory network for the developing Nematostella vectensis gut.
PLoS One
9(7), e103341.
-
Proceedings
H. Tahir, I. Niculescu, R. Merks, and A. G. Hoekstra.
A cellular Potts model of a stented arterial vessel to study the role of initial smooth muscle cells migration in neointimal development.
In:
Virtual Physiological Human 2014.
-
Proceedings
C. Bona-Casas, H. Tahir, J. Borgdorff, and A. G. Hoekstra.
A 3D Multiscale In-Stent Restenosis Model: A Milestone For The Next Generation of In-stent Restenosis Modelling.
In:
Virtual Physiological Human 2014.
-
Book
-
Article
A. L. Pyayt, I. I. Mokhov, and A. P. Kozionov.
Интеллектуальная система мониторинга состояния объектов критической инфраструктуры.
Integral
2013(4), pp. 84-86.
-
Article
L. Mountrakis, E. Lorenz, and A. G. Hoekstra.
Where do the platelets go? A simulation study of fully resolved blood flow through aneurysmal vessels.
Interface Focus
3(2), p. 20120089.
-
Proceedings
E. R. Dugundji and L. Gulyás.
Understanding Emergence in a Fully-Specified Nested Logit Model.
-
Article
R. Quax, A. Apolloni, and P. M. A. Sloot.
Towards understanding the behavior of physical systems using information theory.
The European Physical Journal - Special Topics
222(6), pp. 1389-1401.
-
PhD Thesis
-
Article
P. Ramos-Silva, J. Kaandorp, L. Huisman, B. Marie, I. Zanella-Cléon, N. Guichard, D. J. Miller, and F. Marin.
The skeletal proteome of the coral Acropora millepora: the evolution of calcification by co-option and domain shuffling.
Molecular Biology and evolution
30(9), pp. 2099-2112.
-
Article
B. Marie, D. J. Jackson, P. Ramos-Silva, I. Zanella-Cléon, N. Guichard, and F. Marin.
The shell-forming proteome of Lottia gigantea reveals both deep conservations and lineage-specific novelties.
The FEBS Journal
280(1), pp. 214-232.
-
Article
N. Toth, L. Gulyas, R. O. Legendi, P. Duijn, P. M. A. Sloot, and G. Kampis.
The importance of centralities in dark network value chains.
The European Physical Journal - Special Topics
222(6), pp. 1413-1439.
-
Article
R. Quax, A. Apolloni, and P. M. A. Sloot.
The diminishing role of hubs in dynamical processes on complex networks.
Journal of the Royal Society Interface
10(88), 20130568.
-
Article
V. S. Lebanin, V. V. Krzhizhanovskaya, and S. E. Alexandrov.
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.
Technical Physics Letters
.
-
PhD Thesis
P. Sequeira dos Ramos Silva.
The biocalcification of mollusk shells and coral skeletons: Integrating molecular, proteomics and bioinformatics methods.
ISBN
9789810785635.
Supervised by
P. M. A. Sloot, J. A. Kaandorp, and F. G. Marin.
-
Article
T. Ishiyama, S. Rieder, J. Makino, S. Portegies Zwart, D. Groen, K. Nitadori, C. de Laat, S. McMillan, K. Hiraki, and S. Harfst.
The Cosmogrid simulation: Statistical properties of small dark matter halos.
Astrophysical Journal
767(2), 146.
-
Article
I. Bartha, M. Assel, P. M. A. Sloot, M. Zazzi, C. Torti, E. Schülter, A. De Luca, A. Sönnerborg, A. B. Abecasis, K. Van Laethem, A. Rosi, J. Svärd, R. Paredes, D. A. M. C. van de Vijver, and A.-M. Vandamme.
Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort.
BMC Infectious Diseases
13, p. 537.
-
Article
A. Czaplicka, J. A. Hołyst, and P. M. A. Sloot.
Stochastic resonance for information flows on hierarchical networks.
The European Physical Journal - Special Topics
222(6), pp. 1335-1345.
-
MSc Thesis
J. Hofman.
SPVAs: Grid GPU Implementation \& Risk Assessment of Investment Strategies.
Supervised by
B. D. Kandhai, D. Schrager, and V. Sergeev.
-
Article
J. T. I. Tanzil, B. E. Brown, R. P. Dunne, J. N. Lee, J. A. Kaandorp, and P. A. Todd.
Regional decline in growth rates of massive Porites corals in Southeast Asia.
Global Change Biology
19(10), pp. 3011-3023.
-
Article
P. Libin, G. Beheydt, K. Deforche, S. Imbrechts, F. Ferreira, K. Van Laethem, K. Theys, A. P. Carvalho, J. Cavaco-Silva, G. Lapadula, C. Torti, M. Assel, S. Wesner, J. Snoeck, and J. Ruelle.
RegaDB: Community-driven data management and analysis for infectious diseases.
Bioinformatics
29(11), pp. 1477-1480.
-
Article
L. B. Carey, D. van Dijk, P. M. A. Sloot, J. A. Kaandorp, and E. Segal.
Promoter sequence determines the relationship between expression level and noise.
PLoS Biology
11(4), e1001528.
-
Proceedings
-
Article
A. Afanasyeva, S. Ponyaev, and V. Krgiganovskaya.
Numerical simulation of synthesis of fullerenes by the arc discharge method.
Journal of Physics. Conference Series
461, 012043.
-
Article
A. Czaplicka, J. A. Holyst, and P. M. A. Sloot.
Noise enhances information transfer in hierarchical networks.
Scientific Reports
3, 1223.
-
Article
J. Borgdorff, M. Mamonski, B. Bosak, D. Groen, M. Ben Belgacem, K. Kurowski, and A. G. Hoekstra.
Multiscale Computing with the Multiscale Modeling Library and Runtime Environment.
Procedia Computer Science
18, pp. 1097-1105.
-
MSc Thesis
A. M. Abdol.
Multi-objective optimization approach to infer Drosophila gene regulatory parameters.
Supervised by
J. A. Kaandorp and F. R. Jansson.
Publications of the CSL group