Publications of the CSL group2015
-
Article. On the Possible Interaction Mechanism between Collateral Vessels and Restenosis. Procedia Computer Science pp. 412-418.
-
Article. Numerical prediction of the IJkDijk trial embankment failure. Proceedings of the Institution of Civil Engineers. Geotechnical Engineering pp. 158-171.
-
Article. Multiscale Modelling and Simulation Workshop: 12 Years of Inspiration. Procedia Computer Science pp. 1082-1087.
-
Article. Modeling chemical vapor deposition of silicon dioxide in microreactors at atmospheric pressure. Journal of Physics. Conference Series .
-
Article. Information impact on transportation systems. Journal of Computational Science pp. 88-93.
-
Article. How to Speed up Optimization? Opposite-Center Learning and Its Application to Differential Evolution. Procedia Computer Science pp. 805-814.
-
Article. From Data to Disruption. Digital Investigation pp. 39-45.
-
Article. Fluid Simulations with Atomistic Resolution: Multiscale Model with Account of Nonlocal Momentum Transfer. Procedia Computer Science pp. 1108-1117.
-
Article. Experience of using FEM for real-time flood early warning systems: Monitoring and modeling Boston levee instability. Journal of Computational Science pp. 13-25.
-
Article. Evolving agent-based models using self-adaptive complexification. Journal of Computational Science pp. 351-359.
-
Article. Differential evolution for system identification of self-excited vibrations. Journal of Computational Science pp. 360-369.
-
Proceedings. Detecting erosion events in earth dam and levee passive seismic data with clustering. In: 2015 IEEE 14th International Conference on Machine Learning and Applications. pp. 903-910.
-
Article. Density-based evolutionary framework for crowd model calibration. Journal of Computational Science pp. 11-22.
-
Article. Data-driven modeling of transportation systems and traffic data analysis during a major power outage in the Netherlands. Procedia Computer Science pp. 336-345.
-
Article. Computational Science at the Gates of Nature, preface for ICCS 2015. Procedia Computer Science pp. 1-8.
-
Article. Complex agent networks: An emerging approach for modeling complex systems. Applied Soft Computing pp. 311-321.
-
Article. Combining data-driven methods with finite element analysis for flood early warning systems. Procedia Computer Science pp. 2347-2356.
-
Article. An in silico study on the role of smooth muscle cell migration in neointimal formation after coronary stenting. Journal of the Royal Society Interface .
-
Proceedings. An Asynchronous Synchronization Strategy for Parallel Large-scale Agent-based Traffic Simulations. In: SIGSIM-PADS'15. pp. 259-269.
-
Article. A review of interactive narrative systems and technologies. Simulation pp. 126-147.
-
Article. A partition-based match making algorithm for dynamic ridesharing. IEEE Transactions on Intelligent Transportation Systems pp. 2587-2598.
-
Article. A mathematical model and simulation results of plasma enhanced chemical vapor deposition of silicon nitride films. Journal of Physics. Conference Series .
2014
-
Proceedings. Компьютерное моделирование и экспериментальные исследования закономерностей плазмохимического осаждения тонких пленок нитрида кремния. In: Неделя науки СПбГПУ : материалы Научно-практической конференции с международным участием, 2-7 декабря 2013 года. pp. 31-33.
-
Article. Validation of an efficient two-dimensional model for dense suspensions of red blood cells. International Journal of Modern Physics C .
-
Article. Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization. PLoS Computational Biology .
-
Proceedings. Toward Simulation-Based Egress Optimization in Smart Buildings Using Symbiotic Simulation. In: Pedestrian and Evacuation Dynamics 2012. pp. 987-999.
-
Article. Topology dependent epidemic spreading velocity in weighted networks. Journal of Statistical Mechanics : Theory and Experiment .
-
Article. Time-frequency Methods for Structural Health Monitoring. Sensors pp. 5147-5173.
-
MSc Thesis. The use of genetic algorithms to find an optimum MHD as an approximate description of holes. Supervised by S. Markoff and A. Boukhanovsky.
-
Article. The skeleton of the staghorn coral Acropora millepora: molecular and structural characterization. PLoS ONE .
-
Article. The emergence of slums: A contemporary view on simulation models. Environmental Modelling & Software pp. 76-90.
-
Article. The Relative Ineffectiveness of Criminal Network Disruption. Scientific Reports .
-
Article. Super Fast Greeks: An Application to Counterparty Valuation Adjustments. Wilmott pp. 76-80.
-
MSc Thesis. Study of the news spread among social network user with respect to their stakeholdership. Supervised by R. Quax and A. Yakushev.
-
Report. Slope Instability of the Earthen Levee in Boston, UK: Numerical Simulation and Sensor Data Analysis.
-
Proceedings. Simulation of City Evacuation Coupled to Flood Dynamics. In: Pedestrian and Evacuation Dynamics 2012. pp. 485-499.
-
Article. Signal analysis and anomaly detection for flood early warning systems. Journal of Hydroinformatics pp. 1025-1043.
-
Article. Short-Term Forecasting of Taiwanese Earthquakes Using a Universal Model of Fusion-Fission Processes. Scientific Reports .
-
Article. Reducing cross-flow vibrations of underflow gates: experiments and numerical studies. Journal of Fluids and Structures pp. 25-48.
-
Article. Quantitative Comparison Between Crowd Models for Evacuation Planning and Evaluation. The European Physical Journal B. Condensed Matter Physics .
-
Proceedings. Proceedings of the International Conference on Computational Science, ICCS 2014. Procedia Computer Science 29.
-
Article. Performance of distributed multiscale simulations. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences .
-
Article. Multiscale modelling: approaches and challenges. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences .
-
Article. Multiscale modelling and simulation: a position paper. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences .
-
MSc Thesis. Multi-objective optimization approach to infer Drosophila gene regulatory parameters. Supervised by A. S. Z. Belloum and S. Kovalchuk.
-
Chapter. Multi-Scale Modelling and Simulation. In: Computational biomedicine: modelling the human body. pp. 138-160.
-
PhD Thesis. Modelling flow-induced vibrations of gates in hydraulic structures. Supervised by P. M. A. Sloot and V. V. Krzhizhanovskaya.
-
Article. Inference of the Russian drug community from one of the largest social networks in the Russian Federation. Quality and Quantity pp. 2739-2755.
-
Article. Individual decision making can drive epidemics: a fuzzy cognitive map study. IEEE Transactions on Fuzzy Systems pp. 264-273.
-
Article. Identifying Self-excited Vibrations with Evolutionary Computing. Procedia Computer Science pp. 637-647.
-
Article. From histology and imaging data to models for in-stent restenosis. The international journal of artificial organs pp. 786-800.
-
Article. Free-surface flow simulations for discharge-based operation of hydraulic structure gates. Journal of Hydroinformatics pp. 189-206.
-
PhD Thesis. Finite element analysis of levee stability for flood early warning systems. Supervised by P. M. A. Sloot and V. V. Krzhizhanovskaya.
-
Article. Experimental Collapse of the IJkDijk: Numerical Prediction of Failure Mode and Posterior Sensor Data Analysis. Canadian Geotechnical Journal .
-
Article. Evolving Agent-based Models Using Complexification Approach. Procedia Computer Science pp. 310-321.
-
Article. Energy position of the transport path in disordered organic semiconductors. Journal of Physics-Condensed Matter .
-
Article. Endothelial repair process and its relevance to longitudinal neointimal tissue patterns: Comparing histology with in silico modelling. Journal of the Royal Society Interface .
-
Proceedings. 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. pp. 3483-3494.
-
Article. Efficient Computation of Exposure Profiles for Counterparty Credit Risk. International Journal of Theoretical and Applied Finance .
-
Proceedings. 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. pp. 395-406.
-
Proceedings. Dutch-Russian Double Degree Master's Program Curricula in Computational Science and High Performance Computing. In: 2014 IEEE Frontiers in Education Conference.
-
Article. Double-degree Master's Program in Computational Science: Experiences of ITMO University and University of Amsterdam. Procedia Computer Science pp. 1433-1445.
-
Article. Distributed multiscale computing with MUSCLE 2, the Multiscale Coupling Library and Environment. Journal of Computational Science pp. 719-731.
-
PhD Thesis. Distributed multiscale computing. Supervised by P. M. A. Sloot and A. G. Hoekstra.
-
PhD Thesis. Data-driven methods in application to flood defence systems monitoring and analysis. Supervised by P. M. A. Sloot and V. V. Krzhizhanovskaya.
-
Article. Big Data Meets Computational Science: preface for ICCS 2014. Procedia Computer Science pp. 1-7.
-
Proceedings. 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. pp. 1125-1132.
-
Article. Applying Information Theory to Neuronal Networks: From Theory to Experiments. Entropy pp. 5721-5737.
-
Article. Analysing the Effectiveness of Wearable Wireless Sensors in Controlling Crowd Disasters. Procedia Computer Science pp. 1590-1599.
-
PhD Thesis. Agent based modeling of viral infections: an investigation across several spatio-temporal scales. Supervised by P. M. A. Sloot.
-
Article. A novel feature-based approach to extract drug-drug interactions from biomedical text. Bioinformatics pp. 3365-3371.
-
Article. A model of filamentous cyanobacteria leading to reticulate pattern formation. Life (Basel) pp. 433-456.
-
Article. A framework for multi-scale modelling. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences .
-
Article. A computational approach towards a gene regulatory network for the developing Nematostella vectensis gut. PLoS ONE .
2013
-
Article. Интеллектуальная система мониторинга состояния объектов критической инфраструктуры. Integral pp. 84-86.
-
Article. Where do the platelets go? A simulation study of fully resolved blood flow through aneurysmal vessels. Interface Focus p. 20120089.
-
Proceedings. Understanding Emergence in a Fully-Specified Nested Logit Model.
-
Article. Towards understanding the behavior of physical systems using information theory. The European Physical Journal - Special Topics pp. 1389-1401.
-
Proceedings. Topic Crawler for Social Networks Monitoring. In: Knowledge Engineering and the Semantic Web. pp. 214-227.
-
PhD Thesis. The symphony of gene regulation. Supervised by P. M. A. Sloot and J. A. Kaandorp.
-
Article. The skeletal proteome of the coral Acropora millepora: the evolution of calcification by co-option and domain shuffling. Molecular Biology and evolution pp. 2099-2112.
-
Article. The shell-forming proteome of Lottia gigantea reveals both deep conservations and lineage-specific novelties. The FEBS Journal pp. 214-232.
-
Article. The importance of centralities in dark network value chains. The European Physical Journal - Special Topics pp. 1413-1439.
-
Article. The diminishing role of hubs in dynamical processes on complex networks. Journal of the Royal Society Interface .
-
Article. 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. The biocalcification of mollusk shells and coral skeletons: Integrating molecular, proteomics and bioinformatics methods. Supervised by P. M. A. Sloot, J. A. Kaandorp, and F. G. Marin.
-
Article. The Cosmogrid simulation: Statistical properties of small dark matter halos. Astrophysical Journal .
-
Article. Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort. BMC Infectious Diseases p. 537.
-
Article. Stochastic resonance for information flows on hierarchical networks. The European Physical Journal - Special Topics pp. 1335-1345.
-
MSc Thesis. SPVAs: Grid GPU Implementation \& Risk Assessment of Investment Strategies. Supervised by B. D. Kandhai, D. Schrager, and V. Sergeev.
-
Article. Regional decline in growth rates of massive Porites corals in Southeast Asia. Global Change Biology pp. 3011-3023.
-
Article. RegaDB: Community-driven data management and analysis for infectious diseases. Bioinformatics pp. 1477-1480.
-
Article. Promoter sequence determines the relationship between expression level and noise. PLoS Biology .
-
Proceedings. Proceedings of the International Conference on Computational Science, ICCS 2013. Procedia Computer Science 18.
-
Article. Numerical simulation of synthesis of fullerenes by the arc discharge method. Journal of Physics. Conference Series .
-
Article. Noise enhances information transfer in hierarchical networks. Scientific Reports .
-
Article. Multiscale Computing with the Multiscale Modeling Library and Runtime Environment. Procedia Computer Science pp. 1097-1105.
-
MSc Thesis. Multi-objective optimization approach to infer Drosophila gene regulatory parameters. Supervised by J. A. Kaandorp and F. R. Jansson.
-
Article. Modelling the Effect of a Functional Endothelium on the Development of In-Stent Restenosis. PLoS ONE .
-
Article. Modelling processes in the shock tube experiments with ignition of combustible gas mixtures. Technical Physics Letters .