Publications of the CSL group2015
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Article. Computational Science at the Gates of Nature, preface for ICCS 2015. Procedia Computer Science 51, pp. 1-8.
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Article. Complex agent networks: An emerging approach for modeling complex systems. Applied Soft Computing 37, pp. 311-321.
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Article. Combining data-driven methods with finite element analysis for flood early warning systems. Procedia Computer Science 51, pp. 2347-2356.
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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 12(108), 20150358.
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Proceedings. An Asynchronous Synchronization Strategy for Parallel Large-scale Agent-based Traffic Simulations. In: SIGSIM-PADS'15. ISBN 9781450335836, 9781450335652. pp. 259-269.
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Article. A review of interactive narrative systems and technologies. Simulation 91(2), pp. 126-147.
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Article. A partition-based match making algorithm for dynamic ridesharing. IEEE Transactions on Intelligent Transportation Systems 16(5), pp. 2587-2598.
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Article. A mathematical model and simulation results of plasma enhanced chemical vapor deposition of silicon nitride films. Journal of Physics: Conference Series 574, 012144.
2014
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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. ISBN 9785742243472, 9785742243243. 2, pp. 31-33.
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Article. Validation of an efficient two-dimensional model for dense suspensions of red blood cells. International Journal of Modern Physics C 25(12), 1441005.
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Article. 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.
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Article. Towards a data-driven approach to scenario generation for serious games. Computer Animation and Virtual Worlds 25(3-4), pp. 393-402.
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Proceedings. Toward Simulation-Based Egress Optimization in Smart Buildings Using Symbiotic Simulation. In: Pedestrian and Evacuation Dynamics 2012. ISBN 9783319024462. pp. 987-999.
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Article. Topology dependent epidemic spreading velocity in weighted networks. Journal of Statistical Mechanics : Theory and Experiment 2014(12), P12020.
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Article. Time-frequency Methods for Structural Health Monitoring. Sensors 14(3), pp. 5147-5173.
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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.
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Article. The skeleton of the staghorn coral Acropora millepora: molecular and structural characterization. PLoS ONE 9(6), e97454.
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Article. The emergence of slums: A contemporary view on simulation models. Environmental Modelling & Software 59, pp. 76-90.
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Article. The Relative Ineffectiveness of Criminal Network Disruption. Scientific Reports 4, 4238.
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Article. Super Fast Greeks: An Application to Counterparty Valuation Adjustments. Wilmott 69, pp. 76-80.
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MSc Thesis. Study of the news spread among social network user with respect to their stakeholdership. Supervised by R. Quax and A. Yakushev.
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Report. Slope Instability of the Earthen Levee in Boston, UK: Numerical Simulation and Sensor Data Analysis.
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Proceedings. Simulation of City Evacuation Coupled to Flood Dynamics. In: Pedestrian and Evacuation Dynamics 2012. ISBN 9783319024462. pp. 485-499.
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Article. Signal analysis and anomaly detection for flood early warning systems. Journal of Hydroinformatics 16(5), pp. 1025-1043.
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Article. Short-Term Forecasting of Taiwanese Earthquakes Using a Universal Model of Fusion-Fission Processes. Scientific Reports 4, 3624.
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Article. Reducing cross-flow vibrations of underflow gates: experiments and numerical studies. Journal of Fluids and Structures 50, pp. 25-48.
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Article. Quantitative Comparison Between Crowd Models for Evacuation Planning and Evaluation. The European Physical Journal B. Condensed Matter Physics 87(2), 27.
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Proceedings. Proceedings of the International Conference on Computational Science, ICCS 2014. Procedia Computer Science 29.
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Article. Performance of distributed multiscale simulations. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 372(2021), 20130407.
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Article. Multiscale modelling: approaches and challenges. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 372(2021), 20130390.
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Article. Multiscale modelling and simulation: a position paper. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 372(2021), 20130377.
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Article. Multi-scale systems in fluids and soft matter: approaches, numerics and applications. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 372(2021).
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MSc Thesis. Multi-objective optimization approach to infer Drosophila gene regulatory parameters. Supervised by A. S. Z. Belloum and S. Kovalchuk.
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Chapter. Multi-Scale Modelling and Simulation. In: Computational biomedicine: modelling the human body. ISBN 9780199658183. pp. 138-160.
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PhD Thesis. Modelling flow-induced vibrations of gates in hydraulic structures. ISBN 9789064648007. Supervised by P. M. A. Sloot and V. V. Krzhizhanovskaya.
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Article. 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.
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Article. Individual decision making can drive epidemics: a fuzzy cognitive map study. IEEE Transactions on Fuzzy Systems 22(2), pp. 264-273.
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Article. Identifying Self-excited Vibrations with Evolutionary Computing. Procedia Computer Science 29, pp. 637-647.
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Article. From histology and imaging data to models for in-stent restenosis. The international journal of artificial organs 37(10), pp. 786-800.
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Article. Free-surface flow simulations for discharge-based operation of hydraulic structure gates. Journal of Hydroinformatics 16(1), pp. 189-206.
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PhD Thesis. Finite element analysis of levee stability for flood early warning systems. ISBN 9789064648069. Supervised by P. M. A. Sloot and V. V. Krzhizhanovskaya.
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Article. Experimental Collapse of the IJkDijk: Numerical Prediction of Failure Mode and Posterior Sensor Data Analysis. Canadian Geotechnical Journal .
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Article. Evolving Agent-based Models Using Complexification Approach. Procedia Computer Science 29, pp. 310-321.
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Article. Energy position of the transport path in disordered organic semiconductors. Journal of Physics-Condensed Matter 26(25), 255801.
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Article. 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.
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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. ISBN 9781479974849. pp. 3483-3494.
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Article. Efficient Computation of Exposure Profiles for Counterparty Credit Risk. International Journal of Theoretical and Applied Finance 17(4), 1450024.
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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. ISBN 9781479974849. pp. 395-406.
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Proceedings. Dutch-Russian Double Degree Master's Program Curricula in Computational Science and High Performance Computing. In: 2014 IEEE Frontiers in Education Conference. ISBN 9781479939213, 9781479939220.
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Article. Double-degree Master's Program in Computational Science: Experiences of ITMO University and University of Amsterdam. Procedia Computer Science 29, pp. 1433-1445.
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Article. Distributed multiscale computing with MUSCLE 2, the Multiscale Coupling Library and Environment. Journal of Computational Science 5(5), pp. 719-731.
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PhD Thesis. Distributed multiscale computing. ISBN 9789462592353. Supervised by P. M. A. Sloot and A. G. Hoekstra.
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PhD Thesis. Data-driven methods in application to flood defence systems monitoring and analysis. ISBN 9789064648052. Supervised by P. M. A. Sloot and V. V. Krzhizhanovskaya.
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Article. Big Data Meets Computational Science: preface for ICCS 2014. Procedia Computer Science 29, pp. 1-7.
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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. ISBN 9781450327381. pp. 1125-1132.
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Article. Applying Information Theory to Neuronal Networks: From Theory to Experiments. Entropy 16(11), pp. 5721-5737.
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Article. Analysing the Effectiveness of Wearable Wireless Sensors in Controlling Crowd Disasters. Procedia Computer Science 29, pp. 1590-1599.
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PhD Thesis. Agent based modeling of viral infections: an investigation across several spatio-temporal scales. Supervised by P. M. A. Sloot.
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Article. A novel feature-based approach to extract drug-drug interactions from biomedical text. Bioinformatics 30(23), pp. 3365-3371.
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Article. A model of filamentous cyanobacteria leading to reticulate pattern formation. Life (Basel) 4(3), pp. 433-456.
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Article. A framework for multi-scale modelling. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 372(2021), 2013037813.
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Article. A computational approach towards a gene regulatory network for the developing Nematostella vectensis gut. PLoS ONE 9(7), e103341.
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Book. 2014 International Conference on Computational Science.
2013
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Article. Интеллектуальная система мониторинга состояния объектов критической инфраструктуры. Integral 2013(4), pp. 84-86.
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Article. Where do the platelets go? A simulation study of fully resolved blood flow through aneurysmal vessels. Interface Focus 3(2), p. 20120089.
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Proceedings. Understanding Emergence in a Fully-Specified Nested Logit Model.
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Article. Towards understanding the behavior of physical systems using information theory. The European Physical Journal - Special Topics 222(6), pp. 1389-1401.
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Proceedings. Topic Crawler for Social Networks Monitoring. In: Knowledge Engineering and the Semantic Web. ISBN 9783642413605. pp. 214-227.
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PhD Thesis. The symphony of gene regulation. Supervised by P. M. A. Sloot and J. A. Kaandorp.
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Article. 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.
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Article. The shell-forming proteome of Lottia gigantea reveals both deep conservations and lineage-specific novelties. The FEBS Journal 280(1), pp. 214-232.
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Article. The importance of centralities in dark network value chains. The European Physical Journal - Special Topics 222(6), pp. 1413-1439.
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Article. The diminishing role of hubs in dynamical processes on complex networks. Journal of the Royal Society Interface 10(88), 20130568.
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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 .
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PhD Thesis. 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.
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Article. The Cosmogrid simulation: Statistical properties of small dark matter halos. Astrophysical Journal 767(2), 146.
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Article. 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.
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Article. Stochastic resonance for information flows on hierarchical networks. The European Physical Journal - Special Topics 222(6), pp. 1335-1345.
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MSc Thesis. SPVAs: Grid GPU Implementation \& Risk Assessment of Investment Strategies. Supervised by B. D. Kandhai, D. Schrager, and V. Sergeev.
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Article. Regional decline in growth rates of massive Porites corals in Southeast Asia. Global Change Biology 19(10), pp. 3011-3023.
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Article. RegaDB: Community-driven data management and analysis for infectious diseases. Bioinformatics 29(11), pp. 1477-1480.
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Article. Promoter sequence determines the relationship between expression level and noise. PLoS Biology 11(4), e1001528.
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Proceedings. Proceedings of the International Conference on Computational Science, ICCS 2013. Procedia Computer Science 18.
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Article. Numerical simulation of synthesis of fullerenes by the arc discharge method. Journal of Physics: Conference Series 461, 012043.
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Article. Noise enhances information transfer in hierarchical networks. Scientific Reports 3, 1223.
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Article. Multiscale Computing with the Multiscale Modeling Library and Runtime Environment. Procedia Computer Science 18, pp. 1097-1105.
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MSc Thesis. Multi-objective optimization approach to infer Drosophila gene regulatory parameters. Supervised by J. A. Kaandorp and F. R. Jansson.
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Article. Modelling the Effect of a Functional Endothelium on the Development of In-Stent Restenosis. PLoS ONE 8(6), e66138.
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Article. Modelling processes in the shock tube experiments with ignition of combustible gas mixtures. Technical Physics Letters .
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Proceedings. Modelling in-stent restenosis: morphological differences in the tissue patterns based on the origin of endothelium recovery.
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Article. Modelling growth and form of the scleractinian coral Pocillopora verrucosa and the influence of hydrodynamics. PLoS Computational Biology 9(1), e1002849.
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PhD Thesis. Modelling and simulating the dynamics of in-stent restenosis in porcine coronary arteries. Supervised by P. M. A. Sloot and A. G. Hoekstra.
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Article. Modeling earthen dikes using real-time sensor data. Journal of Hydrology 496, pp. 154-165.
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Chapter. Modeling and analyzing the human cognitive limits for perception in crowd simulation. In: Transactions on Computational Science XVII. ISBN 9783642358401. pp. 51-72.
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Article. Modeling Earthen Dike Stability: Sensitivity Analysis and Automatic Calibration of Diffusivities Based on Live Sensor Data. Journal of Hydrology .
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Chapter. Modeling Biosilicification at Subcellular Scales. In: Biomedical Inorganic Polymers. ISBN 9783642410048. pp. 117-141.
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Article. Macroscopic modelling of environmental influence on growth and form of sponges and corals using the accretive growth model. ISRN Biomathematics 2013, p. 159170.
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Proceedings. JavaScript distributed agent based discrete event simulation. In: Proceedings - 17th IEEE/ACM International Symposium on Distributed Simulation and Real Time Applications, DS-RT 2013. ISBN 9780769551388.
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Proceedings. Interpreting sensor measurements in dikes - experiences from UrbanFlood pilot sites. In: Comprehensive Flood Risk Management: research for policy and practice. ISBN 9780203374511 . pp. 81-82.
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Book. International Conference on Computational Science, ICCS 2013: Barcelona, Spain, June 5- June 7, 2013.