Publications of the CSL group2016
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PhD Thesis. Biosilicification mechanisms: An investigation using computational modeling and experimentation. ISBN 9789402801125. Supervised by P. M. A. Sloot and J. A. Kaandorp.
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Chapter. Anatomy and Physiology of Multiscale Modeling and Simulation in Systems Medicine. In: Systems Medicine. ISBN 9781493932832. pp. 375-404.
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Article. Abnormally high oscillator strengths of the graphene nanoribbons electronic spectrum. RSC Advances 6(79), pp. 75937-75942.
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Article. A novel three-jet microreactor for localized metal-organic chemical vapour deposition of gallium arsenide. Journal of Physics. Conference Series 741, 012018.
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Article. 3D simulation and analytical model of chemical heating during silicon wet etching in microchannels. Journal of Physics. Conference Series 681, 012035.
2015
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Article. Young Researchers Advancing Computational Science: Perspectives of the Young Scientists Conference 2015. Procedia Computer Science 66, pp. 1-4.
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PhD Thesis. Transport of blood cells studied with fully resolved models. ISBN 9789462597754. Supervised by P. M. A. Sloot and A. G. Hoekstra.
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Article. Topological Characterization of Complex Systems: Using Persistent Entropy. Entropy 17(10), pp. 6872-6892.
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Article. Simulating city-level airborne infectious diseases. Computers, Environment and Urban Systems 51, pp. 97-105.
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Article. Scaling description of positive magnetoresistivity in doped dilute magnetic semiconductors. Journal of Magnetism and Magnetic Materials 383(1), pp. 44-49.
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Article. SIM-CITY: An e-Science Framework for Urban Assisted Decision Support. Procedia Computer Science 51, pp. 2327-2336.
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Article. Russian-Dutch double-degree Master’s programme in computational science in the age of global education. Journal of Computational Science 10, pp. 288-298.
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Article. Perspectives of the International Conference of Computational Science 2014. Journal of Computational Science 10, pp. 247-248.
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Article. Parallel performance of an IB-LBM suspension simulation framework. Journal of Computational Science 9, pp. 45-50.
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Article. On the Possible Interaction Mechanism between Collateral Vessels and Restenosis. Procedia Computer Science 66, pp. 412-418.
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Article. Numerical prediction of the IJkDijk trial embankment failure. Proceedings of the Institution of Civil Engineers. Geotechnical Engineering 168(2), pp. 158-171.
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Article. Multiscale Modelling and Simulation Workshop: 12 Years of Inspiration. Procedia Computer Science 51, pp. 1082-1087.
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Article. Modeling chemical vapor deposition of silicon dioxide in microreactors at atmospheric pressure. Journal of Physics. Conference Series 574, 012145.
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Book. International Conference On Computational Science, ICCS 2015: Computational Science at the Gates of Nature.
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Article. Information impact on transportation systems. Journal of Computational Science 9, pp. 88-93.
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Article. How to Speed up Optimization? Opposite-Center Learning and Its Application to Differential Evolution. Procedia Computer Science 51, pp. 805-814.
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Article. From Data to Disruption. Digital Investigation 11, pp. 39-45.
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Article. Fluid Simulations with Atomistic Resolution: Multiscale Model with Account of Nonlocal Momentum Transfer. Procedia Computer Science 51, pp. 1108-1117.
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Article. Experience of using FEM for real-time flood early warning systems: Monitoring and modeling Boston levee instability. Journal of Computational Science 10, pp. 13-25.
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Article. Evolving agent-based models using self-adaptive complexification. Journal of Computational Science 10, pp. 351-359.
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Article. Differential evolution for system identification of self-excited vibrations. Journal of Computational Science 10, pp. 360-369.
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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. ISBN 9781509002870. pp. 903-910.
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Article. Density-based evolutionary framework for crowd model calibration. Journal of Computational Science 6, pp. 11-22.
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Article. Data-driven modeling of transportation systems and traffic data analysis during a major power outage in the Netherlands. Procedia Computer Science 66, pp. 336-345.
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Article. Convergence of the discrete dipole approximation. I. Theoretical analysis: erratum. Journal of the Optical Society of America. A, Optics, Image Science and Vision 32(12), pp. 2407-2408.
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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: Science Week. Proceedings of the International conference. 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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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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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: May 5-9, 2014, Paris, France. 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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Proceedings. 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.
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Proceedings. A 3D Multiscale In-Stent Restenosis Model: A Milestone For The Next Generation of In-stent Restenosis Modelling. In: Virtual Physiological Human 2014.
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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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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.