Publications of the CSL group2017
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Proceedings. Anomaly detection in earth dam and levee passive seismic data using multivariate Gaussian. In: ICMLA 2017 : 16th IEEE International Conference on Machine Learning and Applications. ISBN 9781538614174, 9781538614181. pp. 685-690.
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Article. Anomaly Detection in Clinical Data of Patients Undergoing Heart Surgery. Procedia Computer Science 108, pp. 99-108.
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Article. Analysis of Computational Science Papers from ICCS 2001-2016 using Topic Modeling and Graph Theory. Procedia Computer Science 108, pp. 7-17.
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Article. A physical description of the adhesion and aggregation of platelets. Royal Society Open Science 4, 170219.
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Article. A novel technique to combine and analyse spatial and temporal expression datasets: A case study with the sea anemone Nematostella vectensis to identify potential gene interactions. Developmental Biology 428(1), pp. 204-214.
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Article. A cell-based mechanical model of coronary artery tunica media. Journal of the Royal Society Interface 14, 20170028.
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Article. A Comparison of Fully-Coupled 3D In-Stent Restenosis Simulations to In-vivo Data. Frontiers in Physiology 8, 284.
2016
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Article. Towards the virtual artery: a multiscale model for vascular physiology at the physics–chemistry–biology interface. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 374(2080), 20160146.
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Article. The influence of memory on indoor environment exploration: A numerical study. Behavior Research Methods 48(2), pp. 621-639.
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Chapter. Systems Biology and Health Systems Complexity. In: The Digital Patient. ISBN 9781118952788. pp. 73-84.
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PhD Thesis. Spatial gene expression quantification in changing morphologies. Supervised by P. M. A. Sloot and J. A. Kaandorp.
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Article. Smile and Default: The Role of Stochastic Volatility and Interest Rates in Counterparty Credit Risk. Quantitative Finance 16(11), pp. 1725-1740.
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Article. Simulating an Impact of Road Network Improvements on the Performance of Transportation Systems under Critical Load: Agent-based Approach. Procedia Computer Science 101, pp. 253-261.
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Article. Scaling of shear-induced diffusion and clustering in a blood-like suspension. Europhysics Letters 114(1), 14002.
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Proceedings. Reproducibility of Two Innate Immune System Models. In: Digital Transformation and Global Society. ISBN 9783319497006. pp. 501-514.
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Article. Partitioning of Arterial Tree for Parallel Decomposition of Hemodynamic Calculations. Procedia Computer Science 80, p. 977–987.
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Article. Nonparametric estimation of Fisher information from real data. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 93(2), 023301.
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Article. Multiscale modelling and simulation, 13th international workshop. Procedia Computer Science 80, pp. 1242-1243.
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Article. Luminescence and density banding patterns in massive Porites corals around the Thai-Malay Peninsula, Southeast Asia. Limnology and Oceanography 61(6), pp. 2003-2026.
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Book. International Conference on Computational Science 2016, ICCS 2016.
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Article. Information geometric analysis of phase transitions in complex patterns: the case of the Gray-Scott reaction-diffusion model. Journal of Statistical Mechanics : Theory and Experiment 2016(4), 043301.
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Article. Immune System Model Calibration by Genetic Algorithm. Procedia Computer Science 101, pp. 161-171.
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Chapter. From Molecules to Morphologies, a Multiscale Modeling Approach to Unravel the Complex System of Coral Calcification. In: The Cnidaria, Past, Present and Future. ISBN 9783319313054. pp. 223-236.
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Article. From MDMA to Lady Gaga. Procedia Computer Science 101, pp. 96-106.
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Article. Efficient computation of exposure profiles on real-world and risk-neutral scenarios for Bermudan swaptions. Journal of Computational Finance 20(1), pp. 139-172.
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PhD Thesis. Efficient PDE based numerical estimation of credit and liquidity risk measures for realistic derivative portfolios. ISBN 978-94-028-0408-9. Supervised by P. M. A. Sloot and B. D. Kandhai.
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Article. Development and simulation of microfluidic Wheatstone bridge for high-precision sensor. Journal of Physics. Conference Series 738, 012071.
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PhD Thesis. Detecting and disrupting criminal networks. ISBN 978-90-77595-41-1. Supervised by A. G. Hoekstra and Z. J. M. H. Geradts.
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Article. Data-driven Travel Demand Modelling and Agent-based Traffic Simulation in Amsterdam Urban Area. Procedia Computer Science 80, pp. 2030-2041.
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Article. Data through the Computational Lens, Preface for ICCS 2016. Procedia Computer Science 80, pp. 1-7.
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Article. Crack detection in earth dam and levee passive seismic data using support vector machines. Procedia Computer Science 80, pp. 577-586.
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Article. Corrigendum to “The discrete dipole approximation: An overview and recent developments” [J. Quant. Spectrosc. Radiat. Transfer 106 (2007) 558–589]. Journal of Quantitative Spectroscopy & Radiative Transfer 171, pp. 82-83.
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Article. Corrigendum to “Experience of using FEM for real-time flood early warning systems: Monitoring and modelling Boston levee instability”. Journal of Computational Science 16, pp. 225-226.
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Article. Computer Simulation Approach in Development of Propane-air Combustor Microreactor. Procedia Computer Science 101, pp. 76-85.
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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: 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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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.