Publications of the CSL group2018
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Article. Survey-based socio-economic data from slums in Bangalore, India. Scientific Data .
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Article. Supplemented alkaline phosphatase supports the immune response in patients undergoing cardiac surgery: Clinical and computational evidence. Frontiers in Immunology .
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Article. Spatial segregation, inequality, and opportunity bias in the slums of Bengaluru. Cities : The International Journal of Urban Policy and Planning pp. 269-276.
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Article. Quantification of complex modular architecture in plants. New Phytologist pp. 859-872.
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PhD Thesis. Patterns for multiscale computing. Supervised by P. M. A. Sloot and A. G. Hoekstra.
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Proceedings. Parallel performance analysis of bacterial biofilm simulation models. In: Computational Science – ICCS 2018. pp. 496-505.
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Article. Numerical investigation of the effects of red blood cell cytoplasmic viscosity contrasts on single cell and bulk transport behaviour. Applied Sciences .
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Article. Multiscale Modeling: recent progress and open questions. Multiscale and Multidisciplinary Modeling, Experiments and Design p. 57–68.
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Article. Morphogenesis in Robot Swarms. Science Robotics .
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Article. Modelling Neutrophils' Response to Various Levels of Insults. Procedia Computer Science pp. 390-397.
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Article. Mesoscopic Energy Minimization Drives Pseudomonas aeruginosa Biofilm Morphologies and Consequent Stratification of Antibiotic Activity Based on Cell Metabolism. Antimicrobial Agents and Chemotherapy .
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Article. Load balancing of parallel cell-based blood flow simulations. Journal of Computational Science pp. 1-7.
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Article. Liquidity risk in derivatives valuation: an improved credit proxy method. Quantitative Finance pp. 467-481.
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Report. IvI Education vision.
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Article. Information processing features can detect behavioral regimes of dynamical systems. Complexity .
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Article. Inflow and outflow boundary conditions for 2D suspension simulations with the immersed boundary lattice Boltzmann method. Computers & fluids p. 312–317.
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Article. Incorporating Contagion in Portfolio Credit Risk Models Using Network Theory. Complexity .
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Article. High-throughput method for extracting and visualizing the spatial gene expressions from in situ hybridization images: A case study of the early development of the sea anemone Nematostella vectensis. Gene expression patterns : GEP pp. 36-45.
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Article. Financial statement networks: an application of network theory in audit. The Journal of Network Theory in Finance pp. 59-85.
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Proceedings. Evolutionary Game Theory Can Explain the Choice Between Apoptotic and Necrotic Pathways in Neutrophils. In: Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine. pp. 1401-1405.
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Article. Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral. Sciences advances .
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Article. Directed nucleation and growth by balancing local supersaturation and substrate/nucleus lattice mismatch. Proceedings of the National Academy of Sciences of the United States of America pp. 3575-3580.
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Article. Coupling Game Theory and Discrete-Event Simulation for Model-Based Ambulance Dispatching. Procedia Computer Science pp. 398-407.
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Article. Combined Lattice–Boltzmann and rigid-body method for simulations of shear-thickening dense suspensions of hard particles. Computers & fluids pp. 474-482.
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Article. Cell-resolved blood flow simulations of saccular aneurysms: effects of pulsatility and aspect ratio. Journal of the Royal Society Interface .
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Article. Categorical and Geographical Separation in Science. Scientific Reports .
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Article. Application of clustering methods for detecting critical acute coronary syndrome patients. Procedia Computer Science pp. 370-379.
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Article. Analysis of publication activity of computational science society in 2001–2017 using topic modelling and graph theory. Journal of Computational Science pp. 193-204.
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Article. A study on the dynamics of temporary HIV treatment to assess the controversial outcomes of clinical trials: An in-silico approach. PLoS ONE .
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Article. A new hypothesis on the role of vessel topology in cerebral aneurysm initiation. Computers in Biology and Medicine pp. 244-251.
2017
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Article. eHealth in the future of medications management: personalisation, monitoring and adherence. BMC Medicine .
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Article. Uncertainty quantification and sensitivity analysis applied to the wind wave model SWAN. Environmental Modelling & Software pp. 344-357.
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Article. The study of the influence of obstacles on crowd dynamics. Procedia Computer Science pp. 215-224.
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Article. The effect of allometric scaling in coral thermal microenvironments. PLoS ONE .
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Article. The Art of Computational Science, Bridging Gaps - Forming Alloys. Procedia Computer Science pp. 1-2.
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Article. Scatter Search Applied to the Inference of a Development Gene Network. Computation .
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Article. Revisiting the use of the immersed-boundary lattice-Boltzmann method for simulations of suspended particles. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics .
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Article. Relaxing Synchronization in Parallel Agent-Based Road Traffic Simulation. ACM Transactions on Modeling and Computer Simulation .
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Article. Quantitative morphological analysis of 2D images of complex-shaped branching biological growth forms: the example of branching thalli of liverworts. BMC Research Notes .
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Article. Quantifying Synergistic Information Using Intermediate Stochastic Variables. Entropy .
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PhD Thesis. Phase transitions in complex systems. Supervised by P. M. A. Sloot, A. G. Hoekstra, and R. Quax.
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Article. Novel approach to investigation of semiconductor MOCVD by microreactor technology. Journal of Physics. Conference Series .
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Article. Multiscale computing in the exascale era. Journal of Computational Science pp. 15-25.
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Article. Multiscale Modelling and Simulation, 14th International Workshop. Procedia Computer Science pp. 1811-1812.
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Chapter. More likely we would be ritually slaughtered. In: 43 Visions for Complexity. pp. 65-66.
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Article. Models of Pedestrian Adaptive Behaviour in Hot Outdoor Public Spaces. Procedia Computer Science pp. 185-194.
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Article. Modelling the impact of household life cycle on slums in Bangalore. Computers, Environment and Urban Systems pp. 275-287.
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Article. Modelling the distance impedance of protest attendance. Physica A : Statistical Mechanics and its Applications pp. 171-182.
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Article. Hemocell: a high-performance microscopic cellular library. Procedia Computer Science pp. 159-165.
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Article. Efficient Estimation of Sensitivities for Counterparty Credit Risk with the Finite Difference Monte Carlo Method. Journal of Computational Finance pp. 83-113.
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Article. Design and evaluation of a data-driven scenario generation framework for game-based training. IEEE Transactions on Computational Intelligence and AI in Games pp. 213-226.
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Article. Data through the Computational Lens. Journal of Computational Science pp. 81-84.
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Article. Cellular Level In-silico Modeling of Blood Rheology with An Improved Material Model for Red Blood Cells. Frontiers in Physiology .
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Article. Automatic model construction for the behavior of human crowds. Applied Soft Computing pp. 368-378.
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Article. Anomaly detection in earth dam and levee passive seismic data using support vector machines and automatic feature selection. Journal of Computational Science pp. 143-153.
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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. pp. 685-690.
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Article. Anomaly Detection in Clinical Data of Patients Undergoing Heart Surgery. Procedia Computer Science 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 pp. 7-17.
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Article. A physical description of the adhesion and aggregation of platelets. Royal Society Open Science .
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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 pp. 204-214.
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Article. A cell-based mechanical model of coronary artery tunica media. Journal of the Royal Society Interface .
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Article. A Comparison of Fully-Coupled 3D In-Stent Restenosis Simulations to In-vivo Data. Frontiers in Physiology .
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 .
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Article. The influence of memory on indoor environment exploration: A numerical study. Behavior Research Methods pp. 621-639.
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Chapter. Systems Biology and Health Systems Complexity. In: The Digital Patient. 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 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 pp. 253-261.
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Article. Scaling of shear-induced diffusion and clustering in a blood-like suspension. Europhysics Letters .
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Proceedings. Reproducibility of Two Innate Immune System Models. In: Digital Transformation and Global Society. pp. 501-514.
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Article. Partitioning of Arterial Tree for Parallel Decomposition of Hemodynamic Calculations. Procedia Computer Science 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 .
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Article. Multiscale modelling and simulation, 13th international workshop. Procedia Computer Science 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 pp. 2003-2026.
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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 .
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Article. Immune System Model Calibration by Genetic Algorithm. Procedia Computer Science 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. pp. 223-236.
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Article. From MDMA to Lady Gaga. Procedia Computer Science 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. 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 .
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PhD Thesis. Detecting and disrupting criminal networks. 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 pp. 2030-2041.
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Article. Data through the Computational Lens, Preface for ICCS 2016. Procedia Computer Science 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 pp. 577-586.
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Article. Computer Simulation Approach in Development of Propane-air Combustor Microreactor. Procedia Computer Science pp. 76-85.
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PhD Thesis. Biosilicification mechanisms: An investigation using computational modeling and experimentation. 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. pp. 375-404.
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Article. Abnormally high oscillator strengths of the graphene nanoribbons electronic spectrum. RSC Advances 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 .
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Article. 3D simulation and analytical model of chemical heating during silicon wet etching in microchannels. Journal of Physics. Conference Series .
2015
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Article. Young Researchers Advancing Computational Science: Perspectives of the Young Scientists Conference 2015. Procedia Computer Science pp. 1-4.
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PhD Thesis. Transport of blood cells studied with fully resolved models. Supervised by P. M. A. Sloot and A. G. Hoekstra.
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Article. Topological Characterization of Complex Systems: Using Persistent Entropy. Entropy pp. 6872-6892.
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Article. Simulating city-level airborne infectious diseases. Computers, Environment and Urban Systems pp. 97-105.
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Article. Scaling description of positive magnetoresistivity in doped dilute magnetic semiconductors. Journal of Magnetism and Magnetic Materials pp. 44-49.
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Article. SIM-CITY: An e-Science Framework for Urban Assisted Decision Support. Procedia Computer Science 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 pp. 288-298.
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Article. Perspectives of the International Conference of Computational Science 2014. Journal of Computational Science pp. 247-248.
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Article. Parallel performance of an IB-LBM suspension simulation framework. Journal of Computational Science pp. 45-50.