Publications of the CSL group2021
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Article. Data-driven equation for drug-membrane permeability across drugs and membranes. Journal of Chemical Physics 154(24), 244114.
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Article. Coupling one-dimensional arterial blood flow to three-dimensional tissue perfusion models for in silico trials of acute ischaemic stroke. Interface Focus 11(1), 20190125.
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Article. Continuous clonal labeling reveals uniform progenitor potential in the adult exocrine pancreas. Cell Stem Cell 28(11), pp. 2009-2019.e4.
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Article. Computer simulations of lipid regulation by molecular semigrand canonical ensembles. Biophysical Journal 120(12), pp. 2370-2373.
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PhD Thesis. Computational models of human response to urban heat. Supervised by P. M. A. Sloot, V. Krzhizhanovskaya, and M. H. Lees.
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Article. Computational compound screening of biomolecules and soft materials by molecular simulations. Modelling and Simulation in Materials Science and Engineering 29(2), 023001.
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Article. Computational biomedicine. Part II. Interface Focus 11(1), 20200082.
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Article. Combination of institutional incentives for cooperative governance of risky commons. iScience 24(8), 102844.
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Article. Biased perceptions explain collective action deadlocks and suggest new mechanisms to prompt cooperation. Authors Vítor Vasconcelos and Fernando Santos on the article. IAS Review 2, 2.2.
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Article. Biased perceptions explain collective action deadlocks and suggest new mechanisms to prompt cooperation. iScience 24(4), 102375.
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Article. Automated Identification of Collective Variables and Metastable States from Molecular Dynamics Data. Biophysical Journal 120(3, Supplement 1), p. 79A.
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Article. Applicability analysis to evaluate credibility of an in silico thrombectomy procedure. Journal of Biomechanics 126, 110631.
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Article. An individualized systems model to optimize Alzheimer’s disease prevention strategies. Alzheimer's & Dementia 17(S10), e050885.
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Article. An efficient, localised approach for the simulation of elastic blood vessels using the lattice Boltzmann method. Scientific Reports 11, 24260.
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Article. Agent-based modelling of post-disaster recovery with remote sensing data. International Journal of Disaster Risk Reduction .
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Article. Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability. APL Materials 9(3), 031107.
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Article. Advancing urban mental health research: from complexity science to actionable targets for intervention. The Lancet. Psychiatry 8(11), pp. 991-1000.
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Article. A well-timed shift from local to global agreements accelerates climate change mitigation. Nature Communications 12, 2908.
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Article. A unifying model to estimate the effect of heat stress in the human innate immunity during physical activities. Scientific Reports 11, 16688.
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Proceedings. A prototype for the treatment of children with selective mutism using interactive 360° VR. In: EuroXR 2021. ISBN 9789513887568. pp. 37-43.
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Article. A porous circulation model of the human brain for in silico clinical trials in ischaemic stroke. Interface Focus 11(1), 20190127.
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Proceedings. A Model-based Analysis of Evacuation Strategies in Hospital Emergency Departments. In: 2021 Winter Simulation Conference (WSC 2021). ISBN 9781665433112. pp. 1583-1594.
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Article. 20 years of computational science: Selected papers from 2020 International Conference on Computational Science. Journal of Computational Science 53, 101395.
2020
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Article. Understanding resilience in slums using an agent-based model. Computers, Environment and Urban Systems 80, 101458.
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Article. Uncovering the multicausality of Alzheimer’s disease: A systems modeling approach. Alzheimer's & Dementia 16(S10), e041105.
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PhD Thesis. Uncertainty quantification of multiscale models. ISBN 9789402819182. Supervised by A. G. Hoekstra and P. V. Coveney.
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Article. Tracing resilience, social dynamics and behavioral change: a review of agent-based flood risk models. Socio-Environmental Systems Modelling 2, 17938.
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Article. The influence of red blood cell deformability on hematocrit profiles and platelet margination. PLoS Computational Biology 16(3), e1007716.
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Article. The impact of pace of life on pedestrian heat stress: A computational modelling approach. Environmental Research 186, 109397.
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Article. Social norms and obesity prevalence: From cohort to system dynamics models. Obesity Reviews 21(9), e13044.
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Article. Sensitivity analysis based dimension reduction of multiscale models. Mathematics and Computers in Simulation 170, pp. 205-220.
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Proceedings. Risk-based AED placement - Singapore case. In: Computational Science – ICCS 2020. ISBN 9783030504236. IV, pp. 577-590.
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PhD Thesis. Risk management in trading activities through the lens of complex systems theory. ISBN 9789464211009. Supervised by B. D. Kandhai and A. G. Hoekstra.
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Article. Regulating Lipid Composition Rationalizes Acyl Tail Saturation Homeostasis in Ectotherms. Biophysical Journal 119(5), pp. 892-899.
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Article. Reducing the complexity of financial networks using network embeddings. Scientific Reports 10, 17045.
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Article. Redistribution of TPA Fluxes in the Presence of PAI-1 Regulates Spatial Thrombolysis. Biophysical Journal 119(3), pp. 638-651.
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Article. Questionnaire data analysis using information geometry. Scientific Reports 10, 8633.
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Article. Probing Nanoparticle/Membrane Interactions by Combining Amphiphilic Diblock Copolymer Assembly and Plasmonics. The journal of Physical Chemistry. B 124(5), pp. 742-750.
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Proceedings. Preface. In: Computational Science – ICCS 2020. ISBN 9783030503710. I, pp. v-vi.
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Proceedings. Preface. In: Computational Science – ICCS 2020. ISBN 9783030504267. V, pp. v-vi.
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Proceedings. Preface. In: Computational Science – ICCS 2020. ISBN 9783030504205. III, pp. v-vi.
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Proceedings. Preface. In: Computational Science – ICCS 2020. ISBN 9783030504366. VII, pp. v-vi.
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Proceedings. Preface. In: Computational Science – ICCS 2020. ISBN 9783030504175. II, pp. v-vi.
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Proceedings. Preface. In: Computational Science – ICCS 2020. ISBN 9783030504335. VI, pp. v-vi.
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Proceedings. Preface. In: Computational Science – ICCS 2020. ISBN 9783030504236. IV, pp. v-vi.
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PhD Thesis. Platelet adhesion and aggregation in high shear blood flow. ISBN 9789402820287. Supervised by A. G. Hoekstra and G. Závodszky.
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Article. Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations. Scientific Data 7, 51.
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Proceedings. Modeling helping behavior in emergency evacuations using volunteer’s dilemma game. In: Computational Science – ICCS 2020. ISBN 9783030503710. I, pp. 513-523.
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PhD Thesis. Microstructure dynamics in shear thickening suspensions. ISBN 9789402818611. Supervised by A. G. Hoekstra and D. Bonn.
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Proceedings. Leadership, Management and Teams: A way of Being Successful. In: Proceedings of the 16th European Conference on Management, Leadership and Governance. ISBN 9781912764778. pp. 239-249.
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Article. Large-scale forecasting of information spreading. Journal of Big Data 7, 72.
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Article. Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids. Journal of Chemical Theory and Computation 16(5), pp. 3194-3204.
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Article. Inverse Uncertainty Quantification of a cell model using a Gaussian Process metamodel. International Journal for Uncertainty Quantification 10(4), pp. 333-349.
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Article. Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders. Machine Learning: Science and Technology 1(1), 015012.
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Article. Inserting Small Molecules across Membrane Mixtures. Biophysical Journal 118(6), pp. 1321-1332.
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Article. In-Silico Trials for Treatment of Acute Ischemic Stroke. Frontiers in Neurology 11, 558125.
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Article. Identification of risk factors for patients with diabetes: diabetic polyneuropathy case study. BMC Medical Informatics and Decision Making 20, 201.
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Article. Hydrodynamic Resistance of Intracranial Flow-Diverter Stents. Cardiovascular Engineering and Technology 11(1), pp. 1-13.
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Article. Hydration free energies from kernel-based machine learning: Compound-database bias. Journal of Chemical Physics 153(1), 014101.
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Proceedings. Future Prospects of the Transitioning Energy. In: Proceedings of the 16th European Conference on Management, Leadership and Governance. ISBN 9781912764778. pp. 57-64.
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Article. Free-energy landscape of polymer-crystal polymorphism. Soft Matter 16(42), pp. 9683-9692.
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Article. Foreseeing the future of mutualistic communities beyond collapse. Ecology Letters 23(1), pp. 2-15.
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Article. Emergence of spatio-temporal variations in chemotherapeutic drug efficacy. BMC Cancer 20, 1201.
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Proceedings. Easing Multiscale Model Design and Coupling with MUSCLE 3. In: Computational Science – ICCS 2020. ISBN 9783030504335. VI, pp. 425-438.
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Proceedings. Early signs of critical slowing down in heart surface electrograms of ventricular fibrillation victims. In: Computational Science – ICCS 2020. ISBN 9783030504236. IV, pp. 334-347.
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Proceedings. Detecting critical transitions in the human innate immune system post-cardiac surgery. In: Computational Science – ICCS 2020. ISBN 9783030503710. I, pp. 371-384.
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Article. Designing exceptional gas-separation polymer membranes using machine learning. Science Advances 6(20), eaaz4301.
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Article. Correction: A Smartphone App to Improve Medication Adherence in Patients With Type 2 Diabetes in Asia: Feasibility Randomized Controlled Trial. JMIR mHealth and uHealth 8(4), e18411.
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Article. Convection and the Extracellular Matrix Dictate Inter- and Intra-Biofilm Quorum Sensing Communication in Environmental Systems. Environmental Science and Technology 54(11), p. 6730–6740.
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Article. Contagious defaults in a credit portfolio: a Bayesian network approach. Journal of Credit Risk 16(1), pp. 1-26.
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Article. Computational Science in the Interconnected World: Selected papers from 2019 International Conference on Computational Science. Journal of Computational Science 47, 101222.
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Article. Coarse-grained conformational surface hopping. Journal of Chemical Physics 153(21), 214110.
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PhD Thesis. Cell resolved blood flow modeling with the Lattice Boltzmann method. ISBN 9789464211191. Supervised by A. G. Hoekstra and G. Závodszky.
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Article. Building Confidence in Simulation: Applications of EasyVVUQ. Advanced Theory and Simulations 3(8), 1900246.
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Article. Bridging the gap between complexity science and clinical practice by formalizing idiographic theories: a computational model of functional analysis. BMC Medicine 18, 99.
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Article. Biorheology of occlusive thrombi formation under high shear: in vitro growth and shrinkage. Scientific Reports 10, 18604.
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Article. An exploratory factor analysis model for slum severity index in Mexico City. Urban Studies 57(4), pp. 789-805.
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Article. Adversarial reverse mapping of equilibrated condensed-phase molecular structures. Machine Learning: Science and Technology 1(4), 045014.
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Book. Adaptive Information Management. ISBN 9789083045801.
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Article. A particle-based model for endothelial cell migration under flow conditions. Biomechanics and Modeling in Mechanobiology 19(2), pp. 681-692.
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Article. A novel virtual flow diverter implantation method with realistic deployment mechanics and validated force response. International Journal for Numerical Methods in Biomedical Engineering 36(6), e3340.
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Article. A data driven typology of electric vehicle user types and charging sessions. Transportation Research. Part C, Emerging Technologies 115, 102637.
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Proceedings. A Heterogeneous Multi-scale Model for Blood Flow. In: Computational Science – ICCS 2020. ISBN 9783030504335. VI, pp. 403-409.
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Article. 20 years of computational Science. Journal of Computational Science 46, 101187.
2019
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Proceedings. Unlocking the LOFAR ITA. In: IEEE 15th International Conference on eScience. ISBN 9781728124513. pp. 467-470.
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Article. Towards heterogeneous multi-scale computing on large scale parallel supercomputers. Supercomputing Frontiers and Innovations 6(4), pp. 20-43.
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Article. The impact of different obstacles on crowd dynamics. Journal of Computational Science 36, 100893.
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PhD Thesis. The emergence of biofilms. Supervised by P. M. A. Sloot.
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Chapter. The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions. In: Biomolecular Simulations. ISBN 9781493996087. p. 255–290.
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Article. Simulation of future electric vehicle charging behavior—effects of transition from PHEV to FEV. World Electric Vehicle Journal 10(2), 42.
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Article. Shear thickening of dense suspensions: The role of friction. Physics of Fluids 31(10), 103103.
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Article. Semi-intrusive uncertainty propagation for multiscale models. Journal of Computational Science 35, pp. 80-90.
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Article. Semi-intrusive multiscale metamodelling uncertainty quantification with application to a model of in-stent restenosis. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 377(2142), 2018154.
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Article. Science at the intersection of data, modelling, and computation. Journal of Computational Science 34, pp. 117-119.
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Article. Risk Factor Evolution for Counterparty Credit Risk under a Hidden Markov Model. Risks 7(2), 66.
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Article. Red blood cell and platelet diffusivity and margination in the presence of cross-stream gradients in blood flows. Physics of Fluids 31(3), 031903.
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Chapter. Quantitative Modelling Approaches. In: Encyclopedia of Bioinformatics and Computational Biology. ISBN 9780128114322. 2, pp. 874-883.
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Proceedings. Preface. In: Computational Science – ICCS 2019. ISBN 9783030227340. I, pp. v-vi.
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Article. Prediction and quantification of bacterial biofilm detachment using Glazier-Graner–Hogeweg method based model simulations. Journal of Theoretical Biology 482, 109994.
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Article. Patterns for High Performance Multiscale Computing. Future Generation Computer Systems 91, pp. 335-346.