Józsa, T. I., Padmos, R. M., Samuels, N., El-Bouri, W. K., Hoekstra, A. G., & Payne, S. J. (2021). A porous circulation model of the human brain for in silico clinical trials in ischaemic stroke. Interface Focus, 11(1), [20190127]. https://doi.org/10.1098/rsfs.2019.0127[details]
Padmos, R. M., Józsa, T. I., El-Bouri, W. K., Konduri, P. R., Payne, S. J., & Hoekstra, A. G. (2021). 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]. https://doi.org/10.1098/rsfs.2019.0125[details]
van Rooij, B. J. M., Závodszky, G., Hoekstra, A. G., & Ku, D. N. (2021). Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined in vitro and cellular in silico study. Interface Focus, 11(1), [20190126]. https://doi.org/10.1098/rsfs.2019.0126[details]
Czaja, B., Gutierrez, M., Závodszky, G., de Kanter, D., Hoekstra, A., & Eniola-Adefeso, O. (2020). The influence of red blood cell deformability on hematocrit profiles and platelet margination. PLoS Computational Biology, 16(3), [e1007716]. https://doi.org/10.1371/journal.pcbi.1007716[details]
Czaja, B., Závodszky, G., & Hoekstra, A. (2020). A Heterogeneous Multi-scale Model for Blood Flow. In V. V. Krzhizhanovskaya, G. Závodszky, M. H. Lees, J. J. Dongarra, P. M. A. Sloot, S. Brissos, & J. Teixeira (Eds.), Computational Science – ICCS 2020: 20th International Conference, Amsterdam, The Netherlands, June 3–5, 2020 : proceedings (Vol. VI, pp. 403-409). (Lecture Notes in Computer Science; Vol. 12142). Springer. https://doi.org/10.1007/978-3-030-50433-5_31[details]
Konduri, P. R., Marquering, H. A., van Bavel, E. E., Hoekstra, A., Majoie, C. B. L. M., & The INSIST Investigators (2020). In-Silico Trials for Treatment of Acute Ischemic Stroke. Frontiers in Neurology, 11, [558125]. https://doi.org/10.3389/fneur.2020.558125[details]
Nikishova, A., Comi, G. E., & Hoekstra, A. G. (2020). Sensitivity analysis based dimension reduction of multiscale models. Mathematics and Computers in Simulation, 170, 205-220. https://doi.org/10.1016/j.matcom.2019.10.013[details]
Shibeko, A. M., Chopard, B., Hoekstra, A. G., & Panteleev, M. A. (2020). Redistribution of TPA Fluxes in the Presence of PAI-1 Regulates Spatial Thrombolysis. Biophysical Journal, 119(3), 638-651. https://doi.org/10.1016/j.bpj.2020.06.020[details]
Uleman, J. F., Melis, R. J. F., Quax, R., van der Zee, E. A., Thijssen, D., Dresler, M., van de Rest, O., van der Velpen, I. F., Adams, H. H. H., Schmand, B., de Kok, I. M. C. M., de Bresser, J., Richard, E., Verbeek, M., Hoekstra, A. G., Rouwette, E. A. J. A., & Olde Rikkert, M. G. M. (2020). Mapping the multicausality of Alzheimer’s disease through group model building. GeroScience. https://doi.org/10.1007/s11357-020-00228-7
Veen, L. E., & Hoekstra, A. G. (2020). Easing Multiscale Model Design and Coupling with MUSCLE 3. In V. V. Krzhizhanovskaya, G. Závodszky, M. H. Lees, J. J. Dongarra, P. M. A. Sloot, S. Brissos, & J. Teixeira (Eds.), Computational Science – ICCS 2020: 20th International Conference, Amsterdam, The Netherlands, June 3–5, 2020 : proceedings (Vol. VI, pp. 425-438). (Lecture Notes in Computer Science; Vol. 12142). Springer. https://doi.org/10.1007/978-3-030-50433-5_33[details]
Zun, P. S., Narracott, A. J., Evans, P. C., van Rooij, B. J. M., & Hoekstra, A. G. (2020). A particle-based model for endothelial cell migration under flow conditions. Biomechanics and Modeling in Mechanobiology, 19(2), 681-692. https://doi.org/10.1007/s10237-019-01239-w[details]
de Vries, K., Nikishova, A., Czaja, B., Závodszky, G., & Hoekstra, A. G. (2020). Inverse Uncertainty Quantification of a cell model using a Gaussian Process metamodel. International Journal for Uncertainty Quantification, 10(4).
van Rooij, B. JM., Závodszky, G., Hoekstra, A. G., & Ku, D. N. (2020). Biorheology of occlusive thrombi formation under high shear: in vitro growth and shrinkage. Scientific Reports, 10(1), 1-11.
2019
Alowayyed, S., Piontek, T., Suter, J. L., Hoenen, O., Groen, D., Luk, O., ... Hoekstra, A. G. (2019). Patterns for High Performance Multiscale Computing. Future Generation Computer Systems, 91, 335-346. https://doi.org/10.1016/j.future.2018.08.045[details]
Alowayyed, S., Vassaux, M., Czaja, B., Coveney, P. V., & Hoekstra, A. G. (2019). Towards heterogeneous multi-scale computing on large scale parallel supercomputers. Supercomputing Frontiers and Innovations, 6(4), 20-43. https://doi.org/10.14529/jsfi190402
Azizi Tarksalooyeh, V., Závodszky, G., & Hoekstra, A. G. (2019). Optimizing Parallel Performance of the Cell Based Blood Flow Simulation Software HemoCell. In J. M. F. Rodrigues, P. J. S. Cardoso, J. Monteiro, R. Lam, V. V. Krzhizhanovskaya, M. H. Lees, J. J. Dongarra, ... P. M. A. Sloot (Eds.), Computational Science – ICCS 2019: 19th International Conference, Faro, Portugal, June 12–14, 2019 : proceedings (Vol. 3, pp. 537-547). (Lecture Notes in Computer Science; Vol. 11538). Cham: Springer. https://doi.org/10.1007/978-3-030-22744-9_42[details]
Hoekstra, A. G., Chopard, B., Coster, D., Portegies Zwart, S., & Coveney, P. V. (2019). Multiscale computing for science and engineering in the era of exascale performance. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences, 377(2142), [20180144]. https://doi.org/10.1098/rsta.2018.0144[details]
Hoekstra, A. G., Portegies Zwart, S., & Coveney, P. V. (2019). Multiscale modelling, simulation and computing: from the desktop to the exascale. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences, 377(2142), [20180355]. https://doi.org/10.1098/rsta.2018.0355[details]
Nikishova, A., Veen, L., Zun, P., & Hoekstra, A. G. (2019). 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]. https://doi.org/10.1098/rsta.2018.0154[details]
Olde Rikkert, M. G. M., van Zuijlen, P. M., de Kleuver, M., van Reekum, A., Hoekstra, A. G., & Sloot, P. M. A. (2019). Complexiteit van ziekten: Een moderne visie in tijden van vergrijzing en multimorbiditeit. Nederlands Tijdschrift voor Geneeskunde, 163(35), [D3970]. https://www.ntvg.nl/artikelen/complexiteit-van-ziekten
Sivadasan, V., Lorenz, E., Hoekstra, A. G., & Bonn, D. (2019). Shear thickening of dense suspensions: The role of friction. Physics of Fluids, 31(10), [103103]. https://doi.org/10.1063/1.5121536[details]
Zun, P. S., Narracott, A. J., Chiastra, C., Gunn, J., & Hoekstra, A. G. (2019). Location-Specific Comparison Between a 3D In-Stent Restenosis Model and Micro-CT and Histology Data from Porcine In Vivo Experiments. Cardiovascular Engineering and Technology, 10(4), 568–582. https://doi.org/10.1007/s13239-019-00431-4[details]
Závodszky, G., van Rooij, B., Czaja, B., Azizi, V., de Kanter, D., & Hoekstra, A. G. (2019). Red blood cell and platelet diffusivity and margination in the presence of cross-stream gradients in blood flows. Physics of Fluids, 31(3), [031903]. https://doi.org/10.1063/1.5085881[details]
van Rooij, B. J. M., Závodszky, G., Azizi Tarksalooyeh, V. W., & Hoekstra, A. G. (2019). Identifying the start of a platelet aggregate by the shear rate and the cell-depleted layer. Journal of the Royal Society Interface, 16(159), [20190148]. https://doi.org/10.1098/rsif.2019.0148[details]
Azizi Tarksalooyeh, V. W., Závodszky, G., van Rooij, B. J. M., & Hoekstra, A. G. (2018). Inflow and outflow boundary conditions for 2D suspension simulations with the immersed boundary lattice Boltzmann method. Computers & fluids, 172, 312–317. https://doi.org/10.1016/j.compfluid.2018.04.025[details]
Chopard, B., Falcone, J-L., Kunzli, P., Veen, L., & Hoekstra, A. G. (2018). Multiscale Modeling: recent progress and open questions. Multiscale and Multidisciplinary Modeling, Experiments and Design, 1(1), 57–68. https://doi.org/10.1007/s41939-017-0006-4[details]
Czaja, B., Závodszky, G., Azizi Tarksalooyeh, V., & Hoekstra, A. G. (2018). Cell-resolved blood flow simulations of saccular aneurysms: effects of pulsatility and aspect ratio. Journal of the Royal Society Interface, 15(146), [20180485]. https://doi.org/10.1098/rsif.2018.0485[details]
Hoekstra, A. G., van Bavel, E. T., Siebes, M., Gijsen, F., & Geris, L. (2018). Virtual physiological human 2016: translating the virtual physiological human to the clinic. Interface Focus, 8(1), [20170067]. https://doi.org/10.1098/rsfs.2017.0067[details]
Lorenz, E., Sivadasan, V., Bonn, D., & Hoekstra, A. G. (2018). Combined Lattice–Boltzmann and rigid-body method for simulations of shear-thickening dense suspensions of hard particles. Computers and Fluids, 172, 474-482. https://doi.org/10.1016/j.compfluid.2018.03.056[details]
Nikishova, A., Veen, L., Zun, P., & Hoekstra, A. G. (2018). Uncertainty Quantification of a Multiscale Model for In-Stent Restenosis. Cardiovascular Engineering and Technology, 9(4), 761-774. https://doi.org/10.1007/s13239-018-00372-4[details]
Quax, R., Chliamovitch, G., Dupuis, A., Falcone, J-L., Chopard, B., Hoekstra, A. G., & Sloot, P. M. A. (2018). Information processing features can detect behavioral regimes of dynamical systems. Complexity, 2018, [6047846]. https://doi.org/10.1155/2018/6047846[details]
de Haan, M., Zavodszky, G., Azizi, V., & Hoekstra, A. G. (2018). Numerical investigation of the effects of red blood cell cytoplasmic viscosity contrasts on single cell and bulk transport behaviour. Applied Sciences, 8(9), [1616]. https://doi.org/10.3390/app8091616[details]
Alowayyed, S., Groen, D., Coveney, P. V., & Hoekstra, A. G. (2017). Multiscale computing in the exascale era. Journal of Computational Science, 22, 15-25. https://doi.org/10.1016/j.jocs.2017.07.004[details]
Chopard, B., Ribeiro de Sousa, D., Lätt, J., Mountrakis, L., Dubois, F., Yourassowsky, C., ... Zouaoui Boudjeltia, K. (2017). A physical description of the adhesion and aggregation of platelets. Royal Society Open Science, 4, [170219]. https://doi.org/10.1098/rsos.170219[details]
Groen, D., Bosak, B., Krzhizhanovskaya, V., Hoekstra, A., & Koumoutsakos, P. (2017). Multiscale Modelling and Simulation, 14th International Workshop. Procedia Computer Science, 108, 1811-1812. https://doi.org/10.1016/j.procs.2017.05.275[details]
Melnikova, N. B., Svitenkov, A. I., Hose, D. R., & Hoekstra, A. G. (2017). A cell-based mechanical model of coronary artery tunica media. Journal of the Royal Society Interface, 14, [20170028]. https://doi.org/10.1098/rsif.2017.0028[details]
Mountrakis, L., Lorenz, E., & Hoekstra, A. G. (2017). Revisiting the use of the immersed-boundary lattice-Boltzmann method for simulations of suspended particles. Physical Review E, 96(1), [013302]. https://doi.org/10.1103/PhysRevE.96.013302[details]
Nikishova, A., Kalyuzhnaya, A., Boukhanovsky, A., & Hoekstra, A. (2017). Uncertainty quantification and sensitivity analysis applied to the wind wave model SWAN. Environmental Modelling & Software, 95, 344-357. https://doi.org/10.1016/j.envsoft.2017.06.030[details]
Zun, P. S., Anikina, T., Svitenkov, A. I., & Hoekstra, A. G. (2017). A Comparison of Fully-Coupled 3D In-Stent Restenosis Simulations to In-vivo Data. Frontiers in Physiology, 8, [284]. https://doi.org/10.3389/fphys.2017.00284[details]
Závodszky, G., van Rooij, B., Azizi, V., & Hoekstra, A. (2017). Cellular Level In-silico Modeling of Blood Rheology with An Improved Material Model for Red Blood Cells. Frontiers in Physiology, 8, [563]. https://doi.org/10.3389/fphys.2017.00563[details]
Har-Shemesh, O., Quax, R., Hoekstra, A. G., & Sloot, P. M. A. (2016). 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]. https://doi.org/10.1088/1742-5468/2016/04/043301[details]
Har-Shemesh, O., Quax, R., Miñano, B., Hoekstra, A. G., & Sloot, P. M. A. (2016). Nonparametric estimation of Fisher information from real data. Physical Review E, 93(2), [023301]. https://doi.org/10.1103/PhysRevE.93.023301[details]
Hoekstra, A. G., Alowayyed, S., Lorenz, E., Melnikova, N., Mountrakis, L., van Rooij, B., ... Zun, P. (2016). 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]. https://doi.org/10.1098/rsta.2016.0146[details]
Mizeranschi, A., Groen, D., Borgdorff, J., Hoekstra, A. G., Chopard, B., & Dubitzky, W. (2016). Anatomy and Physiology of Multiscale Modeling and Simulation in Systems Medicine. In U. Schmitz, & O. Wolkenhauer (Eds.), Systems Medicine (pp. 375-404). (Methods in Molecular Biology; Vol. 1386). New York: Humana Press. https://doi.org/10.1007/978-1-4939-3283-2_17[details]
Mountrakis, L., Lorenz, E., & Hoekstra, A. G. (2016). Scaling of shear-induced diffusion and clustering in a blood-like suspension. Europhysics Letters, 114(1), [14002]. https://doi.org/10.1209/0295-5075/114/14002[details]
Svitenkov, A. I., Zun, P., Rekin, O., & Hoekstra, A. G. (2016). Partitioning of Arterial Tree for Parallel Decomposition of Hemodynamic Calculations. Procedia Computer Science, 80, 977–987. https://doi.org/10.1016/j.procs.2016.05.393[details]
Krzhizhanovskaya, V. V., Groen, D., Bosak, B., & Hoekstra, A. G. (2015). Multiscale Modelling and Simulation Workshop: 12 Years of Inspiration. Procedia Computer Science, 51, 1082-1087. https://doi.org/10.1016/j.procs.2015.05.268[details]
Mountrakis, L., Lorenz, E., Malaspinas, O., Alowayyed, S., Chopard, B., & Hoekstra, A. G. (2015). Parallel performance of an IB-LBM suspension simulation framework. Journal of Computational Science, 9, 45-50. https://doi.org/10.1016/j.jocs.2015.04.006[details]
Svitenkov, A. I., Chivilikhin, S. A., Hoekstra, A. G., & Boukhanovsky, A. V. (2015). Fluid Simulations with Atomistic Resolution: Multiscale Model with Account of Nonlocal Momentum Transfer. Procedia Computer Science, 51, 1108-1117. https://doi.org/10.1016/j.procs.2015.05.279[details]
Tahir, H., Niculescu, I., Bona-Casas, C., Merks, R. M. H., & Hoekstra, A. G. (2015). 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. [20150358]. https://doi.org/10.1098/rsif.2015.0358[details]
Zun, P. S., & Hoekstra, A. G. (2015). On the Possible Interaction Mechanism between Collateral Vessels and Restenosis. Procedia Computer Science, 66, 412-418. https://doi.org/10.1016/j.procs.2015.11.047[details]
Amatruda, C. M., Bona Casas, C., Keller, B. K., Tahir, H., Dubini, G., Hoekstra, A., ... Gunn, J. (2014). From histology and imaging data to models for in-stent restenosis. The international journal of artificial organs, 37(10), 786-800. https://doi.org/10.5301/ijao.5000336[details]
Borgdorff, J., Ben Belgacem, M., Bona-Casas, C., Fazendeiro, L., Groen, D., Hoenen, O., ... Chopard, B. (2014). Performance of distributed multiscale simulations. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences, 372(2021), [20130407]. https://doi.org/10.1098/rsta.2013.0407[details]
Borgdorff, J., Mamonski, M., Bosak, B., Kurowski, K., Ben Belgacem, M., Chopard, B., ... Hoekstra, A. G. (2014). Distributed multiscale computing with MUSCLE 2, the Multiscale Coupling Library and Environment. Journal of Computational Science, 5(5), 719-731. https://doi.org/10.1016/j.jocs.2014.04.004[details]
Chopard, B., Borgdorff, J., & Hoekstra, A. G. (2014). A framework for multi-scale modelling. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences, 372(2021), [2013037813]. https://doi.org/10.1098/rsta.2013.0378[details]
Hoekstra, A., Chopard, B., & Coveney, P. (2014). Multiscale modelling and simulation: a position paper. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences, 372(2021), [20130377]. https://doi.org/10.1098/rsta.2013.0377[details]
Hoekstra, A., Chopard, B., & Lawford, P. (2014). Multi-Scale Modelling and Simulation. In P. V. Coveney, V. Díaz-Zuccarini, P. Hunter, & M. Viceconti (Eds.), Computational biomedicine: modelling the human body (pp. 138-160). Oxford: Oxford University Press. [details]
Karabasov, S., Nerukh, D., Hoekstra, A., Chopard, B., & Coveney, P. V. (2014). Multiscale modelling: approaches and challenges. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences, 372(2021), [20130390]. https://doi.org/10.1098/rsta.2013.0390[details]
Mountrakis, L., Lorenz, E., & Hoekstra, A. G. (2014). Validation of an efficient two-dimensional model for dense suspensions of red blood cells. International Journal of Modern Physics C, 25(12), [1441005]. https://doi.org/10.1142/S0129183114410058[details]
Tahir, H., Bona-Casas, C., Narracott, A. J., Iqbal, J., Gunn, J., Lawford, P., & Hoekstra, A. G. (2014). 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. [20140022]. https://doi.org/10.1098/rsif.2014.0022[details]
Borgdorff, J., Mamonski, M., Bosak, B., Groen, D., Ben Belgacem, M., Kurowski, K., & Hoekstra, A. G. (2013). Multiscale Computing with the Multiscale Modeling Library and Runtime Environment. Procedia Computer Science, 18, 1097-1105. https://doi.org/10.1016/j.procs.2013.05.275[details]
Groen, D., Borgdorff, J., Bona-Casas, C., Hetherington, J., Nash, R. W., Zasada, S. J., ... Coveney, P. V. (2013). Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations. Interface Focus, 3(2), [20120087]. https://doi.org/10.1098/rsfs.2012.0087[details]
Mountrakis, L., Lorenz, E., & Hoekstra, A. G. (2013). Where do the platelets go? A simulation study of fully resolved blood flow through aneurysmal vessels. Interface Focus, 3(2), 20120089. https://doi.org/10.1098/rsfs.2012.0089[details]
Pennella, F., Gentile, P., Deriu, M. A., Gallo, D., Schiavi, A., Ciardelli, G., Lorenz, E., Hoekstra, A. G., Audenino, A., & Morbiducci, U. (2013). A virtual test bench to study transport phenomena in 3D porous scaffolds using lattice boltzmann simulations. In ASME 2013 Summer Bioengineering Conference, SBC 2013 (ASME 2013 Summer Bioengineering Conference, SBC 2013; Vol. 1 A). American Society of Mechanical Engineers. https://doi.org/10.1115/SBC2013-14489
Tahir, H., Bona-Casas, C., & Hoekstra, A. G. (2013). Modelling the Effect of a Functional Endothelium on the Development of In-Stent Restenosis. PLoS ONE, 8(6), e66138. [e66138]. https://doi.org/10.1371/journal.pone.0066138[details]
Borgdorff, J., Bona-Casas, C., Mamonski, M., Kurowski, K., Piontek, T., Bosak, B., ... Hoekstra, A. G. (2012). A distributed multiscale computation of a tightly coupled model using the Multiscale Modeling Language. Procedia Computer Science, 9, 596-605. https://doi.org/10.1016/j.procs.2012.04.064[details]
Bernsdorf, J., Berti, G., Chopard, B., Hegewald, J., Krafczyk, M., Wang, D., ... Hoekstra, A. (2011). Towards distributed multiscale simulation of biological processes. In The Seventh IEEE International Conference on e-Science. Workshops: eScienceW 2011: proceedings: Stockholm, Sweden, 5-8 December 2011 (pp. 89-96). Piscataway, NJ: IEEE. https://doi.org/10.1109/eScienceW.2011.19[details]
Borgdorff, J., Falcone, J-L., Lorenz, E., Chopard, B., & Hoekstra, A. G. (2011). A principled approach to distributed multiscale computing, from formalization to execution. In Workshop Proceedings, 7th IEEE International Conference on eScience (pp. 97-104). Stockholm, Sweden: IEEE. https://doi.org/10.1109/eScienceW.2011.9[details]
Caiazzo, A., Evans, D., Falcone, J-L., Hegewald, J., Lorenz, E., Stahl, B., ... Hoekstra, A. (2011). A Complex Automata approach for in-stent restenosis: two-dimensional multiscale modelling and simulations. Journal of Computational Science, 2(1), 9-17. https://doi.org/10.1016/j.jocs.2010.09.002[details]
Chopard, B., Falcone, J-L., Hoekstra, A. G., & Borgdorff, J. (2011). A framework for multiscale and multiscience modeling and numerical simulations. In C. S. Calude, J. Kari, I. Petre, & G. Rozenberg (Eds.), Unconventional Computation: 10th International Conference, UC 2011, Turku, Finland, June 6-10 2011 : proceedings (pp. 2-8). (Lecture Notes in Computer Science; Vol. 6714). Heidelberg: Springer. https://doi.org/10.1007/978-3-642-21341-0_2[details]
Lorenz, E., & Hoekstra, A. G. (2011). Heterogeneous multiscale simulations of suspension flow. Multiscale Modeling & Simulation, 9(4), 1301-1326. https://doi.org/10.1137/100818522[details]
Maltsev, V. P., Hoekstra, A. G., & Yurkin, M. A. (2011). Optics of white blood cells: optical models, simulations, and experiments. In V. V. Tuchin (Ed.), Advanced optical flow cytometry: methods and disease diagnoses (pp. 63-93). Weinheim: Wiley-VCH. [details]
Murtaza, S., Hoekstra, A. G., & Sloot, P. M. A. (2011). Cellular automata simulations on a FPGA cluster. International Journal of High Performance Computing Applications, 25(2), 193-204. https://doi.org/10.1177/1094342010383138[details]
Naumov, L., Hoekstra, A., & Sloot, P. (2011). Cellular automata models of tumour natural shrinkage. Physica A : Statistical Mechanics and its Applications, 390(12), 2283-2290. https://doi.org/10.1016/j.physa.2011.02.006[details]
Tahir, H., Hoekstra, A. G., Lorenz, E., Lawford, P. V., Hose, D. R., Gunn, J., & Evans, D. J. W. (2011). Multi-scale simulations of the dynamics of in-stent restenosis: impact of stent deployment and design. Interface Focus, 1(3), 365-373. https://doi.org/10.1098/rsfs.2010.0024[details]
Yurkin, M. A., & Hoekstra, A. G. (2011). The discrete-dipole-approximation code ADDA: capabilities and known limitations. Journal of Quantitative Spectroscopy & Radiative Transfer, 112(13), 2234-2247. https://doi.org/10.1016/j.jqsrt.2011.01.031[details]
Hoekstra, A. G. (2010). Multiscale coupling of a Lattice Boltzmann simulation of blood flow to cell- and tissue-level processes: the case of in-stent restenosis. In J. C. F. Pereira, A. Sequeira, & J. M. C. Pereira (Eds.), Proceedings of the V European Conference on Computational Fluid Dynamics (ECCOMAS CFD 2010), Lisbon, Portugal [details]
Hoekstra, A. G., & Coveney, P. (2010). Towards distributed multiscale computing for the VPH. In Conference abstracts VPH 2010, 1st Virtual Physiological Human Conference (pp. 198-200). VPH Network of Excellence. [details]
Hoekstra, A. G., Lawford, P., & Hose, R. (2010). Modelling and simulating in-stent restenosis with complex automata. In Conference abstracts VPH 2010, 1st Virtual Physiological Human Conference (pp. 222-224). VPH Network of Excellence. [details]
Hoekstra, A., Luo, L. S., & Krafczyk, M. (2010). Mesoscopic methods in engineering and science. Computers and Mathematics with Applications, 59(7), 2139-2140. https://doi.org/10.1016/j.camwa.2009.10.029
Naumov, L., Hoekstra, A., & Sloot, P. (2010). The influence of mitoses rate on growth dynamics of a cellular automata model of tumour growth. Procedia Computer Science, 1(1), 971-978. https://doi.org/10.1016/j.procs.2010.04.107[details]
Sloot, P. M. A., & Hoekstra, A. G. (2010). Multi-scale modelling in computational biomedicine. Briefings in Bioinformatics, 11(1), 142-152. https://doi.org/10.1093/bib/bbp038[details]
Streekstra, G. J., Dobbe, J. G. G., & Hoekstra, A. G. (2010). Quantification of the fraction poorly deformable red blood cells using ektacytometry. Optics Express, 18(13), 14173-14182. https://doi.org/10.1364/OE.18.014173[details]
Yurkin, M. A., Min, M., & Hoekstra, A. G. (2010). Application of the discrete dipole approximation to very large refractive indices: Filtered coupled dipoles revived. Physical Review E, 82(3), 036703. https://doi.org/10.1103/PhysRevE.82.036703[details]
Yurkin, M. A., de Kanter, D., & Hoekstra, A. G. (2010). Accuracy of the discrete dipole approximation for simulation of optical properties of gold nanoparticles. Journal of Nanophotonics, 4(1), 041585. https://doi.org/10.1117/1.3335329[details]
van der Pol, E., Hoekstra, A. G., Sturk, A., Otto, C., van Leeuwen, T. G., & Nieuwland, R. (2010). Optical and non-optical methods for detection and characterization of microparticles and exosomes. Journal of Thrombosis and Haemostasis, 8(12), 2596-2607. https://doi.org/10.1111/j.1538-7836.2010.04074.x[details]
2009
Axner, L., Hoekstra, A. G., Jeays, A., Lawford, P., Hose, R., & Sloot, P. M. A. (2009). Simulations of time harmonic blood flow in the Mesenteric artery: comparing finite element and lattice Boltzmann methods. BioMedical Engineering OnLine, 8, 23. https://doi.org/10.1186/1475-925X-8-23[details]
Caiazzo, A., Evans, D., Falcone, J-L., Hegewald, J., Lorenz, E., Stahl, B., ... Hoekstra, A. G. (2009). Towards a Complex Automata multiscale model of in-stent restenosis. In G. Allen, J. Nabrzyski, E. Seidel, G. D. van Albada, J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2009: 9th International Conference Baton Rouge, LA, USA, May 25-27, 2009 : proceedings (Vol. I, pp. 705-714). (Lecture Notes in Computer Science; Vol. 5544). Berlin: Springer. https://doi.org/10.1007/978-3-642-01970-8_70[details]
Caiazzo, A., Falcone, J-L., Chopard, B., & Hoekstra, A. G. (2009). Asymptotic analysis of Complex Automata models for reaction-diffusion systems. Applied Numerical Mathematics, 59(8), 2023-2034. https://doi.org/10.1016/j.apnum.2009.04.001[details]
Evans, D. J. W., Caiazzo, A., Falcone, J. L., Hegewald, J., Lorenz, E., Stahl, B., Wang, D., Bernsdorf, J., Chopard, B., Gunn, J., Walker, D., Hose, R., Krafczyk, M., Hoekstra, A., & Lawford, P. (2009). COAST: Modelling Restenosis and Stent Based Therapies. In S. Vlad, R. V. Ciupa, & A. I. Nicu (Eds.), International Conference on Advancements of Medicine and Health Care through Technology: 23–26 September, 2009, Cluj-Napoca, Romania (pp. 319-322). (IFMBE Proceedings; Vol. 26). Springer. https://doi.org/10.1007/978-3-642-04292-8_71[details]
Geerdink, J. B. W., & Hoekstra, A. G. (2009). Comparing Entropic and Multiple Relaxation Times Lattice Boltzmann Methods for blood flow simulations. International Journal of Modern Physics C, 20(5), 721-733. https://doi.org/10.1142/S0129183109013947[details]
Lorenz, E., Caiazzo, A., & Hoekstra, A. G. (2009). Corrected momentum exchange method for lattice Boltzmann simulations of suspension flow. Physical Review E, 79(3), 036705. https://doi.org/10.1103/PhysRevE.79.036705[details]
Lorenz, E., Hoekstra, A. G., & Caiazzo, A. (2009). Lees-Edwards boundary conditions for lattice Boltzmann suspension simulations. Physical Review E, 79(3), 036706. https://doi.org/10.1103/PhysRevE.79.036706[details]
Murtaza, S., Hoekstra, A. G., & Sloot, P. M. A. (2009). Compute bound and I/O bound Cellular Automata simulations on FPGA logic. ACM Transactions on Reconfigurable Technology and Systems, 1(4), 23. [details]
Strokotov, D. I., Yurkin, M. A., Gilev, K. V., van Bockstaele, D. R., Hoekstra, A. G., Rubtsov, N. B., & Maltsev, V. P. (2009). Is there a difference between T- and B-lymphocyte morphology? Journal of Biomedical Optics, 14(6), 064036. https://doi.org/10.1117/1.3275471[details]
Axner, L., Bernsdorf, J., Zeiser, T., Lammers, P., Linxweiler, J., & Hoekstra, A. G. (2008). Performance evaluation of a parallel sparse lattice Boltzmann solver. Journal of computational Physics, 227(10), 4895-4911. https://doi.org/10.1016/j.jcp.2008.01.013[details]
Caiazzo, A., Falcone, J. L., Chopard, B., & Hoekstra, A. G. (2008). Error investigations in complex automata models for reaction-diffusion systems. In H. Umeo, S. Morishita, K. Nishinari, T. Komatsuzaki, & S. Bandini (Eds.), Cellular Automata: 8th International Conference on Cellular Aotomata for Reseach and Industry, ACRI 2008, Yokohama, Japan, September 23-26, 2008 : proceedings (pp. 260-267). (Lecture Notes in Computer Science; Vol. 5191). Berlin: Springer. https://doi.org/10.1007/978-3-540-79992-4_33[details]
Caiazzo, A., Falcone, J. L., Chopard, B., & Hoekstra, A. G. (2008). Scale-splitting error in complex automata models for reaction-diffusion systems. In M. Bubak, G. D. van Albada, J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2008: 8th International Conference, Kraków, Poland, June 23-25, 2008 : proceedings (Vol. II, pp. 291-300). (Lecture Notes in Computer Science; Vol. 5102). Berlin: Springer. https://doi.org/10.1007/978-3-540-69387-1_32[details]
Chernyshev, A. V., Tarasov, P. A., Semianov, K. A., Nekrasov, V. M., Hoekstra, A. G., & Maltsev, V. P. (2008). Erythrocyte lysis in isotonic solution of ammonium chloride: Theoretical modelling and experimental verification. Journal of Theoretical Biology, 251(1), 93-107. https://doi.org/10.1016/j.jtbi.2007.10.016[details]
Chopard, B., Falcone, J-L., Razakanirina, R., Hoekstra, A., & Caiazzo, A. (2008). On the collision-propagation and gather-update formulations of a cellular automata rule. In H. Umeo, S. Morishita, K. Nishinari, T. Komatsuzaki, & S. Bandini (Eds.), Cellular Automata: 8th International Conference on Cellular Aotomata for Reseach and Industry, ACRI 2008, Yokohama, Japan, September 23-26, 2008 : proceedings (pp. 144-151). (Lecture Notes in Computer Science; Vol. 5191). Berlin: Springer. https://doi.org/10.1007/978-3-540-79992-4_19[details]
Evans, D. J. W., Lawford, P. V., Gunn, J., Walker, D., Hose, D. R., Smallwood, R. H., ... Hoekstra, A. (2008). The application of multiscale modelling to the process of development and prevention of stenosis in a stented coronary artery. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences, 366(1879), 3343-3360. https://doi.org/10.1098/rsta.2008.0081[details]
Hegewald, J., Krafczyk, M., Tölke, J., Hoekstra, A., & Chopard, B. (2008). An agent-based coupling platform for complex automata. In M. Bubak, G. D. van Albada, J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2008: 8th International Conference, Kraków, Poland, June 23-25, 2008 : proceedings (Vol. II, pp. 227-233). (Lecture Notes in Computer Science; Vol. 5102). Berlin: Springer. https://doi.org/10.1007/978-3-540-69387-1_25[details]
Hoekstra, A. G., Falcone, J-L., Caiazzo, A., & Chopard, B. (2008). Multi-scale modeling with cellular automata: The complex automata approach. In H. Umeo, S. Morishita, K. Nishinari, T. Komatsuzaki, & S. Bandini (Eds.), Cellular Automata: 8th International Conference on Cellular Aotomata for Reseach and Industry, ACRI 2008, Yokohama, Japan, September 23-26, 2008 : proceedings (pp. 192-199). (Lecture Notes in Computer Science; Vol. 5191). Berlin: Springer. https://doi.org/10.1007/978-3-540-79992-4_25[details]
Krzhizhanovskaya, V. V., & Hoekstra, A. G. (2008). Simulation of Multiphysics Multiscale Systems, 5th International Workshop. In M. Bubak, G. D. van Albada, J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2008: 8th International Conference, Kraków, Poland, June 23-25, 2008 : proceedings (Vol. II, pp. 165-166). (Lecture Notes in Computer Science; Vol. 5102). Berlin: Springer. https://doi.org/10.1007/978-3-540-69387-1_18[details]
Murtaza, S., Hoekstra, A. G., & Sloot, P. M. A. (2008). Floating point based Cellular Automata simulations using a dual FPGA-enabled system. In V. Kindratenko (Ed.), 2008 Second International Workshop on High-Performance Reconfigurable Computing Technology and Applications (HPRCTA): proceedings: held in conjunction with SC 08, Austin, TX, November 17, 2008 Piscataway, NJ: IEEE. https://doi.org/10.1109/HPRCTA.2008.4745686[details]
Orlova, D. Y., Yurkin, M. A., Hoekstra, A. G., & Maltsev, V. P. (2008). Light scattering by neutrophils: Model, simulation, and experiment. Journal of Biomedical Optics, 13(5), 054057. https://doi.org/10.1117/1.2992140[details]
Yurkin, M. A., Min, M., & Hoekstra, A. G. (2008). Application of the discrete dipole approximation to extreme refractive indices: Filtered coupled dipoles revived. In 11th Electromagnetic & Light Scattering Conference: Extended abstracts: 7-12 September 2008, de Havilland Campus, University of Hertfordshire (pp. 109-112). University of Hertfordshire. [details]
Yurkin, M. A., de Kanter, D., & Hoekstra, A. G. (2008). Study of light scattering by a granulated coated sphere - a model of granulated blood cells. In 11th Electromagnetic & Light Scattering Conference: Extended abstracts: 7-12 September 2008, de Havilland Campus, University of Hertfordshire (pp. 299-302). University of Hertfordshire. [details]
2020
Uleman, J., Melis, R. J. F., Hoekstra, A., Quax, R., & Olde Rikkert, M. G. M. (2020). Uncovering the multicausality of Alzheimer’s disease: A systems modeling approach: Epidemiology/Risk and protective factors in MCI and dementia. Alzheimer's & Dementia, 16(S10), [e041105]. https://doi.org/10.1002/alz.041105[details]
2016
Yurkin, M. A., & Hoekstra, A. G. (2016). 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, 82-83. https://doi.org/10.1016/j.jqsrt.2015.11.025
2015
Yurkin, M. A., Maltsev, V. P., & Hoekstra, A. G. (2015). 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), 2407-2408. https://doi.org/10.1364/JOSAA.32.002407
2013
Borgdorff, J., Falcone, J-L., Lorenz, E., Bona-Casas, C., Chopard, B., & Hoekstra, A. G. (2013). Foundations of distributed multiscale computing: formalization, specification, and analysis. Journal of Parallel and Distributed Computing, 73(4), 465-483. https://doi.org/10.1016/j.jpdc.2012.12.011[details]
2010
Hoekstra, A. G., Caiazzo, A., Lorenz, E., Falcone, J-L., & Chopard, B. (2010). Complex Automata: Multi-scale Modeling with Coupled Cellular Automata. In A. G. Hoekstra, J. Kroc, & P. M. A. Sloot (Eds.), Simulating complex systems by cellular automata (pp. 29-57). (Understanding complex systems). Heidelberg: Springer. https://doi.org/10.1007/978-3-642-12203-3_3[details]
Hoekstra, A. G., Kroc, J., & Sloot, P. M. A. (2010). Introduction to modeling of complex systems using cellular automata. In A. G. Hoekstra, J. Kroc, & P. M. A. Sloot (Eds.), Simulating complex systems by cellular automata (pp. 1-16). (Understanding complex systems). Springer. https://doi.org/10.1007/978-3-642-12203-3_1[details]
Hoekstra, A. G., Kroc, J., & Sloot, P. M. A. (2010). Preface. In A. G. Hoekstra, J. Kroc, & P. M. A. Sloot (Eds.), Simulating Complex Systems by Cellular Automata (pp. xi-xiii). (Understanding Complex Systems). Springer. https://doi.org/10.1007/978-3-642-12203-3[details]
Hoekstra, A. G., Kroc, J., & Sloot, P. M. A. (Eds.) (2010). Simulating complex systems by cellular automata. (Understanding complex systems). Springer. https://doi.org/10.1007/978-3-642-12203-3[details]
2008
Krzhizhanovskaya, V. V., & Hoekstra, A. G. (2008). Special Issue on Simulation of Multiphysics Multiscale Systems. International Journal for Multiscale Computational Engineering, 6(1). https://doi.org/10.1615/IntJMultCompEng.v6.i1
1989
Sloot, P. M. A., van der Liet, H., Hoekstra, A. G., & Figdor, C. G. (1989). Scattering matrix elements of biological particles measured in a flow through system: theory and practice. Applied Optics, 28(10), 1752-1762. https://doi.org/10.1364/AO.28.001752[details]
Hoekstra, A. G. (2008). [Review of: V.V. Tuchin, L.V. Wang (2006) Optical polarization in biomedical applications]. Journal of Quantitative Spectroscopy & Radiative Transfer, 109(3), 531-531. https://doi.org/10.1016/j.jqsrt.2007.08.004[details]
2012
Borgdorff, J., Groen, D., Ferlin, S., Saverchenko, I., Suter, J., Hoekstra, A. G., & Coveney, P. V. (2012). Multiscale Simulations on Distributed European e-Infrastructures. Inside, 10(1), 72-77.
2014
Mountrakis, L., Lorenz, E., Malaspinas, O., Chopard, B., & Hoekstra, A. G. (2014). Looking into the transport of blood cells in flows without walls. 9. Abstract from Conference on Computational Physics (CCP2014), .
2013
Lorenz, E., Mountrakis, L., & Hoekstra, A. G. (2013). Strong Anisotropy in Shear-induced RBC-enhanced Platelet Diffusion. Abstract from 22nd International Conference on the Discrete Simulation of Fluid Dynamics, .
Mountrakis, L., Lorenz, E., & Hoekstra, A. G. (2013). Shape memory and membrane fluctuations of an RBC in shear flow. Abstract from 22nd International Conference on the Discrete Simulation of Fluid Dynamics, .
2011
Lorenz, E., & Hoekstra, A. G. (2011). Distributions of Cluster Sizes in Shear-Thickening, Suspensions derived from a Statistical Clustering Model. Paper presented at 19th Discrete Simulation of Fluid Dynamics: DSFD 2010, Rome, Italy.
2008
Evans, D. J. W., Hoekstra, A., Gunn, J., Walker, D., Hose, D. R., Smallwood, R. H., ... Lawford, P. V. (2008). Multiscale Modelling: Application of the Complex Automata Simulation Technique (COAST). Journal of Biomechanics, 41(S1), 482. https://doi.org/10.1016/S0021-9290(08)70481-0
Mediaoptreden
Hoekstra, A. (13-06-2018). De wereld van morgen. De wereld van morgen.
2016
Duijn, P. A. C. (2016). Detecting and disrupting criminal networks: A data driven approach. [details]
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