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Prof. dr. ir. A.G. (Alfons) Hoekstra

Faculty of Science
Informatics Institute
Photographer: UvA
Visiting address
  • Science Park 900
  • Room number: L5.03
Postal address
  • Postbus 94323
    1090 GH Amsterdam
Contact details
  • Profile
    Personal Homepage Section Computational Science Publications
  • Publications

    2023

    • Miller, C., Konduri, P., Bridio, S., Luraghi, G., Arrarte Terreros, N., Boodt, N., Samuels, N., Rodriguez Matas, J. F., Migliavacca, F., Lingsma, H., van der Lugt, A., Roos, Y., Dippel, D., Marquering, H., Majoie, C., & Hoekstra, A. (2023). In silico thrombectomy trials for acute ischemic stroke. Computer Methods and Programs in Biomedicine, 228, [107244]. https://doi.org/10.1016/J.CMPB.2022.107244
    • van Dijk, J., Závodszky, G., Varbanescu, A. L., Pimentel, A. D., & Hoekstra, A. G. (2023). Building a Fine-Grained Analytical Performance Model for Complex Scientific Simulations. Lecture Notes in Computer Science, 13826. https://doi.org/10.1007/978-3-031-30442-2_14

    2022

    • Czaja, B., de Bouter, J., Heisler, M., Závodszky, G., Karst, S., Sarunic, M., Maberley, D., & Hoekstra, A. (2022). The effect of stiffened diabetic red blood cells on wall shear stress in a reconstructed 3D microaneurysm. Computer Methods in Biomechanics and Biomedical Engineering, 25(15), 1691-1709. https://doi.org/10.1080/10255842.2022.2034794 [details]
    • Padmos, R. M., Arrarte Terreros, N., Józsa, T. I., Závodszky, G., Marquering, H. A., Majoie, C. B. L. M., Payne, S. J., & Hoekstra, A. G. (2022). Modelling collateral flow and thrombus permeability during acute ischaemic stroke. Journal of the Royal Society Interface, 19(195), [20220649]. https://doi.org/10.1098/rsif.2022.0649
    • Petkantchin, R., Padmos, R., Zouaoui Boudjeltia, K., Raynaud, F., Chopard, B., & INSIST investigators (2022). Thrombolysis: Observations and numerical models. Journal of Biomechanics, 132, [110902]. https://doi.org/10.1016/j.jbiomech.2021.110902 [details]
    • Wang, L., Van Poelgeest, E. P., Pronk, A. C., Daams, J. G., Leeflang, M. M. G., Hoekstra, A. G., & Van Der Velde, N. (2022). Impact of cardiovascular evaluations and interventions on fall risk in older adults: a protocol for a scoping review and evidence map. BMJ Open, 12(4), [e057959]. https://doi.org/10.1136/bmjopen-2021-057959
    • Ye, D., Zun, P., Krzhizhanovskaya, V., & Hoekstra, A. G. (2022). Uncertainty quantification of a three-dimensional in-stent restenosis model with surrogate modelling. Journal of the Royal Society Interface, 19(187), [20210864]. https://doi.org/10.1098/rsif.2021.0864 [details]
    • van der Velden, J., Asselbergs, F. W., Bakkers, J., Batkai, S., Bertrand, L., Bezzina, C. R., Bot, I., Brundel, B. J. J. M., Carrier, L., Chamuleau, S., Ciccarelli, M., Dawson, D., Davidson, S. M., Dendorfer, A., Duncker, D. J., Eschenhagen, T., Fabritz, L., Falcão-Pires, I., Ferdinandy, P., ... Thum, T. (2022). Animal models and animal-free innovations for cardiovascular research: current status and routes to be explored. Consensus document of the ESC Working Group on Myocardial Function and the ESC Working Group on Cellular Biology of the Heart. Cardiovascular research. https://doi.org/10.1093/CVR/CVAB370

    2021

    • Coveney, P. V., Groen, D., & Hoekstra, A. G. (2021). Reliability and reproducibility in computational science: implementing validation, verification and uncertainty quantification in silico. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 379(2197), [20200409]. https://doi.org/10.1098/rsta.2020.0409 [details]
    • Coveney, P. V., Hoekstra, A., Rodriguez, B., & Viceconti, M. (2021). Computational biomedicine. Part II: Organs and systems. Interface Focus, 11(1), [20200082]. https://doi.org/10.1098/rsfs.2020.0082 [details]
    • Georgakopoulou, T., van der Wijk, A-E., Bakker, E. N. T. P., vanBavel, E., & INSIST investigators (2021). Quantitative 3D analysis of tissue damage in a rat model of microembolization. Journal of Biomechanics, 128, [110723]. https://doi.org/10.1016/j.jbiomech.2021.110723 [details]
    • Józsa, T. I., Padmos, R. M., El-Bouri, W. K., Hoekstra, A. G., & Payne, S. J. (2021). On the Sensitivity Analysis of Porous Finite Element Models for Cerebral Perfusion Estimation. Annals of Biomedical Engineering, 49(12), 3647–3665. https://doi.org/10.1007/s10439-021-02808-w [details]
    • 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]
    • Luraghi, G., Bridio, S., Miller, C., Hoekstra, A., Rodriguez Matas, J. F., & Migliavacca, F. (2021). Applicability analysis to evaluate credibility of an in silico thrombectomy procedure. Journal of Biomechanics, 126, [110631]. https://doi.org/10.1016/j.jbiomech.2021.110631 [details]
    • Miller, C., Padmos, R. M., van der Kolk, M., Józsa, T. I., Samuels, N., Xue, Y., Payne, S. J., & Hoekstra, A. G. (2021). In silico trials for treatment of acute ischemic stroke: Design and implementation. Computers in Biology and Medicine, 137, [104802]. https://doi.org/10.1016/j.compbiomed.2021.104802 [details]
    • Miller, C., van der Kolk, M., Padmos, R., Józsa, T., & Hoekstra, A. (2021). Uncertainty Quantification of Coupled 1D Arterial Blood Flow and 3D Tissue Perfusion Models Using the INSIST Framework. In M. Paszynski, D. Kranzlmüller, V. V. Krzhizhanovskaya, J. J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2021: 21st International Conference, Krakow, Poland, June 16–18, 2021 : proceedings (Vol. VI, pp. 691-697). (Lecture Notes in Computer Science; Vol. 12747). Springer. https://doi.org/10.1007/978-3-030-77980-1_52 [details]
    • Padmos, R. M., Arrarte Terreros, N., Józsa, T. I., Závodszky, G., Marquering, H. A., Majoie, C. B. L. M., & Hoekstra, A. G. (2021). Modelling the leptomeningeal collateral circulation during acute ischaemic stroke. Medical Engineering and Physics, 91, 1-11. https://doi.org/10.1016/j.medengphy.2021.03.003 [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]
    • Padmos, R. M., Józsa, T. I., El-Bouri, W. K., Závodszky, G., Payne, S. J., & Hoekstra, A. G. (2021). Two-Way Coupling Between 1D Blood Flow and 3D Tissue Perfusion Models. In M. Paszynski, D. Kranzlmüller, V. V. Krzhizhanovskaya, J. J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2021: 21st International Conference, Krakow, Poland, June 16–18, 2021 : proceedings (Vol. III, pp. 670-683). (Lecture Notes in Computer Science; Vol. 12744). Springer. https://doi.org/10.1007/978-3-030-77967-2_56 [details]
    • Spieker, C. J., Závodszky, G., Mouriaux, C., van der Kolk, M., Gachet, C., Mangin, P. H., & Hoekstra, A. G. (2021). The Effects of Micro-vessel Curvature Induced Elongational Flows on Platelet Adhesion. Annals of Biomedical Engineering, 49(12), 3609–3620. https://doi.org/10.1007/s10439-021-02870-4 [details]
    • Suleimenova, D., Arabnejad, H., Edeling, W. N., Coster, D., Luk, O. O., Lakhlili, J., Jancauskas, V., Kulczewski, M., Veen, L., Ye, D., Zun, P., Krzhizhanovskaya, V., Hoekstra, A., Crommelin, D., Coveney, P. V., & Groen, D. (2021). Tutorial applications for Verification, Validation and Uncertainty Quantification using VECMA toolkit. Journal of Computational Science, 53, [101402]. https://doi.org/10.1016/j.jocs.2021.101402 [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. (2021). Mapping the multicausality of Alzheimer’s disease through group model building. GeroScience, 43(2), 829–843. https://doi.org/10.1007/s11357-020-00228-7 [details]
    • Uleman, J. F., Quax, R., Melis, R. JF., Hoekstra, A., & Rikkert, M. GM. O. (2021). An individualized systems model to optimize Alzheimer’s disease prevention strategies. Alzheimer's & Dementia, 17(S10), [e050885]. https://doi.org/10.1002/alz.050885
    • Ye, D., Nikishova, A., Veen, L., Zun, P., & Hoekstra, A. G. (2021). Non-intrusive and semi-intrusive uncertainty quantification of a multiscale in-stent restenosis model. Reliability Engineering and System Safety, 214, [107734]. https://doi.org/10.1016/j.ress.2021.107734 [details]
    • Ye, D., Veen, L., Nikishova, A., Lakhlili, J., Edeling, W., Luk, O. O., Krzhizhanovskaya, V. V., & Hoekstra, A. G. (2021). Uncertainty quantification patterns for multiscale models. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 379(2197), [20200072]. https://doi.org/10.1098/rsta.2020.0072 [details]
    • Zun, P., Svitenkov, A., & Hoekstra, A. (2021). Effects of local coronary blood flow dynamics on the predictions of a model of in-stent restenosis. Journal of Biomechanics, 120, [110361]. https://doi.org/10.1016/j.jbiomech.2021.110361 [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]
      • Related datasets
        • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Video 5: Platelet-rich plasma experiment with Casa's flow chamber from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study. The Royal Society. https://doi.org/10.6084/m9.figshare.13272999.v1
        • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Supplementary material from "Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study". The Royal Society. https://doi.org/10.6084/m9.figshare.c.5215767.v1
        • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Video 2: Whole blood experiment with Van Rooij's flow chamber from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study. The Royal Society. https://doi.org/10.6084/m9.figshare.13272996.v1
        • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Video 3: Platelet-rich plasma experiment with Van Rooij's flow chamber from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study. The Royal Society. https://doi.org/10.6084/m9.figshare.13273005.v1
        • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Video 1: Cell-based simulation of whole blood from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study. The Royal Society. https://doi.org/10.6084/m9.figshare.13273002.v1
        • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Video 4: Whole blood experiment with Casa's flow chamber from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study. The Royal Society. https://doi.org/10.6084/m9.figshare.13272990.v1
    • van der Kolk, M., Miller, C., Padmos, R., Azizi, V., & Hoekstra, A. (2021). des-ist: A Simulation Framework to Streamline Event-Based In Silico Trials. In M. Paszynski, D. Kranzlmüller, V. V. Krzhizhanovskaya, J. J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2021: 21st International Conference, Krakow, Poland, June 16–18, 2021 : proceedings (Vol. III, pp. 648-654). (Lecture Notes in Computer Science; Vol. 12744). Springer. https://doi.org/10.1007/978-3-030-77967-2_53 [details]

    2020

    2019

    2018

    2017

    2016

    2015

    2014

    • 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., Mizeranschi, A., Sutter, J. L., Coster, D., Coveney, P. V., Dubitzky, W., Hoekstra, A. G., Strand, P., & 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., Groen, D., Coveney, P. V., & 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]

    2013

    • 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., Saverchenko, I., Mamonski, M., Kurowski, K., Bernabeu, M. O., Hoekstra, A. G., & 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]

    2012

    • 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]

    2011

    • 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). 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]

    2010

    • Falcone, J-L., Chopard, B., & Hoekstra, A. (2010). MML: towards a Multiscale Modeling Language. Procedia Computer Science, 1(1), 819-826. https://doi.org/10.1016/j.procs.2010.04.089 [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. http://www.vph-noe.eu/vph-repository/doc_download/204-book-of-abstracts-for-vph2010 [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 [details]
    • 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., Wang, D., Bernsdorf, J., Chopard, B., Gunn, J., Hose, R., Krafczyk, M., Lawford, P., Smallwood, R., Walker, D., & 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). 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]

    2008

    • 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). 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). 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). 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). 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). 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). 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). 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]

    2020

    • Hoekstra, A. (2020). Kunnen wij uw toekomst voorspellen? (Oratiereeks; No. 616). Universiteit van Amsterdam. [details]

    2008

    2012

    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

    Media appearance

    2016

    2020

    • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Video 1: Cell-based simulation of whole blood from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study. The Royal Society. https://doi.org/10.6084/m9.figshare.13273002.v1
    • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Video 3: Platelet-rich plasma experiment with Van Rooij's flow chamber from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study. The Royal Society. https://doi.org/10.6084/m9.figshare.13273005.v1
    • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Video 5: Platelet-rich plasma experiment with Casa's flow chamber from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study. The Royal Society. https://doi.org/10.6084/m9.figshare.13272999.v1
    • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Supplementary material from "Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study". The Royal Society. https://doi.org/10.6084/m9.figshare.c.5215767.v1
    • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Video 4: Whole blood experiment with Casa's flow chamber from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study. The Royal Society. https://doi.org/10.6084/m9.figshare.13272990.v1
    • Van Rooij, R. B. J. M., Závodszky, G., Hoekstra, A. G. & Ku, D. N. (2020). Video 2: Whole blood experiment with Van Rooij's flow chamber from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined <i>in vitro</i> and cellular <i>in silico</i> study. The Royal Society. https://doi.org/10.6084/m9.figshare.13272996.v1

    2018

    • Melnikova, N. B., Hoekstra, A. G., Svitenkov, A. I. & Hose, D. R. (2018). Data from: A cell-based mechanical model of coronary artery tunica media. DRYAD. https://doi.org/10.5061/dryad.2t208
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      Lid Wetenschappellijk Adviesraad
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