Prof. dr. ir. A.G. (Alfons) Hoekstra
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Informatics Institute
Bezoekadres
- Science Park 900
- Kamernummer: L5.03
Postadres
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Postbus 94323
1090 GH Amsterdam
Contactgegevens
- Profile
-
Publicaties
- refereed (153)
- wetenschappelijk (11)
- vakpublicatie (2)
- populair wetenschappelijk (1)
- congresbijdragen (4)
- overige (1)
- erkenning (1)
- supervised theses (1)
- datasets (2)
2025
Karanasiou, G., Edelman, E., Boissel, F.-H., Byrne, R., Emili, L., Fawdry, M., Filipović, N., Flynn, D., Geris, L., Hoekstra, A., Jori, M. C., Kiapour, A., Krsmanovic, D., Marchal, T., Musuamba, F., Pappalardo, F., Petrini, L., Reiterer, M., Viceconti, M., ... Fotiadis, D. I. (2025). Advancing In Silico Clinical Trials for Regulatory Adoption and Innovation. IEEE Journal of Biomedical and Health Informatics, 29(4), 2654-2668. https://doi.org/10.1109/JBHI.2024.3486538 [details]
2024
- Dorst, M., Zeevenhooven, N., Wilding, R., Mende, D., Brandt, B. W., Zaura, E., Hoekstra, A., & Sheraton, V. M. (2024). FAIR compliant database development for human microbiome data samples. Frontiers in Cellular and Infection Microbiology, 14, Article 1384809. https://doi.org/10.3389/fcimb.2024.1384809 [details]
- Hao, Y., Hoekstra, A. G., & Závodszky, G. (2024). A Three-Dimensional Fluid-Structure Interaction Model for Platelet Aggregates Based on Porosity-Dependent Neo-Hookean Material. In L. Franco, C. de Mulatier, M. Paszynski, V. V. Krzhizhanovskaya, J. J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2024: 24th International Conference, Malaga, Spain, July 2–4, 2024 : proceedings (Vol. VII, pp. 48-62). (Lecture Notes in Computer Science; Vol. 14838). Springer. https://doi.org/10.1007/978-3-031-63783-4_5 [details]
- Hao, Y., Tersteeg, C., Hoekstra, A. G., & Závodszky, G. (2024). The effect of flow-derived mechanical cues on the growth and morphology of platelet aggregates under low, medium, and high shear rates. Computers in Biology and Medicine, 180, Article 109010. https://doi.org/10.1016/j.compbiomed.2024.109010 [details]
- Hoekstra, A. G., Marquering, H., & GEMINI consortium (2024). Towards a Generation of Digital Twins in Healthcare of Ischaemic and Haemorrhagic Stroke. In L. Franco, C. de Mulatier, M. Paszynski, V. V. Krzhizhanovskaya, J. J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2024: 24th International Conference, Malaga, Spain, July 2–4, 2024 : proceedings (Vol. III, pp. 239-245). (Lecture Notes in Computer Science; Vol. 14834). Springer. https://doi.org/10.1007/978-3-031-63759-9_29 [details]
- Pronk, A. C., Wang, L., van Poelgeest, E. P., Leeflang, M. M. G., Daams, J. G., Hoekstra, A. G., & van der Velde, N. (2024). The impact of cardiovascular diagnostics and treatments on fall risk in older adults: a scoping review and evidence map. GeroScience, 46, 153-169. https://doi.org/10.1007/s11357-023-00974-4 [details]
- Spieker, C. J., Kern, A. Y., Korin, N., Mangin, P. H., Hoekstra, A. G., & Závodszky, G. (2024). Carotid single- and dual-layer stents reduce the wall adhesion of platelets by influencing flow and cellular transport. Computers in Biology and Medicine, 183, Article 109313. https://doi.org/10.1016/j.compbiomed.2024.109313
- Uleman, J. F., Quax, R., Melis, R. J. F., Hoekstra, A. G., & Olde Rikkert, M. G. M. (2024). The need for systems thinking to advance Alzheimer's disease research. Psychiatry Research, 333, Article 115741. https://doi.org/10.1016/j.psychres.2024.115741 [details]
- Ye, D., Krzhizhanovskaya, V., & Hoekstra, A. G. (2024). Data-driven reduced-order modelling for blood flow simulations with geometry-informed snapshots. Journal of computational Physics, 497, Article 112639. https://doi.org/10.1016/j.jcp.2023.112639 [details]
2023
- Hao, Y., Závodszky, G., Tersteeg, C., Barzegari, M., & Hoekstra, A. G. (2023). Image-based flow simulation of platelet aggregates under different shear rates. PLoS Computational Biology, 19(7), Article e1010965. https://doi.org/10.1371/JOURNAL.PCBI.1010965 [details]
- 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, Article 107244. https://doi.org/10.1016/J.CMPB.2022.107244 [details]
- Petkantchin, R., Rousseau, A., Eker, O., Zouaoui Boudjeltia, K., Raynaud, F., Chopard, B., & INSIST investigators (2023). A simplified mesoscale 3D model for characterizing fibrinolysis under flow conditions. Scientific Reports, 13, Article 13681. https://doi.org/10.1038/s41598-023-40973-1 [details]
- Petkantchin, R., Rousseau, A., Eker, O., Zouaoui Boudjeltia, K., Raynaud, F., Chopard, B., & INSIST investigators (2023). Author Correction: A simplified mesoscale 3D model for characterizing fibrinolysis under flow conditions. Scientific Reports, 13, Article 20369. https://doi.org/10.1038/s41598-023-47162-0
- Spieker, C. J., Závodszky, G., Mouriaux, C., Mangin, P. H., & Hoekstra, A. G. (2023). Initial platelet aggregation in the complex shear environment of a punctured vessel model. Physics of Fluids, 35(7), Article 071904 . https://doi.org/10.1063/5.0157814 [details]
- Uleman, J. F., Melis, R. J. F., Hoekstra, A. G., Olde Rikkert, M. G. M., Quax, R., & the Australian Imaging, Biomarker and Lifestyle study of Aging and Alzheimer's Disease Neuroimaging Initiative studies (2023). Exploring the potential impact of multi-factor precision interventions in Alzheimer's disease with system dynamics. Journal of Biomedical Informatics, 145, Article 104462. https://doi.org/10.1016/j.jbi.2023.104462 [details]
- Uleman, J. F., Melis, R. J. F., Ntanasi, E., Scarmeas, N., Hoekstra, A. G., Quax, R., Olde Rikkert, M. G. M., & Alzheimer's Disease Neuroimaging Initiative (2023). Simulating the multicausality of Alzheimer's disease with system dynamics. Alzheimer's and Dementia, 19(6), 2633-2654. https://doi.org/10.1002/alz.12923 [details]
- Wang, L., Pronk, A. C., van Poelgeest, E. P., Briggs, R., Claassen, J. A. H. R., Jansen, S., Klop, M., de Lange, F. J., Meskers, C. C. G. M., Odekerken, V. J. J., Payne, S. J., Trappenburg, M. C., Thijs, R. D., Uleman, J. F., Hoekstra, A. G., & van der Velde, N. (2023). Applying systems thinking to unravel the mechanisms underlying orthostatic hypotension related fall risk. GeroScience, 45(4), 2743-2755. https://doi.org/10.1007/s11357-023-00802-9 [details]
- van Dijk, J., Zavodszky, G., Varbanescu, A.-L., Pimentel, A. D., & Hoekstra, A. (2023). Building a Fine-Grained Analytical Performance Model for Complex Scientific Simulations. In R. Wyrzykowski, J. Dongarra, E. Deelman, & K. Karczewski (Eds.), Parallel Processing and Applied Mathematics: 14th International Conference, PPAM 2022, Gdansk, Poland, September 11–14, 2022 : revised selected papers (Vol. I, pp. 183-196). (Lecture Notes in Computer Science; Vol. 13826). Springer. https://doi.org/10.1007/978-3-031-30442-2_14 [details]
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), Article 20220649. https://doi.org/10.1098/rsif.2022.0649 [details]
- Petkantchin, R., Padmos, R., Zouaoui Boudjeltia, K., Raynaud, F., Chopard, B., & INSIST investigators (2022). Thrombolysis: Observations and numerical models. Journal of Biomechanics, 132, Article 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), Article e057959. https://doi.org/10.1136/bmjopen-2021-057959 [details]
- 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), Article 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, 118(15), 3016-3051. https://doi.org/10.1093/CVR/CVAB370 [details]
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), Article 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), Article 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, Article 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), Article 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, Article 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, Article 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), Article 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, Article 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]
- 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, Article 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), Article 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, Article 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), Article 20190126. https://doi.org/10.1098/rsfs.2019.0126 [details]
- 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
- 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), Article 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, Article 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]
- 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), 333-349. https://doi.org/10.1615/Int.J.UncertaintyQuantification.2020033186 [details]
- van Rooij, B. J. M., 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, Article 18604. https://doi.org/10.1038/s41598-020-74518-7 [details]
2019
- Alowayyed, S., Piontek, T., Suter, J. L., Hoenen, O., Groen, D., Luk, O., Bosak, B., Kopta, P., Kurowski, K., Perks, O., Brabazon, K., Jancauskas, V., Coster, D., Coveney, P. V., & 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 [details]
- 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. III, pp. 537-547). (Lecture Notes in Computer Science; Vol. 11538). 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), Article 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), Article 20180355. https://doi.org/10.1098/rsta.2018.0355 [details]
- Nikishova, A., & Hoekstra, A. G. (2019). Semi-intrusive uncertainty propagation for multiscale models. Journal of Computational Science, 35, 80-90. https://doi.org/10.1016/j.jocs.2019.06.007 [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), Article 2018154. https://doi.org/10.1098/rsta.2018.0154 [details]
- Olde Rikkert, M. G. M., van Zuijlen, P. 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), Article D3970. https://www.ntvg.nl/artikelen/complexiteit-van-ziekten [details]
- Sivadasan, V., Lorenz, E., Hoekstra, A. G., & Bonn, D. (2019). Shear thickening of dense suspensions: The role of friction. Physics of Fluids, 31(10), Article 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), Article 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), Article 20190148. https://doi.org/10.1098/rsif.2019.0148 [details]
2018
- Alowayyed, S., Závodszky, G., Azizi, V., & Hoekstra, A. G. (2018). Load balancing of parallel cell-based blood flow simulations. Journal of Computational Science, 24, 1-7. https://doi.org/10.1016/j.jocs.2017.11.008 [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), Article 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), Article 20170067. https://doi.org/10.1098/rsfs.2017.0067 [details]
- Hoekstra, A. G., van de Vosse, F., & Röhrle, O. (2018). The Virtual Physiological Human Conference 2016. Journal of Computational Science, 24, 65-67. Advance online publication. https://doi.org/10.1016/j.jocs.2017.11.014 [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, Article 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), Article 1616. https://doi.org/10.3390/app8091616 [details]
2017
- 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., Van Antwerpen, P., Eker, O., Vanhamme, L., Perez-Morga, D., Courbebaisse, G., Lorenz, E., Hoekstra, A. G., & Zouaoui Boudjeltia, K. (2017). A physical description of the adhesion and aggregation of platelets. Royal Society Open Science, 4, Article 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, Article 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), Article 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, Article 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, Article 563. https://doi.org/10.3389/fphys.2017.00563 [details]
- Závodszky, G., van Rooij, B., Azizi, V., Alowayyed, S., & Hoekstra, A. (2017). Hemocell: a high-performance microscopic cellular library. Procedia Computer Science, 108, 159-165. https://doi.org/10.1016/j.procs.2017.05.084 [details]
2016
- Groen, D., Krzhizhanovskaya, V., Bosak, B., Scheibe, T., & Hoekstra, A. (2016). Multiscale modelling and simulation, 13th international workshop. Procedia Computer Science, 80, 1242-1243. https://doi.org/10.1016/j.procs.2016.05.494 [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), Article 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), Article 023301. https://doi.org/10.48550/arXiv.1507.00964, https://doi.org/10.1103/PhysRevE.93.023301 [details]
- Hoekstra, A. G., Alowayyed, S., Lorenz, E., Melnikova, N., Mountrakis, L., van Rooij, B., Svitenkov, A., Závodszky, G., & 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), Article 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). 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), Article 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]
2015
- 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), Article 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]
2014
- Amatruda, C. M., Bona Casas, C., Keller, B. K., Tahir, H., Dubini, G., Hoekstra, A., Hose, D. R., Lawford, P., Migliavacca, F., Narracott, A. J., & Gunn, J. (2014). From histology and imaging data to models for in-stent restenosis. The international journal of artificial organs, 37(10), 786-800. Advance online publication. 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), Article 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), Article 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), Article 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 University Press. https://global.oup.com/academic/product/computational-biomedicine-9780199658183 [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), Article 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), Article 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. Article 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), Article 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. Article e66138. https://doi.org/10.1371/journal.pone.0066138 [details]
2012
- Borgdorff, J., Bona-Casas, C., Mamonski, M., Kurowski, K., Piontek, T., Bosak, B., Rycerz, K., Ciepiela, E., Gubala, T., Harezlak, D., Bubak, M., Lorenz, E., & 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., Lorenz, E., & 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). 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). IEEE. https://doi.org/10.1109/eScienceW.2011.9 [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. (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). Wiley-VCH. http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527409343.html [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 http://web.univ-ubs.fr/limatb/EG2M/Disc_Seminaire/ECCOMAS-CFD2010/papers/01547.pdf [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. http://www.vph-noe.eu/vph-repository/doc_download/204-book-of-abstracts-for-vph2010 [details]
- Hoekstra, A., Luo, L-S., & Krafczyk, M. (2010). Mesoscopic methods in engineering and science. Computers and Mathematics with Applications, 59(7), 2139-2140. Advance online publication. 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. http://doi.acm.org/10.1145/1462586.1462592 [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., Chopard, B., Krafczyk, M., Bernsdorf, J., & 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 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. http://star.herts.ac.uk/els/AbstractsBook.pdf [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. http://star.herts.ac.uk/els/AbstractsBook.pdf [details]
2021
- Uleman, J. F., Quax, R., Melis, R. J. F., Hoekstra, A., & Olde Rikkert, M. G. M. (2021). An individualized systems model to optimize Alzheimer’s disease prevention strategies. Alzheimer's & Dementia, 17(S10), Article e050885. https://doi.org/10.1002/alz.050885 [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), Article 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
2008
- 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. http://inside.hlrs.de/assets/pdfs/inside_spring12.pdf
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). http://ccp2014.bu.edu/wp-content/uploads/2014/08/abstracts-parallel.pdf
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. https://dsfd2013.aua.am/2013/03/20/strong-anisotropy-in-shear-induced-rbc-enhanced-platelet-diffusion/
- 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. https://dsfd2013.aua.am/2013/03/20/shape-memory-and-membrane-fluctuations-of-an-rbc-in-shear-flow/
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., Chopard, B., Krafczyk, M., Bernsdorf, J., & 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 [Web]. De wereld van morgen. https://www.youtube.com/watch?v=xMquwHJH2XI
2022
- Czaja, B., de Bouter, J., Heisler, M., Závodszky, G., Karst, S., Sarunic, M., Maberley, D., Hoekstra, A. & Sarunic, M. (2022). The effect of stiffened diabetic red blood cells on wall shear stress in a reconstructed 3D microaneurysm. Taylor & Francis. https://doi.org/10.6084/m9.figshare.19228682.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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Virtual Physiological Human Institute
Karanasiou, G., Edelman, E., Boissel, F.-H., Byrne, R., Emili, L., Fawdry, M., Filipović, N., Flynn, D., Geris, L., Hoekstra, A., Jori, M. C., Kiapour, A., Krsmanovic, D., Marchal, T., Musuamba, F., Pappalardo, F., Petrini, L., Reiterer, M., Viceconti, M., ... Fotiadis, D. I. (2025). Advancing In Silico Clinical Trials for Regulatory Adoption and Innovation. IEEE Journal of Biomedical and Health Informatics, 29(4), 2654-2668.