Prof. dr. P.V. (Peter Vivian) Coveney
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Informatics Institute
Bezoekadres
- Science Park 904
Postadres
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Postbus 94323
1090 GH Amsterdam
Contactgegevens
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Publicaties
- refereed (39)
- wetenschappelijk (1)
- populair wetenschappelijk (1)
- congresbijdragen (1)
- supervised theses (1)
- datasets (6)
2023
Ahmad, K., Javed, A., Lanphere, C., Coveney, P. V., Orlova, E. V., & Howorka, S. (2023). Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nature Communications, 14, Article 3630. https://doi.org/10.1038/s41467-023-38681-5 [details]- Bhati, A. P., Hoti, A., Potterton, A., Bieniek, M. K., & Coveney, P. V. (2023). Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand-Protein Interactions and Allostery in SARS-CoV-2 Targets. Journal of Chemical Theory and Computation, 19(11), 3359-3378. https://doi.org/10.1021/ACS.JCTC.3C00020 [details]
- Bieniek, M. K., Wade, A. D., Bhati, A. P., Wan, S., & Coveney, P. V. (2023). TIES 2.0: A dual-topology open source relative binding free energy builder with web portal. Journal of Chemical Information and Modeling, 63(3), 718-724. https://doi.org/10.1021/ACS.JCIM.2C01596 [details]
- Groen, D., Arabnejad, H., Suleimenova, D., Edeling, W., Raffin, E., Xue, Y., Bronik, K., Monnier, N., & Coveney, P. V. (2023). FabSim3: An automation toolkit for verified simulations using high performance computing. Computer Physics Communications, 283, Article 108596. https://doi.org/10.1016/J.CPC.2022.108596 [details]
- Klöwer, M., Coveney, P. V., Paxton, E. A., & Palmer, T. N. (2023). Periodic orbits in chaotic systems simulated at low precision. Scientific Reports, 13, Article 11410. https://doi.org/10.1038/s41598-023-37004-4 [details]
- McCullough, J. W. S., & Coveney, P. V. (2023). High resolution simulation of basilar artery infarct and flow within the circle of Willis. Scientific Reports, 13, Article 21665. https://doi.org/10.1038/s41598-023-48776-0 [details]
- Ralli, A., Weaving, T., Tranter, A., Kirby, W. M., Love, P. J., & Coveney, P. V. (2023). Unitary partitioning and the contextual subspace variational quantum eigensolver. Physical Review Research, 5(1), Article 013095. https://doi.org/10.1103/PhysRevResearch.5.013095 [details]
- Suter, J. L., Vassaux, M., & Coveney, P. V. (2023). Large-scale molecular dynamics elucidates the mechanics of reinforcement in graphene-based composites. Advanced materials, 35(35), Article e2302237. https://doi.org/10.1002/ADMA.202302237 [details]
- Wan, S., Bhati, A. P., & Coveney, P. V. (2023). Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions. Journal of Chemical Theory and Computation, 19(21), 7846-7860. https://doi.org/10.1021/ACS.JCTC.3C00842 [details]
- Wan, S., Bhati, A. P., Wade, A. D., & Coveney, P. V. (2023). Ensemble-Based Approaches Ensure Reliability and Reproducibility. Journal of Chemical Information and Modeling, 63(22), 6959-6963. https://doi.org/10.1021/acs.jcim.3c01654 [details]
- Weaving, T., Ralli, A., Kirby, W. M., Love, P. J., Succi, S., & Coveney, P. V. (2023). Benchmarking noisy intermediate scale quantum error mitigation strategies for ground state preparation of the HCl molecule. Physical Review Research, 5(4), Article 043054. https://doi.org/10.1103/PHYSREVRESEARCH.5.043054 [details]
- Weaving, T., Ralli, A., Kirby, W. M., Tranter, A., Love, P. J., & Coveney, P. V. (2023). A stabilizer framework for the Contextual Subspace Variational Quantum Eigensolver and the noncontextual projection ansatz. Journal of Chemical Theory and Computation, 19(3), 808-821. https://doi.org/10.1021/ACS.JCTC.2C00910 [details]
- Zacharoudiou, I., McCullough, J. W. S., & Coveney, P. V. (2023). Development and performance of a HemeLB GPU code for human-scale blood flow simulation. Computer Physics Communications, 282(108548), Article 108548. https://doi.org/10.1016/J.CPC.2022.108548 [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. Advance online publication. https://doi.org/10.1098/rsfs.2020.0082 [details]
- Edeling, W., Arabnejad, H., Sinclair, R., Suleimenova, D., Gopalakrishnan, K., Bosak, B., Groen, D., Mahmood, I., Crommelin, D., & Coveney, P. V. (2021). The impact of uncertainty on predictions of the CovidSim epidemiological code. Nature Computational Science, 1(2), 128-135. https://doi.org/10.1038/s43588-021-00028-9 [details]
- Gheorghiu, A., Coveney, P. V., & Arabi, A. A. (2021). The influence of external electric fields on proton transfer tautomerism in the guanine-cytosine base pair. Physical Chemistry Chemical Physics, 23(10), 6252-6265. https://doi.org/10.1039/d0cp06218a [details]
- Groen, D., Arabnejad, H., Jancauskas, V., Edeling, W. N., Jansson, F., Richardson, R. A., Lakhlili, J., Veen, L., Bosak, B., Kopta, P., Wright, D. W., Monnier, N., Karlshoefer, P., Suleimenova, D., Sinclair, R., Vassaux, M., Nikishova, A., Bieniek, M., Luk, O. O., ... Coveney, P. V. (2021). VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences, 379(2197), Article 20200221. https://doi.org/10.1098/rsta.2020.0221 [details]
- McCullough, J. W. S., & Coveney, P. V. (2021). An efficient, localised approach for the simulation of elastic blood vessels using the lattice Boltzmann method. Scientific Reports, 11, Article 24260. https://doi.org/10.1038/s41598-021-03584-2 [details]
- McCullough, J. W. S., & Coveney, P. V. (2021). High fidelity blood flow in a patient-specific arteriovenous fistula. Scientific Reports, 11, Article 22301. https://doi.org/10.1038/s41598-021-01435-8 [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]
- Suter, J. L., & Coveney, P. V. (2021). Principles governing control of aggregation and dispersion of aqueous graphene oxide. Scientific Reports, 11, Article 22460. https://doi.org/10.1038/s41598-021-01626-3 [details]
2020
- Wright, D. W., Richardson, R. A., Edeling, W., Lakhlili, J., Sinclair, R. C., Jancauskas, V., Suleimenova, D., Bosak, B., Kulczewski, M., Piontek, T., Kopta, P., Chirca, I., Arabnejad, H., Luk, O. O., Hoenen, O., Węglarz, J., Crommelin, D., Groen, D., & Coveney, P. V. (2020). Building Confidence in Simulation: Applications of EasyVVUQ. Advanced Theory and Simulations, 3(8), Article 1900246. https://doi.org/10.1002/adts.201900246 [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. Advance online publication. 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]
- Groen, D., Richardson, R. A., Wright, D. W., Jancauskas, V., Sinclair, R., Karlshoefer, P., Vassaux, M., Arabnejad, H., Piontek, T., Kopta, P., Bosak, B., Lakhlili, J., Hoenen, O., Suleimenova, D., Edeling, W., Crommelin, D., Nikishova, A., & Coveney, P. V. (2019). Introducing VECMAtk - Verification, Validation and Uncertainty Quantification for Multiscale and HPC Simulations. 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. IV, pp. 479-492). (Lecture Notes in Computer Science; Vol. 11539). Springer. https://doi.org/10.1007/978-3-030-22747-0_36 [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. Advance online publication. 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. Advance online publication. https://doi.org/10.1098/rsta.2018.0355 [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. Advance online publication. https://doi.org/10.1016/j.jocs.2017.07.004 [details]
2014
- 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]
- 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]
- 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]
2013
- 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]
2012
- Zasada, S. J., Mamonski, M., Groen, D., Borgdorff, J., Saverchenko, I., Piontek, T., Kurowski, K., & Coveney, P. V. (2012). Distributed infrastructure for multiscale computing. In A. Boukerche, V. Cahill, A. El-Saddik, G. Theodoropoulos, & R. Walshe (Eds.), 2012 IEEE/ACM 16th International Symposium on Distributed Simulation and Real Time Applications: DS-RET 2012: Proceedings (pp. 65-74). IEEE Computer Society. https://doi.org/10.1109/DS-RT.2012.17 [details]
2010
- 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]
2009
- Sloot, P. M. A., Coveney, P. V., Ertaylan, G., Müller, V., Boucher, C. A., & Bubak, M. (2009). HIV decision support: From molecule to man. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences, 367(1898), 2691-2703. https://doi.org/10.1098/rsta.2009.0043 [details]
2008
- Sloot, P., Coveney, P., Bubak, M. T., Vandamme, A-M., Ó Nuallain, B., van de Vijver, D., & Boucher, C. (2008). ViroLab: A collaborative decision support system in viral disease treatment. Reviews in Antiviral Therapy, 3, 4-7. http://www.science.uva.nl/research/scs/papers/archive/Sloot2008e.pdf [details]
- Sloot, P., Coveney, P., Bubak, M. T., Vandamme, A-M., Ó Nualláin, B., van de Vijver, D., & Boucher, C. (2008). Multi-science decision support for HIV drug resistance treatment. Studies in Health Technology and Informatics, 138, 188-198. http://www.science.uva.nl/research/scs/papers/archive/Sloot2008c.pdf [details]
2014
- Karabasov, S. (Guest ed.), Nerukh, D. (Guest ed.), Hoekstra, A. (Guest ed.), Chopard, B. (Guest ed.), & Coveney, P. (Guest ed.) (2014). Multi-scale systems in fluids and soft matter: approaches, numerics and applications: papers of a theme issue. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences, 372(2021). http://rsta.royalsocietypublishing.org/content/372/2021 [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
2012
- Groen, D., Borgdorff, J., Zasada, S. J., Bona Casas, C., Hetherington, J., Nash, R., Hoekstra, A. G., & Coveney, P. (2012). A Distributed Infrastructure for Multiscale Biomedical Simulations. Abstract from VPH 2012 Conference of the Virtual Physiological Human Network of Excellence, London, United Kingdom.
2023
- Ahmad, K., Javed, A., Lanphere, C., Coveney, P. V., Orlova, E. V. & Howorka, S. (24-5-2023). Six DNA Helix Bundle nanopore - State 5. Protein Data Bank (PDB). https://doi.org/10.2210/pdb7YWO/pdb
- Ahmad, K., Javed, A., Lanphere, C., Coveney, P. V., Orlova, E. V. & Howorka, S. (24-5-2023). Six DNA Helix Bundle nanopore - State 4. Protein Data Bank (PDB). https://doi.org/10.2210/pdb7YWN/pdb
- Ahmad, K., Javed, A., Lanphere, C., Coveney, P. V., Orlova, E. V. & Howorka, S. (24-5-2023). Six DNA duplex bundle nanopore - State 2. Protein Data Bank (PDB). https://doi.org/10.2210/pdb7YWI/pdb
- Ahmad, K., Javed, A., Lanphere, C., Coveney, P. V., Orlova, E. V. & Howorka, S. (24-5-2023). Six DNA Helix Bundle nanopore - State 3. Protein Data Bank (PDB). https://doi.org/10.2210/pdb7YWL/pdb
- Ahmad, K., Javed, A., Lanphere, C., Coveney, P. V., Orlova, E. V. & Howorka, S. (24-5-2023). Six DNA Helix Bundle nanopore - State 1. Protein Data Bank (PDB). https://doi.org/10.2210/pdb7YWH/pdb
2021
- Arabnejad, H., Groen, D. J., Gopalakrishnan, K., Bosak, B., Crommelin, D., Coveney, P., Suleimenova, D., Edeling, W. & Mahmood, I. (2021). FabCovidSim. Zenodo. https://doi.org/10.5281/zenodo.4445290
This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list. -
Nevenwerkzaamheden
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University of London
Professor Physical Chemistry, Director Centre for Computational Science -
Yale University, USA
Professor Adjunct within the Medical School -
CBK Sci Con, UK
Founder and Scientific / Technical director -
Ensemble MD ltd, UK
Director
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University of London
Ahmad, K., Javed, A., Lanphere, C., Coveney, P. V., Orlova, E. V., & Howorka, S. (2023). Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nature Communications, 14, Article 3630.