Publications

2019

  • R. C. Sinclair, J. L. Suter and P. V. Coveney, “Micromechanical Exfoliation of Graphene on the Atomistic Scale”, Physical Chemistry Chemical Physics, 21, 5716-5722, (2019), DOI:10.1039/C8CP07796G

2018

  • D. Groen, J. Knap, P. Neumann, D. Suleimenova, L. Veen, K. Leiter, “Mastering the scales: A survey on the benefits of multiscale computing software”, Philosophical Transactions A: Mathematical, Physical and Engineering Sciences, In Press (2018), DOI: 10.1098/rsta.2018.0147
  • Adrian S Hamers, Maxwell X Cai, Javier Roa, Nathan Leigh, Stability of exomoons around the Kepler transiting circumbinary planets, Monthly Notices of the Royal Astronomical Society, 480/3, 3800-3811 (2018), DOI: 10.1093/mnras/sty2117
  • Portegies Zwart, Simon F.; Boekholt, Tjarda C. N., Numerical verification of the microscopic time reversibility of Newton’s equations of motion: Fighting exponential divergence, Communications in Nonlinear Science and Numerical Simulation, 61, 160-166 (2018), DOI: 10.1016/j.cnsns.2018.02.002
  • Jumana Dakka, Kristof Farkas-Pall, Matteo Turilli, David W Wright, Peter V Coveney, Shantenu Jha, Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations, arXiv (2018), arXiv:1801.01174
  • Dakka, Jumana; Turilli, Matteo; Wright, David W; Zasada, Stefan J; Balasubramanian, Vivek; Wan, Shunzhou; Coveney, Peter V; Jha, Shantenu, High-throughput Binding Affinity Calculations at Extreme Scales, BioMed Central, In Press (2018), arXiv:1712.09168
  • O. O. Luk, O. Hoenen, O. Perks, K. Brabazon, T. Piontek, P. Kopta, B. Bosak, A. Bottino, B. D. Scott, D. P. Coster, “Application of the Extreme Scaling Computing Pattern on Multiscale Fusion Plasma Modelling”, Philosophical Transactions of the Royal Society A, In Press (2018), DOI: 10.1098/rsta.2018.0152
  • A. G. Hoekstra, B. Chopard, D. Coster, S. Portegies Zwar, P. V. Coveney,” Multiscale Computing for Science and Engineering in the Era of Exascale Performance”, Phil Trans R Soc A, In Press (2018), DOI: 10.1098/rsta.2018.0144
  • M. Vassaux, R. Richardson, P. V. Coveney, “The heterogeneous multiscale method applied to inelastic polymer mechanics”, Phil Trans R Soc A, In Press (2018), DOI: 10.1098/rsta.2018.0150
  • O. Luk, O. Hoenen, A. Bottino, B. Scott, D. Coster, “ComPat Framework for Multiscale Simulations Applied to Fusion Plasmas”, Computer Physics Communications, Submitted (2018)
  • O. Luk, O. Hoenen, A. Bottino, B. Scott, D. Coster, “Optimization of Multiscale fusion Plasma Simulations within the ComPat Framework”, EPS Proceedings, P1.1102 (2018), ISBN: 979-10-96389-08-7
  • S. Alowayyed, G. Zavodszky, V. Azizi, and A. G. Hoekstra, “Load balancing of parallel cell-based blood flow simulations”, Journal of Computational Science, 24, 1-7, DOI: 10.1016/j.jocs.2017.11.008
  • S. Alowayyed, T. Piontek, J. L. Suter, O. Hoenen, D. Groen, O. Luk, B. Bosak, P. Kopta, K. Kurowski, O. Perks, K. Brabazon, V. Jancauskas, D. Coster, P. V. Coveney, A.G. Hoekstra, “Patterns for High Performance Multiscale Computing”, Future Generation Computer Systems, 91, 335-346 (2018), DOI: 10.1016/j.future.2018.08.045
  • B. Chopard, J. Falcone, P. Kunzli, L. Veen, A. Hoekstra, “Multiscale modeling: recent progress and open questions”, Multiscale and Multidisciplinary Modeling, Experiments and Design, 1, 57–68 (2018), DOI: 10.1007/s41939-017-0006-4
  • S. Alowayyed, V. Azizi, G. Zavodszky and A. G. Hoekstra, “Load Balancing Massively Parallel Cell-based Blood Flow Simulations”, Computer Physics Communications, Submitted (2018)
  • V. Jancauskas, T. Piontek, P. Kopta, B. Bosak, “Predicting Queue Wait Time Probabilities for Multi-Scale Computing”, Philosophical Transactions of the Royal Society, In Press (2018)
  • M. S. Fujii, J. Bédorf, J. Baba, S. P. Zwart, “The dynamics of stellar discs in live dark-matter haloes”, Monthly Notices of the Royal Astronomical Society, 477, 1451–1471, DOI: 10.1093/mnras/sty711
  • S. P. Zwart, S. Torres, I. Pelupessy , J. Bédorf, M. X. Cai, “The origin of interstellar asteroidal objects like 1I/2017 U1 `Oumuamua”, Monthly Notices of the Royal Astronomical Society, 479, L17-L22, DOI: 10.1093/mnrasl/sly088
  • D. Groen, R. A. Richardson, R. Coy, U. D. Schiller, H. Chandrashekar, F. Robertson, P. V. Coveney, “Validation of patient-specific cerebral blood flow simulation using transcranial Doppler measurements”, Frontiers in Physiology, 9, 721 (2018), DOI: 10.3389/fphys.2018.00721
  • D. Groen, “Development of a multiscale simulation approach for forced migration”, ICCS 2018, Springer Lecture Notes in Computer Science (LNCS), Accepted (2018)
  • N. T. Chan, D. Suleimenova, D. Bell, D. Groen, “Modelling Refugees Escaping Violent Events: A Feasibility Study From An Input Data Perspective”, Proceedings of the Operational Research Society Simulation Workshop 2018, In Press (2018)
  • A. Nikishova, L. Veen, P. Zun, A. G. Hoekstra, “Uncertainty Quantification of a Multiscale Model for In-Stent Restenosis”, Cardiovascular Engineering and Technology, 1-14 (2018), DOI: 10.1007/s13239-018-00372-4
  • S. Portegies Zwart and S. McMillan. Textbook: “Astrophysical Recipes: the Art of AMUSE” AAS IOP Astronomy (2018).
  • S. Succi, P. V. Coveney,”Big Data: the End of the Scientific Method?” Phil Trans R Soc (Series A) (in press) arxiv.org/abs/1807.09515
  • J. Suter, P. V. Coveney, “Chemically Specific Multiscale Modelling of the Shear-Induced Exfoliation of Clay-Polymer Nanocomposites”, ACS Omega, 3(6), 6439-6445 (2018) DOI: 10.1021/acsomega.8b00542
  • M. O. Bernabeu, M. L. Jones, R. W. Nash, A. Pezzarossa, P. V. Coveney, H. Gerhardt, and C. A. Franco, “PolNet: A Tool to Quantify Network-Level Cell Polarity and Blood Flow in Vascular Remodeling”, Biophysical Journal, 114 (9), 2052-2058 (2018) DOI: 10.1016/j.bpj.2018.03.032
  • A. Bhati, S. Wan, Y. Hu, B. Sherborne, P. V. Coveney, “Uncertainty Quantification in Alchemical Free Energy Methods”, Journal of Chemical Theory and Computation, 14 (6), 2867–2880 (2018), DOI: 10.1021/acs.jctc.7b01143
  • R. C. Sinclair, J. L. Suter, P. V. Coveney, “Graphene-graphene interactions: friction, superlubricity and exfoliation”, Advanced Materials, 30 (2018) 17057091, DOI: 10.1002/adma.201705791

2017

  • Maxwell Xu Cai, Simon Portegies Zwart, Arjen van Elteren, The signatures of the parental cluster on field planetary systems, Monthly Notices of the Royal Astronomical Society, 474/4, 5114-5121 (2017), DOI: 10.1093/mnras/stx3064
  • Pelupessy, Inti; Van Werkhoven, Ben; Van Elteren, Arjen; Viebahn, Jan; Candy, A.S.; Zwart, Simon Portegies; Dijkstra, Henk A., The Oceanographic Multipurpose Software Environment (OMUSE v1.0), Geoscientific Model Development, 10, 3167-3187 (2017), DOI: 10.5194/gmd-10-3167-2017
  • Gábor Závodszky, Britt van Rooij, Victor Azizi, Alfons Hoekstra, Cellular Level In-silico Modeling of Blood Rheology with An Improved Material Model for Red Blood Cells, Frontiers in Physiology, 8, 563 (2017), DOI: 10.3389/fphys.2017.00563
  • Penny Xuran Qian, Maxwell Xu Cai, Simon Portegies Zwart, Ming Zhu, SiMon: Simulation Monitor for Computational Astrophysics, Publications of the Astronomical Society of the Pacific, 129/979, 094503 (2017), DOI: 10.1088/1538-3873/aa7c49
  • G. Zavodszky, B. Rooij, V. Azizi, S. Alowayyed, A. Hoekstra, “Hemocell: a high-performance microscopic cellular library”, Procedia Computer Science, 108, 159-165 (2017), DOI: 10.1016/j.procs.2017.05.084
  • M. X. Cai, M. B. N. Kouwenhoven, S. Portegies Zwart, R. Spurzem, “Stability of multiplanetary systems in star clusters”, Monthly Notices of the Royal Astronomical Society, 470, 4337-4353 (2017), DOI: 10.1093/mnras/stx1464
  • S. Alowayyed, D. Groen, P. V. Coveney, A. G. Hoekstra, “Multiscale Computing in the Exascale Era”, Journal of Computational Science, 22, 15-25, DOI: 10.1016/j.jocs.2017.07.004
  • R. C. Eccleston, S. Wan, N. Dalchau, P. V. Coveney, “The role of multiscale protein dynamics in antigen presentation and T lymphocyte recognition”, Frontiers in Immunology, Available Online
    (2017), DOI: 10.3389/fimmu.2017.00797
  • P. S. Zun, T. Anikina, A. Svitenkov, A. G. Hoekstra, “A Comparison of Fully-Coupled 3D In-Stent Restenosis Simulations to In-vivo Data” Frontiers in Physiology, 8, 1-12 (2017), DOI:10.3389/fphys.2017.00284
  • D. Groen and S. Zwart, “From Thread to Transcontinental Computer: Disturbing Lessons in Distributed Supercomputing”, IEEE 11th International Conference one-Science (e-Science) 2015, 15557226 (2015), DOI: 10.1109/eScience.2015.81
  • S. Schmieschek , L. Shamardin, S. Frijters, T. Krueger, U. D. Schiller, J. Harting, and P. V. Coveney, “LB3D: A Parallel Implementation of the Lattice-Boltzmann Method for Simulation of Interacting Amphiphilic Fluids”, Computer Physics Communications, 217, 149–161 (2017), DOI: 10.1016/j.cpc.2017.03.013
  • S. Wan, A. Bhati, S. Skerratt, K. Omoto, V. Shanmugasundaram, S. Bagal, P. V. Coveney, “Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation”, Journal of Chemical Information and Modelling, 57 (4), 897–909 (2017), DOI: 10.1021/acs.jcim.6b00780
  • S. Wan, A. P. Bhati, S. J. Zasada, I. Wall, D. Green, P. Bamborough, and P. V. Coveney, “Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: a Computational Study”, J. Chem. Theory Comput., 13 (2), 784–795 (2017), DOI: 10.1021/acs.jctc.6b00794
  • A. Bhati, S. Wan, D. Wright, P. V. Coveney, “Rapid, accurate, precise and reliable relative free energy prediction using ensemble based thermodynamic integration”, Journal of Chemical Theory and Computation, 13 (1), 210–222 (2017), DOI: 10.1021/acs.jctc.6b00979

2016

  • Silvia Toonen, Adrian Hamers, Simon Portegies Zwart, The evolution of hierarchical triple star-systems, Computational Astrophysics and Cosmology, 3 (2016), DOI: 10.1186/s40668-016-0019-0
  • Alex Rimoldi, Simon Portegies Zwart, Elena Maria Rossi, Simulations of stripped core-collapse supernovae in close binaries, Computational Astrophysics and Cosmology, 3 (2016), DOI: 10.1186/s40668-016-0015-4
  • Inti Pelupessy, Ben van Werkhoven, Arjen van Elteren, Jan Viebahn, Adam Candy, Simon Portegies Zwart, Henk Dijkstra, The Oceanographic Multipurpose Software Environment, Geoscientific Model Development Discussions, 1-36 (2016), DOI: 10.5194/gmd-2016-178
  • Peter V. Coveney, Shunzhou Wan, On the calculation of equilibrium thermodynamic properties from molecular dynamics, Physical Chemistry Chemical Physics, 18, 30236-30240 (2016), DOI: 10.1039/c6cp02349e
  • A. G. Hoekstra, S. Alowayyed, E. Lorenz, N. Melnikova, L. Mountrakis, B. van Rooij, A. Svitenkov, G. Závodszky, P. Zun, “Towards the virtual artery: a multiscale model for vascular physiology at the physics–chemistry–biology interface”, Philosophical Transactions of the Royal Society A, 374 (2016), DOI: 10.1098/rsta.2016.0146
  • D. Groen, A. Bhati, J. Suter, J. Hetherington, S. Zasada, P. V. Coveney, “FabSim: facilitating computational research through automation on large-scale and distributed e-infrastructures”, Computer Physics Communications, 207, 375–385 (2016), DOI: 10.1016/j.cpc.2016.05.020

2015

  • S. J. Zasada and P. V. Coveney, “A Distributed Multi-agent Market Place for HPC Compute Cycle Resource Trading”, CoRR (2015), arXiv:1512.04343
  • J. Suter, D. Groen, and P. V. Coveney, “Mechanism of exfoliation and prediction of materials properties of clay-polymer nanocomposites from multiscale modeling”, Nano Lett., 15, 8108–8113 (2015), DOI: 10.1021/acs.nanolett.5b03547

COMPAT Deliverables