Publications

Preprints

M. Vassaux, K. Gopalakrishnan, R. C. Sinclair, R. A. Richardson and P. Coveney, “Accelerating heterogeneous multiscale simulations of advanced materials properties with graph-based clustering”, Advanced Theory and Simulations, In Press
W. Edeling, H. Arabnejad, R. Sinclair, D. Suleimenova, K. Gopalakrishnan, B. Bosak, D. Groen, I. Mahmood, D. Crommelin, P. Coveney, “Model uncertainty and decision making: Predicting the Impact of COVID-19 Using the CovidSim Epidemiological Code”, preprint
P. V. Coveney, D. Groen, A. G. Hoekstra (eds), “Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico“, Phil. Trans. R. Soc. A, in preparation (2020)
D. Groen, H. Arabnejad, V. Jancauskas, W. N. Edeling, F. Jansson, R. A. Richardson, J. Lakhlili, L. Veen, B. Bosak, P. Kopta, D. W. Wright, N. Monnieri, P. Karlshoefer, D. Suleimenova, R. Sinclair, M. Vassaux, A. Nikishova, M. Bieniek, O. O. Luk, M. Kulczewski, E. Raffin, D. Crommelin, O. Hoenen, D. P. Coster, T. Piontek, and P. V. Coveney, “VECMAtk: A Scalable Verification, Validation and Uncertainty Quantification toolkit for Scientific Simulations”, Philosophical Transactions A, preprint
P. V. Coveney and R. R. Highfield “When We Can Trust Computers (and When We Can’t)”, Phil. Trans. R. Soc. A., preprint
S. Wan, R. C. Sinclair and P. V. Coveney, “Uncertainty Quantification in Classical Molecular Dynamics”, Phil. Trans. R. Soc. A, In Press

2020

P. V. Coveney and R. R. Highfield, “From Digital Hype to Analogue Reality: Universal Simulation Beyond the Quantum and Exascale Eras”, Journal of Computational Science, 46, 101093 (2020), DOI:10.1016/j.jocs.2020.101093
J. L. Suter, R. C. Sinclair and P. V. Coveney, “Principles Governing Control of Aggregation and Dispersion of Graphene and Graphene Oxide in Polymer Melts”, Adv. Mater. 2003213 (2020), DOI:10.1002/adma.202003213
D. W. Wright, R. A. Richardson, W. Edeling, J. Lakhlili, R. C. Sinclair, V. Jancauskas, D. Suleimenova, B. Bosak, M. Kulczewski, T. Piontek, P. Kopta, I. Chirca, H. Arabnejad, O. O. Luk, O. Hoenen, J. Weglarz, D. Crommelin, D. Groen, and P. V. Coveney, “Building confidence in simulation: Applications of EasyVVUQ”, Advanced Theory and Simulations, 1900246 (2020) DOI:10.1002/adts.201900246
R. A. Richardson, D. W. Wright, W. Edeling, V. Jancauskas, J. Lakhlili and P. V. Coveney, “EasyVVUQ: A library for verification, validation and uncertainty quantification in high performance computing”, Journal of Open Research Software, 8(1), 11 (2020) DOI:10.5334/jors.303
W. Edeling, D. Crommelin, “Reducing data-driven dynamical subgrid scale models by physical constraints”, Journal of Computers & Fluids, 201, 104470 (2020), DOI:10.1016/j.compfluid.2020.104470
S. Wan, G. Tresadern, L. Perez-Benito, H. van Vlijmen, P. V. Coveney, “Accuracy and Precision of Alchemical Relative Free Energy Predictions With and Without Replica-Exchange”, Advanced Theory and Simulations, 3, 1900195 (2020), DOI:10.1002/adts.201900195
D. Groen, D. Bell, H. Arabnejad, D. Suleimenova, S. E. J. Taylor, and A. Anagnostou, “Towards modelling the effect of evolving violence on forced migration”, In Proceedings of the 2019 Winter Simulation Conference, ΙΕΕΕ (2020)
D. W. Wright, F. Husseini, S. Wan, C. Meyer, H. van Vlijmen, G. Tresadern, P. V. Coveney, “Application of the ESMACS binding free energy protocol to a multi-binding site lactate dehydogenase A ligand dataset”, Advanced Theory and Simulations, Advanced Theory and Simulations, 3, 1900194 (2020), DOI:10.1002/adts.201900194.

2019

W. N. Edeling, D. Crommelin, “Reduced model-error source terms for fluid flow”, UNCECOMP19 Conference, Preprint (2019), DOI:10.13140/RG.2.2.36773.35048
W. Edeling, D. Crommelin, “Reducing data-driven dynamical subgrid scale models by physical constraints”, Computers & Fluids, Pre-Print (2019), DOI:10.1016/j.compfluid.2020.104470
C. V. Campos, D. Suleimenova, D Groen, “A Coupled Food Security and Refugee Movement Model for the South Sudan Conflict”, Computational Science – ICCS 2019, 11540, 725-732 (2019), DOI:10.1007/978-3-030-22750-0_71
V. Jancauskas, T. Piontek, P. Kopta and B. Bosak, “Predicting queue wait time probabilities for multi-scale computing”, Scientific Reports, 377 (2019), DOI:10.1098/rsta.2018.0151
A. Nikishova, G. E. Comi, A. G. Hoekstra, “Sensitivity analysis based dimension reduction of multiscale models”, arXiv (2019), arxiv.org/abs/1904.11403
M. Vassaux, R. C. Sinclair, R. A. Richardson, J. L. Suter, P. V. Coveney, “Toward high fidelity materials property prediction from multiscale modelling and simulation”, Advanced Theory and Simulations, 1900122 (2019), DOI:10.1002/adts.201900122
B. M. Boghosian P. V. Coveney, H. Wang, “A New Pathology in the Simulation of Chaotic Dynamical Systems on Digital Computers”, Advanced Theory and Simulations, 1900125 (2019), DOI:10.1002/adts.201900125
A. Nikishova, A. G. Hoekstra, “Semi-intrusive Uncertainty Propagation for multiscale models”, Journal of Computational Science, Available Online (2019), DOI:10.1016/j.jocs.2019.06.007
R. C. Sinclair, P. V. Coveney, “Modeling Nanostructure in Graphene Oxide: Inhomogeneity and the Percolation Threshold”, J. Chem. Inf. Model., Article ASAP (2019), DOI:10.1021/acs.jcim.9b00114
D. Groen, R. A. Richardson, D. W. Wright, V. Jancauskas, R. Sinclair, P. Karlshoefer, M. Vassaux, H. Arabnejad, T. Piontek, P. Kopta, B. Bosak, J. Lakhlili, O. Hoenen, D. Suleimenova, W. Edeling, D. Crommelin, A. Nikishova, P. V. Coveney, “Introducing VECMAtk – verification, validation and uncertainty quantification for multiscale and HPC simulations”, Lecture Notes in Computer Science, 1153, 479-492 (2019), DOI:10.1007/978-3-030-22747-0_36
David W. Wright, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney, “Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4”, Scientific Reports 9, 6017, (2019), DOI:10.26434/chemrxiv.7327019
A. Potterton, F. Husseini, M. Southey, M. Bodkin, A. Heifetz, P. V. Coveney, A. Townsend-Nicholson, “Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A2A Receptor Binders”, J. Chem. Theory Comput., 15 (5), 3316–3330 (2019), DOI:10.1021/acs.jctc.8b01270
W. Edeling, D. Crommelin, ‘Towards data-driven dynamic surrogate models for ocean flow’, Platform for Advanced Scientific Computing Conference, Zurich (2019), DOI:10.1145/3324989.3325713
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
A. G. Hoekstra, B. Chopard, D. Coster, S. Portegies Zwart, P. V. Coveney, “Multiscale Computing for Science and Engineering in the Era of Exascale Performance”, Phil Trans R Soc A, 377 (2019), DOI: 10.1098/rsta.2018.0144
A. G. Hoekstra , S. Portegies Zwart, and P. V. Coveney, “Multiscale modelling, simulation and computing: from the desktop to the exascale”, Phil Trans R Soc A, 377 (2019), DOI: 10.1098/rsta.2018.0355
S. Succi, P. V. Coveney, “Big Data: the End of the Scientific Method?” Phil Trans R Soc (Series A), 377 (2019), DOI: 10.1098/rsta.2018.0145
M. Vassaux, R. Richardson, P. V. Coveney, “The heterogeneous multiscale method applied to inelastic polymer mechanics”, Phil Trans R Soc A, 377 (2019), DOI: 10.1098/rsta.2018.0150
M. Vassaux, R. C. Sinclair, R. A. Richardson, J. L. Suter, P. V. Coveney, “The role of graphene in enhancing the material properties of thermosetting polymers”, Advanced Theory and Simulations, Available Online (2019), DOI:10.1002/adts.201800168

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, 377, 20180147 (2018), DOI: 10.1098/rsta.2018.0147
A. Nikishova, L. Veen, P. Zun, and A. G. Hoekstra “Semi-intrusive Multiscale Metamodeling Uncertainty Quantification with application to a model of In-Stent Restenosis”, Phil Trans A, 377, 20180154 (2018), doi.org/10.1098/rsta.2018.0154.
A. Nikishova, L. Veen, P. Zun, and A. G. Hoekstra, “Uncertainty Quantification of a Multiscale Model for In-Stent Restenosis”, Cardiovasc Eng Tech (2018), doi.org/10.1007/s13239-018-00372-4.