Publications

Publications

2019

  • 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, In Press (2019).
  • 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, In Press (2019)
  • S. Wan, G. Tresadem, 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, In Press (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:10.13140/RG.2.2.11045.86245
  • 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: Mathematical, Physical and Engineering Sciences, 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.