Publications

Publications

Publications

Preprints

  • A. Ralli, P. Love, A. Tranter and P. Coveney, “Implementation of Measurement Reduction for the Variational Quantum Eigensolver”, Preprint

2021

  • M. Vassaux, S. Wan, W. Edeling and P. V. Coveney, “Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation”, J. Chem. Theory Comput., 17, 5187 (2021), DOI: 10.1021/acs.jctc.1c00526
  • D. Suleimenova, H. Arabnejad, W. N. Edeling, D. Coster, O. O. Luk, J. Lakhlili, V. Jancaskas, M Kulczewski, L. Veen, D. Ye, P. Zun, V. Krzhizhanovskaya, A. Hoekstra, D. Crommelin, P. V. Coveney, D. Groen, “Tutorial applications for Verification, Validation and Uncertainty Quantification using VECMA toolkit”, J. Comput. Sci. 53, 101402 (2021), DOI:10.1016/j.jocs.2021.101402
  • P. V. Coveney, D. Groen and A. G. Hoekstra, “Reliability and reproducibility in computational science: implementing validation, verification and uncertainty quantification in silico”, Phil. Trans. R. Soc. A. 379, 20200409 (2021), DOI:10.1098/rsta.2020.0409
  • M. S. Krafczyk, A. Shi, A. Bhaskar, D. Marinov and V. Stodden, “Learning from reproducing computational results: introducing three principles and the Reproduction Package”, Phil. Trans. R. Soc. A. 379, 20200069 (2021), DOI:10.1098/rsta.2020.0069
  • N. C. Clementi and L. A. Barba, “Reproducible validation and replication studies in nanoscale physics”, Phil. Trans. R. Soc. A. 379, 20200068 (2021), DOI:10.1098/rsta.2020.0068
  • V. Volodina and P. Challenor, “The importance of uncertainty quantification in model reproducibility”, Phil. Trans. R. Soc. A. 379, 20200071 (2021), DOI:10.1098/rsta.2020.0071
  • O. O. Luk, J. Lakhlili, O. Hoenen, U. von Toussaint, B. D. Scott and D. P. Coster, “Towards validated multiscale simulations for fusion”, Phil. Trans. R. Soc. A. 379, 20200074 (2021), DOI:10.1098/rsta.2020.0074
  • S. Wan, R. C. Sinclair and P. V. Coveney, “Uncertainty quantification in classical molecular dynamics”, Phil. Trans. R. Soc. A. 379, 20200082 (2021), DOI:10.1098/rsta.2020.0082
  • D. Suleimenova, H. Arabnejad, W. N. Edeling and D. Groen, “Sensitivity-driven simulation development: a case study in forced migrationo”, Phil. Trans. R. Soc. A. 379, 20200409 (2021), DOI:10.1098/rsta.2020.0077
  • D. Ye, L. Veen, A. Nikishova, J. Lakhlili, W. Edeling, O. O. Luk, V. V. Krzhizhanovskaya and A. G. Hoekstra, “Uncertainty quantification patterns for multiscale models”, Phil. Trans. R. Soc. A. 379, 20200072 (2021), DOI:10.1098/rsta.2020.0072
  • E. G. Daub, H. Arabnejad, I. Mahmood and D. Groen, “Uncertainty quantification of dynamic earthquake rupture simulations”, Phil. Trans. R. Soc. A. 379, 20200076 (2021), DOI:10.1098/rsta.2020.0076
  • F. Jansson, W. Edeling, J. Attema and D. Crommelin, “Assessing uncertainties from physical parameters and modelling choices in an atmospheric large eddy simulation model”, Phil. Trans. R. Soc. A. 379, 20200073 (2021), DOI:10.1098/rsta.2020.0073
  • P. V. Coveney and R. R. Highfield, “When we can trust computers (and when we can’t)”, Phil. Trans. R. Soc. A. 379, 20200409 (2021), DOI:10.1098/rsta.2020.0067
  • G. Fursin, “Collective knowledge: organizing research projects as a database of reusable components and portable workflows with common interfaces”, Phil. Trans. R. Soc. A. 379, 20200211 (2021), DOI:10.1098/rsta.2020.0211
  • 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. Monnier, P. Karlshoefer, D. Suleimenova, R. Sinclair, M. Vassaux, A. Nikishova, M. Bieniek, Onnie 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”, Phil. Trans. R. Soc. A. 379, 20200221 (2021), DOI:10.1098/rsta.2020.0221
  • L. Fortunato and M. Galassi, “The case for free and open source software in research and scholarship”, Phil. Trans. R. Soc. A. 379, 20200079 (2021), DOI:10.1098/rsta.2020.0079
  • Odd Erik Gundersen, “The fundamental principles of reproducibility”, Phil. Trans. R. Soc. A. 379, 20200210 (2021), DOI:10.1098/rsta.2020.0210
  • D. Ye, A. Nikishova, L. Veen, P. Zun and A. G. Hoekstra, “Non-intrusive and semi-intrusive uncertainty quantification of a multiscale in-stent restenosis model,” Reliability Engineering and System Safety 214 (2021) 107734. doi.org/10.1016/j.ress.2021.107734
  • A. Gheorghiu, P. V. Coveney and A. A. Arabi, “The influence of external electric fields on proton transfer tautomerism in the guanine-cytosine base pair”, Phys. Chem. Chem. Phys. 23, 6252-6265 (2021), DOI:10.1039/D0CP06218A
  • 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”, Nat Comput Sci 1, 128–135 (2021), DOI:10.1038/s43588-021-00028-9
  • M. Bieniek, A. Bhati, S. Wan and P. V. Coveney, “TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing”, J. Chem. Theory Comput., 17, 2, 1250–1265 (2021), DOI:10.1021/acs.jctc.0c01179

2020

  • 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, 4, 2, 2000234 (2020), DOI:10.1002/adts.202000234
  • 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.