J. Morillo, M. Vassaux, P. V. Coveney, M. Garcia-Gasulla, “Hybrid parallelization of molecular dynamics simulations to reduce load imbalance”, J. Supercomput. (2022)DOI: 10.1007/s11227-021-04214-4
2021
J. L. Suter & P. V. Coveney, “Principles governing control of aggregation and dispersion of aqueous graphene oxide”, Sci. Rep., 11, 22460 (2021)DOI: 10.1038/s41598-021-01626-3
A. Ralli, P. Love, A. Tranter and P. Coveney, “Implementation of Measurement Reduction for the Variational Quantum Eigensolver”, Phys. Rev. Research 3, 033195 (2021), DOI: 10.1103/PhysRevResearch.3.033195
D. P. Coster, R. Fischer, O. Hoenen, J. Lakhlili, O. O. Luk, R. Preuss, B. D. Scott, and U. Toussaint, “Building a Turbulence-Transport workflow incorporating uncertainty quantification for predicting core profiles in a tokamak plasma”, Accepted, Nuclear Fusion, (2021), DOI: 10.1088/1741-4326/ac359f
O. O. Luk, J. Lakhlili, U. Toussaint, L. E. Veen, Y. Yudin, O. Hoenen, B. D. Scott, D. P. Coster, “Performing Validation, Verification, and Sensitivity Analysis on Multiscale Fusion Plasma Simulations with the VECMA Toolkit”, 47th EPS Conference on Plasma Physics (2021)
B. Bosak, T. Piontek, P. Karlshoefer, E. Raffin, J. Lakhlili, P. Kopta, “Verification, Validation and Uncertainty Quantification of Large-Scale Applications with QCG-PilotJob”, ICCS 2021, Lecture Notes in Computer Science, 12746 (2021), DOI: 10.1007/978-3-030-77977-1_39
D. Crommelin, W. Edeling, “Resampling with neural networks for stochastic parameterization in multiscale systems”,Physica D: Nonlinear Phenomena, 422, 132894 (2021), DOI: 10.1016/j.physd.2021.132894
F. Gugole, L. E. Coffeng, W. Edeling, B. Sanderse, S. J. de Vlas, D. Crommelin, “Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model”, PLOS Computational Biology, 17(9): e1009355 (2021), DOI: 10.1371/journal.pcbi.1009355
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
D. Suleimenova and D. Groen, “How policy decisions affect refugee journeys in South Sudan: A study using automated ensemble simulations”, Journal of Artificial Societies and Social Simulation 23 (1) 2 (2020), DOI: 10.18564/jasss.4193
J. Lakhlili, O.Hoenen, O. Luk, D. Coster, “Uncertainty Quantification for Multiscale Fusion Plasma Simulations with VECMA Toolkit”, ICCS 2020, Lecture Notes in Computer Science, 12143 (2020), DOI: 10.1007/978-3-030-50436-6_53
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
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”, Mathematics and Computers in Simulation, 170 (2020), 205-220,DOI: 10.1016/j.matcom.2019.10.013
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:10.1038/s41598-019-41758-1
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.
