Publications

A list of publications from the group.

Preprints

M. Williams de la Bastida, T. M. Bickley and P. V. Coveney, “Optimised Fermion-Qubit Encodings for Quantum Simulation with Reduced Transpiled Circuit Depth”, arXiv (2025) DOI: 10.48550/arXiv.2512.13580
X. Xue, M. F. P. ten Eikelder, M. Gao, X. Cheng, Y. Yang, Y. He, S. Wang, S. Cheng, Y. Hu and P. V. Coveney, “Fast-Forward Lattice Boltzmann: Learning Kinetic Behaviour with Physics-Informed Neural Operators” arXiv (2025) DOI: 10.48550/arXiv.2509.22411
T. Weaving, A. Mingare, A. Ralli and P. V. Coveney, “Towards Compact Wavefunctions from Quantum-Selected Configuration Interaction”, arXiv (2025) DOI: 10.48550/arXiv.2509.02525
X. Xue, M. F. P. ten Eikelder, T. Yang, Y. Li, K. He, S. Wang and P. V. Coveney, “Equivariant U-Shaped Neural Operators for the Cahn-Hilliard Phase-Field Model”, arXiv (2025) DOI: 10.48550/arXiv.2509.01293
X. Xue, T. M. Athawale, J. W. S. McCullough, S. C. Y. Lo, I. Zacharoudiou, B. Joo, A. Georgiadou and P. V. Coveney, “An Uncertainty Visualization Framework for Large-Scale Cardiovascular Flow Simulations: A Case Study on Aortic Stenosis”, arXiv (2025) DOI: 10.48550/arXiv.2508.15420
M. Wang, X. Xue, M. Gao and P. V. Coveney, “Quantum-Informed Machine Learning for Predicting Spatiotemporal Chaos”, arXiv (2025) DOI: 10.48550/arXiv.2507.19861
P. V. Coveney, S. Succi, “The wall confronting large language models”, arXiv (2025) DOI: 10.48550/arXiv.2507.19703
T. Weaving, A. Ralli, V. Wimalaweera, P. J. Love, P. V. Coveney, “Simulating the Antiferromagnetic Heisenberg Model on a Spin-Frustrated Kagome Lattice with the Contextual Subspace Variational Quantum Eigensolver”, arXiv (2025) DOI: 10.48550/arXiv.2506.12391
P. V. Coveney, S. Wan, “Non-Gaussian distributions of absolute free energies in ensemble molecular dynamics simulations”, ChemRxiv (2023) DOI: 10.26434/chemrxiv-2022-s4jw1-v2
P. V. Coveney, S. Wan, A. P. Bhati, A. D. Wade, “Which corners to cut? Guidelines on choosing optimal settings to maximise sampling with limited computational resources”, ChemRxiv (2022) DOI:10.26434/chemrxiv-2022-2jdk2

In Press

B. Akpa, F. J. Alexander, B. Al-Lazikani, A. Attia, C. Blaby-Haas, N. Chia, C. Chung, P. V. Coveney et. al., “Accelerating Goal-driven Science by Optimizing Operational Decisions”, DOE BER/ASCR Workshop (2025)

2026

P. V. Coveney and R. R. Highfield, “AI needs physics more than physics needs AI”, Frontiers in Physics, 2026, 13, 1731777, DOI: 10.3389/fphy.2025.1731777

2025

T. M. Bickley, A. Mingare, T. Weaving, M. Williams de la Bastida, S. Wan, M. Nibbi, P. Seitz, A. Ralli, P. J. Love, M. Chung, M. Hernández Vera, L. Schulz, P. V. Coveney, “Extending quantum computing through subspace, embedding and classical molecular dynamics techniques”, Digital Discovery, 2025, 4, 3427-3444, DOI: 10.1039/D5DD00225G
M. Wang, J. Jiang, P. V. Coveney, “Parameter-efficient quantum anomaly detection method on a superconducting quantum processor”, Physical Review Research, 2025, 7, 043094, DOI: 10.1103/cv9y-2cnj
A. Ralli, T. Weaving, P. V. Coveney, P. J. Love, “Bridging Quantum Chemistry and MaxCut: Classical Performance Guarantees and Quantum Algorithms for the Hartree–Fock Method”, Journal of Chemical Theory and Computation, 2025, 21, 19, 9511–9524, DOI: 10.1021/acs.jctc.5c00948
X. Zhang, S. Wan, A. P. Bhati, P. W. Fowler and P. V. Coveney, “Rapid, accurate, and reproducible de novo prediction of resistance to antituberculars”, mSphere, 2025, 10, 10, e00571-25, DOI: 10.1128/msphere.00571-25
I. Benemerito, J. McCullough, A. Narracott, P. V. Coveney and A. Marzo, “Comparison of Navier-Stokes and lattice Boltzmann solvers for subject-specific modelling of intracranial aneurysms”, Computers in Biology and Medicine, 2025, 197, 111050, DOI: 10.1016/j.compbiomed.2025.111050
P. V. Coveney, R. R. Highfield, E. Stahlberg and M. Vázquez, “Digital twins and Big AI: the future of truly individualised healthcare”, npj Digital Medicine, 2025, 8, 494, DOI: 10.1038/s41746-025-01874-x
S. C. Y. Lo, A. Zingaro, J. W. S. McCullough, X. Xue, P. Gonzalez-Martin, B. Joo, M. Vázquez, P. V. Coveney, “A multi-component, multi-physics computational model for solving coupled cardiac electromechanics and vascular haemodynamics”, Computer Methods in Applied Mechanics and Engineering, 2025, 446, 118185, DOI: 10.1016/j.cma.2025.118185
A. M. Butler, D. R. Chisholm, C. W. E. Tomlinson, T. Khatib, J. Clark, S. Wan, P. V. Coveney, I. R. Greig, P. McCaffery, E. Pohl, A. Whiting, “Synthetic Retinoids for the Modulation of Genomic and Nongenomic Processes in Neurodegenerative Diseases”, ACS Omega, 2025, 10, 22, 23709–23738, DOI: 10.1021/acsomega.5c00934
T. Weaving, A. Ralli, P. J. Love, S. Succi, P. V. Coveney, “Accurately Simulating the Time Evolution of an Ising Model with Echo Verified Clifford Data Regression on a Superconducting Quantum Computer”, Quantum, 2025, 9, 1732, DOI: 10.22331/q-2025-05-05-1732
P. V. Coveney and S. Wan, “Molecular Dynamics: Probability and Uncertainty”, Oxford University Press, 2025, DOI: 10.1093/9780198893479.001.0001
R. Amaro, J. Åqvist, I. Bahar, F. Battistini, A. Bellaiche, D. Beltran, P. C. Biggin, M. Bonomi, G. R. Bowman, R. Bryce, G. Bussi, P. Carloni, D. Case, A. Cavalli, C. A. Chang, T. E. Cheatham III, M. S. Cheung, C. Chipot, L. T. Chong, P. Choudhary, G. A. Cisneros, C. Clementi, R. Collepardo-Guevara, P. V. Coveney et al., “The need to implement FAIR principles in biomolecular simulations”, Nature Methods, 2025, 22, 641-645, DOI: 10.1038/s41592-025-02635-0
A. Georgiadou, H. Monge Camacho, T. Sohail, S. Ghosh, D. N. Asthagiri, D. Bykov, T. Athawale, M. Titov, M. Turilli, S. Jha, K. Maheshwari, R. Ferreira Da Silva, D. Dietz, M. Ghorbani, D. Suleimenova, P. V. Coveney and T. L. Beck, “Workflows for Science: A comprehensive guide for ensemble workflow tools usage with applications on OLCF systems”, Oak Ridge National Laboratory, 2025, DOI: 10.2172/2575304
T. Weaving, A. Ralli, P. J. Love, S. Succi, P. V. Coveney, “Contextual subspace variational quantum eigensolver calculation of the dissociation curve of molecular nitrogen on a superconducting quantum computer”, npj Quantum Information, 2025, 11, 25, DOI: 10.1038/s41534-024-00952-4
J. L. Suter, W. A. Müller, M. Vassaux, A. Anastasiou, M. Simmons, D. Tilbrook, P. V. Coveney, “Rapid, Accurate and Reproducible Prediction of the Glass Transition Temperature Using Ensemble-Based Molecular Dynamics Simulation”, Journal of Chemical Theory and Computation, 2025, 21, 3, 1405–1421, DOI: 10.1021/acs.jctc.4c01364
A. P. Bhati, S. Wan, P. V. Coveney, “Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations”, Journal of Chemical Theory and Computation, 2025, 21, 1, 440–462, DOI: 10.1021/acs.jctc.4c01389

2024

X. Xue, S. Wang, H.-D. Yao, L. Davidson & P. V. Coveney, “Physics informed data-driven near-wall modelling for lattice Boltzmann simulation of high Reynolds number turbulent flows”, Communications Physics, 2024, 7, 338, DOI: 10.1038/s42005-024-01832-1
P. V. Coveney, “Sharkovskii’s theorem and the limits of digital computers for the simulation of chaotic dynamical systems”, Journal of Computational Science, 2024, 83, 102449, DOI: 10.1016/j.jocs.2024.102449
H. Loeffler, S. Wan, M. Klähn, A. Bhati, P. V. Coveney, “Optimal Molecular Design: Generative Active Learning Combining REINVENT with Precise Binding Free Energy Ranking Simulations”, Journal of Chemical Theory and Computation, 2024, 20, 18, 8308–8328, DOI: 10.1021/acs.jctc.4c00576
E. A. Stahlberg, K. K. Van Dam, P. V. Coveney et. al., “The First Virtual Human Global Summit: Prepublication Meeting Report”, U.S. Department of Energy, Office of Scientific and Technical Information, 2024, DOI: 10.2172/2428904
P. V. Coveney and R. R. Highfield, “Artificial Intelligence Must Be Made More Scientific”, Journal of Chemical Information and Modelling, 2024, 64, 15, 5739–5741, DOI: 10.1021/acs.jcim.4c01091
J. W. S. McCullough, P. V. Coveney, “Uncertainty quantification of the lattice Boltzmann method focussing on studies of human-scale vascular blood flow”, Scientific Reports, 2024, 14, 11317, DOI: 10.1038/s41598-024-61708-w
W. Edeling, M. Vassaux, Y. Yang, S. Wan, S. Guillas, P. V. Coveney, “Global ranking of the sensitivity of interaction potential contributions within classical molecular dynamics force fields”, npj Computational Materials, 2024, 10, 87, DOI: 10.1038/s41524-024-01272-z
S. C. Y. Lo, J. W. S. McCullough, X. Xue, P. V. Coveney, “Uncertainty quantification of the impact of peripheral arterial disease on abdominal aortic aneurysms in blood flow simulations”, Journal of the Royal Society Interface, 2024, 21, 213, DOI: 10.1098/rsif.2023.0656
A. Ralli, M. Williams de la Bastida, P. V. Coveney, “Scalable approach to quantum simulation via projection-based embedding”, Physical Review A, 2024, 109, 022418, DOI: 10.1103/PhysRevA.109.022418
J. O’Connor, S. Laizet, A. Wynn, W. Edeling, P. V. Coveney, “Quantifying uncertainties in direct numerical simulations of a turbulent channel flow”, Computers and Fluids, 2024, 268, 106108, DOI: 10.1016/j.compfluid.2023.106108

2023

J. W. S. McCullough, P. V. Coveney, “High resolution simulation of basilar artery infarct and flow within the circle of Willis”, Scientific Reports (2023) DOI: 10.21203/rs.3.rs-2859399/v1
S. Wan, A. Bhati, A. Wade, Alexander,P. V. Coveney, “Ensemble-Based Approaches Ensure Reliability and Reproducibility”, Journal of Chemical Information and Modeling (2023) DOI: 10.1021/acs.jcim.3c01654
S. Wan, A. Bhati, P. V. Coveney, “Comparison of Equilibrium and Non-Equilibrium Approaches for Relative Binding Free Energy Predictions”, J. Chem. Theory Comput. (2023) DOI: 10.1021/acs.jctc.3c00842
T. Weaving, A. Ralli, W. M. Kirby, P. J. Love, S. Succi, and P. V. Coveney, “Benchmarking Noisy Intermediate Scale Quantum Error Mitigation Strategies for Ground State Preparation of the HCl Molecule”, Physical Review Research (2023) DOI: 10.1103/PhysRevResearch.5.043054
J. L. Suter, M. Vassaux, P. V. Coveney, “Large-Scale Molecular Dynamic Elucidates the Mechanics of Reinforcement in Graphene-Based Composites”, Advanced Materials (2023) DOI: 10.1002/adma.202302237
M. Klöwer, P. V. Coveney, E. A. Paxton, T. N. Palmer, “Periodic orbits in chaotic systems simulated at low precision”, Nature Scientific Reports (2023) DOI: 10.1038/s41598-023-37004-4
A. Bhati, A. Hoti, A. Potterton, M. K. Bieniek, P. V. Coveney, “Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets”, Journal of Chemical Theory and Computation (2023) DOI: 10.1021/acs.jctc.3c00020
K. Ahmad, A. Javed, C. Lanphere, P. V. Coveney, E. V. Orlova, S. Howorka, “Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations”, Nature Communications (2023), DOI: 10.1038/s41467-023-38681-5
P. V. Coveney and R. R. Highfield, “Virtual You: How Building Your Digital Twin Will Revolutionize Medicine and Change Your Life”, Princeton University Press (2023) DOI:10.1515/9780691223407
A. Ralli, T. Weaving, A. Tranter, W. M. Kirby, P. J. Love, P. V. Coveney, “Unitary Partitioning and Contextual Subspace Variational Quantum Eigensolver”, Physical Review Research (2023) DOI:10.1103/PhysRevResearch.5.013095
M. Bieniek, A. Wade, A. Bhati, S. Wan and P. V. Coveney, “TIES 2.0: a Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal”, Journal of Chemical Information and Modeling (2023) DOI:10.1021/acs.jcim.2c01596
T. Weaving, A. Ralli, W. M. Kirby, A. Tranter, P. J. Love, P. V. Coveney, “A stabilizer framework for Contextual Subspace VQE and the noncontextual projection ansatz”, Journal of Chemical Theory and Computation (2023) DOI:10.1021/acs.jctc.2c00910
D. Groen, H. Arabnejad, D. Suleimenova, W. Edeling, E. Raffin, Y. Xue, K. Bronik, N. Monnier, P. V. Coveney, “FabSim3: An automation toolkit for verified simulations using high performance computing”, Computer Physics Communications, 283 (2023) DOI:10.1016/j.cpc.2022.108596
I. Zacharoudiou, J. W. S. McCullough, P. V. Coveney, “Development and performance of a HemeLB GPU code for human-scale blood flow simulation”, Computer Physics Communications, 282, 108548 (2023) DOI:10.1016/j.cpc.2022.108548

2022

M. Vassaux, W. M. Roa, J. L. Suter, A. Vijayaraghavan, P. V. Coveney, “Mechanically-Stable Ultra-Thin Layered Graphene Nanocomposites Alleviate Residual Interfacial Stresses”, ACS Applied Nano Materials (2022) DOI:10.1021/acsanm.2c03955
D. Nepal, S Kang, K. M. Adstedt, K. Kanhaiya, M. R. Bockstaller, L. C. Brinson, M. J. Buehler, P. V. Coveney, K. Dayal, J. A. El-Awady, L. C. Henderson, D. L. Kaplan, S. Keten, N. A. Kotov, G. C. Schatz, S. Vignolini, F. Vollrath, Y. Wang, B. I. Yakobson, V. V. Tsukruk, H. Heinz, “Hierarchically Structured Bioinspired Nanocomposites”, Nature Materials (2022) DOI:10.1038/s41563-022-01384-1
Sharp Chim Yui Lo, J. W. S. McCullough, P. V. Coveney, “Parametric Analysis of an Efficient Boundary Condition to Control Outlet Flow Rates in Large Arterial Networks”, Sci. Rep. (2022) DOI:10.1038/s41598-022-21923-9
S. Wan, A. P. Bhati, D. W. Wright, A. D. Wade, G. Tresaderm, H. van Vlijmen, P. V. Coveney, “The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase”, Sci. Rep., 12, 10433 (2022) DOI: 10.1038/s41598-022-13319-6
A. Wade, A. P. Bhati, S. Wan, P. V. Coveney, “Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility”, J. Chem. Theory Comput., 18, 6, 3972 (2022) DOI: 10.1021/acs.jctc.2c00114
S. Wan, A. Bhati, D. Wright, I. Wall, A. Graves, D. Green, P. V. Coveney, “Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors”, J. Chem. Inf. Model., 62, 10, 2561 (2022) DOI: 10.1021/acs.jcim.2c00255
A. P. Bhati and P. V. Coveney, “Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols”, J. Chem. Theory Comput., 18, 4, 2687 (2022) DOI: 10.1021/acs.jctc.1c01288
J. Morillo, M. Vassaux, P. V. Coveney, M. Garcia-Gasulla, “Hybrid parallelization of molecular dynamics simulations to reduce load imbalance”, J. Supercomput., 78, 9184 (2022) DOI: 10.1007/s11227-021-04214-4

2021

J. W. S. McCullough, P. V. Coveney, “An efficient, localised approach for the simulation of elastic blood vessels using the lattice Boltzmann method”, Sci. Rep., 11, 24260 (2021) DOI: 10.1038/s41598-021-03584-2
M. Wilkinson, B. Lawrence, A. Prescott, D. de Roure, D. Ford, M. Parsons, B. Wingate, P. V. Coveney, S. Morrell, E. Birney, N. Chakraborty, & D. Sijacki, “UKRI Supercomputing Science Case”, Zenodo (2021), DOI:10.5281/zenodo.4985325
S. Wan, A. Bhati, A. Wade, D. Alfe, P. V. Coveney, “Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease”, Mol. Syst. Des. Eng., (2021) DOI:10.1039/d1me00124h
J. L. Suter and 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
J. W. S. McCullough and P. V. Coveney, “High fidelity blood flow in patient-specific arteriovenous fistula”, Sci. Rep., 11, 22301 (2021) DOI: 10.1038/s41598-021-01435-8
A. P. Bhati, S. Wan, D. Alfè, A. R. Clyde, M. Bode, L. Tan, M. Titov, A. Merzky, M. Turilli, S. Jha, R. R. Highfield, W. Rocchia, N. Scafuri, S. Succi, D. Kranzlmüller, G. Mathias, D. Wifling, Y. Donon, A. Di Meglio, S. Vallecorsa, H. Ma, A. Trifan, A. Ramanathan, T. Brettin, A. Partin, F. Xia, X. Duan, R. Stevens, P. V. Coveney, “Pandemic Drugs at Pandemic Speed: Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers”, Interface Focus, 11, 20210018, DOI: 10.1098/rsfs.2021.0018
T. Diederichs, K. Ahmed, J. Burns, Q. Nguyen, Z. Siwy, M. Tornow, P. Coveney, R. Tampé, S. Howorka, “Principles of Small-Molecule Transport through Synthetic Nanopores”, ACS Nano (2021) DOI: 10.1021/acsnano.1c05139
A. Ralli, P. J. Love, A. Tranter, P. V. Coveney, “Implementation of Measurement Reduction for the Variational Quantum Eigensolver”, Phys. Rev. Research, 3, 033195 (2021) DOI: 10.1103/PhysRevResearch.3.033195
H. Lee, A. Merzky, L. Tan, M. Titov, M. Turilli, D. Alfe, A. Bhati, A. Brace, A. Clyde, P. V. Coveney, H. Ma, A. Ramanathan, R. Stevens, A. Trifan, H. Van Dam, S. Wan, S. Wilkinson, S. Jha, “Scalable HPC & AI Infrastructure for COVID-19 Therapeutics”, Platform for Advanced Scientific Computing Conference (PASC ’21), July 5-9 (2021), DOI: 10.1145/3468267.3470573
A. Al Saadi, D. Alfe, Y. Babuji, A. Bhati, B. Blaiszik, A. Brace, T. Brettin, K. Chard, R. Chard, A. Clyde, P. V. Coveney, I. Foster, T. Gibbs, S. Jha, K. Keipert, T. Kurth, D. Kranzlmüller, H. Lee, Z. Li, H. Ma, A. Merzky, G. Mathias, A. Partin, J. Yin, A. Ramanathan, A. Shah, A. Stern, R. Stevens, L. Tan, M. Titov, A. Trifan, A. Tsaris, M. Turilli, H. Van Dam, S. Wan, D. Wifling, “IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads”, 50th International Conference on Parallel Processing (ICPP ’21), August 9-12 (2021), DOI: 10.1145/3472456.3473524
M. Vassaux, S. Wan, W. Edeling, P. V. Coveney, “Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation”, J. Chem. Theory Comput., 17, 8, 5187 (2021), DOI:10.1021/acs.jctc.1c00526
S. Wan, D. Kumar, V. Ilyin, U. Al Homsi, G. Sher, A. Knuth, P. V. Coveney, “The effect of protein mutations on drug binding suggests ensuing personalised drug selection”, Sci. Rep., 11, 13452 (2021), DOI: 10.1038/s41598-021-92785-w
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
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
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
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
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
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

X. Zhai, M. Chen, Sa. S. Esfahani, A. Amira, F. Bensaali, J. Abinahed, S. Dakua, R. A. Richardson, and P. V. Coveney, “Heterogeneous System-on-Chip based Lattice-Boltzmann Visual Simulation System”, IEEE Systems Journal, 14(2) 1592-1601 (2020), DOI:10.1109/JSYST.2019.2952459
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
Peter V. Coveney, Alfons Hoekstra, Blanca Rodriguez and Marco Viceconti, “Computational biomedicine. Part II: organs and systems”, J R Soc Interface Focus 11, 20200082 (2020), DOI:10.1098/rsfs.2020.0082
J. W. S. McCullough, R. A. Richardson, A. Patronis, R. Halver, R. Marshall, M. Ruefenacht, B. J. N. Wylie, T. Odaker, M. Wiedemann, B. Lloyd, E. Neufeld, G. Sutmann, A. Skjellum, D. Kranzlmüller and P. V. Coveney, “Towards blood flow in the virtual human: efficient self-coupling of HemeLB”, J R Soc Interface Focus 11, 20190119 (2020), DOI:10.1098/rsfs.2019.0119
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
P. V. Coveney, “Computational biomedicine. Part 1: molecular medicine”, J R Soc Interface Focus 10, 20190128 (2020), DOI:10.1098/rsfs.2020.0047
S. Wan, A. Potterton, F. S. Husseini, D. W. Wright, A. Heifetz, M. Malawski, A. Townsend-Nicholson and P. V. Coveney, “Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors”, J R Soc Interface Focus 10, 20190128 (2020), DOI:10.1098/rsfs.2019.0128
S. J. Zasada, D. W. Wright and P. V. Coveney, “Large-scale binding affinity calculations on commodity compute clouds”, J R Soc Interface Focus 10, 20190133 (2020), DOI:10.1098/rsfs.2019.0133
S. Wan, A. P. Bhati, S. J. Zasada and P. V. Coveney, “Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction”, J R Soc Interface Focus 10, 2020007 (2020), DOI:10.1098/rsfs.2020.0007
A. Gheorghiu, P. V. Coveney and A. A. Arabi, “The influence of base pair tautomerism on single point mutations in aqueous DNA”, J R Soc Interface Focus 10, 20190120 (2020), DOI:10.1098/rsfs.2019.0120
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
S. S. Esfahani, X. Zhai, M. Chen, A. Amira, F. Bensaali, J. AbiNahed, S. Dakua, G. Younes, A. Baobeid, R. A. Richardson and P. V. Coveney, “Lattice-Boltzmann interactive blood flow simulation pipeline”, Int J CARS 15, 629–639 (2020), DOI:10.1007/s11548-020-02120-3
S. S. Esfahani, X. Zhai, M. Chen, A. Amira, F. Bensaali, J. AbiNahed, S. Dakua, G. Younes, R. A. Richardson and P. V. Coveney, “Hemelb Acceleration and Visualization for Cerebral Aneurysms”, 2019 IEEE International Conference on Image Processing (ICIP), Taipei, Taiwan, (2019), pp. 1376-1380, DOI:10.1109/ICIP.2019.8803712
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. 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

S. Alowayyed, M. Vassaux, B. Czaja, Peter V. Coveney, A. G. Hoekstra,”Towards Heterogeneous Multi-scale Computing on Large Scale Parallel Supercomputers”, Journal of Supercomputing Frontiers and Innovations, 6(4), 20-43 (2019), DOI:10.14529/jsfi1904022
A. Tranter, P. J. Love, F. Mintert, N. Wiebe and P. V. Coveney, “Ordering of Trotterization: Impact on Errors in Quantum Simulation of Electronic Structure”, Entropy 21 (12), 1218 (2019), DOI:10.3390/e21121218
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
M. Vázquez, P. V. Coveney, H. E. Grecco, A. Hoekstra, B. Chopard (editors), “Advanced HPC-based Computational Modeling in Biomechanics and Systems Biology”, Frontiers in Physiology, Frontiers in Applied Mathematics and Statistics and Frontiers in Bioengineering and Biotechnology, April 2019, e-Book.
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
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”, International Conference on Computational Science, 479-492 (2019), DOI:10.1007/978-3-030-22747-0_36
R. C. Sinclair, P. V. Coveney, “Modeling Nanostructure in Graphene Oxide: Inhomogeneity and the Percolation Threshold”, J. Chem. Inf. Model., 59 (6), 2741-2745 (2019), DOI:10.1021/acs.jcim.9b00114
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
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
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 (2019), DOI:10.1002/adts.201800168
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 (2019), DOI: 10.1016/j.future.2018.08.045
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

2018

J. Dakka, M. Turilli, D. W. Wright, S. J. Zasada, V. Balasubramanian, S. Wan, P. V. Coveney, S. Jha, “High-throughput binding affinity calculations at extreme scales”, BMC Bioinformatics (2018) DOI: 10.1186/s12859-018-2506-6
J. Dakka, K. Farkas-Pall, M. Turilli, D. W. Wright, P. V. Coveney and S. Jha, “Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations,” 2018 IEEE 14th International Conference on e-Science (e-Science), Amsterdam, Netherlands, 2018, pp. 189-200, DOI: 10.1109/eScience.2018.00034
A. P. Bhati, S. Wan, and P. V. Coveney, “Ensemble-based replica exchange alchemical free energy methods: the effect of protein mutations on inhibitor binding”, J. Chem. Theory Comput., Available Online (2018), DOI: 10.1021/acs.jctc.8b01118
A. Tranter, P. Love, F. Mintert, P. V. Coveney, “A comparison of the Bravyi-Kitaev and Jordan-Wigner transformations for the quantum simulation of quantum chemistry”, Journal of Chemical Theory and Computation, Available Online (2018), DOI: 10.1021/acs.jctc.8b00450
D. S. M. Boulanger, R. C. Eccleston, A. Phillips, P. V. Coveney, T. Elliott, N. Dalchau, “A mechanistic model for predicting cell surface presentation of competing peptides by MHC class I molecules” Frontiers Immunology (2018) DOI: 10.3389/fimmu.2018.01538
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
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 Physiology, (2018) DOI: 10.3389/fphys.2018.00721
J. Dakka, K. Farkas-Pall, V. Balasubramanian, M. Turilli, S. Wan, D. W. Wright, S. Zasada, P. V. Coveney, S. Jha, “Enabling Trade-offs Between Accuracy and Computational Cost: Adaptive Algorithms to Reduce Time to Clinical Insight”, SCALE 2018, 18th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2018), you can download the paper here.
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
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. Patronis, R. A. Richardson, S. Schmieschek, B. J. Wylie, R. W. Nash and P. V. Coveney, “Modelling Patient-Specific Magnetic Drug Targeting within the Intracranial Vasculature”, Frontiers of Physiology, 9:331 (2018), DOI: 10.3389/fphys.2018.00331
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

R. Eccleston, P. V. Coveney, and N. Dalchau, “Host genotype and time dependent antigen presentation of viral peptides: predictions from theory”, Scientific Reports, 7 (1), 14367 (2017), DOI: 10.1038/s41598-017-14415-8
S. Alowayyed, D. Groen, P. V. Coveney, A. G. Hoekstra, “Multiscale Computing in the Exascale Era”, Journal of Computational Science, In Press (2017), DOI: 10.1016/j.jocs.2017.07.004
T. Puurtinen, J. Toivanen, K. Mattila, J. Hyvaluoma, R. Nash, P. V. Coveney, J. Timonen, “Coupling of lattice-Boltzmann solvers with suspended particles using the MPI intercommunication framework”, Advances in Engineering Software, 111, 52-57 (2017) 01, DOI: 10.1016/j.advengsoft.2016.07.008
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, 8:797(2017), DOI: 10.3389/fimmu.2017.00797
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. This article is associated with a new release version of the LB3D code, also published by the Computer Physics Communications library.
N. Altwaijry, M. Baron, D. Wright, P. V. Coveney, A. Townsend-Nicholson, “An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics”, Journal of Chemical Theory & Computation, 13 (5), 2254–2270 (2017), DOI: 10.1021/acs.jctc.6b01246
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
P. V. Coveney and R. Highfield, “Opinion: Is big data just big hype?”, Longevity Bulletin: Big data in health, Institute and Faculty of Actuaries, 11-12 (2017), ISSN 2397-7213
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

P. V. Coveney, J. P. Boon, and S. Saucci (theme editors),”Multiscale modelling at the physics-chemistry-biology interface”, Philosophical Transactions A, 374, Issue 2080, November 2016, Theme Issue available here.
P. V. Coveney, E. R. Dougherty and R. R. Highfield, “Big Data Need Big Theory Too”, Phil Trans R Soc London A, 374, 20160153 (2016), DOI: 10.1098/rsta.2016.0153
P. V. Coveney, J. P. Boon, and S. Saucci,”Bridging the Gaps at the Physics-Chemistry-Biology Interface”, Philosophical Transactions A, 374, 20160335 (2016), DOI: 10.1098/rsta.2016.0335
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
P. V. Coveney and S. Wan, “On the calculation of equilibrium thermodynamic properties from molecular dynamics”, Phys. Chem. Chem. Phys., 2016, 18, 30236-30240, DOI: 10.1039/C6CP02349E
P. V. Coveney and E. R. Dougherty, “Big data has not revolutionised medicine – we need big theory alongside it”, The Conversation (2016)
P. J. J. O’Malley, R. Babbush, I. D. Kivlichan, J. Romero, J. R. McClean, R. Barends, J. Kelly, P. Roushan, A. Tranter, N. Ding, B. Campbell, Y. Chen, Z. Chen, B. Chiaro, A. Dunsworth, A. G. Fowler, E. Jeffrey, A. Megrant, J. Y. Mutus, C. Neill, C. Quintana, D. Sank, A. Vainsencher, J. Wenner, T. C. White, P. V. Coveney, P. J. Love, H. Neven, A. Aspuru-Guzik, J. M. Martinis, “Scalable Quantum Simulation of Molecular Energies”, Physical Review X, 6, 031007 (2016), DOI: 10.1103/PhysRevX.6.031007
C. A. Franco, M. L. Jones, M. O. Bernabeu, A. Vion, P. Barbacena, J. Fan, T. Mathivet, C. Fonseca, A. Ragab, T. P. Yamaguchi, P. V. Coveney, R. A. Lang, H. Gerhardt, “Non-canonical Wnt signalling modulates the endothelial shear stress flow sensor in vascular remodelling”, eLife, 5, e07727 (2016) DOI: 10.7554/eLife.07727

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
M. A. Itani, U. D. Schiller, S. Schmieschek, J. Hetherington, M. O. Bernabeu, H. Chandrashekar, F. Robertson, P. V. Coveney, D. Groen, “An automated multiscale ensemble simulation approach for vascular blood flow”, Journal of Computational Science, 9, 150-155 (2015), DOI: 10.1016/j.jocs.2015.04.008
J. L. Suter, L. Kabalan, M. Khader, P. V. Coveney, “Ab initio molecular dynamics study of the interlayer and micropore structure of aqueous montmorillonite clays”, Geochimica et Cosmochimica Acta, 169, 17-29 (2015), DOI: 10.1016/j.gca.2015.07.013
U. D. Schiller, J. B. Fleury, R. Seemann and G. Gompper, “Collective waves in dense and confined microfluidic droplet arrays”, Soft Matter, 11, 5850-5861 (2015), DOI: 10.1039/C5SM01116G
A. Tranter, S. Sofia, J. Seeley, M. Kaicher, J. McClean, R. Babbush, P. V. Coveney, F. Mintert, P. J. Love, “The Bravyi-Kitaev Transformation”, International Journal of Theoretical Chemistry, Available Online (2015), DOI: 10.1002/qua.24969
D. Groen, D. Abou Chacra, R. W. Nash, J. Jaros, M. O. Bernabeu, P. V. Coveney, “Weighted decomposition in high-performance lattice-Boltzmann simulations: are some lattice sites more equal than others?”, EASC 2014, LNCS 8759, 28–38 (2015), DOI: 10.1007/978-3-319-15976-8_2
H. B. Carver, D. Groen, J. Hetherington, R. W. Nash, M. O. Bernabeu, P. V. Coveney, “Coalesced communication: a design pattern for complex parallel scientific software”, Advances in Engineering Software, arXiv preprint arXiv:1210.4400 (2015)
S. Wan, B. Knapp, D. Wright, C. Deane, P. V. Coveney, “Rapid, Precise and Reproducible Prediction of Peptide-MHC Binding Affinities from Molecular Dynamics that Correlate Well with Experiment”, J. Chem. Theory Comput., 11 (7), 3346-3356 (2015), DOI: 10.1021/acs.jctc.5b00179
B. Knapp, R. Bardenet, M. Bernabeu, R. Bordas, M. Bruna, B. Calderhead, J. Cooper, A. Fletcher, D. Groen, B. Kuijper, “Ten simple rules for a successful cross-disciplinary collaboration”, PLoS Comput Biol, 11(4), e1004214 (2015), DOI: 10.1371/journal.pcbi.1004214
C. A. Franco, M. Jones, I. Geudens, M. O. Bernabeu, A. Ragab, A. Lima, R. T. Collins, L. K. Phng, P. V. Coveney, H. Gerhardt, “Dynamic endothelial cell rearrangements drive developmental vessel regression”, PLoS Biology, 13(4), e1002125 (2015), DOI: 10.1371/journal.pbio.1002125
T. D. Bunney, S. Wan, N. Thiyagarajan, L. Sutto, S. V. Williams, P. Ashford, H. Koss, M. A. Knowles, F. L. Gervasio, P. V. Coveney, M. Katan, “The effect of mutations on drug sensitivity and kinase activity of fibroblast growth factor receptors: a combined experimental and theoretical study”, EBioMedicine, 2 (3), 194–204 (2015), DOI: 10.1016/j.ebiom.2015.02.009
J. Swadling, D. Wright, J. Suter, P. V. Coveney, “Structure, Dynamics and Function of the Hammerhead Ribozyme in Bulk Water and at a Clay Mineral Surface From Replica Exchange Molecular Dynamics”, Langmuir, 31 (8), 2493–2501 (2015), DOI: 10.1021/la503685t
J. Suter, D. Groen, P. V. Coveney, “Chemically specific multiscale modeling of clay-polymer nanocomposites reveals intercalation dynamics, tactoid self-assembly and emergent materials properties”, Advanced Materials, 27 (6), 966–984 (2015), DOI: 10.1002/adma.201403361
I. Deuzing, C. Charpentier, D. Wright, S. Matheron, J. Paton, D. F., D. Vijver, P. V. Coveney, D. Descamps, ANRS CO5 HIV-2 cohort, C. Boucher, and N. Beerens, “Mutation V111I in HIV-2 reverse transcriptase increases the fitness of the nucleoside analogue resistant K65R and Q151M viruses”, Journal of Virology, 89 (1), 833-843 (2015), DOI: 10.1128/JVI.02259-14
K. Sadiq, P. V. Coveney, “Computing the role of near attack conformations in an enzyme-catalyzed nucleophilic bimolecular reaction”, Journal of Chemical Theory and Computation, 11, 316–324 (2015), DOI: 10.1021/ct5008845

2014

P. V. Coveney, “Impact on UK Government funding and decisions relating to the improvement of UK e-infrastructure”, Research Excellence Framework Impact Case Study (2014)
S. Thutupalli, J. Fleury, U. D. Schiller, G. Gompper, S. Herminghaus, and R. Seemann, “Hydrodynamics Mediated Collective Motions in Populations of Microdroplets” Engineering of Chemical Complexity II, 125-148 (2014), DOI: 10.1142/9789814616133_0008
G. Davies, T. Krüger, P. V. Coveney, and J. Harting, “Detachment Energies of Spheroidal Particles from Fluid-Fluid Interfaces”, Journal of Chemical Physics, 141, 154902 (2014), DOI: 10.1063/1.4898071
J. Marés, L.Shamardin, G. Weiler, A. Anguita, S. Sfakianakis, E. Neri, S. J. Zasada, N. Graf, and P. V. Coveney, “p-medicine: A Medical Informatics Platform for Integrated Large Scale Heterogeneous Patient Data”, AMIA Annu Symp Proc, 2014:872-81, eCollection 2014 (2014)
J. M. Osborne, M. O. Bernabeu, M. Bruna, B. Calderhead, J. Cooper, et al., “Ten Simple Rules for Effective Computational Research”, PLoS Comput Biol 10(3): e1003506 (2014), DOI: 10.1371/journal.pcbi.1003506
S. P. Dakua, N. V. Navkar, J. Abi-Nahed, D. Groen, M. O. Bernabeu, M. A. R. Saghir, H. Kamel, A. Al-Ansari, P. V. Coveney, “Towards a computational system to support clinical treatment decisions for diagnosed cerebral aneurysms”, 2014 Middle East Conference on Biomedical Engineering (MECBME), 281-284 (2014), DOI: 10.1109/MECBME.2014.6783259
T. Krüger, D. Holmes and P. V. Coveney, “Deformability-based red blood cell separation in deterministic lateral displacement devices - a simulation study”, Biomicrofluidics, 8, 054114 (2014), DOI: 10.1063/1.4897913
S. Karabasov, D. Nerukh, A. Hoekstra, B. Chopard and P. V. Coveney, “Multiscale systems in fluids and soft matter: approaches, numerics, and applications”, Philosophical Transactions of the Royal Society of London Series A, Theme Issue, Volume 372, Issue 2021, 06 August 2014, ISBN: 978-1-78252-080-1
J. Borgdorff, M. Ben Belgacem, C. Bona-Casas, L. Fazendeiro, D. Groen, O. Hoenen, A. Mizeranschi, J. L. Suter, D. Coster, P. V. Coveney, W. Dubitzky, A. G. Hoekstra, P. Strand, and B. Chopard, “Performance of distributed multiscale simulations”, Phil. Trans. R. Soc. A., 372, 20130407 (2014), DOI: 10.1098/rsta.2013.0407
S. Karabasov, D. Nerukh, A. Hoekstra, B. Chopard, and P. V. Coveney, “Introduction: Multiscale modelling: approaches and challenges”, Phil. Trans. R. Soc. A., 372, 20130390 (2014), DOI: 10.1098/rsta.2013.0390
A. Hoekstra, B. Chopard, and P. V. Coveney, “Discussion: Multiscale modelling and simulation: a position paper”, Phil. Trans. R. Soc. A., 372, 20130377 (2014), DOI: 10.1098/rsta.2013.0377
G. B. Davies, T. Krueger, P. V. Coveney, J. Harting, F. Bresme, “Assembling Ellipsoidal Particles at Fluid Interfaces using Switchable Dipolar Capillary Interactions”, Advanced Materials, 26 (39), 6800 (2014), DOI: 10.1002/adma.201402419
G. B. Davies, T. Krueger, P. V. Coveney, J. Harting and F. Bresme, “Interface Deformations Affect the Orientation Transition of Magnetic Ellipsoidal Particles Adsorbed at Fluid-Fluid Interfaces”, Soft Matter, 10, 6742 (2014) DOI: 10.1039/C4SM01124D
M. O. Bernabeu, M. Jones, J. H. Nielsen, T. Krüger, R. Nash, D. Groen, S. Schmieschek, J. Hetherington, H. Gerhardt, C. A. Franco, P. V. Coveney, “Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis”, Journal of the Royal Society Interface, 11 (99), 20140543 (2014), DOI: 10.1098/rsif.2014.0543
U. D. Schiller, “A unified operator splitting approach for multi-scale fluid–particle coupling in the lattice Boltzmann method”, Computer Physics Communications, 185 (10), 2586–2597 (2014) DOI: 10.1016/j.cpc.2014.06.005
J. Fleury, U. D. Schiller, S. Thutupalli, G. Gompper, R. Seemann, “Mode coupling of phonons in a dense one-dimensional microfluidic crystal”, New J. Phys., 16, 063029 (2014), DOI: 10.1088/1367-2630/16/6/063029
P. V. Coveney, V. Díaz-Zuccarini, P. Hunter, and M. Viceconti, “Computational Biomedicine”, Oxford University Press, (2014)
D. Groen, S. Zasada, P. V. Coveney, “Survey of Multiscale and Multiphysics Applications and Communities,” Computing in Science & Engineering, 16 (2), 34 - 43, (2014), DOI: 10.1109/MCSE.2013.47
J. Borgdorff, M. Mamonski, B. Bosak, K. Kurowski, M. B. Belgacem, B. Chopard, D. Groen, P. V Coveney, A. G. Hoekstra, “Distributed Multiscale Computing with MUSCLE 2, the Multiscale Coupling Library and Environment”, Journal of Computational Science (2014), Available Online, DOI: 10.1016/j.jocs.2014.04.004.
R. W. Nash, H. B. Carver, M. O. Bernabeu, J. Hetherington, D. Groen, T. Krueger and P. V. Coveney, “Choice of boundary condition for lattice Boltzmann simulation of moderate-Reynolds-number flow in complex domains”, Physical Review E, 89, 023303, (2014), DOI: 10.1103/PhysRevE.89.023303
D. Wright, B. Hall, O. Kenway, S. Jha, P. V. Coveney, “Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors”, Journal of Chemical Theory and Computation, (2014), 10 (3), 1228–1241 DOI: 10.1021/ct4007037
H. S. C. Martin, S. Jha, P. V. Coveney, “Comparative Analysis of Nucleotide Translocation through Protein Nanopores using Steered Molecular Dynamics and an Adaptive Biasing Force”, Journal of Computational Chemistry, (2014), 35 (9), 692–702, DOI: 10.1002/jcc.23525
S. J. Zasada, D. Chang, A. H. Haidar, P. V. Coveney, “Flexible Composition and Execution of Large Scale Applications on Distributed e-Infrastructures”, Journal of Computational Science, 5 (2014), pp. 51-62, DOI: 10.1016/j.jocs.2013.10.009

2013

T. Ishiyama, S. Rieder, J. Makino, S. Portegies Zwart, D. Groen, K. Nitadori, C. de Laat, S. McMillan, K. Hiraki, and S. Harfst, “The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos”, Astrophysical Journal (2013), 767, 146, DOI: DOI: 10.1088/0004-637X/767/2/146
J. Borgdorff, M. Mamonski, B. Bosak, D. Groen, M. Ben Belgacem, K. Kurowski, A.G. Hoekstra, “Multiscale computing with the multiscale modeling library and runtime environment”, International Conference on Computational Science 2013, (2013), 18, 1097–1105, DOI: DOI: 10.1016/j.procs.2013.05.275
M. Kunze, D. Wright, N. Werbeck, J. Kirkpatrick, P. V. Coveney, D. Hansen, “Loop Interactions and Dynamics Tune the Enzymatic Activity of the Human Histone Deacetylase 8”, Journal of the American Chemical Society, (2013), 135 (47), pp 17862–17868, DOI: 10.1021/ja408184x
K. Rycerz, E. Ciepiela, G. Dyk, D. Groen, T. Gubala, D. Harezlak, M. Pawlik, J. Suter, S. Zasada, P. Coveney, M. Bubak, “Support for Multiscale Simulations with Molecular Dynamics”, International Conference on Computational Science 2013, (2013), 18, 1116–1125, DOI: DOI: 10.1016/j.procs.2013.05.277
D. Groen, J. Hetherington, H. B. Carver, R. W. Nash, M. O. Bernabeu, P. V. Coveney, “Analyzing and Modeling the Performance of the HemeLB Lattice-Boltzmann Simulation Environment”, Journal of Computational Science, (2013), 4 (5), 412–422, DOI: 10.1016/j.jocs.2013.03.002
O. Henrich , K. Stratford , P. V. Coveney , M. E. Cates , D. Marenduzzo, “Rheology of Cubic Blue Phases”, Soft Matter, (2013), 9, 10243-10256, DOI: 10.1039/C3SM50228G
D. W. Wright, I. P. Deuzing, P. Flandre, P. van den Eede, M. Govaert, P. V. Coveney et al., “A Polymorphism at Position 400 in the Connection Subdomain of HIV-1 Reverse Transcriptase Affects Sensitivity to NNRTIs and RNaseH Activity”, (2013), PLoS ONE 8(10): e74078, DOI: 10.1371/journal.pone.0074078
S. Buchsbaum, N. Mitchell, H. S. Martin , M. Wiggin , A. Marziali, P. V. Coveney, Z. S. Siwy, and S. Howorka, “Disentangling Steric and Electrostatic Factors in Nanoscale Transport Through Confined Space”, Nano Letters, (2013), 13 (8), pp 3890–3896, DOI: 10.1021/nl401968r
D. Lecarpentier, P. Wittenburg, W. Elbers, A. Michelini, R. Kanso, P. V. Coveney, R. Baxter, “EUDAT: A new Cross-Disciplinary Data Infrastructure for Science”, International Journal of Digital Curation, 8, 279-287 (2013), DOI: 10.2218/ijdc.v8i1.260
B. Könnyű, S. K. Sadiq, T. Turányi, R. Hírmondó, B. Müller, H. Kräusslich, P. V. Coveney, V. Müller, “Gag-Pol Processing during HIV-1 Virion Maturation: A Systems Biology Approach”, PLoS Comput Biol 9(6), e1003103, (2013), DOI: 10.1371/journal.pcbi.1003103
P. V. Coveney, V. Diaz-Zuccarini, N. Graf, P. Hunter, P. Kohl, J. Tegner and M. Viceconti, “The virtual physiological human: integrative approaches to computational biomedicine”, J R Soc Interface Focus Theme Issue, 3 (2), (2013)
P, V. Coveney, V. Diaz-Zuccarini, N. Graf, P. Hunter, P. Kohl, J. Tegner and M. Viceconti, “Introduction: Integrative Approaches to Computational Biomedicine”, J R Soc Interface Focus, 3 (2), 20130003, (2013), DOI: 10.1098/rsfs.2013.0003
M. Bernabeu, R. Nash, D. Groen, H. Carver, J. Hetherington, T. Krueger and P. V Coveney, “Impact of blood rheology on wall shear stress in a model of the middle cerebral artery”, J R Soc Interface Focus, 3 (2), 20120094, (2013), DOI: 10.1098/rsfs.2012.0094
D. Groen, J. Borgdorff, C. Bona-Casas, J. Hetherington, R. W. Nash, S. J. Zasada, I. Saverchenko, M. Mamonski, K. Kurowski, M. O. Bernabeu, A. G. Hoekstra and P. V. Coveney, “Flexible composition and execution of high performance, high ﬁdelity multiscale biomedical simulations”, J R Soc Interface Focus, 3 (2), 20120087, (2013), DOI: 10.1098/rsfs.2012.0087
B. Jefferys, I. Nwankwo, E. Neri, D. Chang, L. Shamardin, S. Hänold, N. Graf, N. Forgo and P.V. Coveney, “Navigating legal constraints in clinical data warehousing: a case study in personalised medicine”, J R Soc Interface Focus, 3 (2), 20120088, (2013), DOI: 10.1098/rsfs.2012.0088
P. Hunter, T. Chapman, P. V. Coveney, B. de Bono, V. Diaz, J. Fenner, A. F. Frangi, P. Harris, R. Hose, P. Kohl, P. Lawford, K. McCormack, M. Mendes, S. Omholt, A. Quarteroni, N. Shublaq, J. Skår, K. Stroetmann, J. Tegner, S. R. Thomas, I. Tollis, I. Tsamardinos, J. H. van Beek and M. Viceconti, “A Vision and Strategy for the VPH: 2012 update”, J R Soc Interface Focus, 3 (2), 20130004, (2013), DOI: 10.1098/rsfs.2013.0004
C.Z. Christov, A. Lodola, T.G. Karabencheva-Christova, S. Wan, P.V. Coveney, and A.J. Mulholland, “Conformational Effects on the pro-(S) Hydrogen Abstraction Reaction in Cyclooxygenase-1: An Integrated QM/MM and MD Study”, Biophysical Journal, 104, (5), L5-L7, (2013), DOI: 10.1016/j.bpj.2013.01.040
J. B. Swadling, J. L. Suter, H. C. Greenwell, P. V. Coveney, “Influence of Surface Chemistry and Charge on Mineral-RNA Interactions”, Langmuir, 29 (5), pp 1573–1583, (2013), DOI: 10.1021/la303352g

2012

J. Suter, D. Groen, L. Kabalan and P. V. Coveney,”Distributed Multiscale Simulations of Clay-Polymer Nanocomposites”, MRS Proceedings, 2012 MRS Spring Meeting, Volume 1470, (2012), DOI: 10.1557/opl.2012.1009
D. Groen, S. J. Zasada, P. V. Coveney, “Survey of Multiscale and Multiphysics Applications and Communities”, CiSE, arXiv:1208.6444v1, (2012), Available Online
N. Shublaq, C. Sansom, P. V. Coveney, “Patient-Specific Modelling in Drug Design, Development and Selection Including its Role in Clinical Decision Making”, Chemical Biology and Drug Design, 81, 5-12, (2012), DOI: 10.1111/j.1747-0285.2012.01444.x
B. A. Hall, D. W. Wright, S. Jha, P. V. Coveney, “Quantized water access to the HIV-1 protease active site as a proposed mechanism for cooperative mutations in drug affinity”, Biochemistry, 51(33):6487-9, (2012), DOI: 10.1021/bi300432u
S. Wan, P. V. Coveney, “Regulation of JAK2 Activation by Janus Homology 2: Evidence from Molecular Dynamics Simulations”, Journal of Chemical Information and Modeling, 52 (11), 2992–3000, (2012), DOI: 10.1021/ci300308g
D. W. Wright, S. Wan, N. Shublaq, S. J. Zasada, P. V. Coveney, “From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine”, Wiley Interdisciplinary Reviews: Systems Biology and Medicine, (2012), 4:585–598, DOI: 10.1002/wsbm.1186
D. W. Wright, K. Sadiq, G. De Fabritiis, P. V. Coveney, “Thumbs down for HIV: Domain level rearrangements do occur in the NNRTI bound HIV-1 Reverse Transcriptase”, Journal of the American Chemical Society, Available Online, 134 (31), 12885–12888, (2012), DOI: 10.1021/ja301565k
S. Wan, D. Wright, P. V. Coveney, “Mechanism of Drug Efficacy within the Epidermal Growth Factor Receptor Revealed by Microsecond Molecular Dynamics Simulation”, Molecular Cancer Therapeutics, 11(11), 2394-400, (2012), DOI: 10.1158/1535-7163.MCT-12-0644-T
D. W. Wright, B. A. Hall, P. Kellam and P. V. Coveney, “Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors”, Biology, 2012, 1(2), 222-244; DOI: 10.3390/biology1020222
O. Henrich, K. Stratford, D. Marenduzzo, P.V. Coveney, M.E. Cates, “Confined Cubic Blue Phases under Shear”,J. Phys.: Condens. Matter, 24, 284127, DOI: 10.1088/0953-8984/24/28/284127
J. Borgdorff, D. Groen, S. Ferlin, I. Saverchenko, J. Suter, A. Hoekstra, P. V. Coveney, “Multiscale Simulations on distributed European e-Infrastructures”, inSiDE, Vol. 10, No. 1, Spring 2012
P.V. Coveney, J.B. Swadling, J.A.D. Wattis & H.C. Greenwell, “Theory, Modelling & Simulation in Origins of Life Studies”, Chem. Soc. Rev., (2012), 2012,41, 5430-5446 DOI: 10.1039/C2CS35018A
O. Henrich, K. Stratford, D. Marenduzzo, P.V. Coveney, M.E. Cates, “Rheology of Lamellar Liquid Crystals in Two and Three Dimensions: A Simulation Study”, Soft Matter 8, 3817-3831 (2012).
J. B. Swadling, P. V. Coveney, and H. C. Greenwell, “Stability of Free and Mineral-Protected Nucleic Acids: Implications for the RNA World”, Geochimica et Cosmochimica Acta, (2012) 83, 360–378, DOI: 10.1016/j.gca.2011.12.023
D. W. Wright, S. K. Sadiq, and P. V. Coveney, “Thumbs Down: Subdomain Rearrangements in the Drug Bound HIV-1 Reverse Transcriptase”, Biophysical Journal, (2012), 102(3), 64a, DOI: 10.1016/j.bpj.2011.11.382

2011

Derek Groen, James Suter, Peter Coveney, “Modelling Distributed Multiscale Simulation Performance: An Application to Nanocomposites,” esciencew, pp.105-111, 2011 IEEE Seventh International Conference on e-Science Workshops, (2011), DOI: 10.1109/eScienceW.2011.37
Derek Groen, Stefan J. Zasada, Peter V. Coveney, “Taxonomy of Multiscale Computing Communities,” esciencew, pp.120-127, 2011 IEEE Seventh International Conference on e-Science Workshops, (2011), DOI: 10.1109/eScienceW.2011.11
D. Wright and P. V. Coveney, “Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations”, Journal of Chemical Information and Modeling, (2011), 51(10), 2636-49, DOI: 10.1021/ci200308r
S. J. Zasada , T. Wang , A. Haidar , E. Liu, B. Graf, G. Clapworthy, S. Manos, P. V. Coveney, “IMENSE: An e-Infrastructure Environment for Patient Speciﬁc Multiscale Modelling and Treatment”, Journal of Computational Science, 3, 314-327, (2012), DOI: 10.1016/j.jocs.2011.07.001
D. Groen, S. Rieder, S. Portegies Zwart, “High performance cosmological simulations on a grid of supercomputers”, INFOCOMP, (2011), arXiv:1109.5559v1.
T. Hewer, M. Nekovee, P. V. Coveney, “Universality of Performance Parameters in Vehicular ad hoc Networks”, IEEE Communications Letters, (2011), 15 (9), 947 - 949, DOI: 10.1109/LCOMM.2011.062911.110710
C. Sansom, M. Mendes, P. V. Coveney, “Modelling the Virtual Physiological Human”, BioTechnologia, (2011) 92 (3), 225-229.
N. Shublaq, S. Zasada, P. V. Coveney, “Exciting Times in Computational Science”, Journal of Computational Science, (2011), 2(4), 315, DOI: 10.1016/j.jocs.2011.11.001
P. V Coveney, R. Kenway, R. Perott, D. de Roure, A. Trefethen, D. Groen, N. Shublaq et al., “Strategy for the UK Research Computing Ecosystem”, (2011), Available Online.
K. Sadiq, B. Konnyu, V. Muller, P. V. Coveney, “Reaction Kinetics of Catalyzed Competitive Heteropolymer Cleavage”, The Journal of Physical Chemistry B, (2011), 115 (37), 11017–11027, DOI: 10.1021/jp206321b
J. L. Suter , P. V. Coveney , R. L. Anderson , H. C. Greenwell and S. Cliffe, “Rule based design of clay-swelling inhibitors” Energy Environ. Sci., 2011,4, 4572-4586, DOI: 10.1039/C1EE01280K
S. J. Zasada, A. N. Haidar, and P. V. Coveney, “On the Usability of Grid Middleware and Security Mechanisms”, Philosophical Transactions of the Royal Society A, (2011), 369, 3413-3428 , DOI: 10.1098/rsta.2011.0131
S. Wan and P. V. Coveney, “Molecular Dynamics Simulation Reveals Structural and Thermodynamic Features of Kinase Activation by Cancer Mutations within the Epidermal Growth Factor Receptor”, J. Comput. Chem., (2011), Published Online, DOI: 10.1002/jcc.21866
L. Biferale, P. V. Coveney, S. Ubertini and S. Succi, “Discrete simulation of fluid dynamics: methods”, Phil. Trans. R. Soc. A, (2011), 369, 2152-2154, DOI: 10.1098/rsta.2011.0101
B. M. Boghosian, L. M. Fazendeiro, J. Latt, H. Tang and P. V. Coveney, “New variational principles for locating periodic orbits of differential equations”, Phil. Trans. R. Soc. A, (2011), 369, 2211-2218, DOI: 10.1098/rsta.2011.0066.
B. M. Boghosian, A. Brown, J. Latt, H. Tang, L. M. Fazendeiro and P. V. Coveney, “Unstable periodic orbits in the Lorenz attractor”, Phil. Trans. R. Soc. A, (2011), 369, 2345-2353, DOI: 10.1098/rsta.2011.0067.
P. V. Coveney, V. Diaz, P. Hunter, P. Kohl, and M. Viceconti, “The Virtual Physiological Human” Interface Focus June 6, (2011) 1:281-285; published online before print March 31, 2011, DOI: 10.1098/rsfs.2011.0020.
K. Marias, D. Dionysiou, V. Sakkalis, N. Graf, R. M. Bohle, P. V. Coveney, S. Wan, A. Folarin, P. Büchler, M. Reyes, G. Clapworthy, E. Liu, J. Sabczynski, T. Bily, A. Roniotis, M. Tsiknakis, E. Kolokotroni, S. Giatili, C. Veith, E. Messe, H. Stenzhorn, Yoo-Jin Kim, S. Zasada, A. N. Haidar, C. May, S. Bauer, T. Wang, Y. Zhao, M. Karasek, R. Grewer, A. Franz, and G. Stamatakos, “Clinically driven design of multi-scale cancer models: the ContraCancrum project paradigm”, Interface Focus June 6, 2011 1:450-461; published online before print March 30, (2011), DOI: 10.1098/rsfs.2010.0037.
A. N. Haidar, S. J. Zasada, P. V. Coveney, A. E. Abdallah, B. Beckles, and M. A. S. Jones, “Audited credential delegation: a usable security solution for the virtual physiological human toolkit”, Interface Focus June 6, 2011 1:462-473; published online before print March 30, (2011), DOI: 10.1098/rsfs.2010.0026.
S. Wan, P. V. Coveney, “Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs”, J. R. Soc. Interface, 8, 1114-1127, (2011), DOI: 10.1098/rsif.2010.0609.

2010

P. Hunter, P. V. Coveney, Bernard de Bono, V. Diaz, J. Fenner, A. F. Frangi, P. Harris, R. Hose, P. Kohl, P. Lawford, K. McCormack, M. Mendes, S. Omholt, A. Quarteroni, J. Skår, J. Tegner, S. R. Thomas, I. Tollis, I. Tsamardinos, J. H. G. M. van Beek, and M. Viceconti “A vision and strategy for the virtual physiological human in 2010 and beyond”, Phil. Trans. R. Soc. A, 368, (1920), 2595-2614, (2010), DOI: 10.1098/rsta.2010.0048.
D. R. Flower, K. Phadwal, I. K. Macdonald, P. V. Coveney, M. N. Davies and S. Wan, “T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges”, Immunome Research, 6, (Suppl 2), S4, (2010), DOI: 10.1186/1745-7580-6-S2-S4.
M. Riedel, B. Schuller, M. Rambadt, M. S. Memon, A. S. Memon, A. Streit, Th. Lippert, S. J. Zasada, S. Manos, P. V. Coveney, F. Wolf and D. Kranzlmüller, “Exploring the Potential of Using Multiple e-Science Infrastructures with Emerging Open Standards-based e-Health Research Tools”, International Conference on Cluster, Cloud and Grid Computing (CCGrid), 2010 10th IEEE/ACM, 341 - 348, (2010), DOI: 10.1109/CCGRID.2010.96.
J. B. Swadling, P. V. Coveney, and H. C. Greenwell, “Clay Minerals Mediate Folding and Regioselective Interactions of RNA: A Large-Scale Atomistic Simulation Study”, Journal of the American Chemical Society, 132, 13750–13764, (2010), DOI: idoi:10.1021/ja104106y.
T. D. Hewer, M. Nekovee and P. V. Coveney “Reducing Congestion in Obstructed Highways with Traffic Data Dissemination Using Ad hoc Vehicular Networks”, EURASIP Journal on Advances in Signal Processing, Article ID 169503, (2010), DOI: idoi:10.1155/2010/169503.
R. S. Saksena, M. D. Mazzeo, S. J. Zasada and P. V. Coveney, “Petascale lattice-Boltzmann studies of amphiphilic cubic liquid crystalline materials in a globally distributed high-performance computing and visualization environment”, Phil. Trans. R. Soc. A, 368, 3983-3999, (2010), DOI: 10.1098/rsta.2010.0160 .
J. Cooper, F. Cervenansky, G. De Fabritiis, J. Fenner, D. Friboulet, T. Giorgino, S. Manos, Y. Martelli, J. Villà-Freixa, S. Zasada, S. Lloyd, K. McCormack, and P. V. Coveney, “The Virtual Physiological Human ToolKit”, Phil. Trans. R. Soc. A, 368, 3925-3936, (2010), DOI: 10.1098/rsta.2010.0144.
G. M. Doctors, M. D. Mazzeo, and P. V. Coveney, “A computationally efficient method for simulating fluid flow in elastic pipes in three dimensions”, Computer Physics Communications, 181, 1584-1592, (2010), DOI: 10.1016/j.cpc.2010.05.012.
S. K. Sadiq, D. W. Wright, O. A. Kenway, P. V. Coveney, “Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases”, Journal of Chemical Information and Modeling, 50, 890-905, (2010), DOI: 10.1021/ci100007w.
P. Sloot, P. V. Coveney, J. Dongarra, “Preface”, Journal of Computational Science, 1, 3-4, (2010), DOI: 10.1016/j.jocs.2010.04.003.
L. Fazendeiro, B..M. Boghosian, P. V. Coveney, J. Latt, “Unstable periodic orbits in weak turbulence”, Journal of Computational Science, 1, 13-23, (2010), DOI: 10.1016/j.jocs.2010.03.004.
J. F. Annett, P. V. Coveney, “Special section: CompSci07, Computational Science 2007: Interdisciplinary challenges and perspectives, from the Grid to e-Science”, Future Generation Computer Systems, 26, 504-505, (2010), DOI: 10.1016/j.future.2009.10.009.
R.L. Anderson, I. Ratcliffe, H.C. Greenwell, P.A. Williams, S. Cliffe and P.V. Coveney, “Clay swelling — A challenge in the oilfield”, Earth-Science Reviews, 98, (3-4), 201-216, (2010), DOI: 10.1016/j.earscirev.2009.11.003.
P. V. Coveney, G. Giupponi, S. Jha, S. Manos, J. MacLaren, S. M. Pickles, R. S. Saksena, T. Soddemann, J. L. Suter, M. Thyveetil, and S. J. Zasada, “Large scale computational science on federated international grids: The role of switched optical networks, Future Generation Computer Systems”, Future Generation Computer Systems, 26, (1), 99-110, (2010), DOI: 10.1016/j.future.2008.09.013.
M. D. Mazzeo, S. Manos, P. V. Coveney, “In situ ray tracing and computational steering for interactive blood flow simulation”, Computer Physics Communications, 181, (2), 355-370, (2010). DOI: 10.1016/j.cpc.2009.10.013.
M. Nekovee, R. Saksena, “Simulations of large-scale WiFi-based wireless networks: Interdisciplinary challenges and applications”, Future Generation Computer Systems, 26, (3), 514-520 (2010), DOI: 10.1016/j.future.2008.05.007.

2009

M. Atkinson, D. Britton, P. V. Coveney et al., “Century‐of‐Information Research (CIR): A Strategy for Research and Innovation in the Century of Information”, Prometheus, 27, 27-45 (2009), DOI: 10.1080/08109020802657479.
S. J. Zasada and P. V. Coveney, “From campus resources to federated international grids: bridging the gap with the application hosting environment”, Proceedings of the 5th Grid Computing Environments Workshop, Article No.: 10, (2009), ISBN:978-1-60558-887-2
R. L. Anderson, H. C. Greenwell, J. L. Suter, P. V. Coveney and M. Thyveetil, “Determining materials properties of natural composites using molecular simulation”, Journal of Materials Chemistry, 19, (39), 7251-7262, (2009), DOI: 10.1039/b909119j.
P. V. Coveney and M. P. Atkinson (Eds), “Crossing Boundaries: Computational Science, e-Science and Global e-Infrastructure I”, theme issue of Phil. Trans. R. Soc. A, 367, (1897), 2425-2617, (2009). DOI: 10.1098/rsta.2009.0061.
P. V. Coveney and M. P. Atkinson (Eds), “Crossing Boundaries: Computational Science, e-Science and Global e-Infrastructure II”, theme issue of Phil. Trans. R. Soc. A, 367, (1898), 2621-2806, (2009). DOI: 10.1098/rsta.2009.0102.
D. Gavaghan, P. V. Coveney, and P. Kohl (Eds), “The Virtual Physiological Human: Tools and Applications I”, theme issue of Phil. Trans. R. Soc. A, 367, (1895), 1817-2118, (2009). DOI: 10.1098/rsta.2009.0070.
H. C. Greenwell, P. V. Coveney, “Investigating organic-clay interactions”, Geochimica et Cosmochimica Acta, 73, (13, supplement 1), A463, (2009), DOI: j.gca.2009.05.025.
T. Hewer, M. Nekovee, P. V. Coveney, “Parameter exploration in parallel for dynamic vehicular network efficiency”, Advances in Computational Tools for Engineering Applications, International Conference on, 16-20, (2009), DOI: 10.1109/ACTEA.2009.5227879.
P. Kohl, P. V. Coveney, and D. Gavaghan (Eds), “The Virtual Physiological Human: Tools and Applications II”, theme issue of Phil. Trans. R. Soc. A, 367, (1896), 2121-2421, (2009). DOI: 10.1098/rsta.2009.0071.
H. Martin, S. Jha, S. Howorka, and P. V. Coveney, “Determination of Free Energy Profiles for the Translocation of Polynucleotides through alpha-Hemolysin Nanopores using Non-Equilibrium Molecular Dynamics Simulations”, Journal of Chemical Theory and Computation, 5, (8), 2135-2148, (2009). DOI: 10.1021/ct9000894.
R. S. Saksena, B. Boghosian, L. Fazendeiro, O. A. Kenway, S. Manos, M. D. Mazzeo, S. K. Sadiq, J. L. Suter, D. Wright, and P. V. Coveney, “Real Science at the Petascale”, Philosophical Transactions of the Royal Society A, 367, (1897), 2557-2571, (2009). DOI: 10.1098/rsta.2009.0049.
R. S. Saksena and P. V. Coveney, “Rheological response and dynamics of the amphiphilic diamond phase from kinetic lattice-Boltzmann simulations”, Proceedings of the Royal Society A, 465, (2106), 1977-2002, (2009), DOI: 10.1098/rspa.2008.0479.
R. S. Saksena and P. V. Coveney, “Shear rheology of amphiphilic cubic liquid crystals from large-scale kinetic lattice–Boltzmann simulations”, Soft Matter, 5, (22), 4446–4463, (2009), DOI: 10.1039/b911884e.
P. M. A Sloot, P. V. Coveney, G. Ertaylan, V. Muller, C. A. Boucher, M. Bubak, “HIV decision support: from molecule to man”, Philosophical Transactions of the Royal Society A-Mathematical Physical and Engineering Sciences, 367, (1898), 2691-2703, (2009), DOI: 10.1098/rsta.2009.0043.
J. L. Suter and P. V. Coveney, “Materials properties of clay nanocomposites: onset of negative Poisson ratio in large-scale molecular dynamics simulation”, Soft Matter, 5, (20), 3896-3904, (2009), DOI: 10.1039/b907590a.
J. L. Suter, R. L. Anderson, H. C. Greenwell, and P. V. Coveney, “Recent advances in large-scale atomistic and coarse-grained molecular dynamics simulation of clay minerals”, Journal of Materials Chemistry, 19, (17), 2482-2493, (2009) DOI: 10.1039/b820445d.
J. L. Suter, P. V. Coveney, “Computer simulation study of the materials properties of intercalated and exfoliated poly(ethylene)glycol clay nanocomposites”, Soft Matter, 5, (11), 2239-2251, (2009), DOI: 10.1039/b822666k.
A. Trefethen, N. Higham, I. Duff, P. V. Coveney, “Developing a high-performance computing/numerical analysis roadmap”, International Journal of High Performance Computing Applications, 23, (4), 423-426, (2009), DOI: 10.1177/1094342009347710.
S. Wan and P. V. Coveney, “A Comparative Study of the COX-1 and COX-2 Isozymes Bound to Lipid Membranes”, Journal of Computational Chemistry, 30, (7), 1038-1050, (2009), DOI: 10.1002/jcc.21130.
S. J. Zasada and P. V. Coveney, “Virtualizing Access to Scientific Applications with the Application Hosting Environment”, Computer Physics Communications, 180, (12), 2513-2525, (2009), DOI: 10.1016/j.cpc.2009.06.008.

2008

S. Manos, S. Zasada, P. V. Coveney, “Life or Death Decision-making: The Medical Case for Large-scale, On-demand Grid Computing”, CTWatch Quarterly, 4, (1), (2008).
P. Boulet, H. C. Greenwell, R. M. Jarvis, W. Jones, P. V. Coveney, and S. Stackhouse, “Gaining Insight into the Structure and Dynamics of Clay-Polymer Nanocomposite Systems Through Computer Simulation”, in P. Knauth and J. Shoonman (eds.), Nanocomposites: Ionic Conducting Materials and Structural Spectroscopies, 175-203, Springer (2008).
B. Chen, J. R. G. Evans, H. C. Greenwell, P. Boulet, P. V. Coveney, A. A. Bowden and A. Whiting, “A critical appraisal of polymer-clay nanocomposites”, Chemical Society Reviews, 37, (3), 568-594, (2008), DOI: 10.1039/b702653f.
G. Clapworthy, M. Viceconti, P. V. Coveney, and P. Kohl, “The virtual physiological human: building a framework for computational biomedicine”, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 366, (1878), 2975-2978, (2008), DOI: 10.1098/rsta.2008.0103.
G. De Fabritiis, P. V. Coveney, and J. Villà-Freixa, “Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics”, PROTEINS, 73, (1), 185-194, (2008). DOI: 10.1002/prot.22036.
G. De Fabritiis, S. Geroult, P. V. Coveney, and G. Waksman, “Insights from the energetics of water binding at the domain-ligand interface of the Src SH2 domain”, PROTEINS, (4), 1290-1297, (2008), DOI: 10.1002/prot.22027.
R. Delgado-Buscalioni, P. V. Coveney, and G. De Fabritiis, “Towards multi-scale modelling of complex liquids using hybrid particle-continuum schemes”, Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science, 222, (5), 769-776, (2008), DOI: 10.1243/09544062JMES746.
J. W. Fenner, B. Brook, G. Clapworthy, P. V. Coveney, V. Feipel, H. Gregersen, D. R. Hose, P. Kohl, P. Lawford, K. M. McCormack, D. Pinney, S. R. Thomas, S. Van Sint Jan, S. Waters, and M. Viceconti, “The EuroPhysiome, STEP and a roadmap for the virtual physiological human”, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 366, (1878), 2979-2999, (2008), DOI: 10.1098/rsta.2008.0089.
M. D. Mazzeo and P. V. Coveney, “HemeLB: A high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries”, Computer Physics Communications, 178, (12), 894-914, (2008). DOI: 10.1016/j.cpc.2008.02.013.
S. K. Sadiq, M. D. Mazzeo, S. J. Zasada, S. Manos, I. Stoica, C. V. Gale, S. J. Watson, P. Kellam, S. Brew, and P. V. Coveney, “Patient-specific simulation as a basis for clinical decision-making”, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 366, (1878), 3199-3219, (2008), DOI: 10.1098/rsta.2008.0100.
S. K. Sadiq, D. Wright, S. J. Watson, S. J. Zasada, I. Stoica, Ileana, and P. V. Coveney, “Automated Molecular Simulation-Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases”, Journal of Chemical Information and Modeling, 48, (9), 1909-1919, (2008), DOI: 10.1021/ci8000937.
R. S. Saksena and P. V. Coveney, “Self-Assembly of Ternary Cubic, Hexagonal and Lamellar Mesophases using the Lattice-Boltzmann Kinetic Method”, Journal of Physical Chemistry B, 112, (10), 2950-2957, (2008), DOI: 10.1021/jp0731506.
D. Scott, P. V. Coveney, and S. Manos, “Design of Electroceramic Materials Using Artificial Neural Networks and Multi-Objective Evolutionary Algorithms” Journal of Chemical Information and Modeling, 48, (2), 262-273, (2008), DOI: 10.1021/ci700269r.
D. Scott, S. Manos, P. V. Coveney, J. Rossiny, S. Fearn, J. Kilner, R. Pullar, N. Alford, A-K. Axelsson, Y. Zhang, L. Chen, S. Yang, M. Sebastian, and J. R. G. Evans, “Functional Ceramic Materials Database: An online resource for materials research”, Journal of Chemical Information and Modeling, 48, (2), 449-455, (2008), DOI: 10.1021/ci700270v.
I. Stoica, S. K. Sadiq, and P. V. Coveney, “Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases”, Journal of the American Chemical Society, 130, (8), 2639-2648, (2008). DOI: 1021/ja0779250.
M.-A Thyveetil, P. V. Coveney, H. C. Greenwell, and J. Suter, “Computer Simulation Study of the Structural Stability and Materials Properties of DNA-Intercalated Layered Double Hydroxides”, Journal of the American Chemical Society, 130, (14), 4742-4756, (2008). DOI: 0.1021/ja077679s.
M.-A Thyveetil, P. V. Coveney, H. C. Greenwell, and J. Suter, “Role of Host-Layer Flexibility in DNA Guest Intercalation Revealed by Computer Simulation of Layered Nanomaterials”, Journal of the American Chemical Society, 130, (37), 12485-12495, (2008), DOI: 10.1021/ja8037068.

2007

B. Boghosian, P. Coveney, S. Dong, L. Finn, S. Jha, G. Karniadakis, and N. Karonis, “NEKTAR, SPICE and Vortonics: Using Federated Grids for Large Scale Scientific Applications”, Cluster Computing, 10, (3), 351-364, (2007), DOI: 10.1007/s10586-007-0029-4.
P. V. Coveney, R. S. Saksena, S. J. Zasada, M. McKeown, and S. Pickles, “The application hosting environment: Lightweight middleware for grid-based computational science”, Computer Physics Communications, 176, 406-418, (2007), DOI: 10.1016/j.cpc.2006.11.011.
G. De Fabritiis, M. Serrano, R. Delgado-Buscalioni, and P. V. Coveney, “Fluctuating hydrodynamic modeling of fluids at the nanoscale”, Phys. Rev. E, 75, 026307, (2007), DOI: 10.1103/PhysRevE.75.026307.
G. De Fabritiis, J. Villà-Freixa, and P. V. Coveney, “Multiscale modelling of permeation through membrane channels using pregenerated molecular dynamics trajectories”, International Journal of Modern Physics C, 18, (4), 511-519, (2007), DOI: 10.1142/S0129183107010747.
P. W. Fowler, K. Balali-Mood, S. Deol, P. V. Coveney, and M. S. P. Sansom, “Monotopic Enzymes and Lipid Bilayers: A Comparative Study”, Biochemistry, 46, (11), 3108-3115, (2007), DOI: 10.1021/bi602455n.
P. W. Fowler, S. Geroult, S. Jha, G. Waksman, and P. V. Coveney, “Rapid and accurate calculation of relative binding affinities for the SH2 domain using a computational grid”, Journal of Chemical Theory and Computation, 3, (3), 1193-1202, (2007), DOI: 10.1021/ct6003017.
G. Giupponi, G. De Fabritiis, and P. V. Coveney, “A coupled molecular-continuum hybrid model for the simulation of macromolecular dynamics”, International Journal of Modern Physics C, 18, (4), 520-527, (2007), DOI: 10.1142/S0129183107010759.
G. Giupponi, G. De Fabritiis, and P. V. Coveney, “Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules”, Journal of Chemical Physics, 126, 154903, (2007), DOI: 10.1063/1.2720385.
J. Harting, G. Giupponi, and P. V. Coveney, “Structural transitions and arrest of domain growth in sheared binary immiscible fluids and microemulsions”, Phys. Rev. E, 75, 04150, (2007), DOI: 10.1103/PhysRevE.75.041504.
S. K. Sadiq, S. Wan, and P. V. Coveney, “Insights into a Mutation-Assisted Lateral Drug Escape Mechanism from the HIV-1 Protease Active Site” Biochemistry, 46, (51), 14865-14877, (2007), DOI: 10.1021/bi700864p.
D. J. Scott, P. V. Coveney, J. A. Kilner, J. C. H. Rossiny, and N. Mc N. Alford, “Prediction of the functional properties of ceramic materials from composition using artificial neural networks”, Journal of the European Ceramic Society, 27, (16), 4425-4435, (2007), DOI: 10.1016/j.jeurceramsoc.2007.02.212.
J. L. Suter, P. V. Coveney, H. C. Greenwell, and M.-A. Thyveetil, “Large-scale molecular dynamics study of montmorillonite clay: Emergence of undulatory fluctuations and determination of material properties”, Journal of Physical Chemistry C, 111, (23), 8248-8259, (2007), DOI: 10.1021/jp070294b.
M.-A. Thyveetil, P. V. Coveney, J. L. Suter, and H. C. Greenwell, “Emergence of Undulations and Determination of Materials Properties in Large-Scale Molecular Dynamics Simulation of Layered Double Hydroxides”, Chemistry of Materials, 19, (23), 5510-5523, (2007), DOI: 10.1021/cm070923u.
Marco Viceconti (Editor), “Seeding the EuroPhysiome: A Roadmap to the Virtual Physiological Human”, STEP Consortium, (2007), http://www.europhysiome.org/RoadMap.
S. Wan, D. R. Flower, and P. V. Coveney, “Toward an atomistic understanding of the immune synapse: Large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex”, Molecular Immunology, 45, (5), 1221-1230, (2007), DOI: 10.1016/j.molimm.2007.09.022.
J. A. D. Wattis, and P. V. Coveney, “Sequence Selection During Polymerisation”, Journal of Physical Chemistry B, 111, (32), 9546-9562, (2007), DOI: 10.1021/jp071767h.

2006

P. Boulet, H. C. Greenwell, S. Stackhouse and P. V. Coveney, “Recent advances in understanding the structure and reactivity of clays using electronic structure calculations”, J. Mol. Struct. Theo., 762, (1-3), 33-48, (2006), DOI: 10.1016/j.theochem.2005.10.028.
J. Chin and P. V. Coveney, “Chirality and domain growth in the gyroid mesophase”, Proceedings of the Royal Society of London Series A, 462, 3575-3600, (2006), DOI: 10.1098/rspa.2006.1741.
P. V. Coveney, G. De Fabritiis, M. J. Harvey, S. M. Pickles and A. R. Porter, “Coupled applications on distributed resources”, Computer Physics Communications, 175, (6), 389-396, (2006), DOI: 10.1016/j.cpc.2006.05.008.
P. V. Coveney and J. A. D. Wattis, “Coarse-graining and renormalisation group methods for the elucidation of the kinetics of complex nucleation and growth processes”, Mol. Phys., 104, (1), 177-185, (2006), DOI: 10.1080/00268970500317210.
G. De Fabritiis, R. Delgado-Buscalioni and P. V. Coveney, “Multiscale modelling of liquids with molecular specificity”, Physical Review Letters, 97, 134501, (2006), DOI: 10.1103/PhysRevLett.97.134501.
G. De Fabritiis, M. Serrano, P. Espanol and P. V. Coveney, “Efficient numerical integrators for stochastic models”, Physica A, 361, (2), 429-440, (2006), DOI: 10.1016/j.physa.2005.06.090.
R. Delgado-Buscalioni and P. V. Coveney, “Structure of a tethered polymer under flow using molecular dynamics and hybrid molecular-continuum simulations”, Physica A, 362, (1), 30-35, (2006), DOI: 10.1016/j.physa.2005.09.011.
P. W. Fowler and P. V. Coveney, “A Computational Protocol for the Integration of the Monotopic Protein Prostaglandin H2 Synthase into a Phospholipid Bilayer”, Biophys. J., 91, 401-410, (2006), DOI: 10.1529/biophysj.105.077784.
G. Giupponi and P. V. Coveney, “Non-Newtonian behaviour of the gyroid mesophase: A lattice-Boltzmann study”, Mathematics and Computers in Simulation, 72, (2-6), 124-127, (2006), DOI: 10.1016/j.matcom.2006.05.035.
G. Giupponi, J. Harting and P. V. Coveney, “Emergence of rheological properties in lattice Boltzmann simulations of gyroid mesophases”, Europhysics Letters, 73, (4), 533-539, (2006), DOI: 10.1209/epl/i2005-10438-x.
N. González-Segredo, J. Harting, G. Giupponi and P. V. Coveney, “Stress response and structural transitions in sheared gyroidal and lamellar amphiphilic mesophases: Lattice-Boltzmann simulations”, Phys. Rev. E, 73, 031503, (2006), DOI: 10.1103/PhysRevE.73.031503.
H. C. Greenwell, L. A. Bindley, P. R. Unwin, P. J. Holliman, W. Jones, P. V. Coveney and S. L. Barnes, “In situ monitoring of crystal growth and dissolution of oriented layered double-hydroxide crystals immobilized on silicon”, Journal of Crystal Growth, 294, (1), 53-59, (2006), DOI: j.jcrysgro.2006.05.048.
H. C. Greenwell, A. A. Bowden, B. Chen, P. Boulet, J. R. G. Evans, P. V. Coveney and A. Whiting, “Intercalation and in situ polymerization of poly(alkylene oxide) derivatives within M+-montmorillonite (M = Li, Na, K)”, Journal of Materials Chemistry, 16, (11), 1082-1094, (2006), DOI: 10.1039/b505217c.
H. C. Greenwell and P. V. Coveney, “Layered double hydroxide minerals as possible prebiotic information storage and transfer compounds”, Origins of Life and Evolution of the Biosphere, 36, (1), 13-37, (2006), DOI: 10.1007/s11084-005-2068-2.
H. C. Greenwell, W. Jones, P. V. Coveney and S. Stackhouse, “On the application of computer simulation techniques to anionic and cationic clays: A materials chemistry perspective”, Journal of Materials Chemistry, 16, (8), 708-723, (2006), DOI: 10.1039/b506932g.
M. J. Harvey, D. Scott and P. V. Coveney, “An Integrated Instrument Control and Informatics System for Combinatorial Materials Research”, Journal of Chemical Information and Modeling, 46, (3), 1026-1033, (2006), DOI: 10.1021/ci050399g.
M. Serrano, G. De Fabritiis, P. Español and P. V. Coveney, “A stochastic Trotter integration scheme for dissipative particle dynamics”, Mathematics and Computers in Simulation, 72, (2-6), 190-194, (2006), DOI: 10.1016/j.matcom.2006.05.019.
S. K. Sadiq, S. Wan and P. V. Coveney, “Ensemble molecular dynamics simulations of HIV-1 protease with the inhibitor saquinavir: insights into the molecular basis of drug resistance caused by the G48V and L90M mutations”, Antiviral Therapy, 11, (5), S151-S151, (2006),

2005

R. J. Blake, P. V. Coveney, P. Clarke, S. M. Pickles, “The TeraGyroid Experiment - Supercomputing 2003”, Scientific Computing, 13, Number 1, 1-17, (2005), available online.
B. Boghosian and P. V. Coveney, “Scientific Applications of Grid Computing”, Computing in Science and Engineering, 7 (5), 10-13, (2005), DOI: 10.1109/MCSE.2005.95.
B. Chen, A. A. Bowden, H. C. Greenwell, P. Boulet, P. V. Coveney, A. Whiting, J. R. G. Evans, “Morphology and elastic modulus of novel poly[oligo(ethylene glycol) diacrylate]-montmorillonite nanocomposites”, J. Polym. Sci. Part B: Polym. Phys., 43, (14), 1785-1793, (2005), DOI: 10.1002/polb.20459.
J. Chin, M. J. Harvey, S. Jha and P. V. Coveney, “Scientific grid computing: The first generation”, Computing in Science and Engineering, 7 (5), 24-32, (2005), DOI: 10.1109/MCSE.2005.100.
P. V. Coveney, ed., “Scientific Grid computing”, theme issue of Phil. Trans. R. Soc. A., 363 (1833), 1701-2095, (2005), available online.
P. V. Coveney, “Scientific Grid computing”, Phil. Trans. R. Soc. A., 363 (1833), 1707-1713, (2005), DOI: 10.1098/rsta.2005.1632.
P. V. Coveney and P. W. Fowler, “Modelling biological complexity: a physical scientist’s perspective”, Journal of the Royal Society Interface, 2, (4), 267-280, (2005), DOI: 10.1098/rsif.2005.0045.
P. Coveney, J. Vicary, J. Chin and M. Harvey, “WEDS: a Web services-based environment for distributed simulation”, Phil. Trans. R. Soc. A., 363 (1833), 1807-1816, (2005), DOI: 10.1098/rsta.2005.1608.
R. Delgado-Buscalioni, P. V. Coveney, G. D. Riley and R. W. Ford, “Hybrid molecular-continuum fluid models: implementation within a general framework”, Phil. Trans. R. Soc. A., 363 (1833), 1975-1985, (2005), DOI: 10.1098/rsta.2005.1623.
R. Delgado-Buscalioni, G. De Fabritiis and P. V. Coveney, “Determination of the chemical potential using energy-biased sampling”, J. Chem. Phys., 123, 054105, (2005), DOI: 10.1063/1.2000244.
R. Delgado-Buscalioni, E. G. Flekkøy and P. V. Coveney, “Fluctuations and continuity in particle-continuum hybrid simulations of unsteady flows based on flux-exchange”, Europhys. Lett., 69, Issue 6, 959-965, (2005), DOI: 10.1209/epl/i2004-10431-y.
P. W. Fowler, S. Jha and P. V. Coveney, “Grid-based steered thermodynamic integration accelerates the calculation of binding free energies”, Phil. Trans. R. Soc. A., 363 (1833), 1999-2015, (2005), DOI: 10.1098/rsta.2005.1625.
F. Giordanetto, P. W. Fowler, M. Saqi and P. V. Coveney, “Large scale molecular dynamics simulation of native and mutant dihydropteroate synthase-sulphanilamide complexes suggests the molecular basis for dihydropteroate synthase drug resistance”, Phil. Trans. R. Soc. A., 363 (1833), 2055-2073, (2005), DOI: 10.1098/rsta.2005.1629.
H. C. Greenwell, M. J. Harvey, P. Boulet, A. A. Bowden, P. V. Coveney, and A. Whiting, “Interlayer structure and bonding in nonswelling primary amine intercalated clays”, Macromolecules, 38, (14), 6189-6200, (2005), DOI: 10.1021/ma0503817.
P. Guan, M. Davies, D. J. Taylor, S. Wan, H. McSparron, S. L. Hemsley, C. Toseland, M. J. Blythe, P. D. Taylor, V. Walshe , C. K. Hattotuwagama, I. A. Doytchinova, P. V. Coveney, P. Borrow, D. R. Flower, “Computational Chemistry, Informatics, and the Discovery of Vaccines”, Current Computer-Aided Drug Design, 1, 377-398, (2005).
J. Harting, M. J. Harvey, J. Chin and P. V. Coveney, “Detection and tracking of defects in the gyroid mesophase”, Comp. Phys. Commun., 165, Issue 2, 97-109, (2005), DOI: 10.1016/j.cpc.2004.10.001.
J. Harting, J. Chin, M. Venturoli and P. V. Coveney, “Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational Grids”, Phil. Trans. R. Soc. A., 363 (1833), 1895-1915, (2005). DOI: 10.1098/rsta.2005.1618 .
S. Jha and P. V. Coveney, “Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer”, Journal of Computational Chemistry, 26, (15), 1617-1627, (2005), DOI: 10.1002/jcc.20300.
R. S. Kalawsky, S. P. Nee, I. Holmes and P. V. Coveney, “A grid-enabled lightweight computational steering client: a .NET PDA implementation”, Phil. Trans. R. Soc. A., 363 (1833), 1885-1894, (2005). DOI: 10.1098/rsta.2005.1617.
R. S. Kalawsky, J. O’Brien and P. V. Coveney, “Improving scientists’ interaction with complex computational—visualization environments based on a distributed grid infrastructure”, Phil. Trans. R. Soc. A., 363 (1833), 1867-1884, (2005), DOI: 10.1098/rsta.2005.1616.
K. R. Mayes, M. Luján, G. D. Riley, J. Chin, P. V. Coveney and J. R. Gurd, “Towards performance control on the Grid”, Phil. Trans. R. Soc. A., 363 (1833), 1793-1805, (2005), DOI: 10.1098/rsta.2005.1607.
S. P. Newman, S. J. Clifford, P. V. Coveney, V. Gupta, J. D. Blanchard, F. Serafin, D. Ben-Amotz and S. Diamond, “Anomalous fluorescence in near-infrared Raman spectroscopy of cementitious materials”, Cem. Concr. Res., 35 (8), 1620-1628, (2005), DOI: 10.1016/j.cemconres.2004.10.001.
S. Wan, P. V. Coveney and D. Flower, “Molecular basis of peptide recognition by the TCR: affinity differences calculated using large scale computing”, J. Immunol., 175, 1715-1723, (2005). available online.
S. Wan, P. V. Coveney and D. R. Flower, “Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations”, Phil. Trans. R. Soc. A., 363 (1833), 2037-2053, (2005), DOI: 10.1098/rsta.2005.1627.

2004

M. Al-Ghoul, J. P. Boon and P. V. Coveney, Preface, Phil. Trans. R. Soc. Lond. A, 362, Number 1821, 1551-1552, (2004), DOI: 10.1098/rsta.2004.1417.
S. Barsky, R. Delgado-Buscalioni and P. V. Coveney, “Comparison of Molecular Dynamics with Hybrid Continuum-Molecular Dynamics for a Single Tethered Polymer in a Solvent”, Journal of Chemical Physics, 121, Issue 5, 2403-2411, (2004); DOI: 10.1063/1.1767996. selected for Virtual Journal of Biological Physics Research, 8 (Issue 2, July 15 2004), Fundamental Polymer Statics/Dynamics section; http://www.vjbio.org.
D. M. Benoit, “Fast vibrational self-consistent field calculations through a reduced mode-mode coupling scheme”, J. Chem. Phys., 120, 562-573, (2004); DOI: 10.1063/1.1631817.
B. M. Boghosian, P. J. Love, J. Yepez and P. V. Coveney, “Galilean-invariant multi-speed entropic lattice Boltzmann models”, Physica D: Nonlinear Phenomena, 192, Issues 1-4, 169-181, (2004); DOI: 10.1016/j.physd.2004.01.018.
P. Boulet, P. V. Coveney and S. Stackhouse, “Simulation of hydrated Li+-, Na+- and K+-montmorillonite/polymer nanocomposites using large-scale molecular dynamics.” Chemical Physics Letters, 389, Issues 4-6, 261-267, (2004); DOI: 10.1016/j.cplett.2004.03.084.
J. Chin and P. V. Coveney, “Towards tractable toolkits for the Grid: a plea for lightweight, usable middleware.” UK e-Science Technical Report, number UKeS-2004-01; available online as PDF or HTML.
J. Chin, P. V. Coveney and S. Jha, “The Current State of the Grid”, a book review of “Grid Computing: Making the Global Infrastructure a Reality”, by F. Berman, G. Fox, and A. J. G. Hey, Computing in Science and Engineering, 6, Number 5, (2004); available from CiSE.
P. V. Coveney, H. C. Greenwell and M. J. Harvey, “Large-scale MD Simulations for Studying the Interlayer Structure in Cationic and Anionic Clays and Nanocomposite Materials”, Geochem. Cosmica Acta, 68, A106, (2004).
P. V. Coveney and M. J. Harvey, “Europe: AG aids RealityGrid and the TeraGyroid Project”, AG Focus, Vol 2, Issue 1, page 4, Spring 2004; available online (5.7MB).
P. V. Coveney, J. Vicary, J. Chin, M. J. Harvey, “Introducing WEDS: a WSRF-based Environment for Distributed Simulation”, UK e-Science Technical Report, number UKeS-2004-07; available online.
P. V. Coveney, M. Watkinson, A. Whiting, E. S. Boek, “Stabilizing clayey formations”, US Patent Number, 6,787,507, Link to US Patent Office website.
G. De Fabritiis, R. Delgado-Buscalioni and P. V. Coveney, “Energy controlled insertion of polar molecules in dense fluids”, J. Chem. Phys., 121, Issue 24, 12139-12142, (2004), DOI: 10.1063/1.1835957.
R. Delgado-Buscalioni and P. V. Coveney, “Hybrid molecular-continuum fluid dynamics”, Phil. Trans. R. Soc. Lond. A, 362, Number 1821, 1639-1654, (2004), DOI: 10.1098/rsta.2004.1401.
N. González-Segredo and P. V. Coveney, “Coarsening dynamics of ternary amphiphilic fluids and the self-assembly of the gyroid and sponge mesophases: Lattice-Boltzmann simulations.” Phys. Rev. E, 69, 061501 (2004); DOI: 10.1103/PhysRevE.69.061501; selected for Virtual Journal of Nanoscale Science & Technology, 9, (Issue 23, June 14 2004), Supramolecular and Biochemical Assembly section; http://www.vjnano.org.
N. González-Segredo and P. V. Coveney, “Self-assembly of the gyroid cubic mesophase: lattice-Boltzmann simulations.” Europhys. Lett., 65, 6, 795-801 (2004); DOI: 10.1209/epl/i2003-10129-8 , or here.
C. Grindon, S. Harris, T. Evans, K. Novik, P. Coveney and C. Laughton, “Large Scale Molecular Dynamics Simulation of DNA: Implementation and Validation of the Amber98 Forcefield in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator).” Phil. Trans. R. Soc. London Series A, 362, Number 1820, 1373-1386, (2004); DOI: 10.1098/rsta.2004.1381.
Patrick Grosfils, Jean Pierre Boon, Jonathan Chin, and E. S. Boek, “Structural and dynamical characterization of Hele-Shaw viscous fingering”, Phil. Trans. R. Soc. Lond. A, 362, Number 1821, 1723-1734, DOI: 10.1098/rsta.2004.1398.
J. Harting, M. Venturoli and P. V. Coveney, “Large-scale grid-enabled lattice Boltzmann simulations of complex fluid flow in porous media and under shear”, Phil. Trans. R. Soc. Lond. A, 362, Number 1821, 1703-1722, DOI: 10.1098/rsta.2004.1402.
S. M. Pickles, R. J. Blake, B. M. Boghosian, J. M. Brooke, J. Chin, P. E. L. Clarke, P. V. Coveney, N. González-Segredo, R. Haines, J. Harting, M. Harvey, M. A. S. Jones, M. McKeown, R. L. Pinning, A. R. Porter, K. Roy, M. Riding, “The TeraGyroid Experiment.” Proceedings of GGF10, 2004. .
S. Stackhouse, P. V. Coveney, and D. M. Benoit, “Density Functional Theory Based Study of the Dehydroxylation Behaviour of Aluminous Dioctahedral 2:1 Layer Type Clay Minerals”, J. Phys. Chem. B, 108, (28), 9685-9694, (2004); DOI: 10.1021/jp037608p.
S. Wan, P. V. Coveney and D. Flower, “Large scale molecular dynamics simulations of HLA-A*0201 complexed with a tumour-specific antigenic peptide: Can the α3 and β2m domains be neglected?”, Journal of Computational Chemistry, 25 (15), 1803-1813, (2004); DOI: 10.1002/jcc.20100.
J. A. D. Wattis, C. D. Bolton and P. V. Coveney, “The Becker-Döring equations with exponentially size-dependent rate coefficients.” J. Phys. A: Math. Gen., 37, 2895-2912 (2004); available online.
J. A. D. Wattis and P. V. Coveney, “Symmetry-breaking in chiral polymerisation,” Origins of Life and Evolution of the Biosphere, (in press, 2004) available online.

2003

E. S. Boek, J. Chin and P. V. Coveney, “Lattice Boltzmann Simulation of the Flow of Non-Newtonian Fluids in Porous Media,” International Journal of Modern Physics B, 17, Nos. 1 & 2, 99-102 (2003); available online as a PS file (210KB).
B. M. Boghosian, P. J. Love, P. V. Coveney, I. V. Karlin, S. Succi, and J. Yepez, “Galilean-Invariant Lattice-Boltzmann Models with H-Theorem,” Phys. Rev. E , 68, 025103(R) (2003); DOI: 10.1103/PhysRevE.68.025103.
A. A. Bowden, P. Boulet, P. V. Coveney and A. Whiting, “Combined experimental and theoretical investigations of clay-polymer nanocomposites: intercalation of single bifunctional organic compounds in Na+-montmorillonite and Na+-hectorite clays for the design of new materials,” J. Mater. Chem., 13, 2540-2550 (2003); DOI: 10.1039/b307752g.
J. M. Brooke, P. V. Coveney, J. Harting, S. Jha, S. M. Pickles, R. L. Pinning, A. R. Porter, “Computational Steering in RealityGrid,” Proceedings of the UK e-Science All Hands Meeting 2003, published online at http://www.nesc.ac.uk/events/ahm2003/AHMCD/ , article is available here.
J. Chin, J. Harting, S. Jha, P. V. Coveney, A. R. Porter, and S. M. Pickles, “Steering in computational science: mesoscale modelling and simulation,” Contemporary Physics, 44, 417-434 (2003); DOI: 10.1080/00107510310001605046.
P. V. Coveney, “Modeling structure and properties in mesoscale fluid systems,” Fiona Case and Paschalis Alexandridis, eds., Mesoscale Phenomena in Fluid Systems, 206-226, (ACS Symposium Series), Oxford University Press 2003.
P. V. Coveney, “Self-organization and complexity: a new age for theory, computation and experiment,” Phil. Trans. R. Soc. Lond. A 361, Number 1807, 1057 (2003); available online.
R. Delgado-Buscalioni and P. V. Coveney, “Continuum-particle hybrid coupling for mass, momentum, and energy transfers in unsteady fluid flow,” Phys. Rev. E 67, 046704 (2003); available online from the American Physical Society.
R. Delgado-Buscalioni and P. V. Coveney, “USHER: An algorithm for particle insertion in dense fluids,” J. Chem. Phys. 119, 2, 978-987 (2003); available online from the American Institute of Physics.
G. De Fabritiis and P. V. Coveney, “Dynamical geometry for multiscale dissipative particle dynamics,” Comp. Phys. Commun., 153, Issue 2, 209-226 (2003); DOI: 10.1016/S0010-4655(03)00199-1.
D. Flower, H. McSparron, M. J. Blythe, C. Zygouri, D. Taylor, P. Guan, S. Wan, P. V. Coveney, V. Walshe, P. Borrow, and I. A. Doytchinova, “Computational vaccinology: quantitative approaches,” Novartis Found. Symp., 254, 102-20 (2003); discussion 120-5, 216-22, 250-2; abstract available online.
N. González-Segredo, M. Nekovee, and P. V. Coveney, “Three-dimensional lattice-Boltzmann simulations of critical spinodal decomposition in binary immiscible fluids,” Phys. Rev. E 67, 046304 (2003); available online from the American Physical Society.
H. C. Greenwell, W. Jones, S. P. Newman, and P. V. Coveney, “Computer simulation of interlayer arrangement in cinnamate intercalated layered double hydroxides,” J. Mol. Struct. 647, 75 (2003).
H. C. Greenwell, S. Stackhouse, P. V. Coveney, and W. Jones, “A density functional theory study of catalytic trans -esterification by tert -butoxide MgAl anionic clays,” J. Phys. Chem. B 107, 3476 (2003); DOI: 10.1021/jp027663i.
J. Harting, S. Wan, and P. V. Coveney, “RealityGrid: high performance computing, visualisation, computational steering and teragrids”, Capability Computing: The newsletter of the HPCx community, issue 2, 4-7 (2003); available online.
P. J. Love, M. Nekovee, P. V. Coveney, J. Chin, N. González-Segredo, and J. M. R. Martin, “Simulations of amphiphilic fluids using mesoscale lattice-Boltzmann and lattice-gas methods,” Comp. Phys. Commun. 153, Issue 3, 340-358 (2003); DOI: 10.1016/S0010-4655(03)00200-5.
J. Skår and P. V. Coveney, eds., “Self-organization: the quest for the origin and evolution of structure.” Proceedings of the 2002 Nobel Symposium on self-organization. Phil. Trans. R. Soc. Lond. A 361, Number 1807 (2003);
J. Skår and P. V. Coveney, “Preface,” Phil. Trans. R. Soc. Lond. A 361, Number 1807, 1047 (2003); available online.
J. Skår and P. V. Coveney, “Developmental and physiological circuits: dissecting complexity. A report on a talk given by Dr Leroy Hood,” Phil. Trans. R. Soc. Lond. A 361, Number 1807, 1313 (2003); available online.
D. A. Tilbrook, G. J. Pearson, M. Braden, and P. V. Coveney, “Prediction of polymerisation shrinkage using molecular modelling,” J. Polym. Sci. Part B: Polym. Phys. 41, 528 (2003).

2002

B. M. Boghosian, P. J. Love, and D. A Meyer, “Towards the simplest hydrodynamic lattice-gas model,” Phil. Trans. R. Soc. Lond. A 360, 333 (2002); available as a PDF file (750 kB).
D. Bosbach, P. V. Coveney, J. L. W. Griffin, A. Putnis, P. Risthaus, S.Stackhouse, and A. Whiting, “The rational design, synthesis and demonstration of the recognition and binding of a diaza-dioxa-12-crown-4 diphosphonate macrocycle to all crystal growth faces of barium sulfate,” J. Chem. Soc. Perkin Trans. II 7, 1238 (2002); available online from the Royal Society of Chemistry.
J. Chin, E. S. Boek, and P. V. Coveney, “Lattice Boltzmann simulation of the flow of binary immiscible fluids with different viscosities using the Shan-Chen microscopic interaction model,” Phil. Trans. R. Soc. Lond. A 360, 547 (2002); available as a PDF file (640 kB).
J. Chin and P. V. Coveney, “Lattice Boltzmann study of spinodal decomposition in two dimensions,” Phys. Rev. E 66 016303 (2002); available from the American Physical Society Online Journal Publishing Service.
P. V. Coveney, J. L. W. Griffin, M. Watkinson, A. Whiting, and E. S. Boek, “Novel exfoliated clay-nanoncomposite materials by in situ co-polymerisation of intercalated monomers: A combinatorial discovery approach,” Mol. Simul. 28, 295 (2002).
P. V. Coveney and S. Succi, eds., “Discrete modelling and simulation of fluid dynamics,” Proceedings of the 2-6 July 2001 Cargese Conference, Phil. Trans. R. Soc. Lond. A 360 293 (2002); available online from the Royal Society.
P. V. Coveney and S. Succi, “Jean Pierre Boon,” Phil. Trans. R. Soc. Lond. A 360, 293 (2002); available as a PDF file (130 kB).
P. V. Coveney and S. Succi, “Preface,” Phil. Trans. R. Soc. Lond. A 360, 295 (2002); available as a PDF file (64 kB).
G. De Fabritiis, P. V. Coveney, and E. G. Flekkøy, “Multiscale dissipative particle dynamics,” Phil. Trans. R. Soc. Lond. A 360, 317 (2002); available as a PDF file (290 kB).
G. De Fabritiis, S. Succi, and P. V. Coveney, “Electronic structure calculations using self-adaptive multiscale Voronoi basis functions,” J. Stat. Phys. 107, 159 (2002).
P. J. Love, “A particulate basis for a lattice-gas model of amphiphilic fluids,” Phil. Trans. R. Soc. Lond. A 360, 345 (2002); available as a PDF file (270 kB).
P. J. Love and P. V. Coveney, “Three-dimensional hydrodynamic lattice-gas simulations of ternary amphiphilic fluids under shear flow,” Phil. Trans. R. Soc. Lond. A 360, 357 (2002); available as a PDF file (5.7 MB).
S. P. Newman, T. Di Cristina, P. V. Coveney, and W. Jones, “Molecular dynamics simulation of cationic and anionic clays containing amino acids,” Langmuir 18 2933 (2002); available online from the American Chemical Society.
M. Serrano, G. De Fabritiis, P. Español, E. G. Flekkøy, and P. V. Coveney, “Mesoscopic dynamics of Voronoi fluid particles,” J. Phys. A: Math. Gen. 35, 1605 (2002); also available as a gzipped PostScript file (170 kB).
S. Stackhouse and P. V. Coveney, “Study of thermally treated lithium montmorillonite by ab initio methods,” J. Phys. Chem. B 106, 12470 (2002); available online from the American Chemical Society.

2001

A. S. Bains, E. S. Boek, P. V. Coveney, S. J. Williams, and M. V. Akbar, “Molecular modelling of the mechanism of action of organic clay-swelling inhibitors,” Mol. Sim. 26, 101 (2001).
O. F. Bandtlow and P. V. Coveney, “On the existence of dynamical systems with exponentially decaying collision operators,” J. Phys. A: Math. Gen. 34, 4585 (2001); available as a gzipped PostScript file (92 kB).
D. M. Benoit, D. Sebastiani and M. Parrinello, “Accurate total energies without self-consistency”, Phys. Rev. Lett., 87, 226401 (2001); DOI: 10.1103/PhysRevLett.87.226401.
B. M. Boghosian, P. V. Coveney, P. Love, and J.-B. Maillet, “Mesoscale modeling of amphiphilic fluid dynamics,” Mol. Sim. 26, 85 (2001); .
B. M. Boghosian, J. Yepez, P. V. Coveney, and A. J. Wagner, “Entropic lattice Boltzmann methods” Proc. R. Soc. London A 457, 717 (2001); cf. cond-mat/0005260.
J. R. G. Evans, M. J. Edirisinghe, P. V. Coveney, and J. Eames, “Combinatorial searches of inorganic materials using the ink-jet printer: Science, philosophy and technology,” Journal of the European Ceramic Society, 21, 2291 (2001).
R. Gaudoin, M. Nekovee, W. M. C. Foulkes, R. J. Needs, and G. Rajagopal, “Inhomogeneous random-phase approximation and many-electron trial wave functions,” Phys. Rev. B 63, 115115 (2001); available from the American Physical Society Online Journal Publishing Service.
C. R. Grindon, S. A. Harris, T. J. Evans, K. E. Novik, P. V. Coveney, and C. A. Laughton, “Porting the AMBER force field to LAMMPS: Massively parallel molecular dynamics simulations of DNA,” CSAR Focus 7, 5 (2001).
M. B. Hoffman and P. V. Coveney, “Lattice molecular dynamics,” Mol. Simul. 27, 157 (2001).
P. J. Love, P. V. Coveney, and B. M. Boghosian, “Three dimensional hydrodynamic lattice-gas simulations of domain growth and self-assembly in binary immiscible and ternary amphiphilic fluids,” Phys. Rev. E 64, 021503 (2001); available from the American Physical Society Online Journal Publishing Service.
P. J. Love, J.-B. Maillet, and P. V. Coveney, “Three-dimensional hydrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic flow through porous media,” Phys. Rev. E 64 , 061302 (2001); available from the American Physical Society Online Journal Publishing Service.
M. Nekovee, J. Chin, N. González-Segredo, and P. V. Coveney, “A parallel lattice-Boltzmann method for large scale simulations of complex fluids,” E. Ramos et al., eds., Computational Fluid Dynamics, Proceedings of the Fourth UNAM Supercomputing Conference, Singapore (World Scientific, 2001); available as a gzipped PostScript file (1.2 MB).
M. Nekovee and P. V. Coveney, “Lattice-Boltzmann simulations of self-assembly of a binary water-surfactant system into ordered bicontinous cubic and lamellar phases” J. Am. Chem. Soc. 123, 12380 (2001); available from the American Chemical Society, and cf. cond-mat/0101379.
M. Nekovee, W. M. C. Foulkes, and R. J. Needs, “Quantum Monte Carlo analysis of exchange and correlation in the strongly inhomogeneous electron gas” Phys. Rev. Lett. 87, 036401 (2001); available from the American Physical Society Online Journal Publishing Service, and cf. cond-mat/0008181.
M. Nekovee and J. M. Pitarke, “Recent progress in computational many-body theory of metal surfaces,” Comp. Phys. Commun. 137, 123-142 (2001); available online.
S. P. Newman, C. H. Greenwell, P. V. Coveney, and W. Jones, “Computer Simulations of Layered Double Hydroxides,” V. Rives, ed., Layered Double Hydroxides: Present and Future (Nova Science Publishers, 2001).
S. Stackhouse, P. V. Coveney, and E. Sandré, “Plane-wave density functional theoretic study of formation of clay-polymer nanocomposite materials by self-catalyzed in situ intercalative polymerization”, J. Am. Chem. Soc. 123 , 11764 (2001); available from the American Chemical Society.
J. A. D. Wattis and P. V. Coveney, “Renormalisation theoretic analysis of non-equilibrium phase transitions I: The Becker-Döring equations with power law rate coefficients,” J. Phys. A: Math. Gen. 34, 8679 (2001); available as a gzipped PostScript file (72 kB).
J. A. D. Wattis and P. V. Coveney, “Renormalisation theoretic analysis of non-equilibrium phase transitions II: The effect of perturbations on rate coefficients in the Becker-Döring equations,” J. Phys. A: Math. Gen. 34, 8697 (2001); available as a gzipped PostScript file (110 kB).

2000

B. M. Boghosian and P. V. Coveney, “A particulate basis for an immiscible lattice-gas model,” Comp. Phys. Comm. 129, 46 (2000); cf. cond-mat/9911340.
B. M. Boghosian and P. V. Coveney, “Lattice Models of Amphiphilic Fluid Hydrodynamics: Simulations and Results,” D. P. Landau, S. P. Lewis, and H.-B. Schluettler, eds., Computer Simulation Studies in Condensed Matter Physics XIII, Proceedings of the Thirteenth Workshop, Athens, Georgia, USA, February 2000; available as a PDF file (910 kB).
B. M. Boghosian, P. V. Coveney, and P. J. Love, “A three dimensional lattice-gas model for amphiphilic fluid dynamics,” Proc. R. Soc. London A 456, 1431 (2000); cf. cond-mat/9907298.
H. Chen, B. M. Boghosian, P. V. Coveney, and M. Nekovee, “A lattice-Boltzmann model of ternary amphiphilic fluids,” Proc. R. Soc. London A 456, 2043 (2000); available as a gzipped PostScript file (400 kB).
P. V. Coveney, “A clash of doctrines: The arrow of time in modern physics,” P. Baert, ed., Time in Contemporary Intellectual Thought (Elsevier, Amsterdam, 2000).
P. V. Coveney, R. Davey, J. L. W. Griffin, Y. He, J. D. Hamlin, S. Stackhouse, and A. Whiting, “A new design strategy for molecular recognition in heterogeneous systems: a universal crystal-face growth inhibitor for barium sulfate,” J. Am. Chem. Soc. 122, 11557 (2000); available from the American Chemical Society.
P. V. Coveney, H. De Silva, A. Gomtsyan, A. Whiting, and E. S. Boek, “Molecular simulation approaches to cross-linking high molecular weight polysaccharides: Application to guar-based hydraulic fracturing fluids,” Mol. Sim. 25, 265 (2000).
E. G. Flekkøy, P. V. Coveney, and G. De Fabritiis, “Foundations of dissipative particle dynamics,” Phys. Rev. E 62, 2140 (2000); available from the American Physical Society Online Journal Publishing Service, and cf. cond-mat/0002174.
N. González-Segredo and M. Foster, “pLRME2D: A parallel implementation of a two-dimensional hydrodynamic lattice-gas model with long-range interactions,” Proceedings of the Sixth European SGI/Cray MPP Workshop, Manchester, UK (2000); available online.
A. Heinzmann, X.-Q. Mao, M. Akaiwa, R. T. Kroemer, P.-S. Gao, K. Ohshima, R. Umeshita, Y. Abe, S. Braun, T. Yamashita, M. H. Roberts, R. Sugimoto, K. Arima, Y. Arinobu, B. Yu, S. Kruse, T. Enomoto, Y. Dake, M. Kawai, S. Shimazu, S. Sasaki, C. N. Adra, M. Kitaichi, H. Inoue, K. Yamauchi, N. Tomichi, F. Kurimoto, N. Hamasaki, J. M. Hopkin, K. Izuhara, T. Shirakawa, and K. A. Deichmann, “Genetic variants of IL-13 signalling and human asthma and atopy,” Hum. Mol. Genet. 9, 549 (2000); available from Oxford University Press.
T. Loerting, C. Tautermann, R. T. Kroemer, I. Kohl, A. Hallbrucker, E. Mayer, and K. R. Liedl, “On the surprising kinetic stability of carbonic acid (H2CO3),” Angew. Chem. Int. Ed. 39, 891 (2000).
J.-B. Maillet and P. V. Coveney, “Two-dimensional hydrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic fluid flow through porous media,” Phys. Rev. E 62, 2898 (2000); available from the American Physical Society Online Journal Publishing Service, and cf. cond-mat/0005259.
M. Nekovee, P. V. Coveney, H. Chen, and B. M. Boghosian, “Lattice-Boltzmann model for interacting amphiphilic fluids,” Phys. Rev. E 62, 8282 (2000); available from the American Physical Society Online Journal Publishing Service, and cf. cond-mat/0006319.
K. E. Novik and P. V. Coveney, “Spinodal decomposition of off-critical quenches with a viscous phase using dissipative particle dynamics in two and three spatial dimensions,” Phys. Rev. E 61, 435 (2000); available from the American Physical Society Online Journal Publishing Service, and cf. cond-mat/9911344.

1999

P. V. Coveney and J. A. D. Wattis, “Cluster renormalization in the Becker-Döring equations,” J. Phys. A: Math. Gen. 32, 7145 (1999); available as a PDF file (120 kB), and cf. cond-mat/9908402.
G. De Fabritiis, P. V. Coveney, and E. G. Flekkøy, “Multiscale modelling of complex fluids,” Proceedings of the Fifth European SGI/Cray MPP Workshop, Bologna, Italy (1999); available as a gzipped PostScript file (124 kB).
E. G. Flekkøy and P. V. Coveney, “From molecular dynamics to dissipative particle dynamics,” Phys. Rev. Lett. 83, 1775 (1999); available from the American Physical Society Online Journal Publishing Service, and cf. cond-mat/9908334.
R. J. Graham, R. T. Kroemer, M. Mons, E. G. Robertson, L. C. Snoek, and J. P. Simons, “Infrared ion dip spectroscopy of a Noradrenaline analogue: Hydrogen bonding in 2-Amino-1-phenylethanol and its singly hydrated complex,” J. Phys. Chem. A 103, 9706 (1999); available from the American Chemical Society.
J. L. W. Griffin, P. V. Coveney, A. Whiting, and R. Davey, “Design and synthesis of macrocylic ligands for specific interaction with crystalline ettringite and demonstration of a viable mechanism for the setting of cement,” J. Chem. Soc. Perkin Trans. II 10, 1973 (1999); available as a PDF file (1.0 GB).
R. T. Kroemer, “Molecular Modelling,” B. Z. Chowdhry and S. E. Harding, eds., Protein-Ligand Interactions (IRL Press, New York, 1999).
J.-B. Maillet, V. Lachet, and P. V. Coveney, “Large scale molecular dynamics simulation of self-assembly processes in short and long chain cationic surfactants,” Phys. Chem. Chem. Phys. 1, 5277 (1999); available as a PDF file (790 kB) from the Royal Society of Chemistry, and cf. cond-mat/9911013.
S. P. Newman, W. Jones, and P. V. Coveney, “Computer simulations of layered double hydroxides,” P. A. Williams and A. Dyer, eds., Advances in Ion Exchange for Industry and Research, Proceedings of the Fifth International Conference on Ion Exchange Processes, 5-9 July 1998, NEWI, Wales (Royal Society of Chemistry, 1999).
P. Risthaus, D. Bosbach, P. V. Coveney, and A. Putnis, “Inhibition of barite and celestite growth with different phosphonates: A comparative AFM study,” EUG 10, Strasbourg J. Conf. Abs. 4, 665 (1999).
J. A. D. Wattis and P. V. Coveney, “Mesoscopic models of nucleation and growth processes: A challenge to experiment,” Phys. Chem. Chem. Phys. 1, 2163 (1999); available as a PDF file (230 kB) from the Royal Society of Chemistry.
J. A. D. Wattis and P. V. Coveney, “The origin of the RNA world: A kinetic model,” J. Phys. Chem. B 103, 4231 (1999); available from the American Chemical Society.
S. J. Williams, P. V. Coveney, and W. Jones, “Molecular dynamics simulations of the swelling of terephthalate-containing anionic clays,” Mol. Sim. 21, 183 (1999).