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Publications

Publications

Preprints

2010

  • 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

  • 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.
  • 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.
  • 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.
  • 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. 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.
  • 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. 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • S. Wan, 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.

2008

  • G. De Fabritiis, S. Geroult, P. V. Coveney, G. Waksman, "Insights from the energetics of water binding at the domain-ligand interface of the Src SH2 domain", PROTEINS, 17, (4), 1290-1297, (2008), DOI: 10.1002/prot.22027.
  • M. Thyveetil, P. V. Coveney, H. C. Greenwell, 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.
  • G. Clapworthy, M. Viceconti, P. V. Coveney, 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.
  • S. K. Sadiq, D. Wright, S. J. Watson, S. J. Zasada, I. Stoica, Ileana, P. V. Coveney, "Automated Molecular Simulation-Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases", Journal of Chemical Information and Modeling, , (48), 1909-1919, (2008), DOI: 10.1021/ci8000937.
  • G. De Fabritiis, P. V. Coveney and J. Villa i 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.
  • S. K. Sadiq, M. D. Mazzeo, S. J. Zasada, S. Manos, I. Stoica, C. V. Gale, S. J. Watson, P. Kellam, S. Brew, 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, volnum, (366), 3199-3219, (2008), DOI: 10.1098/rsta.2008.0100.
  • R. Delgado-Buscalion1, P. V. Coveney, 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.
  • I. Stoica, S. K. Sadiq, 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. Thyveetil, P. V. Coveney, H. C. Greenwell, J. Suter, "Computer Simulation Study of the Structural Stability and Materials Properties of DNA-Intercalated Layered Double Hydroxides", Journal of the American Chemical Society, (2008). DOI: 10.1021/ja077679s.
  • M. D. Mazzeo, P. V. Coveney, "HemeLB: A high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries", Computer Physics Communications, (2008). DOI: 10.1016/j.cpc.2008.02.013.
  • R. Saksena, P. Coveney, "Self-Assembly of Ternary Cubic, Hexagonal and Lamellar Mesophases using the Lattice-Boltzmann Kinetic Method", Journal of Physical Chemistry B, (2008). DOI: 10.1021/jp0731506.
  • P. Boulet, H. C. Greenwell, R. M. Jarvis, W. Jones, P. V. Coveney, 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).
  • D. Scott, S. Manos, P. 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 (2008). DOI: 10.1021/ci700270v.
  • D. Scott, P. Coveney and S. Manos, "Design of Electroceramic Materials Using Artificial Neural Networks and Multi-Objective Evolutionary Algorithms", Journal of Chemical Information and Modeling (2008). DOI: 10.1021/ci700269r.
  • 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.

2007

  • I. R. Holmes and R. S. Kalawsky, "Delivering Effective and Usable Interactive 3D Visualization on Lightweight Mobile Devices", Theory and Practice of Computer Graphics 2007 (TPCG'07), Bangor, Wales, UK, Eurographics Association, 2007.
  • R. S. Kalawsky and I. R. Holmes, "Overcoming engineering challenges of providing an effective user interface to a large scale distributed synthetic environment on the US Teragrid: A systems engineering success story", INCOSE, San Diego, INCOSE, 2007.
  • R. S. Kalawsky and I. R. Holmes, " Overcoming Engineering Challenges of Providing an Effective User Interface to a Large Scale Distributed Synthetic Environment on the US Teragrid: A Systems Engineering Success Story", Systems Engineering: Key to Intelligent Enterprises, San Diego, California, USA, 2007.
  • J. T. O'Brien and R. S. Kalawsky, "A novel control mechanism for distributed stream rendering", Theory and Practice of Computer Graphics (TPCG'07), Bangor, Wales, UK, Eurographics Association, 2007.
  • J. T. O'Brien, and R. S. Kalawsky (2007), "A Service Agreement Framework for Grid based Distributed Rendering", EPSRC e-Science All Hands Meeting, 2007.
  • 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). Available for download here. DOI:10.1016/j.molimm.2007.09.022.
  • S. Kashif Sadiq, Shunzhou Wan and P. V. Coveney, "Insights into a Mutation-Assisted Lateral Drug Escape Mechanism from the HIV-1 Protease Active Site". Biochemistry, 46, 14865-14877 (2007). Available for download here.
  • M-A Thyveetil, P. V. Coveney, J. L. Suter, and H. Chris Greenwell, "Emergence of Undulations and Determination of Materials Properties in Large-Scale Molecular Dynamics Simulation of Layered Double Hydroxides", Chem. Mater., 19(23), 5510-5523 (2007). DOI: 10.1021/cm070923u
  • 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., 74, 041504 (2007). DOI: 10.1103/PhysRevE.75.041504
  • J. A. D. Wattis and P. V. Coveney, "Sequence Selection during Copolymerization", J. Phys. Chem. B, 111(32), 9546-9562 (2007). DOI: 10.1021/jp071767h
  • P. W. Fowler, K. Balali-Mood, S. Deol, P. V. Coveney and M. S. P. Sansom, "Monotopic proteins and lipid bilayers: a compartive study", Biochemistry, 46, 3108-3115 (2007). DOI: 10.1021/bi60455n
  • B. Boghosian, P. V. Coveney, S. Dong, L. Finn, S. Jha, G. Karniadakis, N. Karonis, "NEKTAR, SPICE and Vortonics: Using Federated Grids for Large Scale Scientific Applications", Journal of Cluster Computing, 10(3), 351-364 (2007). DOI: 10.1007/s10586-007-0029-4
  • G. Giupponi, G. De Fabritiis and P. V. Coveney, "Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules", J. Chem. Phys, 126, 154903 (2007). DOI: 10.1063/1.2720385
  • G. Giupponi, G. De Fabritiis and P. V. Coveney, "An hybrid model for the simulation of macromolecular dynamics". Int, J. Mod. Phys. C, 18 (4), 520-527 (2007). Available for download here
  • 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". J. Phys. Chem. C, 111, 8248-8259 (2007). DOI: 10.1021/jp070294b
  • P. W. Fowler, S. Geroult, S. Jha, G. Waksman and P. V. Coveney, "Rapid, accurate and precise calculation of relative binding affinities for the SH2 domain using a computational grid". Journal of Chemical Theory and Computation, 3(3), 1193-1202 (2007). Available for download here. DOI: 10.1021/ct6003017
  • 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). Available for download here. DOI: 10.1103/PhysRevE.75.026307.
  • 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", Comp. Phys. Comm., 176, 406-418 (2007). Available for download here. DOI: 10.1016/j.cpc.2006.11.011.

2006

  • S. J. Zasada, R. S. Saksena, P. V. Coveney, M. McKeown and S. Pickles, "Facilitating User Access to the Grid: A Lightweight Application Hosting Environment for Grid Enabled Computational Science". In Proceedings of the Second IEEE International Conference on e-Science and Grid Computing, 50 (2006). DOI: 10.1109/E-SCIENCE.2006.66.
  • M. Harvey, S. Jha and M-A. Thyveetil, "Using Lambda Networks to Enhance Performance of Interactive Large Simulations". In Proceedings of the Second IEEE International Conference on e-Science and Grid Computing, 40 (2006). ISBN: 0-7695-2734-5. DOI: 10.1109/E-SCIENCE.2006.150. Available for download here.
  • 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", J. Crystal Growth, 294, 53-59 (2006). Available for download here.
  • A. Sen, J. Brooke, B. Harbulot, M. Mc Keown, S. Pickles and A. Porter, "Combining AJAX and WSRF for Web-browser based Grid clients". Accepted for presentation at the Second International Workshop on Grid Computing Environments, Supercomputing 2006, Tampa, Florida. Available for download here.
  • J. MacLaren, M. Mc Keown and S. Pickles, "Co-Allocation, Fault Tolerance and Grid Computing", Proceedings of the UK e-Science All Hands Meeting 2006, 155-162(2006). Available for download here.
  • 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. Available for download here.
  • S. K. Sadiq, S. J. Zasada and P. V. Coveney, "Grid Assisted Ensemble Molecular Dynamics Simulations of HIV-1 Proteases Reveal Novel Conformations of the Inhibitor Saquinavir", LNB1 4216, Berthold, M. R., GLen, R. and Fischer I. (eds.) CompLife 2006, Springer-Verlag, pp. 150-161
  • S. K. Sadiq, S. Wan and P. V. Coveney, "Ensemble molecular dynamics of HIV-1 protease with the inhibitor saquinavir: Insights into the molecular basis of drug resistance cause by the G48V and L90M mutations", Antiviral Therapy 2006, 11:S151.
  • P. V. Coveney, S. K. Sadiq, R. Saksena, M. Thyveetil, S. J. Zasada, M. McKeown and S. Pickles, "A Lightweight Application Hosting Environment for Grid Computing", Proceedings of the UK e-Science All Hands Meeting 2006, 217-224(2006). Available for download here.
  • P. V. Coveney, S. K. Sadiq, R. S. Saksena and S. J. Zasada, "Constructing Chained Molecular Dynamics Simulations of HIV-1 Protease Using the Application Hosting Environment", Proceedings of the UK e-Science All Hands Meeting 2006, 428-431(2006).
  • B.M. Boghosian, P.V. Coveney, S. Dong, L.I. Finn, S. Jha, G. Karniadakis and N. Karonis, "Nektar, SPICE and Vortonics: Using Federated Grids for Large Scale Scientific Applications". In Proceedings of Challenges of Large Applications in Distributed Environments, 34-42 (2006). IEEE Catalog Number: 06EX1397 ISBN 1-4244-0420-7 Library of Congress 2006925560. Available for download here.
  • G. De Fabritiis, R. Delgado-Buscalioni and P. V. Coveney, "Multiscale modelling of liquids with molecular specificity", Physical Review Letters, 97(13), 134501(2006), DOI: 10.1103/PhysRevLett.97.134501. Published online, 29 September 2006 at http://link.aps.org/abstract/PRL/v97/e134501. Available for download here.
  • M. Serrano, G. De Fabritiis, P. Espanol and P. V. Coveney, "A stochastic Trotter integration scheme for dissipative particle dynamics", Mathematics and Computers in Simulations, 72, 190-194(2006), DOI: 10.1016/j.matcom.2006.05.019. Available for download here.
  • H. C. Greenwell, L. A. Bindley, P. R. Unwin, P. J. Holliman, W. Jones and P. V. Coveney, "In situ monitoring of crystal growth and dissolution in immobilized oriented layered double hydroxide crystals", J. Cryst. Growth, 249, 53-59(2006).
  • G. Giupponi and P. V. Coveney, "Non-Newtonian behaviour of the gyroid mesophase: A lattice-Boltzmann study", Mathematics and Computers in Simulations, 72, 124-127(2006), DOI: 10.1016/j.matcom.2006.05.035. Available for download here.
  • P. V. Coveney, G. De Fabritiis, M. J. Harvey, S. M. Pickles and A. R. Porter, "Coupled applications on distributed resources", Comp. Phys. Comm., 175, 389-396(2006), DOI: 10.1016/j.cpc.2006.05.008. Available for download here.
  • P. V. Coveney, S. K. Sadiq, R. Saksena, S. J. Zasada, M. Mc Keown and S. Pickles, "The Application Hosting Environment: Lightweight Middleware for Grid Based Computational Science", TeraGrid '06 Conference. Available for download here.
  • 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)
  • M. Parkin, J. Brooke, "A PDA Client for the Computational Grid". Accepted for publication in Concurrency and Computation: Practice and Experience.
  • M. Parkin, D. Kuo, J. Brooke, "A Framework & Protocols for Service Contract Agreement". Accepted for Service Computing Conference 2006 (SCC '06).
  • M. Parkin, D. Kuo, J. Brooke, A. MacCulloch, "Challenges in EU Grid Contracts". Accepted for e-Challenges 2006 Conference (e-Challenges e-2006).
  • D. Kuo, M. Parkin, J. Brooke, "Negotiating Contracts on the Grid". Accepted for the e-Challenges 2006 Conference (e-Challenges e-2006).
  • M.J. Harvey, D. Scott and P. V. Coveney, "An Integrated Instrument Control and Informatics System for Combinatorial Materials Research", J. Chem. Inf. Model., 46(3), 1026-1033 (2006) DOI: 10.1021/ci050399g. Available for download here.
  • B.M. Boghosian, L.I. Finn and P.V. Coveney, "Moving the data to the computation: multi-site distributed parallel computation", (2006). Available for download here.
  • R. Delgado-Buscalioni and P.V. Coveney, "Structure of a tethered polymer under flow using molecular dynamics and hybrid molecular-continuum simulations", Physica A (Proceedings of the 13th International Conference on Discrete Simulation of Fluid Dynamics), 362, 30-35 (2006). DOI: 10.1016/j.physa.2005.09.011.
  • R.W. Ford, G.D. Riley, M.K. Bane, C.W. Armstrong, T.L. Freeman, "GCF: A General Coupling Framework", Concurrency and Computation: Practice and Experience, Special Issue: Computational Frameworks, Vol 18, pages 163-181 (2006). DOI: 10.1002/cpe.910.
  • G. Giupponi, J. Harting, P.V. Coveney, "Emergence of rheological properties in lattice Boltzmann simulations of gyroid mesophases", Europhysics Letters, 73, 533-539 (2006). Available here
  • N. Gonzalez-Segredo, J. Harting, G. Giupponi, P.V. Coveney "Stress response and structural transitions in sheared gyroidal and lamellar amphiphilic mesophases: lattice-Boltzmann simulations", Phys. Rev. E. 73, 031503 DOI: 10.1103/PhysRevE.73.031503.
  • 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", J. Mater. Chem., 16, 708-723 (2006) DOI: 10.1039/b506932g. Also available for download here.
  • M. Serrano, G. De Fabritiis, P. Español and P.V.Coveney "A stochastic Trotter integration scheme for dissipative particle dynamics", preprint.
  • P. Stansell, K. Stratford, J.-C.Desplat, R. Adhikari, M. E. Cates, "Nonequilibrium Steady States in Sheared Binary Fluids", accepted for publication in Physical Review Letters. cond-mat/0511745.
  • M. Venturoli and E.S. Boek, "Two-dimensional lattice-Boltzmann simulations of single phase flow in a pseudo two-dimensional micromodel", Physica A (Proceedings of the 13th International Conference on Discrete Simulation of Fluid Dynamics), 362, 23-29 (2006). DOI: 10.1016/j.physa.2005.09.006.

2005

The August 2005 issue of Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences contains papers of a theme issue entitled Scientific Grid computing, compiled and edited by Peter Coveney.

  • R. Adhikari, M. E. Cates, K. Stratford, A. Wagner, "Fluctuating lattice Boltzmann", Europhys.Lett, 71(3), 473-479, (2005)
  • R. Adhikari, J.-C. Desplat, K. Stratford, "Sliding periodic boundary conditions for lattice Boltzmann and lattice kinetic equations", submitted to Physical Review E (2005). cond-mat/0503175
  • S. K. Allison, J. P. Fox, R. Hargreaves and S. P. Bates, "Clustering and microimmiscibility in alcohol-water mixtures: Evidence from molecular-dynamics simulations", Phys. Rev. B, 024201 (2005).
  • C.W. Armstrong, R.W. Ford, J.R. Gurd, M. Lujan, K.R. Mayes, G.D. Riley, "Performance Control of Scientific Coupled Models in Grid Environments. Concurrency and Computation Practice and Experience", Special Issue: Grid Computing. Eds. J. Gurd, T. Hey, J, Papay and G. Riley. Vol. 17, No. 2-4, pp. 259-295, February-April 2005.
  • M. Ashworth, I.J. Bush, M.F. Guest, A.G. Sunderland, S. Booth, J. Hein, L. Smith, K. Stratford and A. Curioni, "HPCx: towards capability computing", Concurrency and Computation-Practice and Experience, 17(10), 1329-1361, (2005)
  • R. J. Blake, P. V. Coveney, P. Clarke, S. M. Pickles, "The TeraGyroid Experiment-Supercomputing 2003", Scientific Programming, 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.
  • A. A. Bowden, P. Boulet, H. C. Greenwell, B. Chen, J. R. G. Evans, P .V. Coveney, A. Whiting, "Intercalation and in situ polymerization of poly(alkylene oxide) derivatives within M+-montmorillonite (M= Li, Na, K)", J. Mater. Chem., Accepted pending revision (2005).
  • J. Brooke, M. Mc Keown, S. Pickles and S. Zasada, "Implementing WS-Security in Perl", UK e-Science All Hands Meeting 2005, available online.
  • J. Brooke and M. Parkin, "A PDA Client for the Computational Grid in proceedings of Emerging Technologies for Next Generation Grid (ETNGRID-2005)". Linkoping University, Sweden, June 2005, IEEE Press.
  • M.E. Cates, R. Adhikari, K. Stratford, "Colloidal arrest by capillary forces", J. Phys. Condens. Matter, 17, S2771-S2778 (2005), DOI: 10.1088/0953-8984/17/31/001.
  • M. E. Cates, J.-C. Desplat, P. Stansell, A.J. Wagner, K. Stratford, R. Adhikari, I. Pagonabarraga, "Physical and Computational Scaling Issues in Lattice Boltzmann Simulations of Binary Fluid Mixtures", P.V. Coveney, ed., "Scientific Grid computing", theme issue of Phil. Trans. R. Soc. A., DOI: 10.1098/rsta.2005.1619 (2005).
  • Jonathan 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.
  • Jay Chin, M. Parkin, N. Zhang, A. Nenadic and J. Brooke. "GridFAME: Flexible Authentication Middleware Extension for Grids". In Proceedings of Grid Computing & Applications Workshop, Grid Asia 2005. Singapore, May 2005, IEEE Press
  • Jay Chin, M. Parkin, N. Zhang, A. Nenadic, J.M. Brooke, "An Authentication Strength Linked Access Control"; Middleware for the Grid International Journal of Information Technology, 11(4):1, (2005)
  • J. Cohen, A.S. McGough, J. Darlington, N. Furmento, G. Kong, and A. Mayer, "RealityGrid: An Integrated Approach to Middleware through ICENI". Philosophical Transactions: Mathematical, Physical and Engineering Sciences, 363(1833):1817--1827,(2005)
  • 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, 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.
  • P.V. Coveney, G. De Fabritiis, M.J. Harvey, S.M. Pickles and A.R. Porter, "On steering coupled models", UK e-Science All Hands Meeting 2005, available online.
  • P.V. Coveney, M.J. Harvey, L. Pedesseau, D. Mason, A. Sutton, M. Mc Keown and S. Pickles, "Development and deployment of an application hosting environment for grid based computational science", UK e-Science All Hands Meeting 2005, available online.
  • 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.
  • L. Dougan, R. Hargreaves, S.P. Bates, J.L. Finney, V. Reat, A.K. Soper and J. Crain, "Segregation in aqueous methanol enhanced by cooling and compression", J. Chem. Phys. 122, 174514 (2005).
  • E. G. Flekkøy, R. Delgado-Buscalioni and P.V. Coveney, "Flux boundary conditions in particle simulations", Phys. Rev. E 72, 026703 (2005). DOI: 10.1103/PhysRevE.72.026703
  • 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, A. Whiting, "Interlayer structure and bonding in non-swelling primary amine intercalated clays", Macromolecules, 38, 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. Gurd, T. Hey, J. Papay and G. Riley, Special Issue: Grid Performance; Licklider and the Grid, Concurrency and Computation Practice and Experience, Special Issue: Grid Computing. Eds. J. Gurd, T. Hey, J, Papay and G. Riley. Vol. 17, No. 2-4, pp. 95-98, February-April 2005.
  • R. Haines, M. Mc Keown, S.M. Pickles, R.L. Pinning, A.R. Porter and M. Riding, "The Service Architecture of the TeraGyroid Experiment", Phil Trans R Soc, 363, 1743-1755, (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 .
  • M. Humphrey, G. Wasson, K. Jackson, J. Boverhof, M. Rodriguez, J. Gawor, J. Bester, S. Lang, I. Foster, S. Meder, S. Pickles, M. Mc Keown, "State and Events for Web Services: A Comparison of Five WS-Resource Framework and WS-Notification Implementations", Proceedings of 14th IEEE International Symposium on High Performance Distributed Computing HPDC-14, 24-27 July 2005, pages:3-13. DOI: 10.1109/HPDC.2005.1520928.
  • H. Hurchand, S.D. Kenny, C. F. Sanz-Navarro, R. Smith and P.E.J. Flewitt, "The influence of P solutes on an irradiated alpha-Fe matrix", NIM B 229, 92-102 (2005).
  • S. Jha, P.V. Coveney and C. Laughton, "Forcefield validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer.", J. Comp. Chem., 26(15), 1617-1627 (2005). DOI: 10.1002/jcc.20300.
  • S. Jha, P. V. Coveney and M. J. Harvey, "SPICE: Simulated Pore Interactive Computing Environment", Proceedings of the 2005 ACM/IEEE Conference on Supercomputing (2005), DOI:10.1109/SC.2005.65. Available here.
  • S. Jha, M. J. Harvey, P.V. Coveney, N. Pezzi, S. Pickles, R. Pinning and P. Clarke, "SPICE: Simulated Pore Interactive Computing Environment - Using Grid computing to understand DNA translocation across protein nanopores embedded in lipid membranes", UK e-Science All Hands Meeting 2005, available online.
  • S. Jha, S. Wan and P.V. Coveney, "Computing free energies for `real' systems using molecular dynamics simulations", Capability Computing, the Newsletter of the HPCx community, 6, 8-10, (2005). Available here.
  • 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.
  • R.S. Kalawsky and G. Simpkin, "Automating the Display of Third Person/Stealth Views of Virtual Environments," Presence, In press.
  • S.D. Kenny, D. Mulliah, C.F. Sanz-Navarro and R. Smith, "Molecular dynamics simulations of nanoindentation and nanotribology". Phil. Trans. R. Soc. A., 363 (1833), 1949-1959 (2005). DOI: 10.1098/rsta.2005.1621.
  • W. Lee, S. McGough, J. Darlington, "Performance Evaluation of the GridSAM Job Submission and Monitoring System", UK e-Science All Hands Meeting 2005, available online.
  • 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.
  • D.R. Mason, "Faster neighbour list generation using a novel lattice vector representation", Computer Physics Communications 170, 31-41 (2005)
  • D.R. Mason and A.P. Sutton "Computational steering in Monte Carlo simulations of thin film polystyrene", Phil. Trans. R. Soc. A., 363 (1833), 1793-1805, (2005), DOI: 10.1098/rsta.2005.1622.
  • D.R. Mason, T.S. Hudson and A.P. Sutton, "Fast recall of state-history in kinetic Monte Carlo simulations utilizing the Zobrist key", Computer Physics Communications, 165 (1), 37-48, (2005)
  • S. McGough, A. Afzal, J. Darlington, N. Furmento, A. Mayer, and L. Young, "Making the Grid Predictable through Reservations and Performance Modelling", The Computer Journal, 48(3):358--368, (2005)
  • S. McGough, W. Lee and J. Darlington, "ICENI II Architecture", UK All Hands Meeting 2005, available online.
  • S.M. Pickles, R. Haines, R.L. Pinning and A.R. Porter, "A Practical Toolkit for Computational Steering", Phil Trans R Soc, 363 (1833), 1843-1853, (2005). DOI: 10.1098/rsta.2005.1611.
  • C. Nieto-Draghi, R. Hargreaves and S.P. Bates, "Structure and dynamics of water in aqueous methanol", J. Phys. Cond. Matt., 17, S3265-S3270 (2005)
  • K. Stratford, R. Adhikari, I. Pagonabarraga, J.-C. Desplat, M. E. Cates "Colloidal Jamming at Interfaces: A Route to Fluid-Bicontinuous Gels", Science Vol 309, 2198-2201 (2005). Available here.
  • K. Stratford, R. Adhikari, I. Pagonabarraga, J.-C. Desplat, "Lattice Boltzmann for Binary Fluids with Suspended Colloids", Journal of Statistical Physics, Vol 121, pages 163-178 (2005). DOI: 10.1007/s10955-005-8411-1.
  • M. Venturoli , M.J. Harvey, G. Giupponi, P.V. Coveney, R.L. Pinning, A.R. Porter and S.M. Pickles, "Robust Grid-based environment for large scale lattice-Boltzmann simulations", UK e-Science All Hands Meeting 2005, available online.
  • 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.
  • T.W. Whitfield, G.J. Martyana, S.K. Allison, S.P. Bates and J. Crain, "Liquid N-methylacetamide: A surprisingly realistic model for H-bonding motifs in proteins"; under review at Chem. Phys. Lett (2005).

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.
  • J.M. Brooke, D. Fellows, J. MacLaren, "Interoperability of Resource Descriptions across Grid Domain Boundaries" in Proceedings of European Congress on Computational Methods in Applied Sciences and Engineering, Eds. P. Neittaanmäki, T. Rossi, S. Korotov, E. Onate, J. Péiaux and D. Knörper, ECCOMAS 2004, Jyväskylä, July 24-28 2004, proceedings available at http://www.mit.jyu.fi/eccomas2004/proceedings/proceed.html .
  • M.E. Cates, K. Stratford, R. Adhikari, P. Stansell, J.-C. Desplat, I. Pagonabarraga and A.J. Wagner, "Simulating colloid hydrodynamics with lattice Boltzmann methods", J. Phys.: Condens. Matter 16, S3903-S3915 (2004).
  • 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.
  • J. Chin, P.V. Coveney and J. Harting, "The TeraGyroid project - collaborative steering and visualization in an HPC grid for modelling complex fluids", in Proceedings of the UK e-Science All Hands Meeting 2004, available online.
  • J. Cohen, N. Furmento, G. Kong, A. Mayer, S. Newhouse, and J. Darlington, "RealityGrid: An Integrated Approach to Middleware through ICENI", In UK e-Science All Hands Meeting, p. 451--456, Nottingham, UK, Sep. 2004, ISBN 1-904425-21-6
  • 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 and M. Harvey, "Introducing WEDS: a WSRF-based Environment for Distributed Simulation", NeSC Technical Report UKeS-2004-07 PDF.
  • 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.
  • L. Dougan, S. P. Bates, R. Hargreaves, J. P. Fox, J. Crain, J. L. Finney, V. Reat, A. K. Soper, "Methanol-water solutions: A bi-percolating liquid mixture", J. Chem. Phys. 121, 6456-6462 (2004).
  • M.D. Egbert, P.J. Graham, K. Stratford and J.-C. Desplat, "The RealityGrid Web Portal" in Proceedings of the UK e-Science All Hands Meeting 2004, 847-848, available online.
  • D.R. Flower, et al, "Computational vaccinology: quantitative approaches.", Novartis Found Symp. 2003; 254: 102-20; discussion 120-5, 216-22, 250-2. Available here.
  • P.W. Fowler, P.V. Coveney, S. Jha and S. Wan, "Exact calculation of peptide-protein binding energies by steered thermodynamic integration using high performance computing grids", In Proceedings of the UK e-Science All Hands Meeting, Nottingham, UK, Sep. 2004, available online.
  • N. Furmento, J. Hau, W. Lee, S. Newhouse, and J. Darlington, "Implementations of a Service-Oriented Architecture on top of Jini, JXTA and OGSI" In Grid Computing: Second European AcrossGrids Conference, AxGrids 2004, volume 3165 of Lecture Notes in Computer Science, 90-99, Nicosia, Cyprus, Jan. 2004
  • 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.V. 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.
  • 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, (2004) DOI: 10.1098/rsta.2004.1402.
  • S. Jha, S. Pickles, A. Porter, "A Computational Steering API for Scientific Grid Applications: Design, Implementation and Lessons", Workshop on Grid Application Programming Interfaces, September 20, 2004, Brussels, Belgium.
  • W.E. Johnston, J.M. Brooke, R. Butler,D. Foster and M. Mazzucato, "Production Deployment: Experiences and Recommendations" In, I. Foster, C. Kesselman (Eds.), The Grid: Blueprint for a New Computing Infrastructure (2nd Edn.), Morgan Kaufmann Publishers pp 537-566 (2004), ISBN 1-55860-933-4
  • R. S. Kalawsky, Nee, S.P., "Important issues concerning interactive user interfaces in grid based computational steering systems," presented at EPSRC e-Science All Hands Meeting, Nottingham, 2004, available online.
  • R. S. Kalawsky and S. P. Nee, "e-Science RealityGrid - Interim Human Factors Audit Requirements and Context Analysis," Loughborough University 2004, available online.
  • W. Lee, S. McGough, S. Newhouse, and J. Darlington, "A Standard Based Approach to Job Submission through Web Services", In UK e-Science All Hands Meeting, p. 901--905, Nottingham, UK, Sep. 2004, ISBN 1-904425-21-6
  • K. Mayes, G.D. Riley, R.W. Ford, M. Lujan, T.L. Freeman, C. Addison, "The Design of a Performance Steering System for Component-based Grid Applications." In, V. Getov, M. Gerndt, A. Hoisie, A. Malony, B. Miller (Eds.). Performance Analysis and Grid Computing, Kluwer Academic Publishers, pp. 111--127, (2004). ISBN: 1-4020-7693-2
  • S. McGough, L. Young, A. Afzal, S. Newhouse, and J. Darlington, "Workflow Enactment in ICENI" , In UK e-Science All Hands Meeting, p. 894--900, Nottingham, UK, Sep. 2004, ISBN 1-904425-21-6
  • S. McGough, L. Young, A. Afzal, S. Newhouse, and J. Darlington, "Performance Architecture within ICENI" , In UK e-Science All Hands Meeting, p. 906--911, Nottingham, UK, Sep. 2004 , ISBN 1-904425-21-6
  • Mulliah, D., Kenny, S.D. and Smith, R., ''Modelling of stick-slip phenomena using molecular dynamics'' , Physical Review B , 69, 205407 (2004).
  • Mulliah, D., Smith, R. and Kenny, S.D., "Molecular Dynamics simulations of nanoscratching of silver(100)", Nanotechnology, 15, 243-249 (2004).
  • S. P. Nee and R. S. Kalawsky, "Developing a Roaming PDA-Based Interface for a Steering Client for OGSI:Lite using.Net: Practical Lessons Learned," presented at EPSRC e-Science All Hands Meeting, Nottingham, 2004 available online.
  • 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. M. Pickles et al, "The TeraGyroid Experiment", Workshop on Case Studies on Grid Applications, March 13, 2004, Berlin, Germany.
  • S. M. Pickles, R. Haines, R. L. Pinning and A. R. Porter, "Practical Tools for Computational Steering", Proceedings of the UK e-Science All Hands Meeting, Sept 1-3, 2004, available online.
  • S. Pickles, "On the use of checkpoint/recovery in RealityGrid", Global Grid Forum, January 2004, Available online.
  • 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 a3 and ß 2 m domains be neglected?", Journal of Computational Chemistry, 25 (15), 1803-1813, (2004); DOI: 10.1002/jcc.20100.
  • Sanz-Navarro C.F., Kenny, S.D. and Smith, R., '' Atomistic Simulations of Structural Transformations of Silicon Surfaces under Nanoindentation '', Nanotechnology, 15, 692-697 (2004).
  • Sanz-Navarro C.F., Kenny, S.D., Porter A.R. and Pickles S.M., "Real-time visualization and computational steering of molecular dynamics simulations of materials science". Proc. of the UK e-Science All Hands Meeting, Nottingham, UK, September (2004), available online.
  • P. Stodghill, R. Badia, R.t Hood, T. Kielmann, C. Morin, S. Pickles, M. Sgaravatto, N. Stone, H. Y. Yeom, "Use Cases for Grid Checkpoint and Recovery, GGF informational document (draft)", (2004). Available online.

2003

  • R. Allan, et al., "Building the e-Science Grid in the UK: Middleware, Applications and Tools deployed at Level 2", Proceedings of the UK e-Science All Hands Meeting 2003, article is available online.
  • 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, available online.
  • M. E. Cates, J. Vollmer, A. Wagner, D. Vollmer, "Phase separation in binary fluid mixtures with continuously ramped temperature", Phil. Trans. Roy. Soc. A 361, 793-804 (2003)
  • 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, "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.
  • K. Czajkowski, S. Pickles, J. Pruyne, V. Sander, "Usage Scenarios for a Grid Resource Allocation Agreement Protocol", GGF Memo, February 2003.
  • 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.
  • 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.
  • R.W. Ford and G.D. Riley, "Towards the Flexible Composition and Deployment of Coupled Models.", In proc. Tenth ECMWF Workshop on the Useof High Performance Computing in Meteorology; Realizing TeraComputing. ECMWF, Reading, England, 4-8 November 2002. World Scientific, pp. 189--195, (2003). ISBN: 981-238-376-X.
  • N. Furmento, W. Lee, S. Newhouse, and J. Darlington, "Test and Deployment of ICENI, An Integrated Grid Middleware on the UK e-Science Grid", In UK e-Science All Hands Meeting, p. 192--195, Nottingham, UK, Sep. 2003, ISBN 1-904425-11-9
  • N. Furmento, J. Hau, W. Lee, S. Newhouse, and J. Darlington, "Implementations of a Service-Oriented Architecture on top of Jini, JXTA and OGSA", In UK e-Science All Hands Meeting, p. 703--710, Nottingham, UK, Sep. 2003 , ISBN 1-904425-11-9
  • 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.
  • G. Kong, J. Stanton, S. Newhouse, and J. Darlington, "Collaborative Visualisation over the Access Grid using the ICENI Grid Middleware", In UK e-Science All Hands Meeting, p. 393--396, Nottingham, UK, Sep. 2003, ISBN 1-904425-11-9
  • Lorenz S, Walsh TR, Sutton AP, "Towards an anisotropic bead-spring model for ribbonlike polymers: Monte Carlo simulations of liquid benzene", J. Chem. Phys. 119 (5), 2903-2907 (2003)
  • 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.
  • A. Mayer, S. McGough, N. Furmento, W. Lee, S. Newhouse, and J. Darlington, "ICENI Dataflow and Workflow: Composition and Scheduling in Space and Time", In UK e-Science All Hands Meeting, p. 627--634, Nottingham, UK, Sep. 2003, ISBN 1-904425-11-9
  • J. Skår and P. V. Coveney, "Preface", Phil. Trans. R. Soc. Lond. A 361, Number 1807, 1047 (2003); available online.
  • Smith Roger, Christopher D., Kenny S. D., Richter Asta, and Wolf Bodo "Defect generation and pileup of atoms during nanoindentation of Fe single crystals", Physical Review B vol. 67; 245405 (2003).
  • A. J. Wagner, L. M. Wilson, M. E. Cates, "Role of inertia in two-dimensional deformation and breakdown of a droplet", Phys. Rev. E. 68, 045301 (2003)
  • A. J. Wagner, "The origin of spurious velocities in lattice Boltzmann", Int. J. Mod. Phys. B 17, 193-196 (2003)
  • L. Young, S. McGough, S. Newhouse, and J. Darlington, "Scheduling Architecture and Algorithms within the ICENI Grid Middleware", In UK e-Science All Hands Meeting, p. 5--12, Nottingham, UK, Sep. 2003, ISBN 1-904425-11-9

2002

  • N. Furmento, A. Mayer, S. McGough, S. Newhouse, T. Field, and J. Darlington, "ICENI: Optimising Component Applications within a Grid Environment", Software Components for High-Performance Scientific Computing, SIAM Activity Group on Supercomputing, Invited contribution, July 2002
  • The London E-Science Centre, "ICENI, An Integrated Grid Middleware to support e-Science", All Hands Meeting, Sheffield, UK, Sep. 2002
  • I. Pagonabarraga, A. J. Wagner, M. E. Cates, "Binary fluid demixing: the crossover region", J. Stat. Phys. 107, 39-52 (2002)
  • J. Stanton, S. Newhouse, and J. Darlington, "Implementing a Scientific Visualisation Capability Within a Grid Enabled Component Framework", In 8th International Euro-Par Conference, volume 2400 of Lecture Notes in Computer Science, Paderborn, Germany, Aug. 2002
  • D. Vollmer, J. Vollmer, A. J. Wagner, "Oscillatory kinetics of phase separation in a binary mixture under constant heating", Phys. Chem. Chem. Phys. 4, 1380-1385 (2002)
  • A. J. Wagner and I. Pagonabarraga, "Lees Edwards boundary conditions for lattice Boltzmann", J. Stat. Phys. 107, 521-537 (2002)

2000-2001

  • N. Furmento, A. Mayer, S. McGough, S. Newhouse, T. Field, and J. Darlington, "Optimisation of Component-based Applications within a Grid Environment", In SuperComputing 2001, Denver, USA, Nov. 2001
  • N. Furmento, A. Mayer, S. McGough, S. Newhouse, T. Field, and J. Darlington, "An Integrated Grid Environment for Component Applications", In 2nd International Workshop on Grid Computing, Grid 2001, volume 2242 of Lecture Notes in Computer Science, Denver, USA, Nov. 2001
  • 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. 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).
  • S. Newhouse, A. Mayer, and J. Darlington, "A Software Architecture for HPC Grid Applications" In 6th International Euro-Par Conference, volume 1900 of Lecture Notes in Computer Science, p. 686--689, Munich, Germany, Aug. 2000
  • J.K. Stanton, "Enabling Computational Steering through Visualization in a Distributed Environment", Master's thesis, Imperial College, Department of Computing, (2001)

MUST publications

Publications of the MUST Project.
  • J. Brooke, M. Daw, M. Nekovee, S. Olafsson, I. Skenderoski, "MUST - Multicast Streaming Technology for the Grid", UK e-Science All Hands Meeting 2003. available online
  • M. P. Barcellos, M. Nekovee, M. Daw, J. Brooke, S. Olafsson, "Reliable Multicast for the Grid: a comparison of protocol implementations", UK e-Science All Hands Meeting 2004". available online
  • M. P. Barcellos, M. Nekovee, M. Koyabe, M. Daw, J.Brooke, "Evaluating High-Throughput Reliable Multicast for Grid Applications in Production Networks", in Proceedings of GAN'05, Eds. P. Lefevre, P. Primet, CCGrid 2005, Cardiff, UK. IEEE Press

Documentation

RealityGrid technical notes, documentation and software can be found here.

Resources, documentation and tutorials for OGSI::Lite and WSRF::Lite are available here.

See also the RealityGrid Middleware page.

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