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Environment from the Molecular Level

A NERC eScience testbed project

Documents and publications

UK All Hands meeting 2006

  1. "A Lightweight, Scriptable, Web-based Frontend to the SRB". TOH White, RP Tyer, RP Bruin, MT Dove, KF Austen

  2. "A virtual research organization enabled by eMinerals minigrid: An integrated study of the transport and immobilisation of arsenic species in the environment". Z Du, VN Alexandrov, M Alfredsson, KF Austen, ND Bennett, M Blanchard, JP Brodholt, RP Bruin, CRA Catlow, C Chapman, DJ Cooke, TG Cooper, MT Dove, W Emmerich, SM Hasan, S Kerisit, NH de Leeuw, GJ Lewis, A Marmier, SC Parker, GD Price, W Smith, IT Todorov, R Tyer, AM Walker, TOH White, K Wright.

  3. "Managing Scientific Processes on the eMinerals Mini-Grid using BPEL". C Chapman, AM Walker, Mark Calleja, RP Bruin, MT Dove and W Emmerich.

  4. "Application and Uses of CML within the eMinerals project". TOH White, P Murray-Rust, PA Couch, RP Tyer, RP Bruin, IT Todorov, DJ Wilson, MT Dove, KF Austen.

  5. "Job submission to grid computing environments". RP Bruin, TOH White, AM Walker, KF Austen, MT Dove, RP Tyer, PA Couch, IT Todorov, MO Blanchard.

  6. "Automatic metadata capture and grid computing". RP Tyer, PA Couch, K Kleese van Dam, IT Todorov, RP Bruin, TOH White, AM Walker, KF Austen, MT Dove, MO Blanchard.

  7. "Using eScience to calibrate our tools: parameterisation of quantum mechanical calculations with grid technologies". KF Austen, TOH White, RP Bruin, MT Dove, E Artacho, RP Tyer.

  8. "Anatomy of a grid-enabled molecular simulation study: the compressibility of amorphous silica". MT Dove, LA Sullivan, AM Walker, K Trachenko, RP Bruin, TOH White, P Murray-Rust, RP Tyer, PA Couch, IT Todorov, W Smith, K Kleese van Dam.

  9. "A Lightweight, Scriptable, Web-based Frontend to the SRB". TOH White, RP Tyer, RP Bruin, MT Dove, KF Austen.

UK All Hands meeting 2005

  1. "eScience usability: the eMinerals experience." MT Dove, TO White, RP Bruin, MG Tucker, M Calleja, E Artacho, P Murray-Rust, RP Tyer, I Todorov, RJ Allan, K Kleese van Dam, W Smith, C Chapman, W Emmerich, A Marmier, SC Parker, GJ Lewis, SM Hasan, A Thandavan, V Alexandrov, M Blanchard, K Wright, CRA Catlow, Z Du, NH de Leeuw, M Alfredsson, GD Price, J Brodholt. Proceedings of All Hands 2005 (ISBN 1-904425-53-4), pp 30–37, 2005

  2. "Towards Data Integration for Computational Chemistry." PA Couch, P Sherwood, S Sufi, IT Todorov, RJ Allan, PJ Knowles, RP Bruin, MT Dove and P Murray-Rust. Proceedings of All Hands 2005 (ISBN 1-904425-53-4), pp 426–432, 2005

  3. "Multicast Application Sharing Tool for the Access Grid Toolkit." SM Hasan, GJ Lewis, VN Alexandrov, MT Dove, and MG Tucker. Proceedings of All Hands 2005 (ISBN 1-904425-53-4), pp 433–440, 2005

  4. "eScience methods for the combinatorial chemistry problem of adsorption of pollutant organic molecules on mineral surfaces." TO White, RP Bruin, J Wakelin, C Chapman, D Osborn, P Murray-Rust, E Artacho, MT Dove, M Calleja. Proceedings of All Hands 2005 (ISBN 1-904425-53-4), pp 773–780, 2005

  5. "Condor Birdbath: Web Service interfaces to condor." C Chapman, C Goonatilake, W Emmerich, M Farrellee, T Tannenbaum, M Livny, M Calleja and M Dove, Proceedings of All Hands 2005 (ISBN 1-904425-53-4), pp 737–744, 2005

  6. "eMinerals: Science Outcomes enabled by new Grid Tools." M Alfredsson, E Artacho, M Blanchard, JP Brodholt, CRA Catlow, DJ Cooke, MT Dove, Z Du, NH de Leeuw, A Marmier, SC Parker, GD Price, JMA Pruneda, W Smith, I Todorov, K Trachenko, and K Wright. Proceedings of All Hands 2005 (ISBN 1-904425-53-4), pp 788–795, 2005

  7. "The eMinerals project: developing the concept of the virtual organisation to support collaborative work on molecular-scale environmental simulations." MT Dove, E Artacho, TO White, RP Bruin, MG Tucker, P Murray-Rust, RJ Allan, K Kleese van Dam, W Smith, RP Tyer, I Todorov, W Emmerich, C Chapman, SC Parker, A Marmier, V Alexandrov, GJ Lewis, SM Hasan, A Thandavan, K Wright, CRA Catlow, M Blanchard, NH de Leeuw, Z Du, GD Price, J Brodholt, M Alfredsson. Proceedings of All Hands 2005 (ISBN 1-904425-53-4), pp 1058–1065, 2005

UK All Hands meeting 2004

  1. "Collaborative tools in support of the eMinerals Virtual Organisation." MT Dove, M Calleja, R Bruin, J Wakelin, M Keegan, S Ballard, G Lewis, SM Hasan, V Alexandrov, RP Tyer, I Todorov, P Wilson, M Alfredsson, GD Price, C Chapman, W Emmerich, S Wells, A Marmier, S Parker, Z Du. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 127–134, 2004

  2. "CamGrid: Experiences in constructing a university-wide, Condor-based grid at the University of Cambridge." M Calleja, B Beckles, M Keegan, MA Hayes, A Parker and MT Dove. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 173–178, 2004

  3. "Science outcomes from the use of Grid tools in the eMinerals project." S Wells, M Alfredsson, J Bowe, J Brodholt, R Bruin, M Calleja, R Catlow, DJ Cooke, MT Dove,, Z Du, S Kerisit, N de Leeuw, A Marmier, S Parker, GD Price, B Smith, H Spohr, I Todorov, K Trachenko, J Wakelin, K Wright. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 240–247, 2004

  4. "Leveraging HTC for UK eScience with Very Large Condor pools: Demand for transforming untapped power into results". P Wilson, W Emmerich and J Brodholt. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 308-315, 2004

  5. "Environmental Molecular Processes: Management of Simulation Data and Annotation." L Blanshard, R Tyer, M Calleja, K Kleese, MT Dove. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 637–644, 2004

  6. "Portal Framework for Computation within the eMinerals Project." R Tyer, M Calleja, R Bruin, C Chapman, MT Dove, RJ Allan. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 660–665, 2004

  7. "Deploying a distributed data storage system on the UK National Grid Service using federated SRB". AS Manandhar, K Kleese, P Berrisford and GD Brown. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 725-731, 2004

  8. "Grid tool integration within the eMinerals project." M Calleja, L Blanshard, R Bruin, C Chapman, A Thandavan, R Tyer, P Wilson, V Alexandrov, RJ Allen, J Brodholt, MT Dove, W Emmerich, K Kleese van Dam. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 812–817, 2004

  9. "Condor services for the Global Grid: Interoperability between Condor and OGSA." C Chapman, P Wilson, T Tannenbaum, M Farrellee, M Livny, J Brodholt, and W Emmerich. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 870-877, 2004

  10. "JUMBO: An XML infrastructure for eScience." Y Zhang, P Murray-Rust, MT Dove, RC Glen, HS Rzepa, JA Townsend, S Tyrrell, J Wakelin, EG Willighagen. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 930–934, 2004

  11. "The use of XML and CML in Computational Chemistry and Physics Programs". A. García, P. Murray-Rust, J. Wakelin. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 1111-1114, 2004

UK All Hands meeting 2003

  1. "SRB in Action". M Doherty, K Kleese, M Williams, B Strong, L Blanshard, R Tyer, T Folkes, D Corney, A Sansum, M Bly, and N White. Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9) pp 51-58

  2. "An Interdisciplinary model for the representation of Scientific Studies and associated data holdings". S Sufi, B Mathews and K Kleese van Dam. Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9) pp 103-110

  3. "Database Cluster for e-Science". M Doherty, K Kleese and S Sufi. Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9), pp 268-271

  4. "Environment from the molecular level: an escience testbed project." MT Dove, M Calleja, J Wakelin, K Trachenko, G Ferlat, P Murray-Rust, NH de Leeuw, Z Du, GD Price, PB Wilson, JP Brodholt, M Alfredsson, A Marmier, RP Tyer, LJ Blanshard, RJ Allan, K Kleese van Dam, IT Todorov, W Smith, VN Alexandrov, GJ Lewis, A Thandavan, SM Hasan. Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9) pp 302–305

  5. "Building the eMinerals Minigrid." RP Tyer, LJ Blanshard, K Kleese van Dam, RJ Allan, AJ Richards and MT Dove. Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9), pp 483–487

  6. "The CCLRC data portal". G Drinkwater, K Kleese, S Sufi, L Blanshard, A Manandhar, R Tyer, K O'Neill, M Doherty, M Williams and A Woolf. Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9), pp 540-547

  7. "OGSA First Impressions - A Case Study Re-engineering a Scientific Application with the Open Grid Services Architecture". B Butchart, C Chapman and W Emmerich. Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9) pp 810-816

Grid/escience papers

  1. "Calculating activation energies in diffusion processes using a Monte Carlo approach in a grid environment." M Calleja and MT Dove. Lecture Notes in Computer Science, 3039, Part 4, pp 483–490, 2004

  2. "The eMinerals minigrid: An infrastructure to support molecular simulation scientists." MT Dove. ERCIM News 59, 48-49, 2004

  3. "Grid computing and molecular simulations: the vision of the eMinerals project." MT Dove and NH de Leeuw. Molecular Simulation 31, 297–301, 2005

  4. "Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated compute and data grid." M Calleja, R Bruin, MG Tucker, MT Dove, RP Tyer, LJ Blanshard, K Kleese van Dam, RJ Allan, C Chapman, W Emmerich, PB Wilson, JP Brodholt, A Thandavan, VN Alexandrov. Molecular Simulation 31, 303–313, 2005

  5. "The eMinerals collaboratory: tools and experience." MT Dove, M Calleja, R Bruin, J Wakelin, MG Tucker, GJ Lewis, SM Hasan, VN Alexandrov, M Keegan, S Ballard, RP Tyer, I Todorov, PB Wilson, M Alfredsson, GD Price, C Chapman, W Emmerich, SA Wells, A Marmier, SC Parker, Zhimei Du. Molecular Simulation 31, 329–337, 2005

  6. "Building and managing the eMinerals clusters - a case study in grid-enabled cluster operation." RP Bruin, M Calleja , MG Tucker and MT Dove. Computers in Science and Engineering 7, 30–37, 2005

  7. "Multicast application sharing tool – Facilitating the eMinerals virtual organisation." GJ Lewis, SM Hasan, VN Alexandrov, MT Dove and M Calleja. Lecture Notes in Computer Science 3516, 359–366, 2005

Science papers

  1. "Computer modeling study of the effect of hydration on the stability of a silica nanotube". NH de Leeuw, Z Du, J Li, S Yip, and T Zhu. Nanoletters 3, 1347-1352, 2003

  2. "Modelling inorganic solids and their interfaces: A combined approach of atomistic and electronic structure simulation techniques". SC Parker, S Kerisit, A Marmier, S Grigoleit and GW Watson. Faraday Discussisions, 124, 155–170, 2003

  3. "A combined density functional theory and interatomic potential-based simulation study of the hydration of nano-particulate silicate surfaces." Z Du, NH de Leeuw. Surface Science 554, 193-210, 2004

  4. "Free energy of adsorption of water and calcium on the {1014} calcite surface". S Kerisit and S. Parker. Chemical Communications, 2004, 52–53

  5. "Ab initio morphology and surface thermodynamics of a-Al2O3". A Marmier and SC Parker. Physical Review B 69, art no 115409, 2004

  6. "Radiation damage effects in perovskite, CaTiO3, and resistance of materials to amorphization", K Trachenko, M Pruneda, E Artacho and MT Dove, Physical Review B 70, art no 134112, 2004

  7. "Radiation damage effects and percolation theory." K Trachenko, MT Dove, T Geisler, I Todorov and B Smith. Journal of Physics: Condensed Matter 16, S2623–S2627, 2004

  8. "From HADES to PARADISE - atomistic simulation of defects in minerals". SC Parker, DJ Cooke, S Kerisit, AS Marmier, SL Taylor and SN Taylor. Journal of Physics: Condensed Matter 16, S2735–S2749, 2004

  9. "DL_POLY_3: the CCP5 national UK code for molecular-dynamics simulations". IT Todorov and W Smith. Philosophical Transactions of the Royal Society of London A 362, 1835-1852, 2004

  10. "A computational study of the effect of Li-K solid solutions on the structures and stabilities of layered silicate materials – an application of the use of Condor pools in molecular simulation". Z Du, NH de Leeuw, R Grau-Crespo, PB Wilson, JP Brodholt, M Calleja and MT Dove. Molecular Simulation, 31, 339-347, 2005

  11. "Calculation of the effect of intrinsic point defects and volume swelling in the nuclear magnetic resonance spectra of ZrSiO4". JM Pruneda,  L Le Polles, I Farnan, K Trachenko, MT Dove, and E Artacho. Molecular Simulation, 31, 349-354, 2005

  12. "Radiation damage in the bulk and at the surface." K Trachenko, MT Dove, EKH Salje, I Todorov, W Smith, M Pruneda and E Artacho. Molecular Simulations 31, 355–359, 2005

  13. "Two exchange-correlation functionals compared for first-principles liquid water". MV Fernández-Serra, G Ferlat and E Artacho. Molecular Simulation 31, 361-366, 2005

  14. "Structural and magnetic phase transitions in simple oxides using hybrid functionals". M Alfredsson, JP Brodholt, PB Wilson, GD Price, F Corà, M Calleja, R Bruin, LJ Blanshard and RP Tyer. Molecular Simulation, 31, 367-377, 2005

  15. "Ab-initio simulations of magnetic iron sulphides". SA Wells, D Alfe, L Blanchard, J Brodholt, M Calleja, CA Catlow, GD Price, RP Tyler, K Wright. Molecular Simulation, 31 379-384, 2005

  16. "Self Diffusion of Argon in Flexible, Single Wall, Carbon Nanotubes." A Marmier, H Spohr, DJ Cooke, S Kerisit, JP Brodholt, PB Wilson and SC Parker. Molecular Simulation, 31, 385-389, 2005

  17. "DL_POLY_3: science on a grand scale via massively parallelised molecular dynamics simulations." IT Todorov, W Smith, K Trachenko and MT Dove. Capability Computing, 6, 12–14, 2005

  18. "Simulation of radiation damage in gadolinium pyrochlores". IT Todorov, JA Purton, NL Allan and MT Dove. Journal of Physics: Condensed Matter 18, 2217-2234, 2006

  19. "DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism". IT Todorov,W Smith, K Trachenko and MT Dove. Journal of Materials Chemistry 16, 1911-1918, 2006

  20. "Atomistic simulations of resistance to amorphization by radiation damage". K Trachenko, MT Dove, E Artacho, IT Todorov and W Smith. Physical Review B 73, art no 174207, 2006