Environment from the Molecular Level

A NERC eScience testbed project

 

Last update:
4/22/05

eMinerals project documents

All Hands 2003

  1. M Doherty, K Kleese, M Williams, B Strong, L Blanshard, R Tyer, T Folkes, D Corney, A Sansum, M Bly, and N White. "SRB in Action". Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9) pp 51-58 [pdf]
  2. S Sufi, B Mathews and K Kleese van Dam. "An Interdisciplinary model for the representation of Scientific Studies and associated data holdings". Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9) pp 103-110 [pdf]
  3. M Doherty, K Kleese and S Sufi. "Database Cluster for e-Science". Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9), pp 268-271 [pdf]
  4. 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 and SM Hasan. "Environment from the molecular level: an escience testbed project". Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9) pp 302-305 [pdf]
  5. RP Tyer, LJ Blanshard, K Kleese van Dam, RJ Allan, AJ Richards and MT Dove. "Building the eMinerals Minigrid". Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9), pp 483-487 [pdf]
  6. G Drinkwater, K Kleese, S Sufi, L Blanshard, A Manandhar, R Tyer, K O'Neill, M Doherty, M Williams and A Woolf. "The CCLRC data portal". Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9), pp 540-547 [pdf]
  7. B Butchart, C Chapman and W Emmerich. "OGSA First Impressions - A Case Study Re-engineering a Scientific Application with the Open Grid Services Architecture". Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9) pp 810-816 [pdf]

All Hands 2004

  1. 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. "Collaborative tools in support of the eMinerals Virtual Organisation". Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 127-134, 2004 [pdf]
  2. M Calleja, B Beckles, M Keegan, MA Hayes, A Parker and MT Dove. "CamGrid: Experiences in constructing a university-wide, Condor-based grid at the University of Cambridge". Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 173-178, 2004 [pdf]
  3. 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. "Science outcomes from the use of Grid tools in the eMinerals project". Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 240-247, 2004 [pdf]
  4. P Wilson, W Emmerich and J Brodholt. "Leveraging HTC for UK eScience with Very Large Condor pools: Demand for transforming untapped power into results". Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 308-315, 2004 [pdf]
  5. L Blanshard, R Tyer, M Calleja, K Kleese, MT Dove. "Environmental Molecular Processes: Management of Simulation Data and Annotation". Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 637-644, 2004 [pdf]
  6. R Tyer, M Calleja, R Bruin, C Chapman, MT Dove, RJ Allan. "Portal Framework for Computation within the eMinerals Project". Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 660-665, 2004 [pdf]
  7. AS Manandhar, K Kleese K, Berrisford and GD Brown. "Deploying a distributed data storage system on the UK National Grid Service using federated SRB". Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 725-731, 2004 [pdf]
  8. 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. "Grid tool integration within the eMinerals project". Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 812-817, 2004 [pdf]
  9. C Chapman, P Wilson, T Tannenbaum, M Farrellee, M Livny, J Brodholt, and W Emmerich. Condor services for the Global Grid: Interoperability between Condor and OGSA. Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 870-877, 2004 [pdf]
  10. Y Zhang, P Murray-Rust, MT Dove, RC Glen, HS Rzepa, JA Townsend, S Tyrrell, J Wakelin, EG Willighagen. "JUMBO – An XML infrastructure for ecience". Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 930-934, 2004 [pdf]
  11. A. García, P. Murray-Rust, J. Wakelin. "The use of XML and CML in Computational Chemistry and Physics Programs". Proceedings of the UK e-Science All Hands Meeting 2004, (ISBN 1-904425-21-6), pp 1111-1114, 2004 [pdf]

Grid/escience papers

  1. LJ Blanshard, K Kleese and MT Dove. "Environment from the Molecular Level e-Science Project and its use of CLRC's Web Services Based Data Portal". In Proceedings of the First International Conference on Web Services (ed LJ Zhang, CSREA Press, ISBN: 1-892512-40-8), pp 164-167, 2003 [pdf]
  2. G Drinkwater, K Kleese K, S Sufi, L Blanshard, A Manandhar, R Tyer, K O'Neill, M Doherty, M Williams and A Woolf. "The CCLRC Dataportal". In Proceedings of the First International Conference on Web Services (ed LJ Zhang, CSREA Press, ISBN: 1-892512-40-8), pp 285-291, 2003 [pdf]
  3. L Blanshard, R Tyer, G Drinkwater, A Manandhar, S Sufi, K Kleese van Dam and M Dove. "Case study: Using Web services for the management of environmental data". in 2004 IEEE International conference on services computing, proceedings (ed LJ Zhang, M Li, AP Sheth and KG Jeffery), pp 132-136, 2004 [pdf]
  4. M Calleja and MT Dove. "Calculating activation energies in diffusion processes using a Monte Carlo approach in a grid environment". Lecture Notes in Computer Science, 3039, Part 4, pp 483-490, 2004 [pdf]
  5. 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. "Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated compute and data grid". Molecular Simulations (in press) [pdf preprint]
  6. C Chapman, J Wakelin, E Artacho, MT Dove, M Calleja, R Bruin and W Emmerich. "Workflow issues in atomistic simulations". Molecular Simulations (in press) [pdf preprint]
  7. M Dove. "The eMinerals Minigrid: An Infrastructure to Support Molecular Simulation Scientists." ERCIM News No. 59, October 2004, 48-49 [pdf]
  8. MT Dove and NH de Leeuw. "Grid computing and molecular simulations: the vision of the eMinerals project". Molecular Simulations (in press) [pdf preprint]
  9. 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, Z Du. "The eMinerals collaboratory: tools and experience". Molecular Simulations (in press) [pdf preprint]
  10. J Wakelin, P Murray-Rust, S Tyrrell, Y Zhang, HS Rzepa and A García. CML Tools and Information Flow in Atomic Scale Simulations". Molecular Simulations (in press) [pdf preprint]
  11. RP Bruin, M Calleja, MG Tucker and MT Dove. "Building and managing the eMinerals clusters - a case study in grid-enabled cluster operation". Computers in Science and Engineering (submitted) [pdf preprint]

Science papers

  1. M Alfredsson, JP Brodholt, PB Wilson, GD Price, F Corà, M Calleja, R Bruin, LJ Blanshard and RP Tyer. "Structural and magnetic phase transitions in simple oxides using hybrid functionals". Molecular Simulations (in press) [pdf preprint]
  2. NH de Leeuw, Z Du, J Li, S Yip, and T Zhu. "Computer modeling study of the effect of hydration on the stability of a silica nanotube". Nanoletters 3, 1347-1352, 2003 [pdf]
  3. Z Du, NH de Leeuw. A combined density functional theory and interatomic potential-based simulation study of the hydration of nano-particulate silicate surfaces. Surface Science 554, 193-210, 2004 [pdf]
  4. Z Du, NH de Leeuw, R Grau-Crespo, PB Wilson, JP Brodholt, M Calleja and MT Dove. "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". Molecular Simulations (in press) [pdf preprint]
  5. MV Fernández-Serra, G Ferlat and E Artacho. "Two exchange-correlation functionals compared for first-principles liquid water". Molecular Simulations (in press) [pdf preprint]
  6. S Kerisit and S. Parker. "Free energy of adsorption of water and calcium on the {1014} calcite surface". Chemical Communications, 2004, 52–53 [pdf]
  7. A Marmier and SC Parker. "Ab initio morphology and surface thermodynamics of a--Al2O3". Physical Review B 69, 115409 (2004) [pdf]
  8. A Marmier, H Spohr, DJ Cooke, S Kerisit, JP Brodholt, PB Wilson and SC Parker. "Self Diffusion of Argon in Flexible, Single Wall, Carbon Nanotubes". Molecular Simulations (in press) [pdf preprint]
  9. P Maul, D Savage, S Benbow, R Walke, and R Bruin. "Development of a FEP database for the geological storage of carbon dioxide". In Proceedings of the 7th International conference on Greenhouse gas control technologies.
  10. SC Parker, S Kerisit, A Marmier, S Grigoleit and GW Watson. "Modelling inorganic solids and their interfaces: A combined approach of atomistic and electronic structure simulation techniques". Faraday Discussisions, 124, 155–170, 2003 [pdf]
  11. SC Parker, DJ Cooke, S Kerisit, AS Marmier, SL Taylor and SN Taylor. "From HADES to PARADISE - atomistic simulation of defects in minerals". Journal of Physics: Condensed Matter 16, S2735–S2749, 2004 [pdf]
  12. JM Pruneda,  L Le Polles, I Farnan, K Trachenko, MT Dove, and E Artacho. "Calculation of the effect of intrinsic point defects and volume swelling in the nuclear magnetic resonance spectra of ZrSiO4". Molecular Simulations [pdf preprint]
  13. IT Todorov and W Smith. "DL_POLY_3: the CCP5 national UK code for molecular-dynamics simulations". Philosophical Transactions of the Royal Society of London A 362, 1835-1852, 2004
  14. K Trachenko, MT Dove, M Pruneda, E Artacho, E Salje, T Geisler, I Todorov, B Smith. "Radiation-induced structural changes, percolation effects and resistance to amorphization by radiation damage". In Radiation Effects and Ion-Beam Processing of Materials (Editors: Wang LM, Fromknecht R, Snead LL, Downey DF, Takahashi H), Materials Research Society Symposium Proceedings 792, 509–524, 2004
  15. K Trachenko, MT Dove, T Geisler, I Todorov and B Smith. "Radiation damage effects and percolation theory". Journal of Physics: Condensed Matter 16, S2623–S2627, 2004 [pdf]
  16. K Trachenko, MT Dove, EKH Salje, I Todorov, W Smith,  M Pruneda and E Artacho. "Radiation damage in the bulk and at the surface". Molecular Simulations (in press) [pdf preprint]
  17. K Trachenko, M Pruneda, E Artacho and MT Dove, "Radiation damage effects in perovskite, CaTiO3, and resistance of materials to amorphization", Physical Review B 70, 134112, 2004
  18. SA Wells, D Alfe, L Blanchard, J Brodholt, M Calleja, CA Catlow, GD Price, RP Tyler, K Wright. "Ab-initio simulations of magnetic iron sulphides". Molecular Simulations (in press) [pdf preprint]

Reports and documentation

  • eMinerals minigrid userguide [pdf]

Presentations

  • Talk given by Martin Dove to the RealityGrid conference [ppt]
  • Building the UK e-Science Grid: Middleware, Applications and Tools (Managing the transition from Globus to an Open Service Architecture), talk by Rob Allen [ppt]
  • Set of three talks given by Martin Dove to a Spring School in Oxford in March 2004, based on the tools used by the eMinerals project [ppt1, ppt2, ppt3]

eMinerals Newsletters

  1. First date [pdf]
  2. Next date [pdf]
  3. Next date [pdf]
  4. Next date [pdf]

Maintained by Martin Dove