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Details of Grant 

EPSRC Reference: EP/D500028/1
Title: SPICE: Simulated Pore Interactive Computing Environment
Principal Investigator: Coveney, Professor P
Other Investigators:
Pickles, Dr SM Laughton, Professor C Clarke, Professor P
Smith, Dr LA Blake, Dr R
Researcher Co-Investigators:
Project Partners:
Pittsburgh Supercomputing Centre Teragrid NCSA
Department: Chemistry
Organisation: UCL
Scheme: Standard Research (Pre-FEC)
Starts: 01 October 2005 Ends: 31 March 2007 Value (£): 114,808
EPSRC Research Topic Classifications:
Biological membranes eScience
EPSRC Industrial Sector Classifications:
No relevance to Underpinning Sectors
Related Grants:
Panel History:  
Summary on Grant Application Form
It is almost impossible to overstate the importance and ubiquity of the translocation of biomolecules like RNA, DNA and polypeptides across membrane channels (often formed by proteins) in biological cells. However, details of the transport mechanism of such biomolecules across pores in membranes are not well understood. The lack of any serious attempt at an atomistic simulation of the translocation process can be attributed to two reasons,: (i) the construction of such models (requiring high quality and resolution structures of appropriate pores and membranes) relies on experimental data that have only recently become available; (ii) the computational requirements for simulations of systems of such sizes and for the required timescales were hitherto not possible. As a consequence of the emergence of scalable molecular dynamics codes and appropriate platforms along with significant advances in the computational approach, it is now possible to perform meaningful simulations of the translocation process. Our aim in this project is to use our unique capabilities to determine the free-energy profile for DNA across a alpha-hemolysin pore. This requires dozens of simulations of models of approximately 200,000 atoms but including some as large as a million atoms over effective time scales of microseconds which is possible only using high performing codes that scale on the many heterogenous platforms that we will utilize, through the use of steered molecular dynamics.Under the EPSRC e-Science Pilot Project Grant GR/R67699, RealityGrid has made important contributions to grid computing at both national and international levels. The project has developed a reputation for achievement within all areas of its activities in the past three years; we have played a leading role inter alia in the evolution of usable grid middleware, computational steering and scientific research. Global progress toward realisation of the vision of grid computing as providing transparent access to computational resources across multiple administrative boundaries, whether national or global in scale, has been slower than originally anticipated. RealityGrid has been developing new approaches that put a premium on allowing users to exploit the underlying infrastructure as easily as possible.Two years ago, the TeraGyroid project demonstrated RealityGrid's ability to successfully federate high-end performance computing grids on both sides of the Atlantic. Significant changes in the Grid middleware and infrastructure have taken place since, partly due to the project's own endeavours. The aim of this proposal is to utilize the numerous new and enhanced grid features together with the capabilities developed during the course of the RealityGrid project to advance high-performance computing into a new domain by integrating simulations and instrumentation, to solve a focussed biophysical problem. Our approach will build on RealityGrid developments and specific experiences gained during the TeraGyroid and Steered Thermodynamic Integration (STIMD) projects as well as that accumulated more generally in working with computational grids for the past three years. The pinnacle of the activity will take place within computational experiments performed during SuperComputing 2005 (SC05). However a very great deal of scientific effort will need to continue well beyond SC05. Just as turned out to be the case in the TeraGyroid & STIMD projects, the amount of power available on HPC grids produces orders of magnitude more data than conventional HPC work, and a large amount of time is needed to interpret it all and to turn the results into scientific publications.
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