SPICE: Simulated pore interactive computing environment

Shantenu Jha, Peter Coveney, Matt Harvey, Robin Pinning

Research output: Chapter in Book/Report/Conference proceedingConference contribution

15 Scopus citations

Abstract

SPICE aims to understand the vital process of translocation of biomolecules across protein pores by computing the free energy profile of the translocating biomolecule along the vertical axis of the pore. Without significant advances at the algorithmic, computing and analysis levels, understanding problems of this size and complexity will remain beyond the scope of computational science for the foreseeable future. A novel algorithmic advance is provided by a combination of Steered Molecular Dynamics and Jarzynski's Equation (SMD-JE); Grid computing provides the required new computing paradigm as well as facilitating the adoption of new analytical approaches. SPICE uses sophisticated grid infrastructure to couple distributed high performance simulations, visualization and instruments used in the analysis to the same framework. We describe how we utilize the resources of a federated trans-Atlantic Grid to use SMD-JE to enhance our understanding of the translocation phenomenon in ways that have not been possible until now.

Original languageEnglish (US)
Title of host publicationProceedings of the ACM/IEEE SC 2005 Conference, SC 2005
PublisherAssociation for Computing Machinery
ISBN (Electronic)1595930612
DOIs
StatePublished - 2005
Externally publishedYes
Event2005 ACM/IEEE Conference on Supercomputing, SC 2005 - Seattle, United States
Duration: Nov 12 2005Nov 18 2005

Publication series

NameProceedings of the International Conference on Supercomputing
Volume2005-November

Conference

Conference2005 ACM/IEEE Conference on Supercomputing, SC 2005
Country/TerritoryUnited States
CitySeattle
Period11/12/0511/18/05

All Science Journal Classification (ASJC) codes

  • General Computer Science

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