SPICE: Simulated Pore Interactive Computing Environment

— 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. This paper outlines the scientific motivation and describes why distributed resources are critical for the project. We describe how we utilize the resourc...

• Type: Conference
• Year: 2005
• Where: SC
• Authors: Shantenu Jha, Peter V. Coveney, Matt J. Harvey
• Keywords: Applied Computing, Federated Transatlantic Grid, Grid Computing, SC 2005, Sophisticated Grid Infrastructure