Accelerating Electrostatic Surface Potential Calculation with Multiscale Approximation on Graphics Processing Units

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dc.contributor.authorAnandakrishnan, Ramuen
dc.contributor.authorScogland, Thomas R. W.en
dc.contributor.authorFenley, Andrew T.en
dc.contributor.authorGordon, Johnen
dc.contributor.authorFeng, Wu-chunen
dc.contributor.authorOnufriev, Alexey V.en
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2013-06-19T14:36:47Zen
dc.date.available2013-06-19T14:36:47Zen
dc.date.issued2009en
dc.description.abstractTools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function. However, determining the surface potential for large biomolecules on a typical desktop computer can take days or longer using currently available tools and methods. This paper demonstrates how one can take advantage of graphic processing units (GPUs) available in today’s typical desktop computer, together with a multiscale approximation method, to significantly speedup such computations. Specifically, the electrostatic potential computation, using an analytical linearized Poisson Boltzmann (ALPB) method, is implemented on an ATI Radeon 4870 GPU in combination with the hierarchical charge partitioning (HCP) multiscale approximation. This implementation delivers a combined 1800-fold speedup for a 476,040 atom viral capsid.en
dc.format.mimetypeapplication/pdfen
dc.identifierhttp://eprints.cs.vt.edu/archive/00001081/en
dc.identifier.sourceurlhttp://eprints.cs.vt.edu/archive/00001081/01/gpu.pdfen
dc.identifier.trnumberTR-09-15en
dc.identifier.urihttp://hdl.handle.net/10919/20295en
dc.language.isoenen
dc.publisherDepartment of Computer Science, Virginia Polytechnic Institute & State Universityen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectBioinformaticsen
dc.titleAccelerating Electrostatic Surface Potential Calculation with Multiscale Approximation on Graphics Processing Unitsen
dc.typeTechnical reporten
dc.type.dcmitypeTexten

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