Long time-scale simulations of in vivo diffusion using GPU hardware

Elijah Roberts, John E. Stone, Leonardo Sepúlveda, Wen-Mei W Hwu, Zaida Ann Luthey-Schulten

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

Abstract

To address the problem of performing long time simulations of biochemical pathways under in vivo cellular conditions, we have developed a lattice-based, reaction-diffusion model that uses the graphics processing unit (GPU) as a computational co-processor. The method has been specifically designed from the beginning to take advantage of the GPU's capacity to perform massively parallel calculations by not only executing a core set of mathematical calculations, but also running much of the underlying algorithmic logic on the GPU. In this study we present our three-dimensional model for in vivo diffusion that exploits the calculation capabilities of the GPU. The implementation of the diffusion operator on the GPU is subject to architectural constraints, and we discuss its structure and the trade-offs made to accommodate the GPU hardware.

Original languageEnglish (US)
Title of host publicationIPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium
DOIs
StatePublished - Nov 25 2009
Event23rd IEEE International Parallel and Distributed Processing Symposium, IPDPS 2009 - Rome, Italy
Duration: May 23 2009May 29 2009

Publication series

NameIPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium

Other

Other23rd IEEE International Parallel and Distributed Processing Symposium, IPDPS 2009
CountryItaly
CityRome
Period5/23/095/29/09

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Hardware and Architecture
  • Software

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  • Cite this

    Roberts, E., Stone, J. E., Sepúlveda, L., Hwu, W-M. W., & Luthey-Schulten, Z. A. (2009). Long time-scale simulations of in vivo diffusion using GPU hardware. In IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium [5160930] (IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium). https://doi.org/10.1109/IPDPS.2009.5160930