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

Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-Mei W. Hwu, Zaida Luthey-Schulten
Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA
IEEE International Symposium on Parallel & Distributed Processing, 2009. IPDPS 2009.

@conference{roberts2009long,

   title={Long time-scale simulations of in vivo diffusion using GPU hardware},

   author={Roberts, E. and Stone, J.E. and Sep{‘u}lveda, L. and Hwu, W.M.W. and Luthey-Schulten, Z.},

   booktitle={Parallel & Distributed Processing, 2009. IPDPS 2009. IEEE International Symposium on},

   pages={1–8},

   issn={1530-2075},

   year={2009},

   organization={IEEE}

}

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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.
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