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IPPS
2009
IEEE

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

14 years 6 months ago
Long time-scale simulations of in vivo diffusion using GPU hardware
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 threedimensional 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.
Elijah Roberts, John E. Stone, Leonardo Sepulveda,
Added 24 May 2010
Updated 24 May 2010
Type Conference
Year 2009
Where IPPS
Authors Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-mei W. Hwu, Zaida Luthey-Schulten
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