Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-mei W. Hwu, and Zaida
Luthey-Schulten.
Long time-scale simulations of in vivo diffusion using GPU
hardware.
In Proceedings of the IEEE International Parallel &
Distributed Processing Symposium, pp. 1-8, 2009.
ROBE2009-ZLS
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.
