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arXiv · 1512.03126

Accurate Reaction-Diffusion Operator Splitting on Tetrahedral Meshes for Parallel Stochastic Molecular Simulations

I. Hepburn·W. Chen·E. De Schutter
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Abstract

Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in sub-cellular models. This calls for parallel simulations that can take advantage of the power of modern supercomputers; however exact methods are known to be inherently serial. We introduce an operator splitting implementation for irregular grids with a novel method to improve accuracy, and demonstrate potential for scalable parallel simulations in an initial MPI version. We foresee that this groundwork will enable larger scale, whole-cell stochastic simulations in the near future.

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I. Hepburn, W. Chen, E. De Schutter. 2015-12-10. Accurate Reaction-Diffusion Operator Splitting on Tetrahedral Meshes for Parallel Stochastic Molecular Simulations. https://doi.org/10.1063/1.4960034

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