Accurate Reaction-Diffusion Operator Splitting on Tetrahedral Meshes for Parallel Stochastic Molecular Simulations
arXiv:1512.03126 · doi:10.1063/1.4960034
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.
arXiv comment33 pages, 10 figures
References in corpus (4)
- Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions
- Simulation of stochastic reaction-diffusion processes on unstructured meshes
- Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm
- Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting