1. Accurate Reaction-Diffusion Operator Splitting on Tetrahedral Meshes for Parallel Stochastic Molecular Simulations
- Author
-
Hepburn, I., Chen, W., and De Schutter, E.
- Subjects
Quantitative Biology - Quantitative Methods ,Computer Science - Distributed, Parallel, and Cluster Computing ,Physics - Biological Physics ,Physics - Chemical Physics ,Quantitative Biology - Biomolecules - 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., Comment: 33 pages, 10 figures
- Published
- 2015
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