title: Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations.
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, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.
authors: Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan.
authors: I
authors: I
authors: Hepburn
authors: Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan.
authors: W
authors: W
authors: Chen
authors: Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan.
authors: E
authors: E
authors: De Schutter
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D000242:Cyclic AMP / Q000737:chemistry; D004058:Diffusion; D004926:Escherichia coli; D008958:Models, Molecular; D013269:Stochastic Processes; D013997:Time Factors
chemical_list: D000242:Cyclic AMP