Parallel and Distributed Spatial Simulation of Chemical Reactions

Matthias Jeschke, Alfred Park, Roland Ewald, Richard Fujimoto, Adelinde M. Uhrmacher
2008 2008 22nd Workshop on Principles of Advanced and Distributed Simulation  
The application of parallel and distributed simulation techniques is often limited by the amount of parallelism available in the model. This holds true for large-scale cellbiological simulations, a field that has emerged as data and knowledge concerning these systems increases and biologists call for tools to guide wet-lab experimentation. A promising approach to exploit parallelism in this domain is the integration of spatial aspects, which are often crucial to a model's validity. We describe
more » ... n optimistic, parallel and distributed variant of the Next-Subvolume Method (NSM), a method that augments the well-known Gillespie Stochastic Simulation Algorithm (SSA) with spatial features. We discuss requirements imposed by this application on a parallel discrete event simulation engine to achieve efficient execution. First results of combining NSM and the grid-inspired simulation system AURORA are shown. 22nd Workshop on Principles of Advanced and Distributed Simulation
doi:10.1109/pads.2008.20 dblp:conf/pads/JeschkePEFU08 fatcat:jzsqtvpytba2tkujfxd74cqq2q