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Matthias Jeschke, Alfred Park, Roland Ewald, Richard Fujimoto, and Adelinde M Uhrmacher (2008)

Parallel and Distributed Spatial Simulation of Chemical Reactions

In: Proceedings of the 22nd ACM/IEEE/SCS Workshop on Principles of Advanced and Distributed Simulation (PADS 2008), pp. 51-59.

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 cell-biological 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 a 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, and conduct a thorough performance analysis in the context of a grid-inspired simulation system called Aurora.

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