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EFFICIENT PARALLELIZATION OF STOCHASTIC SIMULATION ALGORITHM FOR CHEMICALLY REACTING SYSTEMS ON THE GRAPHICS PROCESSING UNIT

  • Author(s): Li, Hong
  • Petzold, Linda
  • et al.
Abstract

The small number of some reactant molecules in biological systems formed by living cells can result in dynamical behavior which cannot be captured by traditional deterministic models. In such a problem, a more accurate simulation can be obtained with discrete stochastic simulation (Gillespie's stochastic simulation algorithm – SSA). Many stochastic realizations are required to capture accurate statistical information of the solution. This carries a very high computational cost. The current generation of graphics processing units (GPU) is well-suited to this task. In this paper we describe our implementation and present some computational experiments illustrating the power of this technology for this important and challenging class of problems.

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