Exploring the performance of spatial stochastic simulation algorithms

Jeschke, Matthias and Ewald, Roland and Uhrmacher, Adelinde M. (2011) Exploring the performance of spatial stochastic simulation algorithms. Journal of Computational Physics, 230 (7), pp. 2562-2574. ISSN 0021-9991.

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Official URL: http://dx.doi.org/10.1016/j.jcp.2010.12.030


Since the publication of Gillespie’s direct method, diverse methods have been developed to improve the performance of stochastic simulation methods and to enter the spatial realm. In this paper we discuss a spatial τ-leaping variant (Sτ) that extends the basic leap method. Sτ takes reaction and both outgoing and incoming diffusion events into account when calculating a leap candidate. A performance analysis shall reveal details on the achieved success in balancing speed and accuracy in comparison to other methods. However, performance analysis of spatial stochastic algorithms requires significant effort — it is crucial to choose suitable (benchmark) models and to carefully define model and simulation setups that take problem and simulation design spaces into account.

Item Type: Article
Projects: DiErMoSiS, GRK dIEM oSiRiS, VASSiB