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Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods


Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods. Journal of Chemical Physics, 135(24):244103.

Abstract

Stochastic reaction-di usion systems frequently exhibit behavior that is not predicted by deterministic simulation models. Stochastic simulation methods, however, are computationally expensive. We present a more efficient stochastic reaction-di usion simulation algorithm that samples realizations from the exact solution of the reaction-di usion master equation. The present algorithm, called Partial-propensity Stochastic Reaction-Di usion (PSRD) method, uses an on-lattice discretization of the reaction-di usion system and relies on partial-propensity methods for computational efficiency. We describe the algorithm in detail, provide a theoretical analysis of its computational cost, and demonstrate its computational performance in benchmarks. We then illustrate the application of PSRD to two- and three-dimensional pattern-forming Gray-Scott systems, highlighting the role of intrinsic noise in these systems.

Abstract

Stochastic reaction-di usion systems frequently exhibit behavior that is not predicted by deterministic simulation models. Stochastic simulation methods, however, are computationally expensive. We present a more efficient stochastic reaction-di usion simulation algorithm that samples realizations from the exact solution of the reaction-di usion master equation. The present algorithm, called Partial-propensity Stochastic Reaction-Di usion (PSRD) method, uses an on-lattice discretization of the reaction-di usion system and relies on partial-propensity methods for computational efficiency. We describe the algorithm in detail, provide a theoretical analysis of its computational cost, and demonstrate its computational performance in benchmarks. We then illustrate the application of PSRD to two- and three-dimensional pattern-forming Gray-Scott systems, highlighting the role of intrinsic noise in these systems.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Research, Technology and Development Projects > LipidX
Special Collections > SystemsX.ch > Research, Technology and Development Projects > WingX
Special Collections > SystemsX.ch > Research, Technology and Development Projects
Dewey Decimal Classification:570 Life sciences; biology
Date:2011
Deposited On:05 Jul 2013 10:46
Last Modified:07 Dec 2017 21:38
Publisher:American Institute of Physics
ISSN:0021-9606
Publisher DOI:https://doi.org/10.1063/1.3666988
PubMed ID:22225140

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