S-leaping: an adaptive, accelerated stochastic simulation algorithm, bridging -leaping and R-leaping

DOI10.1007/S11538-018-0464-9MaRDI QIDQ2325575zbMATH OpenOpenAlexWikidataFDO

Authors Jana Lipková, Georgios Arampatzis, Philippe Chatelain, Bjoern Menze, Petros Koumoutsakos

Publication date 26 September 2019

Published in Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1802.00296

zbMATH Keywords

accelerated simulationstiff systemsstochastic simulation algorithms

Mathematics Subject Classification ID

Computational methods for stochastic equations (aspects of stochastic analysis) (60H35) Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Abstract: We propose the $S$-leaping algorithm for the acceleration of Gillespie's stochastic simulation algorithm that combines the advantages of the two main accelerated methods; the $au$-leaping and $R$-leaping algorithms. These algorithms are known to be efficient under different conditions; the $au$-leaping is efficient for non-stiff systems or systems with partial equilibrium, while the $R$-leaping performs better in stiff system thanks to an efficient sampling procedure. However, even a small change in a system's set up can critically affect the nature of the simulated system and thus reduce the efficiency of an accelerated algorithm. The proposed algorithm combines the efficient time step selection from the $au$-leaping with the effective sampling procedure from the $R$-leaping algorithm. The $S$-leaping is shown to maintain its efficiency under different conditions and in the case of large and stiff systems or systems with fast dynamics, the $S$-leaping outperforms both methods. We demonstrate the performance and the accuracy of the $S$-leaping in comparison with the $au$-leaping and $R$-leaping on a number of benchmark systems involving biological reaction networks.

Recommendations

• \(L\)-leap: Accelerating the stochastic simulation of chemically reacting systems
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Cites work

• Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems
• Adaptive mesh refinement for stochastic reaction-diffusion processes
• Analysis of Brownian dynamics simulations of reversible bimolecular reactions
• Inverse Gillespie for inferring stochastic reaction mechanisms from intermittent samples
• Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
• Multiscale stochastic simulations of chemical reactions with regulated scale separation

Cited in

(7)

• Stochastic simulation of biochemical systems: in memory of Dan T. Gillespie's contributions
• The DFAPS-leaping algorithm for the biochemical reaction systems with delays
• Efficient unbiased -leap methods for simulating coupled chemical reactions
• Boosted hybrid method for solving chemical reaction systems with multiple scales in time and population size
• Exploring the performance of spatial stochastic simulation algorithms
• Modelling catastrophic extinction in stochastic birth-death process: analytical insights, estimation, and efficient simulation
• Slow-scale tau-leaping method

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