D-leaping: accelerating stochastic simulation algorithms for reactions with delays

DOI10.1016/J.JCP.2009.05.004MaRDI QIDQ834135zbMATH OpenOpenAlexWikidataFDO

Authors Basil Bayati, Philippe Chatelain, Petros Koumoutsakos

Publication date 19 August 2009

Published in Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jcp.2009.05.004

zbMATH Keywords

stochastic simulationdelayed reactionsR-leapingTau-leaping

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Qualitative investigation and simulation of models involving functional-differential equations (34K60) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

Recommendations

• The DFAPS-leaping algorithm for the biochemical reaction systems with delays
• Accelerated stochastic simulation algorithm for coupled chemical reactions with delays
• Efficient unbiased \(\tau\)-leap methods for simulating coupled chemical reactions
• \(L\)-leap: Accelerating the stochastic simulation of chemically reacting systems
• A new approach to simulating stochastic delayed systems

Cites work

• Dissecting the dynamics of the Hes1 genetic oscillator
• Stochastic processes in physics and chemistry.

Cited in

(8)

• The DFAPS-leaping algorithm for the biochemical reaction systems with delays
• Accelerated stochastic simulation algorithm for coupled chemical reactions with delays
• Delay stochastic simulation of biological systems: a purely delayed approach
• Error analysis for D-leaping scheme of chemical reaction system with delay
• Discrete Modeling of Biochemical Signaling with Memory Enhancement
• A new approach to simulating stochastic delayed systems
• Ergodic approximation to chemical reaction system with delay
• The nondeterministic waiting time algorithm: a review

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