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  4. Optimal explicit stabilized postprocessed τ-leap method for the simulation of chemical kinetics
 
research article

Optimal explicit stabilized postprocessed τ-leap method for the simulation of chemical kinetics

Abdulle, Assyr  
•
Gander, Lia
•
de Souza, Giacomo Rosilho  
September 13, 2023
Journal Of Computational Physics

The simulation of chemical kinetics involving multiple scales constitutes a modeling challenge (from ordinary differential equations to Markov chains) and a computational challenge (multiple scales, large dynamical systems, time step restrictions). In this paper, we propose a new discrete stochastic simulation algorithm: the postprocessed second kind stabilized orthogonal τ-leap Runge-Kutta method (PSK-τ-ROCK). In the context of chemical kinetics, this method can be seen as a stabilization of Gillespie's explicit τ-leap algorithm combined with a postprocessor. The stabilized procedure allows to simulate problems with multiple scales (stiff), while the postprocessing procedure allows to approximate the invariant measure (e.g. mean and variance) of ergodic stochastic dynamical systems. We prove stability and accuracy of the PSK-τ-ROCK for a reference system. Numerical experiments illustrate the high reliability and efficiency of the scheme when compared to other τ-leap methods.

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Type
research article
DOI
10.1016/j.jcp.2023.112482
Web of Science ID

WOS:001079097100001

Author(s)
Abdulle, Assyr  
Gander, Lia
de Souza, Giacomo Rosilho  
Date Issued

2023-09-13

Publisher

Academic Press Inc Elsevier Science

Published in
Journal Of Computational Physics
Volume

493

Article Number

112482

Subjects

Technology

•

Physical Sciences

•

Tau-Leap Methods

•

Explicit Stabilized Methods

•

Discrete Noise

•

Chemical Reaction Systems

•

Postprocessor

•

Invariant Measure

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
ANMC  
FunderGrant Number

Swiss National Science Foundation

200020_172710

Swiss National Science Foundation (SNF)

200020_172710

Available on Infoscience
February 14, 2024
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/203717
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