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Title: D-leaping: Accelerating stochastic simulation algorithms for reactions with delays

Abstract

We propose a novel, accelerated algorithm for the approximate stochastic simulation of biochemical systems with delays. The present work extends existing accelerated algorithms by distributing, in a time adaptive fashion, the delayed reactions so as to minimize the computational effort while preserving their accuracy. The accuracy of the present algorithm is assessed by comparing its results to those of the corresponding delay differential equations for a representative biochemical system. In addition, the fluctuations produced from the present algorithm are comparable to those from an exact stochastic simulation with delays. The algorithm is used to simulate biochemical systems that model oscillatory gene expression. The results indicate that the present algorithm is competitive with existing works for several benchmark problems while it is orders of magnitude faster for certain systems of biochemical reactions.

Authors:
;  [1];  [1]
  1. Chair of Computational Science, ETH Zurich, CH-8092 (Switzerland)
Publication Date:
OSTI Identifier:
21308107
Resource Type:
Journal Article
Journal Name:
Journal of Computational Physics
Additional Journal Information:
Journal Volume: 228; Journal Issue: 16; Other Information: DOI: 10.1016/j.jcp.2009.05.004; PII: S0021-9991(09)00243-5; Copyright (c) 2009 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0021-9991
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; ACCURACY; ALGORITHMS; APPROXIMATIONS; BENCHMARKS; DIFFERENTIAL EQUATIONS; FLUCTUATIONS; SIMULATION; STOCHASTIC PROCESSES; TIME DELAY

Citation Formats

Bayati, Basil, Chatelain, Philippe, and Koumoutsakos, Petros. D-leaping: Accelerating stochastic simulation algorithms for reactions with delays. United States: N. p., 2009. Web. doi:10.1016/j.jcp.2009.05.004.
Bayati, Basil, Chatelain, Philippe, & Koumoutsakos, Petros. D-leaping: Accelerating stochastic simulation algorithms for reactions with delays. United States. https://doi.org/10.1016/j.jcp.2009.05.004
Bayati, Basil, Chatelain, Philippe, and Koumoutsakos, Petros. 2009. "D-leaping: Accelerating stochastic simulation algorithms for reactions with delays". United States. https://doi.org/10.1016/j.jcp.2009.05.004.
@article{osti_21308107,
title = {D-leaping: Accelerating stochastic simulation algorithms for reactions with delays},
author = {Bayati, Basil and Chatelain, Philippe and Koumoutsakos, Petros},
abstractNote = {We propose a novel, accelerated algorithm for the approximate stochastic simulation of biochemical systems with delays. The present work extends existing accelerated algorithms by distributing, in a time adaptive fashion, the delayed reactions so as to minimize the computational effort while preserving their accuracy. The accuracy of the present algorithm is assessed by comparing its results to those of the corresponding delay differential equations for a representative biochemical system. In addition, the fluctuations produced from the present algorithm are comparable to those from an exact stochastic simulation with delays. The algorithm is used to simulate biochemical systems that model oscillatory gene expression. The results indicate that the present algorithm is competitive with existing works for several benchmark problems while it is orders of magnitude faster for certain systems of biochemical reactions.},
doi = {10.1016/j.jcp.2009.05.004},
url = {https://www.osti.gov/biblio/21308107}, journal = {Journal of Computational Physics},
issn = {0021-9991},
number = 16,
volume = 228,
place = {United States},
year = {Tue Sep 01 00:00:00 EDT 2009},
month = {Tue Sep 01 00:00:00 EDT 2009}
}