Literature DB >> 15606235

The numerical stability of leaping methods for stochastic simulation of chemically reacting systems.

Yang Cao1, Linda R Petzold, Muruhan Rathinam, Daniel T Gillespie.   

Abstract

Tau-leaping methods have recently been proposed for the acceleration of discrete stochastic simulation of chemically reacting systems. This paper considers the numerical stability of these methods. The concept of stochastic absolute stability is defined, discussed, and applied to the following leaping methods: the explicit tau, implicit tau, and trapezoidal tau. (c) 2004 American Institute of Physics.

Year:  2004        PMID: 15606235     DOI: 10.1063/1.1823412

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  10 in total

1.  Understanding intracellular transport processes pertinent to synthetic gene delivery via stochastic simulations and sensitivity analyses.

Authors:  Anh-Tuan Dinh; Chinmay Pangarkar; Theo Theofanous; Samir Mitragotri
Journal:  Biophys J       Date:  2006-11-03       Impact factor: 4.033

2.  Algorithms and software for stochastic simulation of biochemical reacting systems.

Authors:  Hong Li; Yang Cao; Linda R Petzold; Daniel T Gillespie
Journal:  Biotechnol Prog       Date:  2007-09-26

3.  Stochastic simulation of enzyme-catalyzed reactions with disparate timescales.

Authors:  Debashis Barik; Mark R Paul; William T Baumann; Yang Cao; John J Tyson
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

4.  Exploration of effective potential landscapes using coarse reverse integration.

Authors:  Thomas A Frewen; Gerhard Hummer; Ioannis G Kevrekidis
Journal:  J Chem Phys       Date:  2009-10-07       Impact factor: 3.488

5.  Stiffness detection and reduction in discrete stochastic simulation of biochemical systems.

Authors:  Yang Pu; Layne T Watson; Yang Cao
Journal:  J Chem Phys       Date:  2011-02-07       Impact factor: 3.488

6.  Perspective: Stochastic algorithms for chemical kinetics.

Authors:  Daniel T Gillespie; Andreas Hellander; Linda R Petzold
Journal:  J Chem Phys       Date:  2013-05-07       Impact factor: 3.488

7.  Stochastic regulation in early immune response.

Authors:  Tomasz Lipniacki; Pawel Paszek; Allan R Brasier; Bruce A Luxon; Marek Kimmel
Journal:  Biophys J       Date:  2005-11-11       Impact factor: 4.033

8.  Ensembles of signal transduction models using Pareto Optimal Ensemble Techniques (POETs).

Authors:  Sang Ok Song; Anirikh Chakrabarti; Jeffrey D Varner
Journal:  Biotechnol J       Date:  2010-07       Impact factor: 4.677

9.  Simulation methods with extended stability for stiff biochemical Kinetics.

Authors:  Pau Rué; Jordi Villà-Freixa; Kevin Burrage
Journal:  BMC Syst Biol       Date:  2010-08-11

10.  Quasi-Monte Carlo Methods Applied to Tau-Leaping in Stochastic Biological Systems.

Authors:  Casper H L Beentjes; Ruth E Baker
Journal:  Bull Math Biol       Date:  2018-05-25       Impact factor: 1.758

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.