Stiffness detection and reduction in discrete stochastic simulation of biochemical systems

TitleStiffness detection and reduction in discrete stochastic simulation of biochemical systems
Publication TypeJournal Article
Year of Publication2011
AuthorsPu, Y., L. T. Watson, and Y. Cao
JournalJOURNAL OF CHEMICAL PHYSICS
Volume134
Issue5
Date PublishedFEB 7
Type of ArticleArticle
ISSN0021-9606
Abstract

{Typical multiscale biochemical models contain fast-scale and slow-scale reactions, where ``fast{''} reactions fire much more frequently than ``slow{''} ones. This feature often causes stiffness in discrete stochastic simulation methods such as Gillespie's algorithm and the Tau-Leaping method leading to inefficient simulation. This paper proposes a new strategy to automatically detect stiffness and identify species that cause stiffness for the Tau-Leaping method, as well as two stiffness reduction methods. Numerical results on a stiff decaying dimerization model and a heat shock protein regulation model demonstrate the efficiency and accuracy of the proposed methods for multiscale biochemical systems. (C) 2011 American Institute of Physics. {[}doi:10.1063/1.3548838]}

DOI10.1063/1.3548838