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Stiffness detection and reduction in discrete stochastic simulation of biochemical systems.
- Source :
-
Journal of Chemical Physics . 2/7/2011, Vol. 134 Issue 5, p054105. 10p. 5 Diagrams, 1 Chart, 6 Graphs. - Publication Year :
- 2011
-
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. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 00219606
- Volume :
- 134
- Issue :
- 5
- Database :
- Academic Search Index
- Journal :
- Journal of Chemical Physics
- Publication Type :
- Academic Journal
- Accession number :
- 57854981
- Full Text :
- https://doi.org/10.1063/1.3548838