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


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.

SUBMITTER: Pu Y 

PROVIDER: S-EPMC3045418 | BioStudies | 2011-01-01

REPOSITORIES: biostudies

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