Michaelis–Menten speeds up tau-leaping under a wide range of conditions
نویسندگان
چکیده
منابع مشابه
Michaelis-Menten speeds up tau-leaping under a wide range of conditions.
This paper examines the benefits of Michaelis-Menten model reduction techniques in stochastic tau-leaping simulations. Results show that although the conditions for the validity of the reductions for tau-leaping remain the same as those for the stochastic simulation algorithm (SSA), the reductions result in a substantial speed-up for tau-leaping under a different range of conditions than they d...
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For chemical systems involving both fast and slow scales, stiffness presents challenges for efficient stochastic simulation. Two different avenues have been explored to solve this problem. One is the slow-scale stochastic simulation (ssSSA) based on the stochastic partial equilibrium assumption. The other is the tau-leaping method. In this paper we propose a new algorithm, the slow-scale tau-le...
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Tau-leaping is a popular discretization method for generating approximate paths of continuous time, discrete space, Markov chains, notably for biochemical reaction systems. To compute expected values in this context, an appropriate multilevel Monte Carlo form of tau-leaping has been shown to improve efficiency dramatically. In this work we derive new analytic results concerning the computationa...
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We propose the S-leaping algorithm for the acceleration of Gillespie’s stochastic simulation algorithm that combines the advantages of the two main accelerated methods; the τ -leaping and R-leaping algorithms. These algorithms are known to be efficient under different conditions; the τ -leaping is efficient for non-stiff systems or systems with partial equilibrium, while the R-leaping performs ...
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The existing tau-selection strategy, which was designed for explicit tau leaping, is here modified to apply to implicit tau leaping, allowing for longer steps when the system is stiff. Further, an adaptive strategy that identifies stiffness and automatically chooses between the explicit and the (new) implicit tau-selection methods to achieve better efficiency is proposed. Numerical testing demo...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2011
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.3576123