Asynchronous τ-leaping

Zbigniew Jȩdrzejewski-Szmek

doi:10.1063/1.4944575

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Asynchronous τ-leaping

2016-03-28

Zbigniew Jȩdrzejewski-Szmek

Kim T. Blackwell *

DOI：10.1063/1.4944575

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Abstract

En 中文

Stochastic simulation of cell signaling pathways and genetic regulatory networks has contributed to the understanding of cell function; however, investigation of larger, more complicated systems requires computationally efficient algorithms. tau-leaping methods, which improve efficiency when some molecules have high copy numbers, either use a fixed leap size, which does not adapt to changing state, or recalculate leap size at a heavy computational cost. We present a hybrid simulation method for reaction-diffusion systems which combines exact stochastic simulation and tau-leaping in a dynamic way. Putative times of events are stored in a priority queue, which reduces the cost of each step of the simulation. For every reaction and diffusion channel at each step of the simulation the more efficient of an exact stochastic event or a tau-leap is chosen. This new approach removes the inherent trade-off between speed and accuracy in stiff systems which was present in all tau-leaping methods by allowing each reaction channel to proceed at its own pace. Both directions of reversible reactions and diffusion are combined in a single event, allowing bigger leaps to be taken. This improves efficiency for systems near equilibrium where forward and backward events are approximately equally frequent. Comparison with existing algorithms and behaviour for five test cases of varying complexity shows that the new method is almost as accurate as exact stochastic simulation, scales well for large systems, and for various problems can be significantly faster than tau-leaping. (C) 2016 AIP Publishing LLC.

Keywords:

ACCELERATED STOCHASTIC SIMULATION

SIZE SELECTION

ALGORITHM

KINETICS

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