An efficient hybrid method for stochastic reaction-diffusion biochemical systems with delay
Many chemical reactions, such as gene transcription and translation in living cells, need a certain time to finish once they are initiated. Simulating stochastic models of reaction-diffusion systems with delay can be computationally expensive. In the present paper, a novel hybrid algorithm is propos...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
AIP Publishing LLC
2017-12-01
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| Series: | AIP Advances |
| Online Access: | http://dx.doi.org/10.1063/1.5001760 |
| Summary: | Many chemical reactions, such as gene transcription and translation in living cells, need a certain time to finish once they are initiated. Simulating stochastic models of reaction-diffusion systems with delay can be computationally expensive. In the present paper, a novel hybrid algorithm is proposed to accelerate the stochastic simulation of delayed reaction-diffusion systems. The delayed reactions may be of consuming or non-consuming delay type. The algorithm is designed for moderately stiff systems in which the events can be partitioned into slow and fast subsets according to their propensities. The proposed algorithm is applied to three benchmark problems and the results are compared with those of the delayed Inhomogeneous Stochastic Simulation Algorithm. The numerical results show that the new hybrid algorithm achieves considerable speed-up in the run time and very good accuracy. |
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| ISSN: | 2158-3226 |