Accelerating Algorithm for Biochemical Reaction Systems with Multiple Delays
Pages 39 - 43
Abstract
Delay in the study of biochemical reaction system can't be ignored and the complex time delay systems are integrated to get the multiple time delayed biochemical reactions. An improved acceleration algorithm based on MD-Leaping algorithm for multi-delayed biochemical reaction systems is proposed in this paper. The number of the waiting records generated during the operation of the MD-Leaping algorithm slows down its rate. We use a novel method that can reduce the size of the wait queue to add the wait records. The new algorithm greatly reduces the memory requirements without losing accuracy and runs faster. At last, this paper makes a numerical simulation analysis of a multiple time delayed model, and this case further demonstrates the accuracy and efficiency of the proposed algorithm.
References
[1]
Gillespie, D. T. 1976. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comp. Phys. 22(4): 403--434.
[2]
Lewin, B. 2000. Genes VII. USA: Oxford University Press.
[3]
Barrio, M., Burrage, K., Leier, A. and Tian, A. T. 2006. Oscillatory regulation of hes1: discrete stochastic delay modelling and simulation. Plos. Comp. Biol. 2(9):e117.
[4]
Bratsun, D., Volfson, D., Tsimring, L.S. and Hasty, J. 2005. Delay-induced stochastic oscillations in gene regulation. Proc. Natl. Acad. Sci. USA. 102(41): 14593--14598.
[5]
Cai, X. D. 2007. Exact stochastic simulation of coupled chemical reactions with delays. J. Comp. Phys. 126(12): 124108.
[6]
Tian, T. H. and Burrage, K. 2004. Binomial leap methods for simulating stochastic chemical kinetics. J. Comp. Phys. 121(21): 10356.
[7]
Peng, X., Zhou, W. and Wang, Y. F. 2007. Efficient binomial leap method for simulating chemical kinetics. J. Comp. Phys. 126(22): 224109.
[8]
Leier, A., Marque-Lago, T. T. and Burrage, K. 2008. Generalized binomial tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise. J. Comp. Phys. 128(20): 4861.
[9]
Bayati, B., Chatelain, P. and Koumoutsakos, P. 2009. D-leaping: Accelerating stochastic simulation algorithms for reactions with delays. J. Comp. Phys. 228(16): 5908--5916.
[10]
Yi, N., Zhuang, G., Da, L. and Wang, Y. F. 2012. Improved delay-leaping simulation algorithm for biochemical reaction systems with delays. J. Comp. Phys. 136(14): 144108.
[11]
Zhu, R., Ribeirob, A. S., Salahub, D. and Kauffman, S. A. 2007. Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models. J. Theor. Biol. 246(4):725--745.
[12]
Thanh, V. H., Priami, C. and Zunio, R. 2014. Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays. J. Comp. Phys. 141(13):134116.
[13]
Thanh, V. H. and Priami, C. 2015. Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm. J. Comp. Phys. 143(5):054104.
[14]
Roussel, M. R. and Zhu, R. 2006. Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression. Phys. Biol. 3(4): 274--284.
[15]
Ribeiro, A. S. 2010. Stochastic and delayed stochastic models of gene expression and regulation. Math. Bios. 221(1):1--11.
[16]
Zhuang, G., Yi, N., Da, L. and Wang, Y. F. 2013. MD-Leaping algorithm for multi-delayed biochemical reaction systems. J. Shanghai Univ. 19(1): 75--79.
[17]
Cao, Y., Gillespie, D.T. and Petzold, L. R. 2006. Efficient step size selection for the tau-leaping simulation method. J. Comp. Phys. 124(4): 044109.
Index Terms
- Accelerating Algorithm for Biochemical Reaction Systems with Multiple Delays
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May 2017
123 pages
ISBN:9781450348799
DOI:10.1145/3093293
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In-Cooperation
- Department of Computer Science, University of Szeged: Department of Computer Science, University of Szeged
- University of Lisbon: University of Lisbon
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Association for Computing Machinery
New York, NY, United States
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Published: 14 May 2017
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ICBBT '17
ICBBT '17: 9th International Conference on Bioinformatics and Biomedical Technology
May 14 - 16, 2017
Lisbon, Portugal
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