# COAST: Controllable approximative stochastic reaction algorithm

Wagner H, Moeller M, Prank K (2006)

JOURNAL OF CHEMICAL PHYSICS 125(17).

*Journal Article*|

*Published*|

*English*

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Author

Wagner, Holger
;
Moeller, Mark
;
Prank, Klaus

Abstract

We present an approximative algorithm for stochastic simulations of chemical reaction systems, called COAST, based on three different modeling levels: for small numbers of particles an exact stochastic model; for intermediate numbers an approximative, but computationally more efficient stochastic model based on discrete Gaussian distributions; and for large numbers the deterministic reaction kinetics. In every simulation time step, the subdivision of the reaction channels into the three different modeling levels is done automatically, where all approximations applied can be controlled by a single error parameter for which an appropriate value can easily be found. Test simulations show that the results of COAST simulations agree well with the outcomes of exact algorithms; however, the asymptotic run times of COAST are asymptotically proportional to smaller powers of the particle numbers than exact algorithms. (c) 2006 American Institute of Physics.

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### Cite this

Wagner H, Moeller M, Prank K. COAST: Controllable approximative stochastic reaction algorithm.

*JOURNAL OF CHEMICAL PHYSICS*. 2006;125(17).Wagner, H., Moeller, M., & Prank, K. (2006). COAST: Controllable approximative stochastic reaction algorithm.

*JOURNAL OF CHEMICAL PHYSICS*,*125*(17).Wagner, H., Moeller, M., and Prank, K. (2006). COAST: Controllable approximative stochastic reaction algorithm.

*JOURNAL OF CHEMICAL PHYSICS*125.Wagner, H., Moeller, M., & Prank, K., 2006. COAST: Controllable approximative stochastic reaction algorithm.

*JOURNAL OF CHEMICAL PHYSICS*, 125(17).H. Wagner, M. Moeller, and K. Prank, “COAST: Controllable approximative stochastic reaction algorithm”,

*JOURNAL OF CHEMICAL PHYSICS*, vol. 125, 2006.Wagner, H., Moeller, M., Prank, K.: COAST: Controllable approximative stochastic reaction algorithm. JOURNAL OF CHEMICAL PHYSICS. 125, (2006).

Wagner, Holger, Moeller, Mark, and Prank, Klaus. “COAST: Controllable approximative stochastic reaction algorithm”.

*JOURNAL OF CHEMICAL PHYSICS*125.17 (2006).
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### 3 Citations in Europe PMC

Data provided by Europe PubMed Central.

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PMID: 19518479

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Biochemical simulations: stochastic, approximate stochastic and hybrid approaches.

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### 19 References

Data provided by Europe PubMed Central.

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

Hybrid simulation of cellular behavior.

Kiehl TR, Mattheyses RM, Simmons MK.,

PMID: 14960457

Kiehl TR, Mattheyses RM, Simmons MK.,

*Bioinformatics*20(3), 2004PMID: 14960457

AUTHOR UNKNOWN, 0

A multi-algorithm, multi-timescale method for cell simulation.

Takahashi K, Kaizu K, Hu B, Tomita M.,

PMID: 14990450

Takahashi K, Kaizu K, Hu B, Tomita M.,

*Bioinformatics*20(4), 2004PMID: 14990450

Grid cellware: the first grid-enabled tool for modelling and simulating cellular processes.

Dhar PK, Meng TC, Somani S, Ye L, Sakharkar K, Krishnan A, Ridwan AB, Wah SH, Chitre M, Hao Z.,

PMID: 15546936

Dhar PK, Meng TC, Somani S, Ye L, Sakharkar K, Krishnan A, Ridwan AB, Wah SH, Chitre M, Hao Z.,

*Bioinformatics*21(7), 2005PMID: 15546936

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

Mechanisms of noise-resistance in genetic oscillators.

Vilar JM, Kueh HY, Barkai N, Leibler S.,

PMID: 11972055

Vilar JM, Kueh HY, Barkai N, Leibler S.,

*Proc. Natl. Acad. Sci. U.S.A.*99(9), 2002PMID: 11972055

Box,

*Ann. Math. Stat.*29(), 1958

AUTHOR UNKNOWN, 0

Buchner,

*Elemente der Mathematik*6(), 1951

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

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