A Constrained Approach to Multiscale Stochastic Simulation of Chemically Reacting Systems
| Autor: | Ioannis G. Kevrekidis, Simon L. Cotter, Konstantinos C. Zygalakis, Radek Erban |
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| Rok vydání: | 2016 |
| Předmět: |
Computer science
Computation General Physics and Astronomy Physics and Astronomy(all) 01 natural sciences 03 medical and health sciences 0103 physical sciences Stochastic simulation Computer Simulation Statistical physics Physical and Theoretical Chemistry Diffusion (business) 030304 developmental biology Variable (mathematics) Medicine(all) Stochastic Processes 0303 health sciences 010304 chemical physics Stochastic process Fokker-Planck equation Conditional probability distribution molecular dynamics method Models Chemical Fokker–Planck equation reaction kinetics stochastic processes Realization (systems) Algorithms |
| Zdroj: | Cotter, S L, Zygalakis, K C, Kevrekidis, I G & Erban, R 2011, ' A constrained approach to multiscale stochastic simulation of chemically reacting systems ', Journal of Chemical Physics, vol. 135, no. 9, 094102 . https://doi.org/10.1063/1.3624333 |
| Popis: | Stochastic simulation of coupled chemical reactions is often computationally intensive, especially if a chemical system contains reactions occurring on different time scales. In this paper, we introduce a multiscale methodology suitable to address this problem, assuming that the evolution of the slow species in the system is well approximated by a Langevin process. It is based on the conditional stochastic simulation algorithm (CSSA) which samples from the conditional distribution of the suitably defined fast variables, given values for the slow variables. In the constrained multiscale algorithm (CMA) a single realization of the CSSA is then used for each value of the slow variable to approximate the effective drift and diffusion terms, in a similar manner to the constrained mean-force computations in other applications such as molecular dynamics. We then show how using the ensuing Fokker-Planck equation approximation, we can in turn approximate average switching times in stochastic chemical systems. © 2011 American Institute of Physics. |
| Databáze: | OpenAIRE |
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