A Constrained Approach to Multiscale Stochastic Simulation of Chemically Reacting Systems
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. It is based on the Conditional Stochast...
| Main Authors: | , , , |
|---|---|
| Format: | Journal article |
| Published: |
2011
|
| _version_ | 1826280075666915328 |
|---|---|
| author | Cotter, S Zygalakis, K Kevrekidis, I Erban, R |
| author_facet | Cotter, S Zygalakis, K Kevrekidis, I Erban, R |
| author_sort | Cotter, S |
| collection | OXFORD |
| description | 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. 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 Stochastic Differential Equation (SDE) approximation, we can in turn approximate average switching times in stochastic chemical systems. |
| first_indexed | 2024-03-07T00:08:16Z |
| format | Journal article |
| id | oxford-uuid:784ef862-9571-4880-b074-a4a30e1b094c |
| institution | University of Oxford |
| last_indexed | 2024-03-07T00:08:16Z |
| publishDate | 2011 |
| record_format | dspace |
| spelling | oxford-uuid:784ef862-9571-4880-b074-a4a30e1b094c2022-03-26T20:29:49ZA Constrained Approach to Multiscale Stochastic Simulation of Chemically Reacting SystemsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:784ef862-9571-4880-b074-a4a30e1b094cMathematical Institute - ePrints2011Cotter, SZygalakis, KKevrekidis, IErban, RStochastic 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. 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 Stochastic Differential Equation (SDE) approximation, we can in turn approximate average switching times in stochastic chemical systems. |
| spellingShingle | Cotter, S Zygalakis, K Kevrekidis, I Erban, R A Constrained Approach to Multiscale Stochastic Simulation of Chemically Reacting Systems |
| title | A Constrained Approach to Multiscale Stochastic Simulation of
Chemically Reacting Systems |
| title_full | A Constrained Approach to Multiscale Stochastic Simulation of
Chemically Reacting Systems |
| title_fullStr | A Constrained Approach to Multiscale Stochastic Simulation of
Chemically Reacting Systems |
| title_full_unstemmed | A Constrained Approach to Multiscale Stochastic Simulation of
Chemically Reacting Systems |
| title_short | A Constrained Approach to Multiscale Stochastic Simulation of
Chemically Reacting Systems |
| title_sort | constrained approach to multiscale stochastic simulation of chemically reacting systems |
| work_keys_str_mv | AT cotters aconstrainedapproachtomultiscalestochasticsimulationofchemicallyreactingsystems AT zygalakisk aconstrainedapproachtomultiscalestochasticsimulationofchemicallyreactingsystems AT kevrekidisi aconstrainedapproachtomultiscalestochasticsimulationofchemicallyreactingsystems AT erbanr aconstrainedapproachtomultiscalestochasticsimulationofchemicallyreactingsystems AT cotters constrainedapproachtomultiscalestochasticsimulationofchemicallyreactingsystems AT zygalakisk constrainedapproachtomultiscalestochasticsimulationofchemicallyreactingsystems AT kevrekidisi constrainedapproachtomultiscalestochasticsimulationofchemicallyreactingsystems AT erbanr constrainedapproachtomultiscalestochasticsimulationofchemicallyreactingsystems |