Hierarchical algorithm for the reaction-diffusion master equation.
Journal
The Journal of chemical physics
ISSN: 1089-7690
Titre abrégé: J Chem Phys
Pays: United States
ID NLM: 0375360
Informations de publication
Date de publication:
21 Jan 2020
21 Jan 2020
Historique:
entrez:
24
1
2020
pubmed:
24
1
2020
medline:
24
1
2020
Statut:
ppublish
Résumé
We have developed an algorithm coupling mesoscopic simulations on different levels in a hierarchy of Cartesian meshes. Based on the multiscale nature of the chemical reactions, some molecules in the system will live on a fine-grained mesh, while others live on a coarse-grained mesh. By allowing molecules to transfer from the fine levels to the coarse levels when appropriate, we show that we can save up to three orders of magnitude of computational time compared to microscopic simulations or highly resolved mesoscopic simulations, without losing significant accuracy. We demonstrate this in several numerical examples with systems that cannot be accurately simulated with a coarse-grained mesoscopic model.
Identifiants
pubmed: 31968960
doi: 10.1063/1.5095075
pmc: PMC6964990
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
034104Subventions
Organisme : NIBIB NIH HHS
ID : R01 EB014877
Pays : United States
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