Hierarchical algorithm for the reaction-diffusion master equation.

Content Provider	Europe PMC
Author	Hellander, Stefan Hellander, Andreas
Copyright Year	2020
Abstract	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.
Related Links	https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6964990&blobtype=pdf
Page Count	10
ISSN	00219606
Volume Number	152
DOI	10.1063/1.5095075
PubMed Central reference number	PMC6964990
Issue Number	3
PubMed reference number	31968960
Journal	The Journal of Chemical Physics [J Chem Phys]
e-ISSN	10897690
Language	English
Publisher	AIP Publishing LLC
Publisher Date	2020-01-01
Access Restriction	Open
Rights License	0021-9606/2020/152(3)/034104/10/$0.00 © 2020 Author(s).
Content Type	Text
Resource Type	Article
Subject	Physics and Astronomy Medicine Physical and Theoretical Chemistry