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A hybrid method for micro-mesoscopic stochastic simulation of reaction-diffusion systems.
Math Biosci 2019; 312:23-32MB

Abstract

The present paper introduces a new micro-meso hybrid algorithm based on the Ghost Cell Method concept in which the microscopic subdomain is governed by the Reactive Multi-Particle Collision (RMPC) dynamics. The mesoscopic subdomain is modeled using the Reaction-Diffusion Master Equation (RDME). The RDME is solved by means of the Inhomogeneous Stochastic Simulation Algorithm. No hybrid algorithm has hitherto used the RMPC dynamics for modeling reactions and the trajectories of each individual particle. The RMPC is faster than other molecular based methods and has the advantage of conserving mass, energy and momentum in the collision and free streaming steps. The new algorithm is tested on three reaction-diffusion systems. In all the systems studied, very good agreement with the deterministic solutions of the corresponding differential equations is obtained. In addition, it has been shown that proper discretization of the computational domain results in significant speed-ups in comparison with the full RMPC algorithm.

Authors+Show Affiliations

Department of Mathematics, Ryerson University, 350 Victoria St, M5B 2K3 Toronto, Canada. Electronic address: Asayyidmousavi@ryerson.ca.Department of Mathematics, Ryerson University, 350 Victoria St, M5B 2K3 Toronto, Canada.Department of Mathematics, Ryerson University, 350 Victoria St, M5B 2K3 Toronto, Canada.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

30998936

Citation

Sayyidmousavi, Alireza, et al. "A Hybrid Method for Micro-mesoscopic Stochastic Simulation of Reaction-diffusion Systems." Mathematical Biosciences, vol. 312, 2019, pp. 23-32.
Sayyidmousavi A, Rohlf K, Ilie S. A hybrid method for micro-mesoscopic stochastic simulation of reaction-diffusion systems. Math Biosci. 2019;312:23-32.
Sayyidmousavi, A., Rohlf, K., & Ilie, S. (2019). A hybrid method for micro-mesoscopic stochastic simulation of reaction-diffusion systems. Mathematical Biosciences, 312, pp. 23-32. doi:10.1016/j.mbs.2019.04.001.
Sayyidmousavi A, Rohlf K, Ilie S. A Hybrid Method for Micro-mesoscopic Stochastic Simulation of Reaction-diffusion Systems. Math Biosci. 2019;312:23-32. PubMed PMID: 30998936.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A hybrid method for micro-mesoscopic stochastic simulation of reaction-diffusion systems. AU - Sayyidmousavi,Alireza, AU - Rohlf,Katrin, AU - Ilie,Silvana, Y1 - 2019/04/15/ PY - 2018/08/24/received PY - 2019/04/13/revised PY - 2019/04/14/accepted PY - 2019/4/19/pubmed PY - 2019/4/19/medline PY - 2019/4/19/entrez KW - Hybrid method KW - Inhomogeneous Stochastic Simulation Algorithm KW - Multi-Particle Collision dynamics KW - Reaction-diffusion systems KW - Stochastic simulation SP - 23 EP - 32 JF - Mathematical biosciences JO - Math Biosci VL - 312 N2 - The present paper introduces a new micro-meso hybrid algorithm based on the Ghost Cell Method concept in which the microscopic subdomain is governed by the Reactive Multi-Particle Collision (RMPC) dynamics. The mesoscopic subdomain is modeled using the Reaction-Diffusion Master Equation (RDME). The RDME is solved by means of the Inhomogeneous Stochastic Simulation Algorithm. No hybrid algorithm has hitherto used the RMPC dynamics for modeling reactions and the trajectories of each individual particle. The RMPC is faster than other molecular based methods and has the advantage of conserving mass, energy and momentum in the collision and free streaming steps. The new algorithm is tested on three reaction-diffusion systems. In all the systems studied, very good agreement with the deterministic solutions of the corresponding differential equations is obtained. In addition, it has been shown that proper discretization of the computational domain results in significant speed-ups in comparison with the full RMPC algorithm. SN - 1879-3134 UR - https://www.unboundmedicine.com/medline/citation/30998936/A_hybrid_method_for_micro_mesoscopic_stochastic_simulation_of_reaction_diffusion_systems_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0025-5564(18)30500-5 DB - PRIME DP - Unbound Medicine ER -