Stochastic self-tuning hybrid algorithm for reaction-diffusion systems

Ruiz-Martínez, Á.; Bartol, T. M.; Sejnowski, T. J.; Tartakovsky, D. M.

doi:10.1063/1.5125022

Title: Stochastic self-tuning hybrid algorithm for reaction-diffusion systems

Journal Article · Fri Dec 27 00:00:00 EST 2019 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.5125022· OSTI ID:1803580

Ruiz-Martínez, Á. ^[1]; Bartol, T. M. ^[2]; Sejnowski, T. J. ^[3];

^[4]

Univ. of California San Diego, La Jolla, CA (United States)
Salk Institute for Biological Studies, La Jolla, CA (United States). Computational Neurobiology Lab.
Salk Institute for Biological Studies, La Jolla, CA (United States). Computational Neurobiology Lab.; Univ. of California San Diego, La Jolla, CA (United States)
Stanford Univ., CA (United States)

Many biochemical phenomena involve reactants with vastly different concentrations, some of which are amenable to continuum-level descriptions, while the others are not. We present a hybrid self-tuning algorithm to model such systems. The method combines microscopic (Brownian) dynamics for diffusion with mesoscopic (Gillespie-type) methods for reactions and remains efficient in a wide range of regimes and scenarios with large variations of concentrations. Furthermore, its accuracy, robustness, and versatility are balanced by redefining propensities and optimizing the mesh size and time step. We use a bimolecular reaction to demonstrate the potential of our method in a broad spectrum of scenarios: from almost completely reaction-dominated systems to cases where reactions rarely occur or take place very slowly. The simulation results show that the number of particles present in the system does not degrade the performance of our method. This makes it an accurate and computationally efficient tool to model complex multireaction systems.

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Research Organization:: Stanford Univ., CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); US Air Force Office of Scientific Research (AFOSR)

Grant/Contract Number:: SC0019130; FA9550-17-1-0417

OSTI ID:: 1803580

Alternate ID(s):: OSTI ID: 1580549

Journal Information:: Journal of Chemical Physics, Vol. 151, Issue 24; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 3 works

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