Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

Changho Kim, Andy Nonaka, John B. Bell, Alejandro L. Garcia, Aleksandar Donev

Research output: Contribution to journalArticle

Abstract

We develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules, to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two-dimensional Turing-like pattern and examine the effect of fluctuations on three-dimensional chemical front propagation. By comparing stochastic simulations to deterministic reaction-diffusion simulations, we show that fluctuations accelerate pattern formation in spatially homogeneous systems and lead to a qualitatively different disordered pattern behind a traveling wave.

Original languageEnglish (US)
Article number124110
JournalJournal of Chemical Physics
Volume146
Issue number12
DOIs
StatePublished - Mar 28 2017

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Hydrodynamics
hydrodynamics
reaction-diffusion equations
simulation
partial differential equations
Partial differential equations
Molecules
molecules
Numerical methods
eccentrics
thermodynamic equilibrium
Thermodynamics
traveling waves
constrictions
formulations
thermodynamics
propagation
predictions
cells

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Stochastic simulation of reaction-diffusion systems : A fluctuating-hydrodynamics approach. / Kim, Changho; Nonaka, Andy; Bell, John B.; Garcia, Alejandro L.; Donev, Aleksandar.

In: Journal of Chemical Physics, Vol. 146, No. 12, 124110, 28.03.2017.

Research output: Contribution to journalArticle

Kim, Changho ; Nonaka, Andy ; Bell, John B. ; Garcia, Alejandro L. ; Donev, Aleksandar. / Stochastic simulation of reaction-diffusion systems : A fluctuating-hydrodynamics approach. In: Journal of Chemical Physics. 2017 ; Vol. 146, No. 12.
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