Efficient reactive Brownian dynamics

Aleksandar Donev, Chiao Yu Yang, Changho Kim

Research output: Contribution to journalArticle

Abstract

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently process reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.

Original languageEnglish (US)
Article number034103
JournalJournal of Chemical Physics
Volume148
Issue number3
DOIs
StatePublished - Jan 21 2018

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Association reactions
Thermodynamics
grids
thermodynamic equilibrium
Reaction rates
continuums
association reactions
reaction-diffusion equations
packing density
schedules
predictions
reaction kinetics
Processing
strings
diffusion coefficient
reactivity
dissociation
augmentation
cells
approximation

ASJC Scopus subject areas

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

Cite this

Efficient reactive Brownian dynamics. / Donev, Aleksandar; Yang, Chiao Yu; Kim, Changho.

In: Journal of Chemical Physics, Vol. 148, No. 3, 034103, 21.01.2018.

Research output: Contribution to journalArticle

Donev, Aleksandar ; Yang, Chiao Yu ; Kim, Changho. / Efficient reactive Brownian dynamics. In: Journal of Chemical Physics. 2018 ; Vol. 148, No. 3.
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