Efficient reactive Brownian dynamics
We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reactiondiffusion 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 diffusiononly and reactiononly subproblems exactly, even at high packing densities. To efficiently process reactions without uncontrolled approximations, SRBD employs an eventdriven algorithm that processes reactions in a timeordered 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 gridbased methods such as reactiondiffusion 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 reactionlimited and diffusionlimited irreversible association in three dimensions and compare tomore »
 Authors:

^{[1]};
^{[2]};
^{[3]}
 New York Univ. (NYU), NY (United States)
 New York Univ. (NYU), NY (United States); Univ. of California, Berkeley, CA (United States)
 Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
 Publication Date:
 Grant/Contract Number:
 AC0205CH11231; SC0008271
 Type:
 Accepted Manuscript
 Journal Name:
 Journal of Chemical Physics
 Additional Journal Information:
 Journal Volume: 148; Journal Issue: 3; Related Information: © 2018 Author(s).; Journal ID: ISSN 00219606
 Publisher:
 American Institute of Physics (AIP)
 Research Org:
 Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
 Sponsoring Org:
 USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC21)
 Country of Publication:
 United States
 Language:
 English
 Subject:
 97 MATHEMATICS AND COMPUTING
 OSTI Identifier:
 1435110
 Alternate Identifier(s):
 OSTI ID: 1417424
Donev, Aleksandar, Yang, ChiaoYu, and Kim, Changho. Efficient reactive Brownian dynamics. United States: N. p.,
Web. doi:10.1063/1.5009464.
Donev, Aleksandar, Yang, ChiaoYu, & Kim, Changho. Efficient reactive Brownian dynamics. United States. doi:10.1063/1.5009464.
Donev, Aleksandar, Yang, ChiaoYu, and Kim, Changho. 2018.
"Efficient reactive Brownian dynamics". United States.
doi:10.1063/1.5009464.
@article{osti_1435110,
title = {Efficient reactive Brownian dynamics},
author = {Donev, Aleksandar and Yang, ChiaoYu and Kim, Changho},
abstractNote = {We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reactiondiffusion 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 diffusiononly and reactiononly subproblems exactly, even at high packing densities. To efficiently process reactions without uncontrolled approximations, SRBD employs an eventdriven algorithm that processes reactions in a timeordered 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 gridbased methods such as reactiondiffusion 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 reactionlimited and diffusionlimited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study longtime 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 Turinglike instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusionlimited 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.},
doi = {10.1063/1.5009464},
journal = {Journal of Chemical Physics},
number = 3,
volume = 148,
place = {United States},
year = {2018},
month = {1}
}