A first-passage kinetic Monte Carlo method for reaction-drift-diffusion processes

DOI10.1016/J.JCP.2013.12.023zbMATH Open1349.82047DBLPjournals/jcphy/MauroSSAI14arXiv1302.0793OpenAlexW2054171947WikidataQ60140968 ScholiaQ60140968MaRDI QIDQ348732FDOQ348732

Authors: Ava J. Mauro, Jon Karl Sigurdsson, Justin Shrake, Paul J. Atzberger, Samuel A. Isaacson 

Publication date: 5 December 2016

Published in: Journal of Computational Physics (Search for Journal in Brave)

Abstract: Stochastic reaction-diffusion models are now a popular tool for studying physical systems in which both the explicit diffusion of molecules and noise in the chemical reaction process play important roles. The Smoluchowski diffusion-limited reaction model (SDLR) is one of several that have been used to study biological systems. Exact realizations of the underlying stochastic process described by the SDLR model can be generated by the recently proposed First-Passage Kinetic Monte Carlo (FPKMC) method. This exactness relies on sampling analytical solutions to one and two-body diffusion equations in simplified protective domains. In this work we extend the FPKMC to allow for drift arising from fixed, background potentials. As the corresponding Fokker-Planck equations that describe the motion of each molecule can no longer be solved analytically, we develop a hybrid method that discretizes the protective domains. The discretization is chosen so that the drift-diffusion of each molecule within its protective domain is approximated by a continuous-time random walk on a lattice. New lattices are defined dynamically as the protective domains are updated, hence we will refer to our method as Dynamic Lattice FPKMC or DL-FPKMC. We focus primarily on the one-dimensional case in this manuscript, and demonstrate the numerical convergence and accuracy of our method in this case for both smooth and discontinuous potentials. We also present applications of our method, which illustrate the impact of drift on reaction kinetics.

Full work available at URL: https://arxiv.org/abs/1302.0793

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zbMATH Keywords

cell biologyFokker-Planck equationstochastic chemical kineticsfirst-passage kinetic Monte Carlostochastic reaction-diffusion

Mathematics Subject Classification ID

Monte Carlo methods (65C05) Stochastic particle methods (65C35) Stochastic methods (Fokker-Planck, Langevin, etc.) applied to problems in time-dependent statistical mechanics (82C31) Classical flows, reactions, etc. in chemistry (92E20)

Cites Work

• On Information and Sufficiency
• A Brownian dynamics model of kinesin in three dimensions incorporating the force-extension profile of the coiled-coil cargo tether
• Stochastic processes in physics and chemistry.
• The immersed boundary method
• Handbook of linear partial differential equations for engineers and scientists
• Handbook of stochastic methods for physics, chemistry and natural sciences.
• A second-order-accurate symmetric discretization of the Poisson equation on irregular domains
• Stochastic approach to chemical kinetics
• Some Continuous Monte Carlo Methods for the Dirichlet Problem
• A robust numerical algorithm for studying biomolecular transport processes
• A random walk on rectangles algorithm
• Efficient kinetic Monte Carlo method for reaction-diffusion problems with spatially varying annihilation rates
• Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems
• Analysis of Brownian dynamics simulations of reversible bimolecular reactions
• Simulation of stochastic reaction-diffusion processes on unstructured meshes
• How a protein searches for its site on DNA: the mechanism of facilitated diffusion
• Stochastic reaction-diffusion kinetics in the microscopic limit
• The reaction-diffusion master equation as an asymptotic approximation of diffusion to a small target
• Relationship between the reaction–diffusion master equation and particle tracking models
• Flexible single molecule simulation of reaction-diffusion processes
• Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations
• Adaptive mesh refinement for stochastic reaction-diffusion processes
• Second-order, \(L_ 0\)-stable methods for the heat equation with time-dependent boundary conditions
• A first-passage kinetic Monte Carlo algorithm for complex diffusion-reaction systems

Cited In (10)

• First-passage time statistics on surfaces of general shape: surface PDE solvers using generalized moving least squares (GMLS)
• Reactive boundary conditions as limits of interaction potentials for Brownian and Langevin dynamics
• Stochastic reaction-diffusion processes with embedded lower-dimensional structures
• Simulation of stochastic diffusion via first exit times
• On the Green's function of the partially diffusion-controlled reversible ABCD reaction for radiation chemistry codes
• An exact and efficient first passage time algorithm for reaction-diffusion processes on a 2D-lattice
• A first-passage kinetic Monte Carlo algorithm for complex diffusion-reaction systems
• Efficient Green's function reaction dynamics (GFRD) simulations for diffusion-limited, reversible reactions
• Numerical algorithms based on Galerkin methods for the modeling of reactive interfaces in photoelectrochemical (PEC) solar cells
• First passage Monte Carlo algorithms for solving coupled systems of diffusion-reaction equations

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