A Comparison of Bimolecular Reaction Models for Stochastic Reaction Diffusion Systems

TL;DR

This paper compares two spatially-continuous stochastic reaction-diffusion models, the Smoluchowski and Doi models, analyzing their relationship and differences through rigorous proofs and numerical simulations relevant to biological systems.

Contribution

The paper establishes a rigorous convergence result between the Doi and Smoluchowski models as the reaction rate parameter increases, and investigates their differences through simulations.

Findings

Doi model converges to Smoluchowski model as reaction rate increases

Differences between models grow inversely with reaction radius at fixed high reaction rates

Numerical simulations confirm theoretical convergence and highlight parameter sensitivities

Abstract

Stochastic reaction-diffusion models have become an important tool in studying how both noise in the chemical reaction process and the spatial movement of molecules influences the behavior of biological systems. There are two primary spatially-continuous models that have been used in recent studies: the diffusion limited reaction model of Smoluchowski, and a second approach popularized by Doi. Both models treat molecules as points undergoing Brownian motion. The former represents chemical reactions between two reactants through the use of reactive boundary conditions, with two molecules reacting instantly upon reaching a fixed separation (called the reaction-radius). The Doi model uses reaction potentials, whereby two molecules react with a fixed probability per unit time, $\lambda$, when separated by less than the reaction radius. In this work we study the rigorous relationship between the two models. For the special case of a protein diffusing to a fixed DNA binding site, we prove that the solution to the Doi model converges to the solution of the Smoluchowski model as $\lambda \to \infty$, with a rigorous $O(\lambda^{-1/2 + \epsilon})$ error bound (for any fixed $\epsilon > 0$). We investigate by numerical simulation, for biologically relevant parameter values, the difference between the solutions and associated reaction time statistics of the two models. As the reaction-radius is decreased, for sufficiently large but fixed values of $\lambda$, these differences are found to increase like the inverse of the binding radius.