Chemical continuous time random walks

TL;DR

This paper generalizes chemical reaction modeling by introducing arbitrary inter-reaction time distributions, leading to a non-Markovian framework that captures delays and non-equilibrium effects in reaction kinetics.

Contribution

It develops a generalized chemical master equation and Gillespie algorithm for arbitrary delay distributions, extending traditional Markovian reaction models.

Findings

Derives modified rate laws for different delay distributions.

Shows non-Markovian kinetics exhibit weak ergodicity breaking.

Predicts time-nonlocal reaction kinetics due to broad delay distributions.

Abstract

Kinetic Monte Carlo methods such as the Gillespie algorithm model chemical reactions as random walks in particle number space. The inter-reaction times are exponentially distributed under the assumption that the system is well mixed. We introduce an arbitrary inter-reaction time distribution, which may account for the impact of incomplete mixing on chemical reactions, and in general stochastic reaction delay, which may represent the impact of extrinsic noise. This process defines an inhomogeneous continuous time random walk in particle number space, from which we derive a generalized chemical master equation. This leads naturally to a generalization of the Gillespie algorithm. Based on this formalism, we determine the modified chemical rate laws for different inter-reaction time distributions. This framework traces Michaelis--Menten-type kinetics back to finite-mean delay times, and predicts time-nonlocal macroscopic reaction kinetics as a consequence of broadly distributed delays. Non-Markovian kinetics exhibit weak ergodicity breaking and show key features of reactions under local non-equilibrium.