Gated reactions in discrete time and space

TL;DR

This paper develops a discrete-time theoretical framework for gated molecular reactions on networks, extending continuous-time models, and reveals new phenomena like resonances, with practical case studies demonstrating its effectiveness.

Contribution

It introduces a discrete-time approach to gated reactions, providing formulas for reaction-time distributions and analyzing new dynamic features such as resonances.

Findings

Gated reaction times can be expressed via ungated first-passage times.

Long-time asymptotics are inherited from ungated reactions when mean times diverge.

Discretization introduces resonances and anti-resonances absent in continuous models.

Abstract

How much time does it take two molecules to react? If a reaction occurs upon contact, the answer to this question boils down to the classic first-passage time problem: find the time it takes the two molecules to meet. However, this is not always the case as molecules switch stochastically between reactive and non-reactive states. The reaction is then said to be "gated" by the internal states of the molecules involved which could have a dramatic influence on kinetics. A unified, continuous-time, approach to gated reactions on networks was presented in [Phys. Rev. Lett. 127, 018301, 2021]. Here, we build on this recent advancement and develop an analogous discrete-time version of the theory. Similar to continuous-time, we employ a renewal approach to show that the gated reaction time can always be expressed in terms of the corresponding ungated first-passage and return times; which yields formulas for the generating function of the gated reaction-time distribution and its corresponding mean and variance. In cases where the mean reaction time diverges, we show that the long-time asymptotics of the gated problem is inherited from its ungated counterpart. However, when molecules spend most of their time non-reactive, an interim regime of slower power-law decay emerges prior to the terminal asymptotics. The discretization of time also gives rise to resonances and anti-resonances, which were absent from the continuous time picture. These features are illustrated using two case studies that also demonstrate how the general approach presented herein greatly simplifies the analysis of gated reactions.