Molecular search with conformational change: One-dimensional discrete-state stochastic model

TL;DR

This paper models molecular search processes involving conformational changes using a one-dimensional stochastic framework, revealing multiple dynamic regimes influenced by system parameters, supported by analytical and simulation results.

Contribution

It introduces a novel one-dimensional stochastic model for molecular search with conformational transitions, providing a comprehensive dynamic phase diagram and analytical insights.

Findings

Multiple dynamic regimes identified based on length scales.

Theoretical results validated by Monte Carlo simulations.

Conformational transitions significantly affect search efficiency.

Abstract

Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic modes. To understand the mechanisms of molecular search with alternating dynamics, we investigate the search dynamics with stochastic transitions between two conformations in a one-dimensional discrete-state stochastic model. It is explicitly analyzed using the first-passage time probabilities method to obtain a full dynamic description of the search process. A general dynamic phase diagram is developed. It is found that there are several dynamic regimes in the molecular search with conformational transitions, and they are determined by the relative values of the relevant length scales in the system. Theoretical predictions are fully supported by Monte Carlo computer simulations.