Brownian ratchets driven by asymmetric nucleation of hydrolysis waves

TL;DR

This paper introduces a stochastic model where asymmetric nucleation of hydrolysis waves on a track causes directed particle motion, offering an alternative to molecular motors for biophysical transport mechanisms.

Contribution

It presents a novel fluctuating-frame mean field theory to analyze asymmetric hydrolysis wave nucleation and its role in particle transport, expanding understanding beyond traditional molecular motors.

Findings

Identified parameter regimes for maximal domain wall flux.

Demonstrated directed particle motion without molecular conformational changes.

Developed a new theoretical approach for steady-state velocity computation.

Abstract

We propose a stochastic process wherein molecular transport is mediated by asymmetric nucleation of domains on a one-dimensional substrate. Track-driven mechanisms of molecular transport arise in biophysical applications such as Holliday junction positioning and collagenase processivity. In contrast to molecular motors that hydrolyze nucleotide triphosphates and undergo a local molecular conformational change, we show that asymmetric nucleation of hydrolysis waves on a track can also result in directed motion of an attached particle. Asymmetrically cooperative kinetics between ``hydrolyzed'' and ``unhydrolyzed'' states on each lattice site generate moving domain walls that push a particle sitting on the track. We use a novel fluctuating-frame, finite-segment mean field theory to accurately compute steady-state velocities of the driven particle and to discover parameter regimes which yield maximal domain wall flux, leading to optimal particle drift.