Force-dependent diffusion coefficient of molecular Brownian ratchets

Abstract

We study the mean velocity and diffusion constant in three related models of molecular Brownian ratchets. Brownian ratchets can be used to describe translocation of biopolymers like DNA through nanopores in cells in the presence of chaperones on the trans side of the pore. Chaperones can bind to the polymer and prevent it from sliding back through the pore. First, we study a simple model that describes the translocation in terms of an asymmetric random walk. It serves as an introductory example but already captures the main features of a Brownian ratchet. We then provide an analytical expression for the diffusion constant in the classical model of a translocation ratchet that was first proposed by Peskin et al. . This model is based on the assumption that the binding and unbinding of the chaperones is much faster than the diffusion of the DNA strand. To remedy this shortcoming, we propose a modified model that is also applicable if the (un)binding rates are finite. We calculate the force dependent mean velocity and diffusivity for this new model and compare the results to the original one. Our analysis shows that for large pulling forces the predictions of both models can differ strongly even if the (un)binding rates are large in comparison to the diffusion time-scale but still finite. Furthermore, implications of the thermodynamic uncertainty relation on the efficiency of Brownian ratchets are discussed.

17 pages, 10 figures

References in corpus (8)

• The large deviation approach to statistical mechanics
• Thermodynamic uncertainty relation for biomolecular processes
• Work and information processing in a solvable model of Maxwell's demon
• Proof of the Finite-Time Thermodynamic Uncertainty Relation for Steady-State Currents
• Finite-time generalization of the thermodynamic uncertainty relation
• Introduction to dynamical large deviations of Markov processes
• Universal bound on the efficiency of molecular motors
• Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations

Cited by in corpus (4)

• Thermodynamic uncertainty relation to assess biological processes
• Exponential volume dependence of entropy-current fluctuations at first-order phase transitions in chemical reaction networks
• Propagator for a driven Brownian particle in step potentials
• Mean velocity and effective diffusion constant for translocation of biopolymer chains across membrane