Characteristics of the polymer transport in ratchet systems

TL;DR

This study investigates how polymer molecules with complex structures are transported in time-dependent periodic potentials, revealing how structural and environmental changes influence transport efficiency and mechanisms using numerical and graph analysis methods.

Contribution

It extends previous work by analyzing deterministic potential switching, energetic efficiency, and charge distributions, providing new insights into polymer transport mechanisms in ratchet systems.

Findings

Small structural changes can significantly increase drift.

Deterministic flashing potentials enhance transport and coherence.

Graph analysis identifies dominant transport mechanisms.

Abstract

Molecules with complex internal structure in time-dependent periodic potentials are studied by using short Rubinstein-Duke model polymers as an example. We extend our earlier work on transport in stochastically varying potentials to cover also deterministic potential switching mechanisms, energetic efficiency and non-uniform charge distributions. We also use currents in the non-equilibrium steady state to identify the dominating mechanisms that lead to polymer transportation and analyze the evolution of the macroscopic state (e.g., total and head-to-head lengths) of the polymers. Several numerical methods are used to solve the master equations and nonlinear optimization problems. The dominating transport mechanisms are found via graph optimization methods. The results show that small changes in the molecule structure and the environment variables can lead to large increases of the drift. The drift and the coherence can be amplified by using deterministic flashing potentials and customized polymer charge distributions. Identifying the dominating transport mechanism by graph analysis tools is found to give insight in how the molecule is transported by the ratchet effect.