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arXiv · 2307.01821

Polymer translocation driven by longitudinal and transversal time-dependent end-pulling forces

Alejandro Sainz-Agost·Fernando Falo·Alessandro Fiasconaro
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Abstract

Polymer translocation has long been a topic of interest in the field of biological physics given its relevance in both biological (protein and DNA/RNA translocation through nuclear and cell membranes) and technological processes (nanopore DNA sequencing, drug delivery). In this work, we simulate the translocation of a semiflexible homopolymer through an extended pore, driven by both a constant and a time-dependent end-pulled force, employing a model introduced in previous studies. The time dependence is simplistically modeled as a cosine function, and we distinguish between two scenarios for the driving -- longitudinal force and transversal force -- depending on the relative orientation of the force, parallel or perpendicular respectively, with respect to the pore axis. Beside some key differences between the two drivings, the mean translocation times present a large minimum region as function of the frequency of the force that is typical of the Resonant Activation effect. The presence of the minimum is independent on the elastic characteristics of the polymeric chains and reveals a linear relation between the optimum mean translocation time and the corresponding period of the driving. The mean translocation times show different scaling exponent with the polymer length for different flexibilities. Lastly, we derive an analytical expression of the mean translocation time for low driving frequency, which clearly agrees with the simulations.

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Alejandro Sainz-Agost, Fernando Falo, Alessandro Fiasconaro. 2023-07-04. Polymer translocation driven by longitudinal and transversal time-dependent end-pulling forces. https://doi.org/10.1103/physreve.108.034501

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