Pore shapes effects on polymer translocation
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THE EUROPEAN PHYSICAL JOURNAL E
Regular Article
Pore shapes effects on polymer translocation Rouhollah Haji Abdolvahaba and Mohammadreza Niknam Hamidabad Physics Department, Iran University of Science and Technology (IUST), 16846-13114, Tehran, Iran Received 31 August 2020 / Received in final form 4 November 2020 / Accepted 12 November 2020 Published online: 3 December 2020 c EDP Sciences / Societ` a Italiana di Fisica / Springer-Verlag GmbH Germany, part of Springer Nature, 2020 Abstract. We translocated polymers through pores of different shapes and interaction patterns in three dimensions by Langevin molecular dynamics. There were four simple cylindrical pores of the same length but with different diameters. The results showed that even though decreasing the pore diameter would always decrease the translocation velocity, it was strongly dependent on the shape of the increased pore diameter. Although increasing the pore diameter made the translocation faster in simple cylindrical pores, it was complicated in different pore shapes, e.g. increasing the diameter in the middle decreased the translocation velocity. Investigating polymer shapes through the translocation process and comparing the shapes by the cumulative waiting time for different pore structures reveals the non-equilibrium properties of translocation. Moreover, polymer shape parameters such as gyration radius, polymer center of mass, and average aspect ratio help us to distinguish different pore shapes and/or different polymers.
1 Introduction The human body is composed of many individual cells. More than 90% of the dried weight of the cells comprises different biopolymers. Thus, polymer physics is of fundamental importance in modeling human life on a micro-scale. Polymer translocation is one of the most active fields in soft matter, including polymer physics [1]. Biomolecules’ translocation through biological channels is ubiquitous in cell metabolism. The translocation of proteins through endoplasmic reticulum or organelles such as mitochondria [2–4], and mRNA translocation through nuclear pore complexes in gene expression [2] are some examples. Moreover, biotechnological applications such as rapid DNA sequencing [5,6], protein sensing [7], controlled drug delivery, gene therapy, and disease detection [8] have made it a very fertile field for research [6, 9–14]. Bezrukov et al. in 1994 counted polymers’ translocation through an alamethicin channel [15]. Two years later, in 1996, Kasianowicz et al. translocated an ssRNA through an α-hemolysin channel [16]. They measured the ionic current through the pore and found a distribution function of translocation times. Since then, there have been many theoretical, experimental, and simulation studies on polymer translocation [1, 17–19]. Although people usually use strong electric fields to translocate polymers in vitro, there are several mechanisms for creating the chemical potential difference between cis and trans sides. Crowding [20], pressure, cona
e-mail: [email protected] (corresponding author)
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