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Pore shapes effects on polymer translocation

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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.

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Authors and Affiliations

  1. Physics Department, Iran University of Science and Technology (IUST), 16846-13114, Tehran, Iran

    Rouhollah Haji Abdolvahab & Mohammadreza Niknam Hamidabad

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  1. Rouhollah Haji Abdolvahab
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  2. Mohammadreza Niknam Hamidabad
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Correspondence to Rouhollah Haji Abdolvahab.

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Haji Abdolvahab, R., Niknam Hamidabad, M. Pore shapes effects on polymer translocation. Eur. Phys. J. E 43, 76 (2020). https://doi.org/10.1140/epje/i2020-12001-y

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