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arXiv · 2402.19187

Controlling polymer translocation with crowded medium and polymer length asymmetry

Vrinda Garg·Rejoy Mathew·Riyan Ibrahim·Kulveer Singh·Surya K. Ghosh
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Abstract

Polymer translocation in crowded environments is a ubiquitous phenomenon in biological systems. We studied polymer translocation through a pore in free, one-sided (asymmetric), and two-sided (symmetric) crowded environments. Extensive Langevin dynamics simulation is employed to model the dynamics of the flexible polymer and crowding particles. We studied how crowding size and packing fraction play a crucial role in the translocation process. After determining the standard scaling properties of the translocation probability, time, and MSD, we observed that the translocation rate and bead velocities are location-dependent as we move along the polymer backbone, even in a crowd-free environment. Counter-intuitively, translocation rate and bead velocities showed the opposite behavior; for example, middle monomers near the pore exhibit maximum bead velocity and minimum translocation rate. Free energy calculation for asymmetrically placed polymer indicates there exists a critical number of segments that make the polymer to prefer the receiver side for translocation. For one-sided crowding, we have identified a critical crowding size above which there exists a non-zero probability to translocate into the crowding side instead of the free side. Moreover, we have observed that shifting the polymer towards the crowded side compensates for one-sided crowding, yielding an equal probability akin to a crowder-free system. Under two-sided crowding, the mechanism of how a slight variation in crowder size and packing fraction can force a polymer to switch its translocation direction is proposed, which has not been explored before. Using this control we achieved an equal translocation probability like a crowd-free scenario. These conspicuous yet counter-intuitive phenomena are rationalized by simple theoretical arguments based on osmotic pressure and radial entropic forces.

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Vrinda Garg, Rejoy Mathew, Riyan Ibrahim, Kulveer Singh, Surya K. Ghosh. 2024-02-29. Controlling polymer translocation with crowded medium and polymer length asymmetry. https://arxiv.org/abs/2402.19187

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