Controlling polymer translocation with crowded medium and polymer length asymmetry
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| Autores principales: | , , , , |
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| Formato: | Preprint |
| Publicado: |
2024
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| _version_ | 1866909123385229312 |
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| author | Garg, Vrinda Mathew, Rejoy Ibrahim, Riyan Singh, Kulveer Ghosh, Surya K. |
| author_facet | Garg, Vrinda Mathew, Rejoy Ibrahim, Riyan Singh, Kulveer Ghosh, Surya K. |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2402_19187 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Controlling polymer translocation with crowded medium and polymer length asymmetry Garg, Vrinda Mathew, Rejoy Ibrahim, Riyan Singh, Kulveer Ghosh, Surya K. Soft Condensed Matter Biological Physics Chemical Physics Computational Physics 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. |
| title | Controlling polymer translocation with crowded medium and polymer length asymmetry |
| topic | Soft Condensed Matter Biological Physics Chemical Physics Computational Physics |
| url | https://arxiv.org/abs/2402.19187 |