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arXiv · 2407.18872

Packing and ejection dynamics of polymers: Role of confinement, polymer stiffness and activity

Gokul Upadhyay·Rajeev Kapri·Anil Kumar Dasanna·Abhishek Chaudhuri
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Abstract

The translocation of biopolymers, such as DNA and proteins, across cellular or nuclear membranes is essential for numerous biological processes. The translocation dynamics are influenced by the properties of the polymers, such as polymer stiffness, and the geometry of the capsid. In our study, we aim to investigate the impact of polymer stiffness, activity, and different capsid geometries on the packing and ejection dynamics of both passive and active polymers. We employ Langevin dynamics simulations for a systematic investigation. We observe that flexible polymers exhibit packing times that are faster than those of their semi-flexible counterparts. Interestingly, for large polymers compared to the capsid size, sphere facilitates faster packing and unpacking compared to ellipsoid, mimicking the cell nucleus and suggesting a geometrical advantage for biopolymer translocation. In summary, we observe that increasing activity accelerates both the packing and ejection processes for both flexible and semi-flexible polymers. However, the effect is significantly more pronounced for semi-flexible polymers, highlighting the crucial role of polymer flexibility in these dynamics. These findings deepen our understanding of the intricate interplay between polymer flexibility, capsid geometry, and activity, providing valuable insight into the dynamics of polymer packing and ejection processes.

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Gokul Upadhyay, Rajeev Kapri, Anil Kumar Dasanna, Abhishek Chaudhuri. 2024-07-26. Packing and ejection dynamics of polymers: Role of confinement, polymer stiffness and activity. https://arxiv.org/abs/2407.18872

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