Packing and Ejection Dynamics of Polymers: Role of Confinement, Polymer Stiffness, and Activity

G Upadhyay and R Kapri and AK Dasanna and A Chaudhuri, ADVANCED THEORY AND SIMULATIONS, 8 (2025).

DOI: 10.1002/adts.202500420

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. This study aims to investigate the impact of polymer stiffness, activity, and different capsid geometries on the packing and ejection dynamics of both passive and active polymers. Langevin dynamics simulations are employed for a systematic investigation. It is observed 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, it is observed 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 the 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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