Polymer translocation: Effects of confinement

Manish Dwivedi; Sumitra Rudra; Sanjay Kumar

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arXiv · 2401.04610

Polymer translocation: Effects of confinement

Manish Dwivedi·Sumitra Rudra·Sanjay Kumar

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Abstract

We investigate the influence of varying confinement on the dynamics of polymer translocation through a cone shaped channel. For this, a linear polymer chain is modeled by a self voiding walks (SAWs) on a square lattice. The cis-side of a cone-shaped channel has a finite volume, whereas the trans-side has a semi-infinite space. The confining environment is varied either by changing the position of the back wall while keeping the apex angle fixed or altering the apex angle while keeping the position of the back wall fixed. In both cases, the effective space {\phi}, which represents the number of monomers in a chain relative to the total number of accessible sites within the cone, is reduced due to the imposed confinement. Consequently, the translocation dynamics are affected. We analyze the entropy of the confined system as a function {\phi}, which exhibits non-monotonic behaviour. We also calculate the free energy associated with the confinement as a function of a virtual coordinate for different positions of the back wall (base of the cone) along the conical axis for various apex angles.Employing the Fokker-Planck equation, we calculate the translocation time as a function of {\phi} for different solvent conditions across the pore. Our findings indicate that the translocation time decreases as {\phi} increases, but it eventually reaches a saturation point at a certain value of {\phi}. Moreover, we highlight the possibility to control the translocation dynamics by manipulating the solvent quality across the pore. Furthermore, our investigation delves into the intricacies of polymer translocation through a cone-shaped channel, considering both repulsive and neutral interactions with the pore wall. This exploration unveils nuanced dynamics and sheds light on the factors that significantly impact translocation within confined channels.

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Manish Dwivedi, Sumitra Rudra, Sanjay Kumar. 2024-01-09. Polymer translocation: Effects of confinement. https://arxiv.org/abs/2401.04610

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