Spontaneous Unknotting of a Polymer Confined in a Nanochannel

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Mobius, Wolfram
Frey, Erwin
Gerland, Ulrich
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Abstract
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We study the dynamics of a knot in a semiflexible polymer confined to a narrow channel of width comparable to the polymers' persistence length. Using a combination of Brownian dynamics simulations and a coarse-grained stochastic model, we characterize the coupled dynamics of knot size variation and knot diffusion along the polymer, which ultimately leads to spontaneous unknotting. We find that the knot grows to macroscopic size before disappearing. Interestingly, an external force applied to the ends of the confined polymer speeds up spontaneous unknotting.
Comment: 4 pages, 3 figures
Keywords
Condensed Matter - Soft Condensed Matter, Quantitative Biology - Biomolecules
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