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Abstract Based on polymer scaling theory and numerical evidence, Orlandini, Tesi, Janse van Rensburg and Whittington conjectured in 1996 that the limiting entropy of knot-typeKlattice polygons is the same as that for unknot polygons, and that the entropic critical exponent increases by one for each prime knot in the knot decomposition ofK. This Knot Entropy (KE) conjecture is consistent with the idea that for unconfined polymers, knots occur in a localized way (the knotted part is relatively small compared to polymer length). For full confinement (to a sphere or box), numerical evidence suggests that knots are much less localized. Numerical evidence for nanochannel or tube confinement is mixed, depending on how the size of a knot is measured. Here we outline the proof that the KE conjecture holds for polygons in the lattice tube and show that knotting is localized when a connected-sum measure of knot size is used. Similar results are established for linked polygons. This is the first model for which the knot entropy conjecture has been proved.
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Diffusion of knots in nanochannel-confined DNA molecules
We used Langevin dynamics simulations without hydrodynamic interactions to probe knot diffusion mechanisms and the time scales governing the evolution and the spontaneous untying of trefoil knots in nanochannel-confined DNA molecules in the extended de Gennes regime. The knot untying follows an “opening up process,” wherein the initially tight knot continues growing and fluctuating in size as it moves toward the end of the DNA molecule before its annihilation at the chain end. The mean knot size increases significantly and sub-linearly with increasing chain contour length. The knot diffusion in nanochannel-confined DNA molecules is subdiffusive, with the unknotting time scaling with chain contour length with an exponent of 2.64 ± 0.23 to within a 95% confidence interval. The scaling exponent for the mean unknotting time vs chain contour length, along with visual inspection of the knot conformations, suggests that the knot diffusion mechanism is a combination of self-reptation and knot region breathing for the simulated parameters.
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- Award ID(s):
- 2016879
- PAR ID:
- 10413352
- Publisher / Repository:
- AIP
- Date Published:
- Journal Name:
- The Journal of Chemical Physics
- Volume:
- 158
- Issue:
- 19
- ISSN:
- 0021-9606
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1063/5.0151025
