Effects of Side Chains on Polymer Knots
Name
acs.macromol.9b01425.pdf
Description
Published version
Size
2.46 MB
Format
Adobe PDF
Checksum (MD5)
0ff79c2e37da1274c36763270e07c615
Author(s)
Dai, Liang
Soh, Beatrice W
Doyle, Patrick S
Date Issued
August 2019
Journal
Macromolecules
Publisher
American Chemical Society (ACS)
Citation
Dai, Liang et al. "Effects of Side Chains on Polymer Knots." Macromolecules 52, 17 (August 2019): 6792-6800 © 2019 American Chemical Society
Version
Final published version
Abstract
As an intriguing phenomenon, knotting in DNA, proteins, and other molecules has been extensively investigated in recent years, not only because of fundamental interest in knotting but also because of significant effects of knotting on mechanical, rheological, chemical, and biological properties. Some polymers contain side chains, and the effects of side chains on polymer knots are not clear. In this work, we investigate the effects of side chains on knots through Langevin dynamics simulations of knot diffusion along a stretched polymer with side chains. When the gap between side chains is larger than the knot size; each side chain acts as a barrier to slow down the knot diffusion. We find that how a knot crosses the barrier by a side chain resembles how a polymer translocates a pore. Inspired by the latter, we find a simple empirical expression for the free energy barrier caused by a side chain: Fbarrier/kBT ≈ 75Rg/Lknot, where kB is the Boltzmann constant, T is the temperature, Rg is the radius of gyration of a side chain, and Lknot is the contour length of the knot core. The equations and numerical results obtained in this work can guide the rational control of knot diffusivity along a polymer by side chains. In addition, our results provide insights into the understanding of knots in peptides and single-stranded DNA where side chains are common. Furthermore, this work makes a connection between two interesting phenomena for polymers - knotting and pore translocation.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
Terms of Use
Creative Commons Attribution-NonCommercial-NoDerivs License
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1021/acs.macromol.9b01425
