Next Article in Journal
Visible Light-Induced Metal Free Surface Initiated Atom Transfer Radical Polymerization of Methyl Methacrylate on SBA-15
Next Article in Special Issue
Trapping a Knot into Tight Conformations by Intra-Chain Repulsions
Previous Article in Journal
A Biodegradable Microneedle Cuff for Comparison of Drug Effects through Perivascular Delivery to Balloon-Injured Arteries
Previous Article in Special Issue
Theory of Semiflexible Filaments and Networks
Open AccessArticle

Entropic Interactions between Two Knots on a Semiflexible Polymer

Department of Physics, Johannes Gutenberg University Mainz, Staudinger Weg 9, 55128 Mainz, Germany
Graduate School Materials Science in Mainz, 55128 Mainz, Germany
Author to whom correspondence should be addressed.
Academic Editor: Martin Kröger
Polymers 2017, 9(2), 55;
Received: 30 December 2016 / Revised: 27 January 2017 / Accepted: 31 January 2017 / Published: 9 February 2017
(This article belongs to the Special Issue Semiflexible Polymers)
Two knots on a string can either be separated or intertwined, and may even pass through each other. At the microscopic scale, such transitions may occur spontaneously, driven by thermal fluctuations, and can be associated with a topological free energy barrier. In this manuscript, we study the respective location of a trefoil ( 3 1 ) and a figure-eight ( 4 1 ) knot on a semiflexible polymer, which is parameterized to model dsDNA in physiological conditions. Two cases are considered: first, end monomers are grafted to two confining walls of varying distance. Free energy profiles and transition barriers are then compared to a subset of free chains, which contain exactly one 3 1 and one 4 1 knot. For the latter, we observe a small preference to form an intertwined state, which can be associated with an effective entropic attraction. However, the respective free energy barrier is so small that we expect transition events to occur spontaneously and frequently in polymers and DNA, which are highly knotted for sufficient strain lengths. View Full-Text
Keywords: knots; DNA; free energy barriers knots; DNA; free energy barriers
Show Figures

Figure 1

MDPI and ACS Style

Richard, D.; Stalter, S.; Siebert, J.T.; Rieger, F.; Trefz, B.; Virnau, P. Entropic Interactions between Two Knots on a Semiflexible Polymer. Polymers 2017, 9, 55.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

Back to TopTop