Next Article in Journal
Comparative Analysis of the Thermal Insulation of Traditional and Newly Designed Protective Clothing for Foundry Workers
Next Article in Special Issue
Microstructure of Sheared Entangled Solutions of Semiflexible Polymers
Previous Article in Journal
A New Flexible Soy-Based Adhesive Enhanced with Neopentyl Glycol Diglycidyl Ether: Properties and Application
Previous Article in Special Issue
Particle-Based Modeling of Living Actin Filaments in an Optical Trap
Article Menu
Issue 10 (October) cover image

Export Article

Open AccessArticle
Polymers 2016, 8(10), 347;

Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers

Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
Department of Physics, Faculty for Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
Department of Theoretical Physics, J. Stefan Institute, SI-1000 Ljubljana, Slovenia
Computational Physics Group, University of Vienna, Sensengasse 8, 1090 Vienna, Austria
Author to whom correspondence should be addressed.
Academic Editor: Martin Kröger
Received: 16 July 2016 / Revised: 25 August 2016 / Accepted: 15 September 2016 / Published: 22 September 2016
(This article belongs to the Special Issue Semiflexible Polymers)
PDF [1775 KB, uploaded 22 September 2016]


Knots appear frequently in semiflexible (bio)polymers, including double-stranded DNA, and their presence can affect the polymer’s physical and functional properties. In particular, it is possible and indeed often the case that multiple knots appear on a single chain, with effects which have only come under scrutiny in the last few years. In this manuscript, we study the interaction of two knots on a stretched semiflexible polymer, expanding some recent results on the topic. Specifically, we consider an idealization of a typical optical tweezers experiment and show how the bending rigidity of the chain—And consequently its persistence length—Influences the distribution of the entanglements; possibly more importantly, we observe and report how the relative chirality of the otherwise identical knots substantially modifies their interaction. We analyze the free energy of the chain and extract the effective interactions between embedded knots, rationalizing some of their pertinent features by means of simple effective models. We believe the salient aspect of the knot–knot interactions emerging from our study will be present in a large number of semiflexible polymers under tension, with important consequences for the characterization and manipulation of these systems—Be they artificial or biologica in origin—And for their technological application. View Full-Text
Keywords: semiflexible polymers; dsDNA; knots; chirality; topology semiflexible polymers; dsDNA; knots; chirality; topology

Graphical abstract

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Share & Cite This Article

MDPI and ACS Style

Najafi, S.; Podgornik, R.; Potestio, R.; Tubiana, L. Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers. Polymers 2016, 8, 347.

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.

Related Articles

Article Metrics

Article Access Statistics



[Return to top]
Polymers EISSN 2073-4360 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top