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

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 com...

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Autores principales: Najafi, Saeed, Podgornik, Rudolf, Potestio, Raffaello, Tubiana, Luca
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431951/
https://www.ncbi.nlm.nih.gov/pubmed/30974623
http://dx.doi.org/10.3390/polym8100347
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author Najafi, Saeed
Podgornik, Rudolf
Potestio, Raffaello
Tubiana, Luca
author_facet Najafi, Saeed
Podgornik, Rudolf
Potestio, Raffaello
Tubiana, Luca
author_sort Najafi, Saeed
collection PubMed
description 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.
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spelling pubmed-64319512019-04-02 Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers Najafi, Saeed Podgornik, Rudolf Potestio, Raffaello Tubiana, Luca Polymers (Basel) Article 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. MDPI 2016-09-22 /pmc/articles/PMC6431951/ /pubmed/30974623 http://dx.doi.org/10.3390/polym8100347 Text en © 2016 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Najafi, Saeed
Podgornik, Rudolf
Potestio, Raffaello
Tubiana, Luca
Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers
title Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers
title_full Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers
title_fullStr Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers
title_full_unstemmed Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers
title_short Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers
title_sort role of bending energy and knot chirality in knot distribution and their effective interaction along stretched semiflexible polymers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431951/
https://www.ncbi.nlm.nih.gov/pubmed/30974623
http://dx.doi.org/10.3390/polym8100347
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