Special Issue "Semiflexible Polymers III"

A special issue of Polymers (ISSN 2073-4360). This special issue belongs to the section "Polymer Physics and Theory".

Deadline for manuscript submissions: 15 November 2023 | Viewed by 2808

Special Issue Editors

Prof. Dr. Martin Kröger
E-Mail Website1 Website2
Guest Editor
Polymer Physics, Department of Materials, ETH Zurich, Leopold-Ruzicka-Weg 4, CH-8093 Zurich, Switzerland
Interests: polymer physics; computational physics; applied mathematics; stochastic differential equations; coarse-graining; biophysics
Special Issues, Collections and Topics in MDPI journals
Department of Physics, Kyungpook National University, Daugu, Korea
Interests: statistical mechanics of polymers; semiflexible polymers; elasticity

Special Issue Information

Dear Colleagues,

Continuing on the success of the Special Issue of Polymers, “Semiflexible Polymers I and II”, we are delighted to open a new Special Issue entitled, “Semiflexible Polymers III”. 

Semiflexible chains serve as a coarse-grained representation of macromolecules whenever random or self-avoiding walk statistics do not apply, i.e., when the dimensions of a macromolecule do not significantly exceed its persistence length. Semiflexibility also manifests itself when a polymer is strongly stretched, or when it is confined by boundaries. Prominent systems containing semiflexible chains include various biomolecules, such as DNA and the cytoskeletal filaments (F-actin, nanotubes, intermediate filaments), dendronized polymers, and their networks and brushes. Semiflexible chains are an integral part of polymer physics education. However, even if fundamental results have been obtained for linear semiflexible chains, the number of open issues is larger. The minimal theoretical model which acts as the classical paradigm in the field is the worm-like chain (WLC), a locally inextensible, fluctuating, one-dimensional curve with bending stiffness. Despite its appeal and success with long dsDNA, however, it is inadequate to describe the conformations and elasticity of many semiflexible systems. Electrostatic interactions, quenched or reversible inhomogeneities along the polymer contour, supramolecular structures (e.g., actin bundles and DNA nanotubes, which themselves may act as semiflexible building blocks of higher-order assemblies), cross-links, helicity, and twist stiffness modify the simple, uniform WLC behavior. Besides thermal and possibly quenched disorders, semiflexible polymers in living matter also experience active noise. The polymer itself may have activity, converting chemical energy to mechanical work, or it can be passive, interacting with an active environment. 

This Special Issue is concerned with the statics and dynamics, simulation and application of semiflexible polymers in the WLC framework and beyond, including linear, branched, ring, and thick polymers and their networks or gels. Topics may include polymer solutions or scaling behavior, knots, entanglements, interactions, lattice and continuous representations, buckling, bond breaking, translocation, and scattering properties in both equilibrium and out-of-equilibrium situations. Papers may also address semiflexible chains subjected to flow and external stimuli or fields, and semiflexible chains in composites or in biological systems subjected to confinement or as part of nematic or other networks. Ideally, contributions will focus on fundamental results, algorithms, mechanisms, statistical physics, and/or applications that will help to compile the current state-of-the-art findings. Both original contributions and reviews are welcome. 

Prof. Dr. Martin Kröger
Dr. Panayotis Benetatos
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Polymers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • semiflexible polymers
  • worm-like polymers
  • polymer brushes
  • polymer physics
  • bending
  • buckling
  • tumbling
  • translocation
  • networks
  • entanglements
  • liquid crystals
  • composites
  • confinement
  • actin filaments
  • dna
  • supramolecular structures
  • bundles
  • electrostatic interactions
  • active matter
  • twist
  • helicity
  • disorder
  • phase transitions

Published Papers (3 papers)

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Research

Article
Elasticity of a Grafted Rod-like Filament with Fluctuating Bending Stiffness
Polymers 2023, 15(10), 2307; https://doi.org/10.3390/polym15102307 - 15 May 2023
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Abstract
Quite often polymers exhibit different elastic behavior depending on the statistical ensemble (Gibbs vs. Helmholtz). This is an effect of strong fluctuations. In particular, two-state polymers, which locally or globally fluctuate between two classes of microstates, can exhibit strong ensemble inequivalence with negative [...] Read more.
Quite often polymers exhibit different elastic behavior depending on the statistical ensemble (Gibbs vs. Helmholtz). This is an effect of strong fluctuations. In particular, two-state polymers, which locally or globally fluctuate between two classes of microstates, can exhibit strong ensemble inequivalence with negative elastic moduli (extensibility or compressibility) in the Helmholtz ensemble. Two-state polymers consisting of flexible beads and springs have been studied extensively. Recently, similar behavior was predicted in a strongly stretched wormlike chain consisting of a sequence of reversible blocks, fluctuating between two values of the bending stiffness (the so called reversible wormlike chain, rWLC). In this article, we theoretically analyse the elasticity of a grafted rod-like semiflexible filament which fluctuates between two states of bending stiffness. We consider the response to a point force at the fluctuating tip in both the Gibbs and the Helmholtz ensemble. We also calculate the entropic force exerted by the filament on a confining wall. This is done in the Helmholtz ensemble and, under certain conditions, it yields negative compressibility. We consider a two-state homopolymer and a two-block copolymer with two-state blocks. Possible physical realizations of such a system would be grafted DNA or carbon nanorods undergoing hybridization, or grafted F-actin bundles undergoing collective reversible unbinding. Full article
(This article belongs to the Special Issue Semiflexible Polymers III)
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Article
Activation/Inhibition of Gene Expression Caused by Alcohols: Relationship with the Viscoelastic Property of a DNA Molecule
Polymers 2023, 15(1), 149; https://doi.org/10.3390/polym15010149 - 28 Dec 2022
Cited by 1 | Viewed by 858
Abstract
Alcohols are used in the life sciences because they can condense and precipitate DNA. Alcohol consumption has been linked to many diseases and can alter genetic activity. In the present report, we carried out experiments to make clear how alcohols affect the efficiency [...] Read more.
Alcohols are used in the life sciences because they can condense and precipitate DNA. Alcohol consumption has been linked to many diseases and can alter genetic activity. In the present report, we carried out experiments to make clear how alcohols affect the efficiency of transcription-translation (TX-TL) and translation (TL) by adapting cell-free gene expression systems with plasmid DNA and RNA templates, respectively. In addition, we quantitatively analyzed intrachain fluctuations of single giant DNA molecules based on the fluctuation-dissipation theorem to gain insight into how alcohols affect the dynamical property of a DNA molecule. Ethanol (2–3%) increased gene expression levels four to five times higher than the control in the TX-TL reaction. A similar level of enhancement was observed with 2-propanol, in contrast to the inhibitory effect of 1-propanol. Similar alcohol effects were observed for the TL reaction. Intrachain fluctuation analysis through single DNA observation showed that 1-propanol markedly increased both the spring and damping constants of single DNA in contrast to the weak effects observed with ethanol, whereas 2-propanol exhibits an intermediate effect. This study indicates that the activation/inhibition effects of alcohol isomers on gene expression correlate with the changes in the viscoelastic mechanical properties of DNA molecules. Full article
(This article belongs to the Special Issue Semiflexible Polymers III)
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Article
Elasticity of Semiflexible ZigZag Nanosprings with a Point Magnetic Moment
Polymers 2023, 15(1), 44; https://doi.org/10.3390/polym15010044 - 22 Dec 2022
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Abstract
Kinks can appear along the contour of semiflexible polymers (biopolymers or synthetic ones), and they affect their elasticity and function. A regular sequence of alternating kink defects can form a semiflexible nanospring. In this article, we theoretically analyze the elastic behavior of such [...] Read more.
Kinks can appear along the contour of semiflexible polymers (biopolymers or synthetic ones), and they affect their elasticity and function. A regular sequence of alternating kink defects can form a semiflexible nanospring. In this article, we theoretically analyze the elastic behavior of such a nanospring with a point magnetic dipole attached to one end while the other end is assumed to be grafted to a rigid substrate. The rod-like segments of the nanospring are treated as weakly bending wormlike chains, and the propagator (Green’s function) method is used in order to calculate the conformational and elastic properties of this system. We analytically calculate the distribution of orientational and positional fluctuations of the free end, the force-extension relation, as well as the compressional force that such a spring can exert on a planar wall. Our results show how the magnetic interaction affects the elasticity of the semiflexible nanospring. This sensitivity, which is based on the interplay of positional and orientational degrees of freedom, may prove useful in magnetometry or other applications. Full article
(This article belongs to the Special Issue Semiflexible Polymers III)
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