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Polymers
Special Issues
Models of Polymer Physics for Biological System
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Models of Polymer Physics for Biological System

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

Deadline for manuscript submissions: closed (5 January 2023) | Viewed by 7808

Special Issue Editors

Dr. Andrea Maria Chiariello

E-Mail Website
Guest Editor
Dipartimento di Fisica "E. Pancini", Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
Interests: polymer physics; chromatin organization; epigenetics; complex systems; statistical physics; computational biology; biophysics
Dr. Simona Bianco

E-Mail Website
Guest Editor
Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany
Interests: statistical physics; complex systems; chromatin organization; polymer physics; computational biology; biophysics; epigenetics

Special Issue Information

Dear Colleagues,

Polymer physics is a powerful tool for investigating several biological processes occurring in the cell. Indeed, models from polymer physics have a broad range of applications and have been successfully employed to study, for example, the three-dimensional structure of chromosomes at multiple scales, the phase-separation of protein aggregates, single-cell chromatin organization, DNA–protein interaction mechanisms and gene regulation. Furthermore, the constant advances in experimental technologies, integrated with polymer physics-based computational methods, is rapidly improving our understanding of cell structure, activity and dynamics. 

This Special Issue is dedicated to review or research articles in this interdisciplinary research field where physics and biology meet. The issue will cover a broad range of experimental, computational and theoretical studies based on polymer physics aiming to describe those aspects relevant to the cell. The research topics will also include molecular dynamics simulations, predictive methods, data analysis, meso-scale and coarse-grained polymer models, equilibrium and off-equilibrium processes and further applications. 

This issue will provide progress in and state-of-art applications of polymer physics to tackle specific and general questions arising in cell biology. 

Dr. Andrea Maria Chiariello
Dr. Simona Bianco
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

  • Polymer physics
  • Phase transitions
  • Molecular dynamics
  • Nucleic acids
  • Proteins
  • Chromatin
  • Computational biology
  • Soft matter
  • Bioinformatics

Published Papers (3 papers)

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Research

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29 pages, 811 KiB  
Article
Theory of Weakly Polydisperse Cytoskeleton Filaments
by Vadim Warshavsky and Marcelo Marucho
Polymers 2022, 14(10), 2042; https://doi.org/10.3390/polym14102042 - 17 May 2022
Cited by 1 | Viewed by 1313
Abstract
Cytoskeleton filaments have the extraordinary ability to change conformations dynamically in response to alterations of the number density of actins/tubulin, the number density and type of binding agents, and the electrolyte concentration. This property is crucial for eukaryotic cells to achieve specific biological [...] Read more.
Cytoskeleton filaments have the extraordinary ability to change conformations dynamically in response to alterations of the number density of actins/tubulin, the number density and type of binding agents, and the electrolyte concentration. This property is crucial for eukaryotic cells to achieve specific biological functions in different cellular compartments. Conventional approaches to biopolymers’ solution break down for cytoskeleton filaments because they entail several approximations to treat their polyelectrolyte and mechanical properties. In this article, we introduce a novel density functional theory for polydisperse, semiflexible cytoskeleton filaments. The approach accounts for the equilibrium polymerization kinetics, length and orientation filament distributions, as well as the electrostatic interaction between filaments and the electrolyte. This is essential for cytoskeleton polymerization in different cell compartments generating filaments of different lengths, sometimes long enough to become semiflexible. We characterized the thermodynamics properties of actin filaments in electrolyte aqueous solutions. We calculated the free energy, pressure, chemical potential, and second virial coefficient for each filament conformation. We also calculated the phase diagram of actin filaments’ solution and compared with the corresponding results in in vitro experiments. Full article
(This article belongs to the Special Issue Models of Polymer Physics for Biological System)
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Review

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15 pages, 2814 KiB  
Review
The Physics of DNA Folding: Polymer Models and Phase-Separation
by Andrea Esposito, Alex Abraham, Mattia Conte, Francesca Vercellone, Antonella Prisco, Simona Bianco and Andrea M. Chiariello
Polymers 2022, 14(9), 1918; https://doi.org/10.3390/polym14091918 - 09 May 2022
Cited by 5 | Viewed by 2675
Abstract
Within cell nuclei, several biophysical processes occur in order to allow the correct activities of the genome such as transcription and gene regulation. To quantitatively investigate such processes, polymer physics models have been developed to unveil the molecular mechanisms underlying genome functions. Among [...] Read more.
Within cell nuclei, several biophysical processes occur in order to allow the correct activities of the genome such as transcription and gene regulation. To quantitatively investigate such processes, polymer physics models have been developed to unveil the molecular mechanisms underlying genome functions. Among these, phase-separation plays a key role since it controls gene activity and shapes chromatin spatial structure. In this paper, we review some recent experimental and theoretical progress in the field and show that polymer physics in synergy with numerical simulations can be helpful for several purposes, including the study of molecular condensates, gene-enhancer dynamics, and the three-dimensional reconstruction of real genomic regions. Full article
(This article belongs to the Special Issue Models of Polymer Physics for Biological System)
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18 pages, 1077 KiB  
Review
Insights into Fluctuations of Structure of Proteins: Significance of Intermediary States in Regulating Biological Functions
by Zahoor Ahmad Parray, Mohammad Shahid and Asimul Islam
Polymers 2022, 14(8), 1539; https://doi.org/10.3390/polym14081539 - 11 Apr 2022
Cited by 2 | Viewed by 2685
Abstract
Proteins are indispensable to cellular communication and metabolism. The structure on which cells and tissues are developed is deciphered from proteins. To perform functions, proteins fold into a three-dimensional structural design, which is specific and fundamentally determined by their characteristic sequence of amino [...] Read more.
Proteins are indispensable to cellular communication and metabolism. The structure on which cells and tissues are developed is deciphered from proteins. To perform functions, proteins fold into a three-dimensional structural design, which is specific and fundamentally determined by their characteristic sequence of amino acids. Few of them have structural versatility, allowing them to adapt their shape to the task at hand. The intermediate states appear momentarily, while protein folds from denatured (D) ⇔ native (N), which plays significant roles in cellular functions. Prolific effort needs to be taken in characterizing these intermediate species if detected during the folding process. Protein folds into its native structure through definite pathways, which involve a limited number of transitory intermediates. Intermediates may be essential in protein folding pathways and assembly in some cases, as well as misfolding and aggregation folding pathways. These intermediate states help to understand the machinery of proper folding in proteins. In this review article, we highlight the various intermediate states observed and characterized so far under in vitro conditions. Moreover, the role and significance of intermediates in regulating the biological function of cells are discussed clearly. Full article
(This article belongs to the Special Issue Models of Polymer Physics for Biological System)
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