Topology in soft and biological matter

Autor(en)

, Luca Tubiana, Gareth P. Alexander, Agnese Barbensi, Dorothy Buck, Julyan H.E. Cartwright, Mateusz Chwastyk, Marek Cieplak, Ivan Coluzza, Simon Čopar, David J. Craik, Marco Di Stefano, Ralf Everaers, Patrícia F.N. Faísca, Franco Ferrari, Achille Giacometti, Dimos Goundaroulis, Ellinor Haglund, Ya Ming Hou, Nevena Ilieva, Sophie E. Jackson, Aleksandre Japaridze, Noam Kaplan, Alexander R. Klotz, Hongbin Li, Christos N. Likos, Emanuele Locatelli, Teresa López-León, Thomas Machon, Cristian Micheletti, Davide Michieletto, Antti Niemi, Wanda Niemyska, Szymon Niewieczerzal, Francesco Nitti, Enzo Orlandini, Samuela Pasquali, Agata P. Perlinska, Rudolf Podgornik, Raffaello Potestio, Nicola M. Pugno, Miha Ravnik, Renzo Ricca, Christian M. Rohwer, Angelo Rosa, Jan Smrek, Anton Souslov, Andrzej Stasiak, Danièle Steer, Joanna Sułkowska, Piotr Sułkowski, De Witt L. Sumners, Carsten Svaneborg, Piotr Szymczak, Thomas Tarenzi, Rui Travasso, Peter Virnau, Dimitris Vlassopoulos, Primož Ziherl, Slobodan Žumer

Abstrakt

The last years have witnessed remarkable advances in our understanding of the emergence and consequences of topological constraints in biological and soft matter. Examples are abundant in relation to (bio)polymeric systems and range from the characterization of knots in single polymers and proteins to that of whole chromosomes and polymer melts. At the same time, considerable advances have been made in the description of the interplay between topological and physical properties in complex fluids, with the development of techniques that now allow researchers to control the formation of and interaction between defects in diverse classes of liquid crystals. Thanks to technological progress and the integration of experiments with increasingly sophisticated numerical simulations, topological biological and soft matter is a vibrant area of research attracting scientists from a broad range of disciplines. However, owing to the high degree of specialization of modern science, many results have remained confined to their own particular fields, with different jargon making it difficult for researchers to share ideas and work together towards a comprehensive view of the diverse phenomena at play. Compelled by these motivations, here we present a comprehensive overview of topological effects in systems ranging from DNA and genome organization to entangled proteins, polymeric materials, liquid crystals, and theoretical physics, with the intention of reducing the barriers between different fields of soft matter and biophysics. Particular care has been taken in providing a coherent formal introduction to the topological properties of polymers and of continuum materials and in highlighting the underlying common aspects concerning the emergence, characterization, and effects of topological objects in different systems. The second half of the review is dedicated to the presentation of the latest results in selected problems, specifically, the effects of topological constraints on the viscoelastic properties of polymeric materials; their relation with genome organization; a discussion on the emergence and possible effects of knots and other entanglements in proteins; the emergence and effects of topological defects and solitons in complex fluids. This review is dedicated to the memory of Marek Cieplak.

Organisation(en)

Computergestützte Physik und Physik der Weichen Materie

Externe Organisation(en)

Università degli Studi di Trento, INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, University of Warwick, University of Queensland, Duke University, Universidad de Granada, Instituto Andaluz de Ciencias de La Tierra (IACT), Polish Academy of Sciences (PAS), Rice University, University of Ljubljana, Université de Montpellier, Laboratoire de Physique ENS de Lyon, Universidade de Lisboa, University of Szczecin, Universita Ca' Foscari, Venezia, European Centre for Living Technology, Baylor College of Medicine, University of Hawaii at Manoa, Thomas Jefferson University, Bulgarian Academy of Sciences (BAS), University of Cambridge, Delft University of Technology, Technion - Israel Institute of Technology, California State University, Long Beach, University of British Columbia (UBC), Università degli Studi di Padova, Istituto Nazionale di Fisica Nucleare (INFN), Roma, Archéologie et Philologie d'Orient et d'Occident - AOROC, University of Bristol, Scuola Internazionale Superiore di Studi Avanzati, University of Edinburgh, MRC Human Genetics Unit, Uppsala University, Beijing Institute of Technology, University of Warsaw, Université Paris VII - Paris-Diderot, University of the Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), University of London, Jožef Stefan Institute (IJS), Università degli Studi di Milano-Bicocca, Beijing University of Technology, University of Cape Town, Max Planck Institut für Intelligente Systeme, Center for Integrative Genomics, Université de Lausanne, Schweizer Institut für Bioinformatik, École Normale Supérieure, Paris, Florida State University, University of Southern Denmark (SDU), University of Birmingham, Universidade de Coimbra, Johannes Gutenberg-Universität Mainz, Foundation for Research and Technology—Hellas (FORTH), University of Crete

Journal

Physics Reports

Band

1075

Seiten

1-137

Anzahl der Seiten

137

ISSN

0370-1573

DOI

https://doi.org/10.1016/j.physrep.2024.04.002

Publikationsdatum

07-2024

Peer-reviewed

Ja

ÖFOS 2012

103015 Kondensierte Materie, 106006 Biophysik

Schlagwörter

ASJC Scopus Sachgebiete

Allgemeine Physik und Astronomie

Link zum Portal

https://ucrisportal.univie.ac.at/de/publications/cc26523d-24af-4856-a2b3-77892ae1b87b