Topology in soft and biological matter
Luca Tubiana
(1)
,
Gareth P Alexander
(2)
,
Agnese Barbensi
(3)
,
Dorothy Buck
(4)
,
Julyan H.E Cartwright
(5)
,
Mateusz Chwastyk
(6)
,
Marek Cieplak
(6)
,
Ivan Coluzza
(7)
,
Simon Čopar
(8)
,
David J Craik
(3)
,
Marco Di Stefano
(9, 10)
,
Ralf Everaers
(11)
,
Patrícia F.N Faísca
(12)
,
Franco Ferrari
(13)
,
Achille Giacometti
(14)
,
Dimos Goundaroulis
(7)
,
Ellinor Haglund
(15)
,
Ya-Ming Hou
(16)
,
Nevena Ilieva
(17)
,
Sophie E Jackson
(18)
,
Aleksandre Japaridze
(19)
,
Noam Kaplan
(20)
,
Alexander R Klotz
,
Hongbin Li
,
Christos N Likos
,
Emanuele Locatelli
(21)
,
Teresa López-León
(22)
,
Thomas Machon
(23)
,
Cristian Micheletti
(24)
,
Davide Michieletto
(25)
,
Antti Niemi
(26)
,
Wanda Niemyska
(27)
,
Szymon Niewieczerzal
(27)
,
Francesco Nitti
(28)
,
Enzo Orlandini
(29)
,
Samuela Pasquali
(30)
,
Agata P Perlinska
(27)
,
Rudolf Podgornik
(31)
,
Raffaello Potestio
(1)
,
Nicola M Pugno
(1)
,
Miha Ravnik
(8)
,
Renzo Ricca
(32)
,
Christian M Rohwer
(33)
,
Angelo Rosa
(24)
,
Jan Smrek
,
Anton Souslov
,
Andrzej Stasiak
,
Danièle Steer
(28, 34)
,
Joanna Sułkowska
,
Piotr Sułkowski
,
de Witt L Sumners
,
Carsten Svaneborg
,
Piotr Szymczak
,
Thomas Tarenzi
,
Rui Travasso
,
Peter Virnau
,
Dimitris Vlassopoulos
(35)
,
Primož Ziherl
(8)
,
Slobodan Žumer
(8)
1
UNITN -
Università degli Studi di Trento = University of Trento
2 University of Warwick [Coventry]
3 UQ [All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations] - The University of Queensland
4 Duke University [Durham]
5 UGR - Universidad de Granada = University of Granada
6 Institute of Physics, Polish Academy of Sciences
7 Rice University [Houston]
8 University of Ljubljana
9 UM2 - Université Montpellier 2 - Sciences et Techniques
10 IGH - Institut de génétique humaine
11 Phys-ENS - Laboratoire de Physique de l'ENS Lyon
12 Faculdade de Ciências [Lisboa]
13 University of Szczecin
14 University of Ca’ Foscari [Venice, Italy]
15 UHM - University of Hawai‘i [Mānoa]
16 Jefferson (Philadelphia University + Thomas Jefferson University)
17 BAS - Bulgarian Academy of Sciences
18 Department of Chemistry [Cambridge, UK]
19 KI-NANO - Kavli Institute of Nanosciences [Delft]
20 Technion - Israel Institute of Technology [Haifa]
21 Universität Wien = University of Vienna
22 ESPCI Paris - Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris
23 University of Bristol [Bristol]
24 SISSA / ISAS - Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies
25 Edin. - University of Edinburgh
26 NORDITA - Nordic Institute for Theoretical Physics
27 UW - University of Warsaw
28 APC (UMR_7164) - AstroParticule et Cosmologie
29 Unipd - Università degli Studi di Padova = University of Padua
30 BFA (UMR_8251 / U1133) - Unité de Biologie Fonctionnelle et Adaptative
31 Wenzhou University
32 UNIMI - Università degli Studi di Milano = University of Milan
33 University of Cape Town
34 Cosmologie et Gravitation
35 FORTH - Foundation for Research and Technology - Hellas
2 University of Warwick [Coventry]
3 UQ [All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations] - The University of Queensland
4 Duke University [Durham]
5 UGR - Universidad de Granada = University of Granada
6 Institute of Physics, Polish Academy of Sciences
7 Rice University [Houston]
8 University of Ljubljana
9 UM2 - Université Montpellier 2 - Sciences et Techniques
10 IGH - Institut de génétique humaine
11 Phys-ENS - Laboratoire de Physique de l'ENS Lyon
12 Faculdade de Ciências [Lisboa]
13 University of Szczecin
14 University of Ca’ Foscari [Venice, Italy]
15 UHM - University of Hawai‘i [Mānoa]
16 Jefferson (Philadelphia University + Thomas Jefferson University)
17 BAS - Bulgarian Academy of Sciences
18 Department of Chemistry [Cambridge, UK]
19 KI-NANO - Kavli Institute of Nanosciences [Delft]
20 Technion - Israel Institute of Technology [Haifa]
21 Universität Wien = University of Vienna
22 ESPCI Paris - Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris
23 University of Bristol [Bristol]
24 SISSA / ISAS - Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies
25 Edin. - University of Edinburgh
26 NORDITA - Nordic Institute for Theoretical Physics
27 UW - University of Warsaw
28 APC (UMR_7164) - AstroParticule et Cosmologie
29 Unipd - Università degli Studi di Padova = University of Padua
30 BFA (UMR_8251 / U1133) - Unité de Biologie Fonctionnelle et Adaptative
31 Wenzhou University
32 UNIMI - Università degli Studi di Milano = University of Milan
33 University of Cape Town
34 Cosmologie et Gravitation
35 FORTH - Foundation for Research and Technology - Hellas
Alexander R Klotz
- Fonction : Auteur
Hongbin Li
- Fonction : Auteur
Christos N Likos
- Fonction : Auteur
Samuela Pasquali
- Fonction : Auteur
- PersonId : 772677
- ORCID : 0000-0003-1487-0894
- IdRef : 184520533
Jan Smrek
- Fonction : Auteur
Anton Souslov
- Fonction : Auteur
Andrzej Stasiak
- Fonction : Auteur
Joanna Sułkowska
- Fonction : Auteur
Piotr Sułkowski
- Fonction : Auteur
de Witt L Sumners
- Fonction : Auteur
Carsten Svaneborg
- Fonction : Auteur
Piotr Szymczak
- Fonction : Auteur
Thomas Tarenzi
- Fonction : Auteur
Rui Travasso
- Fonction : Auteur
Peter Virnau
- Fonction : Auteur
Résumé
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.