Topology in soft and biological matter

L Tubiana; GP Alexander; A Barbensi; D Buck; JHE Cartwright; M Chwastyk; M Cieplak; I Coluzza; S Copar; DJ Craik; M Di Stefano; R Everaers; PFN Faísca; F Ferrari; A Giacometti; D Goundaroulis; E Haglund; YM Hou; N Ilieva; SE Jackson; A Japaridze; N Kaplan; AR Klotz; H Li; CN Likos; E Locatelli; T Lopez-Leon; T Machon; C Micheletti; D Michieletto; A Niemi; W Niemyska; S Niewieczerzal; F Nitti; E Orlandini; S Pasquali; AP Perlinska; R Podgornik; R Potestio; NM Pugno; M Ravnik; R Ricca; CM Rohwer; A Rosa; J Smrek; A Souslov; A Stasiak; D Steer; J Sulkowska; P Sulkowski; DWL Sumners; C Svaneborg; P Szymczak; T Tarenzi; R Travasso; P Virnau; D Vlassopoulos; P Ziherl; S Zumer

doi:10.1016/j.physrep.2024.04.002

Topology in soft and biological matter

L Tubiana^*, GP Alexander, A Barbensi, D Buck, JHE Cartwright, M Chwastyk, M Cieplak, I Coluzza, S Copar, DJ Craik, M Di Stefano, R Everaers, PFN Faísca, F Ferrari, A Giacometti, D Goundaroulis, E Haglund, YM Hou, N Ilieva, SE JacksonA Japaridze, N Kaplan, AR Klotz, H Li, CN Likos, E Locatelli, T Lopez-Leon, T Machon, C Micheletti, D Michieletto, A Niemi, W Niemyska, S Niewieczerzal, F Nitti, E Orlandini, S Pasquali, AP Perlinska, R Podgornik, R Potestio, NM Pugno, M Ravnik, R Ricca, CM Rohwer, A Rosa, J Smrek, A Souslov, A Stasiak, D Steer, J Sulkowska, P Sulkowski, DWL Sumners, C Svaneborg, P Szymczak, T Tarenzi, R Travasso, P Virnau, D Vlassopoulos, P Ziherl, S Zumer

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

Abstract

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.

Original language	English
Pages (from-to)	1-137
Number of pages	137
Journal	Physics Reports
Volume	1075
Early online date	16 May 2024
DOIs	https://doi.org/10.1016/j.physrep.2024.04.002
Publication status	Published - 18 Jul 2024

Keywords / Materials (for Non-textual outputs)

DNA topology & genome organization
Entangled proteins
Polymers and polymer melts
Topologically complex fluids
Topology in living matter - protein folding
Topology in soft condensed matter

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10.1016/j.physrep.2024.04.002Licence: Creative Commons: Attribution (CC-BY)

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Tubiana, L., Alexander, GP., Barbensi, A., Buck, D., Cartwright, JHE., Chwastyk, M., Cieplak, M., Coluzza, I., Copar, S., Craik, DJ., Di Stefano, M., Everaers, R., Faísca, PFN., Ferrari, F., Giacometti, A., Goundaroulis, D., Haglund, E., Hou, YM., Ilieva, N., ... Zumer, S. (2024). Topology in soft and biological matter. Physics Reports, 1075, 1-137. https://doi.org/10.1016/j.physrep.2024.04.002

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title = "Topology in soft and biological matter",

abstract = "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.",

keywords = "DNA topology & genome organization, Entangled proteins, Polymers and polymer melts, Topologically complex fluids, Topology in living matter - protein folding, Topology in soft condensed matter",

author = "L Tubiana and GP Alexander and A Barbensi and D Buck and JHE Cartwright and M Chwastyk and M Cieplak and I Coluzza and S Copar and DJ Craik and {Di Stefano}, M and R Everaers and PFN Fa{\'i}sca and F Ferrari and A Giacometti and D Goundaroulis and E Haglund and YM Hou and N Ilieva and SE Jackson and A Japaridze and N Kaplan and AR Klotz and H Li and CN Likos and E Locatelli and T Lopez-Leon and T Machon and C Micheletti and D Michieletto and A Niemi and W Niemyska and S Niewieczerzal and F Nitti and E Orlandini and S Pasquali and AP Perlinska and R Podgornik and R Potestio and NM Pugno and M Ravnik and R Ricca and CM Rohwer and A Rosa and J Smrek and A Souslov and A Stasiak and D Steer and J Sulkowska and P Sulkowski and DWL Sumners and C Svaneborg and P Szymczak and T Tarenzi and R Travasso and P Virnau and D Vlassopoulos and P Ziherl and S Zumer",

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Tubiana, L, Alexander, GP, Barbensi, A, Buck, D, Cartwright, JHE, Chwastyk, M, Cieplak, M, Coluzza, I, Copar, S, Craik, DJ, Di Stefano, M, Everaers, R, Faísca, PFN, Ferrari, F, Giacometti, A, Goundaroulis, D, Haglund, E, Hou, YM, Ilieva, N, Jackson, SE, Japaridze, A, Kaplan, N, Klotz, AR, Li, H, Likos, CN, Locatelli, E, Lopez-Leon, T, Machon, T, Micheletti, C, Michieletto, D, Niemi, A, Niemyska, W, Niewieczerzal, S, Nitti, F, Orlandini, E, Pasquali, S, Perlinska, AP, Podgornik, R, Potestio, R, Pugno, NM, Ravnik, M, Ricca, R, Rohwer, CM, Rosa, A, Smrek, J, Souslov, A, Stasiak, A, Steer, D, Sulkowska, J, Sulkowski, P, Sumners, DWL, Svaneborg, C, Szymczak, P, Tarenzi, T, Travasso, R, Virnau, P, Vlassopoulos, D, Ziherl, P & Zumer, S 2024, 'Topology in soft and biological matter', Physics Reports, vol. 1075, pp. 1-137. https://doi.org/10.1016/j.physrep.2024.04.002

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AU - Tubiana, L

AU - Alexander, GP

AU - Barbensi, A

AU - Buck, D

AU - Cartwright, JHE

AU - Chwastyk, M

AU - Cieplak, M

AU - Coluzza, I

AU - Copar, S

AU - Craik, DJ

AU - Di Stefano, M

AU - Everaers, R

AU - Faísca, PFN

AU - Ferrari, F

AU - Giacometti, A

AU - Goundaroulis, D

AU - Haglund, E

AU - Hou, YM

AU - Ilieva, N

AU - Jackson, SE

AU - Japaridze, A

AU - Kaplan, N

AU - Klotz, AR

AU - Li, H

AU - Likos, CN

AU - Locatelli, E

AU - Lopez-Leon, T

AU - Machon, T

AU - Micheletti, C

AU - Michieletto, D

AU - Niemi, A

AU - Niemyska, W

AU - Niewieczerzal, S

AU - Nitti, F

AU - Orlandini, E

AU - Pasquali, S

AU - Perlinska, AP

AU - Podgornik, R

AU - Potestio, R

AU - Pugno, NM

AU - Ravnik, M

AU - Ricca, R

AU - Rohwer, CM

AU - Rosa, A

AU - Smrek, J

AU - Souslov, A

AU - Stasiak, A

AU - Steer, D

AU - Sulkowska, J

AU - Sulkowski, P

AU - Sumners, DWL

AU - Svaneborg, C

AU - Szymczak, P

AU - Tarenzi, T

AU - Travasso, R

AU - Virnau, P

AU - Vlassopoulos, D

AU - Ziherl, P

AU - Zumer, S

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Topology in soft and biological matter

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Topologically Active Polymers

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Topology in soft and biological matter

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Topologically Active Polymers

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