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 , Slobodan Žumer
{"title":"Topology in soft and biological matter","authors":"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 , Slobodan Žumer","doi":"10.1016/j.physrep.2024.04.002","DOIUrl":null,"url":null,"abstract":"<div><p>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.</p><p>This review is dedicated to the memory of Marek Cieplak.</p></div>","PeriodicalId":404,"journal":{"name":"Physics Reports","volume":"1075 ","pages":"Pages 1-137"},"PeriodicalIF":23.9000,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Physics Reports","FirstCategoryId":"4","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0370157324001339","RegionNum":1,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PHYSICS, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
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.
This review is dedicated to the memory of Marek Cieplak.
过去几年中，我们对生物和软物质中拓扑约束的出现和后果的理解取得了显著进步。与（生物）聚合物系统有关的例子比比皆是，从单个聚合物和蛋白质的结的表征到整个染色体和聚合物熔体的表征，不一而足。与此同时，在描述复杂流体中拓扑和物理特性之间的相互作用方面也取得了长足的进步，研究人员现在可以通过开发技术来控制各种类型液晶中缺陷的形成及其相互作用。由于技术进步以及实验与日益复杂的数值模拟相结合，拓扑生物和软物质是一个充满活力的研究领域，吸引着来自广泛学科的科学家。然而，由于现代科学的高度专业化，许多成果仍然局限于各自的特定领域，不同的行话使得研究人员难以分享观点，也难以共同对正在发生的各种现象形成全面的看法。在这些动机的驱使下，我们在此全面概述了从 DNA 和基因组组织到纠缠蛋白质、高分子材料、液晶和理论物理等系统中的拓扑效应，旨在减少软物质和生物物理不同领域之间的障碍。我们特别注意对聚合物和连续材料的拓扑特性进行连贯的正式介绍，并突出不同系统中拓扑对象的出现、特征和效应的基本共同点。综述的后半部分专门介绍了某些问题的最新成果，特别是拓扑约束对聚合物材料粘弹性能的影响；拓扑约束与基因组组织的关系；讨论蛋白质中结和其他纠缠的出现及其可能的影响；复杂流体中拓扑缺陷和孤子的出现及其影响。
期刊介绍：
Physics Reports keeps the active physicist up-to-date on developments in a wide range of topics by publishing timely reviews which are more extensive than just literature surveys but normally less than a full monograph. Each report deals with one specific subject and is generally published in a separate volume. These reviews are specialist in nature but contain enough introductory material to make the main points intelligible to a non-specialist. The reader will not only be able to distinguish important developments and trends in physics but will also find a sufficient number of references to the original literature.
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