Michieletto Topological Interactions in Ring Polymers

1. Auflage 2016
ISBN: 978-3-319-41042-5
Verlag: Springer Nature Switzerland
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 135 Seiten

Reihe: Springer Theses

Ring polymers are one of the last big mysteries in polymer physics, and this thesis tackles the problem of describing their behaviour when interacting in dense solutions and with complex environments and reports key findings that help shed light on these complex issues. The systems investigated are not restricted to artificial polymer systems, but also cover biologically inspired ensembles, contributing to the broad applicability and interest of the conclusions reached. One of the most remarkable findings is the unambiguous evidence that rings inter-penetrate when in dense solutions; here this behaviour is shown to lead to the emergence of a glassy state solely driven by the topology of the constituents. This novel glassy state is unconventional in its nature and, thanks to its universal properties inherited from polymer physics, will attract the attention of a wide range of physicists in the years to come. 

After his undergraduate studies in Padova (Italy) Davide Michieletto moved to the UK in 2011 where he attended the Doctoral Training Centre in Complexity Science at the University of Warwick until 2015. During this time he worked on a number of projects, the main one with Prof. Matthew Turner leading to his PhD in Physics and Complexity Science for a study of Topological Interactions in Ring Polymers.  In September 2015 he  became a Post-Doctoral Research Associate at the University of Edinburgh, working with Prof. Davide Marenduzzo on biophysical models for DNA and chromatin organisation in the cell nucleus.

Autoren/Hrsg.

Michieletto, Davide

Inhaltsverzeichnis

1;Publications related to this thesis:(1) D. Michieletto, D. Marenduzzo, E. Orlandini, G.P. Alexander, M.S. Turner, Threading Dynamics of Ring Polymers in a Gel, ACS Macro Lett., 3, 255–259 (2014)(2) D. Michieletto, D. Marenduzzo, E. Orlandini, G.P. Alexander, M.S. Turner, Dynamics of Self-Threading Polymers in a Gel, Soft Matter, 10, 5936–5944 (2014)(3) D. Michieletto, E. Orlandini, M.S. Turner, Rings in Random Environments: Sensing Disorder Through Topology, Soft Matter, 11, 1100–1106 (2015)(4) D. Michieletto, D. Marenduzzo, E. Orlandini, Is the Kinetoplast DNA a Percolating Network of Linked Rings at its Critical Point?., Phys. Biol., 12, 036001 (2015)(5) D. Michieletto, D. Marenduzzo, E. Orlandini, Topological Patterns in Two-dimensional Gel Electrophoresis of DNA Knots, Proc. Natl. Acad. Sci. USA, 112 (40), E5471–E5477 (2015)(6) D. Michieletto and M.S. Turner, A Topologically Driven Glass in Ring Polymers, Proc. Natl. Acad. Sci. USA, doi:10.1073/pnas.1520665113 (2016);6
2;Supervisor’s Foreword;7
3;Abstract;10
4;Acknowledgments;11
5;Contents;12
6;1 Introduction;14
6.1;References;22
7;2 Predicting the Behaviour of Rings in Solution;24
7.1;2.1 Statics;25
7.1.1;2.1.1 The Size of a Crumpled Coil;25
7.1.2;2.1.2 Contact Exponents for the Crumpled Globule;30
7.1.3;2.1.3 The Structure Factor;32
7.2;2.2 Dynamics;33
7.2.1;2.2.1 Diffusion Coefficient and Relaxation Time;33
7.2.2;2.2.2 How Rings Relax Stress;36
7.2.3;2.2.3 Inter-Coil Correlations Probed by Dynamic Scattering;37
7.3;References;39
8;3 Molecular Dynamics Models;41
8.1;3.1 Molecular Dynamics Scheme;42
8.1.1;3.1.1 Non-bonded Potentials;42
8.1.2;3.1.2 Bonded Potentials;43
8.1.3;3.1.3 Brownian Dynamics;45
8.2;3.2 Modelling;48
8.2.1;3.2.1 Modelling (Knotted) Ring Polymers;48
8.2.2;3.2.2 Modelling a Physical Gel;53
8.3;References;55
9;4 Threading Rings;58
9.1;4.1 Threading of Rings in a Gel;59
9.1.1;4.1.1 Detecting Threadings Between Rings;61
9.1.2;4.1.2 Extensive Threading Leads to Extensive Correlations;64
9.1.3;4.1.3 The Emergence of a Spanning Network of Inter-Threaded Chains;69
9.2;4.2 Threading of Rings in Dense Solutions;71
9.2.1;4.2.1 Overlapping Crumpled Globules;72
9.2.2;4.2.2 The Slow Exchange Dynamics of Rings;75
9.2.3;4.2.3 Inducing a Topological Glass by Randomly Pinning Rings;77
9.3;4.3 Conclusions;85
9.4;References;87
10;5 A Bio-Physical Model for the Kinetoplast DNA;90
10.1;5.1 Modelling the Network Replication;93
10.2;5.2 The Stable Point Is a Marginally Linked Network;96
10.3;5.3 Redundancy in the Genetic Material Allows for Faster Replication Times;99
10.4;5.4 Conclusions;102
10.5;References;103
11;6 The Role of Topology in DNA Gel Electrophoresis;106
11.1;6.1 Gel Electrophoresis of DNA Rings and Strands;109
11.1.1;6.1.1 Linear Polymers Are Insensitive to Microscopic Disorder;110
11.1.2;6.1.2 Getting More from Pushing Less;112
11.1.3;6.1.3 Topology Can Sense Disorder;114
11.2;6.2 Gel Electrophoresis of DNA Knots;116
11.2.1;6.2.1 Non-monotonic Speed of DNA Knots in Gel;117
11.2.2;6.2.2 Entanglement with Dangling Ends;120
11.2.3;6.2.3 An Equivalent Random Walk Description;124
11.3;6.3 Conclusions;127
11.4;References;129
12;7 Conclusions;132
13;Appendix AIdentifying Knots;134
14;References;135