Regulation of topological entanglement in ring polymers
dc.contributor.advisor
Marenduzzo, Davide
dc.contributor.advisor
Michieletto, Davide
dc.contributor.author
Bonato, Andrea
dc.date.accessioned
2023-03-28T16:21:39Z
dc.date.available
2023-03-28T16:21:39Z
dc.date.issued
2023-03-28
dc.description.abstract
Entanglement abundance and complexity can be both beneficial and detrimental to the biological and mechanical function of polymers. In living organisms, for instance, DNA entanglement is so impactful that its proliferation might have catastrophic consequences, such as mutation and death.
Even though entanglement regulation is therefore necessary to keep the behaviour of both biological and synthetic polymer systems under control, how it is practically achieved is currently not well understood for many systems. To fill this void, by formulating analytic predictions and performing computer simulations, we study the equilibrium properties of sets of geometrically and topologically constrained ring polymers, and model how entanglement abundance and complexity is regulated in both biological and synthetic polymer systems.
We find that a complex of rings undergoing recombination under confinement is distinguished by the presence of a topological gelation transition, which can be controlled by the stiffness or the concentration of the rings. Furthermore, we show that an efficient and controlled way to resolve entanglement by transient cross stranding is having it compete entropically with a slip-linked polymer network. Finally, we study multicomponent polymer links where the monomers can be distributed among the components in all possible ways, and show that, asymptotically, due to entropy maximisation, one of the rings grows at the expense of the others, which behave as roots sliding along the contour of the growing component.
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dc.identifier.uri
https://hdl.handle.net/1842/40450
dc.identifier.uri
http://dx.doi.org/10.7488/era/3218
dc.language.iso
en
en
dc.publisher
The University of Edinburgh
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dc.relation.hasversion
A. Bonato, D. Marenduzzo, D. Michieletto, and E. Orlandini. Topological gelation of reconnecting polymers. Proceedings of the National Academy of Sciences, 119(44):e2207728119, 2022.
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dc.relation.hasversion
A. Bonato, D. Marenduzzo, and D. Michieletto. Simplifying topological entanglements by entropic competition of slip-links. Physical Review Research, 3(4):043070, 2021
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dc.relation.hasversion
A. Bonato, E. Orlandini, and S .G. Whittington. Asymptotics of linked polygons. Journal of Physics A: Mathematical and Theoretical, 53(38):385002, 2020
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dc.relation.hasversion
A. Bonato, E. Orlandini, and S. G. Whittington. Asymptotics of multicomponent linked polygons. Journal of Physics A: Mathematical and Theoretical, 54(23):235002, 2021.
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dc.relation.hasversion
J. K. Ryu, C. Bouchoux, H. W. Liu, E. Kim, M. Minamino, R. de Groot, A. J. Katan, A. Bonato, D. Marenduzzo, D. Michieletto, F. Uhlmann, and C. Dekker. Phase separation induced by cohesin SMC protein complexes. Sci. Adv., 7(7):1–10, 2021
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dc.relation.hasversion
A. Bonato, C. A. Brackley, J. Johnson, D. Michieletto, and D. Mareduzzo. Chromosome Compaction and Chromatin Stiffness Enhance Diffusive Loop Extrusion by Slip-Link Proteins. Soft Matter, 16:2406– 2414, 2020.
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dc.subject
polymers
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dc.subject
analytic predictions
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dc.subject
entangled polymers
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dc.subject
constrained ring polymers
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dc.title
Regulation of topological entanglement in ring polymers
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dc.type
Thesis or Dissertation
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dc.type.qualificationlevel
Doctoral
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dc.type.qualificationname
PhD Doctor of Philosophy
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