Topological Friction and Relaxation Dynamics of Spatially Confined Catenated Polymers.

Giulia Amici,Michele Caraglio,Cristian Micheletti,Enzo Orlandini

doi:10.1021/acsmacrolett.1c00594

Abstract

We study catenated ring polymers confined inside channels and slits with Langevin dynamics simulations and address how the contour position and size of the interlocked or physically linked region evolve with time. We show that the catenation constraints generate a drag, or topological friction, that couples the contour motion of the interlocked regions. Notably, the coupling strength decreases as the interlocking is made tighter, but also shorter, by confinement. Though the coupling strength differs for channel and slit confinement, the data outline a single universal curve when plotted against the size of the linked region. Finally, we study how the relaxation kinetics changes after one of the rings is cut open and conclude that considering interlocked circular polymers is key for isolating the manifestations of topological friction. The results ought to be relevant for linked biomolecules in experimental or biological confining conditions.

Highlights

We study catenated ring polymers confined inside channels and slits with Langevin dynamics simulations and address how the contour position and size of the interlocked or physically linked region evolve with time
The convergent theoretical and experimental focus on interlocked molecular systems has given us much insight about the unusual physical properties of these systems, e.g., how they typically establish low-dimensional extended structures, how they elongate and flatten when sheared,[13−15] and how they are affected by adsorbing surfaces[6] or varying quality of the solvent.[16]
Multichain entanglement is found in genomic DNA subject to anisotropic spatial confinement in vivo, such as intertwined sister nucleoids inside newly divided bacteria[17] and intermingled chromosomes inside eukaryotic nuclei.[4]

Summary

Corresponding Author

Authors Giulia Amici − Scuola Internazionale Superiore di Studi Avanzati - SISSA, 34136 Trieste, Italy Michele Caraglio − Institut für Theoretische Physik, Universität Innsbruck, A-6020 Innsbruck, Austria; orcid.org/0000-0001-6567-6923 Enzo Orlandini − Department of Physics and Astronomy, University of Padova, I-35100 Padova, Italy; orcid.org/ 0000-0003-3680-9488 Complete contact information is available at: https://pubs.acs.org/10.1021/acsmacrolett.1c00594 Notes The authors declare no competing financial interest.

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■ REFERENCES