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Efficient sampling of knotting-unknotting pathways for semiflexible Gaussian chains

Micheletti, Cristian
•
Orland, Henri
2017
  • journal article

Periodico
POLYMERS
Abstract
We propose a stochastic method to generate exactly the overdamped Langevin dynamics of semi-flexible Gaussian chains, conditioned to evolve between given initial and final conformations in a preassigned time. The initial and final conformations have no restrictions, and hence can be in any knotted state. Our method allows the generation of statistically independent paths in a computationally efficient manner. We show that these conditioned paths can be exactly generated by a set of local stochastic differential equations. The method is used to analyze the transition routes between various knots in crossable filamentous structures, thus mimicking topological reconnections occurring in soft matter systems or those introduced in DNA by topoisomerase enzymes. We find that the average number of crossings, writhe and unknotting number are not necessarily monotonic in time and that more complex topologies than the initial and final ones can be visited along the route.
DOI
10.3390/polym9060196
WOS
WOS:000404218500012
Archivio
http://hdl.handle.net/20.500.11767/63581
info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85020250087
http://www.mdpi.com/2073-4360/9/6/196/pdf
https://arxiv.org/abs/1704.01743
Diritti
open access
Soggetti
  • Knot

  • Langevin bridge

  • Reconnection path

  • Chemistry (all)

  • Polymers and Plastics...

  • Settore FIS/03 - Fisi...

Scopus© citazioni
1
Data di acquisizione
Jun 14, 2022
Vedi dettagli
Web of Science© citazioni
2
Data di acquisizione
Mar 24, 2024
Visualizzazioni
2
Data di acquisizione
Apr 19, 2024
Vedi dettagli
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