Random state transitions of knots: a first step towards modeling unknotting by type II topoisomerases

DOI10.1016/J.TOPOL.2006.05.010zbMATH Open1114.57005OpenAlexW2035767281WikidataQ37422803 ScholiaQ37422803MaRDI QIDQ876535FDOQ876535

M. Vazquez, Diana M. H. Nguyen, J. Arsuaga, Xia Hua, Barath Raghavan

Publication date: 18 April 2007

Published in: Topology and its Applications (Search for Journal in Brave)

Full work available at URL: http://europepmc.org/articles/pmc2778028

zbMATH Keywords

polymer modelscubic latticeBFACF-algorithmDNA knotslattice knotsrandom knottingtopoisomerase II

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Biology and other natural sciences (92-XX)

Cites Work

• A new polynomial invariant of knots and links
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• Classification of knot projections
• The first 1,701,936 knots
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• Knots in self-avoiding walks
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• A calculus for rational tangles: applications to DNA recombination
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• Tangle solutions for a family of DNA-rearranging proteins
• Rational tangle distances on knots and links
• BIOLOGICAL DISTANCES ON DNA KNOTS AND LINKS: Applications to XER recombination
• Tangle analysis of Gin site-specific recombination
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• Entanglement complexity of graphs in Z³
• The BFACF algorithm and knotted polygons
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• A general limitation on Monte Carlo algorithms of the Metropolis type
• Computer evaluation of Homfly polynomials by using Gauss codes, with a skein-template algorithm
• DNA KNOT FORMATION IN AQUEOUS SOLUTIONS
• The Writhe of Knots in the Cubic Lattice
• The writhe of a self-avoiding walk

Cited In (6)

• The abundance of unknots in various models of polymer loops
• Minimum lattice length and ropelength of knots
• The local topological free energy of proteins
• Models of random knots
• Minimum lattice length and ropelength of 2-bridge knots and links
• New evidence on the asymptotics of knotted lattice polygons via local strand-passage models

   Recommendations

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• New evidence on the asymptotics of knotted lattice polygons via local strand-passage models 👍 👎
• Knotting probabilities after a local strand passage in unknotted self-avoiding polygons 👍 👎
• Mean unknotting times of random knots and embeddings 👍 👎

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