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

DOI10.1016/J.TOPOL.2006.05.010MaRDI QIDQ876535zbMATHOpenAlexWikidataFDO

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

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)

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Cites work

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• DNA KNOT FORMATION IN AQUEOUS SOLUTIONS
• Entanglement complexity of graphs in Z³
• Knots in self-avoiding walks
• MINIMAL KNOTS IN THE CUBIC LATTICE
• Rational tangle distances on knots and links
• Tangle analysis of Gin site-specific recombination
• Tangle solutions for a family of DNA-rearranging proteins
• The BFACF algorithm and knotted polygons
• The Writhe of Knots in the Cubic Lattice
• The first 1,701,936 knots
• The writhe of a self-avoiding walk

Cited in

(8)

• The local topological free energy of proteins
• Minimum lattice length and ropelength of 2-bridge knots and links
• Models of random knots
• Minimum lattice length and ropelength of knots
• The abundance of unknots in various models of polymer loops
• New evidence on the asymptotics of knotted lattice polygons via local strand-passage models
• Modelling state transitions in knot space motivated by type II topoisomerase action
• The effect of juxtaposition angle on knot reduction in a lattice polygon model of strand passage

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