Literature DB >> 16576754

Scaling behavior of random knots.

Akos Dobay1, Jacques Dubochet, Kenneth Millett, Pierre-Edouard Sottas, Andrzej Stasiak.   

Abstract

Using numerical simulations we investigate how overall dimensions of random knots scale with their length. We demonstrate that when closed non-self-avoiding random trajectories are divided into groups consisting of individual knot types, then each such group shows the scaling exponent of approximately 0.588 that is typical for self-avoiding walks. However, when all generated knots are grouped together, their scaling exponent becomes equal to 0.5 (as in non-self-avoiding random walks). We explain here this apparent paradox. We introduce the notion of the equilibrium length of individual types of knots and show its correlation with the length of ideal geometric representations of knots. We also demonstrate that overall dimensions of random knots with a given chain length follow the same order as dimensions of ideal geometric representations of knots.

Year:  2003        PMID: 16576754      PMCID: PMC156249          DOI: 10.1073/pnas.0330884100

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  9 in total

1.  A topological invariant to predict the three-dimensional writhe of ideal configurations of knots and links.

Authors:  C Cerf; A Stasiak
Journal:  Proc Natl Acad Sci U S A       Date:  2000-04-11       Impact factor: 11.205

2.  Critical exponents for random knots

Authors: 
Journal:  Phys Rev Lett       Date:  2000-10-30       Impact factor: 9.161

3.  Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads.

Authors:  S B Smith; L Finzi; C Bustamante
Journal:  Science       Date:  1992-11-13       Impact factor: 47.728

4.  Electrophoretic mobility of DNA knots.

Authors:  A Stasiak; V Katritch; J Bednar; D Michoud; J Dubochet
Journal:  Nature       Date:  1996-11-14       Impact factor: 49.962

5.  Sedimentation and electrophoretic migration of DNA knots and catenanes.

Authors:  A V Vologodskii; N J Crisona; B Laurie; P Pieranski; V Katritch; J Dubochet; A Stasiak
Journal:  J Mol Biol       Date:  1998-04-24       Impact factor: 5.469

6.  Effect of excluded volume on topological properties of circular DNA.

Authors:  K V Klenin; A V Vologodskii; V V Anshelevich; A M Dykhne; M D Frank-Kamenetskii
Journal:  J Biomol Struct Dyn       Date:  1988-06

7.  Knotting of a DNA chain during ring closure.

Authors:  S Y Shaw; J C Wang
Journal:  Science       Date:  1993-04-23       Impact factor: 47.728

8.  Probability of DNA knotting and the effective diameter of the DNA double helix.

Authors:  V V Rybenkov; N R Cozzarelli; A V Vologodskii
Journal:  Proc Natl Acad Sci U S A       Date:  1993-06-01       Impact factor: 11.205

9.  Tightness of random knotting.

Authors:  V Katritch; W K Olson; A Vologodskii; J Dubochet; A Stasiak
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  2000-05
  9 in total
  16 in total

1.  Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots.

Authors:  Alessandro Flammini; Amos Maritan; Andrzej Stasiak
Journal:  Biophys J       Date:  2004-08-23       Impact factor: 4.033

2.  Topologically driven swelling of a polymer loop.

Authors:  Nathan T Moore; Rhonald C Lua; Alexander Y Grosberg
Journal:  Proc Natl Acad Sci U S A       Date:  2004-08-31       Impact factor: 11.205

3.  Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields.

Authors:  C Weber; A Stasiak; P De Los Rios; G Dietler
Journal:  Biophys J       Date:  2006-02-10       Impact factor: 4.033

4.  Simulations of knotting in confined circular DNA.

Authors:  C Micheletti; D Marenduzzo; E Orlandini; D W Sumners
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

5.  A semiflexible polymer ring acting as a nano-propeller.

Authors:  H Wada
Journal:  Eur Phys J E Soft Matter       Date:  2009-01       Impact factor: 1.890

6.  Facile Characterization of Topology of DNA Catenanes.

Authors:  Lin Li; Ran An; Jiaxuan Tang; Zhe Sui; Guoqing Wang; Makoto Komiyama; Xingguo Liang
Journal:  Biophys J       Date:  2020-02-15       Impact factor: 4.033

7.  Action at hooked or twisted-hooked DNA juxtapositions rationalizes unlinking preference of type-2 topoisomerases.

Authors:  Zhirong Liu; Lynn Zechiedrich; Hue Sun Chan
Journal:  J Mol Biol       Date:  2010-05-10       Impact factor: 5.469

8.  Inferring global topology from local juxtaposition geometry: interlinking polymer rings and ramifications for topoisomerase action.

Authors:  Zhirong Liu; E Lynn Zechiedrich; Hue Sun Chan
Journal:  Biophys J       Date:  2006-04-01       Impact factor: 4.033

9.  The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture.

Authors:  Julien Dorier; Andrzej Stasiak
Journal:  Nucleic Acids Res       Date:  2010-07-31       Impact factor: 16.971

10.  Topological origins of chromosomal territories.

Authors:  Julien Dorier; Andrzej Stasiak
Journal:  Nucleic Acids Res       Date:  2009-09-02       Impact factor: 16.971

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