Literature DB >> 17911269

Spontaneous knotting of an agitated string.

Dorian M Raymer1, Douglas E Smith.   

Abstract

It is well known that a jostled string tends to become knotted; yet the factors governing the "spontaneous" formation of various knots are unclear. We performed experiments in which a string was tumbled inside a box and found that complex knots often form within seconds. We used mathematical knot theory to analyze the knots. Above a critical string length, the probability P of knotting at first increased sharply with length but then saturated below 100%. This behavior differs from that of mathematical self-avoiding random walks, where P has been proven to approach 100%. Finite agitation time and jamming of the string due to its stiffness result in lower probability, but P approaches 100% with long, flexible strings. We analyzed the knots by calculating their Jones polynomials via computer analysis of digital photos of the string. Remarkably, almost all were identified as prime knots: 120 different types, having minimum crossing numbers up to 11, were observed in 3,415 trials. All prime knots with up to seven crossings were observed. The relative probability of forming a knot decreased exponentially with minimum crossing number and Möbius energy, mathematical measures of knot complexity. Based on the observation that long, stiff strings tend to form a coiled structure when confined, we propose a simple model to describe the knot formation based on random "braid moves" of the string end. Our model can qualitatively account for the observed distribution of knots and dependence on agitation time and string length.

Entities:  

Year:  2007        PMID: 17911269      PMCID: PMC2034230          DOI: 10.1073/pnas.0611320104

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


  10 in total

1.  Knots and random walks in vibrated granular chains.

Authors:  E Ben-Naim; Z A Daya; P Vorobieff; R E Ecke
Journal:  Phys Rev Lett       Date:  2001-02-19       Impact factor: 9.161

2.  Dynamic patterns and self-knotting of a driven hanging chain.

Authors:  A Belmonte; M J Shelley; S T Eldakar; C H Wiggins
Journal:  Phys Rev Lett       Date:  2001-08-24       Impact factor: 9.161

3.  Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids.

Authors:  Javier Arsuaga; Mariel Vázquez; Sonia Trigueros; De Witt Sumners; Joaquim Roca
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-16       Impact factor: 11.205

4.  Knot complexity and the probability of random knotting.

Authors:  Miyuki K Shimamura; Tetsuo Deguchi
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2002-10-14

5.  A Lemma on Systems of Knotted Curves.

Authors:  J W Alexander
Journal:  Proc Natl Acad Sci U S A       Date:  1923-03       Impact factor: 11.205

6.  Knotting probability of a shaken ball-chain.

Authors:  J Hickford; R Jones; S Courrech du Pont; J Eggers
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2006-11-15

7.  Statistical mechanics and topology of polymer chains.

Authors:  M D Frank-Kamenetskii; A V Lukashin; A V Vologodskii
Journal:  Nature       Date:  1975-12-04       Impact factor: 49.962

8.  Knotting of random ring polymers in confined spaces.

Authors:  C Micheletti; D Marenduzzo; E Orlandini; D W Sumners; D W Summers
Journal:  J Chem Phys       Date:  2006-02-14       Impact factor: 3.488

9.  Duplex DNA knots produced by Escherichia coli topoisomerase I. Structure and requirements for formation.

Authors:  F B Dean; A Stasiak; T Koller; N R Cozzarelli
Journal:  J Biol Chem       Date:  1985-04-25       Impact factor: 5.157

10.  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

  10 in total
  19 in total

Review 1.  Knot theory in understanding proteins.

Authors:  Rama Mishra; Shantha Bhushan
Journal:  J Math Biol       Date:  2011-11-22       Impact factor: 2.259

2.  Slipknotting upon native-like loop formation in a trefoil knot protein.

Authors:  Jeffrey K Noel; Joanna I Sułkowska; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-11       Impact factor: 11.205

3.  Experimental detection of knotted conformations in denatured proteins.

Authors:  Anna L Mallam; Joseph M Rogers; Sophie E Jackson
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-14       Impact factor: 11.205

4.  The tangled web of self-tying knots.

Authors:  Andrew Belmonte
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-24       Impact factor: 11.205

5.  Dodging the crisis of folding proteins with knots.

Authors:  Joanna I Sułkowska; Piotr Sułkowski; José Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-11       Impact factor: 11.205

6.  Exploring knotting mechanisms in protein folding.

Authors:  Anna L Mallam; Elizabeth R Morris; Sophie E Jackson
Journal:  Proc Natl Acad Sci U S A       Date:  2008-11-17       Impact factor: 11.205

7.  Compression and self-entanglement of single DNA molecules under uniform electric field.

Authors:  Jing Tang; Ning Du; Patrick S Doyle
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-12       Impact factor: 11.205

8.  The energy landscape, folding pathways and the kinetics of a knotted protein.

Authors:  Michael C Prentiss; David J Wales; Peter G Wolynes
Journal:  PLoS Comput Biol       Date:  2010-07-01       Impact factor: 4.475

9.  Tying up the Loose Ends: A Mathematically Knotted Protein.

Authors:  Shang-Te Danny Hsu; Yun-Tzai Cloud Lee; Kornelia M Mikula; Sofia M Backlund; Igor Tascón; Adrian Goldman; Hideo Iwaï
Journal:  Front Chem       Date:  2021-05-24       Impact factor: 5.221

10.  Spontaneous knotting of peritoneal catheter: A report of an asymptomatic patient.

Authors:  Sandeep Mohindra; Manish Sharma
Journal:  J Pediatr Neurosci       Date:  2012-05
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