Literature DB >> 16241470

Diffusion-controlled first contact of the ends of a polymer: crossover between two scaling regimes.

Jeff Z Y Chen1, Heng-Kwong Tsao, Yu-Jane Sheng.   

Abstract

We report on Monte Carlo simulations of loop formation of an ideal flexible polymer consisting of N bonds with two reactive ends. We determine the first-passage time associated with chain looping that yields a conformation in which the end monomers are separated by a distance a--the reaction radius. In particular, our numerical results demonstrate how this time scale crosses over from tau(first) approximately N(3/2)/a to the a-independent tau(first) approximately N2 as N is increased. The existence and characteristics, of the two scaling regimes and the crossover between the two, are further illuminated by a scaling argument.

Entities:  

Year:  2005        PMID: 16241470     DOI: 10.1103/PhysRevE.72.031804

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  6 in total

1.  Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics.

Authors:  Peter J Mulligan; Yi-Ju Chen; Rob Phillips; Andrew J Spakowitz
Journal:  Biophys J       Date:  2015-08-04       Impact factor: 4.033

2.  Renormalization group analysis of polymer cyclization with non-equilibrium initial conditions.

Authors:  B A Friedman; C Yeung
Journal:  Eur Phys J E Soft Matter       Date:  2006-10-06       Impact factor: 1.890

3.  Sequence and temperature dependence of the end-to-end collision dynamics of single-stranded DNA.

Authors:  Takanori Uzawa; Takashi Isoshima; Yoshihiro Ito; Koichiro Ishimori; Dmitrii E Makarov; Kevin W Plaxco
Journal:  Biophys J       Date:  2013-06-04       Impact factor: 4.033

4.  Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics.

Authors:  Charles H Starr; Zev Bryant; Andrew J Spakowitz
Journal:  Biophys J       Date:  2022-04-11       Impact factor: 3.699

5.  The rate of intramolecular loop formation in DNA and polypeptides: the absence of the diffusion-controlled limit and fractional power-law viscosity dependence.

Authors:  Ryan R Cheng; Takanori Uzawa; Kevin W Plaxco; Dmitrii E Makarov
Journal:  J Phys Chem B       Date:  2009-10-22       Impact factor: 2.991

6.  The length and viscosity dependence of end-to-end collision rates in single-stranded DNA.

Authors:  Takanori Uzawa; Ryan R Cheng; Kevin J Cash; Dmitrii E Makarov; Kevin W Plaxco
Journal:  Biophys J       Date:  2009-07-08       Impact factor: 4.033

  6 in total

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