DNA confined in a two-dimensional strip geometry

    Authors

    A. Q. Huang;A. Bhattacharya

    Comments

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    Abbreviated Journal Title

    Epl

    Keywords

    SEMIFLEXIBLE POLYMERS; CHAIN MODEL; ROD LIMIT; DYNAMICS; CHANNELS; NANOCHANNELS; STATISTICS; EXTENSION; Physics, Multidisciplinary

    Abstract

    Semiflexible polymers characterized by the contour length L and persistent length lp confined in a spatial region D have been described as a series of " spherical blobs" and " deflecting lines" by de Gennes and Odjik for l(p) < D and lp > > D, respectively. Recently new intermediate regimes (extended de Gennes and Gauss- de Gennes) have been investigated by Tree et al. (Phys. Rev. Lett., 110 (2013) 208103). In this letter we derive scaling relations to characterize these transitions in terms of universal scaled fluctuations in d- dimension as a function of Lp, and D, and show that the Gauss- de Gennes regime is absent and the extended de Gennes regime is vanishingly small for polymers confined in a 2D strip. We validate our claim by an extensive Brownian dynamics (BD) simulation which also reveals that the prefactor A used to describe the chain extension in the Odjik limit is independent of the physical dimension d and is the same as previously found by Yang et al. (Phys. Rev. E, 76 (2007) 011804). Our studies are relevant for optical maps of DNA stretched inside a nanostrip.

    Journal Title

    Epl

    Volume

    106

    Issue/Number

    1

    Publication Date

    1-1-2014

    Document Type

    Article

    Language

    English

    First Page

    6

    WOS Identifier

    WOS:000335657300021

    ISSN

    0295-5075

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