English

DNA confined in a two-dimensional strip geometry

Biological Physics 2015-06-18 v2 Soft Condensed Matter Biomolecules

Abstract

Semiflexible polymers characterized by the contour length LL and persistent length p\ell_p confined in a spatial region DD have been described as a series of ``{\em spherical blobs}'' and ``{\em deflecting lines}'' by de Gennes and Odjik for p<D\ell_p < D and pD\ell_p \gg D respectively. Recently new intermediate regimes ({\em extended de Gennes} and {\em Gauss-de Gennes}) have been investigated by Tree {\em et al.} [Phys. Rev. Lett. {\bf 110}, 208103 (2013)]. In this letter we derive scaling relations to characterize these transitions in terms of universal scaled fluctuations in dd-dimension as a function of L,pL,\ell_p, and DD, and show that the Gauss-de Gennes regime is absent and extended de Gennes regime is vanishingly small for polymers confined in a 2D strip. We validate our claim by extensive Brownian dynamics (BD) simulation which also reveals that the prefactor AA used to describe the chain extension in the Odjik limit is independent of physical dimension dd and is the same as previously found by Yang {\em et al.}[Y. Yang, T. W. Burkhardt, G. Gompper, Phys. Rev. E {\bf 76}, 011804 (2007)]. Our studies are relevant for optical maps of DNA stretched inside a nano-strip.

Keywords

Cite

@article{arxiv.1312.1298,
  title  = {DNA confined in a two-dimensional strip geometry},
  author = {Aiqun Huang and Aniket Bhattacharya},
  journal= {arXiv preprint arXiv:1312.1298},
  year   = {2015}
}

Comments

6 pages, 4 figures

R2 v1 2026-06-22T02:20:57.495Z