title: Effect of hydrodynamic interaction on partially stretched polymers.
abstract: We compute the effect of hydrodynamic interaction and stretching on the fluctuation properties of a polymer, with its end points held fixed. Computing the preaveraged hydrodynamic tensor exactly for this geometry, we study both flexible and semiflexible polymer chains, such as Zimm, freely jointed chain, and wormlike chain (WLC) models. We compare the spectra of relaxation-time scales for the effective normal modes of these models. The spectra differ across models with respect to the degree of stretch, but their power-law scaling with low mode numbers turns out to be the same. The characteristics of the transverse modes of WLC agree very well with the experimental data on DNA. The crossover scaling function for (1/r), the inverse of the distance along the polymer contour, yields a modified formula for the size of a "Pincus blob," appropriate for the fixed-end boundary condition.
authors.affiliation: Physics Department, Indian Institute of Technology-Bombay, Powai, Mumbai, India.
authors.forename: Anirban
authors.initials: A
authors.lastname: Sain
mesh_terms: D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D004867:Equipment Design; D005456:Fluorescent Dyes / Q000737:chemistry; D008956:Models, Chemical; D015233:Models, Statistical; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D011108:Polymers / Q000737:chemistry; D013499:Surface Properties
chemical_list: D005456:Fluorescent Dyes; D011108:Polymers; D004247:DNA