title: Tethered DNA dynamics in shear flow.
abstract: We study the cyclic dynamics of a single polymer tethered to a hard wall in shear flow using Brownian dynamics, the lattice Boltzmann method, and a recent stochastic event-driven molecular dynamics algorithm. We focus on the dynamics of the free end (last bead) of the tethered chain and we examine the cross-correlation function and power spectral density of the chain extensions in the flow and gradient directions as a function of chain length N and dimensionless shear rate Wi. Extensive simulation results suggest a classical fluctuation-dissipation stochastic process and question the existence of periodicity of the cyclic dynamics, as previously claimed. We support our numerical findings with a simple analytical calculation for a harmonic dimer in shear flow.
authors: Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1691, USA.
authors: Yu
authors: Y
authors: Zhang
authors: Aleksandar
authors: A
authors: Donev
authors: Todd
authors: T
authors: Weisgraber
authors: Berni J
authors: BJ
authors: Alder
authors: Michael D
authors: MD
authors: Graham
authors: Juan J
authors: JJ
authors: de Pablo
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008956:Models, Chemical; D011108:Polymers / Q000737:chemistry*; D012996:Solutions
chemical_list: D011108:Polymers; D012996:Solutions; D004247:DNA