Tethered DNA dynamics in shear flow.
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.
Zhang
Yu
Y
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1691, USA.
Donev
Aleksandar
A
Weisgraber
Todd
T
Alder
Berni J
BJ
Graham
Michael D
MD
de Pablo
Juan J
JJ
D000465:Algorithms; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008956:Models, Chemical; D011108:Polymers / Q000737:chemistry*; D012996:Solutions
D011108:Polymers; D012996:Solutions; D004247:DNA