Tethered DNA dynamics in shear flow

Yu Zhang, Aleksandar Donev, Todd Weisgraber, Berni J. Alder, Michael D. Graham, Juan J. De Pablo

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number234902
JournalJournal of Chemical Physics
Volume130
Issue number23
DOIs
StatePublished - 2009

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Stochastic Processes
Periodicity
Molecular Dynamics Simulation
Shear flow
shear flow
Polymers
deoxyribonucleic acid
DNA
Power spectral density
stochastic processes
Random processes
Chain length
beads
Dimers
Shear deformation
cross correlation
Molecular dynamics
periodic variations
dissipation
dimers

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry
  • Medicine(all)

Cite this

Zhang, Y., Donev, A., Weisgraber, T., Alder, B. J., Graham, M. D., & De Pablo, J. J. (2009). Tethered DNA dynamics in shear flow. Journal of Chemical Physics, 130(23), [234902]. https://doi.org/10.1063/1.3149860

Tethered DNA dynamics in shear flow. / Zhang, Yu; Donev, Aleksandar; Weisgraber, Todd; Alder, Berni J.; Graham, Michael D.; De Pablo, Juan J.

In: Journal of Chemical Physics, Vol. 130, No. 23, 234902, 2009.

Research output: Contribution to journalArticle

Zhang, Y, Donev, A, Weisgraber, T, Alder, BJ, Graham, MD & De Pablo, JJ 2009, 'Tethered DNA dynamics in shear flow', Journal of Chemical Physics, vol. 130, no. 23, 234902. https://doi.org/10.1063/1.3149860
Zhang Y, Donev A, Weisgraber T, Alder BJ, Graham MD, De Pablo JJ. Tethered DNA dynamics in shear flow. Journal of Chemical Physics. 2009;130(23). 234902. https://doi.org/10.1063/1.3149860
Zhang, Yu ; Donev, Aleksandar ; Weisgraber, Todd ; Alder, Berni J. ; Graham, Michael D. ; De Pablo, Juan J. / Tethered DNA dynamics in shear flow. In: Journal of Chemical Physics. 2009 ; Vol. 130, No. 23.
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