Effect of hydrodynamic interactions on DNA dynamics in extensional flow: Simulation and single molecule experiment

Charles M. Schroeder, Eric S.G. Shaqfeh, Steven Chu

Research output: Contribution to journalArticlepeer-review


Intramolecular hydrodynamic interactions (HI) in flexible polymer chains influence both the equilibrium and nonequilibrium physical properties of macromoecules. In this work, we utilize a combination of single molecule experimental techniques and Brownian dynamics (BD) simulation to investigate the role of HI and excluded-volume (EV) interactions for DNA molecules ranging in contour length from 150 to 1300 μm. Epifluorescence microscopy is used to directly observe the dynamics of DNA molecules in planar extensional flow, and a semiimplicit bead-spring BD algorithm with fluctuating HI and EV interactions is presented. Quantitatitative agreement between ensemble average transient molecular extension in experiment and BD simulation is shown for DNA with 150 μm contour length. Simulations show polymer conformation hysteresis for larger DNA chains (1300 μm in length) when HI and EV parameters are chosen such that simulation results match the experimental polymer relaxation time and polymer stretch at flow strengths below the coil-stretch transition. Furthermore, conformation-dependent resistivities are extracted from BD simulation for DNA chains 1300 μm in length, and this drag functionality is utilized in a coarse-grained Brownian dumbbell model with variable resistivity. Finally, steady-state molecular extension results from the coarse-grained model are compared to simple polymer kinetic theory for a dumbbell with variable resistivity.

Original languageEnglish (US)
Pages (from-to)9242-9256
Number of pages15
Issue number24
StatePublished - Nov 30 2004
Externally publishedYes

ASJC Scopus subject areas

  • Organic Chemistry
  • Polymers and Plastics
  • Inorganic Chemistry
  • Materials Chemistry


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