Dynamics of DNA in the Flow-Gradient Plane of Steady Shear Flow:  Observations and Simulations

• Published in: Macromolecules 2005-03, Vol.38 (5), p.1967-1978
• Main Authors: Schroeder, Charles M, Teixeira, Rodrigo E, Shaqfeh, Eric S. G, Chu, Steven
• Format: Article
• Language: English
• Subjects: Applied sciences; Biological and medical sciences; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; In solution. Condensed state. Thin layers; Miscellaneous; Molecular biophysics; Natural polymers; Physico-chemical properties of biomolecules; Physicochemistry of polymers
• ISSN: 0024-9297; 1520-5835
• DOI: 10.1021/ma0480796

The dynamical behavior of DNA in steady shear flow has been elucidated using a combination of Brownian dynamics (BD) simulation and single molecule visualization using fluorescence microscopy. Observations of DNA motion in the flow-gradient plane of shear flow using a novel flow apparatus allow for measurement of the gradient-direction polymer thickness (δ2), a microscopic conformational property that has direct influence on macroscopic polymer solution properties. To complement experimental results for λ-phage DNA (22 μm in length) and 84 μm DNA, we present BD simulation results for DNA in terms of both free-draining bead−spring models and models including both intramolecular hydrodynamic interactions (HI) and excluded volume (EV) interactions. Good agreement between experiments and BD simulations is obtained for ensemble averaged measurements of polymer extension, δ2, and orientation angle over a wide range of flow strengths. Macroscopic solution properties, including the polymer contribution to the shear viscosity (ηp) and first normal stress coefficient ( ), are calculated in BD simulations. Power law scalings of ηp and from the single molecule experiment and BD simulation agree well with bulk rheological characterization of dilute polymer solutions. Histograms of polymer extension demonstrate good agreement between experiment and BD simulation, though histograms of δ2 from BD simulation slightly differ from experimental results. Cross-correlations of polymer extension and δ2 display rich dynamical polymer behavior, which we discuss on a physical basis. Finally, the power spectral density of polymer extension and δ2 is presented for DNA for both single molecule experiment and BD simulation.