Single molecule visualization of DNA in the nonhomogeneous shear flow in a microchannel
Smith, Connie Kathleen
Doctor of Philosophy
The dynamics of individual DNA molecules were analyzed under the nonhomogeneous shear flow in a rectangular microchannel. The effects of a complex flow field on individual molecular behavior have never before been experimentally studied. Understanding the specific behavior of complex fluids in flow can lead to enhanced control of applications from synthetic polymer coatings to microfluidics and DNA microarrays. The molecular dynamics were measured though fluorescence microscopy with digital image acquisition. The flow channel, which was plasma etched into a silicon wafer for precise control of features, allowed for visualization of molecules in the plane defined by the velocity and velocity gradient. The extension of each DNA molecule in the ultra-dilute solution was measured in flow as a function of its position in the channel, which was then related to the Weissenberg number (Wi = lambdagamma). Wi values ranging from 0 to 30 were simultaneously studied in this work. Even at relatively high Wi, the molecules stretched to less than 50% of their full contour length because shear flow is a combination of elongation and rotation. The combination of these two forces caused partially extended molecules to tumble onto themselves before reaching maximum extension. These results were found to be in good agreement with data previously acquired for molecules in homogeneous shear flow. The molecules were not evenly distributed across the channel width or depth while flowing. Regions devoid of molecules extended 7 mum from each wall due to hydrodynamic interactions between the DNA molecules and the walls of the channel. Molecules also moved away from the centerline of the channel in both width and depth due to normal stresses. After cessation of flow, the depletion region in the middle of the channel disappeared and the width of the depletion regions adjacent to the walls was reduced to 4 mum because weaker static boundary layer effects replaced the flow-induced hydrodynamic interactions. This research brings us closer to fully understanding how individual molecules in solution respond to nonhomogeneous shear flow.