Experimental and numerical studies of tethered DNA dynamics in shear flow

Polymer physics has a rich tradition spanning nearly two centuries. In the 1830s, Henri Braconnot and coworkers were perhaps the first to work on what is today known as polymer science when they derived semi-synthetic materials from naturally occurring cellulose. However, the true nature of polymers, as long chain molecules, had not been proposed until 1910 by Pickles. It was not until the 1950's when polymer models were developed using statistical mechanics. Recently, the field has been revitalized by the ability to study individual polymer molecules for the first time. The development of DNA single molecule fluorescence microscopy coupled with ever increasing computational power has opened the door to molecular level understanding of polymer physics, resolving old disputes and uncovering new interesting phenomena.;In this work, we use a combination of theoretical predictions and lambda-phage DNA single molecule fluorescence microscopy to study the behavior of polymers tethered to surfaces. Brownian dynamics simulations of a number of coarse-grained polymer models---dynamic and equilibrium Kratky-Porod chains as well as bead-spring chains---were completed and compared with analytical and experimental results.;First, an expression is developed for the entropic exclusion force experienced by a tethered polymer chain. We propose that, for a freely jointed chain, a modification to the free entropic force of kBT/y is needed in the direction normal to the surface. Analogously, we propose that for a wormlike chain, a modification of 2kBT/y is needed, due to the finite curvature of the model. Then, the reliability of discretized bead spring simulations containing this modified entropic force are analyzed using Kratky-Porod simulations and are found to reproduce most statistics, except for those very near the surface, such as end-wall contact.;Next, experiments of tethered lambda-phage DNA in shear flow are presented for the first time in the flow-gradient plane. The tethering surface chemistry proved to be arduous work, but with the aide of contact angle and ellipsometry measurements, success was achieved. Extension behavior was shown to agree well with bead spring simulations, but deviations were discovered for weak flows in the extensional fluctuations, mean distance from the wall, and orientation angle. Cyclic dynamics---where the polymer continuously diffuses away from the wall, subsequently undergoes stretch in the flow direction, is then "entropically pulled back" towards the wall, and finally recoils---was observed and quantified through correlation and power spectral densities. Again, quantitative agreement was observed between experiments and bead spring simulations. The onset of cyclic dynamics was found to occur at Wi ≈ 3 and was found to decline with increasing Wi up to ≈ 200.;Finally, a reliable procedure was developed utilizing Dip Pen Nanolithography to controllably tether DNA to gold surfaces. Preliminary experiments were performed and successful tethering was achieved, an important first step toward creating DNA scaffolds for molecular wires. However, further research is needed to fully develop the process and successfully double tether DNA molecules between gold electrodes.