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Doctor of Philosophy / Department of Chemistry / Daniel A. Higgins / This dissertation describes the application of wide-field single-molecule fluorescence microscopy techniques to investigations of DNA-surface interactions on chemically graded organosilane surfaces. The adsorption and desorption behaviors of double-stranded (ds) plasmid DNA along the amino-trimethoxysilane and octyl-trichlorosilane gradients were explored as a function of solution pH, solution ionic strength and surface properties. The results provide an improved fundamental understanding of DNA interactions with different surfaces and are certain to aid in the development and advancement of DNA-based biological and biomedical devices. Three distinct experiments were performed in completion of the work for this dissertation. In the first study, total internal reflection fluorescence (TIRF) microscopy was employed to study DNA interactions with aminosilane gradient surfaces under relatively acidic and basic environments. Electrical potentials were applied to assist DNA adsorption and desorption. The single-molecule data clearly showed that DNA capture and release was achieved on the monolayer and submonolayer coated regions of the aminosilane gradient surface under relatively basic pH conditions, with the help of an electrical potential. Meanwhile, DNA adsorption was found to be quasi-reversible on the multilayers at the high aminosilane end of the gradient in the relatively acidic solution. The results of these studies demonstrate the importance of manipulating the electrostatic interactions of DNA with charged surfaces in order to achieve DNA capture and release. The fundamental knowledge of the DNA-surface interactions gained in these studies will be helpful in diverse fields ranging from the layer-by-layer assembly of polyelectrolyte-based thin films to the selective electronic sensing of charged biomolecules. In the second study, the local dielectric properties of the least polar environments in dsDNA were assessed by using the solvatochromic dye, nile red, as a polarity-sensitive probe. TIRF spectroscopic imaging methods were employed in these studies. Although the dielectric constant within the least polar regions of dsDNA was previously predicted by theoretical and computational methods, no experimental measurements of its value had been reported to date. The results provide important knowledge of the factors governing the polarity of DNA microenvironments to which intercalators bind, and provide vital experimental support for the values determined in computational studies. In the third study, TIRF microscopy and single molecule tracking methods were employed to study DNA interactions with an opposed two-component C8-silane and aminosilane gradient surface as a function of solution pH. The mobility of surface-adsorbed DNA molecules was explored and quantified in these studies. The preliminary results further demonstrated the importance of electrostatic interactions over hydrophobic interactions in governing the adsorption of DNA to surfaces. The mobility of surface-adsorbed DNA was found to be largely independent of position along the two-component gradient. These studies were originally undertaken as a route to observation of cooperative effects that are believed to govern DNA-surface binding. Unfortunately, no clear evidence of cooperative effects was observed at the mixed regions of the two-component gradient surface.

Deposition of nanoscale thickness films is ubiquitous in micro- and nano-scale device manufacturing. Current techniques such as spin-coating and chemical vapor deposition are designed to create only uniform thin films, and can be wasteful in material consumption. They lack the ability to adaptively prescribe desired film thickness profiles. This dissertation presents a novel inkjet-based zero-waste polymer deposition process referred to as Jet and Coat of Adaptive Sustainable Thin Films or J-CAST. The core of this process is built on an experimentally validated multi-scale fluid evolution model, based on extensions of lubrication theory. This model involves a nano-scale fluid film sandwiched between two flat plates: a compliant superstrate and a rigid substrate, with spatial topography on both surfaces. Accounting for the flexural elasticity of the compliant superstrate, and describing the temporal evolution of the fluid film in the presence of different boundary conditions reveals that instead of seeking process equilibrium, non-equilibrium transients should be exploited to guide film deposition. This forms the first core concept behind the process. This concept also enables robust full-wafer processes for creation of uniform films as well as nanoscale films with prescribed variation of thickness at mm-scale spatial wavelengths. The use of inkjets enables zero-waste adaptive material deposition with the preferred drop volumes and locations obtained from an inverse optimization formulation. This forms the second core concept behind the process. The optimization is based on the prescribed film thickness profile and typically involves >100,000 integer parameters. Using simplifying approximations for the same, three specific applications have been discussed - gradient surfaces in combinatorial materials science and research, elliptical profiles with ~10km radius of curvature for X-ray nanoscopy applications and polishing of starting wafer surfaces for mitigation of existing nanotopography. In addition, the potential of extending the demonstrated process to high throughput roll-roll systems has also been mentioned by modifying the model to incorporate the compliance of the substrate along with that of the superstrate. / text

The research topic of liquid drop interaction with solid surfaces is being actively pursued to gain in-depth understanding of several practical cases such as the impingement of fuel spray droplets on surfaces like combustion chamber walls and piston top of an I.C. engine, heat transfer via spray impingement, ink-jet printing, etc. In most of the cases, the physical and flow properties of the liquid drop/spray may be fixed whereas it may be possible to tune the physical and chemical properties of the solid surface thereby enabling to control the interaction process. The present work belongs to the study of liquid drop-solid surface interaction process with special focus on the physical characteristics of solid surface. The thesis reports an experimental study of the dynamics of millimetric water drops impacted onto the junction of dual-textured substrates made of stainless steel. The dual-textured substrates consisted of hydrophobic (textured) and hydrophilic (smooth) portions. The entire textured portion comprised of parallel groove-like structures separated by solid posts/pillars. Two dual-textured substrates, which differ only in the geometry of their textured portions, were employed. Surface topography features of the dual-textured substrates were characterized using scanning electron microscopy (SEM) and optical surface profilometer. The wetting behavior of the textured and smooth portions of the substrates, quantified in terms of the equilibrium, advancing, and receding contact angles adopted by a water drop on the surface portions, was characterized experimentally through the methods of sessile drop formation, captive needle volume addition, and drop evaporation under ambient conditions. Free-falling water drops were impacted from a height onto the junction between the hydrophobic (textured) and hydrophilic (smooth) portions of the dual-textured substrates. A set of twelve different impact experiments were conducted on each of the target substrates with drop impact velocity (Uo) ranging from 0.37 to 1.50 m/sec. The dynamics of drop impact were captured using a high speed camera with frame rate ranging from 3000 to 10000 frames per second. From the captured frames, the temporal variations of the impacting drop parameters were measured using a MATLAB-assisted program. A systematic analysis of experimental data revealed the existence of four distinct regimes of drop dynamics on the dual-textured substrate: (a) early inertia driven drop spreading, (b) primary drop receding, (c) secondary spreading on the hydrophilic portion, and (d) final equilibrium regimes. It is shown that the drop impact dynamics during the early inertia driven impact regime remains unaffected by the dual-texture feature of the substrate. A larger retraction speed of impacting drop liquid observed on the hydrophobic portion of the substrate makes the drop liquid on the higher wettability/hydrophilic portion to advance further (secondary drop spreading). The net horizontal drop velocity towards the hydrophilic portion of the dual-textured substrate decreases with increasing drop impact velocity. The available experimental results suggest that the movement of bulk drop liquid away from the impact point during drop impact on the dual-textured substrate is larger for the impact of low inertia drops. A semi-empirical model, based on the balance of the wettability gradient, contact angle hysteresis, and viscous forces acting on impacted drop liquid on the substrate, is formulated to predict the movement of bulk drop liquid away from the impact point (ξ). A satisfactory comparison between the model predictions and the experimental measurements is reported for the variation of ξ with Uo.