Controlling the orientation of liquid crystal molecules in LC displays is extremely important for optimizing device performance. The method most commonly used in industry today involves rubbing the surface of the polymer-coated glass substrates used in the displays with a velvet cloth to create microscopic grooves. Berreman theory states that the liquid crystal molecules then align along the direction of the grooves. Alternatively, some literature shows that the friction caused by rubbing aligns the polymer chains in the surface layer which then attract and align the liquid crystal molecules along the direction of the chains. Even now, it is still unclear exactly how the process of rubbing the surface causes the liquid crystal molecules to align in an orderly manner. This thesis describes a systematic study of the physical and chemical influence of the substrate on the alignment and orientation of liquid crystal molecules. We used Fourier Transform Infrared spectroscopy (FTIR) to identify surface chemistry, contact angle measurements to determine the surface energy, and atomic force microscopy (AFM) to observe the alignment of liquid crystal on the surfaces. In the course of this study, we have gained insight into how the physical and chemical properties of the surface affect the molecular arrangement in the solid-liquid interface. Our results can be applied not only to LCD technology, but more generally to biochips and biosensor devices.

Atomic force microscopy (AFM) is an important technology that allows researchers to probe local surface properties at nanometer length scales. In addition to surface topography, the AFM can probe many types of tip-surface interactions (including adhesion and friction) to gain a better understanding of the chemical properties of surfaces. This thesis contains two experiments which utilize AFM to in addition to several other techniques to study (1) Self Assembled Monolayer (SAM) formation and corrosion and (2) intermolecular and surface/molecular effects on gramicidin film formation and molecular orientation. In the first experiment, N-octadecyltrichlorosilane (OTS) molecules were self-assembled onto silicon samples. We observed that OTS required a very short time (about 15 seconds) to complete the formation of the monolayer on surface. However, this SAM film was highly susceptible to corrosion by the strong oxidant (KMnO4), resulting in a chemical change to the film from hydrophobic functional groups (CH3) to hydrophilic functional groups (OH). In subsequent experiments, we observed that if the SAMs were formed using longer exposure times (about 24 hours), they were highly resistant to corrosion. Fourier Transform Infrared Spectroscopy (FTIR) and X-Ray Photoelectron Spectroscopy (XPS) also showed that the 24 hour growth SAM films were densely packed. These results indicate that SAM films based on organosilane molecules can protect the surface from corrosion, and further that more densely packed SAMs exhibit better anti-corrosion performance than less dense films. In the second experiment, the antibacterial peptide Gramicidin was used to study how intermolecular and surface energy properties can influence the aggregation and film formation of molecules on several surfaces. Gramicidin has a unique physical and chemical structure with hydrophobic side chain and hydrophilic ends. Here, we have used three different substrates (Silicon, Mica, and Graphite) to study intermolecular interactions, aggregation, and orientation of Gramicidin peptide. Langmuir-Blodgett methods were also used to study aggregation and molecular orientation at the solid-liquid interface.

Self assembled monolayer films (SAMs) deposited on silicon surfaces have gained considerable interest due to their ability to modify surface properties for advanced applications in sensors, MEMS, and NEMS devices. These molecular films are typically deposited on silicon surfaces from solution using a variety of solvents, which can influence the molecular packing and quality of the films. To better understand these effects, we have performed a systematic solvent effect study of the growth of n-Octadecyltrichlorosilane (OTS) on silicon substrates using chloroform, dichloromethane, toluene, benzene and hexadecane. The films were characterized using contact angle measurements, Fourier Transform Infrared Spectroscopy (FTIR), and Atomic Force Microscopy (AFM) to evaluate the SAM growth rate and film quality. Lateral Force Microscopy (LFM) and transmission FTIR were used to characterize the molecular packing. Finally, we used AFM to make adhesion measurements on the films and correlated these results with friction data. These techniques provide a means to characterize the local nanoscale packing of the films. The Hertzian contact model was used to model and describe the adhesion and friction result. Our results show that using hexadecane as the solvent produced OTS films with the highest density molecular packing. By comparing to Langmuir-Blodgett SAM film deposition methods, we show that it is the intermolecular interaction between the solvent molecules and OTS that determines this density. Thus, the structure and chemical properties of the solvent molecule strongly influences the molecular packing, quality, and performance of the SAM film.

Many proteins are known to actively interact with biological, as well as inorganic and synthetic surfaces that are widely used in nano- and bio-technology as biosensing platforms and in tissue engineering. Amyloid fibrils are insoluble protein aggregates in beta-sheet conformation that are implicated in at least 20 diseases for which no cure is currently available. The molecular mechanism of fibril formation, as well as the mechanism of fibril clusters interacting with lipid membrane surfaces is currently unknown. The lipid membrane surface has a complex biochemical composition and is also electrostatically non-homogeneous. Currently, the experimental data available for amyloid fibril formation both on lipid and artificial surfaces is limited. The goal of our study is to investigate how the physical properties of the surfaces affect binding of amyloid peptides and affect the fibril formation. We seek to elucidate the effect of electrostatic interactions of amyloid peptides with surfaces using Atomic Force Microscopy (AFM) and Kelvin probe force microscopy (KPFM). We show using KPFM that electrostatic domains readily form within biological systems such as lung surfactant and lipid monolayers. We compared three different implementations of KPFM to demonstrate that frequency modulated (FM-) KPFM provides significant advantages over other modes. We also present a study of Amyloid beta (1-42) fibril formation on model surfaces, which are uniformly charged or possess periodicity of charges and hydrophobic functionality based on thiol self-assembly. Effect of membrane composition, surface charge, and presence of steroids will be discussed.

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 135-138).

Thesis (Ph. D.)--University of Chicago, Department of Physics, December 2003. / CD-ROM includes PDF files of figures 2.1-4.7. Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (p. 95-103).

Thesis (M.S.)--Worcester Polytechnic Institute. / Keywords: Aniosotropy; scanning instruments; scanning; surface metrology; surface; fractal. Includes bibliographical references (p. 52).

This dissertation will demonstrate the synergy of nanoscopic materials and surface metrology methods by the fabrication and implementation of CNT atomic force microscopy (AFM) tips, CNT scanning tunneling microscopy (STM) tips, Pt spike AFM tips, and Pt spike near-field scanning optical microscopy (NSOM) tips for the methods of critical dimension metrology, STM, AFM phase imaging, scanning surface potential AFM (SSPM), NSOM, and three-dimensional AFM. Chapter 1 provides a general overview of the information that will be discussed in this dissertation. Chapter 2 describes two methods for the simultaneous fabrication of carbon nanotube atomic force microscopy and scanning tunneling microscopy probes. The fabrication of these high resolution probes, as well as their imaging characteristics, is described in detail. Resolution standards were used to characterize their behavior and resolution limits. In Chapter 3, the effect of high aspect ratio probe length on AFM phase imaging is studied by fabricating highly controllable Pt spike AFM tips. By monitoring phase shifts on homogenous surfaces as a function of Pt spike length, it is shown that attractive forces at the tip are significantly reduced when high aspect ratio structures are added to conventional AFM probes. In Chapter 4, the effect of probe geometry on scanning surface potential microscopy (SSPM) is described. By studying the effect of scan height in SSPM, it was found that large surface area probe geometries, such as conventional Pt coated AFM tips, have lower surface potential resolution because of contributions from the sides of the tip as well as the cantilever. Spatial resolution standards were probed to evaluate the effect of probe geometry on SSPM sensitivity and resolution. Chapter 5 describes the fabrication of specialized probes for three-dimensional atomic force microscopy, scanning near-field optical microscopy, and scanning electrochemical -- atomic force microscopy (SECM-AFM). Using techniques described in Chapters 2-4, high aspect ratio structures were added to conventional probes used in 3D AFM, NSOM and SECM-AFM to solve limitations inherent to current probe designs for each method. Preliminary data indicates that each probe will have a significant beneficial effect on the resolution limit of its technique.

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