Thesis (Ph. D.)--University of Chicago, Dept. of Chemistry. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph.D)--Mechanical Engineering, Georgia Institute of Technology, 2009. / Committee Chair: Zhu, Cheng; Committee Member: Degertekin, Levent; Committee Member: Fox, Ronald; Committee Member: Garcia, Andres; Committee Member: McIntire, Larry. Part of the SMARTech Electronic Thesis and Dissertation Collection. Non-Latin script record

Thesis (M.S.)--Worcester Polytechnic Institute. / Keywords: Atomic force microscopy; proteins; Pseudomonas aeruginosa. Includes bibliographical references (leaves 107-130).

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 94-102).

The research described in this thesis aimed to evaluate the intrinsic DNA curvature ofthe region of the TP53 tumour suppressor gene that codes for the sequence-specific DNA-binding domain of the p53 protein, a key protein that protects the cell from chemical insultsand tumourogenesis. There have been no previous attempts to experimentally investigate theintrinsic DNA curvature within TP53 or its relation to the functional or structural properties ofthe gene, such as DNA repair and nucleosomal architecture. The present study usedtheoretical models of TP53 in concert with an atomic force microscopy based experimentalinvestigation of TP53 DNA molecules to analyse intrinsic DNA curvature within the gene. Thiswas achieved by developing a novel software platform for the atomic force microscopy basedinvestigation of DNA curvature, named ADIPAS. Dinucleotide wedge models of DNA curvaturewere used to model TP53 in order to investigate the relationship between intrinsic DNAcurvature and the structure and function of the gene. ADIPAS was applied to atomic forcemicroscopy images of TP53 DNA molecules immobilised on a mica surface in order toexperimentally measure intrinsic DNA curvature. The experimental findings were compared totheoretical models of intrinsic curvature in TP53. The resulting intrinsic curvature profilesshowed that exons exhibited significantly lower intrinsic DNA curvature than introns withinTP53, this was also shown to be true for regions of slow DNA repair. This indicated that DNAcurvature may play a role in TP53 as a controlling factor for nucleosomal architecture tofacilitate open chromatin and active DNA transcription. The evolutionary selection for intrinsiccurvature may have played a role in the development of exons with low intrinsic DNAcurvature. Low intrinsic curvature in exon position has also been implicated in the reducedefficiency of DNA repair in a number of cancer specific mutation hotspots.

Nanomaterial composites hold improvement potential for many materials. Improvements arise through known material behaviors and unique nanoscale effects to improve performance in areas including elastic modulus and damping as well as various processes, and products. Review of research spurred development of a load-stage. The load stage could be used independently, or in conjunction with an AFM to investigate bulk and nanoscale material mechanics. The effect of MWCNT content on structural damping, elastic modulus, toughness, loss modulus, and glass transition temperature was investigated using the load stage, AMF, and DMA. Initial investigation showed elastic modulus increased 23% with 1wt.% MWCNT versus pure epoxy and in-situ imaging observed micro/nanoscale deformation. Dynamic capabilities of the load stage were investigated as a method to achieve higher stress than available through DMA. The system showed energy dissipation across all reinforce levels, with ~480% peak for the 1wt.% MWCNT material vs. the neat epoxy at 1Hz. / ND NASA EPSCoR FAR0017788 / NDSU Development Foundation FAR0017503 / National Science Foundation (NSF) Grant# HRD-0811239 to the NDSU Advance FORWARD Program

>Magister Scientiae - MSc / Solid-state reactions of bi-metallic systems can be driven or activated by various external stimuli like pressure, energetic photons, energetic charged particles or heat. For an example, high pressure torsion can be applied to aluminium-copper (Al-Cu) to drive solid-state reaction [1.1]. Oh-ishi et al. [1.1] applied a pressure of 6 GPa to Al and Cu half discs. Following this, x-ray diffraction (XRD) and high-resolution transmission electron microscope (HRTEM) were used to confirm the formation of different intermetallic phases such as Al2Cu and Al4Cu9. One of the first reported case where photons were used to drive solid phase diffusion was reported in 1998 by Ditchfield et al. [1.2]. The study was carried out to study the non-thermal effects of photons illumination on surface diffusion, an important process in microelectronics fabrication. Surface diffusion governs several important steps in microelectronics fabrication including the formation of hemispherical grained silicon used in memory devices [1.2], filling of channels with metals for devices interconnection purposes among others [1.2]. In this study, germanium-indium (Ge-In) on silicon was used because the thermal diffusion of this system was well understood [1.3]. Surface diffusion was measured in ultrahigh vacuum via second harmonic microscopy when the sample was illuminated with pulsed Nd: YAG laser at a wavelength of 1064 nm [1.3]. This study showed conclusively that photons could be used to drive solid-state reactions.

The complex structures of water-soluble wheat arabinoxylans have been mapped along individual molecules, and within populations, using the visualisation of the binding of inactivated enzymes by atomic force microscopy (AFM). It was demonstrated that site-directed mutagenesis (SDM) can be used to produce inactive enzymes as structural probes. For the SDM mutants AFM has been used to compare the binding of different xylanases to arabinoxylans. Xylanase mutant E386A, derived from the Xyn11A enzyme (Neocallimastrix patriciarium), was shown to bind randomly along arabinoxylan molecules. The xylanase binding was also monitored following Aspergillus niger arabinofuranosidase pre-treatment of samples. It was demonstrated that removal of arabinose side chains significantly altered the binding pattern of the inactivated enzyme. Xylanase mutant E246A, derived from the Xyn10A enzyme (Cellvibrio japonicus), was found to show deviations from random binding to the arabinoxylan chains. It is believed that this is due to the effect of a small residual catalytic activity of the enzyme that alters the binding pattern of the probe. Control procedures were developed and assessed to establish that the interactions between the modified xylanases and the arabinoxylans were specific interactions. The experimental data demonstrates the potential for using inactivated enzymes and AFM to probe the structural heterogeneity of individual polysaccharide molecules.

This work explores the stochastic dynamics and important diagnostics of a mechanical resonator (nanobeam) used in cavity optomechanical sensors for atomic force microscopy. Atomic force microscopy (AFM) is a tool to image surface topology down to the level of individual atoms. Conventional AFM has been an essential tool for micro and nanoscale studies in physics, chemistry, and biology. Cavity optomechanical sensors for AFM extend the utility of conventional AFM into a new regime of high sensitivity k is approximately 1 N/m and high frequency f0 is approximately 10 MHz. Cavity optomechanical sensors for AFM are unique because they use near field optics to transduce the position of a nanobeam. The nanobeam is not able to be transduced by more conventional AFM techniques, such as laser interferometry, because the nanobeam is smaller than the spot size of the laser. This work determines the noise spectrum G of a nanobeam in water and in air. Also important diagnostics of the nanobeam are determined in air and in water. These important diagnostics include the quality factor Q and natural frequency in fluid omega_f. It is found that the nanobeam is overdamped in water. However, the nanobeam is underdamped in air and has quality factor of Q is approximately 4. The noise spectrum is determined from deterministic numerical calculations and the Fluctuation-Dissipation Theorem. This is possible because the same molecular processes, Brownian motion, cause both the fluctuations of the nanobeam and the dissipation of the nanobeam. / Master of Science

In this dissertation, experiments are described which elucidate how the ordering of symmetric diblock copolymers affects the dynamics within various geometries. In all studies presented herein, experimental techniques are used to probe the dynamics of symmetric diblock copolymer systems as they progress toward equilibrium and to study the role that nanoscale ordering plays in these processes. In the majority of work presented herein, experiments were performed on symmetric diblock copolymer thin films. This work focuses on the effect of various sample preparation techniques on the equilibration kinetics of lamellar forming films. Films are prepared with varying thicknesses in the homogeneous, disordered state and annealed to form islands and holes as the surface decomposes to form commensurate thicknesses. Both nucleated and spinodal growth patterns were observed for this surface decomposition dependent on the initial thickness and intermediate morphologies formed upon ordering. We also prepare equilibrium commensurate films and induce a step change in surface interactions, switching from asymmetric to symmetric wetting boundaries. Upon equilibration, a perforated lamella forms at the free surface to mediate the order-order transition, inducing hole growth with a ramified shape. In the final project, the effect that lamellar order has on dynamics is studied within unstable polymer melt bridges. Liquid bridges are what is formed when a droplet is stretched between two surfaces, like spit between two fingers. Disordered diblock bridges are shown to evolve similar to their homopolymer counterparts. However, ordered diblock copolymer exhibits an enhanced stability with an inhibition of flow proposed to be induced by the isotropic orientational order within the bridge. As well, shear thinning is observed that is believed to be caused by an alignment of ordered domains along the bridge axis due to shear strain rates, providing pathways for flow of diblock copolymer out of the unstable bridge. / Thesis / Doctor of Philosophy (PhD)