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)

Cold spray (CS) deposition of metals is a process involving deposition of materials in the solid or semi-solid state. It also has lower operating temperatures, and oxidation is greatly reduced in the process. The process is beneficial for refractory metals, such as tantalum, which are tough and difficult to machine. The interface between the CS powder and the substrate is the most important region for the study of mechanical properties as it is where the bonding process occurs first; studying mechanical properties at the nanoscale will give us a better idea of the mechanical properties of the coated surface. The present work investigates multiple-sprayed conventional and low-hydrogen treated tantalum powders on stainless steel substrates and also single-sprayed nitrogen-treated tantalum powders on aluminum substrate using Atomic force microscopy (AFM). It also discusses the effects of topography on the local changes in modulus. AFM is an instrument that measures the site-specific property of the sample. In this work, the local Young's modulus is studied using force-distance curves. Calibration of the AFM cantilever and the photodetector used to measure the cantilever, is a vital step before the actual process. The conventional method of calibration can cause damage to the tip as it arbitrarily penetrates into the sample creating a cantilever deflection vs. tip penetration curve, giving the sensitivity of the photodetector. AFM is highly dependent on topographical features as the cantilever tip-sample interaction can vary, causing variations in the property mapped. This work, however uses a non-contact method of calibration which saves the cantilever tip from potential damages, saving the results from the detrimental effects of tip topography. The work also discusses the effects of local sample deformation and volume of tip-surface contact on local changes in Young's modulus at the interface of coating and substrate. This work uses Electron micro-probe analysis (EPMA) to show the presence of oxides at the interface. The presence of oxides changes the bond energy as compared to a pure tantalum bond, ultimately affecting the local modulus mapped using AFM. The effect of oxides on the local modulus at the coating-substrate interface is theoretically discussed.

Protein-DNA interactions are central to many biological processes and form the bedrock of gene transcription, DNA replication, and DNA repair processes. Many proteins recognize specific sequences in DNA- a restriction enzyme must only cut at the correct sequence and a transcription factor should bind at its consensus sequence. Some proteins are designed to bind to specific structural or chemical features in DNA, such as DNA repair proteins and some DNA modifying enzymes. Target-specific DNA binding proteins initially bind to non-specific DNA and then search for their target sites through different types of diffusion mechanisms. Atomic force microscopy (AFM) is a single-molecule technique that is specifically well-suited to resolve the distinct states of target-specific as well as nonspecific protein-DNA interactions that are vital for a deeper insight into the target site search mechanisms of these enzymes. In this thesis, protein systems involved in epigenetic regulation, base excision repair (BER), and transcription are investigated by single-molecule AFM analyses complemented by biochemical and biophysical experiments. The first chapter of this thesis narrates the establishment of a novel, user-unbiased MatLab-based tool for automated DNA bend angle measurements on AFM data. This tool has then been employed to study the initial lesion detection step of several DNA glycosylases. These results promoted a model describing the altered plasticities of DNA at the target lesions of DNA glycosylases as the fundamental mechanism for their enhanced efficiency of lesion detection. In the second chapter of this thesis, the novel automated tool has been further extended to provide protein binding positions on the DNA along with corresponding DNA bend angles and applied to the study of DNMT3A DNA methyltransferase. These AFM studies revealed preferential co-methylation at specific, defined distances between two CpG sites by the enzyme and when combined with biochemical analyses and structural modelling supported novel modes of CpG co-methylation by DNMT3A. In the third chapter of this thesis, the role of 8-oxo-guanine glycosylase (hOGG1) in Myc-mediated transcription initiation has been investigated. AFM analyses revealed that in the presence of oxidative damage in DNA, Myc is recruited to its target site (E-box) by hOGG1 through direct protein-protein interactions, specifically under oxidizing conditions. Intriguingly, oxidation of hOGG1 was further observed to result in dimerization of hOGG1, which may also play a role in the mechanism of transcription regulation by hOGG1 under oxidative stress. / Protein-DNA-Wechselwirkungen sind für viele biologische Prozesse von zentraler Bedeutung und bilden die Grundlage der Gentranskription, der DNA-Replikation und der DNA-Reparaturprozesse. Viele Proteine erkennen bestimmte Bassen-Sequenzen in der DNA - ein Restriktionsenzym darf nur an der richtigen Sequenz schneiden, und ein Transkriptionsfaktor sollte an seine Konsenssequenz binden. Einige Proteine sind darauf ausgelegt, an bestimmte strukturelle oder chemische Merkmale der DNA zu binden, wie z. B. DNA-Reparaturproteine und verschiedene DNA-modifizierende Enzyme. Zielspezifische DNA-bindende Proteine binden zunächst an unspezifische DNA und suchen dann durch verschiedene Arten von Diffusionsmechanismen nach ihren Zielstellen in der DNA. AFM ist eine Einzelmolekültechnik, die besonders gut geeignet ist, um die verschiedenen Zustände sowohl der spezifisch gebundenen als auch unspezifischen Protein-DNA-Wechselwirkungen aufzulösen, die für einen tieferen Einblick in die Mechanismen der Zielstellensuche unerlässlich sind. In dieser Arbeit werden Proteinsysteme, die an der epigenetischen Regulation, der Basenexzisionsreparatur (BER) und der Transkription beteiligt sind, durch Einzelmolekül- AFM-Analysen untersucht, und diese Studien werden durch biochemische und biophysikalische Experimente komplementiert. ...

This study uses in situ atomic force microscopy (AFM) to directly observe the atomic scale effects of Sr on the monomolecular layer growth of abiotic calcite. These insights are coupled with quantitative measurements of the kinetics and thermodynamics of growth to determine the direction-specific effects of Sr on the positive and negative surface coordination environments that characterize calcite step edges. Low concentrations of strontium enhance calcite growth rate through changes in kinetics. A new conceptual model is introduced to explain this behavior. Higher concentrations of strontium inhibit and ultimately stop calcite growth by a step blocking mechanism. The critical supersaturation required to initiate growth (sigma*) increases with increasing levels of strontium. At higher supersaturations, strontium causes growth rates to increase to levels greater than those for the pure system. The step blocking model proposed by Cabrera and Vermilyea in 1958 does not predict the experimental data reported in this study because the dependence of sigma* upon strontium concentration is not the same for all supersaturations. Strontium inhibits calcite growth by different mechanisms for positive and negative step directions. Preliminary evidence indicates that strontium is preferentially incorporated into the positive step directions suggesting that impurity concentrations are not homogeneous throughout the crystal structure. Despite geochemical similarities, this study demonstrates that strontium and magnesium have different surface interaction mechanisms. The findings of this study demonstrate the importance of understanding microscopic processes and the significance of interpreting biominerals trace element signatures in the context of direction-specific interactions. / Master of Science

Through enhancing aerosol particle measurement accuracy by determining particle shape factors using Atomic Force Microscopy (AFM) combined with machine learning techniques, this study aims to provide a methodology that will improve the precision of aerosol measurements and contribute to the development of more effective filtration technologies. Accurate shape factor measurement is crucial for devices such as the Scanning Mobility Particle Sizer (SMPS), which often assume spherical particles of uniform density. By identifying and analyzing particles in AFM scans using machine learning techniques, this research provides a better understanding of shape factors, improving the quality of aerosol measurements. These advancements contribute to a deeper understanding of aerosol properties and their impact on filtration systems, aiding in the development of more effective filtration technologies and improving our capability to measure and control particulate matter in various environmental and industrial applications.

Microbial infections of medical implants occur in more than 2 million surgical cases each year in the United States alone. These increase patient morbidity and mortality, as well as patient cost and recovery time. Many treatments are available, but none are guaranteed to remove the infection. The purpose of this work is to examine the initial events in microbial adhesion by simulating the approach and contact between a planktonic cell, immobilized on an Atomic Force Microscope (AFM) cantilever, and a biomaterial or biofilm substrate. Distinct adhesive interactions exist between Candida parapsilosis and both unmodified silicone rubber and Pseudomonas aeruginosa biofilms. Using C. parapsilosis cells immobilized on AFM cantilevers with a silicone substrate, we have measured attractive interactions with magnitude of 2.3 ± 0.5 nN (SD) in the approach portion of the force cycle. On P. aeruginosa biofilms, the magnitude of the attractive force increases to 3.5 ± 0.75 nN (SD), and is preceded by a 2.5 nN repulsion at approximately 175 nm from the cell surface. This repulsion may be attributed to steric and electrostatic interactions between the two microbial polymer brushes. Young's moduli for microbes and biofilms were calculated using Hertzian contact models. These produced values of 0.21 ± 0.003 MPa (SD) for the C. parapsilosis-silicone rubber system, and 0.84 ± 0.015 MPa (SD) for the C. parapsilosis-biofilm system. This technique may be extended to calculate the work per unit contact area involved in the attractions in experimental data. For example, the work of adhesion using a spore probe is an order of magnitude greater for unmodified silicone rubber than for a P. aeruginosa biofilm. This indicates a high affinity for silicone rubber, and suggests that this material is vulnerable to infection by C. parapsilosis in vivo. We have also demonstrated that AFM force curve analysis using established qualitative and quantitative models fails to accurately represent the physical interactions taking place between the probe and sample for the case where a polymer brush exists on the substrate, the probe, or both. As such, an approximate method defining the sample surface as the actual surface plus some vertical dimension associated with the maximum compressible thickness of the polymer brush is discussed. Characterization of cell-biomaterial and cell-cell interactions allows for a quantitative evaluation of the materials used for medical implantation. It also provides a link between the physicochemical and physicomechanical properties of these materials and the nanoscale interactions leading to microbial colonization and infection. The goal of this research is to study this link and determine how best to exploit it to prevent microbial infections of medical implant materials.

Integrins are heterodimers that mediate cell adhesion in many physiological processes. Binding of integrins to ligands provides anchorage and signals for the cell. However, how force regulates integrin/ligand dissociation is unclear. Atomic force microscopy was used to measure the force dependence of lifetimes of single bonds between a FN fragment and integrin α₅β₁. First, lifetime-force relationships demonstrated that force prolonged bond lifetimes in the 10-30 pN range, a behavior called catch bonds. Changing divalent cations from Ca²⁺/Mg²⁺ to Mg²⁺/EGTA and to Mn²⁺ caused more pronounced catch bonds. A truncated α₅β₁ construct containing the headpiece but not the legs (trα₅β₁-Fc) formed much longer-lived catch bonds in the same force range. Bindings of two activating mAbs, 12G10 and TS2/16, left shift the catch bond and converted catch bonds to slip bonds, respectively. Catch bonds may provide a mechanical mechanism for the cell to regulate adhesion by applying different forces. Second, FNIII₇₋₁₀/α₅β₁-Fc/GG-7 bond was stretched to ~ 30 pN and then relaxed to ~ 7 pN at which the bond's lifetime was measured. The strong bond state induced by the 30 pN stretching stayed stable even after the force was reduced to 7 pN. In other words, lower the force would not weaken FNIII₇₋₁₀/α₅β₁-Fc bond once it had been stretched. Similar behaviors were observed for FNIII₇₋₁₀/trα₅β₁-Fc and FNIII₇₋₁₀/mα₅β₁interactions. In addition, the efficiency of the force to induce such a strong bond state for FNIII₇₋₁₀/α₅β₁-Fc interaction in 2 mM Mg²⁺/EGTA condition was characterized. The probability of force to induce the strong bond state increased as force increased and when the force reached 26 pN, all bonds were transit to the strong state. Moreover, reversible unbending of α₅β₁binding with FNIII₇₋₁₀ under mechanical force were observed, which proved that integrin bending and unbending was dynamic. Importantly, integrin could restore bent conformation even when engaged with its ligand, providing a mechanism for mechanotransduction. Third, structural changes of α₅β₁under force were observed. The structural changes did not change the trend of lifetime-force relationships of FNIII₇₋₁₀/α₅β₁/GG-7 bond. Moreover, the lifetime for the structural changes to occur and molecular length changes caused by them were characterized.

Polymer brushes provide the responsive smart surfaces which can be used for fabrication of various devices. In this thesis work, adhesion, friction, and wear of polystyrene (PS) - poly(2-vinyl pyridine) (P2VP) and polystyrene - poly(acrylic acid) (PAA) binary brushes and corresponding monobrushes were investigated in dried state under controlled environment. Spin-coated films were also investigated for comparison. The aim was to explore possibilities to control/tune adhesion, friction, and wear between inorganic or polymeric surfaces by use of polymer brushes. Atomic force microscopy (AFM) with sharp silicon nitride tip and colloidal probes was employed to investigate the nanoscale adhesion and friction forces between different inorganic and polymeric surfaces. Adhesion and friction on the polymer brushes were comparable to that on the spin-coated films. Adhesion and friction force values were correlated, and were in accordance with the wettability of the brush surfaces for most of the samples. Switching in the adhesion and friction forces was observed for the PS+P2VP and PS+PAA binary brushes on treatment with selective solvents. Maximum switching in adhesion force and friction coefficient was by a factor of 2.7 and 5.4, respectively. Furthermore, switching of friction for mixed brush surface was observed during macroscale friction measurements using nanoindenter. Friction coefficients at macroscale were higher than those at the nanoscale. Moreover, adhesion and friction forces between the surfaces were significantly influenced by the humidity, grafting density of polymer brushes, chemical composition of top of the binary brush surface, and tip scan velocity. Nanowear studies were carried out with AFM using sharp silicon nitride tip while macrowear studies were carried out using nanoindenter. Nanowear on the surfaces was affected by molecular entanglements, adhesion and friction forces as well as shape and status of the tip. It was observed that the typical wear mode for PS brushes (treated with toluene) was ripple formation. In case of P2VP brushes (treated with ethanol) and PAA brushes (treated with pH 10 water), wear occurred via removal of the polymeric material. Wear mechanism observed for the monobrushes was similar to that observed for the spin-coated thick films of the same polymeric material. However, extent of the wear on the brush surfaces significantly differed from that on the spin-coated films. In case of PS+P2VP and PS+PAA binary brush samples, change in the wear mode was observed on treatment with the different selective solvents. On treatment with toluene (PS on the top), both of these binary brushes showed the wear by formation of the ripples. On the other hand, when these binary brushes were treated with selective solvent for P2VP or PAA, wear occurred mainly via removal of the polymeric material. The amount of wear increased with the number of scans for all the polymer brush samples. Moreover, wear on the polymer brush surfaces was also increased on increase in the applied load and decrease in the scan speed. Wear behavior on macroscale was averaged due to contact between surfaces at large number of asperities. Our results show that adhesion, friction, and wear of polymer surfaces can be controlled/tuned by the use of binary polymer brushes.

Master of Science / Department of Physics / Robert Szoszkiewicz / For proteins in living cells, forces are present at all levels. These range from macroscopic to single molecule levels. Single molecule atomic force microscopy (AFM) in force extension (FX) and force clamp (FC) modes can investigate the mechanical properties of proteins, for example, forces at which proteins unfold, or the kinetics of these processes. In the FX-AFM experiments, proteins are pulled at constant velocity, while in FC-AFM experiments, proteins are pulled at constant force. This thesis describes i) how a single molecule FX/FC-AFM was constructed using various components, ii) how it was calibrated and tested using (I27)4 polyprotein, and iii) how it was applied to the studies of a Notch construct. Building up the single molecule FX/FC-AFM system opened a path to investigate the mechanical properties of proteins. Such a system was tested on a known protein construct, hence the usage of the (I27)4 polyprotein. The Notch protein is a signaling protein that plays a role in triggering breast cancer. It is believed that understanding the mechanical properties of Notch can help to understand its oncogenic functions. We have successfully constructed and calibrated the FX/FC-AFM setup. It was found that the AFM worked for the standard calibration protein of (I27)4. The results on a Notch construct revealed our ability to see some conformational transition state in this molecule under force. These results opened a path for further investigations of a Notch construct at various physiologically relevant conditions.