Thesis (M.S.) -- Mississippi State University. Department of Mechanical Engineering. / Title from title screen. Includes bibliographical references.

Thesis (Ph. D.)--University of Delaware, 2008. / Principal faculty advisor: Eric W. Kaler, College of Engineering. Includes bibliographical references.

Thesis (M. S.)--Mechanical Engineering, Georgia Institute of Technology, 2009. / Committee Chair: Ghiaasiaan, S. Mostafa; Committee Member: Desai, Prateen; Committee Member: Jeter, Sheldon; Committee Member: Kirkconnell, Carl.

Thesis (Ph. D.)--Mechanical Engineering, Georgia Institute of Technology, 2008. / Jeremy P. Harvey, Committee Member ; Carl S. Kirkconnell, Committee Member ; Kurt D. Pennell, Committee Member ; S. Mostafa Ghiaasiaan, Committee Chair ; Prateen V. Desai, Committee Member ; Sheldon M. Jeter, Committee Member.

Thesis (M. S.)--Mechanical Engineering, Georgia Institute of Technology, 2008. / Kirkconnell, Carl S., Committee Member ; Ghiaasiaan, S. Mostafa, Committee Chair ; Desai, Prateen V., Committee Member ; Jeter, Sheldon M., Committee Member.

The study of the three-dimensional structures of biological macromolecules has given us significant insight into life and its mechanisms. Understanding these structures in their native contexts, a challenging but important goal, came closer to reality with the development of electron microscopy. After many years of technological development, we are now starting to understand previously intractable biological phenomena at an unprecedented resolution. One such phenomenon is how neighboring cells interact, both to communicate and send signals, and to adhere and form complex tissue structures. While the molecules that mediate such processes have long been studied in isolation, electron microscopy allows us to examine them in a more native biophysical environment; as hydrated, dynamic molecules tethered to opposed cellular membranes.Imaging unadulterated biological material using electron microscopy requires that the sample be embedded in a thin layer of vitreous ice to immobilize the molecules and protect them from the vacuum of the microscope, and thus is generally referred to as cryogenic electron microscopy (cryo-EM). Samples can be imaged using two common cryo-EM modalities: single particle analysis (SPA), where many two-dimensional projection images of molecules in solution are collected, and cryo-electron tomography (cryo-ET), where the sample is tilted as it is imaged at multiple angles to reconstruct a three-dimensional volume. In this work, I will describe how I have used both SPA and cryo-ET to understand cell surface interactions involving a variety of proteins. The first chapter will look at the cell surface molecules known as the Toll receptors, a family of molecules found in Drosophila melanogaster, with orthologs in mammals known as the Toll-like receptors (TLRs). I will focus on their role in the development of the Drosophila embryo during germ band extension, a kind of convergent extension that is a conserved process through all metazoans. Biophysical assays of the three implicated Toll receptors, Toll-2, -6, and -8, revealed both homophilic and heterophilic interactions. SPA was used to determine the structure of monomeric Toll-2 which closely resembles the overall fold of Toll, whose structure was previously solved by x-ray crystallography. Surface plasmon resonance (SPR) spectroscopy and analytical ultracentrifugation (AUC) showed Toll-6 is a dimer in solution, which I visualized using cryo-EM. The Toll-6 homodimer is a novel dimer interface for Tolls and TLRs, where molecules on the same cell surface have been shown to dimerize in the presence of a wide variety of ligands. In contrast, the Toll-6 dimer is formed in the absence of any ligand and exists in an antiparallel arrangement that could be formed by molecules on opposing cell surfaces. Together, these results provide a biochemical basis for germ band extension which may be further explored through the study of structure-based mutations. While cryo-EM SPA is a powerful tool, cryo-ET allows one to reconstruct three dimensional volumes of highly heterogeneous samples, such as the interior of cells, where molecules of interest may not exist in enough copies to facilitate averaging. This technique, where the sample is imaged multiple times as it is tilted to obtain three-dimensional information of a region of interest, was used to study cell adhesion of a different type: that mediated by the classical cadherins. These calcium-dependent adhesion molecules cluster into adherens junctions, spot-like protein densities found in a wide variety of tissues. In the second chapter, these junctions are recapitulated between synthetic liposome membranes by tethering the adherent cadherin molecules to chemically functionalized lipids. They are then imaged using cryo-ET to reveal higher-order structural details. First, this method is applied to the clustered protocadherins, a family of cadherins that mediate neuronal self-avoidance in mammals. Cryo-ET in combination with x-ray crystallography revealed that clustered protocadherins form extended one-dimensional zippers between membranes, which are a combination of strictly homophilic trans interactions coupled with promiscuous cis interactions. Neurons express unique subsets of the ~50-60 possible isoforms, and when two neuronal processes express identical subsets, which happens only when those processes are a part of the same cell, these linear chains grow and initiate a repulsive signal. If the subsets are different, the chains terminate and no repulsive signal is generated. The same technique has been used previously to study the type I classical cadherins, perhaps the most well-studied members of the cadherin superfamily. In the second half of this chapter, we extend our analysis to include the type II classical cadherins, which possess more complex expression patterns and binding specificities. Cryo-ET of type II cadherin ectodomains tethered to synthetic liposomes revealed that several representative members of this family form only moderately ordered arrays between liposomes, a finding in agreement with their role in cell sorting and migration. However, VE-cadherin, an outlier type II expressed in vascular endothelial cells where it withstands blood pressure, forms extraordinarily ordered junctions. Subtomogram averaging reveals the regularity of this two-dimensional array. In the final chapter, I describe my work on a membrane surface molecule of a different kind, one not involved in cell adhesion but viral infection. The global COVID-19 pandemic gave me the opportunity to contribute to our understanding of SARS-CoV-2 by studying the structure of neutralizing antibodies bound to the viral spike protein, perhaps the most infamous membrane surface protein. The first subchapter describes the initial isolation, neutralization, and structural analysis of antibodies isolated from convalescent COVID-19 patients. This work revealed that patients with severe COVID-19 produce potently neutralizing antibodies that target two spike protein domains: the receptor binding domain (RBD) and the N-terminal domain (NTD). RBD-directed antibodies occlude binding to ACE2, the human receptor that mediates viral fusion, but the neutralization mechanism of NTD-directed antibodies is unknown. The following two subchapters are more detailed structural studies of two specific types of antibodies. The first looks at a class of RBD-directed antibodies derived from the VH1-2 gene, which are some of the most potent and common antibodies against SARS-CoV-2. The heavy chains of these antibodies recognize almost identical epitopes, but the antibodies employ a modular approach to recognize the RBD in either of its possible conformations. The second class are antibodies that target the NTD, which our work revealed all bind to a single antigenic supersite. The final subchapter focuses on emerging SARS-CoV-2 variants and includes the structures of two antibodies that are still capable of neutralizing these new variants. They are also infrequent in the human antibody response to SARS-CoV-2, meaning they put little selective pressure on the virus to produce escape mutations, making them good candidates for monoclonal antibody therapies. Though Drosophila embryogenesis, adherens junction formation, and SARS-CoV-2 neutralization are seemingly unrelated systems, they are united by the incredible flexibility of cryo-EM to visualize biological molecules in more native environments. Whether it is the ability to study multiprotein complexes or assemblies formed between membranes, cryo-EM is a powerful technique that promises to help bridge the divide between structure and function.

This dissertation reports on data acquisition method and the application of world’s first cryogenic apertureless near-field microscope designed for terahertz frequencies. The dissertation briefly summarizes the commonly used data acquisition methods and the existing challenges in applying near-field technology using broadband terahertz sources. We devised, implemented, and validated a novel measurement technique to resolve the challenges. The novel method improves the traditional method by providing the information of the carrier-envelop-phase of the terahertz pulse. The physical properties of WTe₂ microcrystals depend sensitively on the layer number. By applying both the traditional and the novel techniques, we systematically explored the layer-dependent electromagnetic response of mono-layer and few-layer tungsten ditelluride (WTe₂ microcrystals. On tri-layer WTe₂, we discovered the plasmonic response and imaged the real-space pattern of the terahertz plasmon using the novel measurement technique. On bi-layer WTe₂, our measurements support that the band alignment is semi-metallic instead of semi-conducting. Near-field technology at terahertz frequency is sensitive to the Drude behavior of condensed matters. We imaged the electromagnetic response of the transition of cadmium osmate (Cd₂Os₂O₇) crystals from a high temperature metal to a low temperature magnetic insulator. The result is consistent with the temperature dependence in the direct-current conductivity. In the end, the dissertation discusses the theory and simulation of imaging hydrodynamic flow of materials with viscous electron systems via nano-photocurrent technique. In anisotropic material, nano-photocurrent measures the geometrical properties of the Shockley-Ramo auxiliary field or flux. As a result, the nano-photocurrent is a good candidate to detect the boundary layer and vortex flow pattern of a viscous electron system.

A data reduction method has been developed and tested for a high frequency angle probe. The angle probe is designed for unsteady aerodynamic measurements in transonic cryogenic wind tunnels. The probe measures time-resolved total pressure, static pressure, angle of attack, and yaw angle from readings of four pressure transducers. The unique feature of this probe, as compared to a conventional multi-hole directional probe, is that the four high frequency response silicon pressure transducers are mounted flush on the probe tip. The data reduction method is basically an interpolation routine of calibration curves. The calibration curves consist of experimentally determined non-dimensional flow coefficients. Two experiments were conducted to test the probe and the data reduction method. The first experiment tested the angle probe in a Karman vortex street shed from a cylinder. In the second experiment, the angle probe was placed in an open air jet with an exit Mach number of 0.42. Plots of the time-resolved measurements and the Fast Fourier Transform analysis were made for each test. / Master of Science

The objective of the proposed work is to study the behavior of SiGe HBTs at cryogenic temperatures and its relation to device scaling and optimization. Not only is cryogenic operation of these devices required by space missions, but characterizing their cryogenic behavior also helps to investigate the performance limits of SiGe HBTs and provides essential information for further device scaling. Technology computer aided design (TCAD) and sophisticated on-wafer DC and RF measurements are essential in this research. Drift-diffusion (DD) theory is used to investigate a novel negative differential resistance (NDR) effect and a collector current kink effect in first-generation SiGe HBTs at deep cryogenic temperatures. A theory of positive feedback due to the enhanced heterojunction barrier effect at deep cryogenic temperatures is proposed to explain such effects. Intricate design of the germanium and base doping profiles can greatly suppress both carrier freezeout and the heterojunction barrier effect, leading to a significant improvement in the DC and RF performance for NASA lunar missions. Furthermore, cooling is used as a tuning knob to better understand the performance limits of SiGe HBTs. The consequences of cooling SiGe HBTs are in many ways similar to those of combined vertical and lateral device scaling. A case study of low-temperature DC and RF performance of prototype fourth-generation SiGe HBTs is presented. This study summarizes the performance of all three prototypes of these fourth-generation SiGe HBTs within the temperature range of 4.5 to 300 K. Temperature dependence of a fourth-generation SiGe CML gate delay is also examined, leading to record performance of Si-based IC. This work helps to analyze the key optimization issues associated with device scaling to terahertz speeds at room temperature. As an alternative method, an fT -doubler technique is presented as an attempt to reach half-terahertz speeds. In addition, a roadmap for terahertz device scaling is given, and the potential relevant physics associated with future device scaling are examined. Subsequently, a novel superjunction collector design is proposed for higher breakdown voltages. Hydrodynamic models are used for the TCAD studies that complete this part of the work. Finally, Monte Carlo simulations are explored in the analysis of aggressively-scaled SiGe HBTs.

Pulse tube cryocoolers (PTCs) are among the most attractive choices of refrigerators for applications requiring up to 1 kW of cooling in the temperature range of 4-123 K as a result of the high relative efficiency of the Stirling cycle, the reliability of linear compressors, and the lack of cryogenic moving parts resulting in long life and low vibration signature. Recently, PTCs have been successfully used in applications in the 150 K range, extending the useful range of the device beyond the traditional cryogenic regime. A carefully designed cylindrical cavity referred to as the pulse tube replaces the mechanical expander piston found in a Stirling machine. A network consisting of the pulse tube, inertance tube, and surge volume invoke out-of-phase pressure and mass flow oscillations while eliminating all moving parts in the cold region of the device, significantly improving reliability over Stirling cryocoolers. Terrestrial applications of PTCs expose a fundamental flaw. Many PTCs only function properly in a narrow range of orientations, with the cold end of the pulse tube pointed downward with respect to gravity. Unfavorable orientation of the cold head often leads to a catastrophic loss of cooling, rendering the entire cryocooler system inoperable. Previous research indicates that cooling loss is most likely attributed to secondary flow patterns in the pulse tube caused by free convection. Convective instability is initiated as a result of non-uniform density gradients within the pulse tube. The ensuing secondary flow mixes the cryogen and causes enhanced thermal transport between the warm and cold heat exchangers of the cryocooler. This study investigates the nonlinear stabilizing effect of fluid oscillation on Rayleigh-Bénard instability in a cryogenic gas subject to misalignment between gravitational body force and the primary flow direction. The results are directly applicable to the flow conditions frequently experienced in PTCs. Research has shown that the convective component can be minimized by parametrically driven fluid oscillation as a result of sinusoidal pressure excitation; however, a reliable method of predicting the influence of operating parameters has not been reported. In this dissertation, the entire PTC domain is first fully simulated in three dimensions at various angles of inclination using a hybrid method of finite volume and finite element techniques in order to incorporate conjugate heat transfer between fluid domains and their solid containment structures. The results of this method identify the pulse tube as the sole contributor to convective instability, and also illustrate the importance of pulse tube design by incorporating a comparison between two pulse tubes with constant volume but varying aspect ratio. A reduced domain that isolates the pulse tube and its adjacent components is then developed and simulated to improve computational efficiency, facilitating the model’s use for parametric study of the driving variables. A parametric computational study is then carried out and analyzed for pulse tubes with cold end temperatures ranging from 4 K to 80 K, frequencies between 25-60 Hz, mass flow - pressure phase relationships of -30◦ and +30◦, and Stokes thickness-based Reynolds numbers in the range of 43-350, where the turbulent transition occurs at 500. In order to validate the computational models reported and therefore justify their suitability to perform parametric exploration, the CFD codes are applied to a commercially developed single stage PTR design. The results of the CFD model are compared to laboratory-measured values of refrigeration power at temperatures ranging from 60 K to 120 K at inclination angles of 0◦ and 91◦. The modeled results are shown to agree with experimental values with less than 8.5% error for simulation times of approximately six days using high performance computing (HPC) resources through Georgia Tech’s Partnership for Advanced Computing (PACE) cluster resource, and 10 days on a common quad-core desktop computer. The results of the computational parametric study as well as the commercial cryocooler data sets are compiled in a common analysis of the body of data as a whole. The results are compared to the current leading pulse tube convective stability model to improve the reliability of the predictions and bracket the range of losses expected as a function of pulse tube convection number. Results can be used to bracket the normalized cooling loss as a function of the pulse tube convection number NPTC. Experimental data and simulated results indicate that a value of NPTC greater than 10 will yield a loss no greater than 10% of the net pulse tube energy flow at any angle. A value of NPTC greater than 40 is shown to yield a loss no greater than 1% of the net pulse tube energy flow at all angles investigated. The computational and experimental study completed in this dissertation addresses static angles of inclination. Recent interest in the application of PTCs to mobile terrestrial platforms such as ships, aircraft, and military vehicles introduces a separate regime wherein the angle of inclination is dynamically varying. To address this research need, the development of a single axis rotating cryogenic vacuum facility is documented. A separate effects apparatus with interchangeable pulse tube components has also been built in a modular fashion to accommodate future research needs.