Physical Sciences and Mathematics Commons^™

Devising A Scalable Synthesis To Probe The G-Protein Cell Receptor Signaling Pathway, Matthew Robert Medcalf

Arts & Sciences Electronic Theses and Dissertations

The G-protein coupled cell receptor signaling pathway is amongst the largest and most diverse class of cell-surface receptors in the body. Nearly 800 different genes encode for these cell membrane receptors which are responsible for mediating a variety of hormones, neurotransmitters, and sensory stimuli through the activation of intracellular G proteins. To date, roughly 34% of pharmaceuticals on the market target GPCR’s, but despite this fact, there are still many difficulties associated with targeting this family of receptors. The vast number of GPCR’s, disease states resulting from a dysregulation of multiple GPCR signaling pathways, and difficulties crystalizing and purifying the …

Sideromycin Pathway Elucidation: Insights Into Salmycin Biosynthesis, Transport Paradigms, And Drug Release, Gerry Sann Macaraeg Rivera

Arts & Sciences Electronic Theses and Dissertations

Antibiotic resistance is an increasing threat in today’s society. In order to overcome resistant bacteria, it is necessary to discover new drugs with novel mechanisms of action. This work focuses on the sideromycin pathway, encompassing the biosynthetic production, mechanism of entry and hydrolysis-mediated drug release. Sideromycins are an interesting approach to combat the rise of antibiotic resistance since they provide a different avenue that overcomes problems that arise when entering the cell. The dissertation is separated into distinct sections dealing with the various areas of interest in the sideromycin pathway, particularly for the sideromycin, salmycin, produced by Streptomyces violaceus. The …

Cyclotron Resonance In Graphene Heterostructurescyclotron Resonance In Graphene Heterostructures, Billy Jordan Russell

Arts & Sciences Electronic Theses and Dissertations

We present observations of cyclotron resonance in graphene Van der Waals heterostructure devices. Such devices provide dramatic improvements in sample quality and allow for ad- vanced electronic control, opening windows on previously inaccessible physics. The design and construction of a dedicated system for the measurement of electronic transport and infrared magnetospectroscopy in microscopic samples of atomically thin materials at cryogenic temperatures is presented. In high-mobility encapsulated monolayer graphene, electron- electron interaction effects are unambiguously observed to impact the interband cyclotron resonance as the Landau level filling factor is varied in a quantizing magnetic field. Additionally, a splitting of transitions involving …

Development And Application Of Mass Spectrometry-Based Protein Footprinting In Structural Proteomics, Ming Cheng

Arts & Sciences Electronic Theses and Dissertations

Integral mass spectrometry (MS) has emerged as an important tool for protein structural characterization. It readouts are a broad range of structural information, including stoichiometry, interactions, conformations and conformation change, and dynamics. Protein footprinting is a pivotal component in the intergral MS toolkit.My dissertation centers around the development and application of protein footprinting to characterize protein structure. It is divided into seven chapters.Chapter 1 serves as the introduction for integral mass spectrometry in structural proteomic.In Chapter 2, we extended the fast-photochemical oxidation of proteins (FPOP) platform by adding the trifluoromethyl radical (•CF3) as a new reagent. We discovered that •CF3 …

Instrumentation For Dynamic Nuclear Polarization And Application Of Electron Decoupling For Electron Relaxation Measurement, Nicholas Howard Alaniva

Arts & Sciences Electronic Theses and Dissertations

Dynamic nuclear polarization nuclear magnetic resonance (DNP NMR) exploits internal electron spin and nuclear spin interactions to increase sensitivity and uncover valuable information regarding structure and dynamics of a system. To manipulate these interactions, instrumentation is developed to combine high-power microwave and radiofrequency irradiation with the ability to spin samples at the magic angle (MAS) at temperatures from 90 K to 4.2 K. Electron decoupling uses frequency-modulated microwaves to mitigate the electron-nuclear dipolar interaction, improving signal intensity and resolution in DNP NMR experiments. Electron decoupling is combined with short DNP periods to encode electron spin information in polarized nuclear signal. …

Magic Angle Spinning Spheres And Improved Microwave Coupling For Magnetic Resonance, Pin-Hui Chen

Arts & Sciences Electronic Theses and Dissertations

Nuclear magnetic resonance (NMR) is a nondestructive technique used to characterize molecular structure and dynamics with atomic resolution. In solid-state NMR, magic angle spinning (MAS) is commonly implemented to improve spectral resolution by partially averaging anisotropic interactions. To further improve NMR sensitivity, dynamic nuclear polarization (DNP) is utilized to transfer the polarization from electron spins to nuclei of interest using microwaves. Advanced MAS DNP NMR instrumentation, such as spherical rotors for stable and fast spinning, dielectric lenses to effectively couple the microwaves into the sample, and the separation of receiving and transmitting circuits to decrease measurement noise, are developed to …

Enhanced Magnetic Ordering In Sm Metal And Search For Superconductivity In Cs And Rb Under Extreme Pressure, Yuhang Deng

Arts & Sciences Electronic Theses and Dissertations

At ambient pressure Sm metal orders antiferromagnetically at 106 K and 14 K. The pressure-dependence of the magnetic ordering temperature To of Sm metal was determined through four-point electrical resistivity measurements in a diamond anvil cell to pressures as high as 150 GPa. A strong increase in To with pressure is observed above 85 GPa. In this pressure range Sm ions alloyed in dilute concentration with superconducting Y exhibit giant Kondo pair breaking. Taken together, these results suggest that for pressures above 85 GPa Sm is in a highly correlated electron state, like a Kondo lattice, with an unusually high …

Understanding The Physiology Of Extracellular Electron Uptake In Purple Nonsulfur Bacteria, Michael Singh Guzman

Arts & Sciences Electronic Theses and Dissertations

Microbially catalyzed oxidation-reduction reactions drive nutrient cycling and energy flux on Earth. Photoautotrophs, which include the cyanobacteria (oxygenic) and purple and green sulfur bacteria (anoxygenic), transform light energy into chemical energy and are responsible for substantial global primary productivity. Anoxygenic phototrophs, in particular, play a crucial role in biogeochemical cycling in anoxic illuminated environments because of their ability to oxidize an array of inorganic compounds for CO2 fixation. Electron donors include molecular hydrogen, nitrite, and reduced sulfur compounds. Recent evidence has also suggested that solid-phase conductive substances (SPCSs), including rust (mixed-valent iron minerals) and their proxies (poised electrodes), can serve …

Adiabatic Dark Matter Density Cusps Around Supermassive Black Holes And Dark Matter Detection, Augusto Medeiros Da Rosa

Arts & Sciences Electronic Theses and Dissertations

The growth of a black hole surrounded by dark matter can lead to a significant enhance- ment of the dark matter density close to the hole. We investigate this effect, focusing on the phenomenologically interesting case where the black hole is supermassive and is embedded in a galactic dark matter halo, although the formalism developed does not depend on that fact. Due to the enhanced gravitational potential, the dark matter will tend to cluster around the black hole. The precise details of this clustering will, in general, depend on the formation process of the black hole. However, if the black …

Correlated Sem, Fib, And Tem Studies Of Material Collected By The Nasa Stardust Spacecraft, Brendan Albert Haas

Arts & Sciences Electronic Theses and Dissertations

The objective of this thesis is to describe the study of cometary materials returned by NASA’s Stardust mission. The majority of the research presented in this thesis focuses on improving our characterization and understanding of the fine (< 1 µm) component of comet Wild 2. Investigations of the Stardust foils are conducted with correlated Scanning Electron Microscopy (SEM), Focused Ion Beam (FIB) sample preparation, and Transmission Electron Microscopy (TEM). Investigations of the Stardust aerogels are conducted with plasma ashing sample preparation followed by detailed characterization of the material with TEM. Additional studies of the Stardust interstellar foils, as well as the use of a Convolutional Neural Network (CNN) to search images of the Stardust foils for impact features, are also presented. As a part of this thesis I have developed a new technique for analyzing the Stardust aerogels through the use of plasma ashing sample preparation. This technique is an improvement upon previous attempts to separate cometary materials from the aerogel through the use of HF vapor etching. Plasma ashing allows for cometary materials trapped within the Stardust aerogels to be deposited directly onto TEM grids allowing for detailed characterization of the cometary material with minimal interference from the aerogel itself. The correlated SEM/FIB/TEM studies of the Stardust foils demonstrated here nearly double the number of Stardust craters that have been elementally and structurally characterized in scientific literature. The crater impactor residues were largely composed of combinations of silicates and iron-nickel sulfides that, following impact, rapidly quenched into amorphous melt layers. Two craters were found to contain signatures of the refractory minerals spinel and taenite, indicating a component of the Wild 2 fines originated in the inner Solar System. However, the lack of crystalline material throughout the crater residues suggests that the fine component may largely be composed of amorphous silicates that likely formed in the outer Solar System. Additionally, the submicron Stardust craters appeared enriched in volatile elements relative to CI chondrites, further suggesting that the fine component of Wild 2 originated from a reservoir that was separate from the more refractory coarse (> 1 µm) component. The Stardust aerogel samples returned carbon-rich and potential oldhamite grains. Carbon-rich materials have not been previously observed in the Stardust foils, likely due to the violent collection methods, and the result suggests the ashing technique may be used to better characterize components of the Wild 2 fines that have been difficult to investigate. The presence of oldhamite in the …

Investigation And Classification Of Planetary Materials And Surfaces Using Novel Methods To Analyze Large Compositional Datasets: Quantitative X-Ray Compositional Mapping And Lunar Reconnaissance Orbiter Narrow Angle Camera Photometric Analysis, Timothy Michael Hahn

Arts & Sciences Electronic Theses and Dissertations

Our understanding of planetary bodies and their surfaces originates from measurements made by spacecraft instruments and laboratory analysis of extraterrestrial materials. Integration of these datasets can significantly advance the fields of planetary geology and geochemistry. The goal of my dissertation research has been to develop novel methods for interrogating extraterrestrial samples and planetary regoliths, with an emphasis on integrating these complementary datasets. Additionally, my research has focused on utilizing ‘big data’ within the geoscience and planetary science communities, whether that data be geospatial or geochemical in nature. My dissertation research involves two separate, but related projects: (1) coupling Apollo 17 …

Electron Decoupling With Chirped Microwave Pulses For Magic Angle Spinning Dynamic Nuclear Polarization Nuclear Magnetic Resonance Spectroscopy, Edward Paul Saliba

Arts & Sciences Electronic Theses and Dissertations

Dynamic nuclear polarization (DNP) is a method of generating hyperpolarization of nuclear spins for nuclear magnetic resonance (NMR) spectroscopy. Coherent, time domain techniques make the possibility of DNP directly to spins of interest at room temperature and higher feasible in magic angle spinning (MAS) NMR, allowing for optimal experimental repetition times to be limited by the T_1 of the electron, rather than a much longer T_1DNP, with excellent resolution. The strong hyperfine couplings that make such direct DNP transfers possible, however, can lead to short nuclear relaxation times that result in broadening of nuclear resonances and reduce sensitivity. This dissertation …

Fast-Forward Protein Folding And Design: Development, Analysis, And Applications Of The Fast Sampling Algorithm, Maxwell Isaac Zimmerman

Arts & Sciences Electronic Theses and Dissertations

Molecular dynamics simulations are a powerful tool to explore conformational landscapes, though limitations in computational hardware commonly thwart observation of biologically relevant events. Since highly specialized or massively parallelized distributed supercomputers are not available to most scientists, there is a strong need for methods that can access long timescale phenomena using commodity hardware. In this thesis, I present the goal-oriented sampling method, Fluctuation Amplification of Specific Traits (FAST), that takes advantage of Markov state models (MSMs) to adaptively explore conformational space using equilibrium-based simulations. This method follows gradients in conformational space to quickly explore relevant conformational transitions with orders of …

Self-Assembly Of Conducting Polymer Nano- And Microstructures For Energy Storage, Luciano Matteo Santino

Arts & Sciences Electronic Theses and Dissertations

Plastics are materials composed of many long chains of molecules with repeating subunits; strong interactions between neighboring molecules lead to the material used throughout the world. Plastics are commonly thought to be insulating, in stark contrast to the conductivity of metals. However, certain polymer structures were discovered to exhibit semiconducting properties, the subject of the Nobel Prize in Chemistry in 2000. Conducting polymers have a unique molecular structure with an electronically conjugated backbone, allowing electrons to freely travel both across the chain and in between chains. This work focuses on controlling the kinetics of the reaction between the vapors of …

Strongly Correlated Systems Under High Magnetic Field: A Mixed Landau Levels Description For Fractional Quantum Hall Effect, Sumanta Bandyopadhyay

Arts & Sciences Electronic Theses and Dissertations

Strong correlation among electrons under high magnetic field gives rise to an entirely new arena of emergent physics, namely fractional quantum Hall effect. Such systems have entirely different elementary degrees of freedom and generally, demand non-perturbative approaches to develop a better understanding. In the literature, there are several analytical methodologies and numerical toolkits available to study such a system. Clustering of zeros, parent Hamiltonian, off-diagonal order parameter, parton construction, matrix product states are to be named among a few of those popular methodologies in the existing literature. Most of these methods work well in the lowest Landau level or holomorphic …

Strongly Correlated Systems Under High Magnetic Field: A Mixed Landau Levels Description For Fractional Quantum Hall Effect, Sumanta Bandyopadhyay

Arts & Sciences Electronic Theses and Dissertations

Strong correlation among electrons under high magnetic field gives rise to an entirely new arena of emergent physics, namely fractional quantum Hall effect. Such systems have entirely different elementary degrees of freedom and generally, demand non-perturbative approaches to develop a better understanding. In the literature, there are several analytical methodologies and numerical toolkits available to study such a system. Clustering of zeros, parent Hamiltonian, off-diagonal order parameter, parton construction, matrix product states are to be named among a few of those popular methodologies in the existing literature. Most of these methods work well in the lowest Landau level or holomorphic …

A Physics-Based Intermolecular Potential For Biomolecular Simulation, Joshua Andrew Rackers

Arts & Sciences Electronic Theses and Dissertations

The grand challenge of biophysics is to use the fundamental laws of physics to predict how biological molecules will move and interact. The atomistic HIPPO (Hydrogen-like Intermolecular Polarizable Potential) force field is meant to address this challenge. It does so by breaking down the intermolecular potential energy function of biomolecular interactions into physically meaningful components (electrostatics, polarization, dispersion, and exchangerepulsion) and using this function to drive molecular dynamics simulations. This force field is able to achieve accuracy within 1 kcal/mol for each component when compared with ab initio Symmetry Adapted Perturbation Theory calculations. HIPPO is capable of this accuracy because …

Wave Function Engineering In Cdse/Pbs Core/Shell Nanocrystal Heterostructures, Brian Matthew Wieliczka

Arts & Sciences Electronic Theses and Dissertations

Colloidal semiconducting nanocrystals hold significant potential for third generation photovoltaics as solution processable materials that can surpass the Shockley-Queisser limit through multiexciton generation. In pursuit of this goal, the synthesis and optical characterization of CdSe/PbS core/shell quantum dots is reported. The spectroscopic behavior of these particles demonstrates their potential for use in optoelectronic devices, taking advantage of wave function engineering of the electron and hole. The rock salt PbS shell grows on all sides of the underlying zinc blende CdSe quantum dot, creating a core/shell structure. With increasing shell thickness, the band edge absorption and photoluminescence transitions decrease in energy …

Solid-State Nmr Of Co2 Mineralization And Nmr Crystallography, Jinlei Cui

Arts & Sciences Electronic Theses and Dissertations

The work described in this dissertation has been accomplished by using solid-state nuclear magnetic resonance (SSNMR) spectroscopy to investigate CO2 mineralization and to refine the positions of protons in the crystalline system. The reaction of forsterite (Mg2SiO4) and 13CO2 is presented here, which is measured using in-situ 13C NMR spectroscopy without removing the sample from the reactor. 29Si SSNMR is used to investigate the reaction of forsterite with 13CO2 in the presence of water or NaCl brine as a function of depth in the sample. Additionally, we also show that NMR crystallography can significantly improve structure refinement of hydrogens’ positions …

Solid-State Nmr Of Co2 Mineralization And Nmr Crystallography, Jinlei Cui

Arts & Sciences Electronic Theses and Dissertations

The work described in this dissertation has been accomplished by using solid-state nuclear magnetic resonance (SSNMR) spectroscopy to investigate CO2 mineralization and to refine the positions of protons in the crystalline system. The reaction of forsterite (Mg2SiO4) and 13CO2 is presented here, which is measured using in-situ 13C NMR spectroscopy without removing the sample from the reactor. 29Si SSNMR is used to investigate the reaction of forsterite with 13CO2 in the presence of water or NaCl brine as a function of depth in the sample. Additionally, we also show that NMR crystallography can significantly improve structure refinement of hydrogens’ positions …

Index Theory For Toeplitz Operators On Algebraic Spaces, Mohammad Jabbari

Arts & Sciences Electronic Theses and Dissertations

This dissertation is about the abstract Toeplitz operators obtained by compressing the multishifts of the usual Hilbert spaces of analytic functions onto co-invariant subspaces generated by polynomial functions. These operators were introduced by Arveson in regard to his multivariate dilation theory for spherical contractions. The main technical issue here is essential normality, addressed in Arveson's conjecture. If this conjecture holds true then the fundamental tuple of Toeplitz operators associated to a polynomial ideal $I$ can be thought as noncommutative coordinate functions on the variety defined by $I$ intersected with the boundary of the unit ball. This interpretation suggests operator-theoretic techniques …

Variational Inference For Quantile Rgression, Bufei Guo

Arts & Sciences Electronic Theses and Dissertations

Quantile regression (QR) (Koenker and Bassett, 1978), is an alternative to classic lin- ear regression with extensive applications in many fields. This thesis studies Bayesian quantile regression (Yu and Moyeed, 2001) using variational inference, which is one of the alternative methods to the Markov chain Monte Carlo (MCMC) in approximating intractable posterior distributions. The lasso regularization is shown to be effective in improving the accuracy of quantile regression (Li and Zhu, 2008). This thesis developed variational inference for quantile regression and regularized quantile regression with the lasso penalty. Simulation results show that variational inference is a computationally more efficient alternative …

Siderophore Pathways And Non-Traditional Antibiotic Strategies In Multi-Drug Resistant Acinetobacter Baumannii, Tabbetha Bohac

Arts & Sciences Electronic Theses and Dissertations

The rise of antibiotic resistance is driving exploration of non-canonical antibiotic approaches, including neutralization of virulence factors. Multi-drug resistant (MDR) Gram-negative pathogens, including Acinetobacter baumannii, are of particular concern because of the small number of clinically useful antibiotics available for use. Here we both expand upon the existing knowledge of two of the siderophores of A. baumannii, acinetobactin and fimsbactin, and utilize this knowledge to synthesize novel compounds for the inhibition of pathogenic A. baumannii in whole cell assays.

Furthering the current knowledge of the natural siderophore systems of A. baumannii, we were able to investigate the interaction of acinetobactin …

Essays On Econometrics And Rational Choice, Junnan He

Arts & Sciences Electronic Theses and Dissertations

Decision and choice theory is a topic of interest in both econometrics and microeconomic theory. We contribute to the theory of decision under both contexts, that is, the theory of model selection in econometrics, and the theory of rational decision in microeconomics.

There is a long-lasting theoretical interest in model selection. More recently, research on sparse estimators, a class of estimation methods that select and estimate important parameters simultaneously, has been the central focus on model selection. The methods become especially relevant when the problem is of high-dimensional nature. Theoretically, sparse methods can perform well when the true data generating …

The Effect Of Depositional Environment And Early Marine Diagenesis On Carbonate-Associated Sulfate, Jocelyn Ann Richardson

Arts & Sciences Electronic Theses and Dissertations

The long-term redox state of Earth’s surface environments is governed by the relative burial proportions of redox-sensitive carbon and sulfur species throughout geologic time. The sulfur isotopic signature of seawater sulfate (δ34SSO4) traces the relative proportions of sulfur buried as sulfide (commonly pyrite) and sulfate (as evaporites, barite or carbonate-associated sulfate) and weathering source to the ocean. Thus, δ34SSO4 is a powerful tool to understand the evolution of redox conditions and the marine biogeochemical sulfur cycle. Due to the spatial and temporal extent of carbonates in the rock record, carbonate-associated sulfate (δ34SCAS) is a common proxy for the isotopic composition …

Limits And Singularities Of Normal Functions., Tokio Sasaki

Arts & Sciences Electronic Theses and Dissertations

On a projective complex variety $X$, constructing indecomposable higher Chow cycles is an interesting question toward the Hodge conjecture, motives, and other arithmetic applications. A standard method to determine whether a given higher cycle is indecomposable or not is to consider it as a general fiber of a degenerate family of higher cycles, and observe the asymptotic behaviors of the associated higher normal functions.

In this thesis, we introduce some known examples of indecomposable cycles and a new method to detect the linearly independence of $\mathbb{R}$-regulator indecomposable $K_1$-cycles which is based on the singularities and limits of admissible normal functions …

A Q-Analogue And A Symmetric Function Analogue Of A Result By Carlitz, Scoville And Vaughan, Yifei Li

Arts & Sciences Electronic Theses and Dissertations

We derive an equation that is analogous to a well-known symmetric function identity: $\sum_{i=0}^n(-1)^ie_ih_{n-i}=0$. Here the elementary symmetric function $e_i$ is the Frobenius characteristic of the representation of $\mathcal{S}_i$ on the top homology of the subset lattice $B_i$, whereas our identity involves the representation of $\cS_n\times \cS_n$ on the top homology of Segre product of $B_n$ with itself. We then obtain a q-analogue of a polynomial identity given by Carlitz, Scoville and Vaughan through examining the Segre product of the subspace lattice $B_n(q)$ with itself. We recognize the connection between the Euler characteristic of the Segre product of $B_n(q)$ with …

Electronic Transport Behavior Of Adatom- And Nanoparticle-Decorated Graphene, Jamie Anne Elias

Arts & Sciences Electronic Theses and Dissertations

To induce a non-negligible spin-orbit coupling in monolayer graphene, for the purposes of realizing the Kane-Mele Hamiltonian, transition metal adatoms have been deposited in dilute amounts by thermal evaporation in situ while holding the device temperature near 4K. Electronic transport studies including measurements such as gate voltage dependent conductivity and mobility, weak localization, high field magnetoresistance (Shubnikov de Haas oscillations), quantum Hall, and nonlocal voltage were performed at low temperature before and after sequential evaporations. Studies of tungsten adatoms are consistent with literature regarding other metal adatoms on graphene but were unsuccessful in producing a spin-orbit signature, at least partially …

Topics In Complex And Large-Scale Data Analysis, Guanshengrui Hao

Arts & Sciences Electronic Theses and Dissertations

Past few decades have witnessed skyrocketed development of modern technologies. As a result, data collected from modern technologies are evolving towards a direction with more complicated structure and larger scale, driving the traditional data analysis methods to develop and adapt. In this dissertation, we study three statistical issues rising in data with complicated structure and/or in large scale. In Chapter 2, we propose a Bayesian framework via exponential random graph models (ERGM) to estimate the model parameters and network structures for networks with measurement errors; In Chapter 3, we design a novel network sampling algorithm for large-scale networks with community …

Extraordinary Magnetoresistance In Encapsulated Graphene Devices, Bowen Zhou

Arts & Sciences Electronic Theses and Dissertations

We report a study on the phenomenon of extraordinary magnetoresistance (EMR) in boron nitride encapsulated monolayer graphene devices. Extremely large EMR values–calculated as the change in magnetoresistance, (R(B)–R0)/R0–can be found in these devices due to the vanishingly small resistance values at zero field. In many devices the zero-field resistance can become negative, which enables R0 to be chosen arbitrarily close to zero depending only on measurement precision, resulting in very large EMR. We critically discuss the dependence of EMR on measurement precision and device asymmetry. On the other hand, we also find the largest reported values of the sensitivity to …