10,516 Works

Insights into the Mechanism of Asparagine-Linked Glycosylation: Kinetic Studies with Substrates and Inhibitors

Tamara Lynn Hendrickson
Investigations into the mechanism of action of oligosaccharyl transferase (OT), the enzyme that catalyzes the first committed step in the biosynthesis of all asparagine-linked glycoproteins, were conducted. Research focused on kinetic studies with small reactive molecules and tripeptide substrates and inhibitors; these experiments were designed to specifically probe the OT active site. Commercially available chemical modification agents were used to identify a reactive cysteine residue in or near the oligosaccharide binding site. Based on this...

Identification of New OPA1 Cleavage Site Reveals that Short Isoforms Regulate Mitochondrial Fusion

Ruohan Wang
OPA1 is a 120kDa large GTPase belonging to the dynamin superfamily. It is the only known mitochondrial inner membrane fusion protein, mediating fusion of the mitochondrial inner membranes following outer membrane fusion. Additionally, OPA1 also regulates cristae morphology and maintains respiratory chain function. OPA1 has two forms—inner-membrane-anchored long forms (l-OPA1) and cleaved inter-membrane-space only short forms (s-OPA1). L-OPA1 are proteolytically processed by two mitochondrial proteases—OMA1 and YME1L, acting at cleavage sites S1 and S2 respectively,...

High Fidelity Probe and Mitigation of Mirror Thermal Fluctuations

Tara Chalermsongsak
Thermal noise arising from mechanical loss in high reflective dielectric coatings is a significant source of noise in precision optical measurements. In particular, Advanced LIGO, a large scale interferometer aiming to observed gravitational wave, is expected to be limited by coating thermal noise in the most sensitive region around 30–300 Hz. Various theoretical calculations for predicting coating Brownian noise have been proposed. However, due to the relatively limited knowledge of the coating material properties, an...

Dynamic Rupture Simulation Integrated with Earthquake Observations

Yihe Huang
Dynamic rupture simulations are unique in their contributions to the study of earthquake physics. The current rapid development of dynamic rupture simulations poses several new questions: Do the simulations reflect the real world? Do the simulations have predictive power? Which one should we believe when the simulations disagree? This thesis illustrates how integration with observations can help address these questions and reduce the effects of non-uniqueness of both dynamic rupture simulations and kinematic inversion problems....

Seismic Structure along Transitions from Flat to Normal Subduction: Central Mexico, Southern Peru, and Southwest Japan

Sara Lyn Dougherty
The fine-scale seismic structure of the central Mexico, southern Peru, and southwest Japan subduction zones is studied using intraslab earthquakes recorded by temporary and permanent regional seismic arrays. The morphology of the transition from flat to normal subduction is explored in central Mexico and southern Peru, while in southwest Japan the spatial coincidence of a thin ultra-slow velocity layer (USL) atop the flat slab with locations of slow slip events (SSEs) is explored. This USL...

Electronic States in Disordered Topological Insulators

Kun Woo Kim
We present a theoretical study of electronic states in topological insulators with impurities. Chiral edge states in 2d topological insulators and helical surface states in 3d topological insulators show a robust transport against nonmagnetic impurities. Such a nontrivial character inspired physicists to come up with applications such as spintronic devices [1], thermoelectric materials [2], photovoltaics [3], and quantum computation [4]. Not only has it provided new opportunities from a practical point of view, but its...

The Search for Gravitational Waves from the Coalescence of Black Hole Binary Systems in Data from the LIGO and Virgo Detectors. Or: A Dark Walk through a Random Forest

Kari Alison Hodge
The LIGO and Virgo gravitational-wave observatories are complex and extremely sensitive strain detectors that can be used to search for a wide variety of gravitational waves from astrophysical and cosmological sources. In this thesis, I motivate the search for the gravitational wave signals from coalescing black hole binary systems with total mass between 25 and 100 solar masses. The mechanisms for formation of such systems are not well-understood, and we do not have many observational...

Model Predictive Control for Deferrable Loads Scheduling

Niangjun Chen
Real-time demand response is essential for handling the uncertainties of renewable generation. Traditionally, demand response has been focused on large industrial and commercial loads, however it is expected that a large number of small residential loads such as air conditioners, dish washers, and electric vehicles will also participate in the coming years. The electricity consumption of these smaller loads, which we call deferrable loads, can be shifted over time, and thus be used (in aggregate)...

Rational Design of Zinc Phosphide Heterojunction Photovoltaics

Jeffrey Paul Bosco
The prospect of terawatt-scale electricity generation using a photovoltaic (PV) device places strict requirements on the active semiconductor optoelectronic properties and elemental abundance. After reviewing the constraints placed on an "earth-abundant" solar absorber, we find zinc phosphide (α-Zn3P2) to be an ideal candidate. In addition to its near-optimal direct band gap of 1.5 eV, high visible-light absorption coefficient (>104 cm-1), and long minority-carrier diffusion length (>5 μm), Zn3P2 is composed of abundant Zn and P...

Protein Structure Refinement Algorithms

Mohsen Chitsaz
Protein structure prediction has remained a major challenge in structural biology for more than half a century. Accelerated and cost efficient sequencing technologies have allowed researchers to sequence new organisms and discover new protein sequences. Novel protein structure prediction technologies will allow researchers to study the structure of proteins and to determine their roles in the underlying biology processes and develop novel therapeutics. Difficulty of the problem stems from two folds: (a) describing the energy...

Fundamental Studies of Carbon Oxygen Bond Activation in Nickel Diphosphine Ether Complexes. And, Metallomacrocycles as Ligands: Synthesis and Characterization of Aluminum-Bridged Bisglyoximato Complexes of Iron and Cobalt

Paul Kelley
In order to develop better catalysts for the cleavage of aryl-X bonds fundamental studies of the mechanism and individual steps of the mechanism have been investigated in detail. As the described studies are difficult at best in catalytic systems, model systems are frequently used. To study aryl-oxygen bond activation, a terphenyl diphosphine scaffold containing an ether moiety in the central arene was designed. The first three chapters of this dissertation focus on the studies of...

Microstructure Control and Iodine Doping of Bismuth Telluride

Nicholas A. Heinz
On the materials scale, thermoelectric efficiency is defined by the dimensionless figure of merit zT. This value is made up of three material components in the form zT = Tα2/ρκ, where α is the Seebeck coefficient, ρ is the electrical resistivity, and κ is the total thermal conductivity. Therefore, in order to improve zT would require the reduction of κ and ρ while increasing α. However due to the inter-relation of the electrical and thermal...

Search for Color Transparency in A(e,e'p) at High Momentum Transfer

Thomas Germano O'Neill
Rates for A(e, e'p) on the nuclei 2H, C, Fe, and Au have been measured at momentum transfers Q2 = 1, 3, 5, and 6.8 (GeV fc)2. We extract the nuclear transparency T, a measure of the importance of final state interactions (FSI) between the outgoing proton and the recoil nucleus. Some calculations based on perturbative QCD predict an increase in T with momentum transfer, a phenomenon known as Color Transparency. No statistically significant rise...

GPU-Accelerated Fourier-Continuation Solvers and Physically Exact Computational Boundary Conditions for Wave Scattering Problems

Timothy James Elling
Many important engineering problems, ranging from antenna design to seismic imaging, require the numerical solution of problems of time-domain propagation and scattering of acoustic, electromagnetic, elastic waves, etc. These problems present several key difficulties, including numerical dispersion, the need for computational boundary conditions, and the extensive computational cost that arises from the extremely large number of unknowns that are often required for adequate spatial resolution of the underlying three-dimensional space. In this thesis a new...

Randomness and Noise in Information Systems

Hongchao Zhou
This dissertation is devoted to the study of randomness and noise in a number of information systems including computation systems, storage systems, and natural paradigms like molecular systems, where randomness plays important and distinct roles. Motivated by applications in engineering and science we address a number of theoretical research questions. In a computation system, randomness enables to perform tasks faster, simpler, or more space efficient. Hence, randomness is a useful computational resource, and the research...

Polarization-Based Navigation in Drosophila

Peter Thomas Weir
Insects maintain a constant bearing across a wide range of spatial scales. Monarch butterflies and locusts traverse continents (Williams, 1957; Wehner, 1984), and foraging bees and ants travel hundreds of meters to return to their nests (Dyer, 1996; Wehner, 1984, 2003), whereas many other insects fly straight for only a few centimeters before changing direction. Despite this variation in spatial scale, the brain region thought to underlie long-distance navigation is remarkably conserved (Loesel et al.,...

Measurement of Thermo-Optic Properties of Thin Film Dielectric Coatings

Gregory H. Ogin
We have carried out an experiment to test the theory of the thermo-optic response of a dielectric stack mirror coating and to measure parameters of interest in calculating thermo-optic noise. Specifically, we measured the coefficient of thermal expansion and the change of index of refraction with temperature (dn/dT ) for thin film silica (SiO2) and tantala (Ta2O5) in mirror coatings. These measurements were achieved by driving thermal fluctuations in such mirrors in one arm of...

A Novel Method for Studying Nucleated Pathways in Membranes: Development and Applications for Gene Delivery

Christina Lei Ting
The development of a safe, selective, and efficient gene delivery system is key to the success of human gene therapy. In polymer-based gene delivery systems, biocompatible polymers electrostatically bind and condense the genetic material into protective nanoparticles. These nanoparticles must subsequently overcome several challenges, which remain poorly understood. In particular, once internalized by the cell, the nanoparticles are trapped inside a membrane-bound compartment called the endosome. In the proton sponge hypothesis, the buffering capacity of...

Tools for Assessing Mitochondrial Dynamics in Mouse Tissues and Neurodegenerative Models

Anh Hoang Pham
Mitochondria are dynamic organelles that undergo membrane fusion and fission and transport. The dynamic properties of mitochondria are important for regulating mitochondrial function. Defects in mitochondrial dynamics are linked to neurodegenerative diseases and affect the development of many tissues. To investigate the role of mitochondrial dynamics in diseases, versatile tools are needed to explore the physiology of these dynamic organelles in multiple tissues. Current tools for monitoring mitochondrial dynamics have been limited to studies in...

Modeling, Simulation, and Design of Self-Assembling Space Systems: Accurate Collision Detection, Robust Time Integration, and Optimal Control

Gwendolyn Brook Johnson
Motivated by issues inherent in modeling and designing self-assembling systems (e.g. multiple collisions, collisions between non-smooth bodies, clumping and jamming behaviors, etc.), the goal of this thesis is to develop robust numerical tools that enable ecient and accurate direct simulation of self assembling systems and the application of optimal control methods to this type of system. The systems will be alternately modeled using linear nite elements, rigid bodies, or chains of rigid bodies. To this...

Topological Quantum Field Theory and the Geometric Langlands Correspondence

Kevin Luke Setter
In the pioneering work of A. Kapustin and E. Witten, the geometric Langlands program of number theory was shown to be intimately related to duality of GL-twisted N=4 super Yang-Mills theory compactified on a Riemann surface. In this thesis, we generalize Kapustin-Witten by investigating compactification of the GL-twisted theory to three dimensions on a circle (for various values of the twisting parameter t). By considering boundary conditions in the three-dimensional description, we classify codimension-two surface...

Chemistry of PNP Bis(phosphide) Pincer Ligands and Palladium(II) Dimers as Robust, Versatile Precatalysts for Olefin Isomerization, Oligomerization, and Oxidation

Matthew Steven Winston
The first half of this thesis details the synthesis and coordination chemistry of a very unusual pyridine-linked bis(secondary phosphine) pincer ligand system. Despite the highly nucleophilic phosphide donors, this dianionic system is an unexpectedly poor pincer ligand. Crystallographic and DFT studies reveal that both phosphide-metal σ- and π-bonding is compromised by long metal-phosphorus bonds, which result in significant distortions to the chelate ring. The neutral ligand coordinates readily κ2 (via phosphines) to late metals, such...

Sec-facilitated Protein Translocation and Membrane Integration

Bin Zhang
The Sec translocon is a central component of the cellular machinery for targeting and delivering nascent proteins. Ubiquitous across all kingdoms of life, it is a protein-conducting channel that facilitates recognition of integral membrane protein domains and the establishment of integral membrane protein topology. Structural, biochemical, and biophysical studies have illuminated the role of the Sec translocon in both cotranslational and posttranslational protein targeting. In particular, quantitative assays have established the dependence of transmembrane domain...

Essays on Information, Competition, and Cooperation

Luke Anthony Boosey
This thesis consists of three papers that study the relationships between information, competition, and cooperation in two novel environments. We first examine the competitive behavior of firms with private information in two-sided matching markets. This part of the thesis employs purely game-theoretic tools. Second, we study voluntary contributions towards a linear public good by players who are connected through a network. In this environment, we use experimental and theoretical techniques to examine the effects of...

Bootstrapping Vehicles: A Formal Approach to Unsupervised Sensorimotor Learning Based on Invariance

Andrea Censi
Could a "brain in a jar" be able to control an unknown robotic body to which it is connected, and use it to achieve useful tasks, without any prior assumptions on the body's sensors and actuators? Other than of purely intellectual interest, this question is relevant to the medium-term challenges of robotics: as the complexity of robotics applications grows, automated learning techniques might reduce design effort and increase the robustness and reliability of the solutions....

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