2,412 Works

Studies of Zγ Production and Constraints on Anomalous Triple Gauge Couplings in pp Collisions at √s = 7 TeV

Jan Veverka
In this thesis, we test the electroweak sector of the Standard Model of particle physics through the measurements of the cross section of the simultaneous production of the neutral weak boson Z and photon γ, and the limits on the anomalous Zγγ and ZZγ triple gauge couplings h3 and h4 with the Z decaying to leptons (electrons and muons). We analyze events collected in proton-proton collisions at center of mass energy of sqrt(s) = 7...

Transcriptional Enhancer Activity of Biochemically Marked Genomic Elements

Gilberto DeSalvo
Functional genomics aspires to explain how a transcription factor (TF) and its measured biochemical occupancy relates to the enhancer activity of the underlying sequence elements. Tissue-specific TFs exhibit remarkable selectivity and reproducibility in the available genome-wide sequence motifs accessed. A consistent central conclusion is that, irrespective of the element selection criteria used, ~50% of candidate Enhancers score as transcriptionally active in both mouse and human cell types, while the remaining 50% of similarly biochemically marked...

Mechanisms of Transposable Element Repression by Piwi Proteins in the piRNA Pathway of Drosophila Germ Cells

Alexandre Webster
The ability to reproduce is a defining characteristic of all living organisms. During reproduction, the integrity of genetic material transferred from one generation to the next is of utmost importance. Organisms have diverse strategies to ensure the fidelity of genomic information inherited between generations of individuals. In sexually reproducing animals, the piRNA pathway is an RNA-interference (RNAi) mechanism that protects the genomes of germ cells from the replication of ‘selfish’ genetic sequences called transposable elements...

Toward Realizable Quantum Computers

Michael Edward Beverland
The work in this thesis splits naturally into two parts: (1) experimentally oriented work consisting of experimental proposals for systems that could be used to implement quantum information tasks with current technology, and (2) theoretical work focusing on universal fault-tolerant quantum computers which we hope can be scaled as experimental capabilities continue to move forward.

New insights into the formation and modification of carbonate-bearing minerals and methane gas in geological systems using multiply substituted isotopologues

Daniel Aaron Stolper
This thesis describes the use of multiply-substituted stable isotopologues of carbonate minerals and methane gas to better understand how these environmentally significant minerals and gases form and are modified throughout their geological histories. Stable isotopes have a long tradition in earth science as a tool for providing quantitative constraints on how molecules, in or on the earth, formed in both the present and past. Nearly all studies, until recently, have only measured the bulk concentrations...

Nonlinear Optics and Wavelength Translation Via Cavity-Optomechanics

Jeffrey Thomas Hill
The field of cavity-optomechanics explores the interaction of light with sound in an ever increasing array of devices. This interaction allows the mechanical system to be both sensed and controlled by the optical system, opening up a wide variety of experiments including the cooling of the mechanical resonator to its quantum mechanical ground state and the squeezing of the optical field upon interaction with the mechanical resonator, to name two. In this work we explore...

Egospace Motion Planning Representations for Micro Air Vehicles

Anthony Thomas Fragoso
Navigation of micro air vehicles (MAVs) in unknown environments is a complex sensing and trajectory generation task, particularly at high velocities. In this work, we introduce an efficient sense-and-avoid pipeline that compactly represents range measurements from multiple sensors, trajectory generation, and motion planning in a 2.5–dimensional projective data structure called an egospace representation. Egospace coordinates generalize depth image obstacle representations and are a particularly convenient choice for configuration flat mobile robots, which are differentially flat...

Dynamics of Granular Crystals with Elastic-Plastic Contacts

Hayden Andrew Burgoyne
We study the behavior of granular crystals subjected to impact loading that creates plastic deformation at the contacts between constituent particles. Granular crystals are highly periodic arrangements of spherical particles, arranged into densely packed structures resembling crystals. This special class of granular materials has been shown to have unique dynamics with suggested applications in impact protection. However, previous work has focused on very low amplitude impacts where every contact point can be described using the...

Characterization of Diverse Megathrust Fault Behavior Related to Seismic Supercycles, Mentawai Islands, Sumatra

Belle Philibosian
Long paleoseismic histories are necessary for understanding the full range of behavior of faults, as the most destructive events often have recurrence intervals longer than local recorded history. The Sunda megathrust, the interface along which the Australian plate subducts beneath Southeast Asia, provides an ideal natural laboratory for determining a detailed paleoseismic history over many seismic cycles. The outer-arc islands above the seismogenic portion of the megathrust cyclically rise and subside in response to processes...

Advanced Density Functional Theory Methods tor Materials Science

Steven Brian Demers
In this work we chiefly deal with two broad classes of problems in computational materials science, determining the doping mechanism in a semiconductor and developing an extreme condition equation of state. While solving certain aspects of these questions is well-trodden ground, both require extending the reach of existing methods to fully answer them. Here we choose to build upon the framework of density functional theory (DFT) which provides an efficient means to investigate a system...

The Polygon Package

Computer Science Technical Reports

Single-Neuron Correlates of Visual Object Representation in the Human Brain: Effects of Attention, Memory, and Choice

Juri Minxha
Neurons in the medial temporal lobe (amygdala and hippocampus) are known to respond selectively to specific object categories, such as faces. This dissertation investigates two novel extensions of this work: (1) how are such neuronal responses influenced by where we attend; (2) how is category information used by the brain to make decisions. The first question evaluated the representation of faces in the primate amygdala during naturalistic conditions, by recording from both human and macaque...

Identification of Fucose-α(1-2)-Galactose Binding Proteins in the Mammalian Brain

Arif Wibowo
Fucose-α(1-2)-galactose (Fucα(1-2)Gal) carbohydrates have been implicated in cognitive functions. However, the underlying molecular mechanisms that govern these processes are not well understood. While significant progress has been made toward identifying glycoconjugates bearing this carbohydrate epitope, a major challenge remains the discovery of interactions mediated by these sugars. Here, we employ the use of multivalent glycopolymers to enable the proteomic identification of weak affinity, low abundant Fucα(1-2)Gal-binding proteins (i.e. lectins) from the brain. End-biotinylated glycopolymers containing...

Iridium and Rhodium Analogues of the Shilov Cycle Catalyst; and The Investigation and Applications of the Reduction-Coupled Oxo Activation (ROA) Mechanistic Motif towards Alkane Upgrading

Ross Fu
This dissertation will cover several disparate topics, with the overarching theme centering on the investigation of organometallic C-H activation and hydrocarbon transformation and upgrading. Chapters 2 and 3 discuss iridium and rhodium analogues of the Shilov cycle catalyst for methane to methanol oxidation, and Chapter 4 on the recently discovered ROA mechanistic motif in catalysts for various alkane partial oxidation reactions. In addition, Chapter 5 discusses the mechanism of nickel pyridine bisoxazoline Negishi catalysts for...

Synthetic Molecular Machines for Active Self-Assembly: Prototype Algorithms, Designs, and Experimental Study

Nadine L. Dabby
Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional. This thesis explores and develops algorithms, molecular implementations, and theoretical...

An Economic Approach to Consumer Product Ratings

Dustin Hughes Beckett
In three essays we examine user-generated product ratings with aggregation. While recommendation systems have been studied extensively, this simple type of recommendation system has been neglected, despite its prevalence in the field. We develop a novel theoretical model of user-generated ratings. This model improves upon previous work in three ways: it considers rational agents and allows them to abstain from rating when rating is costly; it incorporates rating aggregation (such as averaging ratings); and it...

Towards Understanding the Mixing Characteristics of Turbulent Buoyant Flows

Phares Lynn Carroll
This work proposes a new simulation methodology in which variable density turbulent flows can be studied in the context of a mixing layer with or without the presence of gravity. Specifically, this methodology is developed to probe the nature of non-buoyantly-driven (i.e. isotropically-driven) or buoyantly-driven mixing deep inside a mixing layer. Numerical forcing methods are incorporated into both the velocity and scalar fields, which extends the length of time over which mixing physics can be...

Cell-Selective Chemoproteomics for Biological Discovery

Shannon Elizabeth Stone
Cellular protein synthesis changes rapidly in response to internal and external cues in ways that vary from cell to cell. Global proteomic analyses of microbial communities, tissues, and organisms have provided important insights into the behavior of such systems, but can obscure the diversity of responses characteristic of different cellular subpopulations. Recent advances in cell-specific proteomics—fueled in part by the development of bioorthogonal chemistries, more sensitive mass spectrometers and more advanced mining algorithms—have yielded unprecedented...

Dynamics of Cell–Matrix Mechanical Interactions in Three Dimensions

Jacob K. Notbohm
The forces cells apply to their surroundings control biological processes such as growth, adhesion, development, and migration. In the past 20 years, a number of experimental techniques have been developed to measure such cell tractions. These approaches have primarily measured the tractions applied by cells to synthetic two-dimensional substrates, which do not mimic in vivo conditions for most cell types. Many cell types live in a fibrous three-dimensional (3D) matrix environment. While studying cell behavior...

New Techniques for Noble Gas Geochronometry and Thermochronometry

Stephen Ellis Cox
Noble gases were among the first species measured by mass spectrometry and interrogated for geochemical information about the solid Earth. The analytical challenge of measuring them has driven technological development in the field, and new applications have in turn followed from new developments. In the first chapter, I present developments that bolster an existing technique, the (U–Th)/Ne system, by verifying the theoretical underpinnings of the method and by exploring its application in several minerals. In...

Eph Receptor Clustering by Chondroitin Sulfate Inhibits Axon Regeneration

Gregory Martin Miller
Chondroitin sulfate proteoglycans (CSPGs) play important roles in the developing and mature nervous system, where they guide axons, maintain stable connections, restrict synaptic plasticity, and prevent axon regeneration following CNS injury. The chondroitin sulfate glycosaminoglycan (CS GAG) chains that decorate CSPGs are essential for their functions. Through these sugar chains, CSPGs are able to bind and regulate the activity of a diverse range of proteins and through these interactions can regulate neuronal growth. These CS-protein...

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