Physical Sciences and Mathematics Commons^™

Role Of The Cytosolic Chaperonin Cct In The Folding Of Novel Substrates, Theresa M. Smith

Theses and Dissertations

All cells depend on properly folded proteins for survival and function. Misfolding of proteins results in loss of critical functions and may trigger the misfolding of other nearby proteins leading to toxic aggregation. While many proteins can fold on their own, others with complicated domain structures require assistance from protein folding machines called chaperones. The most complex and highly specialized of all chaperones is the eukaryotic chaperonin complex CCT which is necessary for the folding of a wide variety of essential proteins. These include the cytoskeletal proteins actin and tubulin as well as the Gβ subunit of the G protein …

Hierarchical Joint Entity Recognition And Relation Extraction Of Contextual Entities In Family History Records, Daniel Segrera

Theses and Dissertations

Entity extraction is an important step in document understanding. Higher accuracy entity extraction on fine-grained entities can be achieved by combining the utility of Named Entity Recognition (NER) and Relation Extraction (RE) models. In this paper, a cascading model is proposed that implements NER and Relation extraction. This model utilizes relations between entities to infer context-dependent fine-grain named entities in text corpora. The RE module runs independent of the NER module, which reduces error accumulation from sequential steps. This process improves on the fine-grained NER F1-score of existing state-of-the-art from .4753 to .8563 on our data, albeit on a strictly …

Alegaatr The Bandit, Ethan Pedersen

Theses and Dissertations

One design strategy for developing intelligent agents is to create N distinct behaviors. At each time step during task execution, the agent, or bandit, chooses which of the N behaviors to use. Traditional bandit algorithms often (1) assume the environment is stationary, (2) focus on asymptotic performance, and (3) do not incorporate external information available to them. Each of these simplifications limits these algorithms such that they often cannot be used successfully in practice. In this paper, we propose a new algorithm, called AlegAATr, as a step toward overcoming these deficiencies. AlegAATr utilizes a technique called Assumption-Alignment Tracking (AAT), proposed …

Developing Methods For Measuring In Vivo Lipid Metabolism, Russell L. Denton

Theses and Dissertations

Lipid metabolism is critically important to the normal function of individual cells and for signaling between tissues of the human body. There is a great need to quantify changes in lipid metabolism because of its implications in both normal healthy conditions and during disease development. In our first study, we developed a liquid chromatography mass spectrometry based workflow to assess in vivo metabolism of murine brain lipids. This involved sample preparation, data acquisition, and analysis software development and improvements. Regarding sample preparation, we maintained the mice at 5% body water for the duration of the experiment. As mouse metabolism proceeds, …

Characterization Of Telsam Chaperone Linker To Improve Crystallization Resolution And Structural Elucidation Of The Hydrogenase Maturase Complex, Parag Laljibhai Gajjar

Theses and Dissertations

TELSAM crystallization can be a revolutionary tool for the facile crystallization of proteins. TELSAM can increase the rate of crystallization and form crystals at low protein concentrations without direct contact between TELSAM polymers and, in some cases, with very minimal crystal contacts overall. To further understand and characterize TELSAM crystallization, we sought to understand the requirements for the composition of the linker confirmation between TELSAM and the fused target protein. We evaluated four linkers, AlaAla, AlaVal, ThrVal, and ThrThr, between 1TEL and the human CMG2 vWa domain. We compared the number of successful crystallization conditions, the number of crystals, the …

Community Detection Via Persistent Homology Surfaces, Abigail Jenkins

Theses and Dissertations

Network science continues to be an area of growing interest. In this thesis we introduce new methods of analyzing the structure of networks through the use of persistent homology. We propose the notion of a network's persistent surface, which allows us to visualize a vertex's relation to the whole network from a purely homological point of view. We further introduce a method of persistent surface community detection that finds vertices that play the same structural role in the network. We describe how these concepts provide the basis for an equivalence class among the vertices of a network, and provide many …

Gamelan Gong Directivity Dataset, Samuel D. Bellows, Dallin T. Harwood, Kent L. Gee, Micah R. Shepherd

Directivity

No abstract provided.

Short-Range Magnetic Correlations, Spontaneous Magnetovolume Effect, And Local Distortion In Magnetic Semiconductor Mnte, Raju Baral

Theses and Dissertations

The antiferromagnetic semiconductor MnTe has recently attracted significant interest as a potential high-performance thermoelectric material. Its promising thermoelectric properties are due in large part to short-range magnetic correlations in the paramagnetic state, which enhance the thermopower through the paramagnon drag effect. Using magnetic pair distribution function (mPDF) analysis of neutron total scattering data, we present a detailed, real-space picture of the short-range magnetic correlation in MnTe, offering a deeper view into the paramagnon drag effect and the nature of the correlated paramagnetic state. We confirm the presence of nanometer-scale antiferromagnetic correlations far into the paramagnetic state, show the evolution of …

The Unexpected Effectiveness Of Strategically Sparse Cooperation, Neal D. Munson

Theses and Dissertations

In this work, we will show a result derived from a class of economically inspired multi-agent differential games. The result shows that in the class of games we present, only a sparse cooperation structure is needed by the agents to achieve an outcome that is in a particular sense "optimal". One may expect that to achieve such an outcome, a centralized control or full cooperation would be necessary; it is not. Not only is it not necessary - it is never necessary. We precisely characterize what kind of cooperation IS necessary to attain that kind of optimality. Only the sparsest …

Quantifying Volatile Fatty Acid Concentrations During The Pretreatment And Anaerobic Digestion Process, Sascha Boutelle

Theses and Dissertations

Producing renewable energy from biomass or from the wastewater treatment process has gained momentum in the past 20 years. Anaerobic digestion has historically been used as one step in the waste treatment process, to both reduce the mass of waste that needs to be disposed of and to generate biogas. This process is typically only able to reduce 30-40% of the waste mass because of the recalcitrant nature of the waste streams being treated. Anaerobic pretreatment with the thermophilic bacteria Caldicellulosiruptor bescii (C. bescii) has been proven to increase the percentage of mass digested and consequently increase methane production to …

Effect Of X-Ray Illumination On Magnetic Domain Memory In [Co/Pd]/Irmn Multilayers, Colby Singint Walker

Theses and Dissertations

This thesis focuses on investigating the possible x-ray illumination effects on the magnetic domain memory (MDM) in magnetic [Co/Pd]IrMn multilayers. In this material, MDM is induced via exchange couplings between the ferromagnetic Co/Pd layer and the antiferromagnetic IrMn layer. To carry out this investigation, we have used magneto-transport and x-ray resonant magnetic scattering. The use of magneto-transport in-situ at synchrotron x-ray scattering facility has allowed us to follow the gradual effect of x-ray illumination on the amount of exchange bias, initially present after field cooling the material. With our in-situ measurements we have been able to see that x-ray illumination …

Wildfire Modeling With Data Assimilation, Andrew Johnston

Theses and Dissertations

Wildfire modeling is a complex, computationally costly endeavor, but with droughts worsening and fires burning across the western United States, obtaining accurate wildfire predictions is more important than ever. In this paper, we present a novel approach to wildfire modeling using data assimiliation. We model wildfire spread with a modification of the partial differential equation model described by Mandel et al. in their 2008 paper. Specifically, we replace some constant parameter values with geospatial functions of fuel type. We combine deep learning and remote sensing to obtain real-time data for the model and employ the Nelder-Mead method to recover optimal …

Determining Figure Skating Jump Under-Rotation In Real-Time Using Imu Sensors During Practice, Duncan O. Furgeson

Theses and Dissertations

We explore the use of machine learning to detect under-rotation in figure skating jumps. Under- rotation in jumps is difficult for the skater to sense but learning to recognize under-rotation is an impor- tant part of learning proper jump technique. To address this difficulty, we present the Under-rotation Monitor, or UR Monitor, a system for detecting under-rotated figure skating jumps in real-time. UR Monitor uses a single inertial measurement unit (IMU) attached to the skater's waist that sends a stream of accelerometer and gyroscope data to a mobile phone via Bluetooth. The mobile phone creates and sends an input vector …

A Usability Study Of Fido2 Hardware Tokens On Mobile Devices, Stephen Lambert

Theses and Dissertations

Passwords as the primary form of authentication on the web have many issues, such as password re-use across sites and difficulty in remembering secure passwords. The FIDO Alliance has created a passwordless system that has with support from companies like Google, Apple, and Microsoft: FIDO2. Studies have shown so far that users find FIDO2 usable on personal computers, but no work has been published on its usability on mobile devices. I conducted a lab study in which participants used FIDO2 passwordless authentication with hardware tokens on a mobile phone. Participants found FIDO2 usable on mobile devices, but had similar fears …

Computational Studies Of Dinuclear Catalytic Reaction Mechanisms, James Curtis Coombs Iii

Theses and Dissertations

Heterodinuclear and homodinuclear metal complexes with a direct metal-metal interaction offer the potential for unique catalysis due to cooperativity effects that impact reaction mechanisms, reactivity, and selectivity. Quantum-chemical density functional theory (DFT) calculations can directly examine the origin of dinuclear reactivity and selectivity effects. Chapter 1 provides a short overview of heterodinuclear and homodinuclear catalysts that have been experimentally and computationally examined. Chapter 2 reports our study using DFT methods to understand the mechanism and reactivity of a heterodinuclear Co-Zr catalyst with phosphinoamide ligands that catalyzes a Kumada coupling between alkyl halides and alkyl Grignards. Chapter 3 reports DFT calculations …

Structural Reasoning With Rational Expressions, Dana Steinhorst

Theses and Dissertations

Many students struggle to make sense of algebraic expressions in math. This lack of understanding results in students making symbolic manipulation errors, hindering their procedural fluency. Researchers believe these errors are linked to students' lack of structural reasoning. While research has shown that students rarely engage in expert structural reasoning, little is known about how students actually reason structurally. In this study, I interviewed six high school calculus students to study the way they identified, matched, and evaluated structures as they solved problems involving rational expressions and equations. I analyzed the participant interviews and outlined the matching process they used …

Complete Equitable Decompositions, Joseph Paul Drapeau

Theses and Dissertations

A well-known result in spectral graph theory states that if a graph has an equitable partition then the eigenvalues of the associated divisor graph are a subset of the graph's eigenvalues. A natural question question is whether it is possible to recover the remaining eigenvalues of the graph. Here we show that if a graph has a Hermitian adjacency matrix then the spectrum of the graph can be decomposed into a collection of smaller graphs whose eigenvalues are collectively the remaining eigenvalues of the graph. This we refer to as a complete equitable decomposition of the graph.

Determination Of A Catalytic Mechanism By Time Resolved Fourier Transform Infrared Spectroscopy And Time Domain Analysis Of Data From Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Jacob T. Davis

Theses and Dissertations

Heterobimetallic catalysts offer large potential for efficient and selective catalysis of a wide range of reactions. Better understanding of these catalytic mechanisms could yield further improvement in their catalytic abilities. Cp(CO)2Fe-Cu(IPr) (IPr = N,N-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) is a catalyst that has been reported to catalyze arene borylation. The catalytic mechanism of this catalyst that had been previously proposed had the initial step being a metal-metal cleavage. However, computational modeling suggested an alternate mechanism that could be more energetically favorable. Rather than a metal-metal cleavage as the initial step, we proposed a photoactivated carbonyl dissociation. To support this proposition, we performed time resolved …

Developing A Quantitative Understanding Of U-Substitution In First-Semester Calculus, Leilani Camille Heaton Fonbuena

Theses and Dissertations

In much of calculus teaching there is an overemphasis on procedures and manipulation of symbols and insufficient emphasis on conceptual understanding of calculus topics. As such students to struggle to understand and use calculus ideas in applied settings. Research shows that learning calculus topics from a quantitative reasoning-perspective results in more powerful and flexible conceptions of calculus topics like integration. However, topics beyond introducing integrals and the Fundamental Theorem of Calculus, like u-substitution, have yet to be explored from a quantity-based perspective. In this study, I conducted a set of two clinical interviews where we discussed quantitative meanings of integrals, …

Single-Shot, Ultrafast, Multi-Frame X-Ray Imaging Of Defect-Bearing Ablator Materials In Extreme Conditions, Daniel S. Hodge

Theses and Dissertations

Characterization of the dynamic behavior of defect-bearing ablator materials subjected to extreme conditions is essential in advancing fusion energy as an reliable and abundant energy source. By understanding how materials evolve spatially and temporally we can minimize hydrodynamic instabilities, which are major contributing factors to energy yield degradation in inertial confinement fusion (ICF) experiments. In this thesis we demonstrate the capabilities of an ultrafast x-ray imaging (UXI) detector, the Icarus V2, where we capture multiple frames of single void-bearing sample compressed by a high-intensity laser shockwave. Using the Matter in Extreme Conditions (MEC) instrument at the Linac Coherent Light Source …

Identity Work To Teach Mathematics For Social Justice, Navy B. Dixon

Theses and Dissertations

In this thesis, mathematics educators are conceptualized as individuals with multiple, simultaneous figured worlds that inform their decisions while planning. The study explores how two mathematics educators negotiated and orchestrated their figured worlds to plan two mathematics lessons for social justice. The results highlight how numerous the figured worlds each participant surfaced through background interviews. Some of the figured worlds were elicited by the interview questions (i.e., Race, Family, Social Justice Teaching) but other figured worlds organically surfaced through the interviews (i.e., Sexuality, Community, Activism, Critical Information Consumption). A discursive analysis of a selection of these figured worlds revealed conceptualizations …

Zeros Of A Family Of Complex-Valued Harmonic Rational Functions, Alexander Lee

Theses and Dissertations

The Fundamental Theorem of Algebra is a useful tool in determining the number of zeros of complex-valued polynomials and rational functions. It does not, however, apply to complex-valued harmonic polynomials and rational functions generally. In this thesis, we determine behaviors of the family of complex-valued harmonic functions $f_{c}(z) = z^{n} + \frac{c}{\overline{z}^{k}} - 1$ that defy intuition for analytic polynomials. We first determine the sum of the orders of zeros by using the harmonic analogue of Rouch\'e's Theorem. We then determine useful geometry of the critical curve and its image in order to count winding numbers by applying the harmonic …

Focusing Of High-Amplitude Sound Waves Using The Time Reversal Process, Brian D. Patchett

Theses and Dissertations

Time reversal is a method often used to focus sound to a desired location, and works best in a reverberant environment. The effect of focus location within a reverberant environment is presented first, revealing that proximity to reflecting surfaces has a significant effect on the amplitude of the focus both experimentally and when using a modal summation model. These effects are a primary component to creating focus signals at high amplitudes. High-amplitude focusing experiments show that when multiple sources are used simultaneously to generate a focus, a peak amplitude pressure spike of 200 dB can be achieved in air. A …

Improving Spatial Resolution Of Time Reversal Focusing Using Arrays Of Acoustic Resonators, Adam David Kingsley

Theses and Dissertations

Using a near-field array of acoustic resonators, it is possible to modify a focused pressure field and enforce a spatial frequency corresponding to the resonator array spacing. This higher spatial frequency makes it possible to focus and image with a resolution that is better than if the focusing were in free space. This near-field effect is caused by the phase shifting properties of resonators and, specifically, the delayed phase found in waves with a temporal frequency lower than that of the resonators in the array. Using time reversal, arrays of resonators are explored and the subwavelength focusing is used to …

Facies Architecture And Provenance Of The Highly Progradational, Fluvial Dominated Deltaic Depositional System Of The Cretaceous Nanushuk Formation On The North Slope Of Alaska, Sarah N. Naone

Theses and Dissertations

The Cretaceous Nanushuk Formation of northern Alaska records extremely rapid shoreline progradation across the Colville Basin during the Albian-Cenomanian epochs. Additionally, it records a period of tectonic realignment in the region, as the main sediment source began to transition from the Chukotkan orogeny to the west to a more local sediment source of the proximal Brooks Range to the south. Through detailed outcrop characterization and 3-D modeling of three exposed outcrops along the axial trend of the Colville Basin on the North Slope and the Upper section of the Nanushuk, this study clarifies the relative timing of the early Brookian …

Methods For Single-Cell And Low-Input Proteomics, Yiran Liang

Theses and Dissertations

Single-Cell Proteomics (SCP) can provide unique insights into biological processes by resolving heterogeneity that is obscured by bulk measurements. Gains in the overall sensitivity and proteome coverage through improvements in sample processing and analysis increase the information content obtained from each cell, particularly for less abundant proteins. In addition to achieving in-depth proteome coverage from single cells, higher throughput measurements enable large-scale and statistically significant features within single cell populations. This dissertation focuses on method development to improve the sensitivity and throughput of SCP based on the nanoPOTS (nanodroplet Processing in One pot for Trace Samples) platform. The methods discussed …

Evaluating Multi-Agent Modeller Representations, Jonathan Demke

Theses and Dissertations

The way a multi-agent modeller represents an agent not only affects its ability to reason about agents but also the interpretability of its representation space as well as its efficacy on future downstream tasks. We utilize and repurpose metrics from the field of representation learning to specifically analyze and compare multi-agent modellers that build real-valued vector representations of the agents they model. By generating two datasets and analyzing the representations of multiple LSTM- or transformer-based modellers with various embedding sizes, we demonstrate that representation metrics provide a more complete and nuanced picture of a modeller's representation space than an analysis …

Design And Evaluation Of Miniaturized Ion Trap Mass Analyzers Using Simulation, Radhya Weligama Gamage

Theses and Dissertations

Mass spectrometry is a technique that analyzes the chemical compositions of compounds based on the mass-to-charge ratio of their ionized constituents. Miniaturized ion trap mass spectrometry finds application in a wide range of fields where portable, rugged, and reliable analytical instruments are required. Ion traps of various designs have been introduced over the past decades, each with their own unique advantages and capabilities. However, the process of developing a novel miniaturized ion trap mass spectrometer continues to be fraught with challenges. This dissertation discusses simulation studies pertaining to the development of a novel dual ion trap, the simplified coaxial ion …

Stemficohort1preinterviewdata, Rebecca L. Sansom, Bryn Stclair, Jamie Jensen, Richard West

ScholarsArchive Data

The science, technology, engineering, and mathematics faculty institute (STEMFI) is a National Science Foundation funded project designed to provide support, measurement, and training to BYU faculty developing their own student-centered curriculum.

This PDF file contains pre-institute participation interview data from the first cohort of faculty involved in the STEM faculty institute (2018).

Charge Detection Mass Spectrometry Using Printed Circuit Board Arrays For The Analysis Of Microparticles In The Martian Atmosphere, Elaura Luanne Gustafson

Theses and Dissertations

Charge detection mass spectrometry (CDMS) is a single particle technique capable of simultaneously measuring charge and mass-to-charge ratios for individual ions or particles. The linear array CDMS design theoretically has no upper mass limit and is therefore a choice method for the analysis of high mass and heterogeneous samples, such as dust microparticles in the Martian atmosphere. This dissertation describes the development of a novel charge detection mass spectrometer made of printed circuit boards (PCB) for the analysis of dust microparticles in the Martian atmosphere. Development of this device has required investigations in analysis methods and the engineering design of …