Digital Commons Network^™

Computational Advances For Single-Cell Proteomics, Hannah Boekweg

Theses and Dissertations

The overarching goal of biologists is to characterize biological systems. When the workings of a system are understood, they can be fixed, broken, preserved, mimicked, and even replicated. The field of proteomics seeks to characterize systems through the lens of proteins. Proteins are referred to as the 'workhorse' of the cell to illustrate that they perform most functional tasks within the cell. These tasks are highly varied, including enzymatic activity, structural support, transport, storage, cell signaling, gene regulation, immune response, and more. Proteomics has been instrumental in new biological discoveries by characterizing the functional state of cells. A new area …

The Cellular Mechanisms Of Alzheimer's Disease Protection By The Pilra G78r Variant, Wenhan Cheng

Theses and Dissertations

Microglial dysfunction is increasingly linked to Alzheimer’s Disease (AD). Immune receptors like TREM2 and CD33 play opposing roles in microglial activity. TREM2 activation triggers immunoreceptor tyrosine-based activation motif (ITAM) signaling to promote microglial activities, including amyloid-β clearance, but variants in TREM2 such as R47H that impair its function increase AD risk. In contrast, CD33 is an inhibitory receptor that contains an immunoreceptor tyrosine-based inhibitory motif (ITIM) which transmits signals that suppress microglial function. An AD-protective variant in CD33 alters CD33 activity, potentially enhancing TREM2 function. PILRA is another inhibitory immune receptor expressed by microglia that contains an ITIM. A naturally …

Quantum-Chemical Modeling Of Mechanisms And Selectivity In Open-Shell Organometallic Reactions, Michael T. Davenport

Theses and Dissertations

Quantum mechanical calculations have emerged as a powerful approach for directly evaluating reaction mechanisms and selectivity in transition metal-ligand complexes involving organometallic intermediates. Density functional theory (DFT) quantum mechanical methods enable the generation of potential energy surfaces and structures that define reaction mechanisms and allow for the evaluation of selectivity through statistical transition state theory. However, in certain cases, it is necessary to go beyond statistical treatments and incorporate atomic motion through molecular dynamics simulations. Additionally, many transition metal-mediated reactions involve unpaired electrons and spin state crossings. This dissertation focuses on the application of DFT-derived potential energy surfaces and molecular …

From Assistance To Impact: The Expanding Role Of Undergraduate Teaching Assistants In Higher Education, Erin Measom

Theses and Dissertations

This dissertation is presented in a three-article format. It explores the evolving role of undergraduate teaching assistants (UTAs) in higher education, with a particular focus on how they facilitate interaction, engagement, and student success in online courses. As higher education institutions expand online learning and seek innovative ways to enhance student support, UTAs have emerged as key players in bridging the gap between students and instructors. The first article provides a scoping review of the literature on UTAs, tracing their historical evolution and examining their expanding role. While traditionally viewed as logistical or grading assistants, UTAs are increasingly taking on …

A Modular Simulation Environment And B-Spline Trajectory Generation Methods For Multi-Agent Uav Systems, Landon D. Shumway

Theses and Dissertations

Multi-agent UAV systems present a complex challenge requiring solutions to numerous subproblems. This research addresses two key issues: simulation testing and path planning. A modular simulation environment is developed, enabling users to run diverse mission scenarios with heterogeneous UAV teams and to implement custom dynamic models and guidance laws. Additionally, two novel B-spline trajectory generation methods are proposed. The first generates time-synchronized B-spline paths for UAVs with arbitrary initial and final states in 2D space, accommodating scenarios where agents must follow predetermined speed profiles. The second guidance method converts spline paths between MINVO, Bézier, and non-uniform B-spline representations, leveraging the …

The Efficacy Of Open Educational Resources On Achievement Outcomes In Different Higher Education Institutions, Angela Grace Findlay

Theses and Dissertations

Students suffer from achievement gaps in higher education. Achievement gaps refer to differences in graduation rates, retention rates, persistence rates, and student's grades. Achievement gaps may negatively affect students who are culturally or ethnically diverse and/or have a lower socioeconomic status. The use of open educational resources (OER) may mitigate achievement gaps as OER assists student success through higher academic performance and cost savings for students. Average quiz scores were obtained at different higher education institutions using an Introduction to Psychology OER. The scores from each course were analyzed using hierarchical linear modeling. Colleges were nested by demographics to evaluate …

Structural Analysis Of The Aileu Metamorphic Complex And The Laclo Fault Of Timor Leste, Banda Arc-Continent Collision, Emma C. Morrison

Theses and Dissertations

This study presents a structural analysis of the brittle and ductile features within the Aileu Metamorphic Complex of Timor Leste, located in the active Banda Arc–Australian continental collision zone. The deformation history of the complex is interpreted from the Permian–Jurassic deposition of sediments and basalts into intra-arc basins of Gondwana, through to the present- day collision of the Australian continental margin. This collision led to the development of the Wetar Suture and subsequent back-thrusting of the Aileu metamorphic rocks northward over the Banda forearc. Field evidence confirms that the Laclo Fault is currently active, with the most recent movement exhibiting …

How Transitioning Autistic Adults Consciously Perform Neurotypical Communication, Makenna J. Allred

Theses and Dissertations

Using semi-structured interviews this research explored the experiences of transitioning autistic adults with online communication. Participants shared information about navigating online communication, highlighting specific challenges such as interpreting tone and sarcasm, managing unspoken social norms, like emoji use, and responding to ambiguous or unexpected interactions. Participants shared that misunderstandings do occur in their online communication and how they recognize those miscommunications and strategize around preventing and mitigating them. These findings reveal that while computer-mediated communication offers opportunities for connection, it also presents unique obstacles that can exacerbate feelings of frustration due to miscommunications or misunderstandings. To prevent these social frictions …

Modeling And Simulation Of Tensegrity Structures With Continuous Cables, Austin R. Brown

Theses and Dissertations

This thesis presents a novel approach for modeling and simulating tensegrity structures with continuous cables. A Python-based simulation framework package was developed to address limitations in existing tensegrity modeling software, particularly the inability to model cables passing through multiple nodes. The framework utilizes virtual work methods to solve for equilibrium configurations of 2D, 2.5D and 3D tensegrity systems. Key features include: • A YAML-based input system for easy definition of tensegrity topologies. • Algorithms for handling continuous cables spanning multiple nodes. • Optimization techniques to find stable equilibrium states. • Capability to simulate 2.5D structures wrapped around cylindrical surfaces. • …

Semitic Root Encoding: Tokenization Based On The Templatic Morphology Of Semitic Languages In Nmt, Brendan T. Hatch

Theses and Dissertations

The morphological structure of Semitic languages like Arabic and Hebrew is based on non-concatenative roots and templates. This complex word structure used by humans is obscured to neural models that use traditional tokenization algorithms. In this work, I present and evaluate Semitic Root Encoding (SRE), a tokenization method that represents Semitic words with distinct root and template stem tokens, and apply it to neural machine translation (NMT). I evaluate whether tokenization with the SRE method leads to increases in translation quality, whether it allows NMT models to hypothesize unseen word forms needed at inference, and how impervious resulting NMT models …

Building And Demonstrating A Framework And Guide For Human-Centered Threat Modeling, Warda Usman

Theses and Dissertations

As researchers increasingly seek to understand threats faced by people rather than systems, there remains little consensus on how to study these threats in ways that are grounded in human experience. Traditional approaches to threat modeling are often designed for system vulnerabilities and offer limited guidance for eliciting or analyzing threats as understood by individuals in their social and cultural contexts. This dissertation addresses this gap by advancing human-centered threat modeling (HCTM) in security and privacy research as both a conceptual framework and through a set of empirical studies. The dissertation employs a mixed set of qualitative methods across four …

Simulating And Designing Pyro Fx To Communicate A Hostile And Magical Environment, Rebekah L. Tran

Undergraduate Honors Theses

This thesis aims to document the fire FX work completed on this year’s senior capstone film, Love & Gold, for the BYU Center of Animation. The story of the film is brought to life with many different types of effects including snow, sparks, lava, rock shattering, magic, hair, cloth, and the topic of this thesis, fire. The film has three main fire simulation needs: torches, braziers, and fire traps. The FX team on the film created these with Pyro simulations. Pyro simulations are a common type of simulation supported by Houdini FX, the software program that BYU Animation primarily uses …

Bloom Pattern Data, Zhongyuan Wang, Robert J. Lang, Larry L. Howell

ScholarsArchive Data

This data is the supplementary material of the paper "Bloom Patterns: Radially Expansive, Developable, and Flat-Foldable Origami" by Zhongyuan (Kelvin) Wang , Robert J. Lang, and Larry L. Howell.

We present bloom patterns as a family of radially expansive, flat-foldable, and developable origami patterns, many of which are rotationally symmetric. Bloom patterns are defined with a generalized definition and a standardized definition. A classification scheme for bloom patterns is identified, and several types of bloom patterns are analysed. The distinct helical nature that characterizes bloom patterns is described, and a set of compatibility conditions is derived to help determine if …

Refinement And Application Of The Absorption Cross-Section Of Molecular Bromine With Relevance To Atmospheric Chemistry, Callum Flowerday, Ryan Thalman, Jaron C. Hansen, Eric T. Sevy, Jason J. Sorensen, Matthew C. Asplund

ScholarsArchive Data

Defined Br2 XS - is the defined absorption cross-section using the UVvis spectrophotometer.

BBCEAS - This is raw absorption data measured using the BBCEAS (see article for details).

UVvis raw - This is the raw absorption data measured using the UVvis spectrophotometer.

Untying The Knot: All Of Us Strangers And The Transgressive Encounter, Luka Romney

Undergraduate Honors Theses

Trauma is a perennial human problem that has only recently received sustained attention from the academic community. Within the interdisciplinary field of memory studies, there has been a significant push to not only identify and theorize trauma but also map out and propose ways to move through and beyond the constraints of trauma. This article will use Andrew Haigh’s 2023 film All of Us Strangers to theorize an experience that forms a redemptive foil to trauma that I term encounter. These redemptive encounters are sticky and unwieldy, and they require a variety of critical frames to draw out their ultimate …

Exploring The Figured Worlds And Identity Of Religious Women In Mathematics-Related Majors, Rachel K. Reynolds

Undergraduate Honors Theses

This thesis investigates how religious women in mathematics construct and navigate their identities within the intersecting figured worlds of gender, religion, and mathematics. Drawing on Holland et al.’s (1998) theory of figured worlds and informed by identity theory, this study examines how these women experience, negotiate, and position their identities within these figured worlds. Through interviews with women who are simultaneously committed to religious life and mathematical scholarship, the research reveals that rather than perceiving conflict between these domains, participants often find points of integration and mutual reinforcement. Their narratives illuminate how identity is shaped through cultural contexts, institutional expectations, …

Delaunay Keyer For Colorspace-Local Matte Extraction And Spill Suppression, Isaac J. Criddle

Undergraduate Honors Theses

Keying is a fundamental, common, and expensive problem in visual effects. It consists of two subtasks: matte extraction and screen spill removal. Today’s standard keyers often fall short on edge cases including unevenly lit screens, fine detail, and sky replacements. As a result, keying continues to be a laborious process requiring highly trained compositors and complex bespoke setups. Our method does not assume one single saturated screen color, allowing for more versatile workflows. The keyer functions by interpolating over a Delaunay tetrahedralization of user-given sample colors. We evaluate our method relative to the visual effects industry’s standard keyers on a …

New Definitions Of Library Use: Experimentation, Discovery, And Creation (Edc) Within A Library, Holt Zaugg

Faculty Publications

Why did you do this activity, project, or research?

Over the last decade, libraries have shifted from being primarily repositories for information and resources to active learning centers. Physical resources (e.g., books, journals, manuscripts) have moved to online access. Librarian roles have adjusted how they help patrons find and access resources in their local library and beyond, resulting in impactful input on research, learning, and scholarly endeavors. Additionally, due to a reduced need for storing materials, libraries have developed collaborative and innovative spaces to meet patrons’ needs. These spaces include group study rooms, experiential studios, makerspaces, green rooms, and podcast …

Teaching Hygiene Skills To Teenagers With Developmental Disabilities Utilizing Friendship Circles, Nathaniel Medsker

Theses and Dissertations

High school students with intellectual and developmental disabilities (IDD) often struggle with hygiene skills, including table manners. These difficulties are especially noticeable in peer tutoring settings. Peer tutors were utilized to increase the mouth wiping behavior of the students with IDD using peer influence through the friendship circles intervention. The participants included high school age students with IDD and accompanying peer tutors from their classroom. This was done in a social setting during lunch while the peer tutors modeled the appropriate mouth wiping behavior and complimented the students with IDD if they also participated in the mouth wiping behavior. The …

Benchtop-Scale High Temperature Molten Salt Electrochemical Reactors: Experimental Setup And Considerations, Haley Hoover, Ivy Wu, Oluwatamilore Olushina, Robert Bell, Kerry Rippy

Reviews, Analyses, and Instructional Studies in Electrochemistry (RAISE)

Molten salt electrochemical reduction (MSER) is the dominant production method for aluminum and titanium, and emerging technologies for producing other commodity metals with these highly electrified techniques have demonstrated promising results. However, the scale up of MSER of materials such as iron and silicon are limited by the challenging issues of materials compatibility and impurity control. This work describes an experimental MSER setup using both chloride and carbonate salts. This setup is designed for operations outside of a glovebox, which is practical from an industrial perspective, but creates unique challenges. This work serves as a practical guide to discuss some …

From The University To The Universe: Byu’S West Mountain Observatory, Amber Zendejas, Dan Broadbent

BYU West Mountain Observatory Project

Brigham Young University’s West Mountain Observatory (WMO) is a research facility that offers primarily undergraduate students valuable mentoring and hands-on learning opportunities. Established in 1981, the observatory was built in response to increasing light pollution in Provo, Utah, which began affecting research at the Orson Pratt Observatory (OPO) atop the Eyring Science Center on the BYU main campus. Before WMO was created, OPO served as the primary observatory for astronomical research at BYU. Construction plans for a new observatory began in the late 1970s, as university planners and astronomers sought a location with minimal light pollution, favorable elevation, relatively easy …

Bridging The Language Proficiency Gap: Seeking Strategies For High Language Proficiency, Maria Isabelle Lyon

Theses and Dissertations

This study explores factors contributing to high proficiency in German speakers, focusing on university graduates who achieved Advanced High or Superior ratings on the ACTFL Oral Proficiency Interview (OPI) at the end of their university studies. The nine participants, all of whom had significant exposure to German during and/or before their undergraduate studies at Brigham Young University (BYU), shared insights into their language learning experiences. The study uses interviews and surveys to examine key characteristics, strategies, and experiences that influenced participant proficiency. The findings highlight motivation, consistency, and humility as key factors contributing to learners. Participants emphasize intrinsic motivation, consistent …

A Study Of The Parameters Involved In Nir Sintering Of Silver Microparticle-Based, Pad-Printed Features, Jonah Clement Brooks

Theses and Dissertations

This study explores the effectiveness of pad printing and near-infrared (NIR) sintering for producing conductive silver microparticle traces. A new pad printer was set up, and silver inks with varying concentrations of silver particles (17.5 %v/v, 20 %v/v, and 25 %v/v) were manufactured, printed, and sintered. The study identified sintering time and silver concentration as the most influential parameters affecting resistivity, with the best result of 8.73 × 10⁻⁷ Ω·m achieved using 25 %v/v ink sintered for 3 seconds at full power. Although resistivity continued to decrease at this maximum sintering duration, further optimization of parameters, including NIR bulb distance …

Assessing The Impact Of Internal Flow Dynamics On Detection Region Concentrations Of Low-Cost Optical Particle Counters, Livingstone Quarshie

Theses and Dissertations

Particulate matter (PM) poses significant risks to human health and the environment, making accurate measurement essential for exposure assessment and regulatory decisions. While traditional reference methods provide reliable data, they are often bulky, expensive, and difficult to maintain. Optical Particle Counters (OPCs) offer a cost-effective alternative, commonly used in clean rooms, residential spaces, and personal exposure monitoring. These devices rely on light scattering to measure PM concentrations. However, low cost OPCs face challenges related to calibration and measurement accuracy, requiring careful performance evaluation. This study used computational fluid dynamics (CFD) tools, CONVERGE Studio and ANSYS Fluent, to simulate a simplified …

The Conditioning Of Reservoir Computing And Ng-Rc For Forecasting And The Effects Of Temporal Overparameterization, Daniel Jensen

Theses and Dissertations

Reservoir computing and "Next-generation reservoir computing" built on nonlinear vector autoregression are algorithms for predicting time series given past observations. Both algorithms have been successful in predicting some chaotic dynamical systems, but this success is not theoretically well understood. This paper considers the conditioning of both algorithms and the nature of the solutions found. With either algorithm, the least squares problem which is solved to give parameters as a function of the time series data is ill-conditioned, leading to parameter non-identifiability. Both algorithms fall into the class of "sloppy models." Standard practice to regularize either algorithm includes a bias towards …

Focus On Form: Perceptions Of Portuguese Immersion Teacher When Implementing The Capa Model, Priscila Isabel Rebicki Prestes

Theses and Dissertations

This study investigates Portuguese Dual Language Immersion (DLI) teachers' perceptions when implementing the CAPA Model, a structured Focus on Form Instruction (FFI) approach aimed at improving grammatical accuracy in content-based learning. While immersion students develop strong communication skills, research highlights persistent grammatical inaccuracies due to the emphasis on meaning-based instruction. The CAPA Model seeks to bridge this gap by integrating explicit grammar instruction, fostering metalinguistic awareness, and enhancing linguistic accuracy without detracting from content learning. Findings reveal that teachers recognize the model’s benefits but face challenges such as limited planning time, a lack of pre-adapted materials, and difficulties implementing all …

Surface-Texture Fabrication Of Zirconia-Toughened Alumina Using Focused Ion-Beam Machining, Kameron M. Woodruff

Theses and Dissertations

Focused ion-beam machining (FIBM), a precise form of micro-machining, was tested for feasibility in the manufacturing of microscopic dimples in zirconia-toughened alumina (ZTA), a wear resistant ceramic used in artificial joint replacements. The interaction between the ion-beam and the ceramic was characterized in terms of material removal rate (MRR), surface roughness, and notable irregularities (e.g. pitting, steps at vertical faces). These characteristics were used to design and machine patterns of microscopic dimples for tribological testing. The dimple size and pattern area were limited due to a slow MRR and high cost of milling. No significant difference in the coefficient of …

Gnn Convergence And Accuracy Analysis On Contextual Stochastic Block Models, Trevor Garrity

Theses and Dissertations

Contextual Stochastic Block Models (cSBMs) are simple generative graph models commonly used to benchmark the performance of Graph Neural Networks (GNNs). In this thesis, I prove how inducing symmetries on general, nonlinear GNNs improves their cross entropy on cSBMs, and I derive the limiting accuracy of linear Graph Convolutional Networks (GCNs) on cSBMs. I use these results to derive the functional form of cross-entropy optimal GCNs on cSBMs and compare them to accuracy optimal GCNs.

Isolation Structure Simulation And Measurement To Reduce Transmit-Receive Coupling In Compact X-Band Fmcw Radar, Bruce E. Averill

Theses and Dissertations

Transmit-receive isolation in a compact X-band FMCW radar antenna system is critical for system performance. A set of candidate isolation structures are explored. In the process, performance of a commercial FDTD EM simulation software package is evaluated for antenna array modelling. Noise parameters of receiver electronics on a prototype radar processing front-end are tested. Improvements to the BYU Microwave Lab RF anechoic chamber are also reported, with a focus on measurement repeatability and antenna pattern angular resolution.

Exploring Representations And Inductive Bias For Machine Learning Tasks In Knot Theory, Nathaniel Driggs

Theses and Dissertations

Knot theory is a branch of mathematics that studies embeddings of the circle in $\mathbb{R}^3$ that are equivalent up to ambient isotopy. A link is a knot with one or more component. Knots and links have invariants, or functions from each knot to a set such as the integers or a family of polynomials. Predicting invariants can help us approximate them, understand them better, and find useful ways of representing knots and useful models for other machine learning tasks in knot theory. I perform many supervised learning experiments, predicting signature on a large, wide-ranging dataset using 5 different models and …