Physical Sciences and Mathematics Commons^™

Intermountain West Lichen Dna Reference Library, Brian Colgrove

Undergraduate Honors Theses

Accurate estimates of biodiversity can play crucial roles in monitoring ecological health. BYU’s Lichen Air Quality Biomonitoring program (Wright) represents one of the largest biomonitoring programs in the nation. Recently, DNA metabarcoding approaches have shown promise in streamlining lichen biodiversity inventories. However, to date, lichen diversity of western North America is poorly represented in available DNA reference libraries, preventing biologists and land managers from using DNA barcoding to identify unknown specimens. To solve this problem, I have developed a DNA reference library for over 500 species occurring in the Intermountain West region. Using bioinformatic and statistical tools, I created a …

Who Uses Multi-Factor Authentication?, Leah Roberts

Undergraduate Honors Theses

A sample of 47 BYU students were recruited to participate in this study to determine who was using Multi-factor Authentication (MFA) on their online accounts. This study determined that there were many different factors that separated those who used MFA and those who did not. Some of those factors included: time spent on the internet each day, gender, the website itself, and personal privacy behaviors.

A Fret Flow Cytometry-Based Screening Assay For Multiplex Analysis Of Metabolites In T. Brucei, Ronald A. Zegarra

Undergraduate Honors Theses

Kinetoplastid parasites are a significant public health issue in some tropical and subtropical regions of the world. Kinetoplastid parasites all require glycolysis for survival, with host glucose key for ATP production. One such parasite, Trypanosoma brucei, exclusively metabolizes glucose in its bloodstream form. Trypanosomal glycolysis is unique because it displays unconventional structural features. Hence, glucose metabolism has been studied extensively in T. brucei and is a therapeutic target in kinetoplastid parasites.The lack of in vivo analytical techniques for measuring vital glycolytic metabolites in situ has restricted the ability of researchers to test, with high sensitivity and specificity, the essential roles …

Exploration Of Fluorinated Α,Β-Dehydroamino Acids And Their Structure, Austin Lesueur

Undergraduate Honors Theses

This thesis explores the synthesis of fluorinated α,β-dehydroamino acids, specifically a fluorinated dehydrovaline derivative. Previous work has been done on the equivalent dehydrovaline derivative without fluorine present and this work builds toward the fluorinated version with the goal of comparing the two structurally. The synthesis presented here pulls from previous synthetic strategies employed for dehydrovaline while also exploring the synthetic impact of the electronegative fluorine atoms.

Interpretable Fine-Grained Visual Categorization, Pei Guo

Theses and Dissertations

Not all categories are created equal in object recognition. Fine-grained visual categorization (FGVC) is a branch of visual object recognition that aims to distinguish subordinate categories within a basic-level category. Examples include classifying an image of a bird into specific species like "Western Gull" or "California Gull". Such subordinate categories exhibit characteristics like small inter-category variation and large intra-class variation, making distinguishing them extremely difficult. To address such challenges, an algorithm should be able to focus on object parts and be invariant to object pose. Like many other computer vision tasks, FGVC has witnessed phenomenal advancement following the resurgence of …

The Role Of The Cytosolic Chaperonin Cct In Folding Β-Propeller Proteins, William Grant Ludlam

Theses and Dissertations

Many Proteins require the aid of molecular chaperones to achieve a stable folding state and avoid misfolding pathologies. A major eukaryotic chaperone is the cytosolic chaperonin CCT. While CCT is known to fold a significant portion of all cytosolic proteins, there is no general model for the mechanism CCT uses to fold substrate proteins. One class of proteins that CCT is known to fold are β-propeller containing proteins. Here, we present structural and biochemical data on the processes that CCT uses to fold three distinct β-propeller proteins: the G-protein Beta 5 (Gβ5) subunit of the Gβ5-RGS complex, mLST8 of the …

Cationic Steroid Antimicrobials: Applications To Medical Device Coatings, Mechanism Of Pro-Osteogenic Properties, And Potential Synergy With Common Antifungals, Brian J. Hilton

Theses and Dissertations

Cationic steroid antimicrobials (CSAs or ceragenins) are a novel class of synthetic, cholic acid-based mimics of endogenous antimicrobial peptides. These small molecule compounds display broad bactericidal activity against gram-negative and gram-positive bacteria, potent ability against fungal pathogens, and cidal effects against drug resistant and multidrug resistant microbes. Implantable medical devices provide an abiotic surface upon which bacteria and fungi can accumulate--thereby leading to localized or systemic infection. We proposed that CSA antibiotics can be incorporated into medical device surface coatings which can be optimized for the active release or elution of the CSA compounds over time to prevent device-associated infections. …

Simple Ssh Management, Torstein Calvin Collett

Theses and Dissertations

SSH certificates are used by administrators so connections to the server can be verified. This ensures that only authorized administrators can access the server and that the server being accessed is the intended machine. Current solutions for managing SSH certificates are focused on commercial use, which makes them cumbersome for small groups and individuals to use. These solutions require running multiple services that companies already use but add significant overhead for smaller groups. We developed a new standalone system that makes it easy to manage SSH certificates for small amounts of servers and users, without requiring additional servers to be …

Developing The Definite Integral And Accumulation Function Through Adding Up Pieces: A Hypothetical Learning Trajectory, Brinley Nichole Stevens

Theses and Dissertations

Integration is a core concept of calculus. As such, significant work has been done on understanding how students come to reason about integrals, including both the definite integral and the accumulation function. A path towards understanding the accumulation function first, then the definite integral as a single point on the accumulation function has been presented in the literature. However, there seems to be an accessible path that begins first with understanding the definite integral through an Adding Up Pieces (AUP) perspective and extending that understanding to the accumulation function. This study provides a viable hypothetical learning trajectory (HLT) for beginning …

Zeros Of A Family Of Complex Harmonic Polynomials, Samantha Sandberg

Theses and Dissertations

In this thesis we study complex harmonic functions of the form f where f is the sum of a nonconstant analytic and a nonconstant anti-analytic function of one variable. The Fundamental Theorem of Algebra does not apply to such functions, so we ask how many zeros a complex harmonic function can have and where those zeros are located. This thesis focuses on the complex harmonic family of polynomials p_c where p_c is the sum of z+(c/2)z^2 and the conjugate of (c/(n-1))z^(n-1)+(1/n)z^n. We first establish properties of the critical curve, which separates orientation preserving and reversing regions. These properties are then …

Pegylation Stabilizes The Conformation Of Proteins And The Noncovalent Interactions Within Them, Steven R. E. Draper

Theses and Dissertations

PEGylation has been used for decades to enhance the pharmacokinetic properties of protein therapeutics. This method has been effective at increasing the serum half-life of these drugs, but the mechanism of how it does this is unclear. Chapter 1 is an introduction to the methods of PEGylation. In chapter 2 we show that the effect of PEGylation on the conformational stability of the WW domain differs based on amino acid linker and conjugation site. We show that all positions in the WW domain that were tested can be stabilized by at least one amino acid linker. The rate of proteolysis …

Reinforcement Learning With Auxiliary Memory, Sterling Suggs

Theses and Dissertations

Deep reinforcement learning algorithms typically require vast amounts of data to train to a useful level of performance. Each time new data is encountered, the network must inefficiently update all of its parameters. Auxiliary memory units can help deep neural networks train more efficiently by separating computation from storage, and providing a means to rapidly store and retrieve precise information. We present four deep reinforcement learning models augmented with external memory, and benchmark their performance on ten tasks from the Arcade Learning Environment. Our discussion and insights will be helpful for future RL researchers developing their own memory agents.

Spatiospectral Features In Supersonic, Highly Heated Jet Noise, Kevin Matthew Leete

Theses and Dissertations

The sound produced by military aircraft is dominated by noise generated by the turbulent mixing of the jetted exhaust with the ambient air. This jet noise has the potential to annoy the community and pose a hearing loss risk for military personnel. The goal of this dissertation is to characterize spatiospectral features in the field produced by full-scale military aircraft that are not traditionally seen at the laboratory scale and identify potential noise mechanisms for these features. Measurements of two military aircraft jet noise fields are found to be best described as a superposition of spatiospectral lobes, whose relative amplitudes …

The Whole Is Greater Than Its Parts: Ensembling Improves Protein Contact Prediction, Wendy M. Billings, Connor J. Morris, Dennis Della Corte

Faculty Publications

The prediction of amino acid contacts from protein sequence is an important problem, as protein contacts are a vital step towards the prediction of folded protein structures. We propose that a powerful concept from deep learning, called ensembling, can increase the accuracy of protein contact predictions by combining the outputs of different neural network models. We show that ensembling the predictions made by different groups at the recent Critical Assessment of Protein Structure Prediction (CASP13) outperforms all individual groups. Further, we show that contacts derived from the distance predictions of three additional deep neural networks—AlphaFold, trRosetta, and ProSPr—can be substantially …

A Hybrid Method For Auralizing Vibroacoustic Systems And Evaluating Audio Fidelity/Sound Quality Using Machine Learning, Andrew Jared Miller

Theses and Dissertations

Two separate methods are presented to aid in the creation and evaluation of acoustic simulations. The first is a hybrid method that allows separate low and high-frequency acoustic responses to be combined into a single broadband response suitable for auralization. The process consists of four steps: 1) creating separate low-frequency and high-frequency responses of the system of interest, 2) interpolating between the two responses to get a single broadband magnitude response, 3) adding amplitude modulation to the high-frequency portion of the response, and 4) calculating approximate phase information. An experimental setup is used to validate the hybrid method. Listening tests …

The Mechanism Of Ptov1 Regulation By 14-3-3, Huwei1 And Sgk2, Pramoda Sahan Kumari Aththota Gamage

Theses and Dissertations

Prostate tumor overexpressed 1 (PTOV1) is highly expressed in several forms of cancer. High expression of PTOV1 is associated with tumor aggressiveness in several tumor types, including ovarian and breast cancer. Currently, PTOV1 is known to act both as a translational and transcriptional regulator aiding in the expression of prosurvival genes. Although PTOV1 is known to pass in and out of the nucleus in a cell cycle-dependent manner, the regulation of PTOV1 activity is not well understood and here we identify 14-3-3 as a PTOV1 interactor and show that high levels of 14-3-3 expression, like PTOV1, correlate with prostate cancer …

You Do Math Like A Girl: How Women Reason Mathematically Outside Of Formal And School Mathematics Contexts, Katelyn C. Pyfer

Theses and Dissertations

Females continue to have negative dispositions towards mathematics even though the performance gap between females and males has all but disappeared. While there are many hypotheses for why these negative dispositions exist among females towards mathematics, this paper explores the possibility that the field of mathematics could favor more masculine ways of reasoning at the exclusion of valid, non-masculine mathematical thought. To research this idea, the day-to-day, non-formal, non-school mathematical activities of two women were identified and analyzed. The analysis uncovered complex mathematical processes among both women that were fundamentally different from the mathematical processes common in the mathematics field. …

Dynamics Of Systems Driven By An External Force, Xue Liu

Theses and Dissertations

In this dissertation, we study the complicated dynamics of two classes of systems: Anosov systems driven by an external force and partially hyperbolic systems driven by an external force. For smooth Anosov systems driven by an external force, we first study the random specification property, which is on the approximation of an N−spaced arbitrary long finite random orbit segments within given precision by a random periodic point. We prove that if such system is topological mixing on fibers, then it has the random specification property. Furthermore, we prove that the homeomorphism induced by such a system on the space of …

Computing The Rank Of Braids, Justin Meiners

Theses and Dissertations

We describe a method for computing rank (and determining quasipositivity) in the free group using dynamic programming. The algorithm is adapted to computing upper bounds on the rank for braids. We test our method on a table of knots by identifying quasipositive knots and calculating the ribbon genus. We consider the possibility that rank is not theoretically computable and prove some partial results that would classify its computational complexity. We then present a method for effectively brute force searching band presentations of small rank and conjugate length.

Going For Gold: Point Of Care Bio-Diagnostics And Gold Nanoparticles Treating Disease, Trevor M. Godfrey

Theses and Dissertations

Correct diagnosis of disease is essential in the effort to save and improve lives. Point of care (POC) diagnostics are in-vitro tests that assist in patient diagnosis and can be used at the location of patient care. POC diagnostics are easy to use and provide near-instant readouts allowing medical providers and patients to make rapid decisions about treatment. Increased access to POC testing is especially beneficial to low-income and low resource areas that cannot afford expensive lab testing. The World Health Organization (WHO) has outlined at least 113 diseases for which POC diagnostics are needed. Because of this, developing effective, …

Improving Artistic Workflows For Fluid Simulation Through Adaptive And Editable Fluid Simulation Techniques, Sean A. Flynn

Theses and Dissertations

As the fidelity of computer generated imagery has increased, the need to digitally create convincing natural phenomena like fluids has become fundamental to the entertainment production industry. Because fluids are complex, the underlying physics must be computationally simulated. However, because a strictly physics-based approach is both computationally expensive and difficult to control, it does not lend itself well to the way artists and directors like to work. Directors require control to achieve their specific artistic vision. Furthermore, artistic workflows rely on quick iteration and the ability to apply changes late in the production process. In this dissertation we present novel …

The Dns Bake Sale: Advertising Dns Cookie Support For Ddos Protection, Jacob Davis

Theses and Dissertations

The Domain Name System (DNS) has been frequently abused for Distributed Denial of Service (DDoS) attacks and cache poisoning because it relies on the User Datagram Protocol (UDP). Since UDP is connection-less, it is trivial for an attacker to spoof the source of a DNS query or response. DNS Cookies, a protocol standardized in 2016, add pseudo-random values to DNS packets to provide identity management and prevent spoofing attacks. This work finds that 30% of popular authoritative servers and open recursive resolvers fully support cookies and that 10% of recursive clients send cookies. Despite this, DNS cookie use is rarely …

Multilattice Tilings And Coverings, Joshua Randall Linnell

Theses and Dissertations

Let L be a discrete subgroup of \mathbb{R}^n under addition. Let D be a finite set of points including the origin. These two sets will define a multilattice of \mathbb{R}^n. We explore how to generate a periodic covering of the space \mathbb{R}^n based on L and $D$. Additionally, we explore the problem of covering when we restrict ourselves to covering \mathbb{R}^n using only dilations of the right regular simplex in our covering. We show that using a set D= {0,d} to define our multilattice the minimum covering density is 5-\sqrt{13}. Furthermore, we show that when we allow for an arbitrary …

Fourier Decompositions Of Graphs With Symmetries And Equitable Partitions, Darren Scott Lund

Theses and Dissertations

We show that equitable partitions, which are generalizations of graph symmetries, and Fourier transforms are fundamentally related. For a partition of a graph's vertices we define a Fourier similarity transform of the graph's adjacency matrix built from the matrices used to carryout discrete Fourier transformations. We show that the matrix (graph) decomposes into a number of smaller matrices (graphs) under this transformation if and only if the partition is an equitable partition. To extend this result to directed graphs we define two new types of equitable partitions, equitable receiving and equitable transmitting partitions, and show that if a partition of …

Light And Truth: Measuring Unseen Harm In Individuals And Communities, Hannah Pfost

Undergraduate Honors Theses

While the fields of physics and international development may seem disparate, the insights gained from studying each one of them can improve understanding of the other. Here, I demonstrate that concept as applied to computational optics and historical memory. Thus, the purpose of this project is threefold: (1) to computationally model light transport through tissue, and use that model to inform choices about a physical system; (2) to determine the types of historical memory recommended in the final reports of truth commissions; and (3) to give evidence for the usefulness of human-centered design in both areas. To model light transport, …

Terwilliger Algebras For Several Finite Groups, Nicholas Lee Bastian

Theses and Dissertations

In this thesis, we will explore the structure of Terwilliger algebras over several different types of finite groups. We will begin by discussing what a Schur ring is, as well as providing many different results and examples of them. Following our discussion on Schur rings, we will move onto discussing association schemes as well as their properties. In particular, we will show every Schur ring gives rise to an association scheme. We will then define a Terwilliger algebra for any finite set, as well as discuss basic properties that hold for all Terwilliger algebras. After specializing to the case of …

Telsam-Target Protein Fusions Can Form Diffraction-Quality Crystals Without Direct Inter-Polymer Contacts, Moriah Longhurst

Undergraduate Honors Theses

X-ray diffraction is a robust method for determining the detailed 3D structures of specific proteins. However, this requires the formation of well-ordered protein crystals, a process that is time-consuming, expensive, and only has about a 10-30% success rate. New methods are needed to enable the efficient crystallization of challenging proteins. One such technique is explored here, which utilizes a protein polymer (the sterile alpha motif domain of the human protein translocation Ets leukemia, or TELSAM) as a crystallization chaperone to form a more ordered crystal lattice of target proteins and drive crystallization. This method was successfully used to crystallize, collect …

Computational Development Of A Miniature Quantum Dot Spectrometer For Use In Space, Joseph Richardson

Undergraduate Honors Theses

Miniature spectrometers are of great interest to NASA as necessary instrumentation is scaled down and optimized for specific space application. Semiconductor nanocrystals called quantum dots (QD) are being used to create a miniature high-resolution filter-based spectrometer, with the goal of use in space within 5 years. Computational imaging techniques— such as automated image analysis and mathematical spectrum reconstruction algorithms—are key to making the QD spectrometer a reality. This thesis will discuss the process of developing these computational methods, along with the improvements that have occurred from previous work.

Realium: Building The Future Of Real Estate On The Blockchain, Demitri Haddad

Undergraduate Honors Theses

This paper discusses the prospective challenges, limitations and opportunities in the real estate sector for blockchain. It outlines the idea of Realium, a financial technology application that aims to assist in the purchase, sale, and legal compliance of real estate assets. For more information see docs.realium.io

The Communicative Effects Of Anonymity Online: A Natural Language Analysis Of The Faceless, Caleb Johnson

Undergraduate Honors Theses

An ever-increasing number of Americans have an active social media

presence online. As of March 2020, an estimated 79% of Americans were active

monthly users of some sort. Many of these online platforms allow users to

operate anonymously which could potentially lead to shifts in communicative

behavior. I first discuss my compilation process of the Twitter Anonymity

Dataset (TAD), a human-classified dataset of 100,000 Twitter accounts that are

categorized by their level of identifiability to their real-world agent. Next, I

investigate some of the structural differences between the classification levels

and employ a variety of Natural Language Processing models and …