Physical Sciences and Mathematics Commons^™

Comparative Genomics Using The Colored De Bruijn Graph, Cole Andrew Lyman

Theses and Dissertations

Comparing genomes in a computationally efficient manner is a difficult problem. Methods that provide the highest resolution are too inefficient and methods that are efficient are too low resolution. In this thesis, we show that the Colored de Bruijn Graph (CdBG) is a suitable method for comparing genomes because it is efficient while maintaining a useful amount of resolution. To illustrate the usefulness of the CdBG, the phylogenetic tree for 12 species in the Drosophila genus is reconstructed using pseudo-homologous regions of the genome contained in the CdBG.

Supporting Support Engineers, Esdras Kutomi

Theses and Dissertations

The steady and uninterrupted availability of systems is essential for the mission of many companies and other organizations. This responsibility relies mostly upon support engineers, who are responsible to respond to incidents. Incident response is a unique type of task in software engineering, given it carries distinguishing characteristics like risks, pressure, incomplete information and urgency. Despite the importance of this task for many organizations, little can be found in the literature about the incident response task and model. To fill the gap, we created a theoretical foundation to foster research on incident response. We conducted an interview study, asking 12 …

Chaotic Model Prediction With Machine Learning, Yajing Zhao

Theses and Dissertations

Chaos theory is a branch of modern mathematics concerning the non-linear dynamic systems that are highly sensitive to their initial states. It has extensive real-world applications, such as weather forecasting and stock market prediction. The Lorenz system, defined by three ordinary differential equations (ODEs), is one of the simplest and most popular chaotic models. Historically research has focused on understanding the Lorenz system's mathematical characteristics and dynamical evolution including the inherent chaotic features it possesses. In this thesis, we take a data-driven approach and propose the task of predicting future states of the chaotic system from limited observations. We explore …

Superconductivity At Its Limit: Simulating Superconductor Dynamics Near The Superconducting Superheating Field In Eilenberger And Ginzburg-Landau Theory, Alden Roy Pack

Theses and Dissertations

We computationally explore the dynamics of superconductivity near the superheating field in two ways. First, we use a finite element method to solve the time-dependent Ginzburg-Landau equations of superconductivity. We present a novel way to evaluate the superheating field Hsh and the critical mode that leads to vortex nucleation using saddle-node bifurcation theory. We simulate how surface roughness, grain boundaries, and islands of deficient Sn change those results in 2 and 3 spatial dimensions. We study how AC magnetic fields and heat waves impact vortex movement. Second, we use automatic differentiation to abstract away the details of deriving the equations …

Growing Complex Networks For Better Learning Of Chaotic Dynamical Systems, David Joseph Passey Jr.

Theses and Dissertations

This thesis advances the theory of network specialization by characterizing the effect of network specialization on the eigenvectors of a network. We prove and provide explicit formulas for the eigenvectors of specialized graphs based on the eigenvectors of their parent graphs. The second portion of this thesis applies network specialization to learning problems. Our work focuses on training reservoir computers to mimic the Lorentz equations. We experiment with random graph, preferential attachment and small world topologies and demonstrate that the random removal of directed edges increases predictive capability of a reservoir topology. We then create a new network model by …

Stability Of Mhd Shock Waves, Bryn Nicole Barker

Theses and Dissertations

This thesis focuses on the study of spectral stability of planar shock waves in 2-dimensional magnetohydrodynamics. We begin with a numerical approach, computing the Lopatinski determinant and Evans function with the goal of determining if there are parameters for which viscous waves are unstable and the corresponding inviscid waves are stable. We also begin developing a method to obtain an explicit, analytical representation of the Evans function. We demonstrate the capabilities of this method with compressible Navier-Stokes and extend our results to 2-D MHD. Finally, using compressible Navier-Stokes again, we derive an energy estimate as a first step in improving …

Capillary Morphogenesis Gene Protein 2 (Cmg2) Mediates Matrix Protein Uptake And Is Required For Endothelial Cell Chemotaxis In Response To Multiple Vascular Growth Factors, Tsz Ming Jeremy Tsang

Theses and Dissertations

Pathological angiogenesis, or new blood vessel formation, is involved in many pathologies, including cancer and serious eye diseases. While traditional anti-angiogenic therapies target vascular endothelial growth factor receptors to reduce or inhibit new vessel formation, this approach has several downsides, including unpleasant side effects and low efficacy over time. Therefore, identifying new targets to treat pathological angiogenesis is still needed. CMG2, one of the two identified anthrax toxin receptors, has been proposed as an alternative target to treat pathological angiogenesis. CMG2’s role as a cell surface receptor that mediates anthrax toxin internalization is very well documented. One physiological function for …

Design, Synthesis, And Characterization Of New Non-Centrosymmetric Organic Crystals For Terahertz Generation, Gabriel Alejandro Valdivia-Berroeta

Theses and Dissertations

Terahertz (THz) spectroscopy is an emerging technology with promising applications in imaging, homeland security, and material detection and quantification. Frequencies in the THz region can be generated by optical rectification of ultrafast near-infrared laser pulses in the presence of a nonlinear optical (NLO) materials such as organic crystals. Non-centrosymmetric organic THz generating crystals such as DAST, HMQ-TMS, and OH1 have received special attention due to the strong generated fields on the order of MV/cm. The cation of these organic salts is designed by connecting electron-donating with electron-accepting groups via a highly planar aromatic system. To improve the performance of organic …

Bounds On Heat Transfer In The Presence Of Ekman Pumping, Benjamin Alexander Pachev

Theses and Dissertations

Rigorous bounds on heat transfer in rapidly rotating convection have existed for several years in the case of free-slip or stress-free boundary conditions. No-slip boundary conditions result in a phenomenon known as Ekman pumping, which significantly impacts the heat transport. A recent collaborative effort in which the author was involved significantly sharpened the bound on heat transfer in the presence of Ekman pumping. The resulting publication was targeted for an audience consisting primarily of physicists and other non-mathematicians. This work stems from the same effort, but is intended for a mathematical audience. Two additional, new results are presented that provide …

Managing Two-Factor Authentication Setup Through Password Managers, Jonathan William Dutson

Theses and Dissertations

Two-factor authentication (2FA) provides online accounts with protection against remote account compromise. Despite the security benefits, adoption of 2FA has remained low, in part due to poor usability. We explore the possibility of improving the usability of the 2FA setup process by providing setup automation through password managers. We create a proof-of-concept KeePass (a popular password manager) extension that adds browser-based automation to the 2FA setup process and conduct a 30-participant within-subjects user study to measure user perceptions about the system. Our system is found to be significantly more usable than the current manual method of 2FA setup for multiple …

Bountiful City Source Apportionment Study 2019, Jaron Hansen, Delbert Eatough

ScholarsArchive Data

Quality assured data from air sampling campaign conducted in Bountiful City during February-June 2019.

An Actuarial Approach To Personal Injury Protection Severity, Jason Colgrove

Undergraduate Honors Theses

Insurance companies examine the risk of financial losses for their policyholders as a way to accurately price insurance policies. Within the automobile insurance sector, the frequency of crashes and the associated liabilities started to increase in late 2013 when it had been on the decline for close to a decade. The purpose of this research focuses on the possible correlated variables that could lead to a better understanding of this change. To embark on this task, we teamed up with the Society of Actuaries, Casualty Actuarial Society, and the American Property Casualty Insurance Association to obtain data regarding frequency, severity, …

Immobilization Of Copper Nanoparticles Onto Various Supports Applications In Catalysis, Anh Hoang Tu Nguyen Sorenson

Theses and Dissertations

Copper-based materials are one of the most promising catalysts for performing transformations of important organic compounds in both academic and industrial operations. However, it is challenging to consistently synthesize highly active and stable copper species as heterogeneous catalysts due to their relatively high surface energy. As a result, agglomeration usually occurs, which limits the catalytic activities of the copper species. The work presented in this dissertation shows different synthetic strategies for obtaining active and stable copper-based materials by modifying chemical/physical properties of copper nanoparticles (NPs). Emphasis is placed on discussing specific catalytic systems, including carbon-supported catalysts (monometallic and bimetallic copper-based …

Retiming Smoke Simulation Using Machine Learning, Samuel Charles Gérard Giraud Carrier

Theses and Dissertations

Art-directability is a crucial aspect of creating aesthetically pleasing visual effects that help tell stories. A particularly common method of art direction is the retiming of a simulation. Unfortunately, the means of retiming an existing simulation sequence which preserves the desired shapes is an ill-defined problem. Naively interpolating values between frames leads to visual artifacts such as choppy frames or jittering intensities. Due to the difficulty in formulating a proper interpolation method we elect to use a machine learning approach to approximate this function. Our model is based on the ODE-net structure and reproduces a set of desired time samples …

The Investigation Of Functionalized Carbon Nanotubes For The Carbon Dioxide Capture And Ethane Oxidative Dehyrogenation Catalysts, Zheng Zhou

Theses and Dissertations

Carbon nanotubes (CNT) have gained interest for wide use as both support and catalyst due to the ease of uniquely tunable surface chemistry. Increasingly severe greenhouse effects have attracted attention to novel materials and technologies capable of capturing carbon dioxide (CO2). In this context, we develop a CNT based solid state amine for the CO2 capture. CNT are functionalized under various methods as a support for polymeric amines. Polyethyleneimine are physically adsorbed on CNT and are further characterized and studied for reversible CO2 capture. We obtain a high CO2 capture capacity (6.78 mmol∙g-1) for linear polyethyleneimine (LPEI) and 6.18 mmol∙g-1 …

Gamma-Ray Burst Afterglow Dynamics In Inhomogeneous Interstellar Media, Jacob Fields

Undergraduate Honors Theses

Gamma-ray bursts (GRBs) are the most luminous electromagnetic phenomena in the universe, but much remains unknown about them. Many models invoked to explain their highly variable light curves are based on complicated dynamics and interactions involving the GRB progenitor but assume simple circumstellar environments. Many long GRBs, however, show late time optical and x-ray flares that may be an indication of a much richer environment. Relativistic hydrodynamics simulations are used to study a family of initial data with a relativistic blast wave encountering a dense circumstellar shell of matter, similar to what an aging star expelling the outer layers of …

Using Logical Specifications For Multi-Objective Reinforcement Learning, Kolby Nottingham

Undergraduate Honors Theses

In the multi-objective reinforcement learning (MORL) paradigm, the relative importance of environment objectives is often unknown prior to training, so agents must learn to specialize their behavior to optimize different combinations of environment objectives that are specified post-training. These are typically linear combinations, so the agent is effectively parameterized by a weight vector that describes how to balance competing environment objectives. However, we show that behaviors can be successfully specified and learned by much more expressive non-linear logical specifications. We test our agent in several environments with various objectives and show that it can generalize to many never-before-seen specifications.

An Analysis Of Opiate Prescription For Chronic Degenerative Disease And Other Pain Syndromes, Catherine Sawyer

Undergraduate Honors Theses

Utilizing the National Ambulatory Medical Care Survey (NAMCS) database, this thesis explores patterns of opiate prescribing during time period from 1993 to 2016, which includes the time period when the opiate crisis was recognized in the United States and efforts begun to combat it. We analyze these patterns particularly as they relate to patients who were prescribed opiates and who were simultaneously suffering from various chronic conditions, and interactions between prescription of opiates and diagnosis of chronic conditions. We examine which demographic groups were most likely to receive opiates, and considered opiate prescription trends among patients with any pain diagnosis …

Orientable Single-Distance Codes For Absolute Incremental Encoders, Kristian Brian Sims

Theses and Dissertations

Digital encoders are electro-mechanical sensors that measure linear or angular position using special binary patterns. The properties of these patterns influence the traits of the resulting encoders, such as their maximum speed, resolution, tolerance to error, or cost to manufacture. We describe a novel set of patterns that can be used in encoders that are simple and compact, but require some initial movement to register their position. Previous designs for such encoders, called absolute incremental encoders, tend to incorporate separate patterns for the functions of tracking incremental movement and determining the absolute position. The encoders in this work, however, use …

Machine Learning For Effective Parkinson's Disease Diagnosis, Brennon Brimhall

Undergraduate Honors Theses

Parkinson’s Disease is a degenerative neurological condition that affects approximately 10 million people globally. Because there is currently no cure, there is a strong motivation for research into improved and automated diagnostic procedures. Using Random Forests, a computer can effectively learn to diagnose Parkinson’s disease in a patient with high accuracy (94%), precision (95%), and recall (91%) across the data of over 2800 patients. Using similar techniques, I further determine that the most predictive medical tests relate to tremors observed in patients.

Congruences For Coefficients Of Modular Functions In Levels 3, 5, And 7 With Poles At 0, Ryan Austin Keck

Theses and Dissertations

We give congruences modulo powers of p in {3, 5, 7} for the Fourier coefficients of certain modular functions in level p with poles only at 0, answering a question posed by Andersen and Jenkins and continuing work done by the Jenkins, the author, and Moss. The congruences involve a modulus that depends on the base p expansion of the modular form's order of vanishing at infinity.

Data For The Review Of Gamified Fitness Tracker Apps, Aatish Neupane, Derek Hansen, Anud Sharma, Jerry Alan Fails

ScholarsArchive Data

This is a supplemental dataset to a paper that reviews 103 gamified fitness tracker apps and analyzes the presence and usage of various game elements. This dataset contains the list of those apps that were reviewed. It also contains the coding that represents the presence of difference game elements.

Historical Milestones In Astronomy: As Shown Through The Byu Special Collections Archives, Dan Broadbent

Faculty Publications

Science Research: The “Long Conversation”

• Ideas in science can take a long time to develop.
• How do they develop?

• These books document a part of a conversation that began 447 years ago and spanned a 153 year period… documenting:
• how the overall nature of the universe was worked out,
• the establishment of the scientific method, and the boundaries of religious authority,
• and culminated in Isaac Newton’s book that presented his three laws of motion that allow us to explore the universe to this day.

Automatic Detection And Prevention Of Fake Key Attacks In Signal, Tarun Kumar Yadav

Theses and Dissertations

The Signal protocol provides end-to-end encryption for billions of users in popular instant messaging applications like WhatsApp, Facebook Messenger, and Google Allo. The protocol relies on an app-specific central server to distribute public keys and relay encrypted messages between the users. Signal prevents passive attacks. However, it is vulnerable to some active attacks due to its reliance on a trusted key server. A malicious key server can distribute fake keys to users to perform man-in-the-middle or impersonation attacks. Signal applications support an authentication ceremony to detect these active attacks. However, this places an undue burden on the users to manually …

Cell Velocity Is Asymptotically Independent Of Force: A Differential Equation Model With Random Switching., J. C. Dallon, Emily J. Evans, Christopher P. Grant, William V. Smith

Faculty Publications

Numerical simulations suggest that average velocity of a biological cell depends largely on attachment dynamics and less on the forces exerted by the cell. We determine the relationship between two models of cell motion, one based on finite spring constants modeling attachment properties (a randomly switched differential equation) and a limiting case (a centroid model-a generalized random walk) where spring constants are infinite. We prove the main result of this paper, the Expected Velocity Relationship theorem. This result shows that the expected value of the difference between cell locations in the differential equation model at the initial time and at …

Controller Design For Coordinated Encirclement Of Moving Targets, Puneet Jain

Theses and Dissertations

This thesis presents controllers that use relative range and bearing measurements to steer unmanned aerial vehicles (UAVs) to circular trajectories around stationary, constantly moving and constantly accelerating targets. The range and bearing to the target, along with their derivaties are estimated. These, along with the estimated local heading of the UAVs, are used in the control law, and to estimate the velocity of the target. In this work, six controllers are presented. The controller for a stationary target is derived using Lyapunov's direct method, and feedback linearization is used for the constant velocity and accelerating targets. A new controller is …

Inclusion Of Kinetic Proteomics In Multi-Omics Methods To Analyze Calorie Restriction Effects On Aging, Richard Hajime Carson

Theses and Dissertations

One of the greatest risk factors for disease is advanced age. As the human lifespan has increased, so too have the burdens of caring for an increasingly older population suffering from rising rates of cardiovascular disease, kidney disease, diabetes, and dementia. The need for improving medical technology and developing new therapies for age-related diseases is manifest. Yet our understanding of the processes of aging and how to attenuate the effects of aging remains incomplete. Various studies have established calorie restriction as a robust method for extending lifespan in laboratory organisms; however the mechanism is a topic of much debate. Advancing …

Exploring The Relationship Between Vocabulary Scaling And Algorithmic Performance In Text Classification For Large Datasets, Wilson Murray Fearn

Theses and Dissertations

Text analysis is a significant branch of natural language processing, and includes manydifferent sub-fields such as topic modeling, document classification, and sentiment analysis.Unsurprisingly, those who do text analysis are concerned with the runtime of their algorithmsSome of these algorithms have runtimes that depend jointly on the size of the corpus beinganalyzed, as well as the size of that corpus's vocabulary. Trivially, a user may reduce theamount of data they feed into their model to speed it up, but we assume that users will behesitant to do this as more data tends to lead to better model quality. On the other …

Coordinated Persistent Homology And An Application To Seismology, Nickolas Brenten Callor

Theses and Dissertations

The theory of persistent homology (PH), introduced by Edelsbrunner, Letscher, and Zomorodian in [1], provides a framework for extracting topological information from experimental data. This framework was then expanded by Carlsson and Zomorodian in [2] to allow for multiple parameters of analysis with the theory of multidimensional persistent homology (MPH). This particular generalization is considerably more difficult to compute and to apply than its predecessor. We introduce an intermediate theory, coordinated persistent homology (CPH), that allows for multiple parameters while still preserving the clarity and coherence of PH. In addition to introducing the basic theory, we provide a polynomial time …

Depositional Analysis Of A Holocene Carbonate Strand Plain Using High Resolution Gpr, Sediment Analysis, And C-14 Dating, Kaleb Robert Markert

Theses and Dissertations

Understanding modern carbonate depositional systems gives valuable insights into the interpretation of ancient carbonate systems. Ancient carbonate strand plains have the potential to act as productive hydrocarbon reservoirs because of their relatively high porosity. Unfortunately, they are difficult to identify in the rock record because of the lack of work done on modern analogues. San Salvador Island in the Bahamas hosts a well-exposed and easily accessible Holocene strand plain, ideal as a modern analogue. Sandy Hook, located on the southeast part of the island, consists of approximately 35 ridge-swale features that show signs of four distinct zones of deposition. In …