Physical Sciences and Mathematics Commons^™

Reconstructing Historical Earthquake-Induced Tsunamis: Case Study Of 1852 Event Using The Adjoint Method Combined With Hmc, Chelsey Noorda

Theses and Dissertations

Seismic hazard analysis aims to estimate human risk due to natural disasters such as earthquakes. To improve seismic hazard analysis, our group is focused on earthquake induced tsunamis and the use of statistical models to reconstruct historical earthquakes. Based on the estimated wave heights given in anecdotal historical descriptions, we created observational probability distributions to model the historically recorded observations and constructed a prior distribution on the relevant earthquake parameters based on known seismicity of a given region. Then we used the software package GeoClaw, and a Metropolis-Hastings sampler to obtain a posterior distribution of earthquake parameters that most closely …

Developing Microfluidic Devices For Biomolecule Analysis, Jacob Brent Nielsen

Theses and Dissertations

Microfluidics can take laboratory processes and miniaturize them, which led to the term lab-on-a-chip. Microfluidic devices are fabricated with a variety of materials and methods, each offering distinct advantages for bioanalysis. This dissertation describes two methods to create these devices, with the use of four different materials to achieve different assay needs. In the first application in this dissertation, hot-embossed cyclic olefin copolymer was used to create microdevices to electrophoretically separate seven preterm birth biomarkers. One biomarker, thrombin-antithrombin III, cannot be purchased commercially so I developed methods for its assembly in the lab. Dot blots and mass spectrometry were used …

Soft Contact Lens Tear Film Proteomics For Clinical Diagnostic Biomarker Discovery, Robert Kimball Roden

Theses and Dissertations

Human tear film is an accessible biospecimen rich with useful biological information. As tear protein biomarkers for both ocular and systemic diseases have been identified in tears, efforts are being made to create point-of-care tests useful for clinical diagnoses. However, there are significant obstacles to tear diagnostics, including inadequate sampling methods and biomarkers with insufficient sensitivity and specificity. Furthermore, tear film diagnostics are particularly challenging for dry eye disease (DED) patients, where low tear volume makes sampling more difficult and the multifactorial nature of DED makes identifying the exact pathological subtype very complex. As soft contact lenses (SCLs) are designed …

Navigating Molecular Complexity: A Multidimensional Approach Utilizing Computational Chemistry, Jacob Andrew Parkman

Theses and Dissertations

Preparing molecular coordinate files for molecular dynamics (MD) simulations can be a very time-consuming process. Herein we present the development of a user-friendly program that drastically reduces the time required to prepare these molecular coordinate files for MD software packages such as AmberTools. Our program, known as charge atomtype naming (CAN), creates and uses a library of structures such as amino acid monomers to update the charge, atom type, and name of atoms in any molecular structure (mol2) file. We demonstrate the utility of this new program by rapidly preparing structural files for MD simulations for polypeptides ranging from small …

Context Dependence Of Non-Covalent Interactions Among Amino-Acid Side Chains Along The Solvent-Exposed Surface Of Coiled Coils, Kimberlee Larsen Stern

Theses and Dissertations

Coiled coils are a well-known protein structure prevalent in eukaryotic function, synthetic applications, and de novo protein design. Coiled-coil folding is often described using heptad repeat positions labeled abcdefg where a and d positions occupy the interface between the coils, e and g positions flank the interface, and the b, c, and f positions face the solvent-exposed surface. The a, d, e, and g positions have been extensively studied in the coiled-coil literature. There is a lack of investigation on the impact of the b, c, and f positions on coiled-coil folding. Chapter 1 is an introduction to the heptad …

Design, Synthesis And Immunological Testing Of Minimal Oligosaccharide Epitopes For Glycoconjugate Vaccines Targeting Capsular Polysaccharides Of Serotypes 3, 4, 7f And 9v Of Streptococcus Pneumoniae, Seth A. Taylor

Theses and Dissertations

The rise in antibiotic resistant strains of bacteria has led to the need for new methods of combatting bacterial infection. Since the surfaces of bacteria are covered in uniquely patterned capsular polysaccharides, vaccines targeting these polysaccharides have become a popular field of research for protection against pathogenic bacteria. Though licensed polysaccharide vaccines are commercially available, they lack the efficiency to protect patients that are immunocompromised or at high risk because they elicit T cell independent immune responses, resulting in low-affinity antibodies. To elicit a T cell dependent response and thereby recruit B cells that produce high-affinity antibodies, a vaccine was …

Investigating The Use Of Translational Methods To Characterize Therapeutic Interventions In Models Of Pulmonary Disease, Ashley Rae Chang

Theses and Dissertations

Idiopathic Pulmonary Fibrosis (IPF) is an interstitial lung disease with no known cause or cure. IPF has an incidence of 75/1,000,000 of the population, predominately in men over the age of 60. This relatively rare disease develops in a chronic and progressive way, ultimately leading to death within two to five years of diagnosis. Our use of translatable methodologies in the bleomycin mouse model of IPF led to the novel identification of the similarities between the average percent loss of lung function in previous human clinical trials to that of our mouse model data. There is no treatment for IPF …

The Use Of Artificial Intelligence In Higher Education: A Study On Faculty Perspectives In Universities In Egypt, Farah S. Sharawy

Theses and Dissertations

Artificial Intelligence (AI) is an emerging technology that is transforming various aspects of society, including higher education. This paper examines faculty perspectives from five different institutions; The American University in Cairo (AUC), The German University in Cairo (GUC), The Arab Academy for Science and Technology (AAST), Ain Shams University, and Cairo University, on the use of AI in higher education in teaching and learning in Egypt, with all its challenges and resources available to support it, and how it can be used to achieve equity and accessibility. This research was conducted through a qualitative study using semi-structured one- on-one interviews …

Nutrient Optimization For Vegetable Production Under Decoupled Aquaponics Using Brackish Water, Salma Walid Hany Ahmed Abdelfattah

Theses and Dissertations

As the world moves to more sustainable agriculture methods in the agribusiness industry, decoupled aquaponics is recognized as one of the newest techniques currently being utilized to achieve more local food security. As the topic is still freshly new within the industry, a finite number of publications and studies have been made that address the topic hands-on with its many variables. Subsequently, in this paper, an experiment was conducted to assess the most optimized production conditions of both lacinato kale (Brassica oleracea var.palmifolia) and Swiss chard Bright Light (Beta vulgaris ssp. Cicla var. flavescens) plants through the utilization of a …

Exploring Surface Silanization And Characterization Of Thin Films: From Surface Passivation To Microstructural Characterization Of Porous Silicon/Silica, And Exploratory Data Analysis Of X-Ray Photoelectron Spectroscopy Images, Behnam Moeini

Theses and Dissertations

Surface chemistry plays a key role in science and technology because materials interact with their environments through their surfaces. Understanding surface chemistry can help alter/improve the properties of materials. However, surface characterization and modification often require multiple characterization and synthesis techniques. Silicon/silica-based materials are technologically important, so studying their surface properties can enable future advancements. In this dissertation, I explore surface modification and characterization of different types of Si/SiO2 thin films, including silicon wafers, fused silica capillary columns, and oblique angle sputtered Si/SiO2 thin films. In Chapters 2-5, I first present a method to rapidly silanize silica surfaces using a …

Atomistic Assessment Of Drug-Phospholipid Interactions Consequent To Cancer Treatment: A Study Of Anthracycline Cardiotoxicity, Yara Elsayed Ahmed

Theses and Dissertations

Despite being one of the most effective chemotherapeutic agents developed to date, Anthracyclines are notorious for their cardiotoxicity. Their clinical use is frequently limited both in dosage and in prescription due to the severe cardiac damage they cause. The mechanism of anthracycline-induced cardiotoxicity is not yet fully understood. However, it is hypothesized that interactions with the myocardial membrane play an important role in imparting cardiotoxicity. In this study, we use molecular dynamics simulations and density functional theory calculations to study the anthracycline drug molecules and the interactions that they have with the myocardial membrane. We construct a myocardial membrane model …

Dyonic Taub-Nut-Ads Space Phase Structure, Mohamed Tharwat

Theses and Dissertations

The Taub-NUT spacetime remains to hold many mysteries more than half a century after its discovery. The metric's controversy owes largely to the nut charge and the existence of Misner strings. Traditionally the metric is treated in the euclidean signature, this treatment hides the Misner strings. We treat the Taub-NUT spacetime with the Misner strings visible, not enforcing the time periodicity condition. We examine the phase structure belonging to three different horizon geometries. We deal with the hyperbolic, flat and spherical cases. We consider the stable phases, the phase transitions that exist between them, and find the preferable phases in …

Role Of Defect Type In Optimizing Photoelectrochemical Hydrogen Production Catalysts, Mohamed Mahrous

Theses and Dissertations

The search for new energy sources has become a global challenge due to the increasing demand for energy and the negative impact of traditional energy sources on the environment. The photoelectrochemical water splitting has emerged as a promising alternative source for producing hydrogen, which can be used as a clean fuel. However, it is necessary to tailor the properties of the light-active material that will be used to absorb sunlight and split water. This research project aimed at providing detailed insights into the effect of varying the type and concentration of defects on the optical and electronic properties of diamond …

The Target Model For Genealogical Networks, Kolton Baldwin

Theses and Dissertations

Several large-scale projects including FamilySearch, Ancestry, BALSAC (University of Quebec), and others have gathered incredible amounts of genealogical data ranging from millions to billions of individuals. To study the structure of this data, we propose a model that generates a genealogical network based on real-world genealogical data using two key features: (i) geodesic distance between couples prior to union and (ii) the number of children per couple. The distribution of the distance to a couples' nearest common ancestor in an observed community captures the global scale at which biological cycles form in the underlying genealogical network. Similarly, the number of …

Conodont Sequence Biostratigraphy Of The Upper Honaker Trail Formation, Cheyenne Autumn Pratt

Theses and Dissertations

The Paradox Basin is a northwest-southeast trending intracratonic basin that formed in southwestern Colorado, southeastern Utah and adjacent parts of Arizona and New Mexico during the late Paleozoic Era. During rise of the adjacent Uncompahgre Uplift (Ancestral Rocky Mountains), the rapidly subsiding basin was filled with over 2000 m of Permo-Pennsylvanian sediments that reflect a complex interplay of changing tectonic, paleoecological, and climatic conditions that resulted in cyclic packages of mixed lowstand and non-marine siliciclastics and highstand shallow-platform carbonates. The 150 m-thick Honaker Trail formation straddles the transition from mostly marine carbonates to mostly non-marine siliciclastics on the southwest shelf …

Optimal Ordering To Maximize Mev Arbitrage, Granton Michael White

Theses and Dissertations

The rise of cryptocurrencies has brought with it new math problems with new sets of constraints. The MEV problem entails solving for the ordering of pending trades that maximizes a block creator's profit. In decentralized finance, time is a big constraint, so an exhaustive search of all possible orderings is impossible. I propose a solution to the MEV problem that gives a near optimal result that can be solved in a reasonable amount of time. I layout the method and the formulas required for my solution. Additionally, I test my solution on synthesized data to show that it works as …

Hamiltonian Monte Carlo For Reconstructing Historical Earthquake-Induced Tsunamis, Jacob Paul Callahan

Theses and Dissertations

In many areas of the world, seismic hazards pose a great risk to both human and natural populations. In particular, earthquake-induced tsunamis are especially dangerous to many areas in the Pacific. The study and quantification of these seismic events can both help scientists better understand how these natural hazards occur and help at-risk populations make better preparations for these events. However, many events of interest occurred too long ago to be recorded by modern instruments, so data on these earthquakes are sparse and unreliable. To remedy this, a Bayesian method for reconstructing the source earthquakes for these historical tsunamis based …

A Structural Analysis Of The Simpson Mountains, Hyrum A. Briscoe

Theses and Dissertations

The Simpson Mountains have long been of economic interest and have renewed interest in their potential value. Field mapping of the project area redefined structural relationships between stratigraphic units. Geometric and kinematic analysis of structures in the Simpson Mountains show the range is deformed by the three most recent tectonic events: the Sevier Orogeny, the Laramide Orogeny, and Basin and Range Extension. Laramide structures define the range with a significant E-W normal fault and an E-W thrust fault, which are both likely related to Eocene-age igneous intrusions. Principal component analysis (PCA) of regional quartzite X-ray Fluorescence (XRF) data resulted in …

Adversary Aware Continual Learning, Muhammad Umer

Theses and Dissertations

Continual learning approaches are useful as they help the model to learn new information (classes) sequentially, while also retaining the previously acquired information (classes). However, these approaches are adversary agnostic, i.e., they do not consider the possibility of malicious attacks. In this dissertation, we have demonstrated that continual learning approaches are extremely vulnerable to the adversarial backdoor attacks, where an intelligent adversary can introduce small amount of misinformation to the model in the form of imperceptible backdoor pattern during training to cause deliberate forgetting of a specific class at test time. We then propose a novel defensive framework to counter …

A Multimodal Immune System Inspired Defense Architecture For Detecting And Deterring Digital Pathogens In Container Hosted Web Services, Islam Khalil

Theses and Dissertations

With the increased use of web technologies, microservices, and Application Programming Interface (API) for integration between systems, and with the development of containerization of services on operating system level as a method of isolating system execution and for easing the deployment and scaling of systems, there is a growing need as well as opportunities for providing platforms that improve the security of such services. In our work, we propose an architecture for a containerization platform that utilizes various concepts derived from the human immune system. The goal of the proposed containerization platform is to introduce the concept of slowing down …

Computation Offloading Design For Deep Neural Network Inference On Iot Devices, Asmika Boosarapu

Theses and Dissertations

In recent times, advances in the technologies of Internet-of-Things (IoT) and Deep Neural Networks (DNN) have significantly increased the accuracy and speed of a variety of smart applications. However, one of the barriers to deploying DNN to IoT is the computational limitations of IoT devices as compared with the computationally expensive task of DNN inference. Computation offloading is an approach that addresses this problem by offloading DNN computation tasks to cloud servers. In this thesis we propose a collaborative computation offloading solution, in which some of the work is done on the IoT device, and the remainder of the work …

Non-Tuberculous Mycobacterium Correlation With Geochemical Characteristics Of Soil And Basalt In Hawaii, Leeza Marie Wells

Theses and Dissertations

Non-tuberculous mycobacteria (NTM) cause opportunistic lung disease though environmental exposure pathways. Among the United States, Hawaii has a significantly higher infection rate. Preliminary studies have shown certain environmental factors, such as phosphorus and other select soil geochemical characteristics, to be statistically significant to NTM occurrence. However, a model to predict NTM occurrence based on soil geochemistry had yet to be attempted. A selection of 40 NTM positive and 40 NTM negative soils from Oahu were selected for a geochemical analysis to search for possible correlations to mineralogy and elemental abundances that may promote, or inhibit, NTM growth in the environment. …

Failure Distributions For Parallel Dependent Identical Weibull Components, Gina S. Sigler

Theses and Dissertations

For a parallel system, when one component fails, the failure distribution of the remaining components will have an increased failure rate. This dissertation takes a novel approach to finding the associated failure distribution of the full system using ordinal statistic distributions for correlated Weibull components, allowing for unknown correlations between the dependent components. A Taylor series approximation is presented for the two component; system failure time distributions are also derived for two failures in a two component system, two failures in an n component system, three failures in a three component system, and k failures in an n component system. …

Quantitative Modeling Of Text-Based Intelligence Source Uncertainty, Adam D. Nesmith

Theses and Dissertations

An all-source intelligence analyst’s primary job is delivering timely, well-sourced assessments on relevant targets based on uncertain and incomplete information. Each assessment includes a likelihood that the assessment is true, and a confidence level based on the uncertainty of the sources used. Quantitative all-source intelligence analysis is not widely implemented despite the acknowledged limitations of qualitative intelligence assessments and the existence of proposed quantitative methods. This is due to the challenge of quantitatively representing uncertainty in text-based intelligence reporting (i.e., HUMINT, OSINT, SIGINT), which limits the effectiveness and usability of previously suggested methods. This research creates a novel framework for …

Non-Degenerate Two-Photon Absorption And Excited State Line Shapes In Alkali Vapors, Timothy M. True

Theses and Dissertations

The rubidium 5S-5D two-photon transitions were probed between 758-798 nm, where a six order of magnitude change in the cross section was observed and the polarization dependence was seen explicitly. Collisional rates are measured in cesium on the 6P-9S and 5D-10F transitions, with broadening rates as large as 710 MHz/Torr and shifting rates as large as 273 MHz/Torr. We observe Stark broadening on the cesium 5D-10F line shape, with Lorentzian width increasing from 200 MHz to 40 GHz. The influence of electron impact is discussed under these conditions and with 0-20 Torr of helium. Cascade amplified spontaneous emission is seen …

Methodology For Designing Assistive Robots For Activities Of Daily Living Assistance, Javier Dario Sanjuan De Caro

Theses and Dissertations

The growing prevalence of Upper or Lower Extremities Dysfunctions (ULED), often linked to central nervous disorders such as stroke, Spinal Cord Injury (SCI), and Multiple Sclerosis (MS), underscores the urgent need for innovative support solutions. Over 5.35 million Americans currently live with ULED, a situation that places a significant socioeconomic burden on families and society. Despite invaluable support from caregivers and family members, the need for more scalable, practical solutions persists.

Wheelchair-mounted assistive robots emerge as a promising alternative in this context. These devices, offering continuous and reliable assistance, significantly alleviate caregiver fatigue and enhance the independence and quality of …

Dd Slug Migration: Mathematical Model And Numerical Results, Joy Song

Theses and Dissertations

Amoebae are commonly studied to understand embryogenesis, and the best-characterized amoebozoan species is Dictyostelium discoideum (Dd). Dd has a very simple life cycle with a range of developmental stages, among which we are most interested in the stage of a migrating slug. It has been observed that different sizes of Dd slugs maintain a proportional distribution of prestalk cells and prespore cells: prestalk cells occupy the anterior 20% of the slug, while prespore cells occupy the posterior 80%. However, it remains unknown how the migrating slug forms and preserves this anterior-posterior proportional pattern under so many different dynamics including cell …

Recommending Answers To Math Questions Using Kl-Divergence And The Approximate Xml Tree Matching Approach, Siqi Gao

Theses and Dissertations

Mathematics is the science and study of quality, structure, space, and change. It seeks out patterns, formulates new conjectures, and establishes the truth by rigorous deduction from appropriately chosen axioms and definitions. The study of mathematics makes a person better at solving problems. It gives someone skills that (s)he can use across other subjects and apply in many different job roles. In the modern world, builders use mathematics every day to do their work, since construction workers add, subtract, divide, multiply, and work with fractions. It is obvious that mathematics is a major contributor to many areas of study. For …

A Method Of Reconstructing Historical Destructive Landslides Using Bayesian Inference, Raelynn Wonnacott

Theses and Dissertations

Along with being one of the most populated regions of the world, Indonesia has one of the highest natural disaster rates worldwide. One such natural disaster that Indonesia is particularly prone to are tsunamis. Tsunamis are primarily caused by earthquakes, volcanoes, landslides and debris flows. To effectively allocate resources and create emergency plans we need an understanding of the risk factors of the region. Understanding the source events of destructive tsunamis of the past are critical to understanding the these risk factors. We expand upon previous work focusing on earthquake-generated tsunamis to consider landslide-generated tsunamis. Using Bayesian inference and modern …

"I Think They're Poisoning My Mind": Understanding The Motivations Of People Who Have Voluntarily Adopted Secure Email, Warda Usman

Theses and Dissertations

Secure email systems that use end-to-end encryption are the best method we have for ensuring user privacy and security in email communication. However, the adoption of secure email remains low, with previous studies suggesting mainly that secure email is too complex or inconvenient to use. However, the perspectives of those who have, in fact, chosen to use an encrypted email system are largely overlooked. To understand these perspectives, we conducted a semi-structured interview study that aims to provide a comprehensive understanding of the mindsets underlying adoption and use of secure email services. Our participants come from a variety of countries …