Digital Commons Network^™

A Mutational Analysis Of Thatisin: How Single Point Mutations Impact The Biosynthetic Process Of A Group 16 Graspetide, John F. Boynton Jr

Chemistry and Chemical Biology ETDs

Abstract:

Graspetides are a family of Ribosomally synthesized and Post-translationally modified Peptide (RiPP) natural products named for their ATP Grasp Macrocyclases. We identified several Graspetide Biosynthetic Gene Clusters containing common double glycine cleavage motifs and attempted characterization of the mature Graspetides. One of the resulting peptides, Thatisin, has a topology with two interlocking macrolactones installed by a single ATP Grasp Ligase named ThtC. Here we use single and double point mutations to observe the impact or variation on the installation of these macrocycles. Alanine scan mutagenesis is used to assess leader peptide residues in the precursor peptide ThtA to determine …

Understanding The Metallic And Oxide Phases In Platinum-Based Bimetallic Heterogeneous Catalysts After High-Temperature Oxidation, Stephen John Porter Jr

Nanoscience and Microsystems ETDs

Platinum (Pt) and palladium (Pd) are critical components in diesel emission control systems, enabling the conversion of harmful pollutants under demanding conditions. However, Pt’s effectiveness is hindered by sintering under high-temperature oxidizing environments. This dissertation investigates how Pt and Pd evolve under oxidizing conditions at 800°C, highlighting their distinct thermodynamic behaviors and interactions. Using TEM, EDS, EELS, XRF, XRD, and EXAFS, we show that Pd suppresses Pt sintering by reducing the volatility of PtO₂, leading to the formation of stable particles. Both Pt and Pd are present in metallic and oxide states, forming biphasic 'Janus' particles with conjoined metal and …

Phase Nanoscopy With Correlated Frequency Combs, Xiaobing Zhu

Optical Science and Engineering ETDs

In this dissertation a sensing method applying to any physical quantity that modifies optical phase is developed. Two pulses are produced inside a synchronously pumped Optical Parametric Oscillator, generating two identical, undistinguishable frequency combs. The physical quantity to be measured applies a small phase shift/round trip to one of the pulses, resulting in a frequency shift of the corresponding comb. The latter frequency is measured as a beat by interfering the two combs on a detector. A world record resolution, close to the quantum limit, of 0.033 nanoradian (corresponding to 0.006 fm in displacement) is achieved. A detailed analysis of …

Advancing Diamond Quantum Sensors: Isotropic Flux Concentrators And Phase Noise Mitigation, Maziar Saleh Ziabari

Optical Science and Engineering ETDs

Two methods for improving the sensitivity of nitrogen vacancy quantum sensors in diamond are explored. First, by passively concentrating the magnetic flux, three orthogonally oriented ferrite truncated cone pairs amplify the field isotropically by 19 times, allowing measurement of Earth's field without a bias field and increasing sensitivity. Through thorough analysis, modeling and tuning a novel 3-dimensional flux concentrator system, we achieve a fractional standard deviation of less than 1% anisotropy and quantify minimal deadzones and ambient temperature-limited variations below 40 nT/hour. Second, we characterize, model and calculate phase noise in NV experiments, which in NV sensors is effectively indistinguishable …

Predicting Leakage From Nuclear Material Containers At Los Alamos National Laboratory Through Drop Testing, Leak Testing, Finite Element Analysis And Digital Image Correlation, Jude M. Oka, Yu-Lin Shen, Osman Anderoglu, Pankaj Kumar, Rajendra Vaidya

Mechanical Engineering ETDs

Los Alamos National Laboratory (LANL) relies on containment vessels to safely manage special nuclear material. These containers are subject to rigorous testing—such as drop, fire, and water ingress testing—to ensure integrity under adverse conditions. While elastomer-based seals are well studied, metal-to-metal sealing mechanisms remain under investigation, particularly under dynamic loading. This research focuses on the relationship between container mating surfaces and impact loading through drop testing. Finite Element Analysis (FEA) models were developed and validated using Digital Image Correlation (DIC) to measure strain during impact. Drop tests at varying heights showed strong correlation between FEA and DIC results, confirming the …

Networked Systems: Synchronization, Decomposition And Transient Dynamics, Amirhossein Nazerian

Mechanical Engineering ETDs

This dissertation investigates synchronization, transient dynamics, control, and signal amplification in networked dynamical systems. First, it examines complete and cluster synchronization, including cases with large parametric mismatches, in both natural (e.g., brain networks, fireflies) and technological systems (e.g., power grids, robotics). Second, it studies transient dynamics in consensus processes, designing synchronization strategies that link reactivity, contraction theory, and Lyapunov exponents. Third, it addresses the computational limits of Model Predictive Control (MPC) for large networks by introducing an algebraic decomposition method that enables parallel online computation of smaller subproblems, enhancing MPC performance under hardware constraints. Finally, it analyzes the structural role …

Instability Analysis In Cylindrical Thin Film–Compliant Core Structures: Numerical Simulations And Effects Of Inelastic Deformation, Md Al Rifat Anan

Mechanical Engineering ETDs

When a thin film bonded to a thick compliant substrate is subject to in-plane compression, wrinkles can develop if the critical state for instability is reached. In various applications the film/substrate system may also take the form of cylindrical fibers, where an axial compressive loading can trigger axisymmetric wrinkles. A straightforward computational approach to simulate such wrinkling behavior is needed for material design, to either prevent wrinkling or to exploit its benefits for flexible device applications. In this work a comprehensive numerical study is undertaken by employing the finite element method. The embedded imperfection approach used previously for planar structures …

Multiscale And Multi-Model Studies Of Metal Plasticity, Luo Li

Mechanical Engineering ETDs

Plastic deformation is the process in which the material deforms permanently due to external effects. Twinning and slip are two main mechanisms of plastic deformation in metallic materials. The prominent mechanism of plastic deformation in metals that have FCC crystal structures is slip or gliding movement of dislocations, which is mainly focused on here. In the current study, frameworks for investigating plasticity phenomena of metals at different scales ranging from microscale to macroscale are demonstrated. Specifically, the macroscale modeling of plastic response of metallic materials induced by indentations are emulated by nonlinear FEA simulations. Simulation results of macroscale modeling are …

Advancements In Microarray Manufacturing Enable Emerging Technologies, Kendall Hoff

Biomedical Engineering ETDs

Significant advances in manufacturing technologies have enabled the production of new DNA microarrays for use in emergent technology. Photolithography, wafer scale manufacturing, and improvements in synthesis chemistry and design enable high-throughput production of extremely high-quality arrays. These new arrays offer extremely high oligonucleotide densities, in the range of tens of thousands of oligonucleotides per square micron. They also offer smaller features sizes, with millions of features per square centimeter. Furthermore, they can be manufactured with the DNA tethered at either end to the surface, leaving either the 5’ or 3’ end free and available for use in enzymatic reactions; and …

Composition Portfolio Of Doug Falk, Doug Falk

Music ETDs

This composition portfolio contains six compositions:

Heterogeneity (2020) for solo guitar

Amalgamation (2023) for reed quintet

Oil and Vinegar (2024) for wind symphony (satisfying the requirement of one work for large ensemble)

Shouting into the Abyss (2024) for flute with electronics (satisfying the requirements of a work for electronics and a work for voice)

Movements Come, Movements Cease (2025) for voice, trumpet/flugelhorn, marimba, electric bass, drum set and fixed media; written in collaboration with choreography by Laura Orozco Garrett (satisfying the requirement of one collaborative work)

Celestial Bodies in Motion (2025) for 10 piece wind ensemble (satisfying the requirement for …

Improving Infiltration Model Performance In Arid And Urban Regions, Samuel Stephen Coulter

Civil Engineering ETDs

Flooding in arid regions is infrequent but damaging and limited historical data makes flood modeling an important tool for flood infrastructure design. This study improves flood modeling guidance by using plot-scale tests to determine the impact of slope, compaction, gravel mulch and landscape fabric on infiltration and runoff rates in sandy soil types. This data will be used as guidance for the linear and constant model. The performance of this model was compared with the curve number model for a hypothetical 100-year design storm. Results showed that gravel mulch increased infiltration rates by 66% and reduced erosion on steep and …

Finite Element Investigation Of Blast Load Responses In Nuclear Power Plant Containment Structures, Janak Raj Awasthi

Civil Engineering ETDs

Some significant incidents like the Chernobyl disaster (1986), the Fukushima Daiichi hydrogen explosion (2011), and some frequent military and terror threats to the nuclear Power plant structures have led to studying the capacity of power plant structures to withstand blast loadings. From this research, even one-third of the loss of the coolant is enough to damage the power plant structure. Crack starts from the wall and propagates toward the top of the dome and the foundation. The external blast shows high damage symptoms near the foundation area. Most of the steel members, including the rebars, Liner, and Tendons, showed high …

College Football Or Abortion Education? An Examination Of The University Of Arizona’S 1974 Stadium Bonds Bill, Emma Masterson

History ETDs

In 1974 the University of Arizona renovated their football stadium through a bonds bill passed by the state legislature. The renovations allowed the university to increase the stadium’s capacity by 17,000 seats. While in the state house, an Arizona Congressman attached a rider to the bonds bill banning the university’s medical school from performing abortions in most circumstances, effectively barring the university from teaching the medical students how to perform the procedure as well. This thesis seeks to position the University of Arizona football stadium renovations and abortion ban within the larger histories of American higher education and Arizona. This …

Optimizing Distributed Boundary Exchanges For Benchmarks, Solvers And Sparse Matrix Operations, Gerald Collom

Computer Science ETDs

Boundary exchanges dominate the cost of both stenciled codes and those that rely on sparse matrix operations. The performance of large boundary exchanges is limited by synchronization overheads and injection bandwidth limitations. Irregular boundary exchanges incur additional overheads due to the large number of required messages. This thesis investigates multiple methods for improving the performance and scalability of both Cartesian and irregular boundary exchanges. Since boundary exchanges are typically performed iteratively, persistent communication presents an opportunity for optimization by sharing and amortizing setup costs. Partitioned communication is also explored to increase asynchrony, reducing bottlenecks from synchronization overheads and data congestion. …

Exploring Immune System Through Computational Modeling: A Comprehensive Study Of Lymph Nodes And Immune Response Scaling, Vaccine Efficacy, And Large-Scale Extreme First Passage Time, Jannatul Ferdous

Computer Science ETDs

The adaptive immune response is a complex defense mechanism that develops over time to recognize and eliminate pathogens with remarkable precision and durability. This dissertation investigates the dynamics, scaling, and efficiency of the adaptive immune response through a synthesis of computational modeling, mathematical analysis, and agent-based simulations. First, we analyze the topology of the lymphatic network and investigate the T cell search time to find the lymph node that is containing the matching dendritic cell. Second we show how the scaling of lymph node number and volume with body mass, leads to scale-invariant search times for T cells locating antigen-bearing …

Secured Through Stone: The Power, Monuments, And Memory Of Thyra Danmarkarbót And The Jelling Dynasty, Jacquelyn Truitt

History ETDs

Sometime in the mid-tenth century on the Jutland peninsula of Denmark, the Viking Age Queen Thyra (d. ca. 958/9) passed away and the epithet Danmarkarbót—Denmark’s Adornment—was skillfully carved onto her memorial runestone. Yet Thyra’s story has been clouded by few and unreliable textual sources, by differing assessments of her familial background that have emerged from those sources, and by misrepresentations of the material culture relating to her. This thesis explores Thyra and her place within the Viking Age Jelling dynasty through textual and material evidence and considers how the construction of both medieval and modern memory work and memorialization …

Network Intelligence For Next-Generation Wireless Networks: Advancing Distribution And Coordination, Yonatan Melese Worku

Electrical and Computer Engineering ETDs

Next-generation wireless networks, encompassing 6G and beyond, face rigorous demands for ultra-low latency, ubiquitous connectivity, exceptionally high data rates, and robust security, necessitating innovative approaches to resource optimization and network protection. This dissertation proposes a pioneering framework that synergizes advanced methodologies—deep reinforcement learning, deep learning, blockchain, and multi-agent systems—to address these challenges. Distributed architectures, underpinned by AI-driven multi-agent systems, form the backbone of this framework, enabling seamless integration and intelligent orchestration across diverse domains. The research advances IoT-based systems leveraging machine learning for resource efficiency in healthcare applications, develops reinforcement learning-driven frameworks to optimize energy and coverage for Unmanned Aerial …

The Nature Of Anthropogenically Driven River Drying: Spatiotemporal Causes And Consequences, Eliza Inez Gilbert

Biology ETDs

Streambed drying naturally occurs in over 60% of rivers and streams worldwide. Climate change and human regulation of surface and groundwater have increased drying in naturally intermittent systems and caused perennial systems to transition to intermittency, impacting water security, water quality, and biodiversity. To understand human-induced drying dynamics, we used 12 years of daily drying data along a 154-km regulated reach of the Rio Grande. We conceptualized river drying as a regime analogous to the natural flow regime paradigm and quantified drying magnitude, rate of change, and duration. Although linear models predicting drying magnitude and rate of change were uninterpretable, …

Nitrogen Addition Additively Boosts Climate-Driven Salsola Tragus (Russian Thistle) Invasion Into Southwestern Usa Grasslands, Melissa A. Bacigalupa

Biology ETDs

Effective management of invasive, non-native plants requires understanding key drivers of invasion, including nitrogen enrichment from atmospheric deposition and agriculture. Long-term studies are essential for capturing complex invasion dynamics yet remain uncommon. We used 22 years of observations and 14 years of nitrogen experiments to examine invasion by Salsola tragus (Russian thistle) into three semi-arid grasslands of central New Mexico. Invasion patterns varied, with rapid expansion in Chihuahuan Desert grassland and the Desert-Plains ecotone but stability in Plains grassland. Under ambient nitrogen, precipitation most strongly correlated with Russian thistle biomass and high native grass biomass was associated with Russian thistle …

Does Reliance On Kin Erode With Market Integration? A Social Network Perspective, Ruizhe Liu

Anthropology ETDs

Kinship has long shaped human societies. Yet globalization and market integration (MI) are reshaping social structures. This dissertation investigates how kinship-based networks persist, adapt, or erode amid rapid socioeconomic change. It draws on ethnographic and social network data from 229 Mosuo households in southwest China, a matrilineal society experiencing increasing MI, to examine shifts in everyday cooperation.

The first study analyzes fixed name-generator data and finds a general decline in kin support as MI increases, though with considerable variation. The second study uses count models to explore unbounded support networks, showing that kin ties remain central in reproductive contexts, while …

A Study Of Machine Learning Techniques In Solving Biochemical And Chemical Problems, Kenneth Micheal Plackowski

Chemistry and Chemical Biology ETDs

Data-driven approaches to solving problems in biology and chemistry require utilization of reliable techniques and machine learning algorithms are the modern reliable approach. This work presents three problems that involve use of supervised learning techniques when classification is the goal and unsupervised learning techniques when global data representation is the goal.

In the first problem, we demonstrate the use of unsupervised clustering techniques, self-organizing maps and K-means, to ascertain analyte detection capabilities of carbon nitride dots. In the second problem, we add scalability features to a functional group classification model applied to infrared data and evaluate its ability to inform …

Theoretical And Experimental Investigation Of Liquid-Liquid Phase Separation: Characterizing Elastin-Like-Polypeptides, Adam D. Quintana

Chemical and Biological Engineering ETDs

This dissertation develops and validates a semi-empirical Flory–Huggins-based interaction model, combined with Cahn–Hilliard simulations, for predicting multi-component liquid–liquid phase separation (LLPS) in elastin-like polypeptide (ELP) systems. Equilibrium droplet compositions, measured using a PDMS-based microfluidic device, enabled direct parameterization of interaction coefficients. The model was applied to generate phase diagrams and assess composition dependence in ternary mixtures. Cahn–Hilliard simulations were conducted to explore potential phase morphologies under different interfacial conditions. Multi-component Lattice Boltzmann simulations were implemented to model droplet morphology evolution under varying interfacial and diffusive parameters, reproducing experimentally relevant morphologies. A three-phase wetting study revealed conditions for selective wetting and …

Everyday Life In The U.S.: An Intersectional Approach To A North Korean Refugee Woman’S Identities, And Experiences, Lyounghee Kim

Communication ETDs

This dissertation examines everyday experiences of a North Korean refugee woman in the U.S., centering her narratives as sites of critique, resistance, and meaning-making. Grounded in Critical Refugee Studies, Asian American Studies, and Critical Intercultural Communication and framed by intersectionality, it explores how interlocking structures of power shape and are shaped by her life. Rather than focusing solely on trauma or assimilation, this study highlights her digital storytelling, faith, and mutual aid practices as acts of survival, dignity, and moral agency. Using a qualitative, narrative inquiry approach grounded in critical reflexivity, it thematically analyzes her stories to reveal how she …

Analyzing Environmental Health: Air Pollution And Human Health Using Geospatial Data Science, Yanhong Huang

Geography ETDs

Air pollution from industrial emissions and wildfire smoke poses growing threats to public health. This dissertation employs geospatial data science to examine these challenges through three interrelated studies. The first study investigates the relationship between maternal residential exposure to industrial pollutants and low birth weight, identifying five chemicals as significant risk factors. The second study assesses the impact of industrial air pollution on lung and bronchus cancer survival, finding that exposure to 1,1,1-trichloroethane and cobalt is associated with reduced survival. The third study explores disparities in wildfire smoke PM_2.5 exposure and its association with asthma exacerbations. Results show disparities …

What Can We Learn From The High School Math Reform Efforts In California, Georgia, And Oregon? A Policy Analysis, Yanira Vazquez

Teacher Education, Educational Leadership & Policy ETDs

Using publicly available data sources, this policy analysis examined how three states—California, Georgia, and Oregon—approached high school mathematics reforms to address questions regarding what prompted these states to revise their high school math standards and course pathways; how their approaches to reform were similar or different; and what other states could learn from their methods.

Individual state cases were developed, focusing on content standards, course pathways, and graduation requirements. A cross-case study was created to compare reforms from the three states.

While all states aimed to reform high school mathematics to address equity issues and offer options aligned with students’ …

Ghost Highway: De-Touring Albuquerque's Route 66, Madison A. Garay

Art & Art History ETDs

Route 66 was a U.S. Numbered Highway stretching from Chicago, IL to Santa Monica, CA, rising to fame through music and popular culture. In Albuquerque, New Mexico, Route 66 has a troublesome twin life as Central Avenue, a highly politicized space where bodies are contested. In this thesis, the function of public arts and architecture of Albuquerque’s main street thoroughfare, Central Avenue, will be analyzed as visual devices of U.S. Highway 66, or known in popular culture as “Route 66.” I employ a critical Derridean framework through Mark Fisher’s theorization of hauntology and Gerald Vizenor (White Earth Ojibwe)’s theory of …

Boricua En La Luna: An Ethnographic Case Study On The Spatializations Of Puerto Ricans In New Mexico, Neritza Díaz Cruz

Language, Literacy, and Sociocultural Studies ETDs

This ethnographic case study investigates the spatializations of Puerto Ricans in New Mexico, a state where the community is small, dispersed, and often invisible. The purpose of this study is to examine how Puerto Rican identity is shaped, expressed, and contested across New Mexican spaces. Drawing from critical spatial theory, this study investigates how broader structures such as language ideologies become spatialized in the everyday lives of five Puerto Rican adults living in the Albuquerque area. Data was gathered through interviews, observations, and participatory mapping. Thematic analysis was used to interpret the data with a focus on how lived, perceived, …

Seeking Structure In Complex Systems: From Feature Analysis To Space-Time Causal Discovery With Earth Science Applications, Jeffrey J. Nichol

Computer Science ETDs

Complex systems are difficult to study because of their many interacting parts, emergent phenomena, and feedback loops. These systems underpin all life on Earth. We need improved tools for seeking an understanding of them. This body of research presents my investigations into data-driven methods for understanding complex systems, including my invention of a novel causal discovery meta-algorithm for space-time gridded data. I demonstrated machine learning feature importance and causal discovery capabilities for comparing simulated and observed climate data. I developed a new benchmark for modeling space-time dynamics of locally driven phenomena and examined a prominent causal discovery algorithm. Finding that …

Facilitating Novice Learning In Visual Search: Baseline-Dependent Effects Of Transcranial Electrical Stimulation Over The Right Inferior Frontal Gyrus, Bradley M. Robert

Psychology ETDs

Transcranial electrical stimulation (tES) has shown potential to modulate attention and enhance learning, yet its effects in applied, real-world contexts, remains underexplored. This study investigated the impact of transcranial direct current stimulation (tDCS) and high-frequency transcranial random noise stimulation (hf-tRNS with DC offset) on performance in a synthetic aperture radar (SAR) visual search task requiring both target identification and change detection. Participants (N = 63) were randomly assigned to tDCS, hf-tRNS, or sham conditions, with stimulation applied to the right inferior frontal gyrus (F10) during the training phase. Accuracy served as the primary outcome, with supplementary EEG and eye-tracking data …

Pd-Based Hydrogen Separation Membranes Synthesized Via A Liquid-Phase Route, Chase W. Thompson

Chemical and Biological Engineering ETDs

Palladium (Pd) membranes have gained significant attention for their ability to selectively separate hydrogen, a critical process for clean energy applications such as fuel cells and hydrogen storage. However, challenges such as grain growth, sintering, hydrogen embrittlement, and film uniformity limit their scalability and long-term stability. This thesis focuses on the controlled synthesis, deposition, and stability of Pd nanoparticles to optimize membrane performance for hydrogen separation. This work investigates solution-phase synthesis of Pd nanoparticles, focusing on temperature, precursor concentration, and solvent composition as key variables influencing particle growth and dispersion. Pd membranes were fabricated using nanoparticle deposition onto porous supports, …