Engineering Commons^™

Pan-Cancer Analysis Of Rna Dysregulation, Somatic Mutations, And Matrix Stiffness Using Bioinformatics Approaches, Gongyu Tang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cancer is a complex disease driven by genetic mutations, epigenetic modifications, and alterations in the tumor microenvironment. Understanding these intricate molecular mechanisms is crucial for advancing cancer diagnosis, prognosis, and treatment. RNA sequencing (RNA-seq) has emerged as a powerful tool to study cancer by providing comprehensive insights into gene expression, alternative splicing, and mutations at the transcriptome level. This dissertation leverages RNA-seq data to explore different dimensions of cancer biology through multi-omics integration and computational approaches. The research is divided into three main projects. First, I developed OncoDB, an interactive database to analyze gene expression, methylation patterns, and viral interactions …

Hidden Markov Model For Identifying Local Variants In Human Genomes Using Simulated Data, Scott Mccallum

Electronic Theses and Dissertations

Identifying adaptive mutations in genetic data is challenging due to the low frequency of occurrence of such events, and because signatures of selection are intertwined with the footprints of various other evolutionary forces that shape our genomes. Even when a larger region appears to be under selection, genomic sites that are linked to adaptive mutations have similar statistical signals, and thus can obfuscate the identification of the actual adaptive mutation. The new method described here uses a Hidden Markov Model that allows for classification of neutral, linked, and sweep (adaptive mutation) genomic sites. This model is general and can be …

Development Of Titanium Dioxide Coating For Self-Cleaning Photovoltaic Panels, Chau Pham

Masters Theses

As global energy demands continue to rise amid increasing environmental concerns, the transition to renewable energy sources, particularly solar power, has become imperative. Solar energy, driven by recent advancements in photovoltaic (PV) technology, presents a promising solution for achieving greater sustainability and efficiency. However, despite these technological advancements, the persistent issue of soiling caused by dust, bird droppings, and other contaminants remains a major obstacle, diminishing sunlight absorption and reducing energy conversion efficiency, presenting a significant obstacle to optimal PV performance.

This study explores the application of titanium dioxide (TiO2) nanoparticle coatings to address this challenge by enhancing the self-cleaning …

A Comprehensive Usability And Economic Analysis Of Heat-Related Wearable Technologies: Applications To Occupational Health, Ryan T. Cannady

Theses & Dissertations

The purpose of this research was to analyze the usability and economic considerations of real-time wearable technologies that are implemented in occupational settings to assess risk of heat stress and heat strain. The study population included current agriculture workers and Department of Energy (DOE), Environmental Management (EM) contractors. We employed a mixed-methods approach to comprehensively analyze the usability and economic considerations of heat-related technologies. Specifically, our approach assessed three distinct aspects the applications of these technologies in occupational settings to comprehensively address our research objective: (1) worker perceptions of heat-related wearable technologies, (2) field-based assessment of these heat-related wearable technologies, …

Tensile Strain Validation Of Welded Wire Reinforcement, Alvaro Montes

Theses and Dissertations

There have been historical concerns regarding the ductility of welded wire reinforcement (WWR). Recent changes in ACI 318-19 now require all grades of A615 and Grade 100 A706 nonprestressed steel reinforcement to have a ratio of tensile strength to yield strength greater than 1.10 and 1.17 respectively. Although this code requirement does not currently apply to WWR, this preemptive study investigated the current state of the art of WWR manufactured in North America in preparation for such a possibility. This project included the tensile-testing of approximately 365 WWR material specimens of various cross-sectional sizes to determine the ratio of tensile-to-yield …

Real-Time Control (Rtc)-Based Urban Flood Risk Assessment Framework For Arid And Semi-Arid Regions, Sulaiman Altami

Dissertations - ALL

Global climate change has recently increased Flood Risk (FR) disasters in arid and semi-arid regions, particularly in Gulf countries, such as the Kingdom of Saudi Arabia (KSA). Arid regions generally face low rain on average during a year, but flash floods occur during rainfall of longer return periods due to urbanization and climate change. Flood Risk Assessment (FRA) outcomes enable municipalities (planners and decision-makers) in arid urban areas to develop flood management strategies and mitigate the issues of drainage systems, which may otherwise affect the quality of life. FRA is an effective tool for not only identifying high-risk areas but …

Modeling And Algorithms To Simplify Complex Multi-Clock/Edge Timing Constraints In High Performance Synchronous Digital Circuits, Nagbhushan Veerapaneni

Dissertations - ALL

Complex timing constraints that refer to multiple clocks and/or edges are often used in the design of modern high-performance processors. Such constraints complicate downstream algorithms such as logic synthesis and lead to inefficiencies. The complexity of the overall CAD system can be reduced considerably if we can optimally transform the timing constraints so that they refer only to a single clock and edge. In this dissertation, we show how to model these multi clock/edge timing constraints and describe algorithms to reduce the number of reference clocks/edges. We first introduce the concept of timing specification transformation and define optimality. We formulate …

Studies On The Synthesis, Reactivity, And Stability Of Au Nanoparticles In Ts-1 Zeolites For Propylene Epoxidation Within H2/O2 Mixtures, Weixin Li

Dissertations - ALL

The increasing global demand for energy and materials has highlighted the importance of efficient production of chemical intermediates like propylene oxide (PO), a key compound in manufacturing polyurethanes, propylene glycol, and other industrial products. Traditional methods, such as the chlorohydrin process and organic peroxide methods, pose environmental and economic challenges due to hazardous by-products and complex processes. The need for greener alternatives led to the exploration of gold (Au) catalysts for the direct catalytic epoxidation of propylene using hydrogen (H2) and oxygen (O2). This research focused on understanding the propylene epoxidation process over Au catalysts, specifically Au nanoparticles (AuNPs) supported …

Effects Of Negative Poisson’S Ratio On The Mechanics Of Auxetic Carbon Fiber Composites Under Tensile, Buckling And Low Velocity Impact, Wenhua Lin

Dissertations - ALL

Carbon fiber reinforced polymer (CFRP) matrix composites exhibited superior properties, such as high specific stiffness and specific strength, excellent fatigue and corrosion resistance, and low coefficient of thermal expansion, have been popular across various industries including aerospace, marine, automotive, energy, civil infrastructure, and high-end sports over the past decades. However, one significant drawback of CFRP composites is the susceptibility to low velocity impact damage which, for aircraft, can be results of tool drop, runway debris, and bird strike during takeoff and landing. These impact events could lead to external and internal damages of a CFRP composite structure in various damage …

Thermodynamics And Shear Flow Dynamics Of Block Copolymer Morphologies In Solution, Senyuan Liu

Dissertations - ALL

Block copolymers (BCPs) have been a focal point of research for several decades. They have been engineered to produce various morphologies by altering the combinations of chemically distinct polymer segments that interact selectively with their environment, such as in aqueous or organic solvents, or within a polymer matrix. The ability to tailor morphological features by manipulating polymer chain length, composition, and monomer chemistry has led to applications in advanced material manufacturing, catalysis, emulsification, environmental remediation, targeted drug delivery, gene therapy, and medical diagnostics. Consequently, understanding the relationship between copolymer architecture and the self-assembled morphologies at equilibrium, the pathways of structure …

Pan-Cancer Analysis Of Rna Dysregulation, Somatic Mutations, And Matrix Stiffness Using Bioinformatics Approaches, Gongyu Tang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cancer is a complex disease driven by genetic mutations, epigenetic modifications, and alterations in the tumor microenvironment. Understanding these intricate molecular mechanisms is crucial for advancing cancer diagnosis, prognosis, and treatment. RNA sequencing (RNA-seq) has emerged as a powerful tool to study cancer by providing comprehensive insights into gene expression, alternative splicing, and mutations at the transcriptome level. This dissertation leverages RNA-seq data to explore different dimensions of cancer biology through multi-omics integration and computational approaches. The research is divided into three main projects. First, I developed OncoDB, an interactive database to analyze gene expression, methylation patterns, and viral interactions …

Discrete Element Method For Mining Industrial Applications: Solving The Clumping Problem Caused By Bulk Cohesive Particles In An Iron Ore Beneficiation Process, Shuang Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

The discrete element method (DEM) is a widely used numerical approach for simulating and analyzing the behavior of granular materials in various applications. This research focuses on the iron ore beneficiation process, addressing the clumping issue in cohesive iron ores from existing crushing processes through a novel double-layered disperser design. The significance of this study lies in its potential to enhance the efficiency of the existing crushing phase and improve the linkage to subsequent purification stages that target smaller-sized iron ore pellets, thereby enhancing the overall efficiency of the ore beneficiation process and achieving significant energy savings. This research adopts …

Investigating Catalytic Conversion Of Lignin To Valuable Products, Jialiang Zhang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Lignin is a complex, random, and heterogeneous biopolymer in lignocellulosic biomass. It has significant potential for conversion into valuable chemicals and fuels. However, its natural recalcitrant structure has made selective depolymerization challenging. This dissertation presents a detailed investigation into the mechanisms of lignin disassembly and structural evolution under various catalytic and solvent conditions. The research spans three key studies. In Chapter 2, operando magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy was employed to study reaction pathways and kinetics of lignin model polymers during catalytic hydrogenolysis. We used a Ni-Al2O3 catalyst in methanol under high temperature and pressure, and …

Discrete Element Method For Mining Industrial Applications: Solving The Clumping Problem Caused By Bulk Cohesive Particles In An Iron Ore Beneficiation Process, Shuang Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

The discrete element method (DEM) is a widely used numerical approach for simulating and analyzing the behavior of granular materials in various applications. This research focuses on the iron ore beneficiation process, addressing the clumping issue in cohesive iron ores from existing crushing processes through a novel double-layered disperser design. The significance of this study lies in its potential to enhance the efficiency of the existing crushing phase and improve the linkage to subsequent purification stages that target smaller-sized iron ore pellets, thereby enhancing the overall efficiency of the ore beneficiation process and achieving significant energy savings. This research adopts …

Investigating Catalytic Conversion Of Lignin To Valuable Products, Jialiang Zhang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Lignin is a complex, random, and heterogeneous biopolymer in lignocellulosic biomass. It has significant potential for conversion into valuable chemicals and fuels. However, its natural recalcitrant structure has made selective depolymerization challenging. This dissertation presents a detailed investigation into the mechanisms of lignin disassembly and structural evolution under various catalytic and solvent conditions. The research spans three key studies. In Chapter 2, operando magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy was employed to study reaction pathways and kinetics of lignin model polymers during catalytic hydrogenolysis. We used a Ni-Al2O3 catalyst in methanol under high temperature and pressure, and …

Fail-Safe Logic Design Strategies Within Modern Fpga Architectures, Priya A. Bhakta

Electrical and Computer Engineering ETDs

Field Programmable Gate Arrays (FPGAs) are vulnerable to radiation-induced single event upsets (SEUs) and fault injection attacks, requiring the use of redundancy techniques such as fail-safe computing. Fail-safe computing refers to computing systems that revert to a non-operational safe state when a fault occurs. This work investigates circuit-level techniques and implements fail-safe computing processes as mitigation for SEUs and fault injection attacks on FPGAs. The analysis reveals vulnerabilities that exist in FPGAs over those in application-specific integrated circuits (ASIC); thus, requiring a more elaborate network of redundant circuits and checking logic. The reconfiguration capability of FPGAs adds complexity to fail-safe …

Post-Processing National Water Model Long-Range Forecasts With Random Forest Regression In The Cloud To Improve Forecast Accuracy For Decision-Makers And Water Managers, Jacob Matthew Anderson

Theses and Dissertations

Post-processing bias correction of streamflow forecasts can be useful in the hydrologic modeling workflow to fine-tune forecasts for operations, water management, and decision-making. Hydrologic model runoff simulations include errors, uncertainties, and biases, leading to less accuracy and precision for applications in real-world scenarios. We used random forest regression to correct biases and errors in streamflow predictions from the U.S. National Water Model (NWM) long-range streamflow forecasts, considering U.S. Geological Survey (USGS) gauge station measurements as a proxy for true streamflow. We used other features in model training, including watershed characteristics, time fraction of year, and lagged streamflow values, to help …

Local Food System Planning On Multiple Governance Scales: A Grounded Theory Analysis, Decker Ure

Theses and Dissertations

Local food systems (LFS) comprise the people, policies, infrastructure and practices of food production, distribution, and consumption in localized areas. LFS are becoming an increasingly important part of urban sustainable development and have recently gained significant traction in the urban planning and sustainable community spheres. Worldwide shocks to global food systems such as the COVID-19 pandemic and the Ukraine-Russia war have further elevated global interest in LFS, bringing local food to the forefront of many communities as they try to insulate themselves and their food supply from future risk. However, despite this growing interest in and policy momentum for local …

Kinetic Modeling Of Bacteria Removal From Suspensions By Magnetic Nanoparticle Capture And Magnetic Separation, Bowen J. Houser

Theses and Dissertations

This thesis investigates the kinetic modeling of bacteria removal from suspensions using magnetic nanoparticle (MNP) capture and magnetic separation. Functionalized magnetic nanoparticles, especially those coated with polydopamine (pDA), were employed to bind with various bacterial species in phosphate-buffered saline (PBS), apple juice, whole blood, and its components. By analyzing the capture efficiency and kinetics of capture across different bacterial species and mediums, we developed mathematical models describing the capture kinetics of bacteria by the pDA-MNPs. Experimental results demonstrated that pDA-coated MNPs achieved high capture efficiency with certain Gram-positive species like Staphylococcus aureus, and one Gram-negative species, Neisseria perflava; however, capture …

A Computational And Mathematical Approach To The Preclinical Development Of Alpha Emitting Radiopharmaceutical Therapies, Abdulaziz Said

McKelvey School of Engineering Graduate Student Theses & Dissertations

Numerous candidate nuclides have been undergoing rigorous preclinical development in the pursuit of novel targeted therapies. Successful development of these drugs relies on the understanding of physiological impacts at the macro and micro scales, in addition to a scalable process for their production. Here, mathematical and computerized approaches have been developed to guide this preclinical development. In this report, two alpha emitting nuclides Pb-212 and Ra-223 are modeled. Radium-223 dichloride citrate a newly approved ion indicated for treatment of bone metastatic castrate resistant prostate cancer, irradiates lesions through targeted uptake in bone at sites of disease. We have undertaken the …

Safety And Optimality Monitors For Learning-Enabled Systems Using Conformal Prediction, Jackson Cox

McKelvey School of Engineering Graduate Student Theses & Dissertations

The use of machine learning to create data-driven plant models and controllers has led to an increased need for safety and optimality monitors for model-based systems. System plant models are subject to uncertainty due to learning constraints such as unseen data and overfitting or physical constraints such as unknown dynamics and noise. This uncertainty is detrimental to safety-critical systems and must be properly regulated. To curb this uncertainty, we create prediction sets using the guarantees provided by Conformal Prediction. With a user-specified high probability, these prediction sets contain the true plant system states for an entire prediction horizon, which we …

Phosphorus Adsorption Capacity Of Volcanic Scoria, Easton Jeffrey Perkins

Theses and Dissertations

Phosphorus (P) pollution in stormwater runoff poses a significant threat to water quality, contributing to eutrophication and ecosystem degradation. This research evaluates the potential of volcanic scoria (VSco), an abundant and cost-effective resource in Utah, USA, to influence P concentrations in urban stormwater systems. Batch adsorption experiments examined the behavior of VSco across three particle sizes—fine (<0.841 mm), medium (0.841–2 mm), and granular (2.38–9.5 mm)—under conditions mimicking stormwater scenarios. The results reveal that fine VSco exhibited higher adsorption efficiency than medium and granular sizes, achieving notable P removal at higher concentrations. However, at lower concentrations, fine VSco showed potential for P release due to desorption of pre-existing P. Medium and granular VSco showed minimal adsorption capacity and, in some cases, acted as P sources, highlighting a dual potential depending on stormwater conditions. Adsorption isotherms indicate that the adsorption behavior of fine VSco aligns with the Langmuir model, with a finite and relatively low adsorption capacity. Calculated distribution coefficient (Kd) values for fine VSco ranged from 0.04 to 0.005 L/g, indicating weak adsorption efficiency compared to materials like activated carbon (1–10 L/g) or soils with moderate adsorption capacity (0.1–0.5 L/g). Loss-on-ignition tests confirmed that VSco’s performance is driven by its physical and chemical properties, particularly its calcium content, rather than organic matter. The study emphasizes caution in applying fine VSco for stormwater remediation due to its potential to release P under typical runoff conditions. However, fine VSco may still be viable in specific scenarios where P levels are higher, such as in stormwater hotspots or localized areas with elevated concentrations, allowing for targeted remediation. The research underscores the need for further testing to refine VSco’s applications, particularly in low-impact development (LID) practices, such as infiltration basins and rain gardens, to effectively manage P levels while supporting ecological and aesthetic goals. These findings contribute to understanding the complex role of VSco in urban stormwater systems, offering insights for sustainable water quality management and nutrient cycling in urban landscapes.

Developing A New Liquefaction Ejecta Prediction Model Considering Soil Properties Of Non-Liquifiable Surface Layers Using New Large Database From The 2012 Emilia Romagna, Italy Earthquakes, Jonah Bradley Dundas

Theses and Dissertations

The presence of a non-liquefied crust overlying a liquefied layer has been found to have a significant effect on sand ejecta and surficial liquefaction damage, as observed by Ishihara (1985). Following the 2010-2011 Canterbury seismic sequence in New Zealand, almost no foundation deformation occurred in areas with liquefaction susceptible soils overlain by at least a 3 meter thick crust [1]. In contrast, the 2012 Emilia-Romagna earthquake in Italy provided surface evidence of liquefaction despite 6+ meter thick crusts. Several researchers have proposed liquefaction prediction models [e.g. LPI [2], Ishihara Curves [3], LSN [4], LPIISH [5] and the methods proposed by …

Assessing Coincidence Of Satellite Acquisitions And Flood Events To Predict Suitability For Flood Map Synthesis, Lyle Dale Prince

Theses and Dissertations

Flooding is a global problem that impacts people, communities, and governments every year. Better understanding of flooding in an area can enable improved emergency response before a flood hits. Flood maps are a crucial tool to translate what for most is an abstract flow, into a more understandable and actionable representation of who and what are at risk. Satellite based flood maps are a useful tool that has potentially global applications. We developed methods to determine which areas are suitable for generating satellite-based synthetic flood maps. For our processes we used Forecasting Inundation Extents using REOF analysis (FIER): a data-driven …

A Comparison Of Rfssw And Rsw For Automotive Manufacturing, Damon Michael Gale

Theses and Dissertations

Historically, automotive body panels have been made of steel and joined by a process called resistance spot welding (RSW). However, in efforts to reduce vehicle weight to improve the energy efficiency of the vehicle, automotive manufactures have begun substituting aluminum in place of steel. While aluminum can be joined with RSW, a myriad of challenges arise from doing so. These challenges result in less consistent weld quality and accelerated electrode wear. Refill friction stir spot welding (RFSSW) is an emerging joining technology that could replace RSW as it is believed to be capable of creating superior joints in thin sheet …

Design & Development Of Fr1 Band Antenna For V2x Communication, Sujanth Narayan Kg

Theses and Dissertations

The developing trends in the automotive industry are evolving towards connected and autonomous vehicles that provide various advantages namely enhanced safety & security, congestion less traffic, smart mobility, and environmental sustainability at a lower cost with greater cause to the society. Vehicle to Everything (shortly V2X) Communication plays a significant role in autonomous driving. Salient features of V2X provide improved better driving experience and traffic efficiency even during fast moving scenarios.

V2X technologies are being carried out in sub 6 GHz range mainly at the 5.9 GHz band called the Dedicated Short-Range Communication (DSRC) based on IEEE 802.11p providing support …

Site Amplification In The Salt Lake Valley, Utah, During The 2020 Magna Earthquake, Blair A. Hanson

Theses and Dissertations

Site amplification in the Salt Lake Valley, Utah, has been a focus for both geologists and engineers due to its complex geology and seismic vulnerability. This study utilizes data from the 2020 Magna Earthquake to analyze site amplification from previously unavailable strong ground motion data. Ground motion data from the University of Utah Regional Seismic Network and the National Strong Motion Project, combined with extensive soil profiles, was analyzed using the program DEEPSOIL. The study compares computed motions with measured motions, revealing differences in site amplification across the Salt Lake Valley. Notably, the highest amplification was observed at longer periods …

Discharge-To-Water Level Conversion Using Monthly Duration Curves (Dwl-Mdc): Enhancing The Utility Of The Geoglows Ecmwf Hydrological Model, Darlly Judith Rojas Lesmes

Theses and Dissertations

Flood early warning systems are crucial for disaster risk reduction strategies, enabling communities to take timely action against threats. However, the effectiveness of these systems depends on accurate and timely hydrological data, particularly river discharge and water level measurements. Unfortunately, many regions, face significant challenges in obtaining hydrological data, especially discharge data due to outdated rating curves, high equipment costs, and logistical constraints. Water level measurements, by contrast, offer reduced uncertainty and are often more accessible, providing an alternative for hydrological modeling in data-scarce regions. To address these limitations, we developed and validated the Discharge-to-Water Level Conversion Using Monthly Duration …

Application Of Systems Engineering Principles In A Reliability Assessment Of Air- Cooled Heat Exchangers, Dheerajkumar R Narang

Harrisburg University Experiential Learning Projects

A significant systems engineering challenge exists due to the lack of a comprehensive methodology that holistically addresses both the static and dynamic components of air-cooled heat exchangers. Traditional methodologies often overlook the dynamic components—such as fin blades, electrical motors, gearboxes and propellers (fans)—that are integral to the overall performance and reliability of the air-cooled heat exchangers. The absence of an integrated framework that considers the interdependencies and interactions between mechanical and dynamic components complicates the task of accurately assessing the remaining life and ensuring the reliability of the entire system.

This article proposes a holistic RLA and reliability engineering framework …

A Mechanistic Study Of Silicon Nanocrystal Formation Via Solid State Synthesis, Katherine Mccarthy Weinfurter

Dissertations and Theses

Silicon nanocrystals (SiNCs) show promising physiochemical properties that could be used in industrial applications. The production of SiNCs through solid-state synthesis is ideal due to relatively low cost of equipment and chemical reagents, as well as the ability to scale-up production. A widely known and commonly used precursor previously used in solid-state synthesis for SiNCs, hydrogen silsesquioxane (HSiO_1.5), was discontinued in chemical manufacturing, which has led to researching alternative precursors (or starting materials). We have identified that there is a gap of knowledge related to producing these precursors, as well as the mechanistic understanding of the chemical reactions …