Engineering Commons^™

Calculating The Difference In Stiffness Of Living T Cells Through Micropipette Aspiration, Minju Lee

McKelvey School of Engineering Theses & Dissertations

Cardiovascular disease (CVD) accounted for 17.9 million deaths in 2019, with fibrosis contributing to nearly a quarter of these fatalities [1,2]. Fibrosis, characterized by excessive connective tissue formation, has been strongly linked to T cells, essential components of the immune system. This study explores the mechanisms of T cell activation and the subsequent changes in biophysical properties like diameter, stiffness, and elasticity, aiming to develop therapeutic strategies for fibrosis-related diseases, including CVD. Utilizing the micropipette aspiration technique, we accurately assessed T cell stiffness and observed a change in bulk cell stiffness upon activation. The results demonstrated increased fluid-like behavior in …

A Novel Approach To Detect Modified Cytosines In A Nanopore Sequencer, Benjamin Davidorf

McKelvey School of Engineering Theses & Dissertations

Epigenetic changes, such as DNA methylation, have been seen in various types of cancers, diseases, and neurological disorders. A common form of methylation occurs when a methyl group is added to the C-5 position of a cytosine, which is called 5-methyl-cyosine (5- mC). Hydroxymethylated is a type of methylation where 5mC is oxidized to 5-hydroxy-methyl- cytosine (5hmC), which has been linked to normal brain development. Current methods to sequence DNA methylation patterns (5-mC and 5-hmC) at a genome-wide level have several limitations, so there remains a need for a method to efficiently map DNA methylation. The state- of-the-art method for …

Watch: A Distributed Clock Time Offset Estimation Tool On The Platform For Open Wireless Data-Driven Experimental Research, Cassie Jeng

McKelvey School of Engineering Theses & Dissertations

The synchronization of the clocks used at different devices across space is of critical importance in wireless communications networks. Each device’s local clock differs slightly, affecting the times at which packets are transmitted from different nodes in the network. This thesis provides experimentation and software development on POWDER, the Platform for Open, Wireless Data-driven Experimental Research, an open wireless testbed across the University of Utah campus. We build upon Shout, a suite of Python scripts that allow devices to iteratively transmit and receive with each other and save the collected data. We introduce WATCH, an experimental method to estimate clock …

Design Of Microwave Superconducting Resonators For Materials Characterization, Xinyi Zhao

McKelvey School of Engineering Theses & Dissertations

A resonator is a specialized device capable of storing and transferring energy at precise frequencies. Resonators find widespread use in various fields, such as electrical engineering, physics, and material science, owing to their exceptional ability to accurately measure, filter, and amplify signals. Different types of resonators exist, but coplanar waveguide (CPW) and coupled coplanar waveguide (CCPW) resonators are popular due to their high-frequency operation and easy integration into microfabrication processes.

Performance And Emissions Study Of N+3 And N+4 Engine Models With Several Fuel Types Using Npss, Abel Solomon

McKelvey School of Engineering Theses & Dissertations

The aviation industry is known to be one of the major contributors to greenhouse gases accounting for 4.9% of the global greenhouse emissions. With the ever-increasing threat of climate change to the overall survival of the planet, the exploration of new technologies and alternative energy sources that minimize greenhouse gas emissions are of paramount importance. In this regard, the development of propulsion systems well suited for the performance and emissions requirements of future commercial aircraft plays a crucial role. This thesis investigates N+3 and N+4 technology-level propulsion systems that are proposed by NASA as possible propulsion systems for advanced single-aisle …

Mirror Position Detection In A Catoptric Surface, Run Zhang

McKelvey School of Engineering Theses & Dissertations

The Catoptric Surface research project is a pioneering exploration of controlling daylight effects within built environments. In this thesis, we focus on the mirror position detection problem, which plays a vital role in achieving dynamic control over the direction of reflected light within a space. To address the challenge of mirror position detection, we employ computer vision techniques, specifically edge detection and the RANdom SAmple Consensus (RANSAC) algorithm. Edge detection is utilized to identify significant changes in intensity or color, corresponding to object boundaries, while RANSAC is applied for ellipse fitting. By iteratively selecting minimal subsets of points and fitting …

The Effect Of Spinal Cord Stimulation And Video Games Training On Body-Machine Interface Control, Jie Fei

McKelvey School of Engineering Theses & Dissertations

Damage to the spinal cord causes long-lasting loss of motor and sensory function, and currently, there is no ‘cure’ for paralysis. However, even people with severe spinal cord injuries (SCI) have some residual mobility. Studies have shown that transcutaneous electrical spinal cord stimulation (tSCS) combined with functional training targeting residual mobility can further improve the motor function of individuals with SCI. In this study, we present a technical framework that aims to enhance rehabilitation outcomes by targeting residual mobility through a motor training-based approach. Our technical framework centers around a non-invasive body-machine interface (BoMI) that relies on the use of …

Novel Microfluidic Devices To Model The Interactions Between Lymphatics And Breast Cancer, Jade Weber

McKelvey School of Engineering Theses & Dissertations

The lymphatic system is responsible for immune circulation and fluid balance in the body. It accomplishes this by draining interstitial fluid from local tissue and transferring it to lymph nodes and back into blood circulation. However, this process is implicated in many pathologies, one of the most dangerous being breast cancer metastasis to the lymph nodes. The largest factor in breast cancer patient mortality is metastasis. Lymphangiogenesis, the growth of new lymphatic vessels, has been thought to play a dynamic role in aiding breast cancer metastasis. Breast cancer tumor cells have been shown to remodel the functionality of local lymph …

Targeted Adversarial Attacks Against Neural Network Trajectory Predictors, Kaiyuan Tan

McKelvey School of Engineering Theses & Dissertations

Trajectory prediction is an integral component of modern autonomous systems as it allows for envisioning future intentions of nearby moving agents. Due to the lack of other agents' dynamics and control policies, deep neural network (DNN) models are often employed for trajectory forecasting tasks. Although there exists an extensive literature on improving the accuracy of these models, there is a very limited number of works studying their robustness against adversarially crafted input trajectories. To bridge this gap, in this paper, we propose a targeted adversarial attack against DNN models for trajectory forecasting tasks. We call the proposed attack TA4TP for …

Dual Color Optogenetic Control For Analyzing Cardiac Function In Drosophila, Jiantao Zhu

McKelvey School of Engineering Theses & Dissertations

Prolonged consumption of carbohydrate-rich diets and immobile lifestyles frequently cause metabolic disorders and obesity and, as a result, may lead to progressive heart dysfunction among broad social groups of the population. Drosophila melanogaster serves as an essential model organism in cardiovascular disease research due to conserved physiological and genomic traits shared with humans, its genetic and molecular toolbox versatility, and cost-effective maintenance. Here, we combine optogenetics and optical coherence tomography to study cardiovascular function in D. melanogaster. A new optogenetic pacing system has been developed, employing a transgenic line carrying two opsins: ChR2 and NpHR2.0. A custom-built hardware setup …

A General-Purpose Software Platform For Closed-Loop Neuromodulation, William Engelhardt

McKelvey School of Engineering Theses & Dissertations

Implementing closed-loop neuromodulation therapies is a challenging and expensive endeavor. It requires developing software capable of acquiring signals from a bio-signal amplifier, analysis of these signals, and initiation of precisely timed stimulation, all of which need to be accomplished in real-time with very low latency. Developing this software is difficult, as it requires a wide range of expertise ranging from interfacing with hardware to real-time signal processing. Even when successfully implementing such a system for one set of hardware, it often then only works within the laboratory that conceived it. This is because of the inherent heterogeneity in the devices …

Optical Perturbation Of Protein Kinase A Activity Via Photoactivatable Inhibitor Peptides, Peter Chen

McKelvey School of Engineering Theses & Dissertations

Protein Kinase A (PKA) plays important roles in diverse biological processes such as sleep, long term memory, and synaptic plasticity. In addition, PKA also acts as an integrator of neuromodulator signaling though G protein-coupled receptor activation. However, despite genetic knockout and pharmacological inhibition experiments that demonstrate the importance of PKA, it is unclear where, when, or how PKA plays these roles in cellular physiology and behavior. In order to better understand the function of PKA in these processes, and how neuromodulator signaling drives complex behavioral changes, there exists a need for a method to selectively activate/inactivate PKA with high spatial …

Two-Dimensional Field Effect Transistor, Yimeng Li

McKelvey School of Engineering Theses & Dissertations

As silicon-based field-effect transistors (FETs) approach their physical limits with channel lengths approaching 5 nm, the search for new semiconductor materials that can surpass this limit has become urgent. Two-dimensional layered semiconductor nanomaterials, represented by graphene, have emerged as promising candidates due to their unique physical, mechanical, and chemical properties. Unlike traditional silicon-based FETs, two dimensional (2D) layered nanomaterials are held together by van der Waals forces between layers, with no dangling bonds on the material surface, which can effectively address the short-channel effect issue faced by traditional silicon-based FETs. However, unlike traditional silicon-based FETs, which have matured fabrication systems, …

Development Of A Multispectral Vis-Swir Imaging Modality For Cutaneous Water Assessment, Quinlan Mcgrath

McKelvey School of Engineering Theses & Dissertations

Inflammatory skin diseases are estimated to impact 20% of the global population and are the fourth leading cause of nonfatal disability worldwide. Diagnosis and management are predominantly based on clinician visual assessment of disease related changes in skin morphology. The qualitative nature of this method can result in misdiagnosis and underdiagnoses of treatable diseases. There persists systematic undertreatment of skin of color patients given the more subtle presentation of erythema against pigmented skin. There exists a clinical need for a quantitative and objective inflammation assessment tool that meets the needs of a diverse patient population. The accumulation of interstitial fluid …

A Novel Mrna Delivery Strategy Employing Adenovirus Piggyback Mrna Binders Via Catcher/Tag Molecular Glue, Kexin Geng

McKelvey School of Engineering Theses & Dissertations

mRNA-based therapeutics open a new era for the prevention and treatment of a wide range of diseases. However, existing mRNA delivery vehicles have limited repertoires for dendritic cell targeting and intranasal administration which are two paramount delivery pathways of significant advantages for treating cancer and infectious respiratory diseases. Adenovirus (Ad) with well-deciphered viral genomes and intensive-studied structure biology has been developed for DCs-targeted cancer vaccines and intranasal COVID vaccines. In light of these virtues, Ad presents as the “off-the-shelf” tool possessing well-defined manufacturable capabilities and translatable feasibility that perfectly complements the current limitations of mRNA delivery. In this study, we …

Preparing Non-Human Primates To Study Hand-Eye Coordination In Frontal Eye Fields (Fef) During Delayed Movement Task, Juliusz Cydzik

McKelvey School of Engineering Theses & Dissertations

ABSTRACT OF THE THESIS Preparing Non-Human Primates to Study Hand-Eye Coordination in Frontal Eye Fields (FEF) During Delayed Movement Task by Juliusz Cydzik Master of Science in Biomedical Engineering Washington University in St. Louis, 2023 Professor Lawrence Snyder, Chair Hand-eye coordination enables humans and non-human primates to use their hands and eyes to perform various tasks. We are interested in coordination at the systems level, where saccades and reaches are encoded. The parietal reach region (PRR), situated at the posterior end of the intraparietal sulcus (IPS) and overlapping portions of the medial intraparietal area (MIP) and V6a, is commonly attributed …

Single-Molecule Super-Resolution Imaging Of Geobacter Sulfurreducens Under Anaerobic Conditions, Ziyi Hu

McKelvey School of Engineering Theses & Dissertations

Geobacter sulfurreducens are anaerobic bacteria capable of making electrical contacts with other organisms and extracellular electron acceptors. The challenge of imaging live Geobacter bacteria is maintaining anaerobic conditions during the imaging process. In this thesis, we augment a single-molecule localization microscope (SMLM) with a home-built anaerobic imaging chamber and use constant argon bubbling to maintain oxygen-free imaging conditions. To validate the imaging protocol, we use the transient binding of Nile red to resolve the spherical morphology of lipid-coated glass spheres with nanoscale resolution. However, when imaging Geobacter, the distribution of Nile red localizations is non-uniform, both between different cells …

Pathformer: Interpretable And Powerful Graph Transformer For Gene Network Analysis, Qihang Zhao, Zehao Dong, Muhan Zhang, Philip Payne, Michael Province, Carlos Cruchaga, Tianyu Zhao, Yixin Chen, Fuhai Li

McKelvey School of Engineering Theses & Dissertations

Understanding which gene/pathway expression profiles are related to specific disease phenotypes has been a critical active research area in Bioinformatics. Although graph neural networks (GNNs) have achieved impressive performance on various graph-based real-world applications such as recommendation systems and social network analysis, applying GNNs in gene-network-based Bioinformatical tasks is still challenging due to the effectiveness issue and lack of interpretation methods. In this paper, we propose PathFormer, an interpretable graph Transformer (i.e. GNN), to effectively analyze gene networks and discover meaningful biomarkers/pathways. PathFormer is composed of a stack of PathFormer encoder layers and two subsequent interpretation machines. The PathFormer encoder …

Adversarial Patch Attacks On Deep Reinforcement Learning Algorithms, Peizhen Tong

McKelvey School of Engineering Theses & Dissertations

Adversarial patch attack has demonstrated that it can cause the misclassification of deep neural networks to the target label when the size of patch is relatively small to the size of input image; however, the effectiveness of adversarial patch attack has never been experimented on deep reinforcement learning algorithms. We design algorithms to generate adversarial patches to attack two types of deep reinforcement learning algorithms, including deep Q-networks (DQN) and proximal policy optimization (PPO). Our algorithms of generating adversarial patch consist of two parts: choosing attack position and training adversarial patch on that position. Under the same bound of total …

Confined Growth Of Perovskite Stabilized By Strain Engineering, Xucheng Tao

McKelvey School of Engineering Theses & Dissertations

Halide perovskite has been extensively studied for its excellent optoelectronic properties. In this project, we want to explore some range of band gap that conventional 2D materials could not have. To overcome this challenge, we aimed to produce two-dimensional (2D) perovskites with large scale which is suitable for device fabrication and improve its stability using strain engineering. To prepare such 2D perovskite, we tried 2D transformation first and then decided to use confined growth to optimize result. For strain engineering, we employed sputtered nickel as an external stressor.

So far, we have produced multilayer polycrystalline perovskites material close to atomic …

3-Dimensional Visualization Of Cardiac Plaque Mapping Data, Phan Ly Vy Nguyen

McKelvey School of Engineering Theses & Dissertations

Atrial Fibrillation (AF) of one of the most prevalent cardiac arrythmia in humans, and also the most studied arrythmias due to its high association with cardiovascular morbidity and mortality. Diagnosis of AF, which is highly dependent on the observation of the irregular signal in the atria, is often challenging since AF is often asymptomatic at the onset. There has been a lot of effort in exploring different cardiac mapping techniques to understand the dynamics of AF for better intervention. This study aims at developing a MATLAB interface that assists the development of a cardiac plaque mapping data acquisition system in …

Development Of Methods To Enhance Stem Cell Derived Islet Survival, Aining Fan

McKelvey School of Engineering Theses & Dissertations

No abstract provided.

Synthesis And Characterization Of Sodium Cathode Materials, He Zhou

McKelvey School of Engineering Theses & Dissertations

As sodium batteries hold great promise as a next-generation energy storage device to replace lithium batteries, the development of sodium battery materials has become increasingly urgent. The current study aims to investigate two potential sodium-ion battery cathode materials, Sodium Vanadium Phosphate, and Sodium Manganese Hexacyanoferrate, optimize the experimental procedures, conduct a systematic analysis of material properties and characterization, and ultimately determine the ideal synthesis conditions for these materials.

In the first part of the study, we focused on optimizing the synthesis of Sodium Vanadium Phosphate. By investigating various synthesis conditions, such as annealing temperature, pressure, ascorbic acid content, and material …

Computational Analysis Of Steady Hypersonic Flow Fields Of Nasa Benchmark Geometries Utilizing Ansys Fluent, Aidan Murphy

McKelvey School of Engineering Theses & Dissertations

The Hypersonic International Flight Research Experimentation (HIFiRE) program explores and advances hypersonic aerospace systems by developing a multitude of test flight geometries and conducting experimental test flights to obtain data for use in validation of computational models and results. This study focuses on computational validation of heat flux, and calculation of static pressure profiles, skin friction coefficient profiles, and flow contours. The flow fields studied are for Mach number 7.18 and angles of attack (α) of 0° & 2°. These flow fields include many compressible flow features such as an expansion wave at the intersection of the cone and flat …

Analytical And Experimental Investigation Of Interphase And Dispersion Effects On The Mechanical Stiffness Of Cellulose Nanocomposites, Will Goldberg

McKelvey School of Engineering Theses & Dissertations

The effect of dispersion and interphase properties on the elastic behavior of cellulose nanocomposites was investigated using a number of composite models, experimental data and a thorough literature review. Cellulose nanocomposites consisting of soy protein isolate (SPI) and cellulose nanocrystals (CNC) or polydopamine coated cellulose nanocrystals (PD-CNC) were prepared via solution casting method and tested for mechanical stiffness. These outcomes were compared to standard composite models as well as novel methods adapted from the literature that incorporate data regarding dispersion quality and interphase properties. The literature review verified that both dispersion and interphase properties are highly dependent on interfacial chemistry …

Engineered Material Systems For Mimicking Tissue And Disease, Margrethe Ruding

McKelvey School of Engineering Theses & Dissertations

This thesis comprises two studies involving design and application of soft material systems. The goal of the first study was to design, fabricate, and characterize hydrogel lattice structures with consistent, controllable, anisotropic mechanical properties. Lattices, based on four types of unit cells (cubic, diamond, vintile, and Weaire-Phelan), were printed using stereolithography (SLA) of polyethylene glycol diacrylate (PEGDA). In order to create structural anisotropy in the lattices, unit cell design files were scaled in one direction by a factor of two in each layer and then printed. The mechanical properties of the scaled lattices were measured in shear and compression and …

Synthesis, Radiolabeling And Evaluation Of A Suite Of Tracers With 44Sc For Detecting Extracellular Dna, Zhiyao Li

McKelvey School of Engineering Theses & Dissertations

Neutrophil extracellular traps involve the rapid translocation of DNA to the outside of the cell under certain stimuli. This structure forms a fibrous network that is able to limit the spread of pathogens and to kill microorganisms. It has also been shown to be present in various pathological processes such as inflammation, autoimmune diseases, and cancer metastasis. Currently, the formation process of NETs in vivo is being extensively studied. However noninvasive detection and quantitation has yet to be achieved. A class of PET tracers are described here that consists of a DNA dye as the backbone that is labeled with …

Persistence Of Dna From Biocontained Genetically Engineered Microbes, Wentao Dai

McKelvey School of Engineering Theses & Dissertations

The utilization of genetically engineered microbes in environmental systems requires effective biocontainment mechanisms to ensure their safe operation. CRISPR-based kill switches are a promising solution, inducing cell death through site-specific DNA cleavage under specific environmental conditions. In this study, we aimed to assess the impact of CRISPR-based kill switches on the abundance and persistence of bacterial DNA. Our results revealed that while CRISPR-based kill switches were capable of achieving high reductions in viable Escherichia coli Nissle 1917 (EcN); the DNA largely remained intact. This was observed in two strains of EcN: one enabled with multi-locus genome cleavage, and the other …

Application Of Direct Simulation Monte Carlo Method To Computation Of Rf Signal Degradation During Hypersonic Flight, Andrew Derubertis

McKelvey School of Engineering Theses & Dissertations

In order to further understand the hypersonic blackout problem, the first step is to investigate models to quantify signal degradation and begin implementing these models to representative plasma sheath and flow data. This research is the first attempt at implementing a model to predict RF signal degradation through the plasma sheath surrounding the hypersonic air vehicle. The investigation is performed using a Direct Simulation Monte Carlo (DSMC) based flow solver. The dsmcFoam solver in the OpenFoam library is used to simulate the flow around hypersonic bodies to obtain flow field properties, most importantly the electron number density profile, to aid …

Comparison Of In-Vitro 3d Human Embryoids With Current Models For Gastrulation, Jin Park

McKelvey School of Engineering Theses & Dissertations

Gastrulation is an early morphogenetic process that is conserved across most metazoans and lays out the future body plan through the formation and shaping of the three germ layers: endoderm, mesoderm, and ectoderm. Despite its importance, not much is known about the events surrounding human gastrulation that occurs in utero due to ethical and technical limitations on studying human embryos. Therefore, many researchers have devised protocols for creating in vitro models of gastrulation using embryonic stem cells. Initially starting with mouse embryonic stem cells, the field of in vitro embryo models has advanced rapidly, with protocols using human embryonic stem …