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Multiscale Molecular Modeling Studies Of The Dynamics And Catalytic Mechanisms Of Iron(Ii)- And Zinc(Ii)-Dependent Metalloenzymes, Sodiq O. Waheed

Dissertations, Master's Theses and Master's Reports

Enzymes are biological systems that aid in specific biochemical reactions. They lower the reaction barrier, thus speeding up the reaction rate. A detailed knowledge of enzymes will not be achievable without computational modeling as it offers insight into atomistic details and catalytic species, which are crucial to designing enzyme-specific inhibitors and impossible to gain experimentally. This dissertation employs advanced multiscale computational approaches to study the dynamics and reaction mechanisms of non-heme Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases, including AlkB, AlkBH2, TET2, and KDM4E, involved in DNA and histone demethylation. It also focuses on Zn(II) dependent matrix metalloproteinase-1 (MMP-1), which helps …

Information Use And Decision-Making For Evacuation At Fuego Volcano, Guatemala, Beth A. Bartel

Dissertations, Master's Theses and Master's Reports

For populations living with risk to rapid-onset environmental hazards, an effective early warning system (EWS) may be the most viable short- to mid-term solution for risk reduction. At Fuego volcano, Guatemala, more than 60,000 people distributed between more than 30 small communities live within the identified hazard zones for pyroclastic density currents (PDCS), highly lethal hot avalanches and surges of volcanic gases, rock, and ash. Despite ongoing risk reduction efforts by scientific and civil protection authorities, more than 400 people died during a paroxysmal eruption on 3 June 2018 when PDCs reached populated areas. A high-end resort, La Reunión, evacuated …

An Exploration Of Cloud Droplet Growth By Condensation And Collision-Coalescence In A Convection-Cloud Chamber, Jacob T. Kuntzleman

Dissertations, Master's Theses and Master's Reports

Atmospheric clouds are crucial to weather and climate, and the rate at which droplets collide and coalesce to form precipitation is one of the fundamental controlling processes. The convection-cloud chamber allows the interactions between aerosols and cloud droplets produced by condensation to be investigated within a turbulent environment. Studying the full range of microphysical conditions in atmospheric clouds is not possible, however, unless conditions for droplet growth by collision and coalescence are also achieved. In this study, we explore the conditions favorable to collision-coalescence growth in convection-cloud chambers, extending previous work on steady-state droplet size distributions due to condensation alone. …

Microscopic And Laboratory Scale Characterization Methods To Evaluate Biomass Deconstruction, Meenaa Chandrasekar

Dissertations, Master's Theses and Master's Reports

Renewable fuels from lignocellulosic biomass are an appealing option because they can seamlessly integrate into the existing fuel distribution infrastructure. Lignocellulosic biomass constitutes nonedible plant material obtained from plant cell walls. The natural recalcitrance of lignocellulosic biomass poses a challenge in accessing the cell wall carbohydrates during biochemical conversion. Despite various approaches, enzymatic hydrolysis of lignocellulosic biomass remains economically impractical due to incomplete knowledge about biomass recalcitrance and the influence of environmental factors on biomass quality.

The first goal of this dissertation was to construct a microfluidic imaging reactor to better understand the tissue-specific deconstruction of plant materials. Confocal laser …

Prediction Of Sumoylation Sites In Proteins From Language Model Representations, Evgenii Sidorov

Dissertations, Master's Theses and Master's Reports

Sumoylation is an essential post-translational modification intimately involved in a diverse range of eukaryotic cellular mechanisms and plays a significant role in DNA repair. Some researchers hypothesize that a high level of SUMOylation events in cancer cells improves cells' chances for survival under stress conditions by regulating tumor-related proteins.

This study belongs to a booming field of harnessing computational power to the domain of life. Prediction of protein structure, its molecular function, and the design of new drugs are just a few examples of the applications within this exciting area of research. By leveraging computational power, researchers can analyze vast …

Integrating Lidar, Aeromagnetic, And Geological Field Data To Identify Structural-Lithologic Elements Within The Archean Carney Lake Gneiss Complex, Ian M. Gannon

Dissertations, Master's Theses and Master's Reports

The Archean Carney Lake Gneiss Complex (CLGC) is a suite of rocks on the southern margin of the Superior Province and within the Minnesota River Valley subprovince. It is one of many gneissic domes in Michigan, Wisconsin, and Minnesota whose complex geology is poorly understood due to a previous lack of economic interest in gneissic terranes and significant challenges to their investigation. As a consequence, the CLGC and other gneissic domes in the region are represented on geologic maps as undifferentiated masses surrounded by better defined and understood Paleoproterozoic supracrustal rocks and igneous intrusions. Within the last ten years, however, …

Impacts Of Introduced Earthworms On Sugar Maple Sap Chemistry And The Discourse Of Invasion Ecology, Shelby Nicole Lane-Clark

Dissertations, Master's Theses and Master's Reports

To delve into further understanding of the relationships between introduced earthworms, forest ecosystems, and the human systems they impact, two approaches were taken. In the first approach, we seek to explore ways we can shift the discourse within and regarding the field of invasion ecology by re-framing how we approach discussion, management, and education regarding introduced species. Language issues surrounding introduced species through the example of earthworms in North America are described and potential solutions are provided, including a repositioned perspective that may facilitate better relationships with the natural world. The goal is to shift the language to be more …

Fine Root Respiration In Quercus Rubra Is Influenced By Multidimensional Trade-Offs In Root Trait Space, Emma L. Shedd

Dissertations, Master's Theses and Master's Reports

Economic theory is often applied to plant strategies, arguing that trade-offs exist between maximizing quick returns on investment within short lifespans or producing longer-lived tissues with slower returns. While these trade-offs are well-studied aboveground, their influence on belowground traits, including root respiration, remains unclear. Resource heterogeneity and symbioses with mycorrhizal fungi may complicate root trade-off axes beyond those predicted by economics theory alone. Investigating fine root trade-offs in Quercus rubra populations along a latitudinal gradient in the Midwest, USA, we identified two distinct axes of variation in root traits: one related to a potential “fungal symbiosis” trade-off and another representing …

Near-Surface Soil Nitrogen And Vegetation Response To Invasive Emerald Ash Borer In Forested Black Ash Wetlands Of The Western Upper Peninsula, Michigan, Usa, Daniel A. Beyer

Dissertations, Master's Theses and Master's Reports

Invasive emerald ash borer (EAB) (Agrilus planipennis Fairmaire) poses an imminent threat to the structure and function of North American hardwood forests, particularly black ash (Fraxinus nigra Marshall), and alters the hydrologic and ecological services of their wetlands. Black ash trees regularly grow in seasonally saturated soils and are responsible for hydrologic regulation and nutrient cycling. In this study, a gradient of black ash wetlands impacted by EAB were monitored to assess vegetation changes and near-surface soil nitrogen availability. Vegetation community changes were intertwined with nitrogen cycle disturbances following EAB infestation. As black ash died and fell to …

Uhplc/Ft-Ms Non-Targeted Screening Approach For Biomass Burning Organic Aerosol And Liquid Smoke As Biomass Burning Organic Aerosol Surrogate, D.M.R. Thusitha Dinusha Kumarihami Divisekara

Dissertations, Master's Theses and Master's Reports

Biomass combustion contributes a large amount of aerosol particles to the atmosphere impacting the climate system and human health. Identifying the molecular composition of biomass burning organic aerosol (BBOA) is challenging because of its complex nature. Liquid chromatography mass spectrometric non-targeted screening (NTS) methods provide a comprehensive analysis. However, the instrumentation and data analysis are challenging due to the extreme complexity of environmental samples. In the first part of this study, we implemented a new LC/FT-MS data processing approach by combining existing open-source data processing tools, MZmine2.53 and MFAssignR. The method's validity was checked using the standard polyacrylic acid (PAA) …

Remote Sensing Approach For Terramechanics Applications Utilizing Machine And Deep Learning, Jordan J. Ewing

Dissertations, Master's Theses and Master's Reports

Terrain traversability is critical for developing Go/No Go maps, significantly impacting a mission's success. To predict the mobility of a vehicle over a terrain, one must understand the soil characteristics. In situ measurements performed by soldiers in the field are the current method of collecting this information, which is time-consuming, are only point measurements, and can put soldiers in harm's way. Therefore, this study investigates using remote sensing as an alternative approach to characterize terrain properties.

This approach will explore the relationships between electromagnetic radiation and soil types with varying properties. Optical, thermal, and hyperspectral sensors will be used to …

Rain-Induced Hazards In Remote, Low-Resource Communities: A Case Study Of Flash Flooding In The Usulután Department, El Salvador, Natalea Cohen

Dissertations, Master's Theses and Master's Reports

Rain-induced natural hazards can lead to devastating and potentially life-threatening impacts. Understanding areas susceptible to flash flooding and characterizing the intensity of flash flood events is critical in improving the mitigation and emergency preparedness of vulnerable communities. Flash floods occur on small spatial scales and for short durations making it challenging to classify flash flood susceptibility and forecast events. Modeling flash flooding becomes even more difficult when focusing on data-poor regions. This study is based in California, El Salvador, an agricultural community located in the Central American Dry Corridor (CADC), a region experiencing the impacts of climate change and associated …

The Art And Science Of Wood: From Pyrography To Termites And Wood Decomposition, Joanna D. Walitalo

Dissertations, Master's Theses and Master's Reports

Wood is vital to many natural ecosystems, as it provides energy, nutrients, and habitat for organisms from the micro- to the macro- scale. Wood is also critical to humans for similar reasons, and can be an important medium of art and education. This dissertation addresses three diverse aspects of wood with the contexts of science, art, and education. First, we explored the impact of timber harvest techniques and site preparation on microbial wood decay and subterranean termite responses on a forest-stand scale. The amount of coarse woody debris removed post-harvest, coupled with the location and species of the test wood …

Sequencing Antisense Transcriptome Of Populus Through Antisense/Sense Transcript Pair Enrichment, Emma V. Burke

Dissertations, Master's Theses and Master's Reports

Past transcriptome research on plants focused primarily on protein coding genes, and only recently researchers began looking into the non-protein coding regions that may play significant roles in gene regulation. Antisense RNA transcripts that are found naturally in the cell share complementary sequence with sense transcripts and have been shown to regulate expression of their sense counterparts. Since antisense RNA has been largely under-studied and difficult to sequence because of their low relative abundance, new methods are needed to target antisense RNA for efficient genome-wide profiling. To address this gap in methods to efficiently and cost effectively enrich antisense RNA …

Study Of Nanocomposite Materials Using Molecular Dynamics, Prashik Sunil Gaikwad

Dissertations, Master's Theses and Master's Reports

There is an increase in demand for new lightweight structural materials in the aerospace industry for more efficient and affordable human space travel. Polymer matrix composites (PMCs) with reinforcement material as carbon nanotubes (CNTs) have shown exceptional increase in the mechanical properties. Flattened carbon nanotubes (flCNTs) are a primary component of many carbon nanotube (CNT) yarn and sheet materials, which are promising reinforcements for the next generation of ultra-strong composites for aerospace applications. These flCNT/polymer materials are subjected to extreme pressure and temperature during curing process. Therefore there is a need to investigate the evolution of properties during the curing …

Knowledge Discovery On The Integrative Analysis Of Electrical And Mechanical Dyssynchrony To Improve Cardiac Resynchronization Therapy, Zhuo He

Dissertations, Master's Theses and Master's Reports

Cardiac resynchronization therapy (CRT) is a standard method of treating heart failure by coordinating the function of the left and right ventricles. However, up to 40% of CRT recipients do not experience clinical symptoms or cardiac function improvements. The main reasons for CRT non-response include: (1) suboptimal patient selection based on electrical dyssynchrony measured by electrocardiogram (ECG) in current guidelines; (2) mechanical dyssynchrony has been shown to be effective but has not been fully explored; and (3) inappropriate placement of the CRT left ventricular (LV) lead in a significant number of patients.

In terms of mechanical dyssynchrony, we utilize an …

Changes In Poplar Digestibility Due To Overexpression Of Laccase Genes, Fnu Arunima

Dissertations, Master's Theses and Master's Reports

Woody biomass, particularly poplar, is a sought-after feedstock for lignocellulosic biofuels because of its year-round availability and high productivity. Because of cell wall components like lignin, poplar is inherently resistant to enzymatic saccharification. The experiment aims to determine whether the controlled overexpression of laccase genes alters the biomass composition and whether it can create poplar that is more digestible than the wildtype.

Three sets of transgenic poplar (Populus tremula x alba) samples were evaluated: laccase 18, laccase 27, and STTM. Laccase 18 samples, an target of miRNA397a was overexpressed along with Laccase 27. Short Tandem target Mimic (STTM) technology …

Treating Contaminated Water: Predicting Reactivities Of Aqueous Organic Contaminants With Hydrated Electrons, And Development Of A Biogarden To Manage Greywater Discharge In Monteverde, Costa Rica, Rose C. Daily

Dissertations, Master's Theses and Master's Reports

Advanced reduction processes (ARPs) that generate highly reactive solvated electrons (e^-_aq) are a promising method for the destruction of conventional and emerging aqueous organic contaminants. While there is a large database of contaminant reactivity with e^-_aq in the literature, there is little information on the detailed elementary mechanisms for reduction of multifunctional group compounds and the impact of those functional groups on reactivity. As it is difficult to determine specific mechanisms through experiments and time consuming to measure reactivity, the development of computational approaches to elucidate mechanisms and predict reactivity is becoming increasingly important. In …

Comprehensive Analysis Of Seismic Signals From Pacaya Volcano Using Deep Learning Event Detection, Jessica L. Devlieg

Dissertations, Master's Theses and Master's Reports

Pacaya volcano located 30 km SW of Guatemala City, Guatemala, has been erupting intermittently since 1961. Monitoring of seismicity is crucial to understanding current activity levels within Pacaya. Traditional methods of picking these small earthquakes in this noisy environment are imprecise. Pacaya produces many small events that can easily blend in with the background noise. A possible solution for this problem is a machine learning program to pick first arrivals for these earthquakes. We tested a deep learning algorithm (Mousavi et al., 2020) for fast and reliable seismic signal detection within a volcanic system. Data from multiple deployments were used, …

Explicit Rule Learning: A Cognitive Tutorial Method To Train Users Of Artificial Intelligence/Machine Learning Systems, Anne Linja

Dissertations, Master's Theses and Master's Reports

Today’s intelligent software systems, such as Artificial Intelligence/Machine Learning systems, are sophisticated, complicated, sometimes complex systems. In order to effectively interact with these systems, novice users need to have a certain level of understanding. An awareness of a system’s underlying principles, rationale, logic, and goals can enhance the synergistic human-machine interaction. It also benefits the user to know when they can trust the systems’ output, and to discern boundary conditions that might change the output. The purpose of this research is to empirically test the viability of a Cognitive Tutorial approach, called Explicit Rule Learning. Several approaches have been used …

Has Bollywood Lost The Plot? Analyzing The Influence Of Item Songs On Rape Culture In India, Donna Susan Mathew

Dissertations, Master's Theses and Master's Reports

An item song is a provocative musical song and dance sequence that appears in Bollywood films that have little to no connection to the film’s plot, performed by an item girl for the male gaze. Contemporary Bollywood item songs have become highly contested social and political texts in the discourse surrounding rape culture in India. This research explores the socio-cultural context of rape culture in India and examines what makes item songs a popular and acceptable form of entertainment in a patriarchal, conservative society where sexualized violence against women is a major cause for concern.

The study also addresses the …

Collagen V Promotes Fibroblast Contractility, And Adhesion Formation, And Stability, Shaina P. Royer-Weeden

Dissertations, Master's Theses and Master's Reports

Ehlers-Danlos syndrome, classical type, (cEDS) is a hereditary connective tissue disorder causing excessive elasticity and fragility of the connective tissue and problems with wound healing. Most cases of cEDS are caused by haploinsufficiency for collagen V. Collagen V regulates collagen fibril diameter. In cEDS fibroblast migration is impaired and integrin expression is altered.

The effects of collagen V on collagen gel ultrastructure and how it alters its mechanical properties were measured using scanning electron microscopy (SEM) and rheology respectively. Fibroblast contractility and adhesion dynamics were investigated to better understand the role of fibroblast disfunction in wound healing in cEDS. To …

White-Tailed Deer In A Winter-Wonderland: Long-Term Deer Yard Use And Methodological Considerations For Ungulate Fecal Dna Metabarcoding, Melanie A. Ottino

Dissertations, Master's Theses and Master's Reports

Northern white-tailed deer (Odocoileus virginianus) mitigate the increased energetic costs of severe winter conditions through obligate migration to densely congregated areas with abundant conifer cover, a behavior referred to as yarding. “Deer yards” in the Western Upper Peninsula (UP) of Michigan are principally located within the reduced snowpack and increased ambient temperature microclimates of densely canopied eastern hemlock (Tsuga canadensis) stands, but specific drivers of long-term site fidelity and utilization are largely uncharacterized. As an important game species of high economic and cultural value and a keystone herbivore with critical impact of plant community composition and structure, identifying winter yarding …

Advancing Vehicular Communication Systems: An Evolution From Dsrc To 5g Nr C-V2x Technology For Enhanced Safety, Reliability, And Efficiency In Intelligent Transportation Systems, Mehnaz Tabassum

Dissertations, Master's Theses and Master's Reports

This work focuses on the evolution of connected vehicles communication technologies and performance evaluation of vehicular communication systems, specifically in the context of Cellular Vehicle-to-Everything (C-V2X) technology and the Third Generation Partnership Project (3GPP) specifications. The dissertation also discusses the evolution of vehicle communication systems from Dedicated Short-Range Communication (DSRC) through 5G technologies. It examines the motivation for this shift, which are the growing demand for transportation safety, low latency, high data rate, low energy use, and seamless inter connectivity. The research delves into the greater capabilities and improved performance that 5G offers for direct V2V communications by analyzing the …

Design And Implementation Of A Graphql Mesh Gateway: Federating Api Endpoints Based On A Defined Data Model, Marcus D. Scese

Dissertations, Master's Theses and Master's Reports

This paper introduces the GraphQL Mesh federated API (Application Programming Interface) gateway project, a comprehensive initiative implemented using GraphQL Mesh to solve data related issues within the USW-DSS (Undersea Warfare - Decision Support System). The project contributes to the evolving discourse on the pivotal role of Data Fabrics and Data Meshes in dismantling the barriers imposed by digital data silos. The project is a collaboration between researchers at Michigan Technological University, and engineers at ARiA (Applied Research in Acoustics LLC). The aim of the project is to resolve difficulties in understanding a large collection of API endpoints. By navigating the …

Development And Verification Of Automated Fixtures For Functional Testing Of Space Grade Printed Circuit Board Assemblies, Nicholas A. Wylie

Dissertations, Master's Theses and Master's Reports

Orbion Space Technology is a developer and manufacturer of electric propulsion systems for military and commercial spacecraft. Orbion’s products include a Power Processing Unit (PPU) which is utilized for power and control of the satellite propulsion system. These PPUs are complex electro-mechanical assemblies that include multiple Printed Circuit Board Assemblies (PCBA) and are built to IPC standards. To ensure smooth fabrication and to reduce the risk of complications from in-process rework of PCBAs, comprehensive electrical functional testing at the board-level is required before higher- level assembly. Electrical functional testing provides verification of quality, workmanship, and manufacturing defects of the PCBAs. …

Two Research Perspectives On Sugar Maple Canopy Dieback In The Upper Great Lakes: A Decade Of Herbaceous Community Responses And A Survey Of Michigan Forest Managers, Manuel Eduardo Anderson

Dissertations, Master's Theses and Master's Reports

Sugar maple canopy dieback has been reported in the upper Great Lakes since the mid-2000s. This thesis builds on research conducted to determine some of the underlying causes of canopy dieback, which include invasive earthworm impacts, with a view toward adaptations in management of northern hardwood forests in our region. The first chapter reports a study of understory communities in a subsection of forest health monitoring plots located in four national forests near Lake Superior. Based on plot assessments from 2010 and 2021, responses of plant community composition and traits to earthworm impacts and sugar maple canopy dieback were explored. …

On The Gaussian-Core Vortex Lattice Model For The Analysis Of Wind Farm Flow Dynamics, Apurva Baruah

Dissertations, Master's Theses and Master's Reports

Wind power science has seen tremendous development and growth over the last 40 years. Advancements in design, manufacturing, installation, and operation of wind turbines have enabled the commercial deployment of wind power generation systems. These have been due, in a large part, to the expertise in the simulation and modeling of individual wind turbines. The new generation of wind energy systems calls for a need to accurately predict and model the entire wind farm, and not just individual turbines. The commercial deployment of these wind farms depends on model's ability to accurately capture the different physics involved, each at its …

Memory Optimizations For High-Throughput Computer Systems, Zhiyuan Lu

Dissertations, Master's Theses and Master's Reports

The emergence of new non-volatile memory (NVM) technology and deep neural network (DNN) inferences bring challenges related to off-chip memory access. Ensuring crash consistency leads to additional memory operations and exposes memory update operations on the critical execution path. DNN inference execution on some accelerators suffers from intensive off-chip memory access. The focus of this dissertation is to tackle the issues related to off-chip memory in these high performance computing systems.

The logging operations, required by the crash consistency, impose a significant performance overhead due to the extra memory access. To mitigate the persistence time of log requests, we introduce …

An Investigation Of Microseismicity During The 2018 Kilauea Caldera Collapse, Isabella S. Metts

Dissertations, Master's Theses and Master's Reports

The 2018 Kīlauea volcano eruption and incremental caldera collapse was accompanied by more than 60,000 seismic events cataloged by the Hawaiian Volcano Observatory as well as 62 caldera collapse events that occurred roughly once per day. The majority of seismicity occurred on the eastern side of the caldera between daily collapses. However, the majority of caldera subsidence occurred to the west. To understand the collapse mechanics behind this variance in subsidence and seismicity across the caldera region, repetitive waveforms and source properties can be studied.

Repeating seismic events suggest a common source that is not moving or destroyed. At Kīlauea, …