Physical Sciences and Mathematics Commons^™

Exploring The Impact Of Pretrained Bidirectional Language Models On Protein Secondary Structure Prediction, Dillon G. Daudert

Masters Theses

Protein secondary structure prediction (PSSP) involves determining the local conformations of the peptide backbone in a folded protein, and is often the first step in resolving a protein's global folded structure. Accurate structure prediction has important implications for understanding protein function and de novo protein design, with progress in recent years being driven by the application of deep learning methods such as convolutional and recurrent neural networks. Language models pretrained on large text corpora have been shown to learn useful representations for feature extraction and transfer learning across problem domains in natural language processing, most notably in instances where the …

Deep Reinforcement Learning For Autonomous Search And Rescue, Juan Gonzalo Cárcamo Zuluaga

Masters Theses

Unmanned Aerial Vehicles (UAVs) are becoming more prevalent every day. In addition, advances in battery life and electronic sensors have enabled the development of diverse UAV applications outside their original military domain. For example, Search and Rescue (SAR) operations can benefit greatly from modern UAVs since even the simplest commercial models are equipped with high-resolution cameras and the ability to stream video to a computer or portable device. As a result, autonomous unmanned systems (ground, aquatic, and aerial) have recently been employed for such typical SAR tasks as terrain mapping, task observation, and early supply delivery. However, these systems were …

Use Of Fluorescein Dye For Characterizing Water And Solute Flux Across The Groundwater – Surface Water Interface, Ryan Nicholas Cascarano

Masters Theses

Quantifying groundwater discharge across the sediment—surface water interface remains a challenge due to streambed heterogeneity and the integration of disparate measurements over a continuum of spatial and temporal scales. In this study, mini-piezometers are first used to identify areas of groundwater discharge in lakes and streams, and micro-pulses of fluorescein dye are released at precisely known shallow depths as a conservative tracer. The use of fluorescein dye allows for visual dye detection regardless of light conditions, and measurements of dye concentrations over time using a fluorometer are used to generate high resolution breakthrough curves. Accurate determination of groundwater velocity and …

Computational Study Of The Nature Of Tetrel Bond, Yama Aman

Masters Theses

For more than a hundred years, the type of a chemical bond has been distinguished according to the relative electronegativities of chemical units at the ends of a bond. Whereas, the bond of unequally electronegative on both ends is called a polar covalent or even ionic bond or a non-polar covalent bond in case of both equal. Regardless the type of bonded elements, the whole idea for the bond was believed to be electron driven only. In the 20th century the development of the idea, that not just the electronic relation but specific elements are also able to characterize the …

An Investigation Of Sub-Meter Skill In Stem And Non-Stem Undergraduate Students, Laura A. Tingin

Masters Theses

This study designed a nationally-relevant, valid, and reliable survey that measures STEM and Non-STEM undergraduate student familiarity with sub-meter metric scale and common sub-meter sized science objects. The instrument assesses scalar relationship and scalar magnitude, as explained by Cheek, LaDue, and Shipley (2017). The instrument development was based on an existing Scale of Objects Questionnaire (SOQ) instrument created by Tretter, Jones, Andre, Negishi, & Minogue (2006a) which was modified to be nationally relevant and in an electronic format in two phases: online survey development and undergraduate pilot testing. Online survey development was framed in the tailored design method described by …

Spatio-Temporal Variability Of Precipitation And Drought In The State Of Arizona, Usa, Samuel Nimako Nyarkoh

Masters Theses

As a result of climate change, several dry regions continue to get drier as precipitation amounts decline. This decline impact water resources and hinder economic development. Understanding the variability of precipitation and drought through climatic, agricultural and hydrological studies is therefore critical to decision makers and stakeholders in developing proactive measures that promotes economic development.

This study therefore uses dataset from 55 Meteorological stations containing 110-year (1900-2010) monthly precipitation data and a series of spatial and temporal tests to investigate the spatial and temporal patterns of precipitation and drought as well as the effects of local factors such as topography …

Synthesis And Characterization Of Fluorescent Nanojars, Vageesha Warnajith Liyana Gunawardana

Masters Theses

Self-assembly is a powerful tool utilized by synthetic chemists to create large, intricate structures for a variety of applications such as drug delivery, adaptable materials and electronics. In contrast to stepwise synthesis, this process allows the formation of intricate molecular architectures starting from synthetically rudimentary building blocks. Nanojars are class of self-assembling, cyclic copper(II) pyrazolate coordination compounds that encapsulate oxoanions with negative two or three charge. The strong anion binding characteristics of nanojars have potential towards developing novel tools for detecting biologically and environmentally relevant anions such as carbonate, sulfate and phosphate.

This work addresses the design and synthesis of …

Application Of Handheld Ed-Xrf For High-Resolution Chemostratigraphy In Texturally Homogeneous Carbonate Mudstones: Salina A-1 Carbonate (Silurian), Michigan Basin, Matthew A. Hemenway

Masters Theses

Handheld energy dispersive x-ray fluorescence spectrometry (ED-XRF) is routinely used to observe elemental variability in fine-grained siliciclastics but has been applied rarely in fine-grained carbonates. Here, ED-XRF chemostratigraphy is utilized in the texturally homogenous, mudstones of the Silurian A-1 Carbonate (A-1C), Michigan Basin. Previous studies on the A-1C focused on the stratigraphic relationship with the underlying Niagaran reefs, so little is known about the geological variability in the basin center. In this study, high-resolution elemental data from nine cores were integrated with petrographic and mineralogical observations to evaluate two hypotheses: (1) Texturally homogeneous, basin-center mudstones in the A-1C have spatially …

Peer Attention Modeling With Head Pose Trajectory Tracking Using Temporal Thermal Maps, Corey Michael Johnson

Masters Theses

Human head pose trajectories can represent a wealth of implicit information such as areas of attention, body language, potential future actions, and more. This signal is of high value for use in Human-Robot teams due to the implicit information encoded within it. Although team-based tasks require both explicit and implicit communication among peers, large team sizes, noisy environments, distance, and mission urgency can inhibit the frequency and quality of explicit communication. The goal for this thesis is to improve the capabilities of Human-Robot teams by making use of implicit communication. In support of this goal, the following hypotheses are investigated: …

Synthesis And Evaluation Of Acetylcholine Molecularly Imprinted Polymers, Nathaniel Donald Thiemann

Masters Theses

Polymers imprinted with acetylcholine during synthesis were prepared in order to evaluate their potential for implementation as a novel recognition element in acetylcholine biosensors. Biosensors, such as the glucose monitor, are used to rapidly detect and quantify a target analyte. Acetylcholine biosensors have already been produced using enzymatic recognition elements, but they are currently expensive and plagued by short viability. Molecularly imprinted polymers are not only cheap and durable, but have also been successfully used as a recognition element in biosensors for other analytes. Therefore, computational tools were used to rationally design acetylcholine molecularly imprinted polymers. Three chemicals, itaconic acid, …

Mapping Bedrock Topography Of The Portage And Schoolcraft Nw 7.5’ Quadrangles, Kalamazoo Co. Mi, Using The Hvsr Passive Seismic Method, Benjamin B. Seiderman

Masters Theses

This study utilizes the Horizontal to Vertical Spectral Ratio (HVSR) technique to map bedrock topography in the Portage and Schoolcraft NW quadrangles, Kalamazoo Co., MI, looking for buried bedrock valleys. Glacial sediment-landform assemblages dominate the study area, due to multiple advances of the Laurentide Ice Sheet (LIS). Tunnel valleys, which are one type of buried valley, are eroded by subglacial meltwater and commonly filled with the coarser varieties of glacial outwash, making them potential aquifers. The HVSR technique measures the ratio of horizontal to vertical ground motion, excited by ambient seismic noise, resulting in a peak at the resonance frequency. …

A Survey Of Security And Privacy In Mobile Cloud Computing, Bhuvaneswari Rayapuri

Masters Theses

Cloud Computing is an emerging technology that provides shared processing resources and data to computers and other devices on demand. On the other hand, Mobile Computing allows transmission of data, voice and video. From these two there emerges a new concept Mobile Cloud Computing which not only overcomes the problems of Mobile Computing but also integrates Cloud Computing into Mobile Environments to overcome obstacles related to Performance, Security and Environment. This paper also provides a decent description on Security and Privacy, its related problems, threats and challenges. This paper first provides details on survey of Mobile Cloud Computing, then it …

Determinants Of Household Water Use In The City Of Kalamazoo, Michigan: The Role Of Climate And Socioeconomic Factors, Danielle Molenaar

Masters Theses

Located in the Great Lakes Watershed, the City of Kalamazoo can be considered “water rich”. Therefore, the area has been absent from water use studies. Water use studies are beneficial in all locations; as they can aid city planners, water resource managers, and utility companies. This study examines how household monthly water use in the City of Kalamazoo is impacted by both climate and socioeconomic variables over the period 2006-2016. Household level data were aggregated into census tracts to obtain monthly tract averages for the eleven-year period. Ordinary least squares regression (OLS) was used to determine which variables impact the …

Interannual Variations Of Snowfall In The Lower Peninsula Of Michigan And Impacts Of Local And Remote Meteorological Conditions, Nirjala Koirala

Masters Theses

Inter-annual variation of snowfall and its relation to climate indices will help clarify and improve the prediction of total snowfall in the Lower Peninsula of Michigan (LPM). This study examines the trend and variability of annual snowfall (November- March) using 8 homogeneous weather stations in the LPM. The statistical relationship between snowfall and air temperature, Sea Surface Temperature (SST), North Atlantic Oscillation (NAO), Pacific Decadal Oscillation (PDO) and Maximum Ice Coverage(MIC) of Lake Michigan is calculated. The long-term trend in the snowfall data set from 1950 to 2015 is removed before any statistical correlation analysis is conducted. My analysis suggests …

Geologic Mapping Of The Bronson North And Bronson South 7.5-Minute Quadrangles, Branch County, Michigan, Karl John Backhaus

Masters Theses

This study contributes to a better understanding of the glacial history of southwest Michigan through detailed surficial geologic and bedrock topography mapping within the Bronson North and Bronson South Quadrangles in Branch County, Michigan. This project was supported during the summer of 2017 by the USGS EDMAP program in conjunction with the Michigan Geological Survey. Hand-auger borings, grain size analysis tests, passive seismic depth-to-bedrock measurements, and ground penetrating radar transects were collected for this study. There are 350 feet of bedrock relief from west to east across the quadrangles, including a bedrock cuesta of Mississippian Coldwater Shale. This cuesta underlies …

Organocatalyzed Synthesis Of Epoxides From Chalcones Utilizing Amino Acids, Sabrina N. Kegeler

Masters Theses

The epoxide functional group is important throughout the chemical and pharmaceutical industries, as well as in nature. In the chemical industry, epoxides are present in resins and fragrances. In the pharmaceutical industry, epoxide-containing compounds are used as intermediates in the manufacturing of drugs. In nature, many natural products contain epoxide groups and are used for medicinal purposes, and for models to create synthetic molecules.

One approach to epoxide synthesis involves the use of an alkene precursor, a base, and an oxidizing agent. This is where my investigations began. The first step was to optimize the epoxidation reaction, examining substrate scope, …

Geochemical And Petrological Investigation Of The Prospective Ni-Cu-Pge Mineralization At The Echo Lake Intrusion In The Upper Peninsula Of Michigan, Usa, Alexander J. Koerber

Masters Theses

The Echo Lake Intrusion is located in Houghton and Ontonagon counties in the Upper Peninsula (UP) of Michigan. The intrusion is approximately 200 m below the surface and covers approximately 18 km2 in lateral extent. It is associated with the magmatic activities of a 1.1 Ga geologic event called the Midcontinent Rift. The rift is responsible for the formation of Ni-Cu ± PGE deposits in the Lake Superior Region. Based on its association with the Midcontinent Rift and a Cu and PGE enriched layer, the Echo Lake intrusion is identified as a prospect for an economic magmatic sulfide deposit.

The …

Research And Development Of Optically Transparent Join With Low Processing Temperatures, Eric Kevin Muskovin

Masters Theses

The purpose of this study was to investigate durable solar cell cover glass joins produced by diffusion bonding with deep eutectic solvents (DES) and to develop a novel process of joining optically transparent materials at low temperatures. A joined PV cell-glass specimen was characterized using Raman, μ-FTIR, SEM-EDS, and thin-film XRD. DESs were created with malonic acid (MAL) and choline chloride (ChCl) of varying composition factors (CF; CF=MAL/ChCl). Joining borosilicate glass coupons was attempted using DESs with CF = 0.65 and 1 at temperatures between 100-150 °C for 20 hours. Joining the glass coupons failed at all temperatures and oxygen …

Co-Product Potential Of Algae Biocake, Elizabeth J. Nixon

Masters Theses

Society needs to find replacements for fossil fuels, which are finite resources that may be fully depleted within a few generations. While solar and wind have great potential as alternative energy sources, they are unlikely to completely replace all of the current fuel sources, particularly liquid fuels. Plant biomass has great potential for this market, and is already used in many forms for heat energy (e.g. direct combustion). However, the bulk density of important bioenergy crops, particularly grasses, is often low, which necessitates the use of binders in densification strategies. In the present study, waste algae biocake from a proprietary …

Imaging The Subsurface In Eastern Part Of Lake Chesterfield Using A Combination Of Geophysical Tools, Jiawei Li

Masters Theses

"The Lake Chesterfield North Dam in Wildwood city, Missouri has been leaking, more or less continuously since the dam was constructed in 1986 despite mitigation efforts in 1988, 1994, 1995, 2004, and 2005. Neither the grouting efforts in 1988, 1994, 1995, 2004 or 2005, nor the placement and rehabilitation of an impervious clay liner in 2005 has solved the problem. Indeed, in June of 2017, the water level in Lake Chesterfield dropped at an alarmingly rapid rate.

Prior to authorizing additional mitigation work, the Lake Chesterfield Home Owners Association (LCHOA) decided to acquire geophysical data across the dry lake bed. …

Impact Of Temperature Increase On Freshwater Fish Species: Energetics And Muscle Mechanics Of Two Centrarchids, Israt Jahan

Masters Theses

Fishes have evolved physiologically to live within a specific range of environmental variation and existence outside of that range can be stressful or fatal. These ranges can coincide for fishes that evolved in similar habitats. This study investigates physiological processes limiting thermal tolerance, specifically how changes in water temperature affect the swimming energetics and muscle mechanics in largemouth bass (Micropterus salmoides) and bluegill (Lepomis macrochirus). I focused on the impact of temperature change at the muscle level in these two species and the capacity to adapt to rapid changes in the environment. Fish were housed at …

Pd-Based Photocatalysts For Sonogashira C-C Cross-Coupling Reactions, Komadhie Charuka Dissanayake

Masters Theses

Sonogashira C-C cross-coupling reaction has been heavily used for its simplicity, flexibility and value. Although the original Sonogashira C-C cross coupling reaction conditions entail the use of 0.5 mol% of Pd catalyst, 2 mol% of Cul as co-catalyst at room temperature, the experimental conditions used in laboratories to prepare some compounds vary substantially, especially with respect to the reaction time, temperature and loading amount of the catalysts. The most significant drawback of the conventional Sonogashira reaction is the use of Cul as it leads to the formation of homocoupling product when the reaction is exposed to air or oxidizing agents. …

Processing Different Mixtures Of Regionally Available Resources To Create Pellets That Meet A Minimum Standard, Jacob Hixson

Masters Theses

There are several ways to produce energy today, one of the oldest is the gasification of biomass. This process uses a fire to heat the material until it starts to produce gasses that are used as fuel. There are several types of biomass that can be used, many of which have large pieces with low bulk densities. By pelletizing the biomass bulk density increases and allows the opportunity to add in other biomass materials.

There are standards for condensing large pieces of biomass to smaller pelletized materials. Pellet Fuels Institute has set minimum standards for pellets used in the different …

Defense In Depth Network Perimeter Security, Anuoluwapo Ope Fatokun

Masters Theses

Defense in depth network perimeter security has always be a topic of discussion for a long time as an efficient way of mitigating cyber-attacks. While there are no 100% mitigating method against cyber-attacks, a layered defense in depth network perimeter security can be used to mitigate against cyber-attacks. Research have shown a massive growth in cyber-crimes and there are limited number of cyber security expert to counter this attacks. EIU as an institution is taking up the responsibility of producing cyber security graduates with the new Master of Science in Cyber Security program that started in Fall 2017.

This research …

Synthesis And Characterization Of Biomimetic Dinuclear And Tetranuclear Copper Complexes, Syed Rahmath Ullah Joy

Masters Theses

Seven new copper(II) complexes were prepared from the condensation reaction of 4-tert-butyl-2,6-diformylphenol with two equivalents of bis(pyrazolyl)ethanamine or 3,5-dimethyl-bis(pyrazolyl)ethanamine moieties in the presence of two equivalents of various copper(II) starting materials having different counter ions (i.e. acetate - AcO^-, perchlorate - CIO₄^-, tetrafluoroborate - BF₄^-, nitrate - NO₃^-, and chloride - Cl^-). The resulting copper(II) complexes were characterized in solid state by single crystal X-ray crystallography, and in solution by UV-Vis and ESI/MS spectroscopies.

X-ray crystallographic studies showed that in solid state two types of …

3d Seismic Imaging Of Submarine Stratovolcanic And Salt Structures Beneath The Taranaki Basin, New Zealand And The Gulf Of Mexico, Ersin Erdem Unkaracalar

Masters Theses

"The relationship of submarine stratovolcanic and salt structures with overlying sediments creates a significant role in the petroleum system due to the emplacement and burial of volcano and salt. This study characterizes the spatial and temporal distribution of structural and stratigraphic features associated with submarine stratovolcano and salt body to provide insights for elements and processes of petroleum geology related to regional tectonics.

The stratovolcanic and salt structures are clearly identified on seismic sections. However, distortion of ray paths passing through the salt and turning seismic waves prevents accurate identification of steep flanks of salt. The seismic response to a …

Precise Energy Efficient Scheduling Of Mixed-Criticality Tasks & Sustainable Mixed-Criticality Scheduling, Sai Sruti

Masters Theses

"In this thesis, the imprecise mixed-criticality model (IMC) is extended to precise scheduling of tasks, and integrated with the dynamic voltage and frequency scaling (DVFS) technique to enable energy minimization. The challenge in precise scheduling of MC systems is to simultaneously guarantee the timing correctness for all tasks, hi and lo, under both pessimistic and optimistic (less pessimistic) assumptions. To the best of knowledge this is the first work to address the integration of DVFS energy conserving techniques with precise scheduling of lo-tasks of the MC model.

In this thesis, the utilization based schedulability tests and sufficient conditions for such …

Universal Wavefront Transmission Through Disordered Media, Jayson Robert Summers

Masters Theses

”When electromagnetic waves propagate through random dielectric media, they scatter in a predictable, deterministic way. The process is also fully reversible. If one sends an exiting wave backward through the same material, it will converge back to its original form and location in the same amount of time it took to originally propagate through the material. Due to this predictability, a great deal of research has went into studying these scattering processes in multimode fibers, diffusers, biological tissues, and other media. Scientists have turned random scattering material into focusing lenses, image transmitters, and highly transmitting media by controlling the impinging …

An Approach For Formal Analysis Of The Security Of A Water Treatment Testbed, Sai Sidharth Patlolla

Masters Theses

"This thesis focuses on securing critical infrastructures such as chemical plants, manufacturing units, and power generating plants against attacks that disrupt the information flow from one component to another. Such systems are controlled by an Industrial Control System (ICS) that includes controllers communicating with each other, and with physical sensors and actuators, using a communications network.

Traditional security models partition the security universe into two worlds, secure and insecure, but in the real world the partitions often overlap and information is leaked even through the physical observation which makes it much harder to analyze a Cyber physical system (CPS). To …

An Investigation Of The Influence Of The 2007-2009 Recession On The Day Of The Week Effect For The S&P 500 And Its Sectors, Marcel Alwin Trick

Masters Theses

"Several studies have shown that the mean returns and the volatility structure of stock markets change seasonally or by day of the week. For instance, some authors found out that Monday returns are lower compared to Friday returns or that volatility on Wednesdays are lower compared to the rest of the week. Other researchers showed that these effects have changed after certain periods of economic stress. This led to the question, whether the day of the week effects in returns and volatility are in the US stock market and if patterns have changed from pre-recession through the 2007-2009 recession into …