Physical Sciences and Mathematics Commons^™

Cpsrp43 Is Both Highly Flexible And Stable: Structural Insights Using A Combined Experimental And Computational Approach, Mitchell Benton, Mercede Furr, Vivek Govind Kumar, Adithya Polasa, Feng Gao, Colin David Heyes, Thallapuranam Krishnaswamy Suresh Kumar, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 …

The Alternating Access Mechanism In Mammalian Multidrug Resistance Transporters And Their Bacterial Homologs, Shadi A. Badiee, Ugochi H. Isu, Ehsaneh Khodadadi, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

Multidrug resistance (MDR) proteins belonging to the ATP-Binding Cassette (ABC) transporter group play a crucial role in the export of cytotoxic drugs across cell membranes. These proteins are particularly fascinating due to their ability to confer drug resistance, which subsequently leads to the failure of therapeutic interventions and hinders successful treatments. One key mechanism by which multidrug resistance (MDR) proteins carry out their transport function is through alternating access. This mechanism involves intricate conformational changes that enable the binding and transport of substrates across cellular membranes. In this extensive review, we provide an overview of ABC transporters, including their classifications …

Addressing The Embeddability Problem In Transition Rate Estimation, Curtis Goolsby, James Losey, Ashkan Fakharzadeh, Yuchen Xu, Marie-Christine Düker, Mila Getmansky Sherman, David S. Matteson, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

Markov State Models (MSM) and related techniques have gained significant traction as a tool for analyzing and guiding molecular dynamics (MD) simulations due to their ability to extract structural, thermodynamic, and kinetic information on proteins using computationally feasible MD simulations. The MSM analysis often relies on spectral decomposition of empirically generated transition matrices. This work discusses an alternative approach for extracting the thermodynamic and kinetic information from the so-called rate/generator matrix rather than the transition matrix. Although the rate matrix itself is built from the empirical transition matrix, it provides an alternative approach for estimating both thermodynamic and kinetic quantities, …

Lightning: An X-Ray To Submillimeter Galaxy Sed-Fitting Code With Physically Motivated Stellar, Dust, And Agn Models, Keith Doore, Erik B. Monson, Rafael T. Eufrasio, Bret D. Lehmer, Kristen Garofali, Antara Basu-Zych

Physics Faculty Publications and Presentations

We present an updated version of Lightning, a galaxy spectral energy distribution (SED) fitting code that can model X-ray to submillimeter observations. The models in Lightning include the options to contain contributions from stellar populations, dust attenuation and emission, and active galactic nuclei (AGNs). X-ray emission, when utilized, can be modeled as originating from stellar compact binary populations with the option to include emission from AGNs. We have also included a variety of algorithms to fit the models to observations and sample parameter posteriors; these include adaptive Markov Chain Monte Carlo (MCMC), affine-invariant MCMC, and Levenberg–Marquardt gradient-descent (MPFIT) algorithms. To …

Separation Of Organic Acids Through Direct Catalysis From Sugars, Katelyn Robinson

Chemical Engineering Undergraduate Honors Theses

Society relies on plastic products, whether they are single use or durable. A downside of plastic is that the most common type is a product of oil and oil is not only a limited resource but also a climate-damaging resource. Polylactic acid (PLA) is a bio-based, biodegradable plastic. However, the process of converting biomass to polylactic acid polymer has the largest environmental impact of the PLA production process, so alternative methods of conversion are needed (Moretti et al., 2021). The polylactic acid polymer can be made with lactic acid, which can be converted from glucose.

A Consumer's Guide To Greenwashing, Katie Fowler

Marketing Undergraduate Honors Theses

Over the past 37 years since the term greenwashing was coined, there have been sparse attempts to regulate this deceptive environmental marketing. The Federal Trade Commission (FTC) created its Guides for the Use of Environmental Marketing Claims, also known as the Green Guides, in 1992. The Guides have been revised on three separate occasions – 1996, 1998, and 2012 – in an attempt to remain relevant with the proliferation of environmental marketing claims and trends. However, the Guides were created as interpretive rules that do not give the FTC the authority to enforce the regulations unless they can prove that …

Understanding The Operations And Decision-Making Of Cow-Calf Farmers In Northwest Arkansas, Clayton Weyl

Agricultural Economics and Agribusiness Undergraduate Honors Theses

Societal pressure on farmers has become a more central part of the rhetoric surrounding livestock production. This study includes farmers in the discourse on the rhetoric surrounding climate change via interviews and simulations tailored to their operation. Previous research has addressed regenerative agricultural practices and conditions that influence farmer decision-making, but little research has analyzed decision-making in tandem with environmental practices. The literature reveals that cow-calf producer decision-making is influenced by their reliance on cattle as an income source, and farmers overall choose climate-friendly practices based on their perceptions about climate change. The goal of this research was to gather …

Carbon Dioxide Reduction On Large Area Liquid Metal Gallium-Indium Electrocatalysts, Thomas Hollis

Chemistry & Biochemistry Undergraduate Honors Theses

Carbon dioxide (CO₂) is widely known as a greenhouse gas that contributes to global warming due to the burning of fossil fuels. The carbon dioxide reduction reaction (CO₂RR) is widely studied to reutilize CO₂ to useful products, including methane, ethane, and carbon monoxide. This project studies the use of liquid metal gallium-indium as an electrocatalyst to perform CO₂ reduction to carbon monoxide (CO) or possibly solid carbon in various solutions. Gallium-indium is characterized and studied through its “wetting” properties and adhesion to substrate foil through the measurement of contact angles inside solution. These liquid …

An Investigation On The Effect Of Conserved Hinge Histidine On Influenza Hemagglutinin(Ha2) Protein Conformation Using Md Simulations, Nada Tolba

Chemistry & Biochemistry Undergraduate Honors Theses

Hemagglutinin is a protein on the surface of Human Influenza Viruses.¹ It is composed of two glycopolypeptide domains, the HA1 and HA2 domains. Previous studies have found that across different strains of Influenza viruses, HIS435 residues remain conserved.⁴ In studies where mutations occurred in hinge-site histadine residues, the Influenza virus was inactive.⁴ These investigations indicated a significant role of HIS435 (hinge-site histadines) in virulence. Four systems were created using Molecular dynamics (MD) simulations. Each system was composed of an Isolated HA2 trimer solvated in a 150 mM NaCl rectangular water box at 310 K under isobaric and …

Low-Cost Microstereolithography 3d Printing With Microfluidic Microsampling Applications, Lauren Twombly

Chemistry & Biochemistry Undergraduate Honors Theses

The growing field of stereolithography 3D printing has welcomed a new age ofmicrofluidic device fabrication techniques. When compared to previous planar fabrication techniques such as soft-lithography, stereolithography 3D printing offers highly automated procedures, reduced fabrication times, and greater complexity of device features. To date, the greatest tradeoff for 3D printing in microfluidic device fabrication is poorer resolution when compared to soft-lithography which can produce feature sizes on the nanometer scale. The poorer resolution of 3D printing limits the feasible size of features. While highly sophisticated 3D printers are capable of achieving sub 10 μm resolution, these instruments are incredibly expensive …

Design Of A Hyperstable Endocrine Acting Fibroblast Growth Factot, Sara Armstrong

Chemistry & Biochemistry Undergraduate Honors Theses

A novel chimera protein, consisting of the C-terminus of Fibroblast Growth Factor (FGF) 21 and super FGF1, a mutant of the wild-type FGF1, was studied. The protein retained the stability of sFGF1 and the endocrine acting behaviors and binding efficiency of FGF21, so that it could be more practical for therapeutic uses as a wound healing and angiogenic agent. sFGF1- FGF21 was expressed and purified before utilizing various biophysical techniques to measure its stability, secondary and tertiary characteristics, and metabolic activity.

Detection Of Nitrogen Dioxide Via Graphene-Enhanced Raman Scattering, Spencer Hazeslip

Chemistry & Biochemistry Undergraduate Honors Theses

This paper presents the development of a nitrogen dioxide (NO₂) sensor that utilizes the phenomenon of graphene-enhanced Raman scattering (GERS). The sensor consists of monolayer graphene on a silicon wafer, functionalized noncovalently with Copper(II) 2,9,16,23-tetra-tert-butyl-29H,31H-phthalocyanine (CuTTPc) via the solution soaking method. A custom sensing chamber was constructed to enable Raman spectra to be collected during NO₂ exposure. The response of the sensor was found to be linear between 10 and 100 ppm NO₂, indicating that it could be used for both detection and quantification. Furthermore, the sensor was shown to be reusable after …

Framing How We Think About Curves, Megan Sattler

Mathematical Sciences Undergraduate Honors Theses

A frame defines a basis at a point in R^n, and we can frame a curve by placing one at every point along it. This thesis investigates adapted framed curves in R^2 and R^3 in which they are used to provide information about how a curve twists and turns. We derive differential information from the frames that describe how they change and consequently how the curve changes. We also deduce special properties of each framing and discuss how the differential information suffices to describe the shape of curves.

Internship Thesis - Happy Egg Co., Annelise Koster

Data Science Undergraduate Honors Theses

This paper outlines a data science internship at Happy Egg Co, a producer of free-range eggs committed to sustainable agriculture practices. The internship focused on analyzing customer data to uncover characteristics of Happy Egg Co's target market and identify potential new markets for expansion.

The internship spanned a period of 10 weeks and involved working with the company's marketing and data science teams to gain practical experience in data cleaning, analysis, and visualization. The focus was on uncovering patterns and trends in customer behavior, preferences, and demographics to inform marketing strategies.

The internship began with an introduction to Happy Egg …

Battery Design, Construction, And Characterization For Small Motor Use Focusing On Anodic Zinc For Electron Flow, Amber Veach

Chemical Engineering Undergraduate Honors Theses

This thesis explores the construction, characterization, and application of anodic zinc batteries for powering a small electric motor for the ChemE Car competition. Two zinc galvanic cell batteries were studied: zinc-carbon and zinc-air batteries. Prototype batteries were constructed and tested for voltage, amperage, and power production. In the zinc-carbon trials, a 3:1 mixture of manganese dioxide and graphite was determined to be the best cathode for power production. The size which allowed for sufficient power while maintaining the smallest footprint on the car was a zinc can six cm tall and two cm in diameter. Analysis of paper zinc-air battery …

Developing Methods For Pattern Transfer In Photoelectrochemical Lithography, Ashlyn Descarpentrie

Chemistry & Biochemistry Undergraduate Honors Theses

The microprocessor industry has historically been driven by the goal of shrinking devices. To create features small enough to fit on such devices, photolithography has conventionally been used in the micropatterning of noble metal surfaces. Photolithography is a complicated and expensive process that involves a cleanroom, metallization processes, and photoresist. While this investment makes sense for high revenue applications, a number of microelectronic devices do not require nanometer-scale patterned features. Examples of such applications include specific types of antennae, sensing electrodes, and photocatalysts. Photolithography for these devices is thus too costly in both money and energy. The Coridan lab has …

An Overview Of Serial Depletions Of Global Marine Fisheries 1950 To 2019, Alison Follmer

Biological Sciences Undergraduate Honors Theses

Overfishing is a global issue that poses a significant risk to the entire ocean ecosystem in diminishing biodiversity and ecosystem function. This thesis examined the pattern and pace of fisheries depletions due to commercial fishing during the past 70 years. The Food and Agriculture Organization of the United Nations (FAO) Division of Fisheries and Aquaculture maintains a database of global hauls of marine taxa (reported in metric tonnes) from 1950 – 2019. These data were queried to determine the total number and sequence of fisheries depletions documented by the historic record. Analysis of this database showed progressive, linearly-increasing exploitation of …

Realtime In-Network Cyberattack Detection In Power Grid Systems Using A Programmable Network, Luke Waind

Computer Science and Computer Engineering Undergraduate Honors Theses

Power grid communication networks are important systems to detect intrusions from an attacker due to them being necessary to maintain critical infrastructure. This thesis applies recent advancements in P4 technology to detect cyberattacks in SCADA systems. In previous work, a list has been compiled of potential attacks that exploit one of the most common protocols in SCADA systems, DNP3. Solutions for detecting these attacks can be categorized by the broad methods that they use. The two methods that are focused on are single-packet inspection and multiple-packet inspection. For each of these, a specific attack is chosen and a detection algorithm …

Critical Infrastructure Workforce Development Pods For Teaching Cybersecurity Using Netlab+, Gideon Sutterfield

Computer Science and Computer Engineering Undergraduate Honors Theses

As digital automation for Industrial Control Systems has grown, so has its vulnerability to cyberattacks. The world of industry has responded effectively to this, but the world of academia is still lagging as its emphasis is still almost entirely on information technology. Considering this, we created a workforce development pod that serves as a hands-on learning module for teaching students key cybersecurity ideas surrounding operational technology using the NETLAB+ platform. A pod serves as the virtual environment where the learning exercise takes place. This project’s implementation involved the creation of a segmented network within the pod where a student starts …

Linux Malware Obfuscation, Brian Roden

Computer Science and Computer Engineering Undergraduate Honors Theses

Many forms of malicious software use techniques and tools that make it harder for their functionality to be parsed, both by antivirus software and reverse-engineering methods. Historically, the vast majority of malware has been written for the Windows operating system due to its large user base. As such, most efforts made for malware detection and analysis have been performed on that platform. However, in recent years, we have seen an increase in malware targeting servers running Linux and other Unix-like operating systems resulting in more emphasis of malware research on these platforms. In this work, several obfuscation techniques for Linux …

Analysis Of A Federated Learning Framework For Heterogeneous Medical Image Data: Privacy And Performance Perspective, Julia Brixey

Computer Science and Computer Engineering Undergraduate Honors Theses

The massive amount of data available in our modern world and the increase of computational efficiency and power have allowed for great advancements in several fields such as computer vision, image processing, and natural languages. At the center of these advancements lies a data-centric learning approach termed deep learning. However, in the medical field, the application of deep learning comes with many challenges. Some of the fundamental challenges are the lack of massive training datasets, unbalanced and heterogenous data between health applications and health centers, security and privacy concerns, and the high cost of wrong inference and prediction. One of …

Reverse Engineering Post-Quantum Cryptography Schemes To Find Rowhammer Exploits, Sam Lefforge

Computer Science and Computer Engineering Undergraduate Honors Theses

Post-quantum cryptography is a necessary countermeasure to protect against attacks from quantum computer. However, the post-quantum cryptography schemes are potentially vulnerable to side channel attacks. One such method of attacking involves creating bit-flips in victim memory through a process called Rowhammer. These attacks can vary in nature, but can involve rowhammering bits to raise the encryption scheme's decryption failure rate, or modifying the scheme's random seed. With a high enough decryption failure rate, it becomes feasible to generate sufficient information about the secret key to perform a key recovery attack. This thesis proposed two attacks on proposed post-quantum cryptography algorithms, …

Culture In Computing: The Importance Of Developing Gender-Inclusive Software, Creighton France

Computer Science and Computer Engineering Undergraduate Honors Theses

The field of computing as we know it today exists because of the contributions of numerous female mathematicians, computer scientists, and programmers. While working with hardware was viewed as “a man’s job” during the mid-20th century, computing and programming was viewed as a noble and high-paying field for women to occupy. However, as time has progressed, the U.S. has seen a decrease in the number of women pursuing computer science. The idea that computing is a masculine discipline is common in the U.S. today for reasons such as male-centered marketing of electronics and gadgets, an inaccurate representation of what it …

Chicken Keypoint Estimation, Rohit Kala

Computer Science and Computer Engineering Undergraduate Honors Theses

Poultry is an important food source across the world. To facilitate the growth of the global population, we must also improve methods to oversee poultry with new and emerging technologies to improve the efficiency of poultry farms as well as the welfare of the birds. The technology we explore is Deep Learning methods and Computer Vision to help automate chicken monitoring using technologies such as Mask R-CNN to detect the posture of the chicken from an RGB camera. We use Meta Research's Detectron 2 to implement the Mask R-CNN model to train on our dataset created on videos of chickens …

A Survey And Comparative Study On Vulnerability Scanning Tools, Cassidy Khounborine

Computer Science and Computer Engineering Undergraduate Honors Theses

Vulnerability scanners are a tool used by many organizations and developers as part of their vulnerability management. These scanners aid in the security of applications, databases, networks, etc. There are many different options available for vulnerability scanners that vary in the analysis method they encompass or target for which they scan, among many other features. This thesis explores the different types of scanners available and aims to ease the burden of selecting the ideal vulnerability scanner for one’s needs by conducting a survey and comparative analysis of vulnerability scanners. Before diving into the vulnerability scanners available, background information is provided …

Developing A Multi-Platform Application To Facilitate Internal Campus Hiring, Carissa Patton

Computer Science and Computer Engineering Undergraduate Honors Theses

Undergraduate research has proven to be highly beneficial to students, yet there are many students who do not know how to get involved or who are too timid to approach professors to inquire about potential research opportunities. Our hypothesis is that a cross-platform application has the potential to bridge the gap and help more students get involved in undergraduate research by providing them information about open positions and the faculty or staff members who are mentoring the projects. The key focus of this thesis is to develop an application that provides details about participating faculty or staff including their research …

Characterization Of 2d Quantum Materials Using Ai And Large-Scale Quantum Data Collection, Apoorva Bisht

Computer Science and Computer Engineering Undergraduate Honors Theses

2D materials like hexagonal boron nitride, graphene, and tungsten diselenide are widely utilized for studying their unique mechanical and opto-electronic properties to exploit them to make transistors and fabricating a variety of other devices. All these applications require that the 2D materials used be of specific uniform thickness. Until very recently, this process has been largely manual and tedious. However, few applications exploit the characteristic color-to-thickness correspondence of these near-transparent materials. To continue this effort, in this work we create a large-scale dataset for three different materials (hBN, graphene, and WSe$_2$) to train and test an image segmentation model along …

Universal Computation Using Self-Assembling, Crisscross Dna Slats, Jackson S. Bullard

Computer Science and Computer Engineering Undergraduate Honors Theses

I first give a brief introduction to formal models of computation. I then present three different approaches for computation in the aTAM. I later detail generating systems of crisscross slats given an arbitrary algorithm encoded in the form of a Turing machine. Crisscross slats show potential due to their high levels of cooperativity, so it is hoped that implementations utilizing slats are more robust to various growth errors compared to the aTAM. Finally, my software converts arbitrary crisscross slat systems into various physical representations that assist in analyzing their potential to be realized in experiments.

The Use Of Fluorescence Resonance Energy Transfer And Bent Dna To Study Dna And Ion Interactions, Kaitlin Bullard

Physics Undergraduate Honors Theses

Studying DNA interactions is advantageous to developments in the medical field since DNA and its interactions affect our health greatly. In addition, it is important to understand how the bendability of DNA depends on metal ions, which are essential for various fundamental processes in cells. In this work, we investigate the use of FRET and self-assembled bent DNA molecules to quantify DNA interactions with magnesium ions. We measured that the FRET efficiency increased at higher concentrations of magnesium ions. We also ran simulations to further understand the mechanisms. These observations show that magnesium ions increase the stability and flexibility of …

Analysis On High Mass X-Ray Binary Spectral Shape Dependence On Luminosity For Ngc3310, Izabela Pavel

Physics Undergraduate Honors Theses

In most normal galaxies, the most X-ray luminous sources are high-mass X-ray binaries (HMXBs), which are binary star systems that contain compact objects (black holes or neutron stars) accreting from massive (> 8M⊙) companion stars. These HMXBs are thought to have been important sources of ionizing emission within star-forming galaxies that may have contributed to the heating of the intergalatic medium (gas over large cosmic scales) in the early Universe. When studying how HMXBs contribute to interstellar medium feedback, a single spectral shape of an absorbed power-law is typically assumed to be universal. The goal of this thesis is to …