Digital Commons Network^™

Intrinsic And Extrinsic Drivers Of Bioaerosol Decay: Investigating Pathogen Stability Of Bacteriophage Ms2, Sin Nombre Virus, And Sars-Cov-2 In Simulated Environments, Elizabeth A. Klug

Theses & Dissertations

The threat posed by a virus as a bioaerosol depends largely on its stability under various environmental conditions (relative humidity (RH), sunlight, ozone, etc.). This stability is typically studied through aerosol decay—how the virus' viability changes over time when exposed environmental conditions. The Goldberg rotating drum, a widely used tool for studying bioaerosols, has been the basis of such research (Goldberg et al., 1958). However, it has significant limitations, including an inability to measure initial pathogen infectivity loss and the use of small sample volumes. Additionally, it does not answer the question of what intrinsic factors (lipids, proteins, nucleic acids) …

Feasibility Analysis For The Implementation Of An Anaerobic Digestion System In The City Of Pittsburgh, Pa, Gianna L. Kolencik

Electronic Theses and Dissertations

The current study is investigating the feasibility of an anaerobic digestion system

in Pittsburgh, Pennsylvania, at the old State Correctional Institute (SCI-Pittsburgh)

located at 1922 Westhall St. This location is immediately upstream of the Allegheny

County Sanitary Authority (ALCOSAN) along the Ohio River. Municipal solid waste

from ALCOSAN may be used as the main form of feedstock. ALCOSAN produced

roughly 36,500 tons of dry sludge in the reporting year 2023-2024. Based on the volume

of dry sludge from ALCOSAN it is estimated that an anaerobic digestion system could

yield approximately 29,930,000 kWh of energy, which is enough to power over …

Creasing In Thick Hemispherical Shells As A Model For Foveal Formation, Indigo Skye Peppard

Undergraduate Honors Theses

This research experimentally investigates creasing behavior on the inner surface of hemispherical shells with the ultimate goal of modelling the formation of the foveal pit, a sharp surface deformation present in the retina of the eye of many animals. Creasing is a phenomenon observed in hyperelastic materials and is characterized by sharply localized surface deformations that appear at ~35% compressive strain. The foveal pits of anoles (small iguanian lizards) are funnel-shaped and resemble creases when cut along the central axis. Furthermore, during foveal pit formation the anole eye contracts around 35% along this same axis. Given these similarities we believe …

A Modified Sir Model Used To Investigate The Relationship Between Congenital And Adult Syphilis, Kaleesta R. Waysman

Honors Thesis

A complex SIR model integrating the relationship between adult and congenital syphilis was developed. The goal of the project was to determine the specific population(s) or control strategies that should be enforced, altered, or removed to decrease the number of children experiencing clinical sequelae due to congenital syphilis. Early clinical sequelae include hydrops fetalis, preterm birth, central nervous system infection, hepatosplenomegaly, hyperbilirubinemia, cholestasis, hemolytic anemia, snuffles, osteochondritis, and lesions or rashes in the palms and soles. Late clinical sequelae include interstitial keratitis, hearing loss, Hutchinson teeth, saber shins, Clutton joints, mulberry molars, and saddle nose. After implementing real-world data into …

Evolving Enemy Behavior In Video Games, Hermie H. Adams Iii

Honors Theses

The video game I developed for my senior project lacked complex and engaging enemy artificial intelligence. The standard implementations of AI systems such as finite state machines and behavior trees felt like side-steps rather than innovative solutions. Upon seeing the 'magic' of machine learning in perfecting games such as Snake, Super Mario, and Flappy Bird, I was inspired to seek my answer in the field of evolutionary computation. However, my challenge differed in that the problem space would be defined by dynamic player strategies, making it not well-defined or static. As such, my evaluations are based on enemies exhibiting emergent …

Direct Computations Of Spatially Resolved Viscoelastic Moduli Of Biomolecular Condensates, Liwen Gu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Biomolecular condensates are viscoelastic materials formed by liquid-liquid phase separations (LLPS) of biopolymers. In this study, we develop a modified graph Laplacian-based collective model to characterize viscoelastic heterogeneity within condensates based on results of lattice-based Metropolis Monte Carlo (MMC) simulations. By integrating random graph models and simulations of A1-LCD, a type of intrinsically disordered protein, we examine how network topology influences storage modulus, loss modulus, crossover frequency, and relaxation time spectra. Our results reveal a strong correlation between topological features and mechanical response, with the condensate interior exhibiting higher stiffness and faster relaxation than the interface. The relaxation spectra provide …

Impact Of Unconventional Gas Extraction On Tributaries Of Tenmile Creek, Greene County, Pennsylvania: A 12-Year Perspective, Christian L. Beall

Electronic Theses and Dissertations

Much of southwestern Pennsylvania has been central to a rapid increase in development for unconventional natural gas extraction in the past two decades. The continued monitoring of streams over their lifetime as extraction sites is pivotal to understanding the effects of fracking on local waterways and their ability to provide for wildlife and human use. Here, using multiple indices of biotic integrity (IBI), I perform analyses of fish and macroinvertebrate communities as well as water chemistry on two streams, Bates Fork (with shale wells) and Fonner Run (without), as part of a follow-up to work performed there from 2010-2012. Fish …

Synthesis Of Sensitive Oligodeoxynucleotides Containing Acylated Cytosine, Adenine, And Guanine Nucleobases, Komal Chillar, Rohith Awasthy, Marina Tanasova, Shiyue Fang

Michigan Tech Publications

Background/Objective: Oligodeoxynucleotides (ODNs) containing base-labile modifications such as N4-acetyldeoxycytidine (4acC), N6-acetyladenosine (6acA), N2- acetylguanosine (2acG), and N4-methyoxycarbonyldeoxycytidine (4mcC) are highly challenging to synthesize because standard ODN synthesis methods require deprotection and cleavage under strongly basic and nucleophilic conditions, and there is a lack of ideal alternative methods to solve the problem. The objective of this work is to explore the capability of the recently developed 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) method for the incorporation of multiple 4acC modifications into a single ODN molecule and the feasibility of using the method for the incorporation of the 6acA, 2acG and 4mcC modifications into ODNs. Methods: …

Architecture Of Pseudomonas Aeruginosa Glutamyl-Trna Synthetase Defines A Subfamily Of Dimeric Class Ib Aminoacyl-Trna Synthetases, Michael K. Fenwick, Stephen J. Mayclin, Steve Seibold, Amy E. Derocher, Sandhya Subramanian, Isabelle Q. Phan, David M. Dranow, Donald D. Lorimer, Ariel B. Abramov, James M. Bullard

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

The aminoacyl-tRNA synthetases (AaRSs) are an ancient family of structurally diverse enzymes that are divided into two major classes. The functionalities of most AaRSs are inextricably linked to their oligomeric states. While GluRSs were previously classified as monomers, the current investigation reveals that the form expressed in Pseudomonas aeruginosa is a rotationally pseudosymmetrical homodimer featuring intersubunit tRNA binding sites. Both subunits display a highly bent, “pipe strap” conformation, with the anticodon binding domain directed toward the active site. The tRNA binding sites are similar in shape to those of the monomeric GluRSs, but are formed through an approximately 180-degree rotation …

Detection, Analysis, And Modeling Of Time-Scale Separated Modulatory Brain Dynamics: Methods And Applications In Neurocritical Care, Maren Elizabeth Loe

McKelvey School of Engineering Graduate Student Theses & Dissertations

Clinical monitoring of patients with neurological disease generates large volumes of data, including electrophysiology (e.g. EEG), heart rate, blood pressure, and other physiological measures. The use of these data to generate actionable prognostic measures is a long-held goal in clinical neurophysiology. In this regard, the use of engineering theory, including signal processing methods and computational modeling paradigms, is providing new ways of interpreting neurological data and yielding new insights into brain mechanisms and disease pathophysiology. This research focuses on the analysis and modeling of aberrant brain dynamical phenomena that occur over hours-long temporal epochs. Particularly, we consider time-scale separated electrophysiological …

Preparation, And Characterization Of Gypsum-Levan Composites And Evaluation Of Their Preliminary In Vitro And Antibacterial Characteristics, Jamileh Sultan El Arab

Thesis/ Dissertation Defenses

Orthopedic surgery has to contend with a myriad of issues with bones, injuries such as fractures as well as chronic ailments, like osteoporosis. There is a widespread understanding and execution of polymethylmethacrylate (PMMA) bone cement and calcium phosphate cements (CPCs), however their drawbacks like being non-biodegradable, generating heat, low bioactivity, and other issues reserve the development of better substitutes This study intends to develop and incorporate microbial levan squaring as a β-2,6-linked fructan polysaccharide into gypsum-based formulations of bone cements to make them biodegradable, bioactive and amplify their mechanical properties. The research aims to address the performance drawbacks of traditional …

Existence Of Traveling Waves In A Predator-Prey Invasion Model With Nonlocal Dispersal And Delayed Effects In Dispersal, Austin Simms

Theses and Dissertations

We investigate the existence and stability of traveling wave solutions in a predator--prey population model that incorporates both nonlocal dispersal and time-delayed interactions. The problem arises when species distributions and feeding or reproduction processes do not respond instantaneously, but rather exhibit lags in space and time. Our aim is to understand how these delays and nonlocal effects impact the wavefront speed and the eventual establishment of a predator population in previously prey-dominated regions. To accomplish this, we derive a PDE--integro--delay system from ecological considerations of prey self-regulation, predator ratio dependence, and jump-type dispersal kernels. We then employ a traveling wave …

High-Quality Factor Phase Gradient Metasurfaces With Dynamic Reconfigurability, Lin Lin

Arts & Sciences Graduate Student Theses and Dissertations

Free-space optical communication holds immense potential for surpassing the bandwidth limitations of conventional physically defined channels. Achieving flexible and efficient communication in free space requires compact, robust optical components capable of dynamically tuning laser light without relying on bulky lenses or mechanically driven mirrors. Metasurfaces, or flat optics, have garnered significant attention due to their densely arranged subwavelength nano-resonators, which impart phase, amplitude, and polarization changes comparable to those of traditional bulky optics. However, conventional phase gradient metasurfaces are constrained by passive designs based on geometric configurations and the weak light-matter interaction inherent in most dielectric materials, limiting their applicability …

California Red Hummingbird Flowers: Color Convergence Across Four Biochemical Categories, Melissa León-Osper, Victor Rossi, Katie Conrad, Josephine Hernandez Mena, Elaine Meslow, Amelia A. Fuller, Eduardo Narbona, Justen B. Whittall

Chemistry and Biochemistry

There are 129 red-flowered species in western North America that fit the hummingbird pollination syndrome. Theory predicts that these flowers should produce a specific red color that is conspicuous to hummingbirds but not to bees. In a few well-studied cases, red flowers can be produced with pelargonidin, cyanidin, or both—sometimes complemented with the addition of yellow carotenoids and sometimes not. Which pigment combinations are most common in California and whether they affect conspicuousness to hummingbirds and bees remain unknown. To determine the taxonomic distribution of the pigments responsible for red hummingbird-pollinated flowers, we quantified the color of 36 red-flowered species …

Monitoring Mangrove Dynamics And Evaluating Future Afforestation Potential In The Egyptian Red Sea, Rasha M. Abou Samra, Mansour Almazroui, Wenzhao Li, Hesham El-Askary

Mathematics, Physics, and Computer Science Faculty Articles and Research

Mangrove forests are vital for ecosystem services and coastal management but face stressors from anthropogenic activities and climate change. This study estimates the extent and afforestation potential of mangroves along the Egyptian Red Sea coast from 1984 to 2022 using NDVI derived from Landsat-5 and Sentinel-2 data in Google Earth Engine. Aboveground biomass (AGB), belowground biomass (BGB), carbon (C) stock, and CO₂ sequestration potential were evaluated using Sentinel-2 and elevation data. Future afforestation suitability (2020–2050) under SSP2-4.5 and SSP5-8.5 scenarios was assessed with the MaxEnt model. Mangrove area increased from 0.95 km² in 1984 to 1.46 km^{2 …}

The Impacts Of The Transfer Process Through The Eyes Of Stem Majors, Astrid Y. Lopez Matias

Honors Theses

This study explores the experiences of science, technology, engineering, and math (STEM) transfer students through the lens of Lily, a biology major who transferred from a large Midwestern university to a large Southeastern university. Employing a qualitative case study approach, data were collected via a semi-structured interview to delve into the complexities of her transfer journey. The analysis was guided by the Edalgo and High (2022) framework, which examines the interplay of personal, institutional, and social factors in shaping student experiences.

Lily's narrative highlights several challenges common among STEM transfer students, including unexpected personal and financial pressures, difficulties in navigating …

Simplicity From Complexity: Sensing High-Dimensional Fluctuations Via Regulatory Network, Optimality In Allocating Cellular Resources, And Recovering Functional Groups Via Data-Driven Methods, Fang Yu

Arts & Sciences Graduate Student Theses and Dissertations

Biological systems must navigate dynamic and complex environments while operating under constraints such as limited molecular resources, biochemical noise, and structural trade-offs. This dissertation investigates three distinct cases in which biological systems allocate resources and process information efficiently, revealing emergent simplicity from underlying complexity. The first study develops a generalized end-product inhibition model with cross-talk and an excess of regulators, providing a proof-of-principle that simple biochemical circuits could, in principle, dynamically adjust their responsiveness to high-dimensional environmental variation. This result highlights how such circuits may allow adaptive filtering of both dominant and subdominant fluctuation modes. The second study, conducted in …

Performance Of Lasso And Ridge Regression For Variable Selection In Genome-Wide Association Studies Of Maize Flowering Time, Dipok Deb

Data Science and Data Mining

Genome-Wide Association Studies (GWAS) are instrumental in identifying genetic variants linked to complex traits, providing valuable insights into trait heritability and biological mechanisms. This study applies GWAS to investigate flowering time in maize, a critical adaptive trait, using a diverse dataset of 5,000 recombinant inbred lines across eight environments. Traditional GWAS methods often encounter challenges in high-dimensional datasets due to the presence of multiple small-effect genetic loci. To address this, we compared two penalized regression methods—LASSO and Ridge regression—to perform variable selection and regression analysis within a GWAS framework. LASSO effectively reduced the number of predictors by selecting the most …

Computational Design Of Potent Sirna For Braf Oncogene Silencing For Enhancing Cancer Therapy, Muhammad Hermawan Widyananda, Ricadonna Raissa

Karbala International Journal of Modern Science

The discovery of oncogenic BRAF mutations has prompted the development of inhibitors, yet resistance remains widespread. A more effective strategy involves targeting BRAF mRNA with siRNA to overcome resistance to BRAF inhibitors. This study aims to design potent siRNA for BRAF oncogene silencing using a computational approach. The full coding sequence of BRAF was retrieved from the NCBI database and potential siRNAs were predicted using the Ui-Tei, Reynolds, and Amarzguioui rules. Identified siRNAs were further analyzed using various prediction systems and parameters, including their interaction with the hAgo2 protein. The results identified that seven siRNAs (siRNA 23, siRNA 24, siRNA …

Microplastic Concentrations Within The Winyah Bay River Plume, Daniel C. Haughie

Honors Theses

In the last 20 years, microplastics have become a significant concern for ecosystem and public health. The buoyancy and method of introduction makes river plumes a likely repository for microplastic accumulation. A river plume is a bulge of fresher water that expands radially from the mouth of an estuary, with distinct lines called fronts at the leading edge of the plume. A front is a region of convergence between the fresher plume water and the saltier ocean water. The density differences between the two water masses may create an easily identifiable color and salinity gradient. These fronts often allow for …

Nifuroxazide And 4-Hydroxybenzhydrazone Derivatives As New Antiparasitic (Trypanosoma Cruzi And Leishmania Mexicana) And Anti-Mycobacterium Tuberculosis Agents, Timoteo Delgado-Maldonado, Diana V. Navarrete-Carriola, Lenci K. Vazquez-Jimenez, Alma D. Paz-Gonzalez, Baojie Wan, Scott Franzblau, Othman Mueen Mohammed, Lorena Rodríguez-Páez, Charmina Aguirre-Alvarado, Debasish Bandyopadhyay

School of Integrative Biological & Chemical Sciences Faculty Publications

Background/Objectives: Nifuroxazide (Nfz) is a drug that has been used as a scaffold for designing antimicrobial and antiparasitic agents. This study aimed to synthesize and evaluate in vitro of Nfz and twenty-five 4-hydroxybenzhydrazone derivatives as potential anti-Trypanosoma cruzi, anti-Leishmania mexicana, and anti-Mycobacterium tuberculosis agents.

Methods: The compounds were synthesized by condensing 4-hydroxybenzhydrazide with appropriate aldehydes in acidic conditions and structurally confirmed by spectroscopic techniques. All compounds were evaluated in vitro against T. cruzi strains (NINOA and A1), L. mexicana (M379 and FCQEPS strains), and M. tuberculosis (H37Rv strain), followed by enzymatic assays against T. cruzi …

Experimental Evaluation Of Resource Allocation To Organelles In Eukaryotic Cells, Ronan Hanley

Senior Honors Papers / Undergraduate Theses

Among the hallmarks of the eukaryotic cell is its organization into spatially defined sub-compartments known as organelles. Organelles provide optimized environments for otherwise incompatible biochemical reactions within the cell. It has been shown that there is significant variation in the properties of organelles in a cell, and that cells have access to a limited pool of resources that they can allocate to organelles. This begs the question: by what principles do cells dictate how resources are allocated? To begin to explore this question, we look at resource allocation in S. cerevisiaefrom two perspectives. First, we use a combination of …

Using A Pharmacokinetic Model To Design And Evaluate An Early Ctdna Biomarker For Response To Targeted Therapy, Aaron Li

Spora: A Journal of Biomathematics

Early prediction of response to therapy or lack thereof can help physicians plan treatment more efficiently. Biomarkers based on circulating tumor DNA (ctDNA) are promising. However, biomarkers beyond direct comparison to baseline have not been thoroughly explored. We develop a model for ctDNA shedding under targeted therapy that incorporates pharmacokinetics. Using a simulated cohort of virtual patients with varied parameters, we define and analyze a biomarker based on ctDNA samples at baseline, 12 hours, and 24 hours after initiation of treatment. The biomarker identified patients who would achieve partial or complete response with high sensitivity and specificity and was able …

Flying Safe: Reducing Bird Strikes At Northern Illinois University, Stacey Marcinkowski

Honors Capstones

Bird-window collisions are a major source of avian mortality, particularly in urban environments where glass structures are prevalent. At Northern Illinois University (NIU), systematic monitoring conducted between 2019 and 2024 revealed Montgomery Hall to be the building with the highest incidence of bird strikes. This project aimed to test the effectiveness of a cost efficient bird strike mitigation strategy using grease marker frit dots on Montgomery Hall’s skybridge windows. We applied white dots spaced four inches apart and compared strike data collected during fall migration seasons before (2018–2022) and after (2024) dot application. While limited to one post-treatment season, results …

Weak Formulation For Solving Inverse Problems In Reproducing Kernel Hilbert Spaces (With Applications To Learning Dynamical Systems), Victor William Rielly

Dissertations and Theses

We combine numerical and machine learning techniques to present a general framework for solving inverse problems using vector valued reproducing kernel Hilbert spaces in a variational formulation. We present this framework in two papers. In the first paper, we present an original state-of-the-art method derived in the context of our general framework for learning dynamical systems. In the second paper, we generalize the method from our first paper to arrive at the framework for solving inverse problems. Then we apply our general framework to the task of learning dynamical systems. In both papers we consider numerous applications of our methods …

Vanadyl Phthalocyanine As A Low-Temperature/Low-Pressure Catalyst For The Conversion Of Fructose To Methyl Levulinate, Juan Luna, Mataz Alcoutlabi, Elizabeth M. Fletes, Helia Magali Morales, Jason Parsons

School of Integrative Biological & Chemical Sciences Faculty Publications

In this study, a vanadyl phthalocyanine was synthesized and characterized using XRD, FTIR, and XPS, confirming the successful metalation of the phthalocyanine ring. XRD analysis showed the vanadyl phthalocyanine crystallized in the P-1 crystal lattice, with unit cell parameters a = 12.058 Å, b = 12.598 Å, and c = 8.719 Å, and the lattice angels were 96.203°, 94.941°, and 68.204°. FTIR spectroscopy supported the metalation by the disappearance of the N-H stretch of the non-metalated phthalocyanine. The vanadyl phthalocyanine was tested as a heterogenous catalyst for the conversion of fructose into methyl levulinate in H2SO4–methanol and HCl–methanol systems. The …

Soft Modular Robots: From Modular Tensegrity Structures To Bioinspired Sea Robots, Luyang Zhao

Dartmouth College Ph.D Dissertations

The rapid advancement of robotics necessitates systems capable of adapting to complex, unstructured environments. Soft robots, with their flexibility and compliance, excel in delicate interactions, making them ideal for medical applications and search-and-rescue missions. Modular robots, on the other hand, offer reconfigurability, enabling diverse task-specific adaptations in dynamic settings. Despite their individual advantages, the integration of soft and modular robotics remains underexplored. This proposal aims to develop soft modular robots that combine the adaptability of soft robotics with the versatility of modularity. These systems will be capable of autonomously transitioning between locomotion, manipulation, and infrastructure assembly across land, water, and …

Treatment Wastewater Of Oil Refinery By Fe2o3 Nps Produce By The Novel Alishewanella Jeotgali Strain Haq8., Hawraa Qays Al-Assdy, Wijdan Hussein Al-Tamimi, Asia Fadhile Almansoory

Karbala International Journal of Modern Science

Metal oxide nanoparticles like iron oxide (Fe₂O₃) exhibit strong reactivity and photolytic features in wastewater treatment and serve as an effective adsorbent for water purification due to its substantial surface area and affinity for different functionalized groups. Iron oxide nanoparticles) IONPs) are currently applied to treat oil-contaminated water. Fe₂O₃NPs were produced using an extracellular approach utilizing the Alishewanella jeotgali strain HAQ8. IONPs were characterized using UV-vis, FT-IR, XRD, AFM, SEM-EDX, and Zeta potential. λ max for the synthesized nanoparticles observed at (358) nm. The bands at 485 cm⁻¹ in the FT-IR spectrum confirmed the formation of …

Adding Libraries To The Equation: Mathematical Sciences’ Underutilization Of Academic Librarians, Jennifer L.C. Burke, Elizabeth C. Novosel, Daniel G. Kipnis, Rasitha R. Jayesekere

Libraries Scholarship

Academic librarians do not engage with all disciplinary departments equally. Despite equal or even greater efforts, some departments are less responsive to librarian outreach. One such department is mathematics. To understand mathematics departments’ relationships with their academic librarians, three mathematics librarians created a 20-question survey that was disseminated to mathematics faculty, instructors, and instructional staff in the United States and Canada. Of the 188 survey participants, more than a third reported that they never engage with their librarians, approximately half only do so occasionally, and a mere eight percent of participants collaborated with librarians to provide information literacy instruction (IL) …

Dynamic Riskscapes For Prey: Disentangling The Impact Of Human And Cougar Presence On Deer Behavior Using Gps Smartphone Locations, Heather N. Abernathy, Mark A. Ditmer, David C. Stoner, Kent R. Hersey, Kathryn A. Schoenecker, Pat J. Jackson, Kristin N. Engebretsen, Julie K. Young, George Wittemyer

Wildland Resources Faculty Publications

Prey species adjust their behavior along human-use gradients by balancing risks from predators and humans. During hunting seasons, prey often exhibit strong antipredator responses to humans but may develop tolerance in suburban areas to exploit human-mediated resources. Additionally, areas with high human activity may offer reduced predation risk if apex predators avoid such locations. This study examined mule deer Odocoileus hemionus behavioral responses to risks from humans and their primary predators, cougars Puma concolor, contextualized by differences in risk levels between study sites, individual risk exposure, and human habituation. We framed our investigation using three non-mutually exclusive hypotheses: (H1) …