Digital Commons Network^™

Protein And Water Modeling In Computer-Aided Drug Discovery, Mossa Ghattas

Dissertations, Theses, and Capstone Projects

The field of Computer-Aided Drug Design (CADD) is continuously evolving to improve protein modeling, a crucial step in the drug discovery process. However, limitations exist in how CADD accounts for the various configurations a protein can adopt due to different rotamer and protonation states of its residues. This thesis explores advancements in CADD to address this challenge, focusing on protein modeling and water interactions.

In Chapter 1, I introduce the drug discovery process with a brief overview of its history, the purpose of FDA clinical trials, and the cost and time duration for bringing a drug to the market. I …

Dynamic Difficulty Adjustment For Combat Systems In Role-Playing Genre Video Games, Cheuk Man Chan

Dissertations, Theses, and Capstone Projects

Static difficulty adjustment has been applied to video games since their inception. However, dynamic difficulty adjustment did not become a topic of interest in either the academic fields or the industry until the turn of the century with sufficient advancement in processing power of computers and console systems. Amongst the work done in this area, most of the focus has either been placed on the action/adventure or the strategy game genre. However, there are only a limited number of studies regarding the role playing game genre which, by the nature of such games, generates a massive amount of data regarding …

Building Black Manhattan: Architecture, Art, And The Politics Of Respectability, 1857–1914, Jessica Larson

Dissertations, Theses, and Capstone Projects

“Building Black Manhattan” is the first study to examine the architectural contributions of Black women reformers to the urban development of New York City between the Civil War and the Great Migration. Through the construction of charitable and reform institutions throughout Manhattan, they articulated a strategy of racial uplift through deliberate spatial construction.

As reform work was one of the very few arenas in the nineteenth and early twentieth centuries in which women had a significant public voice, the buildings constructed to facilitate reformers’ work encoded the social, racial, and gendered demands of women into their designs. These institutions included …

Structural Insights Into Bacterial Helicase Loading At A Replication Origin By Cryogenic Electron Microscopy, Abhipsa Shatarupa

Dissertations, Theses, and Capstone Projects

DNA replication is a meticulously regulated and intricate process crucial for cellular viability. Replicative helicases, essential for unwinding DNA during replication, rely on helicase loader proteins for efficient loading and assembly at replication origins. In Escherichia coli, the replicative helicase DnaB forms a complex with six copies of the bacteriophage Lambda λP loader, resulting in a B₆P₆ conformation. The conformation of the BP complex, with a 6:6 stoichiometry, indicates that the isolated DnaB is initially captured by λP (B₆P₆) through its carboxy-terminal domain lassos/grappling hooks, serving as an early intermediate before transitioning …

Perceptual Expectation, Rebecca Keller

Dissertations, Theses, and Capstone Projects

You are currently seeing many things, and, hopefully, you are currently about to see many other things. Many of the things that you are about to see will not be surprising, because you expect to see them. Sometimes, though, when you expect to see one thing and are faced with another, that thing will look like the thing you expected it to be, and not like the thing it actually is. This dissertation is an attempt to get a handle on what is happening in the visual system in these instances. In particular, I am trying to figure out what …

Development Of Collagen Mimetic Mini-Fibrils With Tunable Collagenase Susceptibility, Jui Chaugule

Dissertations, Theses, and Capstone Projects

Collagen fibrils are the primary molecular scaffold of all connective tissues and provide the essential support for cell migration and differentiation. Collagen fibrils represent one of the most complex molecular hierarchies: three polypeptide chains in Gly-Xaa-Yaa repeating amino acid sequences, first form the rod-shaped collagen triple helix. These triple helices further self-assemble laterally in a specific manner to form fibrils having the characteristic 67 nm axially repeating structure known as the D-period. Enzymatic digestion of collagen fibrils by matrix metalloproteinases (MMPs) is critical for several physiological processes and is of particular consequence during wound healing. Many of the mechanisms of …

The Film, The Stadium And The Jail: The Post-Industrial Transformation Of Downtown Durham, Seth Rose

Dissertations, Theses, and Capstone Projects

By the late 1980s, Durham, North Carolina’s downtown-based industrial economy had been replaced by a powerful knowledge economy in the city’s peripheries. Downtown Durham’s vast array of tobacco and textiles manufacturing buildings stood empty, along with most of its commercial spaces, offices and sidewalks. This thesis argues that the local development of two major public works, a baseball stadium (the Durham Bulls Athletic Park) and a jail (the Durham County Detention Center), conceived and constructed on similar timelines in close physical proximity, was indicative of how—and for whom—city and county officials envisioned a revitalized downtown. The first chapter examines the …

Variability In Associations Among Seabirds And Marine Mammals: Causes And Consequences, Samantha A. Monier

Dissertations, Theses, and Capstone Projects

Marine predators today face multifaceted stressors from changing climate to changing prey availability, and these changes are occurring at unprecedented speeds. Any alteration to a species’ environment has the potential to disrupt social networks and thus, how animals obtain and transfer information. Interspecific social interactions in the form of local enhancement and facilitation are a critical, but not yet well-understood, component of seabird foraging; of immediate concern is that anthropogenic changes may be altering the quantity and quality of positive species interactions, with consequences for the species involved.

While we know these interactions are not immutable, less is known about …

Understanding Primate Immunity To African Trypanosomes Through The Characterization Of Trypanosome Lytic Factor Formation And Function, Sara Fresard

Dissertations, Theses, and Capstone Projects

African trypanosomes cause an annual loss of over 1 billion USD due to their economic and agricultural burden in Sub-Saharan Africa. These parasites are unicellular, extracellular parasites, that infect humans, cattle, and other livestock. Humans and some non-human primates are protected against most species of trypanosomes due to an innate immunity factor, Trypanosome Lytic Factor (TLF). This modified High Density Lipoprotein (HDL) contains two unique proteins, Haptoglobin Related Protein (HPR), a ligand to a trypanosome surface receptor, and Apolipoprotein-L1 (APOL1), the lytic component. Our overall goal is to use our understanding of primate immunity to create genetically modified cattle that …

The Impact Of Early Teacher Bias And Academic Risk On Children’S Current And Future Academic Achievement, Damira S. Rasheed

Dissertations, Theses, and Capstone Projects

The racial academic achievement gap continues to plague child academic outcomes in American public schools and teacher bias may be a contributing factor. Through the theoretical lens of critical race theory and the cultural synchrony hypothesis, this study contemplated how longstanding racism in the US may function to hinder the academic achievement outcomes of minority-race children. Moreover, cultural mismatches in the classroom between teachers and students may be associated with lower quality teacher-child relationships and perceived academic risk. A growing body of work has examined the association between teacher bias and child academic-risk factors—with risk defined by children’s sociodemographic characteristics …

Historiography Of The Body And Corporeality In Indonesian Theatre: The Search For Decolonial Aesthetics, Mohamad Ugoran Prasad

Dissertations, Theses, and Capstone Projects

A study on Indonesian theatre historiography, this dissertation explores how and why the body and corporeality serve as the dominant means of theatre-making in Indonesia. Tracing and locating the bodily practice in theatre and performance from Indonesian independence until the turn of the twenty-first century, it locates the frictional relationship between the body and corporeality with modernity and the coloniality of language. That friction occurs in the process of adapting and translating modern theatre in the 1950s as much as during the heyday of folk popular theatre in the 1960s, preferring the body and corporeality as a refuge from ideological, …

Cognitive Flexibility And Stability In Bilingual Older Adults, Lia Pazuelo

Dissertations, Theses, and Capstone Projects

Lifelong bilingual individuals develop expertise in language-switching, requiring a delicate balance between cognitive stability—safeguarding goals from interference—and cognitive flexibility—adapting goals to changing demands. While some studies demonstrate the transferability of these skills to non-linguistic tasks, signifying bilingualism's impact on cognitive processes, others find no direct correlation between non-linguistic task-switching and bilingualism. Our study investigated the cognitive processes underlying bilingual speakers' performance on a switching task, exploring whether varying degrees of bilingual experience in older adults result in different tendencies towards stability (e.g., lower mixing cost and response congruency effect) or flexibility (e.g., smaller switching costs). By treating the bilingual experience …

Active Galactic Nuclei - The Arrhythmic Beat Of A Galactic Heart, Henry James Best V

Dissertations, Theses, and Capstone Projects

Active Galactic Nuclei (AGN) are generally believed to be supermassive black holes (SMBHs) at the center of galaxies which are actively accreting material from the host galaxy. Through this process, they emit radiation across the electromagnetic spectrum both as a smooth continuum and emission lines. However, there is a great variety of the signals we observe–some faint, some bright, some variable and others steady. The wide array of signals produced by AGN is believed to encode both the geometry and the physics surrounding these SMBHs, making them a valuable target for understanding the high gravity limit, their feedback mechanisms to …

Future Land, Futures Lost: Planning The Crisis On The Louisiana Coast, Sheehan Moore

Dissertations, Theses, and Capstone Projects

South Louisiana is rapidly losing coastal land to the combined forces of subsidence, sea-level rise, and worsening storms, accelerated by the effects of flood control engineering and extractive industrial development. With erosion threatening homes and industry alike, the state has marshaled a response on a massive economic and geographic scale: its Coastal Master Plan recommends $50 billion in river sediment diversions, barrier island restoration, and other projects over fifty years. This dissertation is about the emergence of Louisiana’s coast as a place from this knot of human and environmental relations, as an object for governance and a container for political …

The Epigenetic Impact Of Dietary Choline On Growth Outcomes Of Children Exposed To Gestational Diabetes Mellitus, Ismail Kadam

Dissertations, Theses, and Capstone Projects

Maternal insulin resistance and hyperglycemia lead to gestational diabetes mellitus (GDM) which can cause fetal hyperinsulinemia, ultimately leading to excessive fetal growth associated with macrosomia and increased adiposity at birth. Increased placental macronutrient transport and epigenetic changes in growth and metabolic genes affected by GDM contribute to fetal overgrowth and can result in complications such as overweight/obesity, insulin resistance/type 2 diabetes, cardiovascular disease risk factors, as well as cognitive impairment later in life. Choline, an essential nutrient, participates in lipid and energy metabolism by providing methyl groups for DNA methylation and thus may overcome the hypomethylation of growth and metabolic …

Response Styles In Multiscale Measures, Zebing Wu

Dissertations, Theses, and Capstone Projects

Response style, one common aberrancy in non-cognitive assessments in psychological fields, is problematic in terms of inaccurate estimation of item and person parameters, which leads to serious reliability, validity, and fairness issues (Baumgartner & Steenkamp, 2001; Bolt & Johnson, 2009; Bolt & Newton, 2011). Response style refers to systematic individual preference or avoidance of certain response categories (Bolt & Johnson, 2009), especially in self-reported Likert-type scales. When response style occurs, the selection of response options is not only influenced by the trait(s) of interest but also affected by one’s tendency to choose specific options stylistically.

Despite the fact that the …

Intimate Partner Violence And Negotiation During Covid-19: Stressors, Resources, And Perception, Victoria P. Diamond

Dissertations, Theses, and Capstone Projects

Intimate partner violence (IPV) is a serious public health concern that affects millions across the globe. The COVID-19 pandemic created unforeseen stress, and necessitated safety policies that required social isolation, often extended exposure to one’s intimate partner, and an inability to access stress-reduction resources. These factors, along with many others, lead to an abrupt increase in IPV in many couples. Using the couple-adapted family stress model (ABCX), the current study examines both previously defined (e.g., emotional dysregulation, stress, unemployment, communication issues) and COVID-19 specific risk (e.g., quarantine, unprecedented social isolation, fear of contracting COVID-19) and protective factors (e.g., meaning in …

Structural, Electronic And Magnetic Properties Of Vanadium Doped Transition Metal Dichalcogenides (Tmds), Qudsia Ashraf

Dissertations, Theses, and Capstone Projects

Magnetic semiconductors are a prerequisite for spintronic devices but their ferromagnetism disappears at room-temperature hindering application in room temperature electronic devices. Enormous research has been conducted on the room-temperature ferromagnetic order in monolayer form of bulk van der Waals materials but the few layer system has not been extensively explored.

Doping is an effective approach to modulate the structural, electronic and magnetic properties of two-dimensional (2D) Transition metal dichalcogenides (TMDs) and expand their application. The effect of vanadium dopant on structural, electronic and magnetic properties of Tungsten Diselenide (WSe₂) was studied by X-ray Photoelectron Spectroscopy (XPS), Atomic Force …

Meconium: A Potential Means To Predicting Later-Life Cognition, Leah Duran

Dissertations, Theses, and Capstone Projects

Maternal perinatal stress is a commonly experienced, yet chronically undiagnosed condition (CDC, 2010). Literature has suggested that perinatal stress exposure has long lasting implications of the developing child both physically and mentally (Behrman et al., 2007; Hobel et al., 2008; Bowman et al., 2004; Polanska et al., 2017; Van de Bergh et. al, 2020). The use of meconium in the clinical setting has become one that serves a purpose of detection in medical conditions like in utero drug exposure. Using meconium as a predictor for brain behavior, however, is still an emerging concept in the literature. It is quickly gaining …

A Machine Learning Approach To Discovering Physical Models Of Galaxy Formation, Festa Bucinca

Dissertations, Theses, and Capstone Projects

Galaxies are the breathtakingly beautiful starry islands of the Universe. The process of galaxy formation involves the transformation from simple initial conditions in the early Universe to the complex galaxy structures we observe today. Spanning an immense spatial range and tremendous time scales - from the vastness of the Universe to the scale of individual stars - the physics of galaxy formation is both complex and crucial for understanding the Universe we live in. However, despite significant advancements, our theoretical understanding of galaxy formation remains incomplete.

In the era of big data available from hydrodynamical simulations and observations, Machine Learning …

“Hattak Vpi Homma” Mvt Miha Nanta Fehna? What Does “Native American” Really Mean?, Alex R. Steers-Mccrum

Dissertations, Theses, and Capstone Projects

Indigenous identities in North America are much more complex than generally assumed. No single definition of “Native (American),” “(American) Indian,” or related terms provides a set of necessary and sufficient conditions that accurately or usefully describe all and only the right individuals and communities. I argue that understanding Native identities in the contemporary context requires examining multiple interconnected dimensions of Nativeness, articulated here as Enrollment and Recognition, Tribal Ethnicities, Native Race, Indian Panethnicity, and Indigenous Nationhood.

In the U.S., Indigenous identities are usually oversimplified as either Enrollment in a Recognized Tribe or as Native Race. While both of these aspects …

The Effect Of Working Memory Performance Under Stress On The Relationship Between Trauma History, Ptsd Symptoms, And Intimate Partner Violence, Gabriella Robinson

Dissertations, Theses, and Capstone Projects

Background: Over 12 million people annually experience intimate partner violence (IPV) in the United States. Emerging adulthood has the highest rates of IPV across the lifespan. While many theories attempt to explain why IPV rates are markedly increased during this age period, researchers call for more empirical studies to understand processes occurring during this period that result in increased IPV perpetration. Of the studies that assess IPV perpetration, samples generally consisted of male batterers that perpetrated severe IPV. Trauma history and PTSD symptoms have been seen as risk factors for IPV perpetration. Cognitive risk factors for IPV perpetration, such as …

Interplay Of Magnetic Impurities And Superconductivity In Topological Materials, Didier Ndengeyintwali

Dissertations, Theses, and Capstone Projects

The interplay of superconductivity and magnetism has been a long-standing topic of interest since the discovery of superconductivity. In recent years it has been shown that topological superconductivity, which has promising applications such as in topological quantum computing, could result from such interplay. Motivated by the later results I study the effect of magnetic impurities in superconducting doped topological insulators, such as Iron based topological superconductors. I show that topological character of parent materials could lead to modifications in the structure of magnetic impurity induced in-gap states. Moreover, the superconductivity induced interaction between magnetic impurities in doped topological insulator would …

The Beautiful And The Bullshit: Speaker And Listener Mental Representations Influence Bullshit Receptivity, Ryan Tracy

Dissertations, Theses, and Capstone Projects

Bullshit is a topic that has enjoyed an explosion of attention in both cognitive and social psychological research domains. While the picture painted thus far suggests that receptivity to such statements (i.e., perceiving meaning where none exists) hinges upon an individual’s ability to engage in reflective (vs. reflexive) cognitive processing, little attention has been paid to how purveyors of bullshit influence one’s willingness to engage with the message. This is critical to explore, given the status of misinformation in today’s media climate. A critical step involved in determining characteristics of speakers that predict bullshit receptivity is to understand how people …

“Community Thinking Spaces”: Exploring The Openings And Possibilities Of A School-Based Intergenerational Community Of Practice, Lucy A. Robins

Dissertations, Theses, and Capstone Projects

This exploratory case study examines the possibilities of creating generative, collaborative, intergenerational learning communities within a traditional public 6-12 school in the United States, as an antidote to the ideologies of adultism, systems of whiteness, and settler colonial logics. The study is situated within a single public school site, where I have been a science teacher and teacher leader for the past eight years. The school, which self-identifies as a “progressive” public school, serves to reify the history of schools as sites for control through what I term a “we know best” ideology. This ideology serves to dismiss and devalue …

Just Transitions: Critical Exploration Of Environmental Policy And Decision-Making Through The Lens Of Lived Stories, Mariya Marinova

Dissertations, Theses, and Capstone Projects

This research explores perspectives on just transition, what transitional policies and practices are already set in motion, the conditions necessary to achieve it, and how this knowledge can inform environmental policy. Focusing on West Virginia, it employs qualitative methodology with open-ended interviews and develops life sketches of transitions to demonstrate how deeply intertwined just transition is with the lives of the people in places marked by extractive industries. Combining guiding principles from environmental and landscape justice, energy justice, feminist energy systems framework, and place attachment theory, the findings reveal that just transitions need to be transformative, focusing on understanding how …

Competitive And Noncompetitive Credit Assignment To Reward Cues In The Lateral Orbitofrontal Cortex, Mihwa Kang

Dissertations, Theses, and Capstone Projects

This dissertation investigates the mechanisms underlying variations in credit assignment to reward cues, with a focus on the lateral orbitofrontal cortex (lOFC). The lOFC has long been implicated in signaling reward expectancies, with controversy as to whether it signals the economic value of future outcomes, their sensory features to guide behavior or both. However, whether the lOFC signals the relative (competition-dependent) or absolute (contiguity-dependent) credit of cues is unknown. To address this, I employed a combination of novel behavioral assays, in-vivo electrophysiological recordings and optogenetic stimulation in rats. In Chapter 2, I tested the suitability of a self-initiating variant of …

Some New Properties Of Random Groups In The Density And Few-Relator Models, Anastasiia Chorna

Dissertations, Theses, and Capstone Projects

In this dissertation, we delve into the subjects that lie in the intersection of random group theory and first-order theory, or as traditionally referred to in the field, the first-order theory of free groups (Sela (2006) and Kharlampovich and Myasnikov (2006), among others). In particular, we establish the following two findings. First, we demonstrate that for fixed k > 2, among finitely generated groups, those without finite index subgroups of index k are prevalent in the density model (as discussed in Chapter 3). Second, we show that a first-order universal sentence in the language of groups is almost surely true in …

Health Behaviors And Physical Health Among Young Adults With Varying Psychometric Schizotypy, Christopher Liong

Dissertations, Theses, and Capstone Projects

Schizophrenia has consistently been associated with increased rates of physical illness and early mortality. One explanation for this association might be poor health behaviors, as people with schizophrenia are more sedentary, less physically active, and more likely to engage in substance use compared to the general population. Schizotypy may be conceptualized as the phenotypic expression of increased risk for schizophrenia spectrum disorders, and dimensional models of schizotypy suggest that it varies on a continuum ranging from non-clinical (i.e. low schizotypy) to clinical (i.e. high schizotypy and dysfunction, as in schizophrenia). Though schizotypy and schizophrenia appear to share similar deficits and …

Black Horror Film And The Role Of Mood In Race Perception, Nicholas P. Whittaker

Dissertations, Theses, and Capstone Projects

Contemporary discussions of black or antiracist art are often haunted by an air of pessimism. This pessimism rests on the intuition that art cannot change the political realities of antiblackness and/or our relationships with blackness. In this dissertation, I resist this hegemonic view by arguing that black horror films generate a particular, politically-valuable aesthetic experience. Specifically, they allow us to experience blackness and black people as unintelligible. This, I argue, runs counter to everyday experience of blackness; when blackness appears unintelligible, we lose the sense of satisfied comprehension that characterizes our everyday experiences of it. I argue that these films …