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### Computational and Data-Driven Studies of Active Nematics

Chaitanya Joshi
Active nematics are a class of non-equilibrium systems with constituents that consume energy at the molecular level to generate motion at macroscopic scales. In bulk, these materials exhibit turbulent behavior, and the active energy is not converted into meaningful work. One way of taming the turbulence is via confinement in regular geometries, which requires understanding the effect of boundaries on the active flows. Other approaches might involve strategies like optimal control or model-predictive control to...

### Microtubule-based Active Matter: Controlling Microscopic Properties and Characterizing Instabilities

Pooja Chandrakar
Active matter are internally driven non-equilibrium systems, which are made of energy consuming motile entities. They exhibit long-range self-organization phenomena such as pattern formation, collective motion and spontaneous flows. Understanding the physical principles governing these phenomena are of both fundamental and practical interest. They offer promise of improving the fundamental knowledge of non-equilibrium statistical mechanics while also providing a platform for creating novel, programmable synthetic materials with life-like properties. Studying active matter systems is difficult...

### Structural Transitions of Colloidal Membranes in One, Two, and Three Dimensions

Joanna Robaszewski
Directing the geometry of membranes is a goal shared by many disciplines. From designing drug delivery systems in bioengineering to understanding how membranes regulate their size and shape in physics, the study of structural transitions of membranes offers many potential insights into membrane assembly. However, biological membranes operate on small length and time scales that make it difficult to examine the physics behind biomembrane configuration using standard microscopy techniques. Here, we present an experimental model...

### The Mechanisms of DNA Double Strand Break Repair and Mismatch Recognition

Danielle Nicole Gallagher
DNA double-strand breaks (DSBs) are among the most toxic forms of DNA damage and pose a severe threat to genomic integrity. As such, the cell has evolved highly coordinated and complex mechanisms to repair such lesions. Improper repair of DSBs can lead to chromosomal duplication, chromosomal deletions, and chromosomal translocations, all of which are hallmarks of human cancers. Previous work in DNA damage has focused on the mechanistic characterization of how cells repair DNA DSBs,...

### Examining Sleep as a Mechanism Linking Physical Activity and Cognition

Alycia Bisson
Although both physical activity (PA) and sleep have been linked to cognitive functioning, many questions remain with regard to the nature of their relationships. Pathways that link sleep and PA to cognition have been studied separately, but recent work suggests that PA and sleep are also related. Studies have found that more active people sleep better and longer than those who are inactive. Within persons, sleep quantity and quality are better on days when one...

Yi Jin
ABSTRACT

### Atomic Resolution Imaging of Molecular Photoswitches and Their Application in Solar Energy Storage

Mihael Gerkman
Molecular photoswitches that reversibly isomerize when exposed to external stimuli, such as light, heat, and current have been used for diverse applications in drug delivery, sensing, controlling hydrophilicity of surface, actuation, and many other fields. The wide range of applications is achieved primarily due to their significant changes in physical and optical properties upon isomerization. However, the isomerization dynamics of these compounds are typically studied in dilute solution or dispersion in polymer matrices, which is...

This paper describes the context for and explores the claims of insider trading against Eastman Kodak using a mix of quantitative and qualitative analysis. This paper is divided into three different chapters. The first chapter is a general overview of Eastman Kodak in July and the critical information surrounding the US international development finance corporation loan announcement. This chapter includes but is not limited to investments reports, legal reports, Eastman Kodak's press release, and a...

### Spectrum of Chromosomal Repair Mutations Associated with Mitotic Gene Conversions

Qiying Cui
The genome of a cell is continuously subject to damage. By-products from cell metabolism, irradiation, chemical agents, and ultraviolet light are all environmental factors that cause lesions that can block replication progression. Although cells have adapted checkpoint mechanisms and repair pathways, repair failure can lead to deletions, translocations, and fusions in the DNA. These genomic rearrangements are commonly found in cancer cells. Double-strand breaks (DSBs) are problematic and the most lethal type of damage if...

### Paired feed-forward excitation with delayed inhibition allows high frequency computations across brain regions

Alexandra Shan Cao
The transmission of high-frequency temporal information across brain regions is critical to perception, but the mechanisms underlying such transmission remain unclear. Long-range projection patterns across brain areas are often comprised of paired feedforward excitation followed closely by delayed inhibition, including the thalamic triad synapse, thalamic projections to cortex, and projections within hippocampus. Previous studies have shown that these joint projections produce a shortened period of depolarization, sharpening the timing window over which the postsynaptic neuron...

### Exploring the Impact of Computer Science on the Future of Higher Ed

Jessica Liebowitz, Timothy J. Hickey & Matthew Ekins
We bring a new type of data-job posting analytics-to illuminate questions about data scientific expertise in the higher ed workforce. In particular, this allows us to link trends in computer science faculty hiring with demand for data science and predictive analytic skills among non-faculty jobs across the university. Within the context of the US economy as a whole, our findings identify research universities as one of the fastest growing centers of data scientific human capital...

### Investigation into cooperative DNA binding by the Gal4-VP16 transcription factor

Shinji Rho
Gal4-VP16 is an artificial transcription activator with a Gal4 DNA binding domain and aVP16 activation domain, helpful in studying eukaryotic transcription mechanism due to its high

### A D-phenylalanine-benzoxazole derivative uncovers redundancy in the pantothenate biosynthetic pathway of Mycobacterium tuberculosis

Michael Pepi
New drugs and new targets are urgently needed to treat tuberculosis. We discovered the D-phenylalanine-benzoxazole Q112 displays potent antibacterial activity against Mycobacterium tuberculosis in multiple media and in macrophage infections. Metabolomic profiling experiments indicate that Q112 has a unique mechanism of action compared to other antitubercular agents. Q112 perturbs the essential pantothenate/CoA biosynthetic pathway, depleting pantoate while increasing ketopantoate, as would be expected if ketopantoate reductase (KPR) were inhibited. We searched for alternative KPRs since...

### Hippocampal Rem2 in taste learning and memory

Katherine Elizabeth Kimbrell
The molecular/cellular plasticity mechanisms that ensure adaptive animal behaviors remain less than fully understood. Our lab has shown that Rem2, a small GTPase of the Ras-like superfamily, regulates multiple plasticity-related phenomena, including synapse formation and function and dendritic arbor complexity. While the above work involved examination of visual cortex, Rem2 is also expressed the hippocampus, a region that mediates a broad swath of learning and memory behaviors, including Social Transmission of Food Preference (STFP) and...

### Living with 47, XXY: An Emerging Adulthood Perspective

Clare Morris
47, XXY, also known as Klinefelter’s syndrome, is a chromosomal aneuploidy syndrome that can present with a wide array of symptoms that can affect both physical and mental health.This study examines individuals in the emerging adulthood period, ages 18-29, who have 47, XXY. Participants were asked to complete an online survey that focused on their diagnostic experience, relationships, support systems and advice that they have for others. Thirty-six individuals participated and their responses were analyzed...

### Active Filaments In and Out of Confinement

Matthew Peterson
Active matter encompasses systems whose microscopic constituents consume energy at the particle scale to produce forces and motion. Novel macroscale phenomena emerge in these systems when these forces collectively organize into mesoscale `active stresses'. Harnessing these active stresses to drive particular emergent behaviors could enable a new class of materials with life-like properties that would be impossible in traditional equilibrium materials. Similarly, many biological functions, such as cytoplasmic streaming, morphogenesis, and cell migration, are driven...

### L_b-ideals at irregular CM points of weight 1

Tarakaram Gollamudi
Let $f$ be a cuspidal $CM$ modular form of weight $1$ and level $N$ which is irregular at $p$.The primary goal of this thesis is to investigate the behavior $L_b-$ideal at $f$ without knowing the modules of overconvergent modular symbols $M^+$ and $M^-$. These modules are $T-$modules which are free of finite rank $n$ over $R$. We present a full classification such modules for $n=2$ and $3$ and partial classification for $n=4$. We also establish...

### Reassessing Stress: Distinct Neural and Mental Health Correlates of Stress Exposure and Controllability Appraisals

Alyssa Fassett-Carman
Stress is a strong risk factor for internalizing symptoms and can lead to changes in gray matter (GM) structure associated with psychopathology. Adolescence and emerging adulthood is a time of heightened stress, onset of stress-related disorders such as depression, and GM development, and is thus posited to be a sensitive period for the effects of stress. However, not all youth who experience stress develop symptoms. Learned helplessness theory and evidence describes how having control over...

### Redefining the Functional Repertoire and Metal Dependence of Type I Cas3 HD Domain Nucleases

Paul Yanning Jiang
Targeted DNA degradation by the Type I CRISPR-Cas system is performed by Cas3, typically a two-component protein with a nuclease and a helicase domain. The nuclease belongs to the HD-domain metalloprotein superfamily, that harbors functionally diverse representatives including phosphodiesterases, phosphatases and oxygenases. The range of metal ions reported to support Cas3 catalytic activity is diverse, including Mg, Mn, and Ni, demonstrating variability in cofactor requirements. Type IE Cas3 nucleases are dinuclear, whereas for Type IA...

### Dynamics and Rigidity of the Morse Boundary

Qing Liu
Let $X$ be a proper geodesic metric space and let $G$ be a group of isometries of $X$ which acts geometrically. Cordes constructed the Morse boundary of $X$ which generalizes the contracting boundary for CAT(0) spaces and the visual boundary for hyperbolic spaces. For the first part, we characterize Morse elements in $G$ by their fixed points on the Morse boundary $\partial_MX$. The dynamics on the Morse boundary is very similar to that of a...

### The molecular chaperone BiP utilizes electrostatic targeting to specifically bind oligomerized states of a client protein

Judy Lynn Meissner Kotler
Molecular chaperones are crucial machines that maintain protein homeostasis in the cell. In the ER, the two major chaperones performing this function are the Hsp70 BiP and Hsp90 Grp94. While BiP interacts with every nascent polypeptide targeted to the ER and has a specific client binding motif, less is known about how Grp94 chooses its clients. Here, I explore how BiP and Grp94 can work together and set the groundwork for studies exploring a shared...

### Early visual neural circuit development and the role of acute visual experience

Andrea Stacy
Neural circuit development is profoundly influenced by experience-dependent processes. The visual system serves as a robust model for understanding how experience affects sensory perception and the circuit mechanisms required for processing of the visual world. Decades of research have focused on cortical processing of visual receptive field properties and the early plasticity of cortical neurons, with less concentration on the contributing inputs to visual cortex. In this thesis I focus on the lateral geniculate nucleus...

### Statistical Properties and Optogenetic Control of Active Turbulence

Linnea M Lemma
The field of active matter seeks to understand how the collective behavior of many animate constituents leads to large-scale organization and dynamics. In this thesis, I studied an active matter system composed of purified cytoskeletal components to examine the statistical properties of the material dynamics and their microscopic origins.

### Exploring the Patient Perspective of BMD and DMD Transition Planning

Kaitlyn White
Advances in knowledge and medical treatment have worked to extend the lifespan for men affected by Becker and Duchenne muscular dystrophy (BMD and DMD). As these individuals continue to surpass life expectancies of the past, there is now a need for them to transfer care from pediatric to adult providers as well as prepare for this next phase of their lives. Despite the increasing occurrence of this, little is known about the transition process and...

### Impact of Dopamine Synthesis Capacity in Midbrain Regions of Interest on Cognitive Stability and Flexibility in Older Adults

Rebekah Fain
In aging, we see marked alterations to the dopamine system, specifically with losses in the number of dopamine receptors and transporters and increases in dopamine synthesis capacity. While striatal dopamine has been a focus of research, midbrain synthesis capacity has been less thoroughly explored. Here, we developed a protocol that allowed us to accurately define and measure midbrain dopamine synthesis capacity, specifically in the substantia nigra and ventral tegmental area. Using the positron emission tomography...

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