Lyme disease is a common tick-borne illness caused by the Gram-negative bacterium Borrelia burgdorferi. An outer membrane protein of Borrelia burgdorferi, P66, has been suggested as a possible target for Lyme disease treatments. However, a lack of structural information available for P66 has hindered attempts to design medications to target the protein. Therefore, this study attempted to find methods for expressing and purifying P66 in quantities that can be used for structural studies. It was found that by using the PelB signal sequence, His-tagged P66 could be directed to the outer membrane of Escherichia coli, as confirmed by an anti-His Western blot. Further attempts to optimize P66 expression in the outer membrane were made, pending verification via Western blotting. The ability to direct P66 to the outer membrane using the PelB signal sequence is a promising first step in determining the overall structure of P66, but further work is needed before P66 is ready for large-scale purification for structural studies.

The colossal global counterfeit market and advances in cryptography including quantum computing supremacy have led the drive for a class of anti-counterfeit tags that are physically unclonable. Dendrites, previously considered an undesirable side effect of battery operation, have promise as an extremely versatile version of such tags, with their fundamental nature ensuring that no two dendrites are alike and that they can be read at multiple magnification scales. In this work, we first pursue a simulation for electrochemical dendrites that elucidates fundamental information about their growth mechanism. We then translate these results into physical dendrites and demonstrate methods of producing a hash from these dendrites that is damage-tolerant for real-world verification. Finally, we explore theoretical curiosities that arise from the fractal nature of dendrites. We find that uniquely ramified dendrites, which rely on lower ion mobility and conductive deposition, are particularly amenable to wavelet hashing, and demonstrate that these dendrites have strong commercial potential for securing supply chains at the highest level while maintaining a low price point.

Treatment log files for spot scanning proton therapy provide a record of delivery accuracy, but they also contain diagnostic information for machine performance. A collection of patient log files can identify machine performance trends over time. This facilitates the identification of machine issues before they cause downtime or degrade treatment quality. At Mayo Clinic Arizona, all patient treatment logs are stored in a database. These log files contain information including the gantry, beam position, monitor units (MUs), and gantry angle. This data was analyzed to identify trends, which were then correlated with quality assurance measurements and maintenance records.

The use of enzyme-catalyst interfaces is underexplored in the field of biocatalysis, particularly in studies on enabling novel reactivity of enzymes. For this thesis, the HaloTag® protein tagging platform was proposed as a bioconjugation method for a pinacol coupling reaction using lipases, as a model for novel reactivities proceeding via ketyl radical intermediates and hydrogen-bonding-facilitated redox attenuation. After an initial lipase screening of 9 lipases, one lipase (Candida rugosa) was found to perform the pinacol coupling of p-anisaldehyde under standard conditions (fluorescein and 530nm light, 3% yield). Based on a retrosynthetic analysis for the photocatalyst-incorporated HaloTag® linker, the intermediates haloamine 1 and aldehyde 6 were synthesized. Further experiments are underway or planned to complete linker synthesis and conduct pinacol coupling experiments with a bioconjugated system. This project underscores the promising biocatalytic promiscuity of lipases for performing reactions proceeding through ketyl radical intermediates, as well as the underdeveloped potential of incorporating bioengineering principles like bioconjugation into biocatalysis to overcome kinetic barriers to electron transfer and optimize biocatalytic reactions.

Stardust grains can provide useful information about the Solar System environment before the Sun was born. Stardust grains show distinct isotopic compositions that indicate their origins, like the atmospheres of red giant stars, asymptotic giant branch stars, and supernovae (e.g., Bose et al. 2010). It has been argued that some stardust grains likely condensed in classical nova outbursts (e.g., Amari et al. 2001). These nova candidate grains contain 13C, 15N and 17O-rich nuclides which are produced by proton burning. However, these nuclides alone cannot constrain the stellar source of nova candidate grains. Nova ejecta is rich in 7Be that decays to 7Li (which has a half-life of ~53 days). I want to measure 6,7Li isotopes in nova candidate grains using the NanoSIMS 50L (nanoscale secondary ion mass spectrometry) to establish their nova origins without ambiguity. Several stardust grains that are nova candidate grains were identified in meteorite Acfer 094 on the basis of their oxygen isotopes. The identified silicate and oxide stardust grains are <500 nm in size and exist in the meteorite surrounded by meteoritic silicates. Therefore, 6,7Li isotopic measurements on these grains are hindered because of the large 300-500 nm oxygen ion beam in the NanoSIMS. I devised a methodology to isolate stardust grains by performing Focused Ion Beam milling with the FIB – Nova 200 NanoLab (FEI) instrument. We proved that the current FIB instrument cannot be used to prepare stardust grains smaller than 1 𝜇m due to lacking capabilities of the FIB. For future analyses, we could either use the same milling technique with the new and improved FIB – Helios 5 UX or use the recently constructed duoplasmatron on the NanoSIMS that can achieve a size of ~75 nm oxygen ion beam.

Debris disks are a collection of dust grains and planetesimals around a star and are thought to contain the remnants of planet formation. Directly imaging debris disks and studying their morphologies is valuable for studying the planet formation process. In some stellar systems that have a directly imaged debris disk, there are also directly imaged planets. Debris disk structures like gaps and asymmetries can show the gravitational e↵ects of planets that are below the brightness threshold for being detected via direct imaging. We investigate a sample of debris disks in Scorpius-Centaurus (Sco-Cen) that were imaged with the Gemini Planet Imager (GPI), which is an adaptive optics system with a coronagraph to block starlight. We look at two GPI data sets, the GPIES campaign Sco-Cen targets, and a follow-up observing program for Sco-Cen targets. We resolve 5 debris disks in the follow-up program and 13 from the GPIES campaign. By calculating contrast curves, we determine the planet detection limit in each of the GPI images. We find that we could have detected 5 Jupiter mass planets at angular separations greater than about 0.6 arcseconds in our GPIES campaign images. In three of our images we could have detected 2 Jupiter mass planets in wide orbits, but 2 Jupiter masses below the detection limit in our other images. We identify one point source around HD 108904 as a sub-stellar companion candidate. To further check for evidence of planets that are below the detection limit, we measure the surface brightness profile of the disks to check for asymmetries in brightness. We find that one of the edge-on disks has an asymmetric surface brightness profile, HD 106906, and three other edge-on disks have symmetric surface brightness profiles. We also find that two disks, HD 106906 and HD 111520, are asymmetric in radial extent, which is possibly evidence for gravitational interactions with planets.

This thesis project focuses on algorithms that generate good sampling points for function approximation. In one dimension, polynomial interpolation using equispaced points is unstable, with high Oscillations near the endpoints of the interpolated interval. On the other hand, Chebyshev nodes provide both stable and highly accurate points for polynomial interpolation. In higher dimensions, optimal sampling points are unknown. This project addresses this problem by finding algorithms that are robust in various domains for polynomial interpolation and least-squares. To measure the quality of the nodes produced by said algorithms, the Lebesgue constant will be used. In the algorithms, a number of numerical techniques will be used, such as the Gram-Schmidt process and the pivoted-QR process. In addition, concepts such as node density and greedy algorithms will be explored.

This is a study that demonstrates my growing understanding of the factors that influence Latinx engineering students’ sense of belonging in engineering. I conducted a literature review to help me gain perspectives from prior research on this topic. I wanted to investigate Latinx engineering students’ sense of belonging at Arizona State University. This interest was fueled by my own perspectives as an undergraduate first-generation Latina student. I was inspired by the Social Identity Development Theory described in “Becoming La Ingenieria” by Sarah L Rodriguez (2019). I found that science performance, science competence, and science identity recognition were important factors in engineering for Latinx students to thrive and succeed in their chosen major--engineering. Through the literature review, I found that Latinx engineering students need family support, faculty and staff to look up to, and ways to create authentic connections with near peers and professions. Student organization involvement such as in the Society of Hispanic Professional Engineers student chapter can help Latinx students grow their intersectional identities related to their identification as Latinx and as an engineer which then helped strengthen their sense of belonging in engineering. <br/><br/>I conducted a survey of Latinx engineering students at Arizona State University to better understand their perceptions on issues related to their sense of belonging and underlying factors of competence, recognition, and performance in engineering. However, due to the low participation, possibly due to the ongoing COVID-19 pandemic, I could not conduct statistical analyses that could lead inferences to the broad population of Latinx engineering students at ASU. <br/><br/>It is important to continue to create structures within university engineering programs and professional engineering societies to offer formal near-peer and professional mentorship of Latinx students. The integration of families from recruitment to graduation of Latinx engineering students may help build a more supportive structure for students to succeed. Research on the ways in which university faculty, staff, and near-peers can better support Latinx students will be essential to build classroom environments that help all students build a sense of belonging in engineering.

Mutations in the DNA of somatic cells, resulting from inaccuracies in DNA<br/>replication or exposure to harsh conditions (ionizing radiation, carcinogens), may be<br/>loss-of-function mutations, and the compounding of these mutations can lead to cancer.<br/>Such mutations can come in the form of thymine dimers, N-𝛽 glycosyl bond hydrolysis,<br/>oxidation by hydrogen peroxide or other radicals, and deamination of cytosine to uracil.<br/>However, many cells possess the machinery to counteract the deleterious effects of<br/>such mutations. While eukaryotic DNA repair enzymes decrease the incidence of<br/>mutations from 1 mistake per 10^7 nucleotides to 1 mistake per 10^9 nucleotides, these<br/>mutations, however sparse, are problematic. Of particular interest is a mutation in which<br/>uracil is incorporated into DNA, either by spontaneous deamination of cysteine or<br/>misincorporation. Such mutations occur about one in every 107 cytidine residues in 24<br/>hours. DNA uracil glycosylase (UDG) recognizes these mutations and cleaves the<br/>glycosidic bond, creating an abasic site. However, the rate of this form of DNA repair<br/>varies, depending on the nucleotides that surround the uracil. Most enzyme-DNA<br/>interactions depend on the sequence of DNA (which may change the duplex twist),<br/>even if they only bind to the sugar-phosphate backbone. In the mechanism of uracil<br/>excision, UDG flips the uracil out of the DNA double helix, and this step may be<br/>impaired by base pairs that neighbor the uracil. The deformability of certain regions of<br/>DNA may facilitate this step in the mechanism, causing these regions to be less<br/>mutable. In DNA, base stacking, a form of van der Waals forces between the aromatic<br/>nucleic bases, may make these uracil inclusions more difficult to excise. These regions,<br/>stabilized by base stacking interactions, may be less susceptible to repair by<br/>glycosylases such as UDG, and thus, more prone to mutation.