In the midst of the pandemic, our team prototyped a volatile organic compound (VOC) sensor that seeks to detect COVID-19 using mechanisms from our noses: olfactory proteins. In taking the concept from design to testing, a massive amount of data was compiled and produced. Protein sequences were gathered from hundreds of publications on odorant binding proteins (OBPs) and cross-referenced against protein structures in the Protein Data Bank (PDB), sensor molecules were simulated in molecular dynamics, and candidates were screened using multiple experiment methods. I built and deployed the database that tied together signature disease VOCs, protein binding affinities, and protein and peptide sequences, along with molecular dynamics experimental results. In addtion, I had also pulled seqeunces from PDB and had contributed to the literature search. We demonstrate how intelligent data management enabled and accelerated a project to tackle rapid detection of COVID-19.

Pacific sand lance (PSL) are a pelagic plankton feeding forage fish that also exhibit benthic associated behavior, related to burial in sediment on the ocean floor. They represent a key trophic link between plankton and upper-level predators. Despite their ecological importance, these fish are relatively under researched. This study provides new insights related to sediment preference and the effects of light availability on foraging behavior, and quantifies movement patterns related to various response behaviors. We found that PSL may prefer sediments made up of fine and coarse grain sand, as well as require a light cue to leave sediment habitats and forage. Additionally, we quantified a multitude of behaviors exhibited in PSL and found statistically significant relationships therein. We observed positive correlations between fish length and velocity in schooling fish and in fish movement related to burial in sediment. We also observed a negative correlation between fish length and both burial depth and steepness of body position within sediments (burial angle). In short, longer fish were generally faster and buried deeper within sediment at a flatter angle. Schooling distances were compared through two methodologies: stereo camera and video imaging analyses. A significant difference was found between the two, likely due to human error. Further research should be conducted on sediment preference as it relates to spatial habitat, as well as other behavior motion and schooling analysis.

Microplastics (plastics < 5mm) are increasingly prevalent in marine systems and of growing concern, as a source of marine pollution and in potential biomagnification in food webs. This has consequences for high trophic level consumers, including humans. Despite being an emerging area of study with many unknowns, there is increased interest in understanding the abundance and consequences of marine plastics, given evidence that links plastics to degraded ecosystem and organismal health. Microplastics contain and can absorb harmful chemicals, which may serve as endocrine disruptors. This may have implications for growth, reproductive health and longevity. To expand current knowledge on Salish Sea microplastics, I processed and examined 233 Pacific sandlance, sculpin, Pacific salmon, and Arctic cod stomachs for microplastics. 28% of all fish stomachs contained at least one microplastic particle. There was variation of prevalence between sites, ranging from 3% to 49%. Differences between prevalence of plastics differed between beach sites for both sandlance and sculpin and also differed from sandlance sampled in offshore benthic habitats. All forage and benthic samples indicated potential biomagnification to salmon based off of biomagnification factor values (BMF). Comparisons between plastic concentrations and stomach fullness was compared with plastic concentration. Further investigation is needed to develop a more thorough understanding of the microplastic issue in the San Juan Archipelago

The circumgalactic medium (CGM) is the extended gaseous halo that typically surrounds the visible parts of a galaxy - the beautiful spiraling disks that one may recognize from an image captured by the Hubble Space Telescope. Although the CGM harbors no stars, making it only faintly illuminated by the interior galaxy and background sources, it is believed to contain far more mass than the galaxy itself. Understanding the CGM is thus key to understanding galaxy formation and address questions such as: Why are some galaxies red and some blue? Why are we only observing ~20% of the baryons (regular matter, not dark matter) we should observe in galaxies? How do galaxies like our own sustain star formation, enabling the particle diversity we see everywhere around us? The way we currently observe the CGM’s properties is through absorption spectroscopy by using a bright background light source (quasar) and observing how the light is absorbed as it travels through the CGM before reaching our telescopes. However, this limits our observations to only a “pinhole” view of the CGM’s properties. With the advent of instruments sensitive enough to observe the light emitted from the CGM, we will be able to create so-called “emission-maps” of the full state of the gas - including temperature, density, and element abundances. Our project has identified what wavelengths (ionic lines) are most observable with more sensitive telescopes, some of which are already underway. I have run computer simulations in the Cloudy program to identify these emission lines and developed models estimating their intensity. The culmination of our work shows that many of these CGM emission lines are detectable with feasible instruments in the near future, laying the groundwork to justify future missions targeting these specific lines in order to investigate the most pressing questions of galaxy evolution.

 In vivo recordings of neural ensemble activity in non-human primates (NHPs) have contributed to the understanding of how neural activity relates to motor function and intent. Traditionally, neural recording has been conducted in constrained environments, such as head-fixed experiments using bulky wired equipment to achieve high data throughput and reduce measurement noise. To collect more natural data from free-moving NHPs requires a high speed, low power wireless uplink of the neural data. However, wireless communication inside a metal NHP cage suffers from dense multipath interference, due to multiple signal bounces from the cage walls, which decreases communication reliability. We explored an approach called "Electronic Mode Stirring" to obtain better communication reliability. We found that by adding 4 switchable reflecting antennas to the roof of the cage to perform mode-stirring we were able to improve the mean one-way path loss and improved the worst-case signal loss across 126 measured positions in the primate cage. We expect that the reduced signal loss with the mode stirring system will lead to improved wireless communication reliability inside the cage.

Nemaline Myopathy (NM) is a severe genetic muscle disorder defined by muscle weakness and the presence of nemaline rods (rod-shaped intracellular aggregates). This disease is associated with multiple clinical subtypes that result from pathogenic genetic variants across 12 different genes, including skeletal 𝛼-actin (ACTA1). NM-associate mutation H40Y impacts the ACTA1 monomer structure such that it disrupts polymerization. Without efficient and accurate polymerization, ACTA1 monomers form altered protofilaments which do not properly support the cross-bridge cycle and result in contractile dysfunction. The variation and complexity of NM pathology coupled with the rarity of this disease have served as significant barriers to the development of any treatments for NM. Here we show the effects of top performing therapeutic small molecules simulated in the presence of NM-associated mutation H40Y on the structural and mechanical properties of ACTA1. Using Molecular Dynamics simulation data, we have quantified differences between H40Y and wildtype ACTA1. Furthermore, we searched for and designed a target small molecule to fix mutant actin polymerization and mechanical instability. Our results demonstrate how our lead designed small molecule alters the dynamics of the H40Y ACTA1 pentamer when simulated docked in its intended binding pocket. We anticipate that our best small molecule candidate will be tested in vitro for its ability to impact actin polymerization in polymerization assays produced from induced pluripotent stem cells bearing the H40Y mutation. Furthermore, following successful in vitro validation the small molecule may be extensively studied as a potential novel therapy for NM.

Polymers are important in all areas of life from commodity plastics to vaccine delivery. Currently, plasticizers are small molecules used to make rigid polymers into the flexible plastics we need. However, the problem with these plasticizers is that by disrupting intermolecular polymer chain interactions, they can degrade the polymer over time and leach out into the environment. When plasticizers escape, they can be toxic to human health and harmful to the environment. By inserting a plasticizer into the backbone of the polymer rather than into the polymer solution, we reduce the risk of toxic molecules escaping the polymer. To solve this problem, a fluxional molecule such as bullvalene can be inserted into the backbone of the polymer. Bullvalene is a small molecule and due to its fluxional property, it will induce flexibility into the polymer as an internal plasticizer. Bullvalene is considered fluxional because it can undergo Cope rearrangements at room temperature. The purpose of this research is to develop the methods for synthesizing a novel polymer and to analyze its chemical and mechanical properties such as glass transition temperature and tensile strength. My project focuses on polycarbonates, a specific class of polymers. Polycarbonates are in many plastic materials such as water bottles and are increasingly important for consumer electronics. The results will have positive implications for human and environmental health by providing methods to develop safer plastic material.

Designing binders for single beta strand and beta-hairpin peptides could be useful for a wide range of biomedical applications. This project aims to design peptide binders that force unstructured peptides into a beta strand conformation. The computationally designed peptide-binder pairs were expressed and purified utilizing Immobilized Metal Affinity Chromatography (IMAC) and characterized via Size-Exclusion Chromatography (SEC) and biolayer interferometry. Successful binders were redesigned to bind pathogenic fragments of Amyloid-beta, alpha-synuclein and tau. These fragments are known to form beta strand mediated fibrils in the brain that are associated with the development of neurodegenerative diseases like Alzheimer’s and dementia. I am currently characterizing the redesigned binders for Amyloid-beta and expect higher-affinity binding with these designs. Success of this project could provide a new tool in studying the fibril formations and allow for future drug therapies.

When trying to develop the combinatorics of the p-parts of a multiple Dirichlet series given a group of functional equations isomorphic to the Weyl group of a type A root system, one runs into two natural combinatorial defintions of these p-parts in terms of Gelfand-Tsetlin patterns. The fact that these two natural definitions are equivalent is proved in Brubaker, Bump, and Friedberg's Weyl Group Multiple Dirichlet Series: Type A Combinatorial Theory. Their proof is not bijective. Further developing the combinatorics of these generalizations of the Riemann zeta function and other Dirichlet series, and finding a bijective proof of the result of Brubaker-Bump-Friedberg, remains an active area of research. I worked with a large group of undergraduate mathematicians, mentored by Ben Brubaker himself as part of the online collaborative Polymath Jr. Program, and we introduced new combinatorial objects, namely a new kind of colored lattice model, with which we can explicitly conjecture the existence of such a weight-preserving bijection for result of Brubaker-Bump-Friedberg in the most general setting, with p-parts corresponding to certain metaplectic Whittaker functions.