Within STEM, physics ranks among the least aligned with the US population regarding racial and gender representation. This not only has the potential to hinder new discoveries and innovations, it also highlights a lack of equitable opportunities for individuals. In an effort to identify ways in which teaching practices may contribute to this problem, our research explores correlations between active learning strategies and growth in students’ conceptual understanding. The data analyzed are from a pre/post survey in a two-year college calculus-based introductory university physics class with a primarily Vietnamese, Black, and white population. We present topics including force and free-fall that show either substantial or limited improvement in student learning gains. We compare data across several demographics, and relate corresponding learning activities. We provide recommendations to improve both learning outcomes and instructional methods, with the aim of increasing opportunities for all identities to complete degrees and pursue career goals.

Sustainable and effective wastewater treatment is a growing field that incorporates biological and environmentally friendly solutions to many stages in the wastewater treatment process. This study explored the tertiary treatment of wastewater through poplar tree bioreactors with a focus on nitrate and other nitrogen compounds. Synthetic secondary wastewater was made and fed to the bioreactors. The bioreactor effluent was then collected and analyzed. Previous work has shown significantly decreased levels of nitrate found in the poplar bioreactor effluent when compared to the control bioreactors. An important aspect of this bioreactor system is its ability to simultaneously produce biomass. To incentivize this project, the biomass produced can be sold to be synthesized into bioethanol. The latter portion of this study was a woody biomass analysis to compare the different growths between the treated and untreated poplar tree bioreactors. The trees were coppiced, processed, and dried at 60C for roughly seven days until there were little to no changes in the mass between hourly measurements. A leaf nutrient analysis of the treated and untreated trees was made to trace nitrogen pathways. Upon visual inspection, the treated trees appeared significantly larger and more developed. The result of the biomass analysis indicated that were was increased growth in the treated poplar bioreactors. Some of the treated trees had produced over five times the biomass of the untreated trees. The results of the leaf analysis showed greater carbon and nitrogen concentrations in the treated poplar leaves. Additionally, a higher percentage of nitrate was found in the leaf composition of the treated poplars. These results demonstrate that the treated bioreactors possessed an increased nitrogen uptake due to the increased presence of nitrate in the wastewater. There also appears to be a strong correlation between the treatment of the poplar tree bioreactors and their increased growth.

Ferrate is an effective technology for water treatment applications because of its capabilities as an oxidant, coagulant, and disinfectant. Furthermore, ferrate is an environmentally benign chemical derived from a ubiquitous mineral on the Earth’s surface. However, ferrate rapid reduction to ferric species reduces its oxidation capacity. Ferrate-coated sand has been proposed as a better deployable method for ferrate in water treatment applications. Sand has a high composition (>80%) of silica (SiO₂) which has been demonstrated to stabilize ferrate reactivity and increase its oxidation capacity. A previous study on the treatment of phenol, a common surface water contaminant, showed that ferrate-coated sand was better at degrading phenol than ferrate only (in the absence of sand). However, the study was conducted in pure water matrices. Here, we are evaluating the oxidation of phenol by ferrate-coated sand in the presence of effluent organic matter and trace metals (i.e. copper). Organic matter is ubiquitous in the environment and can impact contaminant remediation efficiency. Studies have detected trace metals in surface waters which can pose environmental and health risks. Through batch tests, we observed that effluent organic matter hinders the stability of the ferrate-coated media and reduces its oxidation capacity. The results of this study will provide information about the ferrate-coated sand reactivity and capacity for the treatment of complex water matrices.

We collected and compared the spectra of air plasma and argon plasma in a dirty and clean direct current (DC) plasma discharge device. After cleaning the plasma tube we hypothesize the measured plasma spectrum will have fewer lines because it wont have as many impurities. The fourth state of matter, plasma, is matter that has been superheated, causing the electrons to be ripped from the atoms. This forms an electrically charged gas that consists of negative electrons and positive ions. Our plasma was created using a DC plasma discharge device. This device creates a plasma between two electrodes inside of a vacuum chamber. A high DC voltage is applied across the two electrodes and a current flows between them. DC plasmas can be utilized as sputter sources to deposit thin films for solar panels and the purity of the plasma can affect performance. Our vacuum vessel was accidentally contaminated with oil and dirt. To evaluate the effectiveness of our cleaning practices, spectra was measured for plasmas in the vessel contaminated with oil and other dirt and then again after the vessel was cleaned. Spectra, the range of wavelength produced when light is dispersed, emitted by air plasma and argon plasma were measured between 645 nm and 1050 nm with an Ocean Optics ST-NIR spectrometer. Spectra before and after cleaning were compared to measure the effectiveness of the cleaning. Our research provides evidence for the best way to clean DC plasma discharge devices in order to remove impurities. The conclusion of this analysis is imperative for efficient thin film plating using DC plasma.

The emergence of induced Pluripotent Stem Cells (iPSCs) have allowed researchers to better study the effects of various diseases and mutations on fetal development. One such way of accomplishing this is the breakthrough of the organoid: a complex, iPSC-derived, 3D structure, that provides biologically relevant models for human systems. Lung Organoids (LO) were developed through this technology. However, the current LO models utilize mature lung phenotypes, which do not consider progenitor stages that may be critical for fetal development and the understanding of diseases that may affect this development in utero. The goal of this project is to provide characterization to the early stages of iPSC LO development: the Embryoid Body (EB) and Anterior Foregut (AFE). Using a previously established protocol, the LOs were fixed with 4% paraformaldehyde (PFA) on day 4 (EB stage) and day 6 (AFE stage), then analyzed with immunofluorescence analysis of the corresponding fetal lung (FL) development markers. 135 day old FL tissue sections were used as a positive control. The markers used to establish characterization were SOX17, a marker for the early endoderm germ layer, OCT4, an iPSC marker for pluripotency, and ECAD, a marker for tissue layer separation and cell migration. We hypothesized that all markers would appear in the EB stage, and the AFE stage would experience an upregulation in SOX17 and downregulation in OCT4 and ECAD. My results confirmed an upregulation of 133% for SOX17 and a downregulation of OCT4 by 58% from the EB to AFE stages. Lastly, as hypothesized, ECAD was present in EBs, but not in AFE. In conclusion, the LO stages proved to be similar to developmental stages of in utero development. Further analysis could help with new disease and mutation models for early development in utero, helping prevent devastating outcomes.

6PPD-quinone (6PPDQ), a transformation product of an anti-oxidant used in tire manufacturing, was recently identified as the causal agent of acute mortality in coho salmon. Abrasion on tires by road surfaces create tire wear particles (TWPs). Both TWPs and the accumulation of waste tires pose risks of leaching 6PPDQ into stormwater runoff. Crumb rubbers, which are manufactured to reduce landfill tire waste and applied in turf infills, may also leach 6PPDQ. My research aims to determine the conditions at which crumb rubber can be pyrolyzed to prevent 6PPDQ leaching from tire recycling options. If pyrolysis successfully removes 6PPDQ from crumb rubber, then the resulting material can be applied as an absorbent tire char to remove contaminants from water. Waste tire crumb rubber samples were pyrolyzed in a tube furnace under nitrogen flow for 90 minutes at a range of different temperatures. Methanol-based solvent extraction was used to extract the remaining 6PPDQ from the pyrolyzed samples and diluted until suitable for liquid chromatography-tandem mass spectrometry (LC/MS/MS) analysis. It is observed that as the pyrolysis temperature increases, the mass of 6PPDQ leached from pyrolyzed crumb rubber decreases. The results of this study allow us to understand the limitations of pyrolyzing tire rubber to develop activated carbon. To further investigate the feasibility of waste tire activated carbon, a chemical activation step will be added in pyrolysis to better replicate the creation of activated carbon.

Protein nanoparticles are useful for the design of novel vaccines. We can use these nanomaterials for display of antigens; however, antigens tested thus far have been homooligomers—consisting of a single unique component, and existing protein nanoparticle assemblies are not well-suited for the display of heterooligomeric antigens (such as HCV E1E2). We attempt to solve this problem through designing uniformly symmetric icosahedral nanoparticles that contain two distinct protein chains within their fundamental geometric component—referred to as the asymmetric unit; this allows us to retain the particle symmetry and double the number of accessible linkage points, or chain termini. This doubling of termini could allow us to fuse heterodimeric antigens to our cages. To accomplish this design goal, I utilized RFdiffusion—a generative machine learning model—to generate two-component icosahedral protein backbones, which were then filtered by evaluating subunit packing through a set of contact distance calculations. ProteinMPNN, a DL-based sequence design method, was used to assign candidate sequences to each of the filtered backbones. Finally, complete designs were filtered by using AlphaFold2 to evaluate fidelity to the original design model. I expressed the top 96 designs in E. coli, but saw minimal protein with no indication of assembly. In an attempt to maximize my chances of forming successful cages, I have elected to conditionally generate backbones that favor alpha-helical secondary structure. In this new design round, I hope to see favorable improvements in inter-chain packing; this will lead to an increase in passing design candidates and hopefully allow my computationally generated structures to have a higher chance of assembly in lab. This work serves to streamline the development of a therapeutic platform that can display multi-component antigens, which could enable the creation of new vaccines.

Organs-on-a-chip (OOAC) are biomimetic structures that replicate the physiological environments of human organs. OOACs are growing in popularity as they provide control of parameters including shear stress, concentration gradient, and biological interactions between cells and biofluids; they can be used in pharmacokinetic, physiological, and toxicological studies. The Kelly-Yeung lab works with kidney OOACs to study toxicology and pharmacokinetics. An important component of the chips is the hydrogel that provides a tubular scaffold and biological substrate for the kidney cells. The hydrogel mixture typically consists of decellularized kidney matrix, Collagen I (Col-I), and two types of cell culture media (PTEC and 199x). The matrix mimics the kidney microenvironment, the Col-I is a stabilizer and tissue regeneration agent, and the two cell culture media are used to mimic the extracellular fluids. More matrix in the hydrogel is ideal since it will better mimic a kidney. However, the matrix by itself is not structurally stable, hence the need for a stabilizing agent. The goal of this project is to maximize the ratio of matrix to Col-I while maintaining a stable hydrogel. In order to determine the optimal ratio, stiffness testing of the hydrogels will be performed via AFM (atomic force microscopy) and a Parallel Plate Rheometer to find out how much matrix can be used before the stiffness of the hydrogel composition is compromised. At this stage, we have started testing the collagen hydrogel with the rheometer to gain base measurements before adding the kidney matrix. We aim to incorporate the kidney matrix, achieving measurements closely mirroring those obtained with the collagen hydrogel alone, while supporting healthy cell growth. Creating a more accurate OOAC based on optimized kidney extracellular matrices will help improve the models and recapitulate the effects of drugs, toxins, and diseases on human kidneys more precisely.

Hypoxic ischemia (HI), the loss of blood and oxygen to the brain, is a common cause of neurological impairment and mortality. Astrocytes are one cell type that responds to acute trauma like HI and modulate the vascular-brain interface via their role in maintaining the blood-brain barrier (BBB). Therefore, astrocytes can be a potential therapeutic target; however, to screen methods to target astrocytes, there is still more to be discovered about astrocyte behavior in response to different stimuli. Towards this goal, this project aims to (1) create a robust and detailed characterization of cultured astrocytes over time, (2) evaluate astrocyte changes to different culturing conditions, and (3) measure the uptake of polymer nanoparticles, commonly used as drug delivery systems, on stimuli exposed astrocytes. My results show that after isolation, astrocytes are initially evenly distributed and form snowflake clusters, collectively assuming a star-shaped morphology. Over time, individual astrocytes move away from clusters and independently adopt the characteristic star shape. This suggests a dynamic process wherein astrocytes exhibit both collective and individual behaviors, contributing to the intricate architecture of astrocyte growth. Additionally, changes in the ratio of glial cells were observed. While microglia decreased in number and became less branched over time, oligodendrocyte populations remained relatively stable over time. Neurons that were initially sparse in the population decreased rapidly over time. Current studies involve the application of polymer nanoparticles to oxygen-glucose deprivation (OGD)-exposed cells immediately after OGD to evaluate uptake via imaging co-localization of particles with cells; OGD exposure induces HI injury in vitro. I have confirmed astrocyte response to OGD by analyzing cell morphology using imaging and cell viability assessments. These studies will establish an in vitro astrocyte model of HI and enable future studies incorporating additional BBB cells and other therapeutic platforms.

Bacterial metabolic engineering holds great promise for applications in medicinal, industrial, and climate technologies. A key element of metabolic engineering is the integration of non-native genes and pathways into microorganisms. However, the current state of technology is inefficient and time-intensive. Large cargo sizes of above 2-4 kilobases (kb) reduce integration efficiency, preventing entire metabolic pathways from being integrated into an organism at once. To maintain large heterologous genes and pathways in an organism’s genome, a seamless method for genomic integrations is necessary. A recent breakthrough in genetic engineering uses transposase enzymes and clustered regularly interspaced short palindromic repeat (CRISPR) machinery for more efficient and generalizable genomic integrations. Guided by RNA elements, this genomic integration system improves target site specificity and selection, as well as multiplexing capability (the direct insertion of genes at multiple genomic sites simultaneously). This system is expected to handle cargo insertions of around 10kb, meaning entire metabolic pathways can be implemented into a genome. My research aims to utilize this tool to demonstrate metabolic pathway integrations in non-model organisms and multiplexed knockouts for improved organism engineering. I plan to insert a fluorescent protein in 3 different industrially relevant organisms to demonstrate the generalizability of this genetic engineering toolkit. Additionally, I intend to establish multiplexing capability in multiple organisms by integrating the same genetic cargo at multiple sites using an array of guide RNAs, and determined results using polymerase chain reaction, gel electrophoresis, and DNA sequencing. Finally, using analytical methods such as liquid chromatography-mass spectrometry, I will measure the metabolic effects from integration of complete pathways. I will present the results of ongoing progress for all of the outlined tasks. Overall, my research on CRISPR RNA-guided transposases will enable the targeted, efficient integration of novel genes and pathways in bacteria, leading to significant advancements in therapeutics, biomanufacturing, and sustainable chemical conversion.