The utility of high-throughput, computational screening has become an invaluable asset to the field of materials science. In the hierarchy of computational methods, the most accurate methods are often the most computationally expensive. However, as both the efficiency and fidelity of numerical techniques advance, high-quality screening of large materials datasets...
The focus of this thesis is to design, characterize, and apply novel computational methods and molecular systems to interrogate heterogeneous human gut microbiome-related phenomena. In Chapter 2, I design, implement, and characterize a method for embedding co-occurrence patterns derived from massive 16s amplicon datasets. I use this method to 1....
Fission product yields (FPYs) are used for a wide range of applications including nuclear fission theory, nuclear reactor design, reactor antineutrino anomaly, stellar nucleosynthesis, and nuclear forensics. These applications rely on FPYs that were last evaluated in 1993, which included measurements from all over the world up until 1993. In...
In this dissertation I explore the Arms representation and activities for teaching quantum mechanics invented at Oregon State University. In the Arms representation students embody quantum states. The Arms activities are presented as an exemplar of the unique physics classroom culture of the upper-division Paradigms in Physics program. In the...
Immobilized proteins are integral components of a number of important technologies, including the principal component of many biosensors, as functional coatings in various implants, as catalysts is industrial biosynthesis, and as the building blocks of next-generation nanotechnologies. Despite their ubiquity, relatively little is known about the processes that shape immobilized...
Wastewater treatment plants are considered one of the main sources and reservoirs of antimicrobial resistance (AMR). This study investigated the prevalence of 8 different phenotypes of AMR, multi-drug resistant (MDR), and extended-spectrum beta-lactamases (ESBL) producing E. coli in 17 wastewater treatment plants across Oregon in winter and summer of 2019...
Physics sensemaking is a growing topic of study within the physics education community. Many lenses have been used to study sensemaking but few have considered how time and instruction can impact student sensemaking practices and ideas. In this dissertation, I present four studies that address four major questions: What sensemaking...
Modern plant pathology benefits from integrating methods and concepts from evolutionary biology. For example, evolutionary concepts are used to identify and examine species boundaries of plant pathogens, recognize processes underlying pathogen biogeography, identify traits that characterize emerging species, and discover new molecular interactions that originate under processes of selection. In...
Bioenergy is a rapidly growing subsector of the emerging global bioeconomy, with the potential to create a substantial number of jobs and mitigate climate change. In order to develop bioenergy into a viable industry, capable of providing valuable energy and employment, there is an immediate need for a skilled workforce...
Phenylketonuria (PKU) is a genetic inborn metabolic disorder which inhibits the functional production of the enzyme phenylalanine hydroxylase (PAH). It currently affects one in 15,000 Americans and is the most common amino acid metabolism error found in newborns. Individuals affected with PKU are incapable of metabolizing the amino acid, phenylalanine...
Many ecologists and environmental scientists witnessing the scale of current environmental change are becoming increasingly alarmed about how humanity is pushing the boundaries of the Earth’s systems beyond sustainable levels. The world urgently needs global society to redirect itself toward a more sustainable future: one that moves intergenerational equity and...
The purpose of this study was to make a preliminary
investigation of the productivity of some of the soils
within the Willamette catena under different systems of
soil management. The study was carried out at four experimental
sites near Corvallis, Oregon, during the 1962 growing
season. The soil at each...
Imazamox-resistant wheat (Clearfield®) cultivars carry the Imi1 gene, which confers resistance to the imidazolinone (IMI) herbicide imazamox. Imazamox provides selective control of jointed goatgrass and other weeds in IMI-resistant wheat. Imi1 gene flow between IMI-resistant wheat and jointed goatgrass may occur via hybridization and backcross events. In 2009 and 2010,...
The influence of variety, plant population, and planting date on
corn silage production was studied at Hyslop Agronomy Farm,
Corvallis, Oregon. The corn plants were grown under irrigation with
300 pounds per acre of 16-20-0 (N-P₂0₅-K₂0) and 240 pounds of urea,
providing a total nitrogen application of 158 pounds per...
The nature of inheritance and possible associations for traits
influencing earliness and grain yield were investigated using a four
parent diallel of winter and spring wheat cultivars.
More genetic variability was observed for the traits measured in
segregating populations resulting from crosses between winter and spring
type wheats in contrast...
Investigators have been studying an aggregate
containing enzymes of deoxyribonucleoside triphosphate
biosynthesis in T4-phage infected bacteria. They suggest
that it behaves as an organized complex, efficiently
channeling DNA precursors to the replication apparatus.
Previous work has suggested that about 10 enzyme
activities remain associated through several fractionation
steps. This multi-enzyme...
Bacteriophage T4 gene 42 encodes dCMP hydroxymethylase, an
enzyme unique to the deoxyribonucleotide metabolism of T-even
bacteriophages. To study biochemical and biophysical properties of
the enzyme, as well as the interaction of dCMP hydroxymethylase with
other DNA precursor biosynthetic enzymes in vitro, availability of large
amounts of the enzyme is...
The trans-Pacific atmospheric transport of particulate matter (PM)-bound polycyclic aromatic hydrocarbons (PAHs) to remote sites in western North America has been well documented and has triggered research questions regarding to atmospheric transformation of PM-bound PAHs and the potential impacts on human health from their inhalation exposure. In this dissertation, field...