Major: Physics and Chemistry Academic Year: Senior Lab: David Johnson
Publications related to this research:
Major: Earth Sciences Academic Year: Senior Lab: Samantha Hopkins
Major: Earth Sciences Academic Year: Senior Lab: Josh Roering
Major: Physics and Computer & Information Science Academic Year: Senior Lab: Raghuveer Parthasarathy
Major: Physics and Mathematics Academic Year: Senior Lab: Tristan Ursell
Major: Earth Sciences Academic Year: Senior Lab: Ray Weldon
Major: Chemistry & Biochemistry Academic Year: Senior Lab: Ramesh Jasti
Major: Physics Academic Year: Senior Lab: Stephanie Majewski
back row, from left to right: Karl Reasoner, Eamonn Needham, Annie Gilbert, TJ LaGrow, Michael Womack, Andrew Carpenter
front row, from left to right: Alder Crammond, Michael Haley, Christina Trang, Elizabeth Curtiss, Geraldine Richmond
Major: Physics & Mathematics Academic Year: Senior Lab: Isenberg Lab
Abstract: This research seeks to determine whether the non-Kerrness of a binary black hole system approaches zero as the black holes collide, which is of practical importance for numerical simulations of black hole collisions. The nonKerrness measure is a geometric invariant that calculates whether a slice of spacetime is exactly Kerr spacetime, close to Kerr spacetime, or not Kerr spacetime. Kerr spacetime describes spacetime around a rotating, uncharged back hole. It should be noted that the non-Kerrness of a Kerr black hole is zero, but in the case of a binary system, the non-Kerrness is not equal to zero. Numerical simulations currently do not have standard ways of setting initial conditions for black hole simulations that mimic realistic conditions. Thus, the research seeks to demonstrate that minimizing the non-Kerrness of a set of initial conditions for a black hole simulation will pick the conditions that mimic the state of the system if it were to have evolved naturally. It has been assumed that if this phenomenon is true, the non-Kerrness measure could provide a way to choose initial conditions for simulations that minimize noisy data as the system evolves from the given initial conditions to a natural state.
Major: Mathematics & Computer and Information Science Academic Year: Senior Lab: Ahmadian Lab
Abstract: In the Neuroscience Department at the University of Oregon, Dr. Cris Niell’s lab studies the neurons of mice. The lab recently made novel discoveries on short-term memory with locomotion using trained mice. The mice were 63 trained using a Pavlovian reward system based on water deprivation. While on a dynamically rolling ball, the mice were given a vertical or horizontal visual stimuluses conducted the mice to move either left or right, respectfully. The data were given to the Ahmadian Lab to analyze. Using eigendecompensation, dimensional analysis, singular value decomposition, and principle component analysis, we show the effects of movement maintain the effects of movement maintain a longer dimming time in mice. . The findings suggest that movement increases the dimming time of a neuron cluster, which show that short term memory is improved. The results of this analysis conclude locomotion improves short-term memory.
Major: Chemistry Academic Year: Junior Lab: Boettcher Lab
Abstract: Hydrogen production has been an important aspect of renewable energy research as it can be obtained by splitting water in (photo) electrochemical cells. Due to the slow kinetics of the Oxygen Evolution Reaction (OER), catalysts are widely studied to increase the efficiency of the water-splitting reaction. The development of active, stable, and 100 inexpensive OER catalysts have been studied using first-row transition metals such as Nickel, Cobalt, and Iron. This research identifies activity trends for catalysts based on these elements in relation to compositional and structural changes. Principle characterization techniques include electrochemical measurements, Scanning Electron Microscopy (SEM), and X-ray Photoelectron Spectroscopy (XPS). In addition, a joint experimental and theoretical study is discussed in which the effects of varying cations in electrolyte have been evaluated. Incorporating different cations into solutions such as Na+, K+, Ca2+, and Mg2+ will lead to the analysis of the role of intercalated cations in OER and a better understanding of electrolyte impurities. By evaluating the effects of varying film composition, deposition techniques, and electrolyte counterions, the research provides a more comprehensive understanding of ternary OER catalysts, the role of electrolyte, and illustrates new design principles.
Major: Chemistry Academic Year: Senior Lab: Johnson Lab
Abstract: Anions are small negatively charged particles that have crucial roles in our everyday lives. Nitrate, an anion important for providing nutrients to crops, can also cause devastating environmental impacts in excess. This makes anion sensing an essential field of research in order to regulate and detect high concentrations of anions that are harmful to the environment. A dominate field of anion sensing research is through the development of supramolecular receptors. These small molecule receptors rely on reversible binding interactions taking place around a specially 45 designed binding “pocket” to latch onto any present anions. Typically, a single receptor is designed to exhibit selectivity, affinity, and a response towards one particular anion. This approach, referred to as the Lock-and-Key model, has limitations due to the difficulty finding all three of these components in one receptor. In order to overcome these limitations, a series of previously synthesized cross-reactive receptors from the Darren W. Johnson and Michael M. Haley lab are being incorporated into a sensing assay. This emerging field of supramolecular anion sensing utilizes the composite response of various receptors for detection of several different anions in a quick screening. The research will involve characterization of various receptors by a plate reader to determine response patterns of various probes. In the process, unique responses of receptors can be discovered through this quick screening approach that can be further investigated for the lock-and-key model. This research looks to contribute a unique set of receptors capable of detecting environmentally hazardous anions.
Major: Earth Sciences Academic Year: Senior Lab: Weldon Lab
Abstract: The Sagaing fault is a transform plate boundary between the India and Eurasian plates. The dextral motion of the Sagaing and the Red River faults creates a plateau between them called the Shan Plateau, which spans Myanmar, China, Thailand, and Laos. The Shan Plateau contains 14 active E-W sinistral-slip faults, including the Mae Chan fault (MCF). The ultimate goal of this study is to understand the seismic hazards of the Shan Plateau, by collecting a complete paleoearthquake record of the region. We do this using a combination of field and computational methods to determine the earthquake cycle, slip rates, and slip per event. Using the slip per event measurements, we then calculate the magnitudes that correlate with each event. After returning from the field in March 2017, we now have evidence of at least two events along the MCF. One of these events we have dated to be 500 AD. Once we finish determining dates on all the events, we can average them into an earthquake cycle. For the MCF, we have determined a cycle of 2,000-4,000 years and for the Sagaing fault is 200-500 years, which both are consistent with the slip rates of 1.4 mm/yr and 1-2cm/yr, respectively, determined from displacement features. Using this evidence, we can extrapolate the characteristics to the other 13 sinistral-slip faults along the plateau. This earthquake record will give us an understanding of the seismic hazards at play on this fault system, and thus will help mitigate damage to the surrounding communities.
Major: Earth Sciences Academic Year: Sophomore Lab: Watkins Lab
Abstract: Oxygen isotopes in calcite can indicate the temperature of their formation, which is useful for determining paleoclimate. To calibrate the relationship between oxygen isotope compositions and temperature, we precipitated calcite under controlled conditions. Previous experiments assumed that calcite grown on a timescale of days can grow in near isotopic equilibrium with the host solution. If this were the case, then the δ18O, the ratio of 18O to 16O of the calcite compared to the ratio of the solution, would only change as a function of the temperature of formation. Recent work has called into question whether natural and experimentally precipitated calcite actually grows in isotopic equilibrium with the host solution (Dietzel et. al. 2009, Watkins 2014). Dietzel et al. (2009) demonstrated that the stable oxygen isotope fractionation factor between calcite and water is affected by temperature, the pH of the solution, and the rate of calcite precipitation. Our lab showed that the isotopic disequilibrium in calcite may be derived from the dissolved inorganic carbon species in solution. We developed experiments designed to isolate the temperature, pH, and growth rate-dependence of oxygen isotope fractionation between calcite and water. Using the same setup, we show that salinity also has a significant influence on the oxygen isotopic fractionations; at high salinity, the δ18O of calcite decreases by 2‰ relative to low salinity, corresponding to a temperature difference of 8°C. Since much of the calcite found worldwide occurs in saline environments, the results have implications for the interpretation of oxygen isotope variability in nature.
Major: Chemistry Academic Year: Senior Lab: Pluth Lab
Abstract: Hydrogen sulfide is an important, biologically-produced molecule. It participates in singalling processes throughout the body and its misregulationcan lead to a number of diseases. As a resut, it has potential as a therapeutic agent. We have developed a scaffold that can donate sulfide and has advantages over currently employed systems such as diminished toxicity and potential for additional functionalization.
back row, from left to right: Manju Bangalore, Collin Hickmann, Alexia Smith, and N. Ian Rinehart
front row, from left to right: Selina Robson, Kendra Walters, Victoria Stanfill, and Anna Hickey
not pictured: Brianna Stamas
Major: Physics Academic Year: Sophomore Lab: Corwin Lab
Abstract: Granular materials are ubiquitous in nature. Depending on the thermal and physical conditions, they are capable of acting like a solid or a liquid. A jammed granular system occurs at a critical particle concentration at which the particles can no longer be rearranged by an external force. Oil droplets in oil-in-water emulsion can serve as a simplified model for the jamming of granular materials. The purpose of our project in Dr. Eric Corwin’s lab is to study force networks in granular systems and how individual particles perturb the packingese systems can benefit industries as diverse as agriculture and space exploration.
Major: Biochemistry Academic Year: Junior Lab: De Rose Lab
Abstract: Cisplatin is a commonly used anti-cancer therapeutic; however, its mechanism of inducing cell death is not well understood. In order to identify and isolate cisplatin’s cellular targets for characterization, our lab utilizes the “click” reaction (a physiologically stable and high yielding reaction that produces no harmful byproducts) to attach fluorescent compounds or other small molecules to platinated cellular targets such as DNA, RNA, and proteins. In this project, I optimized an in vitro pull-down procedure using streptavidin-coated magnetic beads to separate platinated cellular targets from unplatinated molecules. I first treated target DNA with a click-functionalized platinum reagent, then clicked that compound to a double-stranded DNA linker. The opposite end of this linker contains a biotin molecule, which interacts strongly with the streptavidin-coated magnetic beads through the streptavidin-biotin interaction. Using a powerful magnet, I separated platinated and clicked DNA attached to the beads from unreacted DNA, then confirmed the desired species of DNA was pulled down using polyacrylamide gel electrophoresis (PAGE), a method by which DNA or proteins can be separated by size. I determined that increasing the incubation time of the beads with the platinated DNA increased elution yields. Furthermore, elution temperatures above 90° C also increase the elution yield. Optimizing this pull-down technology will allow us to better characterize platinated molecules, and will ultimately improve our understanding of cisplatin’s cell-death inducing mechanisms.
Major: Biochemistry Academic Year: Junior Lab: Selker Lab
Abstract: Heterochromatin is a minimally transcribed, densely bundled complex of DNA and associated factors comprising large regions of the eukaryotic genome. It is essential for chromosome stability, genome integrity, gene regulation, and the silencing of transposons. The filamentous fungus Neurospora crassa is often employed as a model organism to study the epigenetic regulation of heterochromatin. In Neurospora, the conserved scaffolding protein heterochromatin protein 1 (HP1) binds H3 histones marked by lysine nine trimethylation (H3K9me3) and recruits other proteins to form at least three distinct complexes. HP1 recruits the DIM-2 DNA methyltransferase, which catalyzes DNA methylation. HP1 is also an essential component of both the HCHC histone deacetylation complex, which facilitates centromeric silencing, and the DMM complex, which limits aberrant heterochromatin spreading. However, it’s unclear how these disparate functions are coordinated. We hypothesized that they are modulated by post-translational modifications (PTMs) of HP1. Previously, we used mass spectrometry to identify HP1 sites harboring methylation, acetylation, formylation, and phosphorylation. I used amino acid substitutions at a subset of these sites to prevent individual PTMs in vivo. Substitutions at multiple sites were found to cause a substantial decrease in centromeric silencing independent of DNA methylation. These results suggest that the recruitment of HCHC to incipient heterochromatin may be selectively mediated by specific PTMs.
N. Ian Rinehart
Major: Chemistry Academic Year: Junior Lab: Tyler Lab
Abstract: Natural gas provided 28% of total energy consumption during 2014 in the United States. Nearly 20% of domestic natural gas wells are contaminated with nitrogen gas, making them unsuitable for use in natural gas burning equipment. Current methods of purification have a large cost, so they are often infeasible. A more feasible purification method is necessary to reduce the cost of purifying contaminated natural gas reserves and dependence on expensive imported natural gas. The Tyler Lab has demonstrated that a certain type of molecule called a coordination complex, which in this case contains phosphine ligands and a central iron atom, can serve as a nitrogen gas sorbent. Since the previous coordination complex bound nitrogen, but degraded too quickly to be applied in industry, current work is focused on creating a longer lived version of this molecule by redesigning the ligands bound to the central iron atom. Progress on the synthesis of this new coordination complex will be presented.
Major: Geology Academic Year: Junior Lab: Hopkins Lab
Abstract: The four modern hyena species are some of the most specialized carnivores on the planet. Three hyena species are bone-crushers—the only living mammals that are specialized for this—and one species is an insect eater, feeding on social insects such as termites. Hyenas are uniquely adapted for both of these diets. However, little is known about how hyenas evolved these capabilities. Unlike their modern relatives, the earliest hyenas were small omnivores that consumed plant material as well as meat. Some of these ancestral hyenas developed more carnivorous traits and 71 eventually became the bone crushers we are familiar with today. We can study the evolution of hyena diets, and by extension hyena ecological niches, by examining the shape and proportions of their teeth. I have applied this method to a hyena species recently discovered in Kyrgyzstan. The new hyena, currently designated as Hyaenictitherium sp. nov., has transitional dentition indicating an omnivorous but meat-dominated diet. The hyena was alive approximately 7 million years ago, making it a relatively young species. I am examining the ecological niche of this new hyena and determining how the specimen enhances our understanding of hyena evolution. Then, I am looking at other hyena species to determine if hyenas are following previously hypothesized patterns of dietary and ecological change.
Major: Biochemistry Academic Year: Junior Lab: Johnson Lab
Abstract: Nanoparticles have been studied for decades due to their optical, chemical, and magnetic properties, leading to a vast array of applications from nanocatalysts to contrast agents in magnetic resonance imaging. Nanoparticles are simply small-scale particles ranging from 1-100 nm in size, roughly the size of the tip of a sewing needle. The given size of nanoparticle plays an important role in their application, as many nanoparticles have size-dependent properties. In particular, magnetic iron oxide nanoparticles offer promise in technological applications such as magnetic inks or precursors for magnetic media devices. In order to effectively synthesize selectively-sized, monodisperse iron oxide nanoparticles, an understanding of their growth mechanisms is necessary. Currently, the parameters to produce selective iron oxide nanoparticles are extensive and each approach has its complications. The synthesis of nanoparticles has been studied extensively in the Hutchison lab in order to understand how to optimize their chemistry, size, and structure. Recent work has shown that a slow-injection synthesis versus a hot injection synthesis produces more monodisperse particles and is a greener method of synthesis. Additionally, particle size is directly related to synthesis temperature, and increases linearly as temperature increases. Many other conditions have been tested to see how the growth of particles is affected: air flow, environment, glassware, precursor used, and volume. Understanding these specific parameters enables synthesis selectivity in order to optimize the nanoparticle size desired for a given application.
Major: Physics Academic Year: Junior Lab: Majewski Lab
Abstract: A basic question about our universe remains unanswered: what is everything fundamentally made of? Everything we know of only makes up 4% of the universe; a significant fraction of the remaining 96% is made of an unknown fundamental particle referred to as dark matter. In an attempt to identify the dark particle, the Large Hadron Collider (LHC) at CERN in Geneva, Switzerland is recreating the conditions of the Big Bang. The ATLAS Experiment is one of two general purpose detectors at the LHC. In anticipation of discovering new physics, the ATLAS detector will undergo numerous hardware upgrades in the coming years, one of which will be an improvement to the existing trigger system which is a 3-level hardware and software based system. This study focuses on the upgrades to the level-1 trigger. The LHC collides bunches of protons every 25 ns, which amounts to a lot of data in an extremely short period of time. Specifically, the missing transverse energy (ETmiss) trigger is crucial in being able to detect a previously undetectable particle. Therefore, we propose implementing a topological clustering inspired algorithm on the level-1 ETmiss trigger. The algorithm will be employed on the gFEX (global feature extractor) with 0.2×0.2 eta-phi granularity to be installed in 2019. This study analyzes the performance the algorithm for future implementation.
Major: Chemistry Academic Year: Junior Lab: Haley Lab
Abstract: Organic field-effect transistors (OFETs) are a type of organic electronic device that determine how and where charge flows throughout a system. They are important to the electronic industry because they are longer lasting and cheaper to synthesize than traditional silicon field-effect transistors. OFETs are ranked on their charge mobility, the speed and quality of the charge transfer. Diindenoanthracenes are a type of organic small molecule with potential to be used in OFETs because of their biradical character, giving them the ability to transport charge. Our research focuses on synthesizing a variety of diindenoanthracene derivatives so we have a large range of molecules with different electronic properties to test in devices. The ultimate goal is to increase the charge mobility of these molecules so that these electronic devices are comparable to traditional inorganic electronics. So far we have created one new diindenoanthracene which has yet to be tested in devices, but we are working towards creating a more generalized synthesis method to make it possible to add a variety of substituents to the general diindenoanthracene scaffold.
Major: Geology Academic Year: Senior Lab: Davis Lab
Abstract: Biodiversity loss is recognized as a global crisis. Current research strives to create models that predict regions that are at high risk for a significant drop in biodiversity levels. These models must be scaled by analyses of historic changes in biodiversity. However, no study has yet to analyze the changes in mammal richness in the United States at a high enough spatial and temporal resolution to produce a predictive model of mammal diversity. Our research is a high-resolution analysis of the changes in mammal richness in the contiguous United States from 1906 to 1995. We collected mammal occurrence data from the online database VertNet and BISON and individual museum collections, divided it into ten year increments, and used scripts in R to produce sampling-standardized patterns of mammal richness for each decade. We then analyzed the geographic distribution of change in richness over the 20th century. From our results, we were able to determine which regions experienced a significant rise in diversity levels and which experienced a significant drop. We also identified regions where sampling intensities remain too low to conclusively determine how mammal diversity has changed. Regions experiencing the most severe biodiversity changes, as well as those without adequate data, should be focal areas for continued research in conservation efforts.
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