Major: Chemistry & Biochemistry Academic Year: Senior Faculty Mentor: Shannon Boettcher
Project title: Semiconductor-Electrocatalyst Interfaces on Photoanodes Designed for Photoelectrochemical Cells
Abstract: Solar water splitting using photoelectrochemical cells is a promising method for storing solar energy in the form of hydrogen bonds. Photoelectrochemical cells consist of two surfaces, the photocathode and photoanode, at which hydrogen and oxygen evolve from an electrolyte solution. Thin metal or metal-oxide electrocatalyst films are often deposited onto silicon based photoanodes in order to catalyze the oxygen evolution reaction and to protect the silicon from corrosion. Previous research has shown that thinner electrocatalyst films are correlated with more efficient photoanodes. However, the underlying physical processes driving this correlation remain unclear. This research uses an electrodeposition technique combined with cyclic voltammetry and atomic force microscopy to gain a deeper understanding of the semiconductor-electrocatalyst interface on photoanodes.
Major: Chemistry & Biochemistry Academic Year: Junior Lab: Cathy Wong
Project title: Correction of evolving background signals in single-shot transient absorption measurements
Abstract: The electronic properties of organic molecules can be tuned to attain target electronic functionality. This feature of organic molecules enables their use in technologies like solar cells and light-emitting diodes (LEDs), in replacement of conventional silicon materials. The electronic properties of organic systems can change depending on way individual molecules pack together to form larger aggregate structures. Understanding how the behavior of organic molecules changes while molecular aggregation occurs enhances our insight into how target electronic functionality can be obtained by altering the environment of the molecular system. Conventional methods of studying the electronic properties of molecular systems are not equipped to measure evolving materials. To examine the changing electronic properties of materials systems, we have developed a single-shot transient absorption (SSTA) spectrometer capable of measuring structurally non-equilibrated samples, like molecules in a solution stacking into a final aggregate structure. However, evolving samples have changing background signals which can hinder SSTA measurements of the electronic properties of a sample. In this work, we demonstrate a shot-to-shot correction of dynamic background signals for SSTA measurements. Our correction scheme improves the robustness of SSTA for measurement of materials systems during molecular aggregation. Characterizing the electronic properties of organic semiconducting molecules during molecular aggregation will ultimately facilitate the achievement of target electronic properties for use in technological devices, like solar cells and LEDs, which are becoming increasingly prevalent in our contemporary society.
Major: Chemistry & Biochemistry Academic Year: Junior Lab: Jim Hutchison
Project title: A Flux Story: Harnessing the Power of a Continuous Growth Synthesis to Study the Formation of Indium Oxide Nanocrystals
Abstract: Nanoparticles have led to incredible technological advances and continue to revolutionize the world around us. In order to pursue novel forms and enhanced synthetic control of these particles, however, we need a fundamental understanding of the growth processes involved. The concept of flux— in this context, the rate at which new material (monomer) adds to a growing particle— is one factor that has remained elusive with traditional synthetic routes. Using a novel slow-injection, continuous growth method developed by the Hutchison lab, we were able to study flux and its influence on the morphology (appearance) of indium oxide nanocrystals, as visualized with transmission electron microscopy. It was found that high flux conditions resulted in relatively branched particle morphologies, while relatively lower flux resulted in cubic particles. We tested several growth mechanisms to explain these observations in the context of different temperatures, and from these experiments, developed a model for nanocrystal growth involving diffusion of monomer across the crystal surface and attachment at reactive edge sites. Our group then utilized this model and the principles of flux to alter the morphology of preexisting particles. The importance of flux during nanoparticle growth, as demonstrated in this study, has far-reaching synthetic implications and should be a consideration in future inquiries.
Major: Earth Sciences Academic Year: Senior Lab: James Watkins
Project title: Palepiezometry Analysis of Recrystallized Quartz from Pre-Main Stage Veins in the Porphyry Copper Deposit in Butte, Montana
Abstract: Recrystallized quartz grains from pre-main stage veins in the porphyry copper deposit in Butte, Montana show microscopic evidence of different temperature and pressure conditions seen through the presence of all three recrystallization regime patterns that imply a range of conditions. In this study new methods are applied to analyze recrystallized quartz veins to generate strain rate conditions not previously constrained for these veins. Thin sections of these recrystallized quartz grains are densely populated with a range of different sized fluid and mineral inclusions. The presence of these inclusions prevents the standard application of the analysis function in ImageJ to accurately measure the area of the grains and create a grain boundary map. In order to overcome this obstacle in the study Fourier transforms were created of the images and a bandpass filter applied to eliminate the frequencies of those inclusions so that the inverse Fourier Transform images did not include them. More image processing was needed to skeletonize and fill left over holes in the images before ImageJ analysis. The grain diameters collected are inputted into paleopiezometry equations from Fazio and Ortlano et al. (2018) with temperature estimates from Fouriner et al. (1999). These determined strain rates can provide insights into the conditions of the porphyry system in early stages.
Major: Chemistry & Biochemistry Academic Year: Senior Lab: Ramesh Jasti
Project title: A Novel Application of Carbon Nanohoops in Ion-Sensitive Devices: A Potential Story
Abstract: Of the many types of ion-sensitive devices, one who’s potential has not been fully realized are chemically modified field effect transistors (CHEMFETs). These devices utilize ion receptors to detect specific target ions, commonly used to detect the presence of pollutants. One possible receptor is cycloparaphenylene (CPP), also called carbon nanohoops. In this research we determined the interaction between CPP and a variety of ions using CHEMFET devices, by measuring a change in output voltage at different ion concentrations. We expected CPPs to interact strongly with cations, as these molecules have an electron rich pore which has been applied as a chemical host in other systems. A preliminary screening showed an interaction between CPP and lithium, ammonium, and sodium cations. In addition control experiments established a baseline, in order to accurately quantify the interaction taking place. Further ion screenings, as well as ionic strength control studies, are future experiments that will be carried out to further characterize the interaction taking place.
Major: Chemistry & Biochemistry Academic Year: Senior Lab: Michael Pluth
Project title: Structure-Activity Relationship Study of the Ortho and Para Positions of Azide Triggers in Self-Immolative Thiocarbamate Donors
Abstract: Since the discovery of hydrogen sulfide (H2S) as a gasotransmitter in the body, there has been a need for organic donors which can release H2S to mimic its endogenous release in cells. H2S is a key molecule for signaling in the body, is a known vasodilator, and is also involved in promoting cell healing. It is important to learn as much as we can about the relationship between structure and activity of H2S donors so that donor design can be optimized. In this study, we used two self-immolative thiocarbamate donors with azide triggers in the ortho and para positions to observe how the position of the trigger affects the rate of H2S release. When the self-immolative thiocarbamate donors are triggered they produce carbonyl sulfide (COS) as a precursor for H2S. The COS is then converted to hydrogen sulfide via carbonic anhydrase (CA) enzyme. Through a methylene blue assay, we were able to measure the rate of release of H2S of both the ortho and para donors. Structural analysis of these donors will allow for more fine-tuning of H2S donors and a better understanding of how to develop fine-tuned donors.
Major: Physics and Chemistry Academic Year: Senior Lab: David Johnson
Publications related to this research:
Title: Properties and Synthesis of Three Component Heterostructure: (BiSe)1+δ(Bi2Se3)1+ δ (BiSe)1+ δ
As potentially applicable in high-performance electronics and quantum computers, topological insulators and
heterostructures containing them have recently garnered significant interest by materials scientists. Despite their imagined
utility, these compounds have proven difficult to synthesize. In a recent study of a series of compounds, [BiSe1+δ]m[TiSe2]
m with m = 1, 2, 3, it was observed that, for the m = 3 compound, the topological insulator Bi2Se3 formed upon deposition
and was present at all annealing temperatures. To test if Bi2Se3 could be incorporated into a heterostructure, a series of (BiSe)3-TiSe2
precursors with varying Bi-Se ratios and layer thicknesses were prepared and annealed at various temperatures for
30 minutes. A combination of specular and in-plane diffraction indicated that select precursors formed a highly crystalline
and crystallographically aligned compound containing BiSe, Bi2Se3, and TiSe2 and high-resolution electron microscopy
revealed the stacking sequence of the constituents. X-ray fluorescence measurements reveal that the compound formed
readily over a range of Bi-Se ratios. Electron transport measurements revealed metallic behavior and surprisingly high carrier
mobility, compared to BiSe1+δ TiSe2. These results provide a synthetic route for preparing a high quality Bi2Se3 containing
heterostructure with unexpected properties and with further research, a material with properties applicable to electronics or
quantum computers may be discovered.
Major: Earth Sciences Academic Year: Senior Lab: Samantha Hopkins
Title: Fossils of Oregon: Mammalian Body Mass Communities in the Miocene
The size of an organism relates to a host of other characteristics about a species such as diet, metabolism, and trophic level.
Changes in body mass through deep time are often the result of changing environments and climates. Previous research has
examined how the patterns of mammalian body size at a community scale are shaped by the environments the organisms
inhabit. However, the fossil record of Eastern Oregon has never been investigated through that lens. The extensive fossil
record and well-studied long-term environmental shifts in Eastern Oregon make it an ideal location to study the effects of
environmental changes on mammalian body masses. This study intends to classify and quantify the effects of the spread
of grasslands on body size structure of mammals in the Miocene. I estimated body mass for Miocene mammals using
measurements from fossil teeth as a proxy. These estimates derive from measurements taken with digital calipers and from
the computer program Image J. I then organized the body masses into size categories and compared the changes in size
structures as Oregon developed from a closed woodland in the middle Miocene to a more open, grassland environment in the
late Miocene. If a pattern is discovered, it could help inform biologists and ecologists which varieties of mammal are at the
greatest risk of climate-change related extinction in the near future.
Major: Physics and Computer & Information Science Academic Year: Senior Lab: Raghuveer Parthasarathy
Title: Using 3D Visualization to Study Immune Cell Distribution in Larval Zebrafish
Advances in microscopy and data visualization are enabling fundamental insights into a wide variety of biological processes.
During the early development of zebrafish, a popular model organism, immune cells grow and migrate. How the distribution
of immune cells in the organism changes with age, however, has been unclear. We therefore used light-sheet microscopy to
image fluorescent neutrophils, a type of immune cell, in larval zebrafish during the first few days of the cells’ development. We
then combined the imaging data with new three-dimensional visualization techniques using virtual reality to develop insights
into the spatial organization of these cells. The virtual reality system is widely applicable and accessible, with the ability to run
on common cell phones and work with various input types of input data. The use of virtual reality coupled with live imaging
data shows the promise of three-dimensional visualization as an avenue for exploring biological data.
Major: Physics and Mathematics Academic Year: Senior Lab: Tristan Ursell
Title: Chemotaxis Expansion Waves in E. Coli
Communities of bacteria respond to environmental changes as a group with the combined behaviors of individual
bacteria giving rise to unique collective behaviors that facilitate the growth and dispersal of bacteria. In particular, bacteria
undergo a process called chemotaxis which utilizes a run and tumble method to move towards higher concentrations
within a given chemical gradient. In liquid environments, collective consumption and chemotaxis towards nutrients
results in a collective behavior known as an expansion wave which facilitates rapid range expansion. How environmental
properties dictate the attributes of expansion waves is poorly understood yet critically important as expansion waves drive
invasiveness, colonization, and may help bacteria define their interspecies boundaries in complex communities. Here we
study the expansion of E. Coli in capillary tubes to replicate a one dimensional expansion environment. The use of various
concentrations of galactose and three amino acids give rise to different expression profiles and observable behaviors. After
inoculating cells into capillary tubes containing different nutrient media, we image the tubes using bright field microscopy
and measure the wave speed and number of waves in each tube. Wave speed allows us to understand how quickly bacteria
enter a new region and how this is affected by nutrient concentration. Because different waves may exhibit different
phenotypic states such as consuming different nutrients and undergoing cell division at different rates, we are interested in
understanding what nutrient concentrations give rise to multiple waves. We hypothesize that slower waves are undergoing
cell division more rapidly, thus devoting more energy to division than to consumption. Results thus far show that expansion
rate is constant until a threshold is met, and lower initial cell concentrations give rise to more waves.
Major: Earth Sciences Academic Year: Senior Lab: Ray Weldon
Title: Petrographic and Geochemical Correlation between Central Oregon Dikes and Flows to the
Columbia River Flood Basalts.
Central Oregon is made up of numerous basalt flows and dikes, having been produced from multiple volcanic events. While
much of the basalt in the region has been mapped Picture Gorge Basalt of the Columbia River Flood Basalts, the local dikes
may have a different source than the type area Picture Gorge Basalt. To further correlate or distinguish the local dikes from
the basalt flows in the Central Oregon region, we used petrographic features observed from thin sections and compared the
geochemistry of two dike samples to the geochemistry of various local basalt samples.
From the X-Ray Fluorescence (XRF) data of each sample, we produced plots that showed relationships and trends between
our samples. There are three clusters in our plots. One cluster contains the dike samples and one of the PGB samples. These
samples are abundant in TiO2, P2O5, SiO2 and K2O while having low percentages of MgO, Al2O3, and CaO. The second
cluster consists of five PGB samples, with low measures of TiO2, P2O5, SiO2 and K2O while containing higher traces of MgO,
Al2O3 and CaO. The last two basalt samples makes a third cluster of data points, which generally falls in the middle of the
trend line created by the two clusters mentioned earlier.
The Petrographic features observed further explain the geochemistry. The dike and NR1 samples are a mixture of glass, albite,
and few orthoclase grains, resulting in higher oxide content of SiO2, K2O and Na2O were as the cluster of five PGB samples
have higher percentages of large pyroxene grains and fewer plagioclase grains and glass, resulting in higher traces of MgO,
Al2O3 and CaO.
All samples plot within Grande Ronde Basalt boundaries, which have high silica content and MgO contents ranging from 2.5-
6.5 wt% and TiO2 ranging from 1.6-2.8 wt% (Reidel 2013). Plotting TiO2, P2O5, MgO and K2O offer the most reliable indicators
used to identify and distinguish flows (Reidel 2016, Hooper 2000). To further our study, we compared the geochemistry of the
PGB to other flow events of the CRFB, such as the Steens and Imnaha basalts. Both the Steens and Imnaha basalts plot below
the Grande Ronde Basalt on an alkali vs. silica plot (Camp 2013), indicating that the dikes in Central Oregon are indeed Picture
Major: Chemistry & Biochemistry Academic Year: Senior Lab: Ramesh Jasti
Title: Synthesis and Characterization of Ru(II) Cycloparaphenylene Complexes
Ruthenium polypyridyl complexes undergo metal-to-ligand charge transfer (MLCT) in the presence of light, allowing energy
from light to be captured in the form of an electron transfer. These molecules possess great potential as catalysts for efficient
and clean chemical processes. To develop light-harvesting complexes that perform advanced functions, new ligands, or
groups around metal ions, must be made. Cycloparaphenylenes (CPPs) are hoop-shaped photoactive molecules with virtually
unexplored roles as ligands. They possess exceptional size-dependent optic and electric properties, and show potential as
a new class of macrocycles for supramolecular chemistry, ultimately making them suitable for charge-transfer complexes.
Through the incorporation of nitrogen atoms into the backbone of CPP, we found that CPPs act as versatile ligands for
a variety of metals including Ru(II). However, the effects of CPP diameter on the electric properties of Ru(II)-based lightharvesting
complexes are unknown. We have recently synthesized CPP ligands of various sizes and coordinated them to
ruthenium centers, which has allowed for the investigation of size/diameter on these properties.
The optic and electric properties of the complexes have been studied using UV-Vis spectroscopy and cyclic voltammetry.
Here, we present our findings.
Major: Physics Academic Year: Senior Lab: Stephanie Majewski
Title: Clustering Algorithm Performance Studies for the ATLAS Trigger System at the HL-LHC
The Large Hadron Collider (LHC) at CERN is a particle accelerator providing massive amounts of data which can reveal new
physics about fundamental particles and forces. An upgrade to the LHC that will increase the luminosity will be enacted in
2026, called the High-Luminosity LHC (HL-LHC). The higher luminosity will increase the rate of proton-proton interactions in
detectors like ATLAS, thus these detectors must increase the speed of sorting through data. This sorting is performed by the
ATLAS Trigger System, which decides whether an interaction is interesting enough to keep within about ten microseconds.
Our group is studying the efficiency of different algorithms that cluster energy for implementation on a Field Programmable
Gate Array (FPGA) in the Global Trigger. These algorithms cluster the most energetic cells in multiple layers of
the detector to reconstruct particle showers. We have implemented the algorithms used on the FPGA in python in order to
validate the performance of the FPGA, analyze the background rejection and trigger efficiency of the clustering algorithms,
and compare these quantities between different algorithms.
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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