Physical Sciences and Mathematics Commons^™

Implementation Of A Constraint And Configuration Interaction Methodology Into Density Functional Tight Binding, Gunnar J. Carlson

WWU Graduate School Collection

This research aims to implement a charge constraint in conjunction with a small configuration interaction scheme into a density-functional tight-binding (DFTB) method within the DFTB+ quantum mechanical software package. This method aims to model the electron transfer rate of chemical systems by calculating the electronic couplings between two constrained states more efficiently. Electronic couplings are directly proportional to electron transfer, making them important parameters to efficiently compute the optimal minimum or maximum of an electron transfer rate, for example, when screening chemical systems based on their ability as a conductor. Other methods such as constrained density-functional theory followed by a …

Synthesis And Reactions Of Medium-Ring Silyl Ethers, Inna A. Fomina

WWU Graduate School Collection

Olefin metathesis is a reaction that creates new carbon-carbon double bonds by rearranging two alkenes. The reaction has undergone significant development since its discovery in the 1950s, from first reports to new catalysts and industrial uses, culminating in the 2005 Nobel Prize in chemistry. Grubbs ruthenium-based catalysts are widely used for such reactions, including ring closing metathesis (RCM) that involves the rearrangement of two alkenes on a single molecule to form a ring. During the course of investigating RCM reactions to produce eight-membered ring silyl ethers, we observed double bond isomerization when using the second-generation Grubbs catalyst and the Hoveyda-Grubbs …

Synthesis Of Guaipyridine Alkaloids Rupestines C, D And K With Studies Toward The Synthesis Of Rupestines B, J, L And M, Briana J. Mulligan

WWU Graduate School Collection

Hepatocellular carcinoma (HCC) is a type of primary liver cancer that is responsible for roughly 700,000 deaths around the world each year. While invasive treatment methods for HCC have proven to be limited, there are drug treatments available that show promising features. The structural elements of these drugs have given rise to an interest in guaipyridine alkaloids, specifically a family of naturally occurring guaipyridine alkaloids known as the rupestines. The rupestines have previously been isolated from the flowers of the plant Artemisia rupestris. This plant has been known for its reported antitumor, antiviral and antibacterial properties when used in traditional …

Pyridinediimine Complexes With Coordination Sphere Interactions Relevant To Copper And Non-Heme Iron Enzymes, Pui Man Audrey Cheung

WWU Graduate School Collection

Primary and secondary coordination sphere interactions with proximal Brønsted-Lowry acid/base sites were investigated using a family of pyridinediimine (PDI) complexes. The PDI ligands used in this project could be easily prepared by the Schiff base reactions with commercially available diamines as proton relays. Upon activation, the pendant Bronsted site and accessible electrons were arranged in a single scaffold that allowed the transportation of both protons and electrons to occur.

Two new PDI complexes with morpholine and pyrrolidine derivatives were introduced to the pendant PDI family. Their proton dissociation constant in acetonitrile were 17.1 and 18.3, respectively. The PDI complexes were …

Provenance Of Early Paleogene Strata In The Bighorn Basin (Wyoming, U.S.A.): Implications For Laramide Tectonism And Basin-Scale Stratigraphic Patterns, Jessica L. Welch

WWU Graduate School Collection

The Bighorn Basin (Wyoming, U.S.A.) contains some of the best exposed and studied nonmarine early Paleogene strata. Over a century of research has produced a highly resolved record of early Paleogene terrestrial climatic and biotic change as well as extensive documentation of spatiotemporal variability in basin-scale stratigraphy. The basin also offers the opportunity to integrate these data with the uplift and erosional history of the Laramide uplifts that surround the Bighorn Basin. Herein we provide a comprehensive provenance analysis of the early Paleogene Fort Union and Willwood formations in the Bighorn Basin from paleocurrent measurements (n = 510 measurements), detrital …

Computational Design Of Novel Materials For Solar Energy Conversion And Catalysis, Corey Teply

WWU Graduate School Collection

As synthetic chemists and materials scientists increasingly gain the ability to precisely arrange the atoms in solids, computation can provide guiding insight toward designing materials for a variety of applications. This work focuses on two distinct projects: 1) the use of biaxial strain in all crystallographic directions to tune the structural and electronic properties of perovskites for solar energy conversion, and 2) the extension of the concept of single-atom alloys to design stable motifs of multiple catalyst atoms on metal surfaces.

Perovskite solar cells have been shown to have band gap tunability when compressive or tensile-biaxial strain is enacted on …

Exploring Biochemical Mechanisms With Hybrid Quantum Mechanics/Molecular Mechanics And Enhanced Sampling Methods, Edwin Enciso

WWU Graduate School Collection

In the field of molecular dynamics (MD), a long-standing issue is the time frame required in order to fully observe a chemical reaction. Enhanced sampling methods have been the primary way of overcoming this issue for the past 40 years. In this experiment our goal was to combine new and existing sampling methods in order to create an efficient and accurate way of retrieving kinetics data from simulations. In order to do this, we examined two test cases: the enzymes chorismate mutase and cytosine deaminase. We did this using hybrid quantum mechanics/molecular mechanics simulations coupled with enhanced sampling methods. The …

Structural Studies Of The Von Willebrand Factor D’ Domain And Its Binding Mechanism To Factor Viii, Ap Wang

WWU Graduate School Collection

Hemophilia A is an X-linked disorder that results in uncontrolled bleeding, which is caused by a lack of activity for blood coagulation factor VIII, an essential protein cofactor in the clotting cascade. Factor VIII consists of multiple domains, and binding disruptions between factor VIII and its circulatory partner, von Willebrand Factor, may cause von Willebrand disease. Von Willebrand Disease type 2N is an autosomal recessive disease, and it is caused by binding disruptions between the D’ domain (also known as TIL’E’) of von Willebrand Factor and a3 domain of factor VIII. A 2.9Å Cryoelectron microscopy structure of the FVIII:vWF complex …

Enhancing Plasmonic Nanomaterials: Colorimetric Sensing And Sers, John Crockett

WWU Graduate School Collection

Nanomaterials, materials with at least one dimension on the nanoscale have become an area of extreme scientific interest due to their many unique properties with applications in catalysis, optics, and sensing, just to name a few. Metal nanoparticles are particularly interesting because of the interactions between light and surface electrons in the metal’s conduction band, called localized surface plasmons. In anisotropic metal nanoparticles these plasmons are especially exciting due to the highly responsive quality of the plasmonic resonance associated with their varied nano dimensions. Gold nanorods and nano dendrites in particular exhibit electromagnetic effects which are specifically associated to the …

Revaluating The Use Of Mollusks For Estimating Paleodepth In The Pacific Northwest, E Worthington

WWU Graduate School Collection

Fossil records have the potential to extract important paleoenvironmental records, and by ground truthing our assumptions with modern mollusks we can improve our interpretations of the fossil record. Modern molluscan death assemblages from Rosario Strait were analyzed to: 1) determine to what extent the molluscan communities were controlled by grain size or depth; and 2) determine the extent to which age mixing was occurring in the death assemblage. Twenty-eight Van Veen grab samples were collected in Rosario Strait to represent range of depth and grain sizes. All samples were wet sieved to isolate mature mollusks (> 2.00 mm), and sediment …

Engineering Segmentally Labeled Intrinsically Disordered Proteins, Erin Rosenkranz

WWU Graduate School Collection

It has long been accepted that a protein’s fold informs its function, but for the vital proteins that don’t adopt one specified fold, this is uninformative. Intrinsically disordered proteins have non-folded regions (IDRs) in their native functional state, which make up 30% of eukaryotic proteins, perform vital cellular processes and contribute to a multitude of disease states. Yet, IDR’s function, interactions and dynamics remain unknown due to their unstable, dynamic, lengthy and solvent-exposed nature. This, along with their tendency for insolubility and aggregation provide formidable challenges to not only their analysis, but their purification, requiring lengthy optimizations. NMR is valuable …

Floodplain Response To Eocene Thermal Maximum 2 In The Southern Bighorn Basin, Wyoming, U.S.A., Eve Lalor

WWU Graduate School Collection

Paleosols in the Willwood Formation of the Bighorn Basin, Wyoming contain a sedimentary and geochemical record of several early Eocene hyperthermal (rapid, global warming) events including the Paleocene-Eocene Thermal Maximum (PETM) and the Eocene Thermal Maximum 2 (ETM2). Numerous studies of the PETM indicate environmental shifts including an overall decrease in precipitation and soil moisture, but the hydrologic response to the subsequent smaller Eocene hyperthermals remains poorly understood. In order to estimate potential precipitation changes during ETM2, I sampled floodplain paleosol horizons from Willwood Formation strata below, within, and above the stratigraphic carbon isotope excursion (CIE) that marks the ETM2. …

Reidentifying Sources Of Tephra In The Izu-Bonin Arc: Recognizing Recent Rear-Arc Volcanism 1.1 – 2.7 Ma, Cassandra King

WWU Graduate School Collection

The focus of volcanic activity in the Izu-Bonin arc has migrated across the arc over time, creating distinct across-arc geochemical regions including the arc front, rift region, and the rear arc seamount chains (RASC). This study challenges the previously held assumptions that the rear arc was inactive after 2.8 Ma and that tephra deposited in the arc younger than 2.8 Ma with K₂O > 1 wt.% and La/Yb > 2.2 was sourced from the SW Japan arc. I studied 1.1 - 2.7 Ma tephra retrieved from core from the rear arc at Site U1437, IODP Expedition 350, in order to …

Grain Size Variability Spanning The Paleocene-Eocene Thermal Maximum In Laramide Basins: Reconstructing Paleoslopes And Overbank Erodibility, Delaney Todd

WWU Graduate School Collection

The Paleocene-Eocene Thermal Maximum (PETM) is an extensively studied global warming event occurring approximately 56 Ma and lasting around 200 kyr. Marked by a negative ¹³C excursion from a massive influx of CO₂ to the atmosphere, the PETM caused environmental alterations including increases in global temperature, changes in hydrology and ocean chemistry, and floral and faunal overturns. Evidence of these alterations during the PETM is found within both marine and continental basins. During the early Paleogene, the Laramide Orogeny formed a series of nonmarine basins within the Western Interior of the United States. Three of these basins, the …

Investigating The Transport, Fate, And Behavior Of Microplastics In Estuarine Systems Through The Application Of Metal-Doped Polystyrene Analogs Using Spicp-Ms, Robert Rauschendorfer

WWU Graduate School Collection

Plastics are a group of materials that are mass produced for their unique properties including durability. This has led to plastics becoming a global contaminant as a bulk material and as micro and nano sized particles termed microplastics and nanoplastics (MP/NPs), respectively. As awareness to MP/NPs has grown, these contaminants are found to be ubiquitous yet the risk to environmental systems remained unclear. Toxicity studies have been performed but the transport, fate, and behavior of these contaminants remains limited by the selectivity and sensitivity of the commonly used analytical techniques. To address this deficiency, MP/NP tracers have been developed using …

Effects Of Environmental Aging On The Acute Toxicity And Chemical Composition Of Various Microplastic Leachates, Allie Johnson

WWU Graduate School Collection

Microplastics have become ubiquitous in the environment and have been intensively studied in recent years. Researchers have documented several toxic effects to aquatic organisms, but the role of different microplastic properties in the toxic responses is not well understood. Toxic effects can be altered by the microplastic pieces themselves, by chemicals from the microplastics, and by sorbed environmental organic or metal pollutants, which microplastics concentrate and transport. I decided to focus on the chemical aspect of microplastic toxicity by observing responses of a marine invertebrate when exposed to several types of leachate solutions, created by soaking microplastics in seawater for …

Evaluating Thresholds In Fluvial Response To The Eocene Thermal Maximum 2 In The Bighorn Basin (Wyoming, U.S.A), Grace Marie Sutherland

WWU Graduate School Collection

Earth's climate experienced a set of hyperthermal events during the greenhouse climate state of the early Paleogene. The Paleocene-Eocene Thermal Maximum (PETM) was the largest of these abrupt global warming events, occurring at ~56 Ma and lasting for ~200,000 years. The PETM is identifiable by a large negative carbon isotope excursion and associated with significant changes in global temperature, hydrology, ocean chemistry, and biology. Subsequent smaller hyperthermal events appear to have commensurately smaller effects on marine environments, but the scaling of the complementary nonmarine environmental responses is unclear.

The Bighorn Basin of northwest Wyoming contains the most detailed nonmarine record …

Structural And Mutational Characterization Of The Blood Coagulation Factor Viii C Domain Lipid Binding Interface, Shaun C. Peters

WWU Graduate School Collection

Blood coagulation factor VIII (fVIII) functions as a cofactor in the blood coagulation cascade for proteolytic activation of factor X by factor IXa. During coagulation, fVIII is activated and subsequently binds to activated platelet surfaces by coordination of the fVIII C1 and C2 domains to the exposed phosphatidylserine of activated platelet membranes. Structural and mutational studies have suggested that both hydrophobic and electrostatic interactions occur between the two tandem C domains and activated lipid surfaces, but models of C domain phospholipid binding propose conflicting regions that directly interact with the membrane surface. This thesis reports the determination of the molecular …

Chemical Modification Of Silk Protein Via Palladium-Mediated Suzuki-Miyaura Reactions, Racine Santen

WWU Graduate School Collection

Suzuki-Miyaura cross-coupling reactions were used to modify the tyrosine residues on Bombyx mori silkworm silk proteins using a water-soluble palladium catalyst. Utilizing this cross-coupling reaction, molecules with specific functions can be introduced to silk in order to broaden the capabilities of silk proteins in biological systems. Model reactions using tyrosine derivatives were first screened to optimize reaction conditions. For these reactions, a variety of aryl boronic acids, solvents, buffers and temperature ranges were explored. Qualitative information on the reaction progress was collected via high performance liquid chromatography (HPLC), mass spectrometry (MS) and nuclear magnetic resonance (NMR). Reactions were then applied …

Using Principal Component Analysis And Hierarchical Clustering To Explore Trends In The Water Quality, Metal Concentrations, And Algal Taxa Richness Of 68 Lakes In Northwest Washington, Jeffrey Pratt

WWU Graduate School Collection

This study analyzed water quality, metals concentrations, and algal taxa richness data from 68 lakes in Northwest Washington that have been sampled by Western Washington University’s Institute of Watershed Studies. The primary goals of this analysis were to survey unmonitored lakes to gain a better understanding of the current conditions and to compare how lakes are characterized using combinations of the three data sets. Higher elevation lakes in the North Cascades were expected to have lower concentrations of metals and nutrients and more sensitive algae taxa than low elevation lakes in the Puget Sound Lowlands. When compared against Washington State …

Effects Of Environmental Weathering On The Acute Toxicity Of Tire Wear Particle Eluate To The Mysid Shrimp, Americamysis Bahia, P. Matt Roberts

WWU Graduate School Collection

For this study seven tire groups (six used-tire groups and one new-tire group) of the same brand and model tire spanning manufacture year 2013 to 2018 were used. Tire particles were artificially created and baseline toxicity was measured using the eluate from unweathered tire particle groups through 96-hour acute toxicity tests using Americamysis bahia. These results were then compared to toxicity results from a subset of the same tire groups that were deployed in a marine environment for weathering. Toxicity of unweathered tire particle groups had an LC50 range of 1.97 to 3.51 g/L and the toxicity of weathered …

Forest Restoration Of The Exposed Lake Mills Bed: Assessing Vegetation, Ectomycorrhizae, And Nitrogen Relative To Riverbank Lupine (Lupinus Rivularis), James Kardouni

WWU Graduate School Collection

This thesis investigated the managed revegetation outcomes of the exposed Lake Mills reservoir bed was investigated following the Glines Canyon dam removal on the Elwha River located in the Pacific Northwest, United States. During the following four years of restoration, one seeded species, riverbank lupine (Lupinus rivularis), quickly established on the coarse textured terraces that also had low organic matter (OM) and low soil nitrogen (N) levels. Nitrogen-fixing lupines may facilitate plant recruitment and conifer establishment, while demonstrating a relationship with ectomycorrhizal (ECM) communities which perform essential forest ecosystem functions. The purpose of this study was to investigate lupine’s influence …

Activation Of Nitrite And Carbon Dioxide By Cobalt Centered Redox Active Ligand Featuring A Hemilabile Pendant Amine, Douglas F. Baumgardner

WWU Graduate School Collection

Carbon dioxide (CO₂) and bioavailable nitrogen in the form of nitrates (NO₃^-) and nitrites (NO₂^-) are serious environmental pollutants. However, without economic incentives there is little interest in remediation of these pollutants outside of laboratory scale experiments. CO₂ can be converted to carbon monoxide (CO), a valuable building block in Fischer-Tropsch sourced fuel, and NO₃^- and NO₂^- can be converted to ammonia, another important chemical building block. However, both require effective, low-cost catalysts to be financially viable options. This thesis seeks to demonstrate the conversion of CO …

Paleomagnetic And Structural Analysis Of Geothermal Drill Core From Akutan, Alaska, Molly Kathleen Johnson

WWU Graduate School Collection

Hot Springs Bay Valley (HSBV) geothermal resource area on Akutan Island, Alaska, has increased fluid output and temperature by almost a magnitude, between 1981 and 2012 (Bergfeld et al., 2014). These increases have been attributed to increased permeability along NW-SE trending faults that may have been activated during a seismic swarm in 1996. In 2010 two unoriented drill cores were collected in Hot Springs Bay geothermal resource area. In this study I reorient sections from one of the highly fractured cores with paleomagnetic data to test this model of geothermal reservoir evolution at Akutan. The core is composed of interlayered …

Interdisciplinary Interspecies Pedagogies For Educating In The Anthropocene: Bringing Critical Animal Studies To Huxley College Of The Environment, Sarah R. (Sarah Rose) Olson

WWU Graduate School Collection

This report examines ENVS 499T Introduction to Critical Animal Studies: Theory, Agency, and Action, a 2-credit environmental humanities seminar designed as a M.Ed. in Environmental Education field project through Western Washington University’s (WWU) Huxley College of the Environment. ENVS 499T was created in response to a lack of critical animal studies course offering at WWU. The seminar was designed to provide WWU undergraduates with an opportunity to engage with interspecies ethical issues through an interdisciplinary lens. This report explores literature relevant to the design and implementation of this field project. It draws on scholars from critical animal studies and other …

Land, Body, Liberation: An Ecofeminist Pedagogical Approach To Place-Based Education, Amy L. Fitkin

WWU Graduate School Collection

Within this project I applied an ecofeminism framework to the tangible practices of place-based education regarding issues of social justice-based sustainability efforts. In order to recognize the impact of identity-based privileges, I explore how place-based education promotes the development of problem-solving skills, critical-thinking techniques and building meaningful relationships within a community. These goals were achieved by shifting the white settler colonist understanding of human conquest and subjugation over land and bodies from an anthropocentric lens to an androcentric lens. In other words, illuminating the oppressive role the patriarchy has continued to play in exploiting natural "resources" and the bodies of …

Using Multispectral Imagery To Interrogate Deposition, Alteration, And Weathering Across Curiosity Rover’S Traverse In Gale Crater, Mars, Christina Seeger

WWU Graduate School Collection

Since landing in 2012, the Mars Science Laboratory (MSL) Curiosity rover has explored over 20 kilometers of Gale crater, climbing almost 400 meters in elevation. The fluvio-deltaic, lacustrine, and aeolian sediments in the crater have been well documented by Curiosity’s suite of in situ and remote science instruments. Indeed, they have traced chemical trends that track changes in lithology and diagenesis over the study area—though most instruments only sample individual rock, vein, and soil targets at a very small scale. The Mast Camera (Mastcam) has periodically acquired much larger (meter-scale) multispectral, visible to near-infrared observations of outcrops throughout this stratigraphic …

Spatial And Temporal Trends Of The Annual First Detections Of Paralytic Shellfish Toxin In Puget Sound, Wa, Margaret Taylor

WWU Graduate School Collection

Since the 1950s, the Washington State Department of Health has routinely monitored the suite of toxins in shellfish associated with Paralytic Shellfish Poisoning. These toxins, known collectively as Paralytic Shellfish Toxins, are produced by species of the marine dinoflagellate in the genus Alexandrium. The role of the monitoring program is primarily to protect public health and safety; and therefore, use of these data for long-term statistical analysis has been limited due to opportunistic and irregular sampling of various shellfish species in space and time. However, some studies suggest that initiation of these toxic events have recently shifted to earlier …

Development Of Ti-Dftb: Transition Dipole Moment Calculations In A Time-Independent Density Functional Tight-Binding Framework, Megan Deshaye

WWU Graduate School Collection

Here we discuss the development of a time-independent excited state computational method that consists of three augmentations to the semi-empirical electronic structure package, DFTB+ 19.1. The density functional based tight binding method (DFTB) is an approximation of Kohn-Sham (KS) density functional theory (DFT) wherein the energy functional is expanded to second order with respect to density fluctuations. Application of a delta self-consistent field (delta-SCF) approach within DFTB has allowed for the variationally optimized calculation of spin-purified excited state (ES) properties, and forms the foundation of our time-independent DFTB (TI-DFTB) framework. Selection of KS spin orbitals based on the character of …

Wave Runup And Morphologic Change On A Mixed-Sediment Beach In The Salish Sea, Wa, Avery Maverick

WWU Graduate School Collection

A primary threat to coastal regions is extreme water levels from tides, storm surges, and waves which drive coastal evolution. Predicting wave runup, the vertical extent of wave uprush on a beach above still water level, and the morphologic responses to storms within the Salish Sea is complex because of the high variability of shoreline exposure to waves and wind, morphology, coastal landforms, and tide range across the region. As part of a USGS study, this project was designed to assess how wave energy offshore drives runup, validate existing runup models (van der Meer, 2002; Stockdon et al., 2006; Didier …