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 …

Community Perspectives Regarding Building Electrification As A Climate Mitigation Strategy In Bellingham, Wa: A Q-Study, Sarah K. Parker

WWU Graduate School Collection

Americans have varying ideas about the validity of climate science, the risk that climate change poses, and what action should be taken to address that risk. To effectively address climate change, policy makers must imagine and implement solutions that are meaningful and affirming to people with fundamentally different ways of perceiving the topic. In this study, I utilized Q-method to uncover distinct perspectives that stakeholders in Bellingham, Washington have regarding two proposed climate mitigation measures that would require the electrification of the City’s building sector. I conclude that the study participants represented three well-developed perspectives regarding the topic—the “Bold Climate …

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 …

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 …

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 …

Signaling And Trafficking In Choanoflagellates And Humans: A Study Of Conserved Peptide-Binding Domains, Haley Wofford

WWU Graduate School Collection

Many crucial cellular processes are regulated by signaling and trafficking pathways, which are largely dependent on protein interactions in the cell. These networks are thought to play a crucial role in the evolution of multicellular organisms from their unicellular ancestors. Choanoflagellates are unicellular organisms that can adopt a multicellular state, called a rosette. Though they evolved independently from and prior to the diversification of metazoans, they are the closest extant nonmetazoan ancestor to animals, making them a compelling model for the study of early multicellularity. Here, we look at two structurally conserved peptide-binding domains that both play important roles in …

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 …

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. …

The Effect Of Large Woody Debris, Direct Seeding, And Distance From The Forest Edge On Species Composition On Novel Terraces Following Dam Removal On The Elwha River, Wa., Sara J. Cendejas-Zarelli

WWU Graduate School Collection

The removal of two dams on the Elwha River, Washington, exposed over 300 hectares of reservoir sediments and created primary successional habitats that posed challenges to revegetation efforts. In order to meet Elwha restoration goals, coarse sediment deposits would require revegetation methods aimed at quickly restoring native vegetation while deterring exotic species invasions. I examined the effect of two restoration treatments—large woody debris translocations and native seed enhancements—on plant species composition on novel terraces in the former Lake Mills reservoir four years after dam removal. I sampled vegetation in seeded and unseeded treatment areas with and without large woody debris. …

Extension Of Restricted Open-Shell Kohn-Sham Methodology To A Density-Functional Tight-Binding Framework, Reuben Szabo

WWU Graduate School Collection

The restricted open-shell Kohn-Sham (ROKS) approach for singlet excited states provides some advantages over the ∆-self-consistent-field (∆SCF) method, requiring only a single SCF procedure and avoiding the problem of variational collapse. While ROKS is a powerful tool for DFT, its application to density functional tight-binding (DFTB) could offer significant improvements in time complexity when compared to DFT, enabling excited-state simulations of extended molecular systems on longer timescales than ROKS. In this work we discuss the implementation of an RO-DFTB approach in the DFTB+ package, as well as its suitability for the study of organic dyes and photoactive compounds. For benchmarking, …

How Science Policies Influence Ecological User-Engaged Research In Brazil And Peru?, Aline C. De Oliveira Machado Prata

WWU Graduate School Collection

As a growing body of literature suggests, to resolve current complex socioenvironmental problems such as climate change, deforestation, and the health crises unraveled by Covid-19 pandemic, requires scientific engagement across disciplines and beyond academia. Through the analysis of written policy documents and 70 semi-structured interviews with researchers in Brazil and Peru, this thesis investigates the Brazilian and Peruvian S&T governance models and policies, looking specifically at academic publication rewards, incentives and requirements, how ecologists and environmental researchers interact with such policies and whether they impact researchers’ ability to do engaged work.

While Peru has just started the process of accrediting …

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 …

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 …

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 …

Partner Preference In The Intertidal: Possible Benefits Of Ocean Acidification To Sea Anemone-Algal Symbiosis, Natalie Coleman

WWU Graduate School Collection

Ocean acidification (OA) threatens many marine species and is projected to become more severe over the next 50 years. Areas of the Salish Sea and Puget Sound that experience seasonal upwelling of low pH water are particularly susceptible to even lower pH conditions. While ocean acidification literature often describes negative impacts to calcifying organisms, including economically important shellfish, and zooplankton, not all marine species appear to be threatened by OA. Photosynthesizing organisms, in particular, may benefit from increased levels of CO₂.

The aggregating anemone (Anthopleura elegantissima), a common intertidal organism throughout the northeast Pacific, hosts two …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

Polybenzoxazine-Grafted Composites: Accelerated Polymerization Of Benzoxazine Resins From Bulk- To Microscale Mesylated Materials, Cassidy L. Crickmore

WWU Graduate School Collection

Benzoxazine-based resins often afford high modulus and high glass transition polymers that are desirable for creating safe and reliable thermoset parts and composites. However, benzoxazine resins have had limited widespread deployment into industry due to their high cure temperature. By blending functionalized glass substrates with the benzoxazine monomer, we hypothesize that the cure temperature of thermosetting resin can be lowered. The structure and purity of the particles, determined by NMR and FTIR, will be presented. DSC studies on the stability and cure accelerating properties of blends composed of functionalized glass substrates and benzoxazine monomer will be determined and compared against …

Integrating Synthetic Biology Derived Variables Into Ecological Risk Assessment Using The Bayesian Network – Relative Risk Model: Gene Drives To Control Nonindigenous M. Musculus On Southeast Farallon Island, Ethan A. Brown

WWU Graduate School Collection

Ecological risk assessment has not been conducted for the proposed environmental applications of synthetic biology. To develop a quantitative framework for risk assessment of synthetic biology, I selected Southeast Farallon Island as a case study for modeling the deployment of gene drive modified house mice to reduce impacts to threatened species. Southeast Farallon Island is part of the Farallon Islands National Wildlife Refuge. The island is populated by invasive house mice that impact indigenous species. Gene drive technology has been proposed as a method to suppress invasive rodent populations through CRISPR-mediated genome editing. I applied the Bayesian Network – Relative …

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 …

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 …

Bio-Preservation Potential Of Sediment In Eberswalde Crater, Mars, Cory Hughes

WWU Graduate School Collection

Within Eberswalde crater, Mars, is one of the most well-preserved river delta deposits identified within Mars’ rock record, and visually traceable from the deposit, is the partially-intact watershed that fed the paleo-lake that once resided within the crater basin. Aqueous alteration minerals, smectite clays and opaline silica, have been previously identified within the deposit, however the origin of those minerals is not well understood. Through analysis of topographic and hyperspectral data, we seek to ascertain the origin and provenance of these minerals to better understand their formative conditions and formation age. We will also assess Eberswalde crater’s potential as a …