Physical Sciences and Mathematics Commons^™

Fluid-Wall Interactions In Pseudopotential Lattice Boltzmann Models, Cheng Peng, Luis F. Ayala, Orlando M. Ayala

Engineering Technology Faculty Publications

Designing proper fluid-wall interaction forces to achieve proper wetting conditions is an important area of interest in pseudopotential lattice Boltzmann models. In this paper, we propose a modified fluid-wall interaction force that applies for pseudopotential models of both single-component fluids and partially miscible multicomponent fluids, such as hydrocarbon mixtures. A reliable correlation that predicts the resulting liquid contact angle on a flat solid surface is also proposed. This correlation works well over a wide variety of pseudopotential lattice Boltzmann models and thermodynamic conditions.

2021 Nebraska Water Leaders Academy Final Report, Mark E. Burbach, Robert Matthew Joeckel, Brooke Mott, Gina S. Matkin

Conservation and Survey Division

Seventeen participants completed the 2021 Water Leaders Academy bringing the total number of graduates to 153 since the inception of the program in 2011. Assessments of participants’ transformational leadership skills, champion of innovation skills, water knowledge, engagement with water issues, civic capacity, entrepreneurial leadership behaviors, and boundary spanner abilities showed significant increases over the course of the year, according to both the participants and their raters. Feedback from the participants was highly positive and constructive. Academy planners are addressing participant concerns. Only minor changes are planned for the 2022 Academy curriculum. Results of the program assessment indicate that the curriculum …

Partially Metal-Coated Tips For Near-Field Nanospectroscopy, Yujia Zhang, Xinzhong Chen, (...), M. M. Qazilbash, Et Al.

Arts & Sciences Articles

Scanning probes with functional optical responses are key components of scanning near-field optical microscopes. For nanospectroscopy performed at IR and terahertz (THz) frequencies, one major challenge is that the commonly used metal-coated silicon tips yield nonadjustable coupling efficiency across the spectrum, which greatly limits the signal-to-noise ratio. Here, we test the possibility of a generic design scheme for wavelength-selective tip enhancement via finite-element numerical modeling. We employ a Si-based tip with various gold-coating lengths on the top, yielding a customizable near-field field strength at the tip apex. Calculations show a wavelength-dependent enhancement factor of the metal-coated tip due to the …

Dimers, Orientifolds And Stability Of Supersymmetry Breaking Vacua, Riccardo Argurio, Matteo Bertolini, Sebastían Franco, Eduardo García-Valdecasas, Shani Meynet, Antoine Pasternak, Valdo Tatitscheff

Publications and Research

We study (orientifolded) toric Calabi-Yau singularities in search for D-brane configurations which lead to dynamical supersymmetry breaking at low energy. By exploiting dimer techniques we are able to determine that while most realizations lead to a Coulomb branch instability, a rather specific construction admits a fully stable supersymmetry breaking vacuum. We describe the geometric structure that a singularity should have in order to host such a construction, and present its simplest example, the Octagon.

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 …

Marine Ecosystem Response To Late Pleistocene Rapid Climate Change In The Salish Sea, Alex Victor Hernandez

WWU Graduate School Collection

The ecologic response of marine invertebrates during collapse of the Cordilleran Ice-sheet through the Late Pleistocene has been insufficiently studied across the lowlands of northwestern Washington State and southern Fraser Valley, British Columbia. Assessment of the response of these nearshore marine assemblages to climatic shifts will improve our understanding of closely related modern taxa in analogous climate-stressed conditions. If we understand the former vulnerability of related genera, meaningful predictions may thus be provided for extant taxa in current and future time. In this thesis, I establish a compilation dataset of all relevant specimens collected within the Salish Sea and Puget …

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 …

Demystifying Denitrification: Coordination Complexes Give Valuable Insight Into The Reduction Of Nitrogen Oxides, Walker R. Marks

WWU Graduate School Collection

Increasing human population is driving the need to produce increasing amounts of food without the ability to dramatically increase farmland area. This has been accomplished by the application of increasing amounts of nitrogen containing fertilizers onto croplands. Nitrogen fertilizer overuse is causing imbalance in the natural nitrogen cycle via excessive amounts of high oxidation-state nitrogen entering both the atmosphere and aquatic ecosystems, which are major contributors to global warming and environmental damage. There is a need to explore synthetic systems which are capable of the reduction of these pollutants through pathways such as denitrification. This thesis will explore the functionalization …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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. …

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 …

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 …

Experimental Investigations Of Contact Friction And Transport Properties Of Monolayer And Bilayer Graphene, Prakash Gajurel

Graduate Theses, Dissertations, and Problem Reports

Results obtained from experimental investigations of contact friction in monolayer and bilayers graphene and the related effects on their transport properties are presented here along with their discussion and interpretation. For this purpose, chemical vapor deposited (CVD) graphene samples on SiO₂/Si were prepared. The samples were characterized by atomic force microscopy (AFM), Raman and X-ray photoelectron spectroscopy (XPS). Summaries of the results are given below.

Defects-controlled friction in graphene is of technological importance but the underlying mechanism remains a subject of debate. The new results obtained from the analysis of lateral force microscopy images revealed that the contact …