Physical Sciences and Mathematics Commons^™

Modeling, Design And Fabrication Of Biocompatible Silk-Based Electronics And Actuators, Nicholas Ostrovsky-Snider

WWU Graduate School Collection

Biocompatible actuators are widely desired for a variety of biomedical devices such as micromanipulators, steerable catheters and artificial muscles but current devices have shortcomings in the range of motion they can achieve. Biocompatible electrodes made from conducting polymers (CPs) have been successfully created but achieving the spatial patterning of these polymers needed for electronic devices like strain gauges, stimulation electrodes and micro circuitry has been difficult. Previous work has relied on complex chemical incorporation of CPs into photoresists or electropolymerization onto vapor-deposited metal substrates. A simple method to produce metal-free flexible electronics would be highly desirable for biomedical electronics. This …

A Computational Investigation Of Bodipy Excited State Properties And Photosensitization Of Molecular Oxygen, Keenan Komoto

WWU Graduate School Collection

Cancer has long been a significant problem that has affected our world’s population for years and continues to this day. With the number of cases expected to increase annually there is a societal pressure to find effective treatment methods for eliminating cancer. Current forms of cancer treatment tend to cause detrimental effects to the human body and are usually quite expensive and long lasting, some costing upwards of $30,000 over an 8 week period. A more recently established form of cancer treatment known as photodynamic therapy is an effective treatment option for ridding cancers that lie on or just below …

Interpreting The Dynamics Of Submarine Landslides Through Hydroacoustic Modeling, West Mata Volcano, Ne Lau Basin, Jonathan G. Drobiarz

WWU Graduate School Collection

Landslides are an integral process in the development of submarine volcanoes, but these events are rarely recorded and observed. Therefore, understanding how the morphology of volcanoes evolve requires information on landslides. Hydroacoustic signals were analyzed for the purposes of characterizing frequent landslides on West Mata volcano during a 5-month eruptive period. Over 200 landslide signals have been compared in conjunction with hydroacoustic modeling to better understand the dynamics that control them. We used interference patterns produced by multipath rays to identify and model these slope failures. Landslides were most clearly captured on the north and west stations, suggesting a source …

Effectiveness Of Salmon Carcass Analogs As A Form Of Nutrient Enhancement For Juvenile Coho Salmon (Oncorhynchus Kisutch) In Three Lower Columbia Watersheds, Matthew T. Sturza

WWU Graduate School Collection

Adult Pacific salmon exhibit a form of parental care after spawning and perishing by depositing a subsidy of marine derived nutrients (MDN) that may be incorporated into the stream food web and feed juvenile salmon. Adult salmon populations have significantly declined since the late 19th century, thereby reducing the amount of MDN within Pacific Northwest Streams. This loss in nutrients within stream food webs may be limiting the growth and survival of juvenile salmon and therefore reducing the population sizes of adult salmon. One strategy to mitigate for nutrient deficiencies within a stream is the use of salmon carcass analogs …

Testing The Time Dependence Of Slip On The Western Klamath Lake Fault Zone, Oregon, Gunnar Speth

WWU Graduate School Collection

New geomorphic mapping and cosmogenic 3He geochronology on the Western Klamath Lake fault zone in southern Oregon reveals moderate, but resolvable changes in the rate of normal-fault slip rates over the past ~170 kyr. We focus on a sequence of glacial and post-glacial surfaces that record progressive offset by the fault zone over multiple time intervals. Thirty-nine new cosmogenic ³He surface exposure dates and a cosmogenic nuclide depth profile establish the first late-Pleistocene glacial chronology in the Cascade Range of Oregon and constrains the timing of the last two major glacial advances in the region at 17.6 ± 2.1 …

Plant Community And Nutrient Development Within Four Estuary Restoration Sites In Kitsap County, Washington, Shannon M. (Shannon Marie) Call

WWU Graduate School Collection

Coastal wetland ecosystems are some of the most productive ecosystems on the planet and link freshwater and marine environments. Coastal wetlands provide invaluable ecosystem services such as carbon sequestration, storm abatement, biogeochemical cycling, and water filtration. However, estuaries affected by physical barriers, such as culverts, experience reduced hydrological inputs and reduced connectivity above and below the site of impact. Loss of connectivity results in loss of ecosystem function such as carbon and nitrogen cycling. We investigated soil nutrients and vegetation composition of estuarine communities in four estuary restoration locations in Kitsap County, Washington and the following questions were addressed: 1) …

Do Conspecific Soil Microorganisms Inhibit Potentilla Recta?, Faythe Duran

WWU Graduate School Collection

In the U.S., Potentilla recta is an invasive, exotic forb. Previous research suggests that the soil microbes of native congeners (relatives within the same genus as P. recta) may inhibit P. recta, presumably because phylogenetically similar species may culture and be susceptible to similar pathogens. Our study aimed to answer three questions: (1) how do the fungal communities within the roots of P. recta compare to the fungal communities within the roots of neighboring congeners Potentilla gracilis and Drymocallis glandulosa (hereinafter referred to as the congeners) and native forbs, (2) what are the effects of the whole microbial …

Intermolecular Interactions That Lead To The Activation And Inhibition Of Ribosome-Dependent Gtpases, Amanda J. Weis

WWU Graduate School Collection

Ribosomes are the macromolecular machines responsible for protein synthesis across all domains of life. Translation of genetic information into a polypeptide by ribosomes is facilitated by a multitude of proteins called translation factors, many of which belong to the guanosine 5’ triphosphate hydrolase (GTPase) superfamily that utilize the hydrolysis of GTP to exert their function. Many naturally occurring antibiotics inhibit protein biosynthesis by targeting the bacterial ribosome or associated translation factors and with increasing antibiotic resistance due to bacterial evolution, the importance of studying ribosome-translation factor interactions is amplified. Determination of high-resolution structures of the ribosome has significantly bolstered our …

Building Arc Crust – Plutonic To Volcanic Connections In An Extensional Island Arc, The Alisitos Arc Crustal Section (Southern Rosario Segment), Baja California, Rebecca A. (Rebecca Anne) Morris

WWU Graduate School Collection

The southern volcano-bounded basin of the Rosario segment of the Cretaceous Alisitos oceanic arc provides outstanding 3-D exposures of the upper 7 km of an extensional arc, where crustal generation processes are recorded in the upper crustal volcanic rocks and underlying plutonic rocks. These exceptional exposures allow for the study of the physical and chemical links between the rock units, and helps constrain the differentiation processes active during the growth and evolution of the arc.

Upper crustal volcanic rocks comprise a 3-5 km thick volcanic-volcaniclastic stratigraphy with shallow sill and dike intrusions. Coarse-grained plutonic rocks intrude these units over a …

Towards The Substrate-Bound Structure Of Streptococcus Pneumoniae Sortase A, Orion Banks

WWU Graduate School Collection

Bacterial sortases have been widely studied for their usefulness in protein modification, however, the variable substrate specificity and activity between homologs of these enzymes is not yet fully characterized. To attempt to further understand sorting signal recognition, we have made advances towards a substrate bound structure of Streptococcus pneumoniae sortase A (SrtA_pneu). This enzyme displays a wide tolerance for alternate amino acids within the canonical LPXTG sorting motif. Our strategy involves a non-cleavable peptide analog that can be docked into the active site, allowing for elucidation of a structure displaying the key contacts that allow the enzyme to …

Clustering Of Epigenetic Methylation And Oxidative Damage: Effects On Duplex Dna Solution Structure, Thermodynamic Stability And Local Dynamics, David R. Gruber

WWU Graduate School Collection

All known living organisms use DNA to store genetic templates used for development, proper function and reproduction. The structural integrity of DNA is therefore of extreme importance and cellular machinery continuously regulates our DNA either through addition of covalent molecules to regulate the transcription of genes or the removal of DNA lesions propagating from the exposure to reactive molecules. One of the most common DNA lesions, 8-oxoguanine (8OG), is a prominent, pro-mutagenic DNA adduct present at a baseline level from consistent generation of reactive oxygen species through oxidative metabolism or at greater concentrations through exposure to ionizing radiation and …

Probing The Secondary Coordination Sphere Of Zn(Ii) And Fe(Ii) Pyridinediimine (Pdi) Complexes, Mayra Delgado

WWU Graduate School Collection

The transformation of many small, abundant molecules is necessary both in a biological setting and in the chemical industry. In Nature, the activation of small molecules is promoted by metalloenzymes. However, many of these chemical transformations are thermodynamically demanding and consist of multi-electron redox processes. Understanding the secondary coordination sphere has played an integral role in determining the catalytic activity and selectivity of such transformations and has led to the development of bioinspired catalysts in order to mimic the native active site of the metalloenzyme. Due to its extensive modularity, the utilization of the pyridinediimine (PDI) metal complexes was targeted …

Structural Characterization Of Factor Viii C2 Domain Activated Platelet Membrane Binding, Serena W. Wo

WWU Graduate School Collection

Hemophilia A is an X-linked blood disorder that results in the inability to form proper blood clots and may also cause spontaneous bleeding in the joints or muscles. This disorder is caused by mutations in the F8 gene that attenuate or abolish the activity of its protein product, factor VIII. Blood coagulation factor VIII (fVIII) is a glycoprotein that serves as a cofactor for the serine protease factor IXa on the surface of activated platelets to form the intrinsic tenase complex, which activates factor X during hemostasis to enable blood clot formation. Previous studies have shown that the C-terminal (C2) …

Structural And Functional Characterization Of The F-Actin Binding Headpiece Domain Of Plant Villin 4, Heather Miears

WWU Graduate School Collection

The villin family of proteins are filamentous actin (F-actin) regulators, which play key roles in cytoskeleton organization regulation in eukaryotes. Recently discovered villin 4, from A. thaliana has been shown to bundle F-actin in root hairs. However, previous work found that mutations to villin 4 result in shorter and sparser root hairs which lead to a weaker capacity for water absorption by A. thaliana. It is previously known that many members of the vertebrate villin protein family contain a highly conserved F-actin binding site within the C-terminal headpiece domain. In order to investigate the headpiece of villin 4, we …

Initiation And Evolution Of Subduction: T-T-D History Of The Easton Metamorphic Suite, Northwest Washington State, Jeremy Cordova

WWU Graduate School Collection

In the Northwest Cascades, results from previous workers show the Easton Metamorphic Suite contains an inverted metamorphic sequence with ultramafic rocks underlain by amphibolite and high-temperature blueschist that are juxtaposed above high-pressure low-temperature Shuksan Greenschist and Darrington Phyllite. In this study, amphibole and white mica ⁴⁰Ar/³⁹Ar geochronology is combined with cation exchange thermometry to constrain the temperature-time-deformation history of the suite. Amphibolite facies fabrics record two deformation events at 10 kbar. The oldest fabric formed at ~760 ̊C prior to 167.4 Ma (2σ). A second fabric formed at ~590 ̊C prior to 164.4 Ma. Na-amphibole schist associated …

Elk Abundance Estimation And Road Ecology In Whatcom And Skagit Counties, Washington, Nathan C. Rice

WWU Graduate School Collection

Chapter 1 – Elk abundance estimation using genetic mark-recapture in the South Fork Nooksack Valley, Whatcom County Washington. Non-invasive genetic mark-recapture is an increasingly useful method for estimating the abundance of elusive wildlife. This method was used to estimate the size of an elk population (Cervus canadensis) in the South Fork Nooksack River valley in northwestern Washington where dense forest cover can hamper aerial surveys. We genotyped 250 elk fecal DNA samples that were collected in a single sampling session. Only 103 samples amplified sufficiently after one PCR for genotype matching, which resulted in 49 unique genotypes. Program Capwire estimated …

Sediment Budget Of The Middle Reach Skagit River, Washington 1937-2015 Reveals Decadal Variations In Sediment Export And Storage, Amelia Deuell Rothleutner

WWU Graduate School Collection

Evaluation of historical meandering since 1937 shows that the active floodplain of the middle reach Skagit River between Rockport and Sedro-Woolley, Washington, has periodically been a significant source of sediment to the lower Skagit River and delta. In response to recent findings that the Sauk-Suiattle on average only supplies approximately 30% of the sediment load observed at Mount Vernon, I examined the geomorphic change and potential sediment production of the middle reach to test whether it is a significant source to the lower river. I tested the hypothesis that the 20-mile (32-km) middle reach has been a net source of …

Schrödinger Theory Of Electrons In Electromagnetic Fields: New Perspectives, Viraht Sahni, Xiao-Yin Pan

Publications and Research

The Schrödinger theory of electrons in an external electromagnetic field is described from the new perspective of the individual electron. The perspective is arrived at via the time-dependent "Quantal Newtonian" law (or differential virial theorem). (The time-independent law, a special case, provides a similar description of stationary-state theory). These laws are in terms of "classical" fields whose sources are quantal expectations of Hermitian operators taken with respect to the wave function. The laws reveal the following physics: (a) in addition to the external field, each electron experiences an internal field whose components are representative of a specific property of the …

Investigating Stress Response Across Integrated Biological Systems, Alice A. Han

Graduate Theses, Dissertations, and Problem Reports

The impact that a stressor has on a living system, whether it is on a cellular, organ, or even a whole organism level, can affect the overall health of the system. Monitoring the biochemical response resulting from a stressful experience offers insight into the numerous potential outcomes ranging on the spectrum of survival and death. Accessing this information not only provides a heightened understanding of the biochemical adaptions that occur, but also allows for the development of prediction models (to assess prospective influences of the stressor) or potential therapeutic treatments (to alleviate adverse effects) using measurable, quantifiable, and comparable metrics. …

Resonant Excitation Spectroscopy And Photon Statistics Of Self-Assembled Semiconductor Quantum Dots, Disheng Chen

Graduate Theses, Dissertations, and Problem Reports

Light-matter interactions in semiconductor nanostructures have attracted significant research interest because of both fundamental physics questions and practical concerns. Epitaxially grown quantum dots (QDs), with their narrow emission linewidths and atom-like density of states in a solid state system, are archetypical elements of study and are potentially useful for many applications, such as on-demand single photon emitters [1,2], efficient entangled photon-pair sources [3,4], and cavity quantum electrodynamics (QED) research [5–11]. Most experiments employ resonant or near-resonant excitation to directly interact with the bound states, which enables high excitation efficiency, precise control of quantum states, and minimal disturbance of the local …

The Programmatic Manipulation Of Planar Diagram Codes To Find An Upper Bound On The Bridge Index Of Prime Knots, Genevieve R. Johnson

Dissertations and Theses @ UNI

The “bridge index” of a knot is the least number of maximal overpasses taken over all diagrams of the knot. A naïve method to determine the bridge index of a knot is to perform Reidemeister moves on diagrams of the knot, and this method quickly becomes tedious to implement by hand. In this paper, we introduce a sequence of Reidemeister moves which we call a “drag the underpass” move and prove how planar diagram codes change as Reidemeister moves are performed. We then use these results to programatically perform Reidemeister moves using Python 2.7 to calculate an upper bound on …

Simulation Study On Jleic High Energy Bunched Electron Cooling, H. Zhang, Y. Roblin, Y. Zhang, Ya. Derbenev, S. Benson, R. Li, J. Chen, H. Huang, L. Luo

Mathematics & Statistics Faculty Publications

In the JLab Electron Ion Collider (JLEIC) project the traditional electron cooling technique is used to reduce the ion beam emittance at the booster ring, and to compensate the intrabeam scattering effect and maintain the ion beam emittance during the collision at the collider ring. Different with other electron coolers using DC electron beam, the proposed electron cooler at the JLEIC ion collider ring uses high energy bunched electron beam, provided by an ERL. In this paper, we report some recent simulation study on how the electron cooling rate will be affected by the bunched electron beam properties, such as …

An Example Of Nature's Mathematics: The Rainbow, John A. Adam

Mathematics & Statistics Faculty Publications

No abstract provided.

A New Formulation Of Time Boundary Integral Equation For Acoustic Wave Scattering In The Presence Of A Uniform Mean Flow, Fang Q. Hu, Michelle E. Pizzo, Douglas M. Nark

Mathematics & Statistics Faculty Publications

It has been well-known that under the assumption of a constant uniform mean flow, the acoustic wave propagation equation can be formulated as a boundary integral equation, in both the time domain and the frequency domain. Compared with solving partial differential equations, numerical methods based on the boundary integral equation have the advantage of a reduced spatial dimension and, hence, requiring only a surface mesh. However, the constant uniform mean flow assumption, while convenient for formulating the integral equation, does not satisfy the solid wall boundary condition wherever the body surface is not aligned with the uniform mean flow. In …

Advances On Software Defined Wireless Networking, D. B. Rawat, M. Song, C. Xin

Electrical & Computer Engineering Faculty Publications

Software defined wireless networking is regarded as an emerging technology to enhance spectrum efficiency and improve the overall network performance. In this paper, we summarise the special issue on recent advances in software defined wireless networking. Specifically, this special issue publishes following findings: i) a novel context aware medium access control scheme for multichannel buffer-aided cognitive networks to reduce the delay by exploiting the packets’ contexts; ii) a utility-based uplink scheduling algorithm that accommodates different performance metrics and adapts its decisions based on user-specified profiles by incorporating an intermediary layer between the MAC and network layer; iii) an opportunistic spectrum …

Preparing Teacher Candidates For Virtual Field Placements Via An Exposure To K-12 Online Teaching, Tian Luo, Laura Hibbard, Teresa Franklin, David R. Moore

STEMPS Faculty Publications

Aim/Purpose The goal of this project was to determine what effects exposure to online K-12 teaching and learning activities had on teacher candidates’ perceptions of K-12 online learning, how the exposure allowed teacher candidates to reach greater understanding of online pedagogy, and what effect such exposure had on teacher candidates’ aspirations to complete virtual field experiences.

Background With an increasing number of K-12 students learning online within full-time online schools and in blended learning environments, universities must prepare future educators to teach in virtual environments including clinical practice. Before engaging in online field placement, preservice teachers must be oriented to …

Light Soaking Phenomena In Organic-Inorganic Mixed Halide Perovskite Single Crystals, Hye Ryung Byun, Dae Young Park, Hye Min Oh, Gon Namkoong, Mun Seok Jeong

Electrical & Computer Engineering Faculty Publications

Recently, organic inorganic mixed halide perovskite (MAPbX₃; MA = CH₃NH₃^+, X = Cl^-, Br^-, or I^-) single crystals with low defect densities have been highlighted as candidate materials for high-efficiency photovoltaics and optoelectronics. Here we report the optical and structural investigations of mixed halide perovskite (MAPbBr_3-xI_x) single crystals. Mixed halide perovskite single crystals showed strong light soaking phenomena with light illumination conditions that were correlated to the trapping and detrapping events from defect sites. By systematic investigation with optical analysis, we found that the …

Femtosecond Laser Induced Structural Dynamics And Melting Of Cu (111) Single Crystal. An Ultrafast Time-Resolved X-Ray Diffraction Study, Runze Li, Omar A. Ashour, Jie Chen, H. E. Elsayed-Ali, Peter M. Rentzepis

Electrical & Computer Engineering Faculty Publications

Femtosecond, 8.04 keV x-ray pulses are used to probe the lattice dynamics of a 150 nm Cu (111) single crystal on a mica substrate irradiated with 400 nm, 100 fs laser pulses. For pump fluences below the damage and melting thresholds, we observed lattice contraction due to the formation of a blast force and coherent acoustic phonons with a period of ∼69 ps. At larger pump fluence, solid to liquid phase transition, annealing, and recrystallization were measured in real time by monitoring the intensity evolution of the probing fs x-ray rocking curves, which agreed well with theoretical simulation results. The …

Deep Models For Engagement Assessment With Scarce Label Information, Feng Li, Guangfan Zhang, Wei Wang, Roger Xu, Tom Schnell, Jonathan Wen, Frederic Mckenzie, Jiang Li

Electrical & Computer Engineering Faculty Publications

Task engagement is defined as loadings on energetic arousal (affect), task motivation, and concentration (cognition) [1]. It is usually challenging and expensive to label cognitive state data, and traditional computational models trained with limited label information for engagement assessment do not perform well because of overfitting. In this paper, we proposed two deep models (i.e., a deep classifier and a deep autoencoder) for engagement assessment with scarce label information. We recruited 15 pilots to conduct a 4-h flight simulation from Seattle to Chicago and recorded their electroencephalograph (EEG) signals during the simulation. Experts carefully examined the EEG signals and labeled …

Teaching Hands-On Cyber Defense Labs To Middle School And High School Students: Our Experience From Gencyber Camps, Peng Jiang, Xin Tian, Chunsheng Xin, Wu He

Electrical & Computer Engineering Faculty Publications

With the high demand of the nation for next generation cybersecurity experts, it is important to design and provide hands-on labs for students at the K-12 level in order to increase their interest in cybersecurity and enhance their confidence in learning cybersecurity skills at the young age. This poster reports some preliminary analysis results from the 2016 GenCyber summer camp held at Old Dominion University (ODU), which is part of a nationwide grant program funded by the National Security Agency (NSA) and the National Science Foundation (NSF). This poster also demonstrates the design of three hands-on labs which have been …