Physical Sciences and Mathematics Commons^™

Biological Control Of Purple Loosestrife (Lythrum Salicaria): Factors Affecting Galerucella Pusilla And Galerucella Calmariensis Establishment In Tidal Areas, Lynda Kathryn Moore

Dissertations and Theses

Galerucella pusilla and G. calmariensis have provided successful biological control of purple loosestrife (Lythrum salicaria L.) in non-tidal areas but only marginal control in areas of tidal influence. While a previous study identified mechanical scour by tidal waters as the main cause of establishment failure, purple loosestrife stem density explained more than 80% of the variability in presence and absence of Galerucella at my study sites in the Columbia River Estuary. A logistic regression model using purple loosestrife stem density, elevation, and their interaction as predictors accurately predicted 92.5% of Galerucella presence or absence observations of a test data …

Model Reduction For Simulation, Optimization And Control, Oleg Edward Roderick

Dissertations and Theses

Many tasks of simulation, optimization and control can be performed more efficiently if the intermediate complexity of the numerical model is reduced. In our work, we investigate model reduction, as applied to reaction-transport systems of atmospheric chemistry. We use a Proper Orthogonal Decomposition-based approach to extract information from a set of model observations, and to project the model equations onto a reduced order space chosen in such a way that the essential model behavior is preserved in the solution of the reduced version. We examine and improve many features of the method. In particular, we show how to measure sensitivities …

Comparison Of The Focal Properties Of Selected Magnetic And Electrostatic Lenses And Tests Of Their Theoretical Models, Luis Thomas Almarez

Dissertations and Theses

The main goal of the present research is to determine whether there is a significant difference between the aberrations of magnetic and electrostatic electron lenses when they are used in the same way. Comparison of the lenses was done in an electron-optical bench, set up to resemble a scanning electron microscope (SEM). Five different lenses, two magnetic and three electrostatic, were compared. Each group included two lenses with different lens-field lengths (pole-face spacing in magnetic lenses and interior length in electrostatic lenses). The lenses were used in turn to focus the electron beam into a demagnified image, or probe. The …

Finite Sample Properties Of Minimum Kolmogorov-Smirnov Estimator And Maximum Likelihood Estimator For Right-Censored Data, Jerzy Wieczorek

Dissertations and Theses

MKSFitter computes minimum Kolmogorov-Smirnov estimators (MKSEs) for several different continuous univariate distributions, using an evolutionary optimization algorithm, and recommends the distribution and parameter estimates that best minimize the Kolmogorov-Smirnov (K-S) test statistic. We modify this tool by extending it to use the Kaplan-Meier estimate of the cumulative distribution function (CDF) for right-censored data. Using simulated data from the most commonly-used survival distributions, we demonstrate the tool's inability to consistently select the correct distribution type with right-censored data, even for large sample sizes and low censoring rates. We also compare this tool's estimates with the right-censored maximum likelihood estimator (MLE). While …

Electron Transport And Sensor Characteristics Of Tin Dioxide Based Nanocrystalline Materials, Allen Chaparadza

Dissertations and Theses

Wide band gap, transparent semiconductor Sn0₂ is an n-type conductor and is widely used as a sensor material as well as transparent electrode material e.g. in solar cells and flat panel displays. Recent discovery of p-type doping with Li has opened exciting possibilities in new classes of sensors and transparent nanoelectronic devices. Li-doping in SnO₂ nanoparticles was explored through a gel-sol method of synthesis to examine the influence of reaction conditions such as pH, dopant concentration, and calcination temperature. The Li doping in nanoparticles was characterized using nuclear reaction analysis and the nanostructure with high-resolution electron transmission microscopy …

Active Site Chemistry Of The Nadph-Dependent:7-Cyano-7-Deazaguanine (Preq0) Nitrile Oxidoreductase, An Enzyme Involved In Queuosine Biosynthesis, Bobby Wai Keung Lee

Dissertations and Theses

Queuosine (Q) is a modified nucleoside found at the wobble position of bacterial and eukaryotic transfer RNAs (tRNAs) that are specific for the amino acids tyrosine, histidine, aspartate and asparagine. A recently discovered enzyme in the biosynthetic pathway of Q, the NADPH-dependent 7-cyano-7-deazaguanine oxidoreductase (QueF), carries out the two-fold, four-electron reduction of Q precursor preQ0 to preQ1 and represents the first example of the enzymatic conversion of the nitrile functional group to an amine. Presented herein are kinetic, spectroscopic, mutational, biophysical, and isotope labeling studies directed at the elucidation of the chemical and kinetic mechanisms of this new class of …

Prediction Of Persistence Of Fertilizer-Derived Cadmium In Oregon Agricultural Soils Using Equilibrium Modeling And Fertilizer Release Kinetics, Fungai Mukome

Dissertations and Theses

Organic farming has become a multimillion dollar industry and while much emphasis is put on subsequent fertilizer inputs onto these fields, very little consideration is given to the prior fertilization activities of these soils. For a farm to be certified organic it means no harmful chemicals have been applied for at least three years.

The overall hypothesis tested by this research was that equilibrium adsorption models can adequately represent the behavior of fertilizer-derived cadmium in Oregon agricultural soils and that such model results can be easily incorporated into risk assessment models, transport study models and persistence studies for organic or …

Quantum Multiplexers, Parrondo Games, And Proper Quantization, Faisal Shah Khan

Dissertations and Theses

A quantum logic gate of particular interest to both electrical engineers and game theorists is the quantum multiplexer. This shared interest is due to the facts that an arbitrary quantum logic gate may be expressed, up to arbitrary accuracy, via a circuit consisting entirely of variations of the quantum multiplexer, and that certain one player games, the history dependent Parrondo games, can be quantized as games via a particular variation of the quantum multiplexer. However, to date all such quantizations have lacked a certain fundamental game theoretic property.

The main result in this dissertation is the development of quantizations of …

Quaternions, Octonions, And The Quantization Of Games, Aden Omar Ahmed

Dissertations and Theses

We present an effect on classical games that is obtained by replacing the notion of probability distribution with the notions of quantum superposition and measurement. Our particular focus will be on two and three player games where each player has precisely two pure strategic choices. Games in normal form are represented as "payoff" functions.

Game quantization requires the extension of these functions to much larger domains. The main result of this work is the co-ordinatization of these extended functions by either the quaternions or octonions in order to obtain computationally friendly versions of these functions. This computational capability is then …

A Framework For Superimposed Applications : Techniques To Represent, Access, Transform, And Interchange Bi-Level Information, Sudarshan Srivivasa Murthy

Dissertations and Theses

Superimposed applications (SAs) superimpose (that is, overlay) new information and structures (such as annotations) on parts (such as sub-documents) of existing base information (BI). In this setting, SA developers and users work with bi-level information, a combination of the superimposed information and the referenced BI parts.

We have designed a framework to assist SAs in the following bi-level-information-management activities: representation, access, transformation, and interchange. This framework defines the abstraction context agent to activate any BI part and to retrieve information from the context of the part. It includes means to represent and access bi-level information in a conceptual model (the …

Data Assimilation, Adaptive Observations And Applications, Humberto Carlos Godinez Vasquez

Dissertations and Theses

Sensitivity analysis, data assimilation and targeting observation strategies are methods that are applied to various complex mathematical models of fluid dynamics. In this research we investigate new directions to improve on the current strategies used to deploy additional observational resources (targeting strategies) for data assimilation in dynamical systems of fluid mechanics.

Targeting strategies aim to determine optimal locations where additional observations will improve the solution of the data assimilation process by identifying regions where state errors in the model have a high potential to grow.

Properly accounting for nonlinear error growth is an unresolved issue in targeted observations for numerical …

Vegetation, Environmental Characteristics, And Their Relationships: Variation Within The Annually Flooded Riparian Zones Of The John Day River Basin, Oregon, Samuel J. Hartsfield

Dissertations and Theses

I hypothesized that vegetation and physical environmental characteristics would differ between the upper and lower extents of the annually flooded riparian zone on the John Day River, and that relationships between species and environmental variables would display differences between these two zones. Vegetation, environmental variables, and relationships between them were assessed for the entire annually flooded riparian zone, and for the proposed upper and lower zones. Data were collected from 60 one-square-meter quadrats: 30 in each the upper and lower zones. Sites were randomly selected and located so that flood duration was roughly equal at all sites within each zone. …

Characterization Of Putative Self-Resistance Genes In The Biosynthetic Gene Cluster Of Hygromycin A From Streptomyces Hygroscopicus Nrrl 2388, Vidya Dhote

Dissertations and Theses

Streptomyces hygroscopicus NRRL 2388 produces an aminocyclitol antibiotic called hygromycin A (HA), which targets bacterial protein synthesis by inhibiting the peptidyl transferase reaction. The hyg6, hygl9, hyg21, hyg28, and hyg29 genes in the biosynthetic gene cluster of HA are predicted to confer self-resistance to the producer strain by different mechanisms. Targeted gene disruptions and in vitro characterization of recombinant proteins were carried out to elucidate the functions of these genes. The hyg21 gene encodes an O-phosphotransferase with a proposed role in HA inactivation by phosphorylation. Disruption of hyg21 led to a significant decrease in HA production but did not …

Synthesis Of Aptamer-Porphyrin Conjugate For Photodynamic Therapy & Synthesis And Stability Of Mixed Thiol/Lipid Coated Gold Nanoparticles, Sarita Sitaula

Dissertations and Theses

An underlying problem in Photodynamic Therapy (PDT) is low selectivity of photosensitizers currently being used for the treatment of tumors. This thesis is focused on developing new PDT drugs and is divided into two parts. The first chapter describes a method for selective delivery of the photosensitizers to the tumor site by conjugating porphyrins to an aptamer for the targeted PDT. To achieve this, a novel synthesis of 2'-porphyrin-modified uridine was developed. The 3'-H-phosphonate derivatives of both 2'-porphyrin and 2'-dithiaporphyrin modified uridine were also synthesized. The 3'41-phosphonate derivative of 2'-porphyrin-modified uridine was conjugated to a 19-mer DNA and to a …

Programmer Friendly Refactoring Tools, Emerson Murphy-Hill

Dissertations and Theses

Tools that perform semi-automated refactoring are currently under-utilized by programmers. If more programmers adopted refactoring tools, software projects could make enormous productivity gains. However, as more advanced refactoring tools are designed, a great chasm widens between how the tools must be used and how programmers want to use them. This dissertation begins to bridge this chasm by exposing usability guidelines to direct the design of the next generation of programmer-friendly refactoring tools, so that refactoring tools fit the way programmers behave, not vice-versa.

The Role Of Water And Other Resources In The Invasion Of Rubus Armeniacus In Pacific Northwest Ecosystems, Joshua Sundance Caplan

Dissertations and Theses

The factors influencing the invasive success of Rubus armeniacus (Himalayan blackberry) in the Pacific Northwest of North America are only partly understood, but have important implications for its management and for our understanding of the processes driving invasive plant proliferation in regions with seasonally fluctuating resources. I identified patterns of R. armeniacus occurrence and growth under widely ranging soil and light conditions in western Oregon. I found that light availability was a primary determinant of R. armeniacus occurrence and growth. I also found that R. armeniacus was tolerant of a wide range of soil conditions, notably coarse texture, and could …

Studies Of Dna Hybridization Reactions And Applications In Genetic Assays, Fidelis Manyanga

Dissertations and Theses

The intent of this study was to investigate two fundamental aspects of short DNA duplex stability and how that stability differs for duplex molecules consisting of either all perfect match Watson/Crick base pairs or a mixture of perfect match Watson/Crick base pairs and mismatch base pairs. Theoretical and experimental investigations of the origins of the nucleation term in the free energy of DNA duplex formation were revisited. Thermodynamic parameters (ΔG, ΔH, Δ S and Tm) of short DNA/DNA duplexes ranging in length from 6 to 35 base pairs were systematically evaluated by Differential Scanning Calorimetry …

Graphical User Interfaces As Updatable Views, James Felger Terwilliger

Dissertations and Theses

In contrast to a traditional setting where users express queries against the database schema, we assert that the semantics of data can often be understood by viewing the data in the context of the user interface (UI) of the software tool used to enter the data. That is, we believe that users will understand the data in a database by seeing the labels, dropdown menus, tool tips, help text, control contents, and juxtaposition or arrangement of controls that are built in to the user interface. Our goal is to allow domain experts with little technical skill to understand and query …

Computational Techniques For Reducing Spectra Of The Giant Planets In Our Solar System, Holly L. Grimes

Dissertations and Theses

The dynamic atmospheres of Jupiter, Saturn, Uranus, and Neptune provide a rich source of meteorological phenomena for scientists to study. To investigate these planets, scientists obtain spectral images of these bodies using various instruments including the Cooled Mid-Infrared Camera and Spectrometer (COMICS) at the Subaru Telescope Facility at Mauna Kea, Hawaii. These spectral images are two-dimensional arrays of double precision floating point values that have been read from a detector array. Such images must be reduced before the information they contain can be analyzed. The reduction process for spectral images from COMICS involves several steps:

1. Sky subtraction: the …