Ion therapy has long been investigated as a potential modality to improve cancer treatments beyond what is currently feasible with photon irradiations. Ions offer both a physical and biological advantage over photons. The physical advantages are well understood, ions deposit their maximum dose at defined penetration depths, allowing for minimal...
Transcriptomics and gene expression profiling enables the elucidation of the genetic response of an organism to various environmental cues. Transcriptomics enables the deciphering of differences between two closely related organisms to the same environment and in contrast, enables the elucidation of genetic responses of the same organism to different environmental...
If P is an integer polynomial denote the degree of P by ∂(P) and let H(P) be the maximum of the absolute value of the coefficients of P. Define Λ(P)=2[superscript ∂(P)]H(P) and for a fixed prime p let C[subscript p] denote the completion of the algebraic closure of the p-adic...
The primary goal of this dissertation is to improve the quality of nuclear data available to the nuclear science community. We propose to accomplish this by applying machine learning algorithms to the large number of available benchmark experiments and simulations, with the goal of determining which nuclear data have strong...
In eukaryotes, the defined loci on each chromosome, the centromeres, accomplish
the critical task of correct cell division. In some organisms, centromeres are
composed of a euchromatic central core region embedded in a stretch of
heterochromatin and the inheritance and maintenance of centromeres are controlled
by dynamic epigenetic phenomena. Although...
Mutation of repetitive DNA by repeat-induced point mutation (RIP) is a process that occurs in many filamentous fungi of the Ascomycota during the sexual cycle. Concurrently, direct DNA repeats are often deleted by homologous recombination at high frequency during the sexual cycle. Thus, the processes of RIP and deletion compete...
In this dissertation, we use Fourier-analytic methods to study questions of equidistribution on the compact abelian group Zp of p-adic integers. In particu- lar, we prove a LeVeque-type Fourier analytic upper bound on the discrepancy of sequences. We establish p-adic analogues of the classical Dirichlet and Fejér kernels on R/Z,...
Two perovskite materials (Bi0.5(A)0.5)(Sc0.5Nb0.5)O3, where A = K+ and Na+ were synthesized phase pure for the first time. Their structures were determined by indexing synchrotron X-ray diffraction data and subsequent combined Rietveld refinement on neutron and synchrotron X-ray diffraction data revealing significant disorder on the A-sites of these materials. A...
We spatially discretize the Sn transport equation using the high-order (HO) discontinuous finite element method (DFEM) on HO meshes. Previous work provided a proof-of-concept for this spatial discretization method in X-Y geometry. Included in the present work, we derive a spatial discretization for the Sn transport equation in both X-Y...
European hazelnut (Corylus avellana L.) is an important crop Oregon's Willamette Valley, producing 99% of the hazelnuts grown in North America and brings over US $60 million dollars to the region annually. Hazelnuts are rich in fiber and vitamins, as well in demand by consumers due to their popularity as...
We present a novel multi-objective optimization methodology built upon a multi-agent blackboard framework. This multi-agent blackboard system (MABS) synthesizes blackboard architectures, multi-agent environments, and optimization theory. The blackboard architecture creates the framework for initializing, storing, and solving a multi-objective optimization problem. Multiple agents allow for an optimization problem to be...
In order to address the energy needs of developing countries and remote communities, Oregon State University has proposed the Multi-Application Small Light Water Reactor (MASLWR) design. In order to achieve five years of operation without refueling, use of 8% enriched fuel is necessary.
This dissertation is focused on core design...
Substantial scientific investment has been directed towards understanding factors that influence distribution patterns and animals' remarkable ability for precise orientation and navigation, yet fundamental gaps in our knowledge remain. In my dissertation, I applied emerging genetic technologies to conduct a top-down and bottom-up investigation of animal movement and cue perception....
Although surface water constitutes less than 1.5% of freshwater supply, historical development of surface water sources continues to mark the landscape. However, over- exploitation of groundwater is now at its highest, and 25% of the world’s 1.7 billion population live in water scare regions. As glaciers and snowpack disappear due...
How can end users efficiently influence the predictions that machine learning systems make on their behalf? Traditional systems rely on users to provide examples of how they want the learning system to behave, but this is not always practical for the user, nor efficient for the learning system. This dissertation...
Dissolved organic matter (DOM) is a critical component of the carbon cycle linking terrestrial and aquatic ecosystems. Although many factors influence DOM fluxes and quality in rivers, controls on DOM compositions in catchments of the western U.S. are poorly understood. UV and fluorescent spectroscopy is a simpler, faster, and less...
Within the past several years the technology of high-throughput sequencing has transformed the study of biology by offering unprecedented access to life's fundamental building block, DNA. With this transformation's potential a host of brand-new challenges have emerged, many of which lend themselves to being solved through computational methods. From de...
A bad software development process leads to wasted effort and inferior products. In order to improve a software process, it must be first understood. In this work I focus on understanding software processes.
The first process we seek to understand is Continuous Integration (CI). CI systems automate the compilation, building,...
We investigate several aspects of the numerical solution of the radiative transfer
equation in the context of coal combustion: the parallel efficiency of two commonly used
opacity models, the sensitivity of turbulent radiation interaction (TRI) effects
to the presence of coal particulate, and an improvement of the order of temporal...
Antineutrino detectors could provide a valuable addition to current safeguards
regimes. Antineutrinos are an attractive emission to monitor due to their low
interaction cross-section that prevents them from being shielded and the dependence
of their spectrum on the power level and isotopic content of a reactor core. While
there are...
The most widely used and versatile medical radioisotope today is technetium-99m. Roughly 30 million people depend on this radioisotope for diagnostic procedures each year, and this demand is expected to grow. Although there are numerous ways of procuring this isotope, the most common and most practical, for reasons to be...
An important improvement in the area of reactor core neutronic modeling is the development and use of the methods based on "quasi-diffusion" (QD) low-order equations. This family of methods takes into account the transport exactly using "functionals" computed by solving transport equations, and is amenable to solution with a variety...
My objectives were to: 1) develop a point count technique for estimating relative
abundance of band-tailed pigeons (Columbafasciata monilis), 2) determine the
availability, distribution, and interspersion of mineral sites, and nesting and foraging cover in relation to abundance of band-tailed pigeons in west-central Oregon, and 3) test the hypothesis that...
Lycopodium alkaloids have generated enormous amounts of interest from the scientific community, both as synthetic targets and for their medicinal properties. Herein is described work towards a unifying approach to large segments of the Lycopodium family. An organocatalyzed intramolecular heteroatom Michael reaction method, for the construction of piperidine and piperizine...
Cellulolytic enzymes capable of efficiently degrading crystalline cellulose are a
complex mixture of endo- (endoglucanases) and exo-acting (cellobiohydrolases)
enzymes. One approach to separating these enzymes is affinity chromatography. A new
ligand, p-aminophenyl l-thio-β-D-cellobioside (APTC), is introduced for this purpose.
The property of APTC in affinity chromatography is demonstrated using Trichoderma...
We present a deterministic spectral method to predict equilibrium temperature distributions, heat flux, and thermal conductivity in homogeneous and heterogeneous media. We solve the Boltzmann transport equation in a second order spatial, self-adjoint angular flux formulation. We implemented this method into the radiation transport code Rattlesnake, built using the MOOSE...
The bi-directional relationships within the personal and contextual environments of adolescents are critical to the development of adolescents and their transition into adulthood. Opportunities for youth to participate in and provide leadership in meaningful programs, gain life skills, and interact with adults in sustained relationships are key features leading to...
Time-dependent electronic transport is increasingly important to the state-of-the-art device design and fabrication. The development of nanoscale sensing, the harnessing and control of structural fluctuations, and the advancement of next-generation materials all require a treatment of quantum dynamics beyond the level of traditional methods and a more nuanced approach to...
Three analytical methods for determination of aroma compounds in alcoholic beverages were developed and validated. These methods are sensitive and reliable that can be applied to analyze volatile phenols, stale aldehydes as well as some highly volatile aromas in alcoholic beverages. In the first study, an ethylene glycol (EG) polydimethylsiloxane...
Small Unmanned Aircraft Systems (sUASs) equipped with optical sensors are capableof remotely sensing landscapes and wildlife at spatial and temporal resolutions that werepreviously inaccessible due to technical and budgetary limitations. Conventional remotesensing and photogrammetric workflows can be applied to the resulting high resolution imageryto facilitate new types of scientific inquiry....
Fungi are capable of growth on a wide variety of carbon sources, both living and dead. They can produce an arsenal of enzymes and transporters for harvesting sugars, polysaccharides, amino acids, lipids and micronutrients from their environments [1]. Within the nucleus of a cell, transcription factors (TF) control whether genes...
Under the label “Supported Employment,” services that promote competitive, integrated employment (CIE) for working-age adult with intellectual and developmental disabilities have been federally funded since the 1980s, alongside other more traditional day habilitation and segregated or sub-minimum wage employment services. However, since the early 2000s, over 30 states have adopted...
Circulating fuel reactor (CFR) kinetics are characterized by delayed neutron precursor (DNP) drift in addition to the neutronic and thermal hydraulic phenomena typical of other reactor types. This environment can be computationally challenging to model, given that the multiphysics phenomena generally have non-linear interdependencies requiring the use of iterative solution...
We present a method for deterministically solving the consistent temperature and frequency dependent phonon radiative transport problem. We use the single relaxation time (SRT) approximation in the Self-Adjoint Angular Flux (SAAF) form with discrete ordinates (S_N) angular discretization method and continuous finite element method (CFEM) for spatial discretization. Included are...
In this dissertation, we attempt to overcome the "curse of dimensionality" inherent to radiation diffusion kinetics problems by employing a novel reduced order modeling technique known as proper generalized decomposition (PGD). After verifying a proposed PGD algorithm and associated solvers through various tests, we explore its performance for computing reduced-order...
Onsite wastewater treatment systems (OWTS; septic systems, compost toilets, etc.) used to treat wastewater in rural areas have the potential to contaminate groundwater (that is used as a water source) with nitrate. There have been decades of scientific and political conflicts concerning the issue of nitrate from OWTS (NOWTS, pronounced...
Radiation therapy is a sophisticated complex process. Systematic methods are needed to quantitatively evaluate the quality of a complex process and hence radiation therapy treatments. An ideal result for a complex process must be established to determine if the complex process is completed acceptably. For radiation therapy, this can be...
DSA (Diffusion Synthetic Acceleration) has been developed to accelerate the SN transport iteration. We have developed solution techniques for the diffusion equations of FLBLD (Fully Lumped Bilinear Discontinuous), SCB (Simple Corner Balance) and UCB (Upstream Corner Balance) modified 4-step DSA in x-y geometry. Our first multi-level method includes a block...
In this dissertation, we derive and implement a new transport-diffusion hybrid algorithm for solving thermal radiative transfer (TRT) problems. Using the method of nonlinear elimination (NLEM), the TRT system of equations can be written in terms of a transport equation with the absence of scattering and a diffusion equation. The...
The implementation of advanced hybrid (Monte Carlo/Deterministic) transport methods for realistic test problems has been a challenge due to the overhead efforts associated with interfacing a solution generated by a deterministic solver with a Monte Carlo based radiation transport code. In this work, with the help of Transpire, Inc., a...
Nuclear fuel management is an optimization problem on many levels. Finding “viable” solutions for the core reload design problem is difficult without expert knowledge and software automation. Small modular reactors with a shared used fuel pool demonstrate a novel opportunity for fuel cycle optimization.
A Python package was developed and...
Pacific sardines (Sardinops sagax) are an economically and ecologically important forage fish which transfer energy from planktonic primary producers and secondary consumers to upper trophic predators. Previous genetics studies of Pacific sardine suggested a panmictic population with a shallow genetic structure. However, more than one subpopulation within the Central California...
Coastal marsh vegetation is an important component in maintaining marsh stability that is threatened by changes in sedimentation, sea level rise, natural and anthropogenic disturbances, and competition from invasive species. Vegetation has been demonstrated to reduce wave energy, increase sedimentation, and decrease erosion in tidal environments under a range of...
Considerable controversy exists about how fish assemblages are
organized. I explicitly took fish movement into account while I
studied the effects of disturbance, habitat complexity, and predation
at different times of the summer to understand the major factors
influencing assemblage structure in a high desert Oregon stream. The
effects of...
Discordance in bone mass between young adult swimmers and soccer players may be a direct result of differences in bone loading patterns that influence bone mineralization during growth. Our aim was to evaluate whether sports participation (soccer and swimming) had an independent effect on bone mass accrual at the hip...
Nearly 3000 juvenile Chinook (Oncorhynchus tshawytscha) and coho (O. kisutch) salmon captured in nearshore waters off the coasts of Washington and Oregon from 1999-2004 were tested for infection by Renibacterium salmoninarum, Nanophyetus salmincola, and skin metacercariae. First, three quantitative PCR primer/probe sets were compared for detection of R. salmoninarum; amplification...
The Northern California Current (NCC) ecosystem exhibits extreme seasonal, interannual and interdecadal shifts in the abiotic environment and shifts in primary and higher production. This variability is also apparent in the spatial structure of the ecosystem with nearshore-shelf waters (<150 m isobath) being highly productive and having a different community...