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Windows of Privilege: Exploring Environmental Catastrophes and Social Responsibility
No full textThis work is a reflection on the stark disparities in how environmental catastrophes impact different communities. While marginalized populations bear the brunt of these crises, many in privileged societies remain insulated from their immediate effects. This disconnect compelled me to create miniature models juxtaposing scenes of comfort and familiarity against backdrops of environmental devastation.Keywords: photography, art, mixed media, privilege, environmental catastrophe, social responsibility, comfort, fait
Towards Resolving Functional and Evolutionary Mysteries of the Large and Heterozygous Genome of Hop (Humulus lupulus) and the Cannabaceae Family Using Genomic Data Science
No full textHop (Humulus lupulus L. var. lupulus) is a diploid, dioecious plant with an extensive history of cultivation and use in brewing, as a textile, and for its therapeutic properties. Hop is prized for its ability to produce a variety of aromatic and flavor compounds, as well as compounds with anti-microbial properties and pharmacological relevance, including terpenes and prenylated flavonoids. Identification of genes and genomic loci involved in response to abiotic and biotic stressors, as well as biosynthesis of secondary metabolites, requires high-quality genomic resources. The hop genome is large (~2.8 Gb) and complex, and early attempts at assembly resulted in fragmented and incomplete assemblies, limiting the extent of investigation that could occur. Fragmented assemblies do not sufficiently capture the surrounding genomic context of genes, including transposable elements and gene duplication. Recent advances in sequencing technology and assembly algorithms have made assembly of the hop genome tractable and have transformed the extent of investigation that can occur. The development of genomic resources for the Cascade hop genome allows for a comprehensive investigation of the evolutionary trajectory of biosynthetic enzymes, as well as genomic features underlying growth, flowering, and stress response. The approaches that we developed to analyze the Cascade hop genome serve to deepen our understanding of the hop genomic landscape and may have broader applicability to the study of other large, complex genomes. Taken together, the genomic resources described in my thesis will inform cultivation strategies and benefit hop researchers and the Cannabaceae genomics community
The Monte Carlo Computational Summit – October 25 & 26, 2023 – Notre Dame, Indiana, USA
No full textThe Monte Carlo Computational Summit was held on the campus of the University
of Notre Dame in South Bend, Indiana, USA on 25–26 October 2023. The goals of
the summit were to discuss algorithmic and software alterations required for successfully porting respective code bases to exascale-class computing hardware, compare software engineering techniques used by various code teams, and consider the
adoption of industry-standard benchmark problems to better facilitate code-to-code
performance comparisons. Participants reported that identifying and implementing
suitable Monte Carlo algorithms for GPUs continues to be a sticking point. They also
report significant difficulty porting existing algorithms between GPU APIs (specifically Nvidia CUDA to AMD ROCm). To better compare code-to-code performance,
participants decided to design a C5G7-like benchmark problem with a defined figure
of merit, with the expectation of adding more benchmarks in the future. The participants also identified the need to explore the intermediate and long-term future
of the Monte Carlo neutron transport community and how best to modernize and
contextualize Monte Carlo as a useful tool in modern industry. Overall the summit
was considered to be a success by the organizers and participants, and the group
shared a strong desire for future, potentially larger, Monte Carlo summits
Development of a Steady State Surrogate Model for an AGN-201 Digital Twin using MOOSE
No full textIncreased interest in nuclear energy as a solution to rising energy demands and climate change will, in turn, increase stress on safeguards measures. Digital twins are a proposed technological solution to the problem this poses, as they could be used to monitor an operating reactor in real time. This necessitates the development of a physics model which can evaluate the state of the physical reactor rapidly and with enough accuracy to detect misuse or diversion. Idaho State University's AGN-201 research reactor is used as a test case to determine the feasibility of the Multiphysics Object-Oriented Simulation Environment to serve as a platform for development of a physics model that meets the aforementioned requirements. A deterministic model is created and used to develop various surrogate models, which are assessed on training efficiency and accuracy when compared to a Serpent model. Polynomial chaos and Gaussian process surrogate models both show promise to serve this purpose. The former more reliably captures the AGN-201 state-points such that all surrogates of that type maintain root mean squared reactivity errors below \$0.07 when compared to the full order model
Destructive measuring instrument precision estimation
No full textMeasuring instrument precision/repeatability is one variance component in a measurement system. Assessing measuring instrument precision is necessary to evaluate its capability for a particular application. Well-known approaches for assessing precision/repeatability rely on repeated measurements of items. However, a destructive measurement destroys measured items, so that repeated measurements are not possible. This research focuses on estimating measuring instrument precision for a destructive measurement instrument. The methodology is based on an assumed polynomial relationship between the squared means and the variance of the measured item/part dimension. A specific dimension of different part types (with different means) are independently measured by a single operator and measuring instrument, and the measurements are assumed to be normally distributed. Additionally, the repeatability is assumed constant. Formulas for repeatability estimation, the variance of the estimator, and confidence intervals are developed for a quadratic polynomial relationship. These formulas are derived under two scenarios. In the first scenario, part type means are assumed known and exact formulas are obtains. In the second scenario, part type means are estimated from measurements and approximate formulas are obtained. Confidence interval coverage evaluation is performed with Monte Carlo simulation to verify the known mean scenario, and to evaluate the accuracy of the estimated mean scenario. A general formula for higher order polynomial relationships is developed and evaluated for cubic and quartic relationships between true means squared and variance. The results indicate that the derived formulas give confidence interval coverage close to 95%
Computational Investigation into the Mechanisms and Origins of Selectivity in Selected Organic and Organometallic Chemical Processes
No full textPut generally, the work I have conducted in my time at Oregon State University has been to answer two questions. The first of these is “Why do I get this particular product from this particular chemical reaction?” and the second is “How do the reagents in this chemical reaction lead to the product I obtain once the reaction is over?” More specifically, my work has been to use chemical modelling software in combination with high-performance computing to determine the origins of selectivity in various chemical reactions, and to determine the mechanism – the exact sequence of bond formation and breakage – by which starting material(s) are converted to product(s). These two goals are often synonymous, and in several cases, determination of the origins of selectivity in a given reaction necessitates the computation of the entire reaction mechanism.
A systematic investigation into an iron-catalyzed [2+2+2] cycloaddition reaction revealed that the selectivity controlling the formation of the observed pyridine product stems from several factors, and that said selectivity is introduced over several steps in the catalytic cycle. Experimental evidence supports the computationally suggested hypothesis that ligand dissociation also occurs during the reaction, aiding in the incorporation of the third π system.
Computational investigation into the ruthenium-catalyzed decarboxylative selenylation of ortho-carborane clusters sought to uncover the mechanism by which this transformation occurred. This necessitated the computation of the entire reaction mechanism. Prior selenylation of the o-carborane was found to be necessary in order for an energetically reasonable decarboxylation to occur.
A study into the observed selectivity of an organo-catalytic Claisen rearrangement led to the observation that an interaction between a C—H bond and the π electrons of an adjacent aromatic ring was responsible for said selectivity. Control computations verified that such interactions are enthalpically favorable, however, neither modification of the aromatic ring, nor replacement of the organic catalyst itself, is predicted to noticeably improve selectivity.
An investigation into the platinum-catalyzed synthesis of indoles from 2-ethynyl anilines with a concomitant 1,3-ipso shift of an aryl ring was also conducted, wherein the computational prediction that an unusual concerted [4+2] cycloaddition of an alkyne and an arene is operative was verified by kinetic isotope experiments. This result highlights the power of joint computational an experimental work.
A computational examination of C(3)-heterofunctionalization of indoles via [3,3]-sigmatropic rearrangements showed that a concerted [3,3] process and stepwise diradical mechanism were both operative for O-functionalization of C(3), and that a concerted pericyclic process is active for N-functionalization of C(3). Electron withdrawing groups on the migratory allyl portion contribute to the experimentally observed decrease in the transition state barrier in O-functionalization through weakening the N—O bond of the N-hydroxy indole derivatives used as substrates. Furthermore, sufficiently electron poor derivatives are postulated to rearrange through ionization rather than concerted [3,3] or stepwise diradical rearrangement
Evaluating the Potential of Protein Supplements and Probiotics for Improving Honey Bee Health and Understanding Honey Bee Behaviors Related to Social Immunity
No full textManaged honey bees (Apis mellifera) play a vital role in pollinating cultivated crops worldwide. Honey bee colony declines reported in the past two decades have been associated with stressors such as pests and diseases, pesticide exposure, and poor nutrition. In the wake of these colony declines, beekeepers have strived to improve honey bee nutrition by feeding probiotic and protein supplements to their colonies, but there exists a significant gap in knowledge regarding the efficacy of these nutritional supplements. The primary objective of this thesis is to evaluate the potential benefits of protein supplements and probiotics that are commonly used by beekeepers to improve honey bee health and survival.
Most studies to date have evaluated protein supplements by measuring colony level parameters, such as colony growth and survival. In our first study, we assessed protein supplements by measuring several physiological parameters directly related to colony fitness. Utilizing both lab and field experiments, we measured several common physiological markers of honey bee health in adult bees raised in colonies that had access to natural pollen and compared them to bees raised in colonies with restricted access to pollen and were instead fed a commercial protein supplement. We measured survival rates, overwintering success, reactive oxygen species, head protein levels, and vitellogenin gene expression in these two groups of experimental colonies. Head protein and reactive oxygen species levels were similar between the two treatments groups. While expression of vitellogenin, which functions as an antioxidant to promote longevity in overwintering bees, was not significantly different between the treatment groups after overwintering, the pollen treatment group experienced a higher increase (33-fold) compared to the protein supplement treatment group (6-fold). Our results suggest that protein supplements could be beneficial during times of limited pollen forage and offer short-term benefits, but are not as effective in sustaining colonies to the same extent as natural pollen.
In a second study, we evaluated the efficacy of a commercial probiotic in improving honey bee health and mitigating pesticide toxicity. The treatments in this study consisted of a combination of a probiotic, lambda-cyhalothrin, and a multifloral pollen. Samples of live bees were obtained to measure head protein levels, reactive oxygen species levels, and microbiome taxa. Survival data revealed that that treatment groups that received the probiotic had lower survival, and the probiotic did not meaningfully affect head protein or reactive oxygen species levels in bees that were exposed to lambda-cyhalothrin. Analysis of gut contents revealed that pollen, rather than the probiotic, played a larger role in influencing the microbiome structure. Our results indicate that the commercial probiotic did not have the desired effects in mitigating pesticide toxicity.
In our final study, we examined honey bee worker behaviors related to social immunity and attempted to collect potential evidence for the behavior of altruistic self-removal. We observed and recorded the behaviors of infected and uninfected bees in experimental observation hives and also examined potential self-removal by monitoring the presence of experimental bees at regular intervals. Our results showed no significant differences in the frequencies and durations of specific interactive behaviors (antennation, inspection, trophallaxis, etc.) among the infected and uninfected bees. Throughout the study, numbers of infected bees were lower compared to the uninfected group. There appears to be a weak, but not conclusive evidence for self-removal, given that there are other important factors contributing to these low numbers. Therefore, it is difficult to discern altruistic self-removal behaviors with the experimental design used in our study
Bioacoustic Variation of Bowhead Whales in a Feeding Hotspot and a Case Study of An Apex Predator’s Increasing Presence in the Arctic
No full textAs the Arctic marine ecosystem continues to alter in the midst of rapid climate change, noninvasive methods, such as passive acoustic monitoring, to answer ecological questions are increasingly important. Since marine mammal species produce unique bioacoustic signals, scientists can largely distinguish species presence by vocalizations alone. Here, I present studies that attempt to answer ecological questions concerning both Bering-Chukchi-Beaufort (BCB) bowhead whales and killer whales in the western Beaufort Sea. In the first study, a BCB bowhead whale call repertoire was synthesized for an offshore environment in the western Beaufort Sea. The second study investigates whether there is variation in BCB bowhead whale acoustic behavior while foraging. Vocalizations were recorded during a biophysical phenomenon in the western Beaufort Sea referred to as the “krill trap”. Acoustic data before and during the krill trap found that bowhead whale vocal behavior changed based on whether or not the krill trap was active. The last study provides documentation of vocalizations of killer whales in the western Beaufort Sea, which appear to be increasing their spatiotemporal residency in this region correlated with reductions in Arctic sea ice. Now, more than ever before, understanding the drivers of animal behavior is vital to accurately assess potential shifts in distribution, abundance and/or behavior under a changing climate. The studies presented here not only bolster established knowledge of marine mammals in the Arctic, but also explore the motivations of specific vocal behaviors in an ecosystem undergoing accelerated, extreme environmental change
Rapid Coded Aperture Imaging of Gamma Rays with Hybrid Pixelated Detectors
No full textGamma imaging of far-field objects – that is, to remotely determine the location and distribution of radioactivity in an environment without having to physically enter the environment – has many advantages for use in routine and emergency situations, but historical systems have commonly been flux limited or required lengthy acquisition times to be used efficiently. To respond to the need for near real-time gamma imaging with high-precision localization for applications such as High Dose Rate (HDR) medical treatments (specifically Brachytherapy) and industrial digital radiography, new gamma imaging approaches and processing techniques have been developed and optimized for rapid processing, fine angular resolution, and high localization precision. A prototype gamma imaging system has been developed, incorporating a unique hybrid pixelated detector and an innovative coded aperture design, enabling near real-time operation. The system is also optimized to support a wide dynamic range of gamma flux rates with high accuracy of localization (<1 cm at 3 meters observed). This elaborates on the design of this new coded aperture imaging system and the new algorithmic approaches that have been developed to significantly increase the dynamic range, sensitivity, and image quality
Exploring the relationship between mindfulness and independence in individuals with disabilities
No full textMindfulness practices are being increasingly acknowledged in psychological studies for their association with enhanced well-being and cognitive functions, achieved through fostering nonjudgmental thinking and self-awareness. Independence, essential for adult development and inherently dynamic and context-specific, relates to mindfulness through its susceptibility to societal attitudes and individual perspectives. This study investigates the degree to which mindfulness levels predict levels of independence among individuals with disabilities, acknowledging a population of individuals often affected by sociocultural bias and systemic oppression. Mindfulness and independence scores were derived from Likert-style survey responses completed by 758 adults with disabilities who participated in the EAMMi2 project available on the Open Science Framework (OSF). Linear regression analyses demonstrated a significant positive relationship between mindfulness and independence, suggesting that higher levels of mindfulness are predictive of higher levels of independence. Subgroup analysis, based on disability identification, showed that participants who reported experiencing a disability but did not identify as disabled (N = 451) exhibited stronger independence levels associated with higher mindfulness, compared to those identified as disabled (N = 307). These findings add to existing mindfulness and independence literature, and highlight the possibilities for future mindfulness-based interventions to increase levels of independence in adults with disabilities. Although the study does acknowledge some limitations (e.g. a small effect size, reliance on self-report measures), the findings underscore the importance of future research endeavors aimed at implementing mindfulness-based interventions and assessing their efficacy in promoting independence across diverse contexts