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Exploring soil-plant relationships to inform seed selection for rangeland restoration

March 21, 2024 12:00 AM
Authors: Mallory Hinton, Matthew Madsen, Raechel Hunsaker, April Hulet. Mentors: April Hulet. Insitution: Brigham Young University. Seeding plants post disturbance on rangelands is a challenge due to unique ecological and environmental conditions such as limited water availability, invasive species, soil health, and native seed supply. One of the key factors to address these challenges and have a successful seedings is understanding the relationships between soil characteristics and the plants that grow within them. Our research evaluated plant growth for seventeen grass species in two degraded rangeland soils (a mine tailings impoundment and Santaquin Wildlife Management Area) in Utah. Grasses (10 PLS/5cm 2 pot) were grown in self-watering growth trays in a complete, randomized block design with four replicates per soil type. After 21 days in the greenhouse, plant densities and aboveground biomass were collected and analyzed. Soils differed in mineral content. Iron and nitrogen were 5- and 4-fold greater in Tailings than Santaquin soil; phosphorus, magnesium, and organic matter were 5.5-, 4-, and 18-folds lower in Tailings than Santaquin soil. The average density of plants was significantly different (p < 0.0001) between the two soil types; in the Santaquin soil plant density was 5.73 plants/pot, in Tailings soil plant density was 2.20 plants/pot. No individual grass species were significantly different from each other in the Tailings soil (p = 0.51). However, individual grass species were significantly different from one another in the Santaquin soil (p = 0.05). Both Tailings and Santaquin soil types had the highest densities of slender wheatgrass (Elymus trachycaulus; 4.75 plants/pot and 8.25 plants/pot, respectively) and tall wheatgrass (Thinopyrum ponticum; 4.75 plants/pot and 10.25 plants/pot, respectively). Sandbergs bluegrass (Poa secunda) had the lowest density in both soil types (zero plants in Tailings soil and 2.50 plants/pot in Santaquin soil). To make informed decisions when selecting plant species for seed mixes, soil characteristics should be considered.
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Advancing Mycotoxin Detection: Multivariate Rapid Analysis on Corn Using Surface Enhanced Raman Spectroscopy (SERS)

March 21, 2024 12:00 AM
Authors: Allison Gabbitas, Kaitlyn Allen, Gene Ahlborn, Shintaro Pang. Mentors: Shintaro Pang. Insitution: Brigham Young University. Mycotoxin contamination on food and feed can have deleterious effect on human and animal health. Agricultural crops may contain one or more mycotoxin compounds; therefore, a good multiplex detection method is desirable to ensure food safety. In this study, we developed a rapid method using label-free surface-enhanced Raman spectroscopy (SERS) to simultaneously detect three common types of mycotoxins found on corn, namely aflatoxin B1 (AFB1), zearalenone (ZEN), and ochratoxin A (OTA). The intrinsic chemical fingerprint from each mycotoxin was characterized by their unique Raman spectra, enabling clear discrimination between them. The limit of detection (LOD) of AFB1, ZEN, and OTA on corn were 10 ppb (32 nM), 20 ppb (64 nM), and 100 ppb (248 nM), respectively. Multivariate statistical analysis was used to predict concentrations of AFB1, ZEN, and OTA up to 1.5 ppm (4.8 µM) based on the SERS spectra of known concentrations, resulting in a correlation coefficient of 0.74, 0.89, and 0.72, respectively. The sampling time was less than 30 min per sample. The application of label-free SERS and multivariate analysis is a promising method for rapid and simultaneous detection of mycotoxins in corn and may be extended to other types of mycotoxins and crops.
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The effect of grass species and soil types on early successional forb species

March 21, 2024 12:00 AM
Authors: Raechel Hunsaker, Matthew Madsen, Mallory Hinton, Derek Tilley, April Hulet. Mentors: April Hulet. Insitution: Brigham Young University. Many early successional plant species have been considered weeds because of their lack of forage value for livestock. However, early successional plant species have the potential to aid rangeland restoration by providing food sources for pollinators, modifying soil in preparation for climax plant communities, and competing against invasive species. To determine which early colonizing species have the greatest restoration potential, interspecific competitive interactions should be evaluated. Our research objective was to evaluate the competitive abilities of two native pioneer forb species, curlycup gumweed (Grindelia squarrosa) and prairie aster (Machaeranthera tanacetifolia), against three common rangeland grasses including 1) native early successional species, bottlebrush squirreltail (Elymus elymoides), 2) invasive colonizing species, cheatgrass (Bromus tectorum), and 3) climax community species, bluebunch wheatgrass (Pseudoroegneria spicata). Treatments included each of the three grass species seeded at high and low densities with curlycup gumweed or prairie aster in two soils (mine tailings and disturbed rangeland) in a greenhouse. After being cultivated for 54 days, above-ground biomass for both forbs were not significantly different when seeded alone, or with high and low densities of grasses in the mine tailings soil (p ≥ 0.05). However, in soil from the disturbed rangeland, forb biomass differed. When planted alone, curlycup gumweed and prairie aster biomass was on average 2.5- and 3-fold greater than when planted with high and low densities of squirreltail and cheatgrass (p ≤ 0.05). Both forbs had significantly lower biomass when planted with a high density of bluebunch (p ≤ 0.05), however, when planted with a low density of bluebunch, biomass was not significantly different than when planted alone (p ≥ 0.05). Results indicate that high densities of squirreltail, cheatgrass, and bluebunch inhibit curlycup gumweed and prairie aster growth on disturbed rangeland soil, and that interspecific competition may be a barrier to the successful establishment of early successional forbs.
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Phylogeny of Hetaerina (Odonata: Calopterygidae): Settling taxonomic issues

March 21, 2024 12:00 AM
Authors: Reganne Leigh Hales, Laura Sutherland, Melissa Sanchez Herrera, Samantha Standring. Mentors: Seth Bybee. Insitution: Brigham Young University. We explore the phylogeny of Hetaeriinae using a targeted enrichment approach (AHE) on gDNA gathered largely from museums. AHE resulted in 20KB (18.5KB of nuclear and 1.5 of mitochondrial DNA) for each taxon. Previous research, based on sanger data generated from three genes, demonstrated that Hetaerina Hagen in Selys, 1853 is not monophyletic but no taxonomic changes were proposed due to the hope of one day having more data. Our goal for this research was to have a larger dataset to test the monophyly of Hetaerina and update the classification. Our results confirm those of the most recent phylogeny of Hetaerina: the genus is non-monophyletic. We recover Mnesarete Cowley 1934 and Ormenophlebia Garrison 2006 within Hetaerina. We have preliminary data (results not shown) demonstrating that both Iridictyon Needham & Fisher 1940 and Bryoplathanon Garrison 2006 are also within Hetaerina. However, due the placement of these genera there is not a clear way to retain these genera and it is likely they will need to be placed within Hetearina due to priority. We further explore the evolution of some characters associated with habitat preference.
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Five-Dimensional Assessment Model for Operation and Maintenance of Stormwater Control Measures - Cedar City Case Study

March 21, 2024 12:00 AM
Authors: Mohamed Askar, Matthew Roberts, Jeremy Matney, Andrew Larsen, Edwin Cansaya Sanchez. Mentors: Mohamed Askar, Matthew Roberts. Insitution: Southern Utah University. Stormwater infrastructures in the U.S. are aging and deteriorating, with most municipalities historically treating stormwater runoff or drainage problems during an emergency or structural failure. What if we could address such issues before they became problematic? Our main objective is to help decision-makers deal effectively with long-term control measures of the budget-limited, ambiguous, and inconsistently applied operation and maintenance of stormwater infrastructures. To this end, an innovative Five-Dimensional Assessment Model (5D-SAM) for the operation and maintenance of stormwater control measures will be developed and tested in the economically disadvantaged rural community of Cedar City, Utah. The model’s strategic approach will employ a prioritized list to create innovative green stormwater infrastructure solutions (clean-energy technologies) for sustainable urban development. The proposed 5D-SAM model includes research on its broader impacts, with a theoretical focus on the nexus of stormwater control measures and design to enhance urban sustainability and resilience. This focus is on the translational and transdisciplinary link between the operation and maintenance of stormwater research outcomes in Cedar City. Performance indicators of the stormwater system will be designed to assess five conditions: assets, functionality, time-effectiveness, cost-effectiveness, and environmental and social impact. 5D-SAM will calculate the performance/health index of the stormwater infrastructure, predict the future state, manage the quantity, and improve stormwater runoff quality. The built-in GIS database will aim to preserve the natural features and functions of stormwater infrastructures while providing a list of cost-effective and environmentally friendly alternatives if a distressed stormwater system is better off demolished, repaired, rehabilitated, or retrofitted. The model benefits society as it applies to other water infrastructure systems, including groundwater wells, dams, reservoirs, treatment facilities, sewer lines, flood prevention, and hydropower. Finally, the proposed research is a valuable and growing resource for students, faculty, urban researchers/practitioners worldwide, and the general public.
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Magnetic Field Spatial Gradient Delivery Optimization For Visualization of Ultrasound Waves During Neuromodulation

March 21, 2024 12:00 AM
Authors: Davi Cavinatto. Mentors: Steven Allen. Insitution: Brigham Young University. Previous work indicates that magnetic gradients oscillating at the same frequency and direction as ultrasound (US) longitudinal displacement can encode particle movement into the complex phase of a magnetic resonance (MR) image. Until now, the coil configuration (Helmholtz) used to generate this oscillating magnetic gradient has constrained the use of this technique to small imaging volumes. Here, we explore the feasibility of using a single coil configuration to improve the versatility of the apparatus, making it possible to visualize US waves as they propagate through tissue that was previously inaccessible through the technique, such as the human brain. This novel approach to the visualization of US waves could potentially be used to establish the missing correlation between the results of neuromodulation treatments and their mechanism of action, thus improving the scientific rigor of this field of research.Wolfram’s Mathematica and COMSOL’s Multiphysics were used for developing a single-coil configuration in silico. The coil design was constrained by the minimum imaging distance from the coil (20mm), gradient needed for an image with signal-to-noise ratio of approximately 10 (0.4 T/m), minimum coil inner radius for fitting the US transducer (20mm), maximum peak current at the coil (20A), and frequency of operation (500kHz). Using Biot-Savart’s Law and Mathematica, we estimated the number of turns needed and the total length of the wire. In order to reduce the skin effect and proximity effect due to the frequency of operation (500kHz), a specific Litz wire configuration was chosen for the windings. Plots for the magnetic gradient over the central axis of the coil were created and compared on both programs to confirm the accuracy of the model.Plots of both the mathematical and in-silicon models matched and proved the high efficiency of the coil system at the frequency of application. The two magnetic field gradient plots corroborate the feasibility of the proposed single coil system for imaging US waves and verification of the functioning of neuromodulation in the extension of the cerebral cortex.
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Pressure Senor Resistance Changes in Varying Biocompatible Metals

March 21, 2024 12:00 AM
Authors: Kasielynn Bussard, Dakota Stringham. Mentors: Matthias Pleil. Insitution: Salt Lake Community College. We are two students from Salt Lake Community College who participated in a summer research workshop in the cleanroom at the University of New Mexico. We were taught the pressure sensor fabrication process, along with the post-production testing methods. For our research project we decided to test how using different biocompatible metals, and different combinations of said metals, for the circuit would affect the pressure sensors functionality. To test this, we prepped five 4” inch wafers and used photolithography to define the Wheatstone bridge pattern, followed by sputter metal deposition. When sputter coating, we coated each wafer in a Venn diagram pattern. This left us with two areas of a single metal on the outside edges, and an area in the middle with both metals present. We then measured the resistance of each section to determine how it changed with different metals.
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Multi-Material Metallurgical Additive Manufacturing

March 21, 2024 12:00 AM
Authors: Joshua Lim. Mentors: Nathan Crane. Insitution: Brigham Young University. Metal additive manufacturing (3D printing) technologies have evolved in the past decade to produce intricate parts in aerospace, car, and biomedical industries. While previous work has been done on single materials, metal-metal composites can expand performance but hasn’t been thoroughly explored. This work investigates ways of creating composites by molted bronze infiltration. At a certain temperature, bronze is melted and seeps through parts that are made via additive manufacturing. By altering the geometry of the pathways that the molten bronze will travel through or the metal particles themselves, one can create unique parts that control where the bronze infiltrates. Initial results indicate that mechanical properties were measurably strengthened by the addition of molten bronze and hypothetically could be used to create thermally graded parts, optimized for specific applications where heat transfer is a parameter of interest.
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Investigating the feasibility of focused ultrasound actuation of shape memory alloy.

March 21, 2024 12:00 AM
Authors: Aldo Chipana, Sarah G Sanderson, Joseph Moore, Jeffery R Hill, Christopher R Dillon. Mentors: Chris Dillon. Insitution: Brigham Young University. Nitinol shape memory alloys have shown immense promise in biomedical engineering, with their exceptional biocompatibility and corrosion resistance. Interestingly, most biomedical applications rely on Nitinol’s super elasticity rather than its hysteretic properties. Previous research in this lab has highlighted the challenges and potential of using focused ultrasound to effectively heat Nitinol wire without causing damage to adjacent tissue. Building upon these findings, our current study presents an extension of the initial experiments, incorporating more realistic in-body conditions. This includes simulating blood flow, which influences the heat transfer taking place in our control volume. Furthermore, we utilize artery mimicking materials to recreate the conditions of human arterial walls. Through comprehensive experimentation and accurate temperature measurements using embedded thermocouples, we aim to enhance our understanding of the interactions between Nitinol wires, surrounding tissues, and focused ultrasound heating. An integral part of our investigation is to discern whether the focused ultrasound directly heats the Nitinol wire or if actuation is achieved indirectly by heating the surrounding tissue. These results will offer insights into the applications of shape memory alloys in diverse biomedical settings, potentially paving the way for more effective and safer medical use.
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Estrous cycle-dependent modulation of psychostimulant effects on striatal neurotransmitter release

March 21, 2024 12:00 AM
Authors: Lauren Ford, Joel Woolley, Ryan Powers, Paulina Medellin, Hillary Wadsworth, Jordan Yorgason. Mentors: Jordan Yorgason. Insitution: Brigham Young University. Women prescribed psychostimulants have self-reported changes in drug efficacy that coincide with menstrual cycling. Furthermore, cocaine and amphetamine effects on dopamine (DA) transmission are more potent in female rodents, an effect that has been linked to cycling hormone levels. However, it is unknown if changes to DA transmission vary by specific psychostimulant, and striatal DA transmission has not yet been well characterized across the estrous cycle. The present study considers dopamine release and reuptake kinetics across various stages of the estrous cycle in the nucleus accumbens (NAc), a key region for dopamine-mediated learning. The effects of cocaine, methamphetamine, and methylphenidate on female dopamine transmission are examined using slice voltammetry. Our data shows that compared to a male control group, baseline (pre-drug) dopamine release in the NAc was lower in females overall, but not at all estrous stages. Applying increasing concentrations of cocaine or methylphenidate revealed similar patterns of enhanced, then diminished release in all mice. Methamphetamine decreased NAc dopamine release similarly in both males and females, but females in estrus were more affected than males, and those in met/diestrus less. Methamphetamine also slowed dopamine uptake in all mice, and at lower concentrations than cocaine or methylphenidate. We find minimal sex differences between cocaine and methylphenidate effects in the NAc, suggesting that the underlying cause of their observed behavioral sex differences may be specific to other striatal regions. On the other hand, methamphetamine-induced DA release fluctuates distinctly with the estrous cycle and peaks when estrogen levels are at their highest, indicating that estrogen and methamphetamine mechanisms share a target in NAc DA terminals that cocaine and methylphenidate do not. This work refines our understanding of DA transmission in females and indicates potential future directions for understanding female psychostimulant abuse.
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A Natural Advantage: An Eye-Tracking Analysis of Indoor and Outdoor Spaces

March 21, 2024 12:00 AM
Authors: Samuel Weisler. Mentors: Brandon Ro. Insitution: Utah Valley University. Contemporary architecture and design increasingly prioritize sustainable, healthy, and aesthetically pleasing indoor environments, acknowledging the fact that we spend most of our lives inside buildings. However, this research brings up a critical question: are we undervaluing the inherent beauty of the outdoors within our built environment? While the concept of beauty is a subject of heavy debate, the universal beauty of nature remains a constant. This study aims to substantiate the superiority of outdoor spaces over their indoor counterparts by comparing the visual appeal of AI-generated images. Specifically, it will create image pairs for five different activity categories: contemplation, recreation, social interaction, education, and creativity. Each image in the pair must embody essential elements: sunlight, biophilic components, and privacy. For each activity category, AI will be instructed to generate an outdoor space image and an indoor equivalent. Next, visual eye-tracking software will analyze these images, enabling us to quantitatively gauge their visual appeal. The analysis will provide insight into whether outdoor spaces surpass their indoor counterparts in aesthetics. Anticipating that outdoor spaces will exhibit greater visual appeal, this research carries valuable implications for the architectural and design industries. In a world increasingly focused on enhancing the human experience, these findings will advocate for the greater incorporation and prioritization of outdoor spaces in built environments. Increasing our access to outdoor living spaces will undoubtedly improve the quality of human experiences.
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Sacred Space Design and Spiritual Experience: A Study of Latter-Day Saint Temples

March 21, 2024 12:00 AM
Authors: Colton Korpi. Mentors: Brandon Ro. Insitution: Utah Valley University. Background: The apparent design shift and style of LDS temples has changed over time moving from a traditional style into a modern era. The ornamentation and architectural style of these sacred spaces play a role in shaping the user's spiritual experience by creating a profound sense of connection to religious tradition. Insights into the evolutionary link between human perception and ornamentation inform this exploration. Architecture, initially rooted in shelter and protection, has evolved into an art form, encompassing subjectivity, creativity, and aesthetics. The effects of architecture on our psychological well-being, makes it an ideal venue to understand its influence on spiritual experiences.Purpose: The purpose of this study is to investigate how the presence of ornamentation and architectural style influences the experience of sacred ordinances within LDS temples.Method: A comprehensive study method combining surveys and Visual Attention Software (VAS) to investigate the effects of temple design on user experiences. Surveys will present participants ranging in age, race, and religious beliefs with questions and visual comparisons of diverse temple styles, form, levels of ornamentation, and site design. Complementing this, VAS will offer a technological perspective by analyzing visual attention patterns. The research includes a selection of LDS temples with varying architectural styles distributed geographically to minimize regional biases.Results: The primary hypothesis is that architectural styles and factors of LDS temples impact the emotional and spiritual experiences of visitors. These results could influence and impact the process and overall thought of designing sacred spaces Conclusion: By utilizing both traditional survey methods and VAS technology, this research aims to provide an understanding of how temple architecture shapes the spiritual journey of visitors. The outcomes could have broader implications for architectural design in sacred spaces and offer valuable insights into the evolving role of architecture in spiritual well-being in a contemporary context.
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Breaking Boundaries

March 21, 2024 12:00 AM
Authors: Arawyn Walter. Mentors: Alexandra Giannell. Insitution: Utah Valley University. “Breaking Boundaries” is an abstract self portrait that describes the duality of distancing myself from relationships, juxtaposed to being entangled in the complex connections I have with family and friends. Boundaries, in my sense of the word, are barriers/rules that are set to make an individual feel comfortable, however these barriers can be complicated and are different from person to person. This piece explores my own personal struggle when it comes to setting boundaries for myself and being able to understand the boundaries of others. The two figures resting in the center of the piece expressing two versions of myself, one in action and one in rest revealing two mental states that portray the emotions showing two extremes of what relationships feel like to me. Parts of the work physically emerges from the canvas from my hands that are tangled up in string. The distance of the tangled and strained strings from the canvas comments on my state now and the physical distance I have put between myself and past relationships in order to feel a sense of freedom from the pressures they put on me and I put on myself.
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Pixels to Pillars: AI's Role in Architectural Design

March 21, 2024 12:00 AM
Authors: Nathaniel Stucki. Mentors: Brandon Ro. Insitution: Utah Valley University. In the field of architectural design, the invention of artificial Intelligence or (AI) has sparked incredible amounts of curiosity and debate in regard to its potential impact on classical design principles. For this Project I will dive into the relationship between AI and classical Architecture and aim to determine whether AI can Measure up to the educated experts of classical architecture and how we can use AI as a tool for design.The project will unravel in three separate phases (1-3). Phase 1 will explore the interior and exterior images provided by AI when describing a building akin to the Pantheon because it is considered to be the pinnacle of beauty. The incremental process of refining the text prompt is essential to obtain quality images to continue into the subsequent phases.In phase 2, the VAS by 3M, will be used to assess which of the AI images are the most captivating for both the exterior images and the interior images. The winning interior image and the winning exterior image will then move on to phase 3.Phase 3 will take these AI images and compare them to photographs of the Pantheon VAS 3M. This phase will evaluate the extent that AI can pull attention and will offer insights into the potential utility for architects or designers to use in the design process during the conceptual phase.In conclusion, I expect findings will show VAS attention percentages are slightly skewed in favor of human design and, while AI can enhance the efficiency in the design process, it cannot replace years of classical training. Architects would be wise to, instead of resisting change, fully embrace AI as a tool for design enhancement. This study emphasizes the importance of collaboration between “man and machine” in shaping the future for architecture.
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Investigating Homeowner Contentment: Exploring areas for improvement in home design and construction

March 21, 2024 12:00 AM
Authors: Josh Lythgoe. Mentors: Brandon Ro. Insitution: Utah Valley University. Is the average American content with their home? If not, why are they discontent? One study suggests that how one perceives their home has more impact on them than the actual physical makeup of their home. This research will be added to by determining how the average homeowner perceives their home, and whether or not they are content with their current home. This research will be executed via a survey with a target sample size of at least one-hundred individuals. Factors such as race, socioeconomics, gender, and education will be studied to see what correlations exist between these factors and contentment in each category. Participants will be gathered by posting the survey on various forms of social media, as well as distributing flyers in public locations and randomly selected neighborhoods. Homeowners will be directed to rate various aspects of their home in the following areas: aesthetics and beauty, layout and flow, spaciousness and comfort, timelessness and longevity, maintenance and upkeep, and neighborhood and location. An average will be taken from each category to assess homeowners contentment by topic. The expected results are that on average homeowners will be more discontent than content in each of the above mentioned categories. A statistical analysis will be conducted to look for correlations between who designed the home and contentment. There is an expected positive correlation between contentment with one's home if they were involved in the design process. Similarly, there is an anticipated positive correlation with contentment if an architect designed the home. This research will be used to help guide design professionals to know how they can improve owner contentment with homes being newly constructed and renovated. The findings will help raise awareness of whether or not the current method of designing and constructing houses is meeting the homeowner’s needs, and expectations.
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The Pagoda at Memory Grove Park Analytique

March 21, 2024 12:00 AM
Authors: Sadie Stutz. Mentors: Ben Felix. Insitution: Utah Valley University. The Pagoda is a World War I memorial located in Memory Grove Park in Salt Lake City Utah. This structure was designed by Slack Winburn who was a WWI veteran and local architect in Salt Lake City. It was built in 1925 and is placed to the right after the entry gates of this park. The structure is built out of marble and has simple but intricate detail around the top of the entablature. The pedestal and urn placed in the middle of the structure was added in later years. As you walk around this pedestal you are able to read the names of those in Utah who have passed on and have fought for our country. This memorial is a very elegant and peaceful structure to pay tribute to those who have passed on. The purpose of this project was to study and research this structure. I went to the structure and measured the different details, I composed this analytique to show the beauty in this structure. This composition is done with pencil and watercolor. I have shown an enlarged Doric column, entablature, and pedestal. There is a flower motif of a forget-me-not flower that is repeated through the ornamentation on the entablature and on the pedestal. I have shown the floor plan and floor details with the broken pieces of colored marble which focuses your attention on the pedestal in the middle to remember these men who fought. In the center of the composition is an elevation of the entire structure, surrounded by rose bushes. file:///C:/Users/sadst/Downloads/Sadie%20Stutz%20-%20Pagoda%20Analytique.pdf
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Application of the Generalized Pareto Distribution to Extreme Stock Trading Volumes

March 21, 2024 12:00 AM
Authors: Rachel Krupnek. Mentors: Jie Liu, Sazib Hasan, Vinodh Chellamuthu. Insitution: Utah Tech University. Many groups are interested in potential market indicators because more than 60% of adults in the United States have investments in the stock market. Extreme stock trading volumes can be an important indicator of unusual market events, including those that precede market crashes. Several studies utilized Extreme Value Theory (EVT) and the Generalized Pareto Distribution (GPD) to examine and model the behavior of these extreme volumes. In particular, various estimation techniques are explored within the GPD framework to best fit the stock trading volume data. The goal of this study is to utilize mathematical approaches in economics. Our results have implications in both mathematical and economic fields, providing benefits by enhancing our ability to analyze and prepare for extreme market occurrences.
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Improving Protein-Ligand Docking Predictions Using Molecular Dynamics Simulations and K-means Clustering

March 21, 2024 12:00 AM
Authors: Matthew Williams. Mentors: Elena Laricheva. Insitution: Utah Valley University. Protein-ligand docking is a computational method widely used in drug discovery to predict binding affinities of small molecules to target receptors. However, despite its widespread utility, the method has inherent limitations that can lead to false negative and false positive results, affecting its reliability. False positives occur when docking predicts strong binding affinities that experimental evidence does not confirm, while false negatives arise when the method fails to identify potent binders validated in experiments.Various factors contribute to these inaccuracies, including limitations in scoring functions and search algorithms, but a significant issue lies in the neglect of protein dynamics, i.e., receptor flexibility. To address this limitation, flexible docking methods, which partially account for receptor flexibility, have been developed, but they come at a considerable computational cost. In this project, we incorporated molecular dynamics simulations and k-means clustering to improve prediction of binding energies of a series of small molecules to the human dopamine 2 receptor, a crucial therapeutic target for neuropsychiatric disorders.Our findings demonstrate that sampling conformational states through molecular dynamics and clustering, followed by docking to representative clusters, offers a more accurate assessment of binding energies. Remarkably, this enhanced predictive capability is achieved with minimal additional computational expense.
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