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Full-Text Articles in Physical Sciences and Mathematics

Mentoring Undergraduates At The Intersection Of Organic Synthesis And Peptide Science, Steven L. Castle Jun 2017

Mentoring Undergraduates At The Intersection Of Organic Synthesis And Peptide Science, Steven L. Castle

Journal of Undergraduate Research

Our academic goals were threefold. First, we aimed to synthesize building blocks and begin assembling them to construct the anticancer peptide yaku’amide A (YA, Figure 1). Our purposes in synthesizing YA were to develop new chemical reactions suitable for efficiently preparing its unusual amino acids (shown in red and blue in Figure 1), and synthesize simplified analogues for use in studies designed to reveal its biological target and mode of action. Our second academic goal was derived from the first and involved investigating the ability of bulky dehydroamino acids (i.e., the amino acids of YA shown in blue in Figure …

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Alzheimer’S Disease: A New Model Defining The Mechanism Of Iron- Catalyzed Radical Damage To Neurons, Richard Watt, Jonathan Wisco Jun 2017

Alzheimer’S Disease: A New Model Defining The Mechanism Of Iron- Catalyzed Radical Damage To Neurons, Richard Watt, Jonathan Wisco

Journal of Undergraduate Research

The MEG proposal focused on understanding how elevated homocysteine levels cause the inability of cells to control iron levels as a cause for Alzheimer’s disease. Iron is associated with the amyloid plaques and tau tangles that are proposed to cause damage to neurons. Dr. Wisco and I previously submitted an NIH R15 proposal that was viewed positively but was not funded due to a lack of preliminary data. Our goal was to use MEG funding to provide preliminary data supporting the hypothesis. We proposed that Homocysteine was a dangerous trigger for disrupting iron metabolism. Biochemical techniques, immunohistochemistry techniques and MRI …

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Calculating Music Similarity With Mobile Device Playlists, Jacob O'Bryant, Dennis Ng Jun 2017

Calculating Music Similarity With Mobile Device Playlists, Jacob O'Bryant, Dennis Ng

Journal of Undergraduate Research

Music recommendation systems, such as Pandora and Spotify, help listeners to discover new music. The similarity of different songs is an important measure used in music recommendation. We have studied manually-created playlists on mobile devices to see if they can be used to accurately calculate song similarity. We collected playlists from 41 research subjects and used a co-occurrence model to calculate similarity between songs in the collection.

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Identifying Binary Brown Dwarf Systems Using Model Point Spread Functions, Kyle Matt, Denise Stephens Jun 2017

Identifying Binary Brown Dwarf Systems Using Model Point Spread Functions, Kyle Matt, Denise Stephens

Journal of Undergraduate Research

The purpose of this project was to improve upon a method for discovering binary brown dwarf systems, and create a program to speed up the implementation of that method. A Brown Dwarf (BD) is a celestial object that is not massive enough to undergo hydrogen fusion in its core, meaning it is too small to be a star, but is also too big to be a planet. BDs can form in low-mass binary pairs. A stellar object located many parsecs away will act as a point source of light for an observer on Earth, therefore the light from such an …

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Using Frequency Noise Feedback To Satabilize Extended Cavity Diode Lasers For Use In Atomic Physics, Mckinley Pugh, Dallin Durfee Jun 2017

Using Frequency Noise Feedback To Satabilize Extended Cavity Diode Lasers For Use In Atomic Physics, Mckinley Pugh, Dallin Durfee

Journal of Undergraduate Research

Diode lasers in particular are useful in atomic physics because they are durable, compact, and relatively inexpensive. Unfortunately diode lasers also have linewidths that are much wider than atomic transitions. One common method to narrow the linewidth of diode lasers is to add a reflection grating outside the laser, creating an extended cavity diode laser (ECDL). While ECDLs are effective at narrowing the linewidth, they also introduce so many variables that affect the wavelength of the laser that small changes in the laser’s environment can cause the laser to mode hop, or jump to an entirely different wavelength.

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Machine Learning With Scattering Transforms, Jacob Hansen, Gus Hart Jun 2017

Machine Learning With Scattering Transforms, Jacob Hansen, Gus Hart

Journal of Undergraduate Research

Our goal was to implement scattering transforms as a mathematical representation of materials. The intention of this project was to build intuition on this technique using model data in one and two dimensions. The tools created here will be used as templates in further projects on real materials data. The intuition built during this project is crucial to the machine learning framework for materials design that we hope to build in the near future.

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Weak Synchronization In Excitatory – Inhibitory Neuronal Networks, Joel Eliason, Benjamin Webb Jun 2017

Weak Synchronization In Excitatory – Inhibitory Neuronal Networks, Joel Eliason, Benjamin Webb

Journal of Undergraduate Research

One ubiquitously observed dynamic phenomenon in the nervous system is that of weak synchronization or clustering, a behavior in which a large group of neurons in a population will all fire synchronously and then fall out of synchronization. When isolated to neurons that only form short-range connections, this behavior is typically referred to as “neuronal avalanches”, and is thought to be particularly important for robustness of information transmission as well as sensitivity to inputs. Given these potential computational benefits, avalanches have been a focus of theoretical biologists for the past 20 years. In particular, my project focused on the conditions, …

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A Photometric Approach To The Redshift Of Galaxies, John Bohman, Joseph Moody Jun 2017

A Photometric Approach To The Redshift Of Galaxies, John Bohman, Joseph Moody

Journal of Undergraduate Research

It is necessary to study the distribution of matter to better understand the universe. There are many difficulties associated with this task however, one of the most basic being that that the universe is an extremely large space, and it takes a lot of time and effort to observe faint objects. Multi fiber spectrometers have made this task much easier, and over 1.4 million spectroscopic redshifts have been obtained. While this is certainly impressive, much remains to be done. This project attempts to develop a survey method capable of detecting and finding the redshift of relatively close (meaning a redshift …

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Characterizing Great Salt Lake Dust Relative Other Regional Dust Sources, Colin Hale, Carling Greg Jun 2017

Characterizing Great Salt Lake Dust Relative Other Regional Dust Sources, Colin Hale, Carling Greg

Journal of Undergraduate Research

Dust storms occur frequently along the Wasatch Front. These dust events may have negative effects on human health and agriculture. To help understand dust events along the Wasatch Front, this study focuses on analyzing dust deposition to better locate dust emission sources. Understanding the source of dust events is important. This is important because Great Salt Lake water levels are dropping exposing lakebed. This newly expose lakebed may result in increased frequency and intensity of dust events. To understand if this lakebed is affecting the Wasatch Front and acting as an emission source.

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Identifying Risk Factors For Interstate Crashes Using Spatial Statistics, Kaitlin Gibson, Matthew Heaton Jun 2017

Identifying Risk Factors For Interstate Crashes Using Spatial Statistics, Kaitlin Gibson, Matthew Heaton

Journal of Undergraduate Research

The goal of systemic highway safety improvement is to identify road characteristics, called risk factors, associated with a higher prevalence of crashes, so that the roads can be modified to avoid these characteristics. However, the statistical analyses these improvement projects are based on generally use methods which are not appropriate for the data. Our project implements novel spatial statistical methodology which is appropriate and state-of-the-art to identify these risk factors.

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Utilizing The Power Of Graphical Processing For Dna Mapping: A Comparison Of Gnumap And Barracuda, Cole Lyman, Mark Clement Jun 2017

Utilizing The Power Of Graphical Processing For Dna Mapping: A Comparison Of Gnumap And Barracuda, Cole Lyman, Mark Clement

Journal of Undergraduate Research

Recent advances in genome sequencing technologies have resulted in a large increase in the amount of genetic data available. Large Genome Wide Association Studies (GWAS) have the potential to identify the causes of cancer, Alzheimer’s disease, heart failure and many other diseases if the large quantities of data that are becoming available can be analyzed effectively. Next-generation read mapping software, a crucial step in analyzing genetic data, is slow while trying to achieve high mapping accuracy. One approach to speeding up next-generation read mapping focuses on using Graphical Processing Units (GPUs). This project compared the effectiveness of two genome mappers, …

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An Algorithm For Multiple Regression Variable Selection For Biochemical Oxygen Demand, Zach White, Dr. William Christensen Jun 2017

An Algorithm For Multiple Regression Variable Selection For Biochemical Oxygen Demand, Zach White, Dr. William Christensen

Journal of Undergraduate Research

Biochemical Oxygen Demand (BOD) is used to measure of the amount of oxygen required by aerobic bacteria and other microorganisms to stabilize decomposable organic matter. It is run as a laboratory based biodegradation test and relies upon the presence of a thriving microbial community that may be naturally present in the sample or artificially introduced by addition of a seed, commonly a known volume of sewage effluent of known BOD. A standard BOD test is run in the dark at a temperature of 20 degrees Celsius for 5 days. This is defined as a five-day BOD (BOD5), which is the …

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Seeing The World Through New Eyes: Implementing Map-Based Mobile Apps In Field Trips And Research, Mariah Chambers, Ron Harris Jun 2017

Seeing The World Through New Eyes: Implementing Map-Based Mobile Apps In Field Trips And Research, Mariah Chambers, Ron Harris

Journal of Undergraduate Research

Mobile apps are a resource that can aid in field trip instruction and enhance students’ learning. Because the specific location of the field trip is often an important element in overall understanding, map-based learning materials can be used to integrate information with the place, providing context for the concepts that will be learned on the field trip. The purpose of this project was twofold. One purpose was to provide professors with information and instructions for using map-based mobile apps to prepare students for, and provide resources during, field trips and study abroad experiences. A second purpose was to implement the …

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Trace Element Analysis Of Quartz Grains In The Wah Wah Springs Tuff And Granodiorite Intrusion, Joel Barker, Dr. Eric Christiansen Jun 2017

Trace Element Analysis Of Quartz Grains In The Wah Wah Springs Tuff And Granodiorite Intrusion, Joel Barker, Dr. Eric Christiansen

Journal of Undergraduate Research

The Wah Wah Springs tuff and cogenetic granodiorite were part of the creation of the Indian Peak-Caliente Caldera Complex, which lies on the Nevada-Utah border (Skidmore, 2013). The complex formed during the middle Cenozoic (36-18 Ma) during an episode of explosive silicic activity (Best et al., 2013). Rollback of the subducting lithosphere likely caused the silicic activity, evidenced by the migration of magmatism southward (Best et al., 2013). The dehydration of the subducting oceanic lithosphere caused mafic magmas high in water to rise and fractionate in continental crust before eruption (Skidmore, 2013). Over twenty-four different ignimbrites have been found in …

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Characterizing The Design Space Of Oscillatory Biological Networks, Leanne Lunsford, Denise Stephens, Eric Hintz Jun 2017

Characterizing The Design Space Of Oscillatory Biological Networks, Leanne Lunsford, Denise Stephens, Eric Hintz

Journal of Undergraduate Research

Characterizing the relevant parameters of a design space in order to satisfy a specific behavior criterion is an important problem throughout all of science and engineering. In this project we proposed to apply model reduction to the case of biological oscillations involving Michaelis-Menten reactions. By removing irrelevant parameters from a fully connected network we were able to reduce a known problem in systems biology to a more general model. Furthermore, significant progress has been made in applying Manifold Boundary Approximation Method (MBAM) to oscillatory models in systems biology.

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The Ogcleaner: Detecting False-Positive Sequence Homology, Masaki Stanley Fujimoto Jun 2017

The Ogcleaner: Detecting False-Positive Sequence Homology, Masaki Stanley Fujimoto

Theses and Dissertations

Within bioinformatics, phylogenetics is the study of the evolutionary relationships between different species and organisms. The genetic revolution has caused an explosion in the amount of raw genomic information that is available to scientists for study. While there has been an explosion in available data, analysis methods have lagged behind. A key task in phylogenetics is identifying homology clusters. Current methods rely on using heuristics based on pairwise sequence comparison to identify homology clusters. We propose the Orthology Group Cleaner (the OGCleaner) as a method to evaluate cluster level verification of putative homology clusters in order to create higher quality …

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Stability Of Planar Detonations In The Reactive Navier-Stokes Equations, Joshua W. Lytle Jun 2017

Stability Of Planar Detonations In The Reactive Navier-Stokes Equations, Joshua W. Lytle

Theses and Dissertations

This dissertation focuses on the study of spectral stability in traveling waves, with a special interest in planar detonations in the multidimensional reactive Navier-Stokes equations. The chief tool is the Evans function, combined with STABLAB, a numerical library devoted to calculating the Evans function. Properly constructed, the Evans function is an analytic function in the right half-plane whose zeros correspond in multiplicity and location to the spectrum of the traveling wave. Thus the Evans function can be used to verify stability, or to locate precisely any unstable eigenvalues. We introduce a new method that uses numerical continuation to follow unstable …

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Active Control Of Cylindrical Shells Using The Weighted Sum Of Spatial Gradients (Wssg) Control Metric, Pegah Aslani Jun 2017

Active Control Of Cylindrical Shells Using The Weighted Sum Of Spatial Gradients (Wssg) Control Metric, Pegah Aslani

Theses and Dissertations

Cylindrical shells are common structures that are often used in industry, such as pipes, ducts, aircraft fuselages, rockets, submarine pressure hulls, electric motors and generators. In many applications it is desired to attenuate the sound radiated from the vibrating structure. There are both active and passive methods to achieve this purpose. However, at low frequencies passive methods are less effective and often an excessive amount of material is needed to achieve acceptable results. There have been a number of works regarding active control methods for this type of structure. In most cases a considerable number of error sensors and secondary …

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Formation Of Rapakivi Feldspars In The Deer Isle Granite Complex, Coastal Maine: In Situ Lead Isotope And Trace Element Analysis, William Desmond Obrien Jun 2017

Formation Of Rapakivi Feldspars In The Deer Isle Granite Complex, Coastal Maine: In Situ Lead Isotope And Trace Element Analysis, William Desmond Obrien

Theses and Dissertations

Rapakivi and alkali feldspar phenocrysts from the Deer Isle Granite Complex were investigated using in situ trace element and Pb isotope geochemistry to see if magma mixing or isothermal decompression was responsible for their formation. Pb isotope and trace element profiles, along with CL imagery of quartz phenocrysts, indicate compositional changes in the magma chamber occurred during rapakivi and alkali feldspar growth. Repeated episodes of magma mixing/replenishment by relatively isotopically primitive and LREE enriched magmas (along with hybridized variations with the host magma) created localized disequilibration. Alkali feldspar phenocrysts proximal to these zones of thermal perturbation were first resorbed and …

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Sedimentology And Taphonomy Of The Abydosaurus Mcintoshi Quarry, (Naturita Formation, Early Cretaceous, Latest Albian), Dinosaur National Monument, Utah, Aaron Daniel Holmes Jun 2017

Sedimentology And Taphonomy Of The Abydosaurus Mcintoshi Quarry, (Naturita Formation, Early Cretaceous, Latest Albian), Dinosaur National Monument, Utah, Aaron Daniel Holmes

Theses and Dissertations

The holotypic locality of the brachiosaurid titanosauriform sauropod, Abydosaurus mcintoshi, is quarry DNM-16, located in Dinosaur National Monument. The bones are preserved near the base of a heterolithic, trough cross stratified to planar bedded sandstone channel complex. The trough cross to planar bedded sandstones mark times of variable flow with times of high flow velocity based on bones whose upper surfaces were eroded before final burial. The abundance of mud with the dominant medium to fine sand, and poorly confined sandstone channels indicate the bones were transported and buried in medial to distal intermittent flows of a distributive fluvial …

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Using Multiview Annotation To Annotate Multiple Images Simultaneously, Timothy C. Price Jun 2017

Using Multiview Annotation To Annotate Multiple Images Simultaneously, Timothy C. Price

Theses and Dissertations

In order for a system to learn a model for object recognition, it must have a lot of positive images to learn from. Because of this, datasets of similar objects are built to train the model. These object datasets used for learning models are best when large, diverse and have annotations. But the process of obtaining the images and creating the annotations often times take a long time, and are costly. We use a method that obtains many images of the same objects in different angles very quickly and then reconstructs those images into a 3D model. We then use …

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Informing The Use Of Hyper-Parameter Optimization Through Meta-Learning, Samantha Corinne Sanders Jun 2017

Informing The Use Of Hyper-Parameter Optimization Through Meta-Learning, Samantha Corinne Sanders

Theses and Dissertations

One of the challenges of data mining is finding hyper-parameters for a learning algorithm that will produce the best model for a given dataset. Hyper-parameter optimization automates this process, but it can still take significant time. It has been found that hyperparameter optimization does not always result in induced models with significant improvement over default hyper-parameters, yet no systematic analysis of the role of hyper-parameter optimization in machine learning has been conducted. We propose the use of meta-learning to inform the decision to optimize hyper-parameters based on whether default hyper-parameter performance can be surpassed in a given amount of time. …

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A Green Form-Based Information Extraction System For Historical Documents, Tae Woo Kim May 2017

A Green Form-Based Information Extraction System For Historical Documents, Tae Woo Kim

Theses and Dissertations

Many historical documents are rich in genealogical facts. Extracting these facts by hand is tedious and almost impossible considering the hundreds of thousands of genealogically rich family-history books currently scanned and online. As one approach for helping to make the extraction feasible, we propose GreenFIE—a "Green" Form-based Information-Extraction tool which is "green" in the sense that it improves with use toward the goal of minimizing the cost of human labor while maintaining high extraction accuracy. Given a page in a historical document, the user's task is to fill out given forms with all facts on a page in a document …

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Robust Object Tracking: A Path-Planning Approach, Bryant Eldon Chandler May 2017

Robust Object Tracking: A Path-Planning Approach, Bryant Eldon Chandler

Theses and Dissertations

When attempting to follow ground-based moving objects (hereafter referred to as ``waldos'') using an unmanned air vehicle (UAV), occlusion can become a significant problem for computer vision algorithms designed to track the object. When a waldo is occluded, the computer vision algorithm loses the track and the UAV's ability to predict movement degrades. We propose a path-planning and replanning method that moves a UAV to a location that maximizes the important waldos that can be seen while accounting for occlusion, and attempts to maximize the area it can see during travel. The proposed work moves beyond state-of-the-art algorithms designed to …

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Diversity And Efficiency: An Unexpected Result, Joseph Smith Johnson May 2017

Diversity And Efficiency: An Unexpected Result, Joseph Smith Johnson

Theses and Dissertations

Empirical evidence shows that ensembles with adequate levels of pairwise diversity among a set of accurate member algorithms significantly outperform any of the individual algorithms. As a result, several diversity measures have been developed for use in optimizing ensembles. We show that diversity measures that properly combine the diversity space in an additive and multiplicative manner, not only result in ensembles whose accuracy is comparable to the naive ensemble of choosing the most accurate learners, but also results in ensembles that are significantly more efficient than such naive ensembles. In addition to diversity measures found in the literature, we submit …

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Desorption Electrospray Ionization (Desi) Mass Spectrometric Imaging Of Spatially Regulated In Vivo Metabolic Rates, Charlotte Reininger Lewis May 2017

Desorption Electrospray Ionization (Desi) Mass Spectrometric Imaging Of Spatially Regulated In Vivo Metabolic Rates, Charlotte Reininger Lewis

Theses and Dissertations

Desorption electrospray ionization (DESI) is an ambient ionization technique used for mass spectrometric imaging of biological samples. When coupled with isotopic ratio measurements of deuterium-labeled tissues, DESI provides a means of measuring metabolic rates on a spatially resolved basis. In vivo metabolic rates are desired to better understand diseases such as Alzheimer's, Parkinson's, Huntington's, and various forms of cancer that negatively impact metabolic rates within different organs of the human body. Although DESI has been used to image lipids and metabolites of a variety of tissues and other imaging techniques, such as NIMS, have been used to study kinetic turnover …

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Network Reconstruction And Vulnerability Analysis Of Financial Networks, Nathan Scott Woodbury May 2017

Network Reconstruction And Vulnerability Analysis Of Financial Networks, Nathan Scott Woodbury

Theses and Dissertations

Passive network reconstruction is the process of learning a structured (networked) representation of a dynamic system through the use of known information about the structure of the system as well as data collected by observing the inputs into a system along with the resultant outputs. This work demonstrates an improvement on an existing network reconstruction algorithm so that the algorithm is capable of consistently and perfectly reconstructing a network when system inputs and outputs are measured without error. This work then extends the improved network reconstruction algorithm so that it functions even in the presence of noise as well as …

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It Is Better To Be Upside Than Sharpe!, Daniele Dapuzzo Apr 2017

It Is Better To Be Upside Than Sharpe!, Daniele Dapuzzo

Theses and Dissertations

Based on the assumption that returns in Commercial Real Estate are normally distributed, the Sharpe Ratio has been the standard risk-adjusted performance measure for the past several years. Research has questioned whether this assumption can be reasonably made. The Upside Potential Ratio as a risk-adjusted performance measure is an alternative to measure performance on a risk-adjusted basis but its values differ from the Sharpe Ratio's only in the assumption of skewed returns. We will provide reasonable evidence that CRE returns should not be fitted with a normal distribution and present the Gaussian Mixture Model as our choice of distribution to …

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Weathering Sequence Of Young Basalts: A Case Study From Kohala, Hawaii, Kimberly Francis Sowards Apr 2017

Weathering Sequence Of Young Basalts: A Case Study From Kohala, Hawaii, Kimberly Francis Sowards

Theses and Dissertations

Exposed weathering profiles of a series of Pololu lava flows in Kohala, Hawaii are ideal for investigating the sequence of reactions/reaction pathways of weathered basalt. Weathering reactions for saprolites show mineral sequences that include feldspar → halloysite ± gibbsite + solutes; clinopyroxene → hematite + minor halloysite + solutes; olivine → hematite + solutes; magnetite → hematite or other Fe-oxides/hydroxides. However, the presence of smectite in four samples suggests that smectite-group clays may form as short lived intermediates at the base of the weathering profile. Regionally, on Kohala, soils and saprolites are dominated by halloysite with small quantities of other …

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Near-Salt Stratal Geometries And Implications For The Evolution Of The Onion Creek Diapir Moab, Ut, Ethan L. Cook Apr 2017

Near-Salt Stratal Geometries And Implications For The Evolution Of The Onion Creek Diapir Moab, Ut, Ethan L. Cook

Theses and Dissertations

The Onion Creek Diapir is one of many salt domes proximal to the Uncompahgre thrust front of the ancestral rockies in the Paradox Basin. It is comprised of Paradox Formation evaporites and large blocks of Honaker Trail Formation carbonates that were deformed by loading of Permian Cutler Formation progradational alluvial to fluvial fans. The history of salt movement in the Onion Creek Diapir is recorded in the near-salt strata. Large salt bodies and their adjacent mini-basins evolve conforming to a complex relationship between salt withdrawal, creating localized accommodation, and sediment deposition. Migrating mini-basin depo-centers, thinned and folded strata, and spatial …

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