Physical Sciences
ProSPr: Protein Structure Prediction via Interatomic Distances
Hedelius, Bryce; Millecam, Todd; Wingate, David; Della Corte, Dennis (Brigham Young University)
Faculty Advisor: Della Corte, Dennis (BYU College of Physical and Mathematical Sciences, Physics); Wingate, David (BYU College of Physical and Mathematical Sciences, Computer Science)
Substantial progress has been made in the past several years towards the accurate prediction of protein tertiary structures from primary sequence, aided greatly by the integration of machine learning. Current success is based on two-stage protocols: first, the training of a deep convolutional neural network (CNN) to predict macromolecular structure restraints, and second, the use of these restraints to construct a folded three-dimensional structure of the target protein. Such a two-stage folding protocol was used by DeepMind in the recent Critical Assessment of Structure Prediction (CASP13), which outperformed all established groups. However, DeepMind has not expressed a plan to publish the code of their AlphaFold protocol. Here we present ProSPr, a network representing the first part of the AlphaFold pipeline for predicting interatomic distances, and demonstrate its abilities in the contact prediction task relative to other state-of-the-art methods. We also investigate and report on the roles of certain input features in prediction quality. ProSPr is made freely available to the scientific community both as source code and a Docker container, which we anticipate will encourage the development of better techniques for assembling protein structures from restraints.
Faculty Advisor: Della Corte, Dennis (BYU College of Physical and Mathematical Sciences, Physics); Wingate, David (BYU College of Physical and Mathematical Sciences, Computer Science)
Substantial progress has been made in the past several years towards the accurate prediction of protein tertiary structures from primary sequence, aided greatly by the integration of machine learning. Current success is based on two-stage protocols: first, the training of a deep convolutional neural network (CNN) to predict macromolecular structure restraints, and second, the use of these restraints to construct a folded three-dimensional structure of the target protein. Such a two-stage folding protocol was used by DeepMind in the recent Critical Assessment of Structure Prediction (CASP13), which outperformed all established groups. However, DeepMind has not expressed a plan to publish the code of their AlphaFold protocol. Here we present ProSPr, a network representing the first part of the AlphaFold pipeline for predicting interatomic distances, and demonstrate its abilities in the contact prediction task relative to other state-of-the-art methods. We also investigate and report on the roles of certain input features in prediction quality. ProSPr is made freely available to the scientific community both as source code and a Docker container, which we anticipate will encourage the development of better techniques for assembling protein structures from restraints.
Measuring the Luminosity Function of Galactic Foreground Stars
Morris, Nathaniel; Jensen, Joseph (Utah Valley University)
Faculty Advisor: Jensen, Joseph (Utah Valley University, Physics)
We measured the brightness of Milky Way stars to determine if they have an effect on extragalactic surface brightness fluctuation (SBF) distance measurements. When SBF measurements are made on background galaxies near the Galactic plane, we observe a large number of stars in the foreground. With most SBF measurements, we can mask out the brightest stars, and make measure SBF with a relatively uncontaminated background. This becomes more difficult with galaxies that are close to the Galactic plane because there are many more foreground stars, and undetected fainter stars that escape the masking process can bias the distance measurement. My research will determine if these unmasked foreground stars have a significant effect on the SBF measurements on these galaxies near the Galactic plane.
Faculty Advisor: Jensen, Joseph (Utah Valley University, Physics)
We measured the brightness of Milky Way stars to determine if they have an effect on extragalactic surface brightness fluctuation (SBF) distance measurements. When SBF measurements are made on background galaxies near the Galactic plane, we observe a large number of stars in the foreground. With most SBF measurements, we can mask out the brightest stars, and make measure SBF with a relatively uncontaminated background. This becomes more difficult with galaxies that are close to the Galactic plane because there are many more foreground stars, and undetected fainter stars that escape the masking process can bias the distance measurement. My research will determine if these unmasked foreground stars have a significant effect on the SBF measurements on these galaxies near the Galactic plane.
Raman Imaging of Single Cellular Metabolism
Ballantyne, Eliza; Buck, Lance; Cox, Zach; Adams, Brittney; Trappett, Matthew; Shipp, Dustin (Utah Valley University)
Faculty Advisor: Shipp, Dustin (Utah Valley University, Physics)
Understanding how cells metabolize the chemicals around them on a single cellular level is paramount to analyzing the effectiveness of pharmaceutical drugs. Discrepancies between pharmaceutical drug results during lab testing versus in actual patients are an expensive and time consuming obstacle. These differences could be alleviated using Raman spectroscopy by testing based on an overall chemical map instead of individual factors. Raman spectroscopy has great potential to aid this process because of its ability to present a chemical fingerprint of an entire cell without interfering with the cell's natural responses to chemical changes.
Using Raman spectroscopy to develop an additional method for observing cell metabolism will enhance understanding of cell function and advance studies focused on the results of chemical effects on cells in vivo. As a step toward this goal, this project is currently focused on obtaining time-lapsed Raman images of glucose uptake. Using glucose metabolism, we are able to model a system for more complicated pharmaceuticals. This study has explored methods for collecting Raman spectra in vivo, balancing time-dependent data collection with the time-constraint of working with living and changing cells. Raman spectra describing the chemical makeup of glioblastoma cancer cells as they metabolize glucose were analyzed and used to create time-lapsed images during uptake.
Our process presents a new lens for understanding cell metabolism and a potential tool for analyzing an additive's effect on a single-cellular level. We developed a platform and method for measuring chemical changes in cells over time. Next stages for this research include observing how metabolism varies depending on what additives are used for uptake and quantifying metabolic differences between types of cells.
Faculty Advisor: Shipp, Dustin (Utah Valley University, Physics)
Understanding how cells metabolize the chemicals around them on a single cellular level is paramount to analyzing the effectiveness of pharmaceutical drugs. Discrepancies between pharmaceutical drug results during lab testing versus in actual patients are an expensive and time consuming obstacle. These differences could be alleviated using Raman spectroscopy by testing based on an overall chemical map instead of individual factors. Raman spectroscopy has great potential to aid this process because of its ability to present a chemical fingerprint of an entire cell without interfering with the cell's natural responses to chemical changes.
Using Raman spectroscopy to develop an additional method for observing cell metabolism will enhance understanding of cell function and advance studies focused on the results of chemical effects on cells in vivo. As a step toward this goal, this project is currently focused on obtaining time-lapsed Raman images of glucose uptake. Using glucose metabolism, we are able to model a system for more complicated pharmaceuticals. This study has explored methods for collecting Raman spectra in vivo, balancing time-dependent data collection with the time-constraint of working with living and changing cells. Raman spectra describing the chemical makeup of glioblastoma cancer cells as they metabolize glucose were analyzed and used to create time-lapsed images during uptake.
Our process presents a new lens for understanding cell metabolism and a potential tool for analyzing an additive's effect on a single-cellular level. We developed a platform and method for measuring chemical changes in cells over time. Next stages for this research include observing how metabolism varies depending on what additives are used for uptake and quantifying metabolic differences between types of cells.
Separation and Detection of Ibuprofen and Warfarin by Capillary Electrophoresis
Covey, Tracy; Alsup, Garrett; Kreinbrink, Alexia (Weber State University)
Faculty Advisor: Covey, Tracy (College of Science, Department of Chemistry and Biochemistry)
Certain over-the-counter medications, such as acetaminophen and ibuprofen, are known to have an effect on the bioavailability of warfarin, enhancing its anticoagulant properties. The goal of this project is to study how varying the concentration of ibuprofen or acetaminophen affects the amount of warfarin bound to blood plasma proteins. To better understand how strong these drug-drug interactions are with warfarin, we proposed capillary electrophoresis (CE) as an analytical method to separate and detect these compounds. Acetaminophen, ibuprofen, and warfarin have all been analyzed using CE in the literature, so we sought to develop a CE method to separate and detect all three drugs together. We are currently optimizing this method and will use this method to investigate warfarin displacement from plasma proteins by ibuprofen and acetaminophen.
Faculty Advisor: Covey, Tracy (College of Science, Department of Chemistry and Biochemistry)
Certain over-the-counter medications, such as acetaminophen and ibuprofen, are known to have an effect on the bioavailability of warfarin, enhancing its anticoagulant properties. The goal of this project is to study how varying the concentration of ibuprofen or acetaminophen affects the amount of warfarin bound to blood plasma proteins. To better understand how strong these drug-drug interactions are with warfarin, we proposed capillary electrophoresis (CE) as an analytical method to separate and detect these compounds. Acetaminophen, ibuprofen, and warfarin have all been analyzed using CE in the literature, so we sought to develop a CE method to separate and detect all three drugs together. We are currently optimizing this method and will use this method to investigate warfarin displacement from plasma proteins by ibuprofen and acetaminophen.
Shocked Electrons: Determination of the Heating Mechanism in Abell 665
Wik, Daniel (University of Utah)
Faculty Advisor: Wik, Daniel (Science, Physics and Astronomy)
Mergers between galaxy clusters are some of the most energetic events in the universe, driving shock fronts in the intracluster medium (ICM), an X-ray hot plasma permeating the cluster. Shock fronts heat thermal electrons, causing an increase in their temperature. The mechanism by which this occurs is undetermined, with two models being proposed to explain the phenomenon. The first proposes direct shock-heating and the second suggests indirect adiabatic compression, with the electrons subsequently equilibrating with ions heated by the shock. We utilize NuSTAR observations, advantaging its effective area at higher energies, of a shock in the merging cluster Abell 665 in order to discriminate between the models. To do so, a temperature profile was constructed across the shock, utilizing spectral fitting, and compared against the models' predictions. In addition, temperature maps across the cluster were generated to better understand the merger event as a whole. We find that the temperature profile is suggestive of the shock model but is not yet statistically significant, due to NuSTAR's comparatively worse spatial resolution. As a result, we apply a novel joint fitting technique to NuSTAR data and Chandra observations in order to statistically distinguish between the models for the first time, accounting for the scattering of photons due to the PSF. Understanding these processes increases our understanding of the magnetic field of the ICM, allowing for mass determination, permitting galaxy clusters to be used to constrain cosmological studies.
Faculty Advisor: Wik, Daniel (Science, Physics and Astronomy)
Mergers between galaxy clusters are some of the most energetic events in the universe, driving shock fronts in the intracluster medium (ICM), an X-ray hot plasma permeating the cluster. Shock fronts heat thermal electrons, causing an increase in their temperature. The mechanism by which this occurs is undetermined, with two models being proposed to explain the phenomenon. The first proposes direct shock-heating and the second suggests indirect adiabatic compression, with the electrons subsequently equilibrating with ions heated by the shock. We utilize NuSTAR observations, advantaging its effective area at higher energies, of a shock in the merging cluster Abell 665 in order to discriminate between the models. To do so, a temperature profile was constructed across the shock, utilizing spectral fitting, and compared against the models' predictions. In addition, temperature maps across the cluster were generated to better understand the merger event as a whole. We find that the temperature profile is suggestive of the shock model but is not yet statistically significant, due to NuSTAR's comparatively worse spatial resolution. As a result, we apply a novel joint fitting technique to NuSTAR data and Chandra observations in order to statistically distinguish between the models for the first time, accounting for the scattering of photons due to the PSF. Understanding these processes increases our understanding of the magnetic field of the ICM, allowing for mass determination, permitting galaxy clusters to be used to constrain cosmological studies.
Discovering the causes of sex-ratio distortion in Drosophila pseudoobscura
White, Michelle; Koury, Spencer; Phadnis, Nitin (University of Utah)
Faculty Advisor: Phadnis, Nitin (University of Utah, School of Biological Sciences)
Sex-ratio chromosomes in Drosophila pseudoobscura are of particular interest because they violate not one, but all three of Mendel's laws of genetics. These special X chromosomes distort the ratio of X and Y-bearing sperm, which leads to biased sex-ratios within the offspring. Although such transmission ratio distortions have been observed from as early as 1928, very little is known about the systems of genes responsible for sex-ratio chromosomal drive due to several complications with traditional methods. Here, we perform one part of a three-part experimental series that attempt to dissect and identify not only the genes involved but also its mechanism. Specifically, this approach will use saturation chemical mutagenesis to knock out every gene on sex-ratio (SR) chromosomes. In order to accomplish this task as efficiently and timely as possible, several preliminary experiments were conducted. We provide the natural variability in SR chromosomal drive and the best statistical framework to analyze the actual mutagenesis experiment. Our results further provide an EMS dosage response curve for the D. pseudoobscura species which has only previously existed for D. melanogaster. These findings propose a reconsideration of the traditional methods used for studying SR chromosomal drive and suggest the mechanism behind the genes or systems of genes involved in this process.
With its rich biological history, the field of genetics has truly grown and expanded into all that we know today. With special regard to our very own Nobel Laureate, Dr. Mario Capecchi, The University of Utah has a dynamic relationship with the field of genetics. The Phadnis Lab plays an active role in this remarkable community and has answered several ideas in evolutionary conflict and speciation. Thus, as a student from the University of Utah studying genetics, it would be greatly interesting to be able to present my work at UCUR.
Faculty Advisor: Phadnis, Nitin (University of Utah, School of Biological Sciences)
Sex-ratio chromosomes in Drosophila pseudoobscura are of particular interest because they violate not one, but all three of Mendel's laws of genetics. These special X chromosomes distort the ratio of X and Y-bearing sperm, which leads to biased sex-ratios within the offspring. Although such transmission ratio distortions have been observed from as early as 1928, very little is known about the systems of genes responsible for sex-ratio chromosomal drive due to several complications with traditional methods. Here, we perform one part of a three-part experimental series that attempt to dissect and identify not only the genes involved but also its mechanism. Specifically, this approach will use saturation chemical mutagenesis to knock out every gene on sex-ratio (SR) chromosomes. In order to accomplish this task as efficiently and timely as possible, several preliminary experiments were conducted. We provide the natural variability in SR chromosomal drive and the best statistical framework to analyze the actual mutagenesis experiment. Our results further provide an EMS dosage response curve for the D. pseudoobscura species which has only previously existed for D. melanogaster. These findings propose a reconsideration of the traditional methods used for studying SR chromosomal drive and suggest the mechanism behind the genes or systems of genes involved in this process.
With its rich biological history, the field of genetics has truly grown and expanded into all that we know today. With special regard to our very own Nobel Laureate, Dr. Mario Capecchi, The University of Utah has a dynamic relationship with the field of genetics. The Phadnis Lab plays an active role in this remarkable community and has answered several ideas in evolutionary conflict and speciation. Thus, as a student from the University of Utah studying genetics, it would be greatly interesting to be able to present my work at UCUR.
CRISPR/Cas9 Mutation of Melanogenic Genes
Backman, Natalia; Bell, Mckenzie; Gostick, Anthony; Kiggins, Kendrick; Koller, Christopher; Naylor, Emily; Porter, Tyrel; Rawlings, Bree; Domyan, Eric, Ph.D (Utah Valley University)
Faculty Advisor: Domyan, Eric (Utah Valley University, Biology/Biotechnology)
The domesticated rock pigeon has been the subject of selective breeding for hounds of years and so displays an immense variety of phenotypes. This variety provides opportunities to further understand the genetic basis of phenotypic evolution. Pigmentation of pigeon feathers is controlled by multiple alleles at different loci, which influences the type and amount of melanin deposited in the feathers. A specific phenotype, known as "recessive red", consists of distinctly red plumage and is caused by a mutation that greatly reduces the expression of the gene Sox10. This gene encodes a transcription factor, known to play a key role in melanocyte maturation and proliferation. Sox10 likely regulates the transcription of multiple downstream genes but the identities of these genes are largely unknown. To identify downstream targets of Sox10, we compared the transcriptomes of regenerating feathers from wild-type and recessive red birds to identify genes that had different expression levels between the two groups. We identified 46 genes that are expressed at different levels between wild-type and recessive red birds, and thus are potential targets of Sox101.
While several of the target genes have known roles in pigmentation, the role that many of the targets play in pigmentation has not been studied, making them interesting candidates for further investigation. Using CRISPR-Cas9, we introduced mutations in candidate genes that were chosen because of their unusually low expression in recessive red birds due to the mutation of Sox10. By observing the effects of the mutated genes, we can determine their roles in pigmentation. The genes that we are mutagenizing in our research is Tbx2, Arsg, and Abcb5 to see if they play a role in the melanin synthesis pathway.
Faculty Advisor: Domyan, Eric (Utah Valley University, Biology/Biotechnology)
The domesticated rock pigeon has been the subject of selective breeding for hounds of years and so displays an immense variety of phenotypes. This variety provides opportunities to further understand the genetic basis of phenotypic evolution. Pigmentation of pigeon feathers is controlled by multiple alleles at different loci, which influences the type and amount of melanin deposited in the feathers. A specific phenotype, known as "recessive red", consists of distinctly red plumage and is caused by a mutation that greatly reduces the expression of the gene Sox10. This gene encodes a transcription factor, known to play a key role in melanocyte maturation and proliferation. Sox10 likely regulates the transcription of multiple downstream genes but the identities of these genes are largely unknown. To identify downstream targets of Sox10, we compared the transcriptomes of regenerating feathers from wild-type and recessive red birds to identify genes that had different expression levels between the two groups. We identified 46 genes that are expressed at different levels between wild-type and recessive red birds, and thus are potential targets of Sox101.
While several of the target genes have known roles in pigmentation, the role that many of the targets play in pigmentation has not been studied, making them interesting candidates for further investigation. Using CRISPR-Cas9, we introduced mutations in candidate genes that were chosen because of their unusually low expression in recessive red birds due to the mutation of Sox10. By observing the effects of the mutated genes, we can determine their roles in pigmentation. The genes that we are mutagenizing in our research is Tbx2, Arsg, and Abcb5 to see if they play a role in the melanin synthesis pathway.
Detection of Protein Biomarkers by Quantum Dot Adsorption
Gomez, Nathaniel; Blumel, Daniel; Dueñas, Davis; Hazel, Matt; Yu, Ming* (Utah Valley University)
Faculty Advisor: Yu, Ming (Utah Valley University, Chemistry)
Kidney cancer in both men and women is among the top ten most common cancers, where the risk in men is estimated at 1:48, and women at 1:83. The issue with kidney disease is that it is difficult to accurately diagnose early-on. Methods of diagnosis that are currently established are expensive and highly invasive if at all accurate. Our research is focused on developing a fast, reliable and cost-effective method of diagnosing kidney disease by the use of fluorescent quantum dots (QDs). When mixed in a solution that contains protein biomarkers, QDs can act as biosensors because the protein alters their fluorescent properties. With QD biosensing, optimal conditions were discovered for the size of QDs and buffers used for detecting different protein biomarkers. The study provides empirical evidence that the alteration is distinguishable between healthy and cancerous levels of protein.
Faculty Advisor: Yu, Ming (Utah Valley University, Chemistry)
Kidney cancer in both men and women is among the top ten most common cancers, where the risk in men is estimated at 1:48, and women at 1:83. The issue with kidney disease is that it is difficult to accurately diagnose early-on. Methods of diagnosis that are currently established are expensive and highly invasive if at all accurate. Our research is focused on developing a fast, reliable and cost-effective method of diagnosing kidney disease by the use of fluorescent quantum dots (QDs). When mixed in a solution that contains protein biomarkers, QDs can act as biosensors because the protein alters their fluorescent properties. With QD biosensing, optimal conditions were discovered for the size of QDs and buffers used for detecting different protein biomarkers. The study provides empirical evidence that the alteration is distinguishable between healthy and cancerous levels of protein.
Continuing Project Atmosniffer
Craig, Michael W. ; Valle, Hugo E. (Weber State University)
Faculty Advisor: Valle, Hugo (Weber State University, Computer Science)
Project atmosniffer has provided me a unique opportunity to work with existing code, updating and maintaining both software and hardware.
Project atmosniffer's purpose is to develop a scientific and comercial air-quality monitoring and recording tool. This project has undergone many transformations over the years since its birth and is continuing to be improved during the period of my contributions.
Most of the learning and developing was self-driven with guidance and learning tools provided by Dr. Valle and the university (pluralsight). The atmosniffer has changed much of its hardware, using a new microprocesser, a new gas board, a new OLED screen, and new drivers. Learning to code to hardware, update legacy code, and reading/coding how each module communicates with each other has been very fascinating.
More details covering the development of Project Atmosniffer will be presented.
Faculty Advisor: Valle, Hugo (Weber State University, Computer Science)
Project atmosniffer has provided me a unique opportunity to work with existing code, updating and maintaining both software and hardware.
Project atmosniffer's purpose is to develop a scientific and comercial air-quality monitoring and recording tool. This project has undergone many transformations over the years since its birth and is continuing to be improved during the period of my contributions.
Most of the learning and developing was self-driven with guidance and learning tools provided by Dr. Valle and the university (pluralsight). The atmosniffer has changed much of its hardware, using a new microprocesser, a new gas board, a new OLED screen, and new drivers. Learning to code to hardware, update legacy code, and reading/coding how each module communicates with each other has been very fascinating.
More details covering the development of Project Atmosniffer will be presented.
Characterizing the grain size distribution of geomorphic units along the Yampa River in Dinosaur National Monument, Colorado.
Schmidt, Jack; Leonard, Christina; Jukes, Thomas (Utah State University)
Faculty Advisor: Schmidt, Jack (S.J. & Jessie E. Quinney College of Natural Resources, Watershed Sciences Department)
Abstract: Western rivers are impounded by a suite of water resource infrastructure that supports human life and has fueled western development. These rivers also support a unique ecosystem for endemic endangered species, whose habitat has been degraded by water resource development that has disrupted the flow and sediment delivered to the system. Channel morphology, and within-channel habitat are the consequence of sediment deposition and erosion. One way to measure the amount of sediment deposition or erosion is by measuring the amount of sediment transported into and out of a river segment to calculate the mass-sediment budget. Such analyses, however, cannot identify the locations within the river segment where aggradation or degradation has occurred, or predict how habitat has changed. In this study, we aim to correlate field-based measurements of channel and habitat change with flux-based sediment budgets. We propose that in order to predict detailed channel response and habitat change, flux-based sediment budgets must be partitioned by grain size class, because different grain size classes are eroded and deposited in different parts of the channel. As part of this study, we have collected samples and observations throughout the study area to analyze and characterize the grain size distribution of the channel and floodplain in units identified as eroding or aggrading. By obtaining information about where different grain size classes of sediment are deposited and eroded, we are working to link the partitioned mass-sediment budget to channel change to understand where and why channel change occurs.
Faculty Advisor: Schmidt, Jack (S.J. & Jessie E. Quinney College of Natural Resources, Watershed Sciences Department)
Abstract: Western rivers are impounded by a suite of water resource infrastructure that supports human life and has fueled western development. These rivers also support a unique ecosystem for endemic endangered species, whose habitat has been degraded by water resource development that has disrupted the flow and sediment delivered to the system. Channel morphology, and within-channel habitat are the consequence of sediment deposition and erosion. One way to measure the amount of sediment deposition or erosion is by measuring the amount of sediment transported into and out of a river segment to calculate the mass-sediment budget. Such analyses, however, cannot identify the locations within the river segment where aggradation or degradation has occurred, or predict how habitat has changed. In this study, we aim to correlate field-based measurements of channel and habitat change with flux-based sediment budgets. We propose that in order to predict detailed channel response and habitat change, flux-based sediment budgets must be partitioned by grain size class, because different grain size classes are eroded and deposited in different parts of the channel. As part of this study, we have collected samples and observations throughout the study area to analyze and characterize the grain size distribution of the channel and floodplain in units identified as eroding or aggrading. By obtaining information about where different grain size classes of sediment are deposited and eroded, we are working to link the partitioned mass-sediment budget to channel change to understand where and why channel change occurs.
Using Redox Active Polymers as Anode and Cathode Species in Redox Flow Batteries
Leininger, Sara; Minteer, Shelley; Rhodes, Zayn; Sigman, Matt; Pancoast, Adam (University of Utah)
Faculty Advisor: Minteer, Shelley (University of Utah College of Science, Chemisty)
In the effort to improve renewable energy as a response to the depletion of fossil fuels, one important aspect to consider is the availability of such sources. The supply of solar and wind power, for example, faces issues with intermittency. Therefore, it is crucial to develop reliable energy storage methods, with redox flow batteries (RFBs) being of particular interest given their potential low cost and high efficiency. RFBs operate similarly to conventional batteries, except the anode and cathode materials are dissolved in electrolyte solutions, and pumped into the electrochemical cell from external storage tanks. Within the cell, the anode and cathode species are separated by a membrane to prevent them from mixing, which would cause the battery to self-discharge. RFBs can utilize aqueous- or organic-based electrolyte solutions, with organic solvents being especially appealing, as the electrochemical potential window is larger than water. However, one major impediment of using organic solvent is the high chemical crossover rate of anode and cathode species through the membrane, causing rapid capacity fade of the battery. Several research studies have shown that the use of redox active polymers (RAPs) with high molecular weights, paired with a size-exclusion membrane effectively counteracts this problem. The resulting steric hindrance between the small pores of the membrane and these large molecules blocks any crossover from the active species. This study will include the construction of an RFB using two previously developed RAPs demonstrated to have high electrochemical cycling stability as electrolytes. By using RAPs as both anode and cathode materials, it is expected that chemical crossover will be minimized, and the lifetime of the battery will be elongated compared to an RFB with one or both species in monomeric form. This study will be significant in the advancement of RFBs, potentially leading to their widespread use for energy storage.
Faculty Advisor: Minteer, Shelley (University of Utah College of Science, Chemisty)
In the effort to improve renewable energy as a response to the depletion of fossil fuels, one important aspect to consider is the availability of such sources. The supply of solar and wind power, for example, faces issues with intermittency. Therefore, it is crucial to develop reliable energy storage methods, with redox flow batteries (RFBs) being of particular interest given their potential low cost and high efficiency. RFBs operate similarly to conventional batteries, except the anode and cathode materials are dissolved in electrolyte solutions, and pumped into the electrochemical cell from external storage tanks. Within the cell, the anode and cathode species are separated by a membrane to prevent them from mixing, which would cause the battery to self-discharge. RFBs can utilize aqueous- or organic-based electrolyte solutions, with organic solvents being especially appealing, as the electrochemical potential window is larger than water. However, one major impediment of using organic solvent is the high chemical crossover rate of anode and cathode species through the membrane, causing rapid capacity fade of the battery. Several research studies have shown that the use of redox active polymers (RAPs) with high molecular weights, paired with a size-exclusion membrane effectively counteracts this problem. The resulting steric hindrance between the small pores of the membrane and these large molecules blocks any crossover from the active species. This study will include the construction of an RFB using two previously developed RAPs demonstrated to have high electrochemical cycling stability as electrolytes. By using RAPs as both anode and cathode materials, it is expected that chemical crossover will be minimized, and the lifetime of the battery will be elongated compared to an RFB with one or both species in monomeric form. This study will be significant in the advancement of RFBs, potentially leading to their widespread use for energy storage.
A Worldwide Phylogenetic Study of the Family Baetidae
Backman, Natalia; Ogden, Heath (Utah Valley University)
Faculty Advisor: Ogden, Heath (Utah Valley University, Biology)
The Family Baetidae, is in the order Ephemeroptera, also commonly known as Mayflies. The first baetids were described around 1815 by Leach, and since there are more than 900 species have been described. The family Baetidae is an important group of mayflies because of their position on the mayfly tree of life in that they are a key to understanding evolutionary trends, such as the origin of wings and flight. Taxon sampling for this study consisted of over 100 taxa, representing ??? genera, from lineages distributed geographically worldwide, except Antarctica. Two main datasets were constructed. The genes 12s, 16s, H3, 18s, 28s and CO1 were used as part of a traditional dataset. Targeted capture sequencing was used to generate a phylogenomic dataset, consisting of over 400 loci. Trees were reconstructed from the aligned datasets, and the results were compared. The phylogenomic data resulted in a much more resolved topology.
Faculty Advisor: Ogden, Heath (Utah Valley University, Biology)
The Family Baetidae, is in the order Ephemeroptera, also commonly known as Mayflies. The first baetids were described around 1815 by Leach, and since there are more than 900 species have been described. The family Baetidae is an important group of mayflies because of their position on the mayfly tree of life in that they are a key to understanding evolutionary trends, such as the origin of wings and flight. Taxon sampling for this study consisted of over 100 taxa, representing ??? genera, from lineages distributed geographically worldwide, except Antarctica. Two main datasets were constructed. The genes 12s, 16s, H3, 18s, 28s and CO1 were used as part of a traditional dataset. Targeted capture sequencing was used to generate a phylogenomic dataset, consisting of over 400 loci. Trees were reconstructed from the aligned datasets, and the results were compared. The phylogenomic data resulted in a much more resolved topology.
A Yarrowing Experience: The Tumor Inhibition and Toxicity of Utah's Native Achillea millefolium
Parada, Michelle (Weber State University)
Faculty Advisor: Schramm, Katharina (Weber State University, Botany)
This research focuses on anti-tumor and the biotoxicity of A. millefollium (yarrow).
Yarrow is an interesting plant with a long history of medicinal uses, but very little has been done to research and prove the different beneficial properties claimed. There are two simple bench-top assays performed in this study, the potato disc assay which inoculates potato slices with Agrobacterium tumefaciens as well as different concentrations of yarrow extracts and assesses the resulting tumor formation and the brine shrimp toxicity assay to assess the LD-50 of the extracts. My results will indicate whether or not the native yarrow extracts inhibit or do not inhibit tumor formation and its toxicity level. The results of this research could lead to further studies of the phytochemicals in the plant to be used for cancer treatments.
Faculty Advisor: Schramm, Katharina (Weber State University, Botany)
This research focuses on anti-tumor and the biotoxicity of A. millefollium (yarrow).
Yarrow is an interesting plant with a long history of medicinal uses, but very little has been done to research and prove the different beneficial properties claimed. There are two simple bench-top assays performed in this study, the potato disc assay which inoculates potato slices with Agrobacterium tumefaciens as well as different concentrations of yarrow extracts and assesses the resulting tumor formation and the brine shrimp toxicity assay to assess the LD-50 of the extracts. My results will indicate whether or not the native yarrow extracts inhibit or do not inhibit tumor formation and its toxicity level. The results of this research could lead to further studies of the phytochemicals in the plant to be used for cancer treatments.
Evaluation of Alternative Methods of Quantifying the Force Involved in a Long Jump
Da Silva, Adrik; Greenwald, Michael; Li, Yongtai; Manseau, Julianna; Woods, Ciera (Westminster College)
Faculty Advisor: Conwell, Peter (Westminster College, Physics); Kamenetzky, Julia (Westminster College, Physics)
The long jump is a track and field event that has a history dating back to 656 BC. Understably, much theorizing and experimenting has been done to find the ideal conditions necessary for an athlete to win such an event. This experiment tests the efficacy of such a theory by using an equation derived by Yongtai Li and comparing its calculations to measurements from a force sensor. Based on Newton's Second Law, the force and its respective range produced from a jump were analyzed and Yongtai's equation proved to be similar to the actual force due to the theoretical results overlapping with the measured results, but will be modified in the future to include angle and initial running velocity to provide an accurate measure of the force necessary to travel a certain horizontal distance. This equation and the ease of calculations will prove useful to long jumper's who attempt to defy the limits of the human body by breaking world records in their events
Faculty Advisor: Conwell, Peter (Westminster College, Physics); Kamenetzky, Julia (Westminster College, Physics)
The long jump is a track and field event that has a history dating back to 656 BC. Understably, much theorizing and experimenting has been done to find the ideal conditions necessary for an athlete to win such an event. This experiment tests the efficacy of such a theory by using an equation derived by Yongtai Li and comparing its calculations to measurements from a force sensor. Based on Newton's Second Law, the force and its respective range produced from a jump were analyzed and Yongtai's equation proved to be similar to the actual force due to the theoretical results overlapping with the measured results, but will be modified in the future to include angle and initial running velocity to provide an accurate measure of the force necessary to travel a certain horizontal distance. This equation and the ease of calculations will prove useful to long jumper's who attempt to defy the limits of the human body by breaking world records in their events
The Power of Wind on Rock: Yardang Formation in Argentina
Sevy, Jonathon; Radebaugh, Jani; McDougall, Dylan; Kerber, Laura; Rabinovitch, Jason (Brigham Young University)
Faculty Advisor: Radebaugh, Jani (Brigham Young University, Geology)
Yardangs are wind-carved linear ridges that are found selectively on Earth and extensively on Mars. The history of the morphologic development of yardangs is not well known. In the Puna high plateau of Argentina there are ignimbrite deposits, many of which have been eroded into yardang fields, commonly called fleets. Yarding fleets are evenly spaced forms, facing into the wind, that resemble a fleet of boats sailing. A prominent fleet, known as Campo de las Piedras Pomez (CCP) was studied to more fully understand their formation and morphology, including field research in December 2018 and 2019. Some physical characteristics looked at in the field included: dedos direction and lengths; heights and lengths of yardangs; structural features; wind and gravel ripple direction. In addition, relationships between yardang organization and structural control have been analyzed. The dedos on the fronts of yardangs averaged 4.0cm in length, while the reverse dedos were 3.3cm. From this it was determined that: Two wind directions, with one dominant, are present; Structural features can shape morphology of yardangs.
Faculty Advisor: Radebaugh, Jani (Brigham Young University, Geology)
Yardangs are wind-carved linear ridges that are found selectively on Earth and extensively on Mars. The history of the morphologic development of yardangs is not well known. In the Puna high plateau of Argentina there are ignimbrite deposits, many of which have been eroded into yardang fields, commonly called fleets. Yarding fleets are evenly spaced forms, facing into the wind, that resemble a fleet of boats sailing. A prominent fleet, known as Campo de las Piedras Pomez (CCP) was studied to more fully understand their formation and morphology, including field research in December 2018 and 2019. Some physical characteristics looked at in the field included: dedos direction and lengths; heights and lengths of yardangs; structural features; wind and gravel ripple direction. In addition, relationships between yardang organization and structural control have been analyzed. The dedos on the fronts of yardangs averaged 4.0cm in length, while the reverse dedos were 3.3cm. From this it was determined that: Two wind directions, with one dominant, are present; Structural features can shape morphology of yardangs.
Chemoselective Macrocyclization of Tyrosine Containing Peptides
Keyes, E. Dalles; Alvey, Brighton; Smith, T. Andrew; Roberts, Andrew G. (University of Utah)
Faculty Advisor: Roberts, Andrew G. (University of Utah, Chemistry)
Medicinal chemistry has long relied on the development of small molecule therapeutics to treat human disease. Small molecules affect change at the cellular level through specific interactions with biological targets (e.g. proteins), thereby eliciting a desired physiological response. Conversely, small molecules can also interact non-specifically, which can complicate their targeted application. In many cases, the use of peptide-based medicines can address this limitation. Like small molecules, peptide-therapeutics are designed to modulate specific biological processes. They often exhibit desirable activity at low concentrations as a result of high selectivity. Being comprised of natural amino acid building blocks, peptides offer an inherent advantage. Their natural breakdown leads to minimally toxic degradation products. However, premature and rapid degradation can result in failure to reach an established target in vivo. The cyclization of peptides has shown to be a promising strategy to address this problem. Inspired by Nature's wide collection of non-ribosomal peptides, specifically those comprising electron-rich aromatic moieties, we have developed a new chemical strategy for the synthesis of cyclic peptides. Our cyclization method leverages the inherent reactivity of the tyrosine (Tyr) phenol nucleus with electrophilic 1,2,4-triazoline-3,5-dione (TAD) moieties. Using this reaction, we can construct macrocyclic peptidomimetic scaffolds. Upon synthesizing an N4-substituted 1,2,4-triazolidine-3,5-dione (aka urazole) at the N-terminus of a solid-supported peptide, the urazole moiety is chemoselectively oxidized under mild conditions to generate a TAD derivative in situ. The TAD moiety reacts with the sidechain phenol nucleus of internally or terminally located Tyr residues and results in the formation of a macrocyclic peptide. We envision that this method will significantly augment current strategies for constructing macrocyclic peptides by enabling the facile synthesis of complex peptidomimetic scaffolds. Furthermore, this approach is anticipated to expand the repertoire of tools used for developing medicinally relevant peptides and, thus, may be suitable for preparing unique peptide-based therapeutics.
Faculty Advisor: Roberts, Andrew G. (University of Utah, Chemistry)
Medicinal chemistry has long relied on the development of small molecule therapeutics to treat human disease. Small molecules affect change at the cellular level through specific interactions with biological targets (e.g. proteins), thereby eliciting a desired physiological response. Conversely, small molecules can also interact non-specifically, which can complicate their targeted application. In many cases, the use of peptide-based medicines can address this limitation. Like small molecules, peptide-therapeutics are designed to modulate specific biological processes. They often exhibit desirable activity at low concentrations as a result of high selectivity. Being comprised of natural amino acid building blocks, peptides offer an inherent advantage. Their natural breakdown leads to minimally toxic degradation products. However, premature and rapid degradation can result in failure to reach an established target in vivo. The cyclization of peptides has shown to be a promising strategy to address this problem. Inspired by Nature's wide collection of non-ribosomal peptides, specifically those comprising electron-rich aromatic moieties, we have developed a new chemical strategy for the synthesis of cyclic peptides. Our cyclization method leverages the inherent reactivity of the tyrosine (Tyr) phenol nucleus with electrophilic 1,2,4-triazoline-3,5-dione (TAD) moieties. Using this reaction, we can construct macrocyclic peptidomimetic scaffolds. Upon synthesizing an N4-substituted 1,2,4-triazolidine-3,5-dione (aka urazole) at the N-terminus of a solid-supported peptide, the urazole moiety is chemoselectively oxidized under mild conditions to generate a TAD derivative in situ. The TAD moiety reacts with the sidechain phenol nucleus of internally or terminally located Tyr residues and results in the formation of a macrocyclic peptide. We envision that this method will significantly augment current strategies for constructing macrocyclic peptides by enabling the facile synthesis of complex peptidomimetic scaffolds. Furthermore, this approach is anticipated to expand the repertoire of tools used for developing medicinally relevant peptides and, thus, may be suitable for preparing unique peptide-based therapeutics.
Hematite Microtextures And (U--TH)/HE Thermochronometry Of The Hurricane Fault, Southwestern Utah: Evidence For A Paleoearthquake?
Taylor, Madison; Ault, Alexis; Newell, Dennis (Utah State University)
Faculty Advisor: Ault, Alexis (College of Science, Geosciences Department)
Hematite-coated fault surfaces offer the potential to characterize and understand the mechanisms and timing of past deformation in exhumed fault zones. We apply integrated micro- to nanoscale microscopy and geochemistry with hematite (U—Th)/He (He) thermochronometry dates to document hematite textural evolution and timing of fault slip on the seismically-active Hurricane fault in southwestern Utah. Hematite is preserved on this bedrock fault scarp that cuts the Triassic Moenkopi Formation. It occurs in elongate, striated, mm- to cm-scale lenses on the slip surface, and we target this material for thermochronometry. Scanning electron microscopy (SEM) shows hematite within ~100—200 μm of the fault surface comprises rounded hematite particles ~100 nm to 2 μm in diameter that lack grain boundaries. Away from the surface and beneath these nanoparticles are randomly-oriented, ~70—150 nm-thick hematite plates. Plate and rounded, "fused" particle morphologies likely reflect initial hematite crystallization from fluids and deformation, respectively. SEM imaging and energy dispersive X-ray spectroscopy also reveal a featureless, ~3 μm-thick, Al-rich silica film enveloping the hematite nanoparticles at the fault surface, suggesting it is amorphous silica. This layer is exclusively found in contact with deformed hematite, implying association with fault slip. A preliminary mean hematite He thermochronometric date is 375 ± 54 ka (±1σ std. dev.; n = 11). This date is appreciably younger than previously-reported, regional apatite He thermochronometry data. This suggests hematite He data may record hematite formation or thermal resetting from friction-generated heat during fault slip. Ongoing hematite He analyses targeting the distinct textural domains will discriminate between these possibilities, and scanning/transmission electron microscopy will evaluate the crystallinity of the surface silica and hematite nanoparticles. Collectively, these data will allow us to decipher the timing and mechanisms of past deformation of the Hurricane fault and understand analogous relationships in other hematite-bearing fault zones.
Faculty Advisor: Ault, Alexis (College of Science, Geosciences Department)
Hematite-coated fault surfaces offer the potential to characterize and understand the mechanisms and timing of past deformation in exhumed fault zones. We apply integrated micro- to nanoscale microscopy and geochemistry with hematite (U—Th)/He (He) thermochronometry dates to document hematite textural evolution and timing of fault slip on the seismically-active Hurricane fault in southwestern Utah. Hematite is preserved on this bedrock fault scarp that cuts the Triassic Moenkopi Formation. It occurs in elongate, striated, mm- to cm-scale lenses on the slip surface, and we target this material for thermochronometry. Scanning electron microscopy (SEM) shows hematite within ~100—200 μm of the fault surface comprises rounded hematite particles ~100 nm to 2 μm in diameter that lack grain boundaries. Away from the surface and beneath these nanoparticles are randomly-oriented, ~70—150 nm-thick hematite plates. Plate and rounded, "fused" particle morphologies likely reflect initial hematite crystallization from fluids and deformation, respectively. SEM imaging and energy dispersive X-ray spectroscopy also reveal a featureless, ~3 μm-thick, Al-rich silica film enveloping the hematite nanoparticles at the fault surface, suggesting it is amorphous silica. This layer is exclusively found in contact with deformed hematite, implying association with fault slip. A preliminary mean hematite He thermochronometric date is 375 ± 54 ka (±1σ std. dev.; n = 11). This date is appreciably younger than previously-reported, regional apatite He thermochronometry data. This suggests hematite He data may record hematite formation or thermal resetting from friction-generated heat during fault slip. Ongoing hematite He analyses targeting the distinct textural domains will discriminate between these possibilities, and scanning/transmission electron microscopy will evaluate the crystallinity of the surface silica and hematite nanoparticles. Collectively, these data will allow us to decipher the timing and mechanisms of past deformation of the Hurricane fault and understand analogous relationships in other hematite-bearing fault zones.
Use of a Portable Handheld X-Ray Fluorescence Unit (pXRF) to Measure Alteration in Exhumed Fault Zones: Implications for Hydrologic Rock Properties and Injection Induced Seismicity
Paulding, Anna (Utah State University)
Faculty Advisor: Bradbury, Kelly (College of Science, Geosciences Department)
A dramatic increase in seismicity has occurred in the midcontinent region since 2009 (Rubinstein and Mahani, 2015), causing public concern for the stability of infrastructure and buildings. Several studies have directly linked this seismicity to the reactivation of buried fault systems near the Paleozoic sedimentary bedrock-Precambrian crystalline basement contact as a result of high volumes of injection of wastewater produced by the oil and gas industry (Ellsworth, 2013; Keranen et al., 2013).
The reactivation of fault zones due to fluid injection is not only influenced by injection rates but also by the ability of fluids to migrate along or across the contact, which is controlled by the rock properties and geologic setting. To better understand the rock property variations that may occur along the nonconformity interface, we use an outcrop analog site of an exhumed fault near Gunnison, Colorado. My undergraduate research focuses on using a portable handheld X-Ray Fluorescence Unit (pXRF) as a tool to measure compositional variations in outcrop. To directly compare data, a calibration using 16 USGS Concentration Standards as well as 12 analog samples will be used to create a calibration optimized for this specific suite of rocks which informs the accuracy of in-situ field data measurements against laboratory measurements of powdered samples, influencing how future pXRF measurements can be analyzed. Micro-scale variations of major and trace element concentrations reflect alteration and related fluid-rock interactions and may serve as a proxy for fluid migration along or across faulted sections of a nonconformity interface. I propose that calibrated pXRF data and whole rock XRF data is a useful tool for understanding the nature and degree of rock alteration in fault zones and across analog sites nonconformity interface. These data can aid in a more broad understanding of how pXRF data can be used in the field to characterize the nonconformity interface and fault zones.
Faculty Advisor: Bradbury, Kelly (College of Science, Geosciences Department)
A dramatic increase in seismicity has occurred in the midcontinent region since 2009 (Rubinstein and Mahani, 2015), causing public concern for the stability of infrastructure and buildings. Several studies have directly linked this seismicity to the reactivation of buried fault systems near the Paleozoic sedimentary bedrock-Precambrian crystalline basement contact as a result of high volumes of injection of wastewater produced by the oil and gas industry (Ellsworth, 2013; Keranen et al., 2013).
The reactivation of fault zones due to fluid injection is not only influenced by injection rates but also by the ability of fluids to migrate along or across the contact, which is controlled by the rock properties and geologic setting. To better understand the rock property variations that may occur along the nonconformity interface, we use an outcrop analog site of an exhumed fault near Gunnison, Colorado. My undergraduate research focuses on using a portable handheld X-Ray Fluorescence Unit (pXRF) as a tool to measure compositional variations in outcrop. To directly compare data, a calibration using 16 USGS Concentration Standards as well as 12 analog samples will be used to create a calibration optimized for this specific suite of rocks which informs the accuracy of in-situ field data measurements against laboratory measurements of powdered samples, influencing how future pXRF measurements can be analyzed. Micro-scale variations of major and trace element concentrations reflect alteration and related fluid-rock interactions and may serve as a proxy for fluid migration along or across faulted sections of a nonconformity interface. I propose that calibrated pXRF data and whole rock XRF data is a useful tool for understanding the nature and degree of rock alteration in fault zones and across analog sites nonconformity interface. These data can aid in a more broad understanding of how pXRF data can be used in the field to characterize the nonconformity interface and fault zones.
The utilization of UV-light and digital photography to measure chemical concentrations during an organic reaction.
Terreros, Eduardo N.; Dr. Roberts, Andrew G. (University of Utah)
Faculty Advisor: Roberts, Andrew G. (University of Utah, Chemistry)
Chromatography is an indispensable tool in most chemistry laboratories, as it provides a way to separate multiple components within a chemical mixture. The separation can be evaluated by the use of various chromatographic methodologies that have been developed to target specific chemical properties (e.g. size, mass, molecular interactions) of the desired compounds. Chromatographic methods are utilized to gather qualitative information in order to observe more general trends, or quantitative data to further explore observations in greater detail.
Thin Layer Chromatography (TLC) is a well-established method for collecting qualitative data from chemical reactions. Although Quantitative TLC (QTLC) methods have been developed, they are limited due to their high complexity, and cost prohibitive nature. The advancement of a Semi-Quantitative Thin Layer Chromatography (S-QTLC) method will provide a quick, low cost method to track organic reactions. We developed a low-cost alternative that uses readily available materials to gather images of TLC plates and process them into semi-quantitative data. In order to achieve this, we have constructed a small image gathering box made of opaque acrylic fitted with two 254 nm UV lamps and a Raspberry Pi Zero W with a camera module to acquire the images. The images are imported to a PC and processed by a custom built MatLab function. We demonstrated that this system can be utilized to gather qualitative data. Current studies will validate semi-quantitative data collection and reaction tracking and work is currently being done to validate semi-quantitative data collection.
Faculty Advisor: Roberts, Andrew G. (University of Utah, Chemistry)
Chromatography is an indispensable tool in most chemistry laboratories, as it provides a way to separate multiple components within a chemical mixture. The separation can be evaluated by the use of various chromatographic methodologies that have been developed to target specific chemical properties (e.g. size, mass, molecular interactions) of the desired compounds. Chromatographic methods are utilized to gather qualitative information in order to observe more general trends, or quantitative data to further explore observations in greater detail.
Thin Layer Chromatography (TLC) is a well-established method for collecting qualitative data from chemical reactions. Although Quantitative TLC (QTLC) methods have been developed, they are limited due to their high complexity, and cost prohibitive nature. The advancement of a Semi-Quantitative Thin Layer Chromatography (S-QTLC) method will provide a quick, low cost method to track organic reactions. We developed a low-cost alternative that uses readily available materials to gather images of TLC plates and process them into semi-quantitative data. In order to achieve this, we have constructed a small image gathering box made of opaque acrylic fitted with two 254 nm UV lamps and a Raspberry Pi Zero W with a camera module to acquire the images. The images are imported to a PC and processed by a custom built MatLab function. We demonstrated that this system can be utilized to gather qualitative data. Current studies will validate semi-quantitative data collection and reaction tracking and work is currently being done to validate semi-quantitative data collection.
Interference Patter Structured Imaging Utilizing Micromirror Display
Gray, Daniel; Durfee, Dallin (Utah Valley University)
Faculty Advisor: Durfee, Dallin (College of Science, Physics)
IPSII is a fully lensless single pixel imaging technique using mechanically scanned interference patterns. The method uses only simple, flat optics; no lenses, curved mirrors, or acousto-optics are used in pattern formation or detection. The resolution is limited by the numerical aperture of the angular access to the object, with a fundamental limit of a quarter wavelength, which is twice the Abbe limit. ISPII also has no fundamental limit on working distance as well as a depth of field and field of view independent of resolution. Normally, an interference pattern is projected across the target object to obtain information. Currently this uses interfering plane waves which produce sinusoidal interference patterns allowing us to measure in the Fourier basis. Mechanically scanning the laser angles to change the interference pattern is slow. Image times usually require hours or days as regular scan times produce approximately one pixel per second. We intend to improve the time to scan an object by utilizing a micromirror array to modify the interference patterns, such that multiple measurements can be made at one angle. Updating the micromirror array is much faster than changing the angles at which the target is scanned. This will greatly reduce the time required as we will not need to measure with as many angles to obtain an image. With the micromirror array we will be able to generate a wider range of basis functions. In addition to increasing the speed this may allow us to better utilize compressive sensing techniques where an n-pixel image may be obtained by scanning only a fraction of n-points on the object.
Faculty Advisor: Durfee, Dallin (College of Science, Physics)
IPSII is a fully lensless single pixel imaging technique using mechanically scanned interference patterns. The method uses only simple, flat optics; no lenses, curved mirrors, or acousto-optics are used in pattern formation or detection. The resolution is limited by the numerical aperture of the angular access to the object, with a fundamental limit of a quarter wavelength, which is twice the Abbe limit. ISPII also has no fundamental limit on working distance as well as a depth of field and field of view independent of resolution. Normally, an interference pattern is projected across the target object to obtain information. Currently this uses interfering plane waves which produce sinusoidal interference patterns allowing us to measure in the Fourier basis. Mechanically scanning the laser angles to change the interference pattern is slow. Image times usually require hours or days as regular scan times produce approximately one pixel per second. We intend to improve the time to scan an object by utilizing a micromirror array to modify the interference patterns, such that multiple measurements can be made at one angle. Updating the micromirror array is much faster than changing the angles at which the target is scanned. This will greatly reduce the time required as we will not need to measure with as many angles to obtain an image. With the micromirror array we will be able to generate a wider range of basis functions. In addition to increasing the speed this may allow us to better utilize compressive sensing techniques where an n-pixel image may be obtained by scanning only a fraction of n-points on the object.
Building a Classifier to Discriminate Bacteria with Raman Spectroscopy
Durrant, Bianca; Bennion, Sean; Shipp, Dustin (Utah Valley University)
Faculty Advisor: Shipp, Dustin (Utah Valley University, Physics)
determine bacteria is growing the bacteria on agar and then identify the bacteria via the API system (analytical profile index). In some medical cases, 24 hours is too long to wait, especially if a patient needs antibiotics. Raman spectroscopy uses laser light to excite a spectrum specific to each molecule. This molecular specificity enables Raman spectroscopy to identify the species of bacteria without a lengthy growth period. Raman spectroscopy is non invasive and only needs one bacterium for detection. It is therefore faster than growing bacteria and identifying via the API system.
From other research groups we know that Raman spectroscopy is able to classify bacteria, albeit with limited breadth of bacterial types. The next step is to implement imaging techniques to make the identification even faster, so that those techniques can be used in hospitals to determine pathological bacteria, so that the treatment can be given faster. Furthermore, when a hospital is unsure whether the patient has a disease caused by bacteria usually they start treating the patient with antibiotics in case they are infected. If identification only take a few hours instead of two to three days, doctors would only prescribe antibiotics when necessary, thus decrease the risk of multiresistant bacteria.
Faculty Advisor: Shipp, Dustin (Utah Valley University, Physics)
determine bacteria is growing the bacteria on agar and then identify the bacteria via the API system (analytical profile index). In some medical cases, 24 hours is too long to wait, especially if a patient needs antibiotics. Raman spectroscopy uses laser light to excite a spectrum specific to each molecule. This molecular specificity enables Raman spectroscopy to identify the species of bacteria without a lengthy growth period. Raman spectroscopy is non invasive and only needs one bacterium for detection. It is therefore faster than growing bacteria and identifying via the API system.
From other research groups we know that Raman spectroscopy is able to classify bacteria, albeit with limited breadth of bacterial types. The next step is to implement imaging techniques to make the identification even faster, so that those techniques can be used in hospitals to determine pathological bacteria, so that the treatment can be given faster. Furthermore, when a hospital is unsure whether the patient has a disease caused by bacteria usually they start treating the patient with antibiotics in case they are infected. If identification only take a few hours instead of two to three days, doctors would only prescribe antibiotics when necessary, thus decrease the risk of multiresistant bacteria.
Binding Trends of simple hosts and guests with CB5, CB6, and Mc5
Dearden, Heravi, Shen, Arslanian, Shrestha, Mismash, Tinsley, Pay (Brigham Young University)
Faculty Advisor: Dearden, David (Brigham Young University, Chemistry)
Using the Spartan and Ion Molecular Spectrometry Suite (IMoS), we use the 3D modeling to predict stability and molecule favorability. Previously in our experimentation we have seen and proper capping of a host molecule with cucurbit[5]uril. This was different than cucurbit[6]uril as the cap in some cases didn't bond to all the upward oxygens because on the molecular symmetry, thus host enclosure was less favorable in cucurbit[6]uril than cucurbit[5]uril. We also observed in our lab the energy differences using the Extensible Computation Chemistry Environment (ECCE) of cucurbit[5]uril host transfer based on cap and host interactions. These studies show that cucurbit[5]uril with methane as a host is more favorable than outside the cavity. It also shows that methane inside cucurbit[5]uril is more favored than in decamethylcucurbit[5]uril. The studies using computational study will be testable using mass spectrometry, and we predict that the same behavior trend will show using other caps and hosts with cucurbit[5]uril and decamethylcucurbit[5]uril.
Faculty Advisor: Dearden, David (Brigham Young University, Chemistry)
Using the Spartan and Ion Molecular Spectrometry Suite (IMoS), we use the 3D modeling to predict stability and molecule favorability. Previously in our experimentation we have seen and proper capping of a host molecule with cucurbit[5]uril. This was different than cucurbit[6]uril as the cap in some cases didn't bond to all the upward oxygens because on the molecular symmetry, thus host enclosure was less favorable in cucurbit[6]uril than cucurbit[5]uril. We also observed in our lab the energy differences using the Extensible Computation Chemistry Environment (ECCE) of cucurbit[5]uril host transfer based on cap and host interactions. These studies show that cucurbit[5]uril with methane as a host is more favorable than outside the cavity. It also shows that methane inside cucurbit[5]uril is more favored than in decamethylcucurbit[5]uril. The studies using computational study will be testable using mass spectrometry, and we predict that the same behavior trend will show using other caps and hosts with cucurbit[5]uril and decamethylcucurbit[5]uril.
An Aperture Correction for GeMS MCAO SBF Distance Measurements
Sundstrom, Rebecca; Jensen, Joseph B. (Utah Valley University)
Faculty Advisor: Jensen, Joseph (Utah Valley University, Physics)
We will measure Surface Brightness Fluctuations (SBF) in three galaxies (ESO137-G006, NGC 3309, and NGC 5128) using images from two cameras: the GeMS Multi-Conjugate Adaptive Optics (MCAO) system and the FLAMINGOS-2 (F-2) near-infrared imaging spectrograph, at the 8-meter Gemini South Telescope in Chile. To make an accurate measurement we need to first determine a photometric calibration for the MCAO system by comparing flux, or captured light, from both detectors. This is necessary because MCAO collects crisp, sharp images but omits some of the total incoming flux from the stars in the galaxies. F-2 takes broader images but includes more measurable flux. By finding the ratio of the flux collected by MCAO to the flux collected by F-2 we can take this "missing" light into account without compromising the crisp, sharp resolution MCAO provides.
Faculty Advisor: Jensen, Joseph (Utah Valley University, Physics)
We will measure Surface Brightness Fluctuations (SBF) in three galaxies (ESO137-G006, NGC 3309, and NGC 5128) using images from two cameras: the GeMS Multi-Conjugate Adaptive Optics (MCAO) system and the FLAMINGOS-2 (F-2) near-infrared imaging spectrograph, at the 8-meter Gemini South Telescope in Chile. To make an accurate measurement we need to first determine a photometric calibration for the MCAO system by comparing flux, or captured light, from both detectors. This is necessary because MCAO collects crisp, sharp images but omits some of the total incoming flux from the stars in the galaxies. F-2 takes broader images but includes more measurable flux. By finding the ratio of the flux collected by MCAO to the flux collected by F-2 we can take this "missing" light into account without compromising the crisp, sharp resolution MCAO provides.
How to create very dark surfaces for applications
Lange, Christian; Shen, T.-C. (Utah State University)
Faculty Advisor: Shen, T.-C. (College of Science, Physics Department)
An ideal black surface should have low reflectance uniformly across the spectrum of electromagnetic radiation. Black paints are not ideal because they have specific reflection peaks and bands. Vertically aligned nanopillars of proper shapes and physical properties are good candidates, but the fabrication and oxidation in air are challenging. Carbon nanotube (CNT) forests could be a cheap alternative but the optical properties are sensitive to the density, length, and alignment of the CNTs in a forest. A model to understand the correlation between the morphology and optical reflectance of CNT forests and strategies to achieve extremely low reflectance in the infrared region will be presented.
Faculty Advisor: Shen, T.-C. (College of Science, Physics Department)
An ideal black surface should have low reflectance uniformly across the spectrum of electromagnetic radiation. Black paints are not ideal because they have specific reflection peaks and bands. Vertically aligned nanopillars of proper shapes and physical properties are good candidates, but the fabrication and oxidation in air are challenging. Carbon nanotube (CNT) forests could be a cheap alternative but the optical properties are sensitive to the density, length, and alignment of the CNTs in a forest. A model to understand the correlation between the morphology and optical reflectance of CNT forests and strategies to achieve extremely low reflectance in the infrared region will be presented.
Distribution of 76 organic compounds and their emission composition throughout the Uintah Basin, Utah
Breitenbach, Makenzie; Lyman, Seth; Tran, Huy (Utah State University)
Faculty Advisor: Lyman, Seth (College of Science, Chemistry and Biochemistry Department); Tran, Huy (College of Science, Chemistry and Biochemistry Department)
The Uintah Basin is a rural area in Northeast Utah where the oil and gas industry is prominent. During multi-day temperature inversions that occur during some winters, locally-emitted air pollutants, particularly from the oil and gas industry, react in the atmosphere to produce ozone. While it is well known that oxides of nitrogen and organic compounds are the main precursors to ozone formation, significant gaps exist in understanding of the sources and composition of organics emitted from various oil and gas-related sources. Better understanding of organic compound emissions will allow regulators and industry to make better decisions to reduce ozone-forming pollution to protect the health of residents and workers in the Uintah Basin.
During the winter of 2018-2019, we are deploying 14 remote measurement stations that collect air samples in silonite-coated canisters (for non-methane hydrocarbons and light alcohols) and on 2,4-dinitrophenylhydrazine-coated sorbent cartridges (for carbonyls). We are analyzing the canister and cartridge samples in our laboratory via gas and liquid chromatography, respectively, to determine concentrations of a suite of 76 organic compounds, all of which are known to be involved in the formation of wintertime ozone in the Uintah Basin. We position these stations in different configurations around the Basin to characterize certain facility types and to characterize organic compound concentrations across the entire Basin. For this presentation, we will use meteorological data and trajectory modeling to determine how facilities in the vicinity of our measurement stations impacted ambient organic compound concentrations and speciation. Later in 2019-20, we will use the 2014 Utah Air Agencies Oil and Gas Emissions Inventory with a three-dimensional photochemical model (WRF-CMAQ) to simulate air concentrations of the measured compounds. We will compare modeled and measured results to determine how well the inventory and model simulate actual ozone precursor concentrations.
Faculty Advisor: Lyman, Seth (College of Science, Chemistry and Biochemistry Department); Tran, Huy (College of Science, Chemistry and Biochemistry Department)
The Uintah Basin is a rural area in Northeast Utah where the oil and gas industry is prominent. During multi-day temperature inversions that occur during some winters, locally-emitted air pollutants, particularly from the oil and gas industry, react in the atmosphere to produce ozone. While it is well known that oxides of nitrogen and organic compounds are the main precursors to ozone formation, significant gaps exist in understanding of the sources and composition of organics emitted from various oil and gas-related sources. Better understanding of organic compound emissions will allow regulators and industry to make better decisions to reduce ozone-forming pollution to protect the health of residents and workers in the Uintah Basin.
During the winter of 2018-2019, we are deploying 14 remote measurement stations that collect air samples in silonite-coated canisters (for non-methane hydrocarbons and light alcohols) and on 2,4-dinitrophenylhydrazine-coated sorbent cartridges (for carbonyls). We are analyzing the canister and cartridge samples in our laboratory via gas and liquid chromatography, respectively, to determine concentrations of a suite of 76 organic compounds, all of which are known to be involved in the formation of wintertime ozone in the Uintah Basin. We position these stations in different configurations around the Basin to characterize certain facility types and to characterize organic compound concentrations across the entire Basin. For this presentation, we will use meteorological data and trajectory modeling to determine how facilities in the vicinity of our measurement stations impacted ambient organic compound concentrations and speciation. Later in 2019-20, we will use the 2014 Utah Air Agencies Oil and Gas Emissions Inventory with a three-dimensional photochemical model (WRF-CMAQ) to simulate air concentrations of the measured compounds. We will compare modeled and measured results to determine how well the inventory and model simulate actual ozone precursor concentrations.
Isotope Paleothermometry of Belemnites from the Jurassic Sundance Sea of Western North America
Perdue, Perdue; Burke, Joshua; Bylund, Kevin; Stephen, Daniel (Utah Valley University)
Faculty Advisor: Stephen, Daniel (Utah Valley University, Earth Science)
The Sundance Sea covered much of western North America during the Middle to Late Jurassic Period. Deposits from this vast epeiric sea are now widely exposed across the region, including the Stump Formation in northeastern Utah, which consists of sandstones and shales reflecting shallow marine deposition. Well-preserved belemnites (Pachyteuthis densus, Oxfordian Stage, ~156 Ma) collected from this unit preserve stable isotope data (_18O and _13C ) that can be used to better understand the paleoceanography and paleoclimatology of the area, as well as possibly some paleobiologic characteristics such as migration patterns through the life cycle and age at sexual maturity and death. Incremental growth of belemnites created growth bands that record isotopic values through various life stages, thus potentially providing information about the life history traits of these organisms, in addition to seasonal temperature variations. Preliminary results suggest our material is consistent with previous reports from other locations in the region, with paleotemperatures in the 17 to 20° C range. In addition, there is some indication of seasonal variations. However, analyses of more samples and further evaluation of potential diagenetic alteration is necessary before more robust conclusions can be drawn.
Faculty Advisor: Stephen, Daniel (Utah Valley University, Earth Science)
The Sundance Sea covered much of western North America during the Middle to Late Jurassic Period. Deposits from this vast epeiric sea are now widely exposed across the region, including the Stump Formation in northeastern Utah, which consists of sandstones and shales reflecting shallow marine deposition. Well-preserved belemnites (Pachyteuthis densus, Oxfordian Stage, ~156 Ma) collected from this unit preserve stable isotope data (_18O and _13C ) that can be used to better understand the paleoceanography and paleoclimatology of the area, as well as possibly some paleobiologic characteristics such as migration patterns through the life cycle and age at sexual maturity and death. Incremental growth of belemnites created growth bands that record isotopic values through various life stages, thus potentially providing information about the life history traits of these organisms, in addition to seasonal temperature variations. Preliminary results suggest our material is consistent with previous reports from other locations in the region, with paleotemperatures in the 17 to 20° C range. In addition, there is some indication of seasonal variations. However, analyses of more samples and further evaluation of potential diagenetic alteration is necessary before more robust conclusions can be drawn.
A Preliminary Paleomagnetic Test for Incremental Pluton Emplacement
Parsons, Travis; Lippert, Peter; Bartley, John (University of Utah)
Faculty Advisor: Lippert, Peter (University of Utah - College of Mines and Earth Science, Geology & Geophysics); Bartley, John (University of Utah - College of Mines and Earth Science, Geology & Geophysics)
Field observations and geochronological measurements of plutons in Yosemite Valley suggest that plutons grow incrementally as a series of stacked sheets of smaller intrusions (i.e., dikes and sills) (Coleman et al., 2004; Glazner et al., 2004; Bartley et al., 2006). This interpretation is in contrast to the traditional view of pluton emplacement through crystallization of a single, massive magma chamber. Most of the observations supporting incremental pluton emplacement use the relationship between zircon U-Pb dating of pluton sections and estimated granitic magma cooling rates to argue that a single magmatic event would crystallize significantly faster than the geochronologic data permit. Incremental pluton emplacement also predicts specific relationships between the age of intruded sheets of magma and the original orientation of these sheets, such that older sheets are expected to be tilted or deformed more than younger sheets. Here we test this prediction of differential tilting by measuring the paleomagnetic inclination preserved in well-dated and structurally characterized sheets of the Tuolumne Intrusive Suite. Magnetic inclination provides a tilt-meter with respect to the Earth's magnetic field direction at the time of pluton emplacement; the reference inclination assuming an untitled pluton is known from independent data sets. We also present rock magnetic data (temperature-dependent magnetic susceptibility, magnetic remanence characteristics) and results from petrographic investigations to characterize the mineralogy and stability of the magnetization. Our results suggest that the low-titanium magnetite remanence carriers are primary and are not biased by secondary magnetizations. The distribution of magnetic inclinations in our sample set — in which older sheets on the periphery of the pluton are shallower than those in younger, more interior sheets, and with respect to the reference inclination — is consistent with predictions from the incremental pluton emplacement hypothesis.
Faculty Advisor: Lippert, Peter (University of Utah - College of Mines and Earth Science, Geology & Geophysics); Bartley, John (University of Utah - College of Mines and Earth Science, Geology & Geophysics)
Field observations and geochronological measurements of plutons in Yosemite Valley suggest that plutons grow incrementally as a series of stacked sheets of smaller intrusions (i.e., dikes and sills) (Coleman et al., 2004; Glazner et al., 2004; Bartley et al., 2006). This interpretation is in contrast to the traditional view of pluton emplacement through crystallization of a single, massive magma chamber. Most of the observations supporting incremental pluton emplacement use the relationship between zircon U-Pb dating of pluton sections and estimated granitic magma cooling rates to argue that a single magmatic event would crystallize significantly faster than the geochronologic data permit. Incremental pluton emplacement also predicts specific relationships between the age of intruded sheets of magma and the original orientation of these sheets, such that older sheets are expected to be tilted or deformed more than younger sheets. Here we test this prediction of differential tilting by measuring the paleomagnetic inclination preserved in well-dated and structurally characterized sheets of the Tuolumne Intrusive Suite. Magnetic inclination provides a tilt-meter with respect to the Earth's magnetic field direction at the time of pluton emplacement; the reference inclination assuming an untitled pluton is known from independent data sets. We also present rock magnetic data (temperature-dependent magnetic susceptibility, magnetic remanence characteristics) and results from petrographic investigations to characterize the mineralogy and stability of the magnetization. Our results suggest that the low-titanium magnetite remanence carriers are primary and are not biased by secondary magnetizations. The distribution of magnetic inclinations in our sample set — in which older sheets on the periphery of the pluton are shallower than those in younger, more interior sheets, and with respect to the reference inclination — is consistent with predictions from the incremental pluton emplacement hypothesis.
Comparative study of humic acids from extracted soils and leaves
Holden, Maliea; Richardson, Spencer; Chilom, Gabriela (Dixie State University)
Faculty Advisor: Chilom, Gabriela (Dixie State University, Physical Sciences)
Humic acids are a key component of the terrestrial ecosystem as they are responsible for many physical and chemical properties of soils; buffering capacity, metal-binding capacity, transport and fate of contaminants, stability of aggregates of soil particles and water-holding capacity all depend on the amount and nature of humic substances in a soil.
The current project is looking into the properties and ability of humic acids extracted from leaves, to improve the stability and fertility of a mineral soil. The humic acid was extracted from fresh and aerobically incubated leaves by traditional alkali extraction. Three species of trees commonly grown in St George, Utah were selected: Prunus x Cistena, Pyrus Calleryana Bradford, and Chilopsis Linearis. The extracts were characterized by the amount and nature of their carbon content as determined by IR, 1H NMR, and 13C NMR spectroscopy. Their properties showed similarities and differences with humic acid extracted from mineral soil and leonardite.
Faculty Advisor: Chilom, Gabriela (Dixie State University, Physical Sciences)
Humic acids are a key component of the terrestrial ecosystem as they are responsible for many physical and chemical properties of soils; buffering capacity, metal-binding capacity, transport and fate of contaminants, stability of aggregates of soil particles and water-holding capacity all depend on the amount and nature of humic substances in a soil.
The current project is looking into the properties and ability of humic acids extracted from leaves, to improve the stability and fertility of a mineral soil. The humic acid was extracted from fresh and aerobically incubated leaves by traditional alkali extraction. Three species of trees commonly grown in St George, Utah were selected: Prunus x Cistena, Pyrus Calleryana Bradford, and Chilopsis Linearis. The extracts were characterized by the amount and nature of their carbon content as determined by IR, 1H NMR, and 13C NMR spectroscopy. Their properties showed similarities and differences with humic acid extracted from mineral soil and leonardite.
Evaluation of Water Quality in Northern British Columbia
Meyr, Katherine (Weber State University)
Faculty Advisor: Matyjasik, Marek (Science, Earth and Environmental Sciences)
The impacts of water quality is among the most highly contested aspects of mining projects. Despite the protection of the majority of land in British Columbia, evidence of the negative environmental impacts of past and present mining activities may be found on the most sacred of lands. Evaluated water samples taken from multiple sites in First Nation territory show evidence of mining contamination, with streams following the sacred Tlingit trail showing the highest percentage of heavy metals. Though British Columbia's regulations have been extensive, mines abandoned before these regulations were put into place may be a source of pollution among current wildlife and vegetation. Abandoned mining sites in British Columbia must be thoroughly evaluated in order to understand the damage that has been done both culturally and environmentally.
Faculty Advisor: Matyjasik, Marek (Science, Earth and Environmental Sciences)
The impacts of water quality is among the most highly contested aspects of mining projects. Despite the protection of the majority of land in British Columbia, evidence of the negative environmental impacts of past and present mining activities may be found on the most sacred of lands. Evaluated water samples taken from multiple sites in First Nation territory show evidence of mining contamination, with streams following the sacred Tlingit trail showing the highest percentage of heavy metals. Though British Columbia's regulations have been extensive, mines abandoned before these regulations were put into place may be a source of pollution among current wildlife and vegetation. Abandoned mining sites in British Columbia must be thoroughly evaluated in order to understand the damage that has been done both culturally and environmentally.
Heavy metals analysis of particulate matter removed by trees
Dustin, Malia; Holden, Maliea; Peterson, Rob; Chilom, Gabriela (Dixie State University)
Faculty Advisor: Chilon, Gabriela (Dixie State University, Chemistry)
Particulate matter (PM) is a complex mixture of extremely small particles and liquid droplets suspended in air. Particles vary in terms of origin, chemical composition and size. Particles with diameter of 10 µm and smaller carry an increased risk for human health as they can penetrate deeper into the lungs, even to the alveolar regions. Recent studies suggest that trees can remove particles from the atmosphere through their leaves and their removal capacity depends on the chemistry and morphology of the leaves.
The goal of this project is to analyze the composition of PM for three species of trees commonly grown in St George, Utah: Pyrus Calleryana Bradford, Prunus x Cistena, and Chilopsis Linearis. The amount of PM accumulated on the surface of leaves was determined gravimetrically for two size fractions (2.5-10µm and 10-100µm). Both fractions were analyzed by inductively coupled plasma-mass spectrometry (ICP MS) after acid digestion of filters that collected PM. The average concentrations of the following metals: Mn, Fe, Co, Ni, Cu, Zn, Ti, V, Cr, As, Zr, Mo, Se, Cd, Sn, Sb, Pt, and Pb is reported.
The accumulation of heavy metals on leaf surfaces can prevent the metals from being airborne, therefore reducing the exposure of residents to PM pollution.
Faculty Advisor: Chilon, Gabriela (Dixie State University, Chemistry)
Particulate matter (PM) is a complex mixture of extremely small particles and liquid droplets suspended in air. Particles vary in terms of origin, chemical composition and size. Particles with diameter of 10 µm and smaller carry an increased risk for human health as they can penetrate deeper into the lungs, even to the alveolar regions. Recent studies suggest that trees can remove particles from the atmosphere through their leaves and their removal capacity depends on the chemistry and morphology of the leaves.
The goal of this project is to analyze the composition of PM for three species of trees commonly grown in St George, Utah: Pyrus Calleryana Bradford, Prunus x Cistena, and Chilopsis Linearis. The amount of PM accumulated on the surface of leaves was determined gravimetrically for two size fractions (2.5-10µm and 10-100µm). Both fractions were analyzed by inductively coupled plasma-mass spectrometry (ICP MS) after acid digestion of filters that collected PM. The average concentrations of the following metals: Mn, Fe, Co, Ni, Cu, Zn, Ti, V, Cr, As, Zr, Mo, Se, Cd, Sn, Sb, Pt, and Pb is reported.
The accumulation of heavy metals on leaf surfaces can prevent the metals from being airborne, therefore reducing the exposure of residents to PM pollution.
Harmonic analysis of mid-latitude temperatures in the mesopause region: TIME-GCM results and sodium resonance lidar observations during 2009
Cutler, Alynne; Hagan, Maura; Yuan, Titus (Utah State University)
Faculty Advisor: Hagan, Maura (College of Science, Physics Department); Yuan, Titus (College of Science, Physics Department)
Analyses of sodium resonance lidar temperature measurements made during a three-day period in August 2009 in the mesopause region (ca. 70-120km) above Fort Collins CO, along with analyses of correlative temperature predictions from the Thermosphere-Ionosphere-Mesosphere-Electrodynamics General Circulation Model (TIME-GCM) reveal diurnal and semidiurnal temperature variations characteristic of solar atmospheric tides. Harmonic analyses via Fourier decomposition of the lidar data reveal a dominant semidiurnal oscillation with amplitudes that are well-represented in TIME-GCM at altitudes below about 92 km. A comparatively weaker diurnal tide was detected in the lidar data. This variation is negligible in the TIME-GCM results below 95km. Downward phase progression associated with upward propagating tides characterizes both tidal model and measurement results. Comparisons between August 2009 mean temperature profiles reveal a cold bias of ~17K in the TIME-GCM mesopause region. Equivalent analyses of temperature during a second three-day period in January 2009 remain in progress.
Faculty Advisor: Hagan, Maura (College of Science, Physics Department); Yuan, Titus (College of Science, Physics Department)
Analyses of sodium resonance lidar temperature measurements made during a three-day period in August 2009 in the mesopause region (ca. 70-120km) above Fort Collins CO, along with analyses of correlative temperature predictions from the Thermosphere-Ionosphere-Mesosphere-Electrodynamics General Circulation Model (TIME-GCM) reveal diurnal and semidiurnal temperature variations characteristic of solar atmospheric tides. Harmonic analyses via Fourier decomposition of the lidar data reveal a dominant semidiurnal oscillation with amplitudes that are well-represented in TIME-GCM at altitudes below about 92 km. A comparatively weaker diurnal tide was detected in the lidar data. This variation is negligible in the TIME-GCM results below 95km. Downward phase progression associated with upward propagating tides characterizes both tidal model and measurement results. Comparisons between August 2009 mean temperature profiles reveal a cold bias of ~17K in the TIME-GCM mesopause region. Equivalent analyses of temperature during a second three-day period in January 2009 remain in progress.