Matching Items (11)
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- All Subjects: Physics
- All Subjects: Genetics
- Creators: Foy, Joseph
Description
This study focused on the connection between the EnvZ/OmpR two-component regulatory system and the iron homeostasis system in Escherichia coli, specifically how a mutant form of EnvZ11/OmpR is able to reduce the expression of fepA::lacZ, a reporter gene fusion in E. coli. FepA is one of several outer membrane siderophore receptors that allow extracellular siderophores bound to iron to enter the cells to power various biological processes. Previous studies have shown that in E. coli cells that expressed a mutant allele of envZ, called envZ11, which led to altered expression of various iron genes including down regulation of fepA::lacZ. The wild type EnvZ/OmpR system is not considered to regulate iron genes, but because these envz11 strains had downregulated fepA::lacZ, this study was undertaken to understand the connection and mechanisms of this downregulation. A large number of Lac+ revertants were obtained from the B32-2483 strain (envz11 and fepA::lacZ) and 7 Lac+ revertants that had reversion mutations not directly correcting the envZ11 allele were further characterized. With P1 phage transduction genetic mapping that involved moving a kanamycin resistance marker linked to fepA::lacZ, two Lac+ revertants were found to have their reversion mutations in the fepA promoter region, while the other five revertants had their mutations mapping outside the fepA region. These two revertants underwent DNA sequencing and found to carry two different single base pair mutations in two different locations of the fepA promoter region. Each one is in the Fur repressor binding region, but one also may have affected the Shine-Dalgarno region involved in translation initiation. All 7 reveratants underwent beta-galactosidase assays to measure fepA::lacZ expression. The two revertants that had mutations in the fepA promoter region had significantly increased fepA activity, with the revertant with the Shine-Dalgarno mutation having the most elevated fepA expression. The other 5 revertants that did not map in the fepA region had fepA expression elevated to the same level as that found in the wild type EnvZ/OmpR background. The data suggest that the negative effect of envZ11 can be overcome by multiple mechanisms, including directly correcting the envZ11 allele or changing the fepA promoter region.
ContributorsKalinkin, Victor Arkady (Co-author) / Misra, Rajeev (Co-author, Thesis director) / Mason, Hugh (Committee member) / Foy, Joseph (Committee member) / Biomedical Informatics Program (Contributor) / School of Life Sciences (Contributor) / W. P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Since the acceptance of Einstein's special theory of relativity by the scientific community, authors of science fiction have used the concept of time dilation to permit seemingly impossible feats. Simple spacecraft acceleration schemes involving time dilation have been considered by scientists and fiction writers alike. Using an original Java program based upon the differential equations for special relativistic kinematics, several scenarios for round trip excursions at relativistic speeds are calculated and compared, with particular attention to energy budget and relativistic time passage in all relevant frames.
ContributorsAlfson, Jonathan William (Author) / Jacob, Richard (Thesis director) / Covatto, Carl (Committee member) / Foy, Joseph (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Physics (Contributor)
Created2015-05
Description
The interaction between England and Scotland is complicated and continually changing. Scottish writer Sir Walter Scott examines this long-standing relationship through his various writings. Scott conveys a presence that is both acutely aware of the damages enacted upon Scotland by various English political efforts, and sensitive to the delicate relationship that the two regions had begun to form during his lifetime. Through a critical analysis of Scott's novel, Rob Roy, one can see the various strategies Scott used to balance the need to address prior controversies within the relationship, and the petition to move beyond the prior conflict and develop a mutual understanding of each culture. Through this, Scott is able to regenerate a sense of Scottish nationalism for his people, and encourage improved relations within the British Isles.
ContributorsChotena, Chelsea (Author) / Facinelli, Diane (Thesis director) / Foy, Joseph (Committee member) / White, Julianne (Committee member) / Barrett, The Honors College (Contributor)
Created2013-05
Description
Dry and steam NanoBonding™ are conceived and researched to bond Si-based surfaces, via nucleation and growth of a two-dimensional SiOxHy or hydrated SiOxHy interphase connecting surfaces at the nanoscale across macroscopic domains. The motivation is to create strong, long lasting, hermetically bonded sensors with their electronics for the development of an artificial pancreas and to bond solar cells to glass panels for robust photovoltaic technology. The first step in NanoBonding™ is to synthesize smooth surfaces with 20 nm wide atomic terraces via a precursor phase, ß-cSiO2 on Si(100) and oxygen-deficient SiOx on the silica using the Herbots-Atluri process and Entrepix’s spin etching. Smooth precursor phases act as geometric and chemical template to nucleate and grow macroscopic contacting domains where cross bridging occurs via arrays of molecular strands in the hydrated SiOxHy interphase. Steam pressurization is found to catalyze NanoBonding™ consistently, eliminating the need for direct mechanical compression that limits the size and shape of wafers to be bonded in turn, reducing the cost of processing. Total surface energy measurements via 3 Liquids Contact Angle Analysis (3L CAA) enables accurate quantitative analysis of the total surface energy and each of its components. 3L CAA at each step in the process shows that surface energy drops to 42.4 ± 0.6 mJ/m2 from 57.5 ± 1.4 mJ/m2 after the Herbots-Atluri clean of an “As Received” wafer. 3L CAA after steam pressurization Nanobonding™ shows almost complete elimination from 13.8 mJ/m2 ± 1.0 to 0.002 ±- 0.0002 mJ/m2 in the contribution of acceptors to the total free surface energy, and an increase from 0.2 ± .03 to 23.8± 1.6 mJ/m2 in the contribution of donors. This is consistent with an increase in hydroxylation of the ß-cSiO2 surface as a consistent precursor phase for cross-bridging. This research optimizes the use of glycerin, water, and α-bromo-naphtalene in the use of 3L CAA to effectively quantify the components of total free surface energy which helps to better understand the most consistent method for NanoBonding™.
ContributorsBennett-Kennett, Ross Buchanan (Author) / Culbertson, Robert (Thesis director) / Herbots, Nicole (Committee member) / Foy, Joseph (Committee member) / Barrett, The Honors College (Contributor) / Materials Science and Engineering Program (Contributor) / Department of Physics (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2013-05
Description
Gle1 is an mRNP export mediator with major activity localized to the nuclear pore complex in eukaryotic cells. The protein's high preservation across vast phylogenetic distances allows us to approximate research on the properties of yeast Gle1 (yGle1) with those of human Gle1 (hGle1). Research at Vanderbilt University in 2016, which provides the research basis of this thesis, suggests that the coiled-coil domain of yGle1 is best crystallized in dicationic aqueous conditions of pH ~8.0 and 10\u201420% PEG 8000. Further exploration of crystallizable microconditions revealed a favorability toward lower pH and lower PEG concentration. Following the discovery of the protein's native crystallography conditions, a comprehensive meta-analysis of scientific literature on Gle1 was conducted on the association of Gle1 mutations with neuron disease.
ContributorsGaetano, Philip Pasquale (Author) / Foy, Joseph (Thesis director) / Dawson, T. Renee (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Because of its massive nature and simple two-body structure, the heavy meson bottomonium (the flavorless bound state of the bottom quark and anti-quark) is among the simplest systems available for the study of the strong force and quantum chromodynamics (QCD)—a feature which has made it of special interest to particle physicists.
Despite being bound by the strong force, bottomonium exhibits a rich spectrum of resonances corresponding to excited states extremely analogous to that of positronium or even familiar atomic systems. Transitions between these levels are possible via the absorption or emission of either a photon, gluon, or gluons manifesting as light hadrons. The goal of this thesis was to establish a theoretical value for the currently unmeasured partial decay width for one such transition—the electromagnetic decay channel hb -> etab gamma. To this end, two methods were utilized.
The first approach relied on the presumption of a nonrelativistic constituent quark model interacting via a simple static potential, allowing for radial wave functions and energy eigenvalues to be obtained for the states of interest via the Schrödinger equation. Upon an application of the standard electromagnetic multipole expansion followed by a utilization of the electric dipole E1 decay width formula, a value of 57.7 ± 0.4 keV was obtained.
The second approach stemmed from the effective Lagrangian describing the bottomonium P to S electromagnetic transitions and relied on the presumption that a single coupling constant could be approximated as describing all nP to mS transitions regardless of spin. A value for this coupling constant could then be extracted from the 1P to 1S spin triplet data and used to predict the width for the singlet 1P to 1S transition. The partial decay width value found in this manner was 47.8 ± 2.0 keV.
Various other methods and models have established a predicted range of 35 to 60 keV for this partial decay width. As the values determined in this thesis fall within the expected range, they agree well with our current understanding of this electromagnetic transition and place further confidence on the expected range.
Despite being bound by the strong force, bottomonium exhibits a rich spectrum of resonances corresponding to excited states extremely analogous to that of positronium or even familiar atomic systems. Transitions between these levels are possible via the absorption or emission of either a photon, gluon, or gluons manifesting as light hadrons. The goal of this thesis was to establish a theoretical value for the currently unmeasured partial decay width for one such transition—the electromagnetic decay channel hb -> etab gamma. To this end, two methods were utilized.
The first approach relied on the presumption of a nonrelativistic constituent quark model interacting via a simple static potential, allowing for radial wave functions and energy eigenvalues to be obtained for the states of interest via the Schrödinger equation. Upon an application of the standard electromagnetic multipole expansion followed by a utilization of the electric dipole E1 decay width formula, a value of 57.7 ± 0.4 keV was obtained.
The second approach stemmed from the effective Lagrangian describing the bottomonium P to S electromagnetic transitions and relied on the presumption that a single coupling constant could be approximated as describing all nP to mS transitions regardless of spin. A value for this coupling constant could then be extracted from the 1P to 1S spin triplet data and used to predict the width for the singlet 1P to 1S transition. The partial decay width value found in this manner was 47.8 ± 2.0 keV.
Various other methods and models have established a predicted range of 35 to 60 keV for this partial decay width. As the values determined in this thesis fall within the expected range, they agree well with our current understanding of this electromagnetic transition and place further confidence on the expected range.
ContributorsIreland, Aurora Nicole (Author) / McCartney, Martha (Thesis director) / Foy, Joseph (Committee member) / Maximon, Leonard (Committee member) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
This research endeavor explores the 1964 reasoning of Irish physicist John Bell and how it pertains to the provoking Einstein-Podolsky-Rosen Paradox. It is necessary to establish the machinations of formalisms ranging from conservation laws to quantum mechanical principles. The notion that locality is unable to be reconciled with the quantum paradigm is upheld through analysis and the subsequent Aspect experiments in the years 1980-1982. No matter the complexity, any local hidden variable theory is incompatible with the formulation of standard quantum mechanics. A number of strikingly ambiguous and abstract concepts are addressed in this pursuit to deduce quantum's validity, including separability and reality. `Elements of reality' characteristic of unique spaces are defined using basis terminology and logic from EPR. The discussion draws directly from Bell's succinct 1964 Physics 1 paper as well as numerous other useful sources. The fundamental principle and insight gleaned is that quantum physics is indeed nonlocal; the door into its metaphysical and philosophical implications has long since been opened. Yet the nexus of information pertaining to Bell's inequality and EPR logic does nothing but assert the impeccable success of quantum physics' ability to describe nature.
ContributorsRapp, Sean R (Author) / Foy, Joseph (Thesis director) / Martin, Thomas (Committee member) / School of Earth and Space Exploration (Contributor) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
With the extreme strides taken in physics in the early twentieth century, one of the biggest questions on the minds of scientists was what this new branch of quantum physics would be able to be used for. The twentieth century saw the rise of computers as devices that significantly aided in calculations and performing algorithms. Because of the incredible success of computers and all of the groundbreaking possibilities that they afforded, research into using quantum mechanics for these systems was proposed. Although theoretical at the time, it was found that a computer that had the ability to leverage quantum mechanics would be far superior to any classical machine. This sparked a wave of interest in research and funding in this exciting new field. General-use quantum computers have the potential to disrupt countless industries and fields of study, like physics, medicine, engineering, cryptography, finance, meteorology, climatology, and more. The supremacy of quantum computers has not yet been reached, but the continued funding and research into this new technology ensures that one day humanity will be able to unlock the full potential of quantum computing.
ContributorsEaton, Jacob (Author) / Foy, Joseph (Thesis director) / Hines, Taylor (Committee member) / Barrett, The Honors College (Contributor) / Mechanical and Aerospace Engineering Program (Contributor)
Created2023-05
Description
In 1757 Edmund Burke published A Philosophical Enquiry into the Sublime and Beautiful. I will be extending his analysis of the sublime and beautiful, and using it to dissect quantum mechanics. Using Burke’s template on the sublime and beautiful, I can evaluate experiments in quantum mechanics, and explore a new side of Burke’s aesthetic theory. For the reader, I have outlined Burke’s aesthetic theory on the sublime and beautiful. I then used this analysis to explore quantum mechanics and assess the components of quantum mechanics that are beautiful and sublime.
ContributorsManrique, Scarlett (Author) / Taylor, Thomas (Thesis director) / Foy, Joseph (Committee member) / Boyce-Jacino, Katherine (Committee member) / Barrett, The Honors College (Contributor) / Department of Information Systems (Contributor) / Historical, Philosophical & Religious Studies, Sch (Contributor) / Department of Finance (Contributor)
Created2022-05
Description
Time travel is closely associated with futuristic science fiction, but it is a concept that dates back to ancient times. Over many generations it has been developed and explored narratively and scientifically. This paper aims to document and analyze the history of the time travel concept and the important role fiction had in its development.
ContributorsElkins, Sydney (Author) / Foy, Joseph (Thesis director) / Maynard, Andrew (Committee member) / School of Earth and Space Exploration (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12