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Description
Supernovae are vital to supplying necessary elements to forming bodies in our solar systems. This project studies the creation of a subset of these necessary elements, called short-lived radionuclides (SLRs). SLRs are isotopes with relatively short half-lives and can serve as heat sources for forming planetary bodies, and their traces

Supernovae are vital to supplying necessary elements to forming bodies in our solar systems. This project studies the creation of a subset of these necessary elements, called short-lived radionuclides (SLRs). SLRs are isotopes with relatively short half-lives and can serve as heat sources for forming planetary bodies, and their traces can be used to date stellar events. Computational models of asymmetric supernovae provide opportunities to study the effect of explosion geometry on the SLR yields. We are most interested in the production of \iso{Al}{26}, \iso{Fe}{60}, and \iso{Ca}{41}, whose decayed products are found in our own solar system. To study the effect of explosion asymmetries in supernovae, we use TYCHO stellar evolution code, SNSHP smooth particle hydrodynamics code for 3D explosion simulations, Burn code for nucleosythesis post-processing, and Python code written to analyze the output of the post-processing code.
ContributorsJohnson, Charlotte (Author) / Young, Patrick (Thesis director) / Lunardini, Cecilia (Committee member) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
Observations of four times ionized iron and nickel (Fe V & Ni V) in the G191-B2B white dwarf spectrum have been used to test for variations in the fine structure constant, α, in the presence of strong gravitational fields. The laboratory wavelengths for these ions were thought to be the

Observations of four times ionized iron and nickel (Fe V & Ni V) in the G191-B2B white dwarf spectrum have been used to test for variations in the fine structure constant, α, in the presence of strong gravitational fields. The laboratory wavelengths for these ions were thought to be the cause of inconsistent conclusions regarding the
variation of α as observed through the white dwarf spectrum. This thesis presents 129 revised Fe V wavelengths (1200 Å to 1600 Å) and 161 revised Ni V wavelengths (1200 Å to 1400 Å) with uncertainties of approximately 3 mÅ. A systematic calibration error
is identified in the previous Ni V wavelengths and is corrected in this work. The evaluation of the fine structure variation is significantly improved with the results
found in this thesis.
ContributorsWard, Jacob Wolfgang (Author) / Treacy, Michael (Thesis director) / Alarcon, Ricardo (Committee member) / Nave, Gillian (Committee member) / Department of Physics (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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Description
The LOw Frequency ARray (LOFAR) is a new and innovative radio telescope designed and constructed by the Netherlands Institute for Radio Astronomy (ASTRON). LOFAR unique capable of operating in very low frequencies (10-240 MHz) and consists of an extensive interferometry array of dipole antenna stations distributed throughout the Netherlands and

The LOw Frequency ARray (LOFAR) is a new and innovative radio telescope designed and constructed by the Netherlands Institute for Radio Astronomy (ASTRON). LOFAR unique capable of operating in very low frequencies (10-240 MHz) and consists of an extensive interferometry array of dipole antenna stations distributed throughout the Netherlands and Europe which allows it to achieve superb angular resolution. I investigate a part of the northern sky to search for rare radio objects such as radio haloes and radio relics that may have not been able to have been resolved by other radio telescopes.
ContributorsNguyen, Dustin Dinh (Author) / Scannapieco, Evan (Thesis director) / Butler, Nathaniel (Committee member) / School of Earth and Space Exploration (Contributor) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
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Description
Radio astronomy is a subfield in astronomy that deals with objects emitting frequencies around 10 MHz to 100 GHz. The Low Frequency Array (LOFAR) is a array of radio antennas in Europe that can reach very low frequencies, roughly between 10-240 MHz. Our project was to image and clean a

Radio astronomy is a subfield in astronomy that deals with objects emitting frequencies around 10 MHz to 100 GHz. The Low Frequency Array (LOFAR) is a array of radio antennas in Europe that can reach very low frequencies, roughly between 10-240 MHz. Our project was to image and clean a field from LOFAR. The data was a 10 degree square in the sky centered at a right ascension of 10:19:34.608 and a declination +49.36.52.482. It was observed for 600 seconds at 141 MHz. To clean the field, we had to flag and remove any stations that were not responding. Using a program called FACTOR, we cleaned the image and reduced the residuals. Next we checked the validity of our sources. We checked positional offsets for our sources using the TGSS survey at 150 MHz, and corrected the declination of our LOFAR sources by a factor of 0.0002 degrees. We also fixed the LOFAR fluxes by a factor of 1.15. After this systematic check, we calculated the spectral index of our sources using the FIRST survey at 1435 MHz. We plotted this spectral index against LOFAR flux as well as redshift of the sources, and compared these to literature.
ContributorsStawinski, Stephanie Mae (Author) / Scannapieco, Evan (Thesis director) / Windhorst, Rogier (Committee member) / Karen, Olsen (Committee member) / Department of Physics (Contributor) / School of International Letters and Cultures (Contributor) / School of Earth and Space Exploration (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
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Description
The Epoch of Reionization (EoR) is the period in the evolution of the universe during which neutral hydrogen was ionized by the first luminous sources, and is closely linked to the formation of structure in the early universe. The Hydrogen Epoch of Reionization Array (HERA) is a radio interferometer currently

The Epoch of Reionization (EoR) is the period in the evolution of the universe during which neutral hydrogen was ionized by the first luminous sources, and is closely linked to the formation of structure in the early universe. The Hydrogen Epoch of Reionization Array (HERA) is a radio interferometer currently under construction in South Africa designed to study this era. Specifically, HERA is dedicated to studying the large-scale structure during the EoR and the preceding Cosmic Dawn by measuring the redshifted 21-cm line from neutral hydrogen. However, the 21-cm signal from the EoR is extremely faint relative to galactic and extragalactic radio foregrounds, and instrumental and environmental systematics make measuring the signal all the more difficult. Radio frequency interference (RFI) from terrestrial sources is one such systematic. In this thesis, we explore various methods of removing RFI from early science-grade HERA data and characterize the effects of different removal patterns on the final 21-cm power spectrum. In particular, we focus on the impact of masking narrowband signals, such as those characteristic of FM radio and aircraft or satellite communications, in the context of the algorithms currently used by the HERA collaboration for analysis.
ContributorsWhitler, Lily (Author) / Jacobs, Daniel (Thesis director) / Bowman, Judd (Committee member) / Beardsley, Adam (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
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Description
Proteins continually and naturally incur evolutionary selection through mutagenesis that optimizes their fitness, which is primarily determined by their function. It is known that allosteric regulation alters a protein's conformational dynamics leading to functional changes. We have computationally introduced a mutation at a predicted regulatory site of a short, 46

Proteins continually and naturally incur evolutionary selection through mutagenesis that optimizes their fitness, which is primarily determined by their function. It is known that allosteric regulation alters a protein's conformational dynamics leading to functional changes. We have computationally introduced a mutation at a predicted regulatory site of a short, 46 residue-long, protein interaction module composed of a WW domain and corresponding polyproline ligand (PDB id: 1k9r). The dynamic flexibility index (DFI) was computed for the binding site of the wild type and mutant WW domains to quantify the mutations effect on the rigidity of the binding pocket. DFI is used as a metric to quantify the resilience of a given position to perturbation along the chain. Using steered molecular dynamics (SMD), we also measure the effect of the point mutation on allosteric regulation by approximating the binding free energy of the system calculated using Jarzynski's Equality. Calculation of the DFI shows that the overall flexibility of the protein complex increases as a result of the distal point mutation. Total change in DFI percentile of the binding site showed a 0.067 increase suggesting an allosteric, loss of function mutation. Furthermore, we see that the change in the binding free energy is greater for that of the mutated complex supporting the idea that an increase in flexibility is correlated to a decrease in proteinlig and binding affinity. We show that sequence mutation of an allosteric site affects the mechanical stability and functionality of the binding pocket.
ContributorsMarianchuk, Tegan (Author) / Ozkan, Sefika (Thesis director) / Ros, Robert (Committee member) / Barrett, The Honors College (Contributor) / Department of Physics (Contributor)
Created2018-05
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Description

Lyme disease is a common tick-borne illness caused by the Gram-negative bacterium Borrelia burgdorferi. An outer membrane protein of Borrelia burgdorferi, P66, has been suggested as a possible target for Lyme disease treatments. However, a lack of structural information available for P66 has hindered attempts to design medications to target

Lyme disease is a common tick-borne illness caused by the Gram-negative bacterium Borrelia burgdorferi. An outer membrane protein of Borrelia burgdorferi, P66, has been suggested as a possible target for Lyme disease treatments. However, a lack of structural information available for P66 has hindered attempts to design medications to target the protein. Therefore, this study attempted to find methods for expressing and purifying P66 in quantities that can be used for structural studies. It was found that by using the PelB signal sequence, His-tagged P66 could be directed to the outer membrane of Escherichia coli, as confirmed by an anti-His Western blot. Further attempts to optimize P66 expression in the outer membrane were made, pending verification via Western blotting. The ability to direct P66 to the outer membrane using the PelB signal sequence is a promising first step in determining the overall structure of P66, but further work is needed before P66 is ready for large-scale purification for structural studies.

ContributorsRamirez, Christopher Nicholas (Author) / Fromme, Petra (Thesis director) / Hansen, Debra (Committee member) / Department of Physics (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

This qualitative study sought to investigate the potential reaction between the 3,3',5,5'-tetramethylbenzidine (TMB) radical and LAF-1 RGG, the N-terminus domain of an RNA helicase which functions as a coacervating intrinsically disordered protein. The study was performed by adding horseradish peroxidase to a solution containing TMB and either LAF-1 or tyrosine

This qualitative study sought to investigate the potential reaction between the 3,3',5,5'-tetramethylbenzidine (TMB) radical and LAF-1 RGG, the N-terminus domain of an RNA helicase which functions as a coacervating intrinsically disordered protein. The study was performed by adding horseradish peroxidase to a solution containing TMB and either LAF-1 or tyrosine in various concentrations, and monitoring the output through UV-Vis spectroscopy. The reacted species was also analyzed via MALDI-TOF mass spectrometry. UV-Vis spectroscopic monitoring showed that in the presence of LAF-1 or tyrosine, the reaction between HRP and TMB occurred more quickly than the control, as well as in the highest concentration of LAF-1, the evolution of a peak at 482 nm. The analysis through MALDI-TOF spectrometry showed the development of a second peak likely due to the reaction between LAF-1 and TMB, as the Δ between the peaks is 229 Da and the size of the TMB species is 240 Da.

ContributorsDavis, Morgan (Author) / Ghirlanda, Giovanna (Thesis director) / Heyden, Matthias (Committee member) / Mazor, Yuval (Committee member) / Barrett, The Honors College (Contributor) / Department of Physics (Contributor) / School of Molecular Sciences (Contributor)
Created2022-12