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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
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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

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
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Description
In this project we are analyzing the diamond-titanium interface as it applies to diamond-based diode devices, including alpha particle, proton, and neutron detectors. This is done through the fabrication of an O-terminated B-doped diamond sample with a 20 Å Ti / 10 Å Pt overlayer which was then annealed and

In this project we are analyzing the diamond-titanium interface as it applies to diamond-based diode devices, including alpha particle, proton, and neutron detectors. This is done through the fabrication of an O-terminated B-doped diamond sample with a 20 Å Ti / 10 Å Pt overlayer which was then annealed and examined via X-ray photoelectron spectroscopy (XPS). It was discovered that after annealing the sample at temperatures ranging from 400 C - 900 C that TiC was not formed at any point during this experiment. Possible reasons for this include a lack of sufficient titanium in order to form TiC and over oxygenating the diamond surface before the metal was deposited.
ContributorsJohnson, Holly (Author) / Zaniewski, Anna (Thesis director) / Nemanich, Robert (Committee member) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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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
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
Description

In this project, we aim to fabricate PIN structure-like diodes for radiation detectors using Boron Nitride (BN). This fabrication is done by performing lithography and metal deposition processes on a Cubic Boron Nitride (cBN) of around 200 nm in thickness layer on top of a boron doped diamond substrate. The

In this project, we aim to fabricate PIN structure-like diodes for radiation detectors using Boron Nitride (BN). This fabrication is done by performing lithography and metal deposition processes on a Cubic Boron Nitride (cBN) of around 200 nm in thickness layer on top of a boron doped diamond substrate. The main goal is to create the most efficient and affordable alpha particle—and ideally neutron—detector in a radiation setting. Thus, making more accessible radiation detectors that can be more easily produced and disposed of, as well as minimizing the size of conventional detectors.

ContributorsGutierrez, Eric (Author) / Nemanich, Robert (Thesis director) / Zaniewski, Anna (Committee member) / Barrett, The Honors College (Contributor) / Department of Physics (Contributor)
Created2023-05