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A Raman Spectroscopic And Computational Study Of The Effects Of Halogen Bonding On Pyrimidine Containing Systems, Peyton Lindsey Reves
A Raman Spectroscopic And Computational Study Of The Effects Of Halogen Bonding On Pyrimidine Containing Systems, Peyton Lindsey Reves
Honors Theses
This thesis involves the study of the effects of halogen bonding on pyrimidine containing systems. Halogen bonding is a type of non-covalent interaction that can occur when a Lewis base interacts with an iodine, bromine, or chlorine atom in a second molecule. The phenomenon of halogen bonding is explained by the presence of a localized region of positive electrostatic potential that exists on the halogen. This positive region is referred to as the σ-hole, and gives halogen bonding its other common name, σ-hole bonding. The magnitude of the positive σ-hole depends on both the type of halogen molecule involved in …
The Effect Of Polyamines On I-Motif Thermal Stablity, Shelby Claire Liddell
The Effect Of Polyamines On I-Motif Thermal Stablity, Shelby Claire Liddell
Honors Theses
Polyamines are present inside cells at varying concentrations anywhere between 10 mM and 60 mM, and because of their molecular structure they contribute a positive charge to the interior of the cell. There has been previous evidence that the concentrations of polyamines have an effect on the stability of the DNA strands, which can affect the cellular processes. The particular DNA conformation studied is the i-motif, which is formed by intermolecular folding in cytosine rich strands. The i-motif studied is C20T, which is found in the promoter region of the oncogene, c-myc. Stabilization of c-myc can have an effect on …
Visualization Techniques Of Shear Wave Propagation In Wormlike Micellar Fluid, Connor M. Tierney
Visualization Techniques Of Shear Wave Propagation In Wormlike Micellar Fluid, Connor M. Tierney
Honors Theses
In an aqueous solution amphiphilic molecules can self-aggregate and form a wormlike micellar fluid. These non-Newtonian fluids have been studied in the context of diagnostic medical imaging due to the fact that the fluids have viscoelastic properties and can act as a nonperishable model for human tissue. They also display flow-birefringence, which is a property that allows for the analysis of shear wave propagation through the fluid. However, one issue encountered at lower micelle concentrations is the inability to see the emergent birefringence pattern that results from shear wave propagation. In this study Experiment 1 was an analysis of shear …
Comparison Of The Spatial Distributions Of Cavitation Damage With The Measured Diffraction Patterns For A High-Power Ultrasonic Transducer, Davis Lane Rogers
Comparison Of The Spatial Distributions Of Cavitation Damage With The Measured Diffraction Patterns For A High-Power Ultrasonic Transducer, Davis Lane Rogers
Honors Theses
The purpose of this study was to evaluate the performance of a model of the propagation of ultrasonic fields produced by an ultrasonic transducer, a device that uses a piezoelectric crystal to produce high-intensity ultrasonic waves. The transducer operates immersed in a water bath where it generates waves of sufficient intensity to produce non-linear phenomena that include acoustic streaming and cavitation. This study used a planar transducer to visualize the damaging effects of high-intensity ultrasonic waves targeted on acrylic plates. Seven plates were targeted and positioned from 8.5 to 11.5 cm from the transducer. The spatial distribution and degree of …
Pro-Aromatic Dye Components For Dye-Sensitized Solar Cells: Thienothiophene And Indolizine, George A. Puneky
Pro-Aromatic Dye Components For Dye-Sensitized Solar Cells: Thienothiophene And Indolizine, George A. Puneky
Honors Theses
Four D-π-A dyes based on a 3,4-thienothiophene Ï€-bridge were synthesized for use in dye-sensitized solar cells (DSCs). The pro-aromatic building block 3,4-thienothiophene has been reported to stabilize dye excited-state oxidation potentials. This lowering of excited-state energy levels permits for increased absorption into the near-infrared (NIR) region using relatively low molecular weight dyes. Strong donor functionality based on triaryl- and diarylamines are employed in the dye designs to raise both the ground and excited-state oxidation potentials to values capable of generating DSC devices with good open-circuit voltages. Solubility, aggregation, and TiO2 surface protection were addressed by examining an ethylhexyl alkyl chain …
Breastfeeding: Physiological And Cultural Influences, Alison R. Cegielski
Breastfeeding: Physiological And Cultural Influences, Alison R. Cegielski
Honors Theses
Within a biological perspective, breasts are indisputably for the use of nourishment of the young. This can be seen by how mammary glands are used by every other species other than humans. Humans are the only species that also looks at breasts within a cultural perspective, and that perspective is where the debate of breastfeeding occurs. There is really no debate that if given the option to breastfeed, breastfeeding is the best choice for the development of infants due to the fact that breast milk has been adapted for the human physique. In spite of the health benefits associated with …
Effects Of Synthetic Blood Plasma On Calcium Dependent Dimerization Of Ncad12, Brent Treadway
Effects Of Synthetic Blood Plasma On Calcium Dependent Dimerization Of Ncad12, Brent Treadway
Honors Theses
Neural Cadherin (NCAD) is one of three Type 1 vertebral classical cadherins that function as the primary transmembrane component in cell-to-cell interactions at adherens junctions. Adhesive interactions mediated by this protein are calcium dependent with three calcium-binding sites between each of its five extracellular domains. NCAD is very important in many cell-to-cell interactions because of its function in development and in immune and neurological synapses. Generally, in vitro studies of calcium dependent dimerization of NCAD are conducted in a nonphysiological buffer (NaCl + HEPES: SEC buffer). In order to study dimerization in more physiologically relevant conditions, I created a synthetic …
Dna I-Motif Stabilization By Ligand Binding To Loop Regions, Harrison Reed Davis
Dna I-Motif Stabilization By Ligand Binding To Loop Regions, Harrison Reed Davis
Honors Theses
DNA i-motifs are a secondary structure of DNA that can be useful in a variety of ways, but this experiment investigates the maximum potential to stabilize i-motifs artificially with a small molecule binding to loop regions. DNA with different position and number of loops was tested to see to what extent the i-motif could be stabilized . A drug, Actinomycin D, was used for its known high affinity for a particular DNA sequence, which we used to make the loops of the i-motif. The binding constant for the drug to the DNA was determined through fluorescense spectroscopy while the presence …
A Visualization Tool For Survey Responses And A Unifying Interface Redesign, Iva Cramer
A Visualization Tool For Survey Responses And A Unifying Interface Redesign, Iva Cramer
Honors Theses
As an intern for financial software company FNC, Inc. during the summer of 2014, my fellow interns and I began an innovation project for creating and analyzing surveys for better client feedback methods. I have continued this project even after the internship, and this thesis covers that continuation: the visualization of survey responses and the redesign of the page on which they are contained. The project detailed here was to revamp the survey statistics page with a coherent layout that matches the rest of the site in addition to overhauling the actual graphs and charts for aesthetic and accuracy.
Non-Covalent Ineteractions Of Trimethylamine N-Oxide (Tmao) And Urea In Water, John Prather
Non-Covalent Ineteractions Of Trimethylamine N-Oxide (Tmao) And Urea In Water, John Prather
Honors Theses
TMAO and urea are important osmolytes. Osmolytes help maintain cell volume with their presence inside and outside cells. Urea is used by kidney cells to neutralize strong osmotic gradients caused by excretion of hypertonic waste. Although urea is for volume- maintaining purposes, it is also known to be a strong denaturant of cellular proteins. The method by which urea destabilizes folded proteins is a debated topic. There is evidence that urea binds directly to amino acid side chains to make protein folding less thermodynamically favored. It has also been suggested that urea acts indirectly to denature proteins by destabilizing the …
A Computational Comparison Of The Hydrophobic Pocket Of Neural And Epithelial Cadherins For The Purpose Of Identifying A Selective Inhibitor, Ross E. Straughan
A Computational Comparison Of The Hydrophobic Pocket Of Neural And Epithelial Cadherins For The Purpose Of Identifying A Selective Inhibitor, Ross E. Straughan
Honors Theses
Classical cadherins are a subfamily of calcium-dependent cellular adhesion molecules that play an important role in the formation of cellular junctions in many tissues. The extracellular portion of cadherins consists of five tandem-repeated domains (EC1-EC5). The critical first step in cadherin-mediated cellular adhesion occurs at the interface between two adjacent EC1 domains in which the transition from monomer to dimer is accomplished by docking the W2 residue of the N-terminal β-strand of one EC1 domain into the hydrophobic pocket of its partner domain. Cancer and many other diseases have been linked to the aberrant expression of Epithelial (E-cad) and Neural …
Effect Of Biochar And Activated Carbon Amendments On Gaseous Mercury Emissions Of Soil And Mercury Methylation Rates In Sediment, Ryan Sessums
Honors Theses
Mercury is a pervasive global contaminant with a complex biogeochemical cycle. In this biogeochemical cycle, methylmercury (MeHg+) tends to biomagnify and concentrate in fish and seafood consumed by humans. This study examines the effect of sorbent amendments on both the mercury emission from soils and the methylation rates of mercury in sediments, both of which are believed to be major contributors to the global cycle. Biochar and activated carbon were used to treat soils and sediments to explore their effects. It was found that biochar and activated carbon reduced gaseous mercury emission by 25% and 49%, respectively. Methylation rates in …
Method Development For The Detection And Quantitation Of Illicit Drugs In Fingerprints Using Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry, Madison Roussel
Honors Theses
The purpose of this research was to develop a method for the detection and quantitation of caffeine and 11-nor-9-carboxy-Δ9- tetrahydrocannabinol in fingerprints using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The matrix used was 2,5-dihydroxybenzoic acid (DHB). The presence of the analytes was confirmed by analysis using liquid chromatography-mass spectrometry (LC-MS). 11-nor-9-carboxy-Δ9- tetrahydrocannabinol was chosen as the drug of interest because it is the major metabolite of tetrahydrocannabinol, the main psychoactive component of marijuana. Marijuana's popularity as a recreational drug continues to increase with its legalization and decriminalization across the country. It is critical to establish methods for the quantification …
Wind Energy Harvesting Utilizing Biaxially Oriented Piezoelectric Polyvinylidenefluoride Film, Matthew Kennedy
Wind Energy Harvesting Utilizing Biaxially Oriented Piezoelectric Polyvinylidenefluoride Film, Matthew Kennedy
Honors Theses
With the growing concern over fossil fuels as a finite source of fuel and as a hazard to the environment, society has developed a growing interest in the use of renewable energy. Advancements in solar, nuclear, geothermal, wind, and vibrational energy harvesting, to name a few, have made the concept of using renewables as a main source of energy more feasible. The research and experimentation conducted for this thesis focused on analyzing the practicality of the future implementation of Biaxially Oriented Piezoelectric Polyvinylidenefluoride in the wind energy harvesting industry. The experiment consisted of data collection and analysis of power output …
From Lazarus To Theophilus: How Manuscript Digitization Led To The Historical, Chemical, And Technological Understanding Of Iron Gall Ink And Its Counterparts, Meredith Oliver
Honors Theses
This paper examines the physical and chemical composition of iron gall ink, how such composition has changed throughout its use in history, and the current chemical, digital, and multi-spectral methods by which the digital humanities use to preserve ancient texts inscribed with such ink. By using spectral technology, I hypothesized it possible to date and locate the geographic origin of ink based on its chemical composition. Uv-vis, fluorescence, and micro-XRF spectrometry were used to analyze elemental composition. Ink samples were made to simulate the ink on ancient manuscripts for UV-vis and fluorescence spectral analysis. Micro-XRF was performed on the Vercelli …
Development Of Methods For Determining Dry Deposition Of Mercury Using An Ion-Exchange Membrane: Relative Rates Of Mercury Dry Deposition At Sardis, Enid, And Grenada Lakes, Ruiqi Feng
Honors Theses
This research focuses on studies developing methods to measure dry deposition of mercury (Hg) using an ion-exchange (IX) membrane to capture gaseous mercury species in the air. Mercury is a toxic heavy metal that is spread globally through the atmosphere. Atmospheric Hg deposits to terrestrial and aquatic ecosystems through wet and dry deposition. While routine methods have been developed to study wet deposition of Hg, measuring dry deposition of Hg is more problematic and often overlooked. In this study, we developed an inexpensive means to deploy a polyethersulfone cation exchange membrane in the field by dangling it within a polycarbonate …
Investigation Into The Initial Electric Field Change Of Lightning Flashes, Ryan Chapman
Investigation Into The Initial Electric Field Change Of Lightning Flashes, Ryan Chapman
Honors Theses
Previously, an initial electric field change (IEC) was found occurring before initial breakdown (IB) pulses by sensors within the reversal distance of 36 lightning flashes [Marshall et al. 2014]. The E-change for a CG flashes was positive within reversal distance, and the E-change for an IC flashes was negative. With this data in mind, an IEC is best defined as occurring from zero slope to gradual increase in E-change at the beginning of a lightning flash, and it ends with the first IB pulse. The purpose of this thesis is to extend said findings to further understand the characteristics of …
Estimating The Number Of Components Of A Spatial—Em Algorithm: An R Package, Aishat O. Aloba
Estimating The Number Of Components Of A Spatial—Em Algorithm: An R Package, Aishat O. Aloba
Honors Theses
The Expectation Maximization algorithm also known as the EM algorithm is an algorithm used to solve the maximum likelihood parameter estimation problem. This problem arises when some of the data involved are missing or incomplete, hence it becomes difficult to know the parameters of the underlying distribution. The EM algorithm mainly comprises of two steps; the E—Step, and the M—Step. In the E—Step, estimated parameter values are used as true values to calculate the maximum likelihood estimate, and in the M—Step, the maximum likelihood calculated is used to estimate the parameters. The E—Step and M—Step iterate through until a speciï¬ed …
Using Technology To Engage Students In The Stem Field, April Elizabeth Steen
Using Technology To Engage Students In The Stem Field, April Elizabeth Steen
Honors Theses
The United States is currently facing a shortage of qualified STEM professionals in the workforce and in research fields. Part of this lack of professionals can be traced back to lack of interest and lack of proficiency in mathematics and science at the secondary level of education as well as STEM major attrition at the college level. In an effort to increase student interest in STEM fields and increase retention of STEM majors, technology was employed to engage student interest. At the high school level, a physical chemistry demonstration on the spectroscopy of light was created. The demonstration was presented …
A Study Of The Impact Of Ph On The Structure And Stability Of Epithelial Cadherin, Catherine Abadie
A Study Of The Impact Of Ph On The Structure And Stability Of Epithelial Cadherin, Catherine Abadie
Honors Theses
Epithelial (E-) cadherin is a transmembrane protein whose function lies in cell-to-cell adhesion. It is a transmembrane component of adherens junctions of epithelial tissues, thereby connecting the actin cytoskeletons of adhered cells. It has five extracellular domains, a small transmembrane portion, and a cytoplasmic tail. The molecule must bind calcium in order to form an adhesive dimer with a cadherin molecule emanating from an adjacent cell. Cancer of the epithelial tissue, carcinoma, is accompanied by acidification of the tissue and a loss in cell adhesion. The long-term goal of this project is to determine the effect of a decrease in …
An Investigation Into The Synthesis Of A Four-Armed Diamino Swallowtail, Christopher Carter Barnett
An Investigation Into The Synthesis Of A Four-Armed Diamino Swallowtail, Christopher Carter Barnett
Honors Theses
Perylenebisimides (PBIs) complex with quadruplex DNA and may influence the formation of telomeres. PBIs with amine groups are ionized at neutral pH and therefore soluble in water [1]. Swallowtails are long alkyl chains usually attached to PBIs to inhibit self-aggregation by pi-stacking [2]. Past attempts to create a PBI with swallowtails containing extra nitrogens were unsuccessful due to purification issues and methylene connectors. The purpose of this research is to investigate the synthesis of a diamino swallowtail with a methine connector. The first step is to create 1,3-bis(dibenzylamino)propan-2-one by way of an SN2 substitution reaction using 1,3-dichloroacetone and dibenzylamine [3]. …
An Investigation Of Protein-Dna Binding Characteristics By Fluorescence Anisotropy, Danna Nobile
An Investigation Of Protein-Dna Binding Characteristics By Fluorescence Anisotropy, Danna Nobile
Honors Theses
Recent studies have illustrated the presence of several secondary, non-B DNA structures that are associated with the promoter regions of several oncogenes, such as the intensely studied MYC gene. Two such secondary structures, G-quadruplexes and i-Motifs, have become topics of interest due to their prevalence within oncogenic promoters and their potential accessibility for future drug targeting due to their globular natures. Though fairly extensive research has been conducted to understand different factors affecting G-quadruplex formation and stability, similar studies for i-Motifs, particularly related to thermodynamics, are still evolving. One factor known to contribute to the additional energy required for duplex …
Modelling Global Climate Variables With Cellular Automata Networks, David Robinson
Modelling Global Climate Variables With Cellular Automata Networks, David Robinson
Honors Theses
Cellular automata are discrete models that can be used to simulate many physical systems. Cellular automata have been used to model gas diffusion, different types of chemical reactions, population growth, and land use change over time. Recent research into cellular automata networks has shown that if sparse long range connections are added to a cellular automata, then it will exhibit properties of complex networks. Furthermore, research into modeling climate systems has shown that modeling the global climate as a complex network can be used to predict individual climate variables. In this work we attempt to connect these ideas by simulating …
Initial Breakdown Pulses In Lightning Flashes, Emily Morgan Smith
Initial Breakdown Pulses In Lightning Flashes, Emily Morgan Smith
Honors Theses
Initial Breakdown (IB) pulses in lightning flashes have been observed since 1937. Using two sensor arrays to determine the location and amplitude of IB pulses, this study examines the largest IB pulse in 55 flashes with 23 pulses from intracloud (IC) flashes and 32 pulses from cloud-to-ground (CG) flashes. The two goals of this project were (1) to compare the range-normalized amplitude of the largest IB pulse to its altitude, duration, and timing within each flash, and (2) to characterize the shapes of the IB pulses. Since all lightning flashes seem to begin with IB pulses, this study is aimed …
X-Dimer Mutations And Their Effects On The Folding Stability And Assembly Of Ecad12 At The K14-D138 Interface, Martha Kaitlyn Coghlan
X-Dimer Mutations And Their Effects On The Folding Stability And Assembly Of Ecad12 At The K14-D138 Interface, Martha Kaitlyn Coghlan
Honors Theses
Classical cadherins were first identified by their function in mediating calcium-dependent cellular adhesion and constitute a large family of cellular adhesion receptor proteins whose differential binding is central to the development and maintenance of tissue architecture. The interface underlying the binding interaction reveals that all classical cadherins share a common adhesive interface in which the portion of the β-A strand closest to the N-terminus is swapped between EC1 domains of the adhesive partner protomers. A second dimeric configuration, known as the 'X-dimer', is the face-to-face association of two protomers in which their orientation is dictated by three symmetrical noncovalent interactions …
Para-Interface: A Novel Interface For Para-Aeh Software Suite, Michael Ginn
Para-Interface: A Novel Interface For Para-Aeh Software Suite, Michael Ginn
Honors Theses
Para-AEH is a software suite designed to the Asymptotic Expansion Homogenization method. This method is commonly used to model structures by using differential equations to represent larger structure from a smaller structure input. In order to facilitate the University of Mississippi's Department of Mechanical Engineering's research purposes the software needed to be installed. A novel interface was designed to remove the overhead of interacting with the software on a command line based level. The software allows the management of users that can access the software and jobs that package several commands together for asynchronous execution without manual intervention.
Characterization Of Epithelial Cadherin Domain 1, Molly Edmondson
Characterization Of Epithelial Cadherin Domain 1, Molly Edmondson
Honors Theses
Cadherins are a family of cell-surface glycoproteins that aid in cell adhesion between two proximal cells. The characteristic cadherin extracellular structure consists of five ~100 amino acid domains connected by seven-residue linker regions. Cadherins mediate adhesion via adherens junctions by forming a strand-swapped structure between identical protomers from apposing cells. Upon calcium binding, the swapping of the N- terminal strands between protomers allows for the symmetrical docking of a conserved tryptophan residue in the N-terminal strand into the hydrophobic pocket of its partner protomer. The two most-well-studied members of the classical cadherin family are Neural- (N-) and Epithelial- (E-) cadherin. …
Electron Cloud Studies With Transverse Beam Islands, Neetish Pradhan
Electron Cloud Studies With Transverse Beam Islands, Neetish Pradhan
Honors Theses
Electron cloud generation has been a rising problem in high energy beam chambers such as the LHC. In order to mitigate this problem, we looked for the best beam configuration to scrub the chambers and reduce its secondary electron yield. Using simulations, a five-island beam and a three-island beam were compared against a normal single beam. The five-island beam was found to work best.
Properties Of A Fluorescent Deoxycytidine Analog In I-Motif Dna, Sara E. Wingate
Properties Of A Fluorescent Deoxycytidine Analog In I-Motif Dna, Sara E. Wingate
Honors Theses
Experiments to determine fluorescence lifetimes and fluorescence quenching constants were performed using oligonucleotides of DNA containing PdC, a fluorescent analog of cytidine, at five different locations in the i-motif. My experiments were chosen in order to better understand the structural characteristics of i-motif DNA, which are thought to have biological importance in cancer and drug delivery. Fluorescent lifetime experiments were carried out using an ISS K2 fluorescence instrument with a modulated LED light source in order to determine if the cytidine bases in DNA replaced by PdC were paired or unpaired in the i-motif structure. The resulting data allowed us …
An Assessment Of The Angular Spectrum Method For The Propagation Of Ultrasound, Taylor Miller
An Assessment Of The Angular Spectrum Method For The Propagation Of Ultrasound, Taylor Miller
Honors Theses
The purpose of this project is to investigate the limitations of the angular spectrum method when it is applied to the propagation of acoustic waves in the ultrasonic frequency waves. In this experiment, broadband acoustic waves at ultrasonic frequencies were propagated through a water bath. Ten planar scans perpendicular to the direction of the wave propagation were taken at 10 different distances from the transducer. These scans recorded the pressure field data at each plane. The angular spectrum method was applied to this data, and used to predict the pressure field data at the other planes. Comparison between this predicted …