Physical Sciences and Mathematics Commons^™

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 …

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 …

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 …

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.

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 …

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

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.

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 …

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 …

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

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

The Dimerization Kinetics Of Ncad12 With A Mutated Cis-X-Pro Bond, Victoria Mcclearn

Honors Theses

VICTORIA RAE McCLEARN: DIMERIZATION KINECTICS OF NCAD12 P16A (Under the direction Dr. Susan Pedigo) Calcium binding causes a conformational change into a strand swapped dimer for the cadherins. However, regardless of the sequence similarity for Epithelial Cadherin (ECAD) and Neural Cadherin (NCAD), they respond to the presence of calcium differently. For NCAD, the rate of assembly and disassembly depends upon the presence of calcium, whereas for ECAD the rate of exchange is independent of calcium. Studies into a kinetic model to explain the differences between the rates have been recently conducted. It is believed that ECAD uses an X-dimer intermediate …

Towards The Synthesis Of A Swallowtailed Perylene Monoimide, Wyatt S. Whicker

Honors Theses

This project was initiated in conjunction with Dr. Justin Youngblood from the University of North Texas. The goal was to synthesize a molecule to be used in solar cell testing. The target molecule involved combining donor and acceptor groups to make a combination that would be able to transfer electricity in a unilateral direction to increase efficiency in solar cells. My project involved the donor portion, a perylene monoimide donor with a long alkyl swallowtail to impart solubility. While the final molecule was not synthesized, the proposed procedure for making such a molecule was improved upon. A perylene tetracarboxylic dianhydride …

The Effects Of Hg2+ On Secondary Structures Formed By T-Rich Dna, Zachary Boynton

Honors Theses

Single stranded DNA that forms secondary structures has been a popular area of research in recent years. Much research has also been done in the field of heavy metals binding to DNA. Recently, it has been discovered that mercury in the presence of thymines will form T-HgII-T bonds. It is our hypothesis that single stranded DNA rich in thymine residues will form into a structure similar to i-motifs, formed from C-rich single strands, in the presence of mercury. Based on spectral changes during a mercuric titration, it is evident that mercury induces a structural change in T-rich DNA. We then …

A Survey Of Shark Population In Winyah Bay, Sc: A Comparison Of Data From 2002-2006 And From 2012-2014, Jessica Bruce

Honors Theses

As a result of a long-term longline study conducted by Coastal Carolina University, data on the population structure of sharks in Winyah Bay, SC have been recorded since 2002. The data are collected from late spring to fall each year. Two separate data sets, from 2002 to 2006 and from 2012 to 2014, were analyzed for catch per unit effort (CPUE), catch composition, sex ratios, and average precaudallengths (PCL) for males and females. The average CPUE for the 2002-2006 data set was 2.68 with a standard deviation of 0.73 while the average for the most recent data set was 3.20 …

Parweb: A Front-End Interface For Cluster Computing., Jacob Potter

Honors Theses

The High Performance Computational Science Laboratory at Western Michigan University operates a cluster of systems for use by students, professors, and professional researchers. Currently users that want to access the cluster, known as “Thor”, require knowledge of the Unix/Linux command line. They also require knowledge of operating a piece of software known as TORQUE to correctly achieve results from the High Performance Computing Lab.

The Web User Interface Framework for High Performance Cluster Computing alleviates the need for intimate knowledge of a command line interface, and replaces the current interaction interface with a more user friendly and graphical oriented system. …

Conservation And Ecological Implications Of The Introgression Between Black Bass Subspecies, Rachel Tessier

Honors Theses

No abstract provided.

Synthesis And Antimicrobial Activity Of Brominated Quaternary Ammonium Compounds, Wendy Pippin

Honors Theses

No abstract provided.

Multisensory Emotion Recognition With Speech And Facial Expression, Jacob P. Roeland

Honors Theses

Computers through both desktop and mobile devices are only becoming more important in our lives leading us to have more involved and longer interactions with them. Because of this our brains actually classify our involvement with them in a manner similar to our interactions with our fellow humans. This can lead to frustration and anxiety when our computers interrupt our work or pleasure with contextually inappropriate messages, much the same way it would if a friend or co-worker was pushy or rude. A way to solve this issue is to give our machines emotional intelligence, or the ability to recognize …

The Nature Conservancy And Aquatic Invasive Species, Rachel Ross

Honors Theses

No abstract provided.

Analysis Of Atmospheric Aerosols Collected In An Urban Area In Upstate Ny Using Proton Induced X-Ray Emission (Pixe) Spectroscopy, Jeremy Smith

Honors Theses

We have performed a PIXE analysis of atmospheric aerosol samples collected in Schenectady, NY, to study airborne pollution in an urban environment. The samples were collected using a PIXE International, 9-stage, cascade impactor that separates the airborne particles according to aerodynamic diameter and deposits them on thin Kapton foils. The impacted foils were bombarded with 2.2-MeV proton beams from the Union College 1.1-MV Pelletron accelerator and the emitted X-rays were detected with an Amptek silicon drift detector. The X-ray energy spectra were analyzed using GUPIX software to determine the elemental concentrations in the samples. A broad range of elements from …