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 …

Synthetic Methods Development Towards The Total Synthesis Of Chlorosulfolipids, Andres Villalpando

LSU Doctoral Dissertations

The focus of this dissertation is the development of a novel chlorination reaction utilizing a triphosgene-amine based mixture towards the total synthesis of chlorosulfolipids, a subclass of naturally occurring organohalogen natural products. This novel, mild chlorination reaction will be utilized under a global chlorination strategy to chlorinate multiple alcohol substituents in one synthetic operation. Chapter one details the history of chlorosulfolipids from the early stages of their isolation, relevant structural elucidation techniques, appropriate biosynthetic discoveries, and their biological relevance to a thorough investigation of the total syntheses completed to date. These compounds demonstrate a range of biological activities and have …

Microstructure And Geotechnical Properties Of St. Peter Sandstone In Clayton, Iowa, Amir Hossein Bagherieh

Doctoral Dissertations

"The St. Peter Sandstone is significantly different from the minerals and rocks which have been studied extensively in mining. It is brittle and characterized by an unusually high friction angle. On the other hand it is friable, and it is nearly cohesionless. The scarcity of the ground control techniques for this particular mining environment has created many difficulties for mine operators. This research aims to establish a fundamental understanding of the basic mechanical and strength properties of the St. Peter Sandstone for engineering design and scientific research. The specific objectives are 1) characterizing the strength of the St. Peter Sandstone, …

Efficient Cryptographic Primitives: Secure Comparison, Binary Decomposition And Proxy Re-Encryption, Feng Li

Doctoral Dissertations

”Data outsourcing becomes an essential paradigm for an organization to reduce operation costs on supporting and managing its IT infrastructure. When sensitive data are outsourced to a remote server, the data generally need to be encrypted before outsourcing. To preserve the confidentiality of the data, any computations performed by the server should only be on the encrypted data. In other words, the encrypted data should not be decrypted during any stage of the computation. This kind of task is commonly termed as query processing over encrypted data (QPED).

One natural solution to solve the QPED problem is to utilize fully …

Synergistic Properties-Driven Synthesis Of Aluminides, Antiomonides, And Bioceramics, Pilanda Watkins-Curry

LSU Doctoral Dissertations

The synthesis, characterization, and properties of selected intermetallics and ceramic materials are presented in this dissertation. In our quest to grow single crystal intermetallics from the metal flux technique, new strategies were employed to avoid thermodynamically stable phases and to ensure sample homogeneity of the crystalline product for structure elucidation and accurate measurements of their magnetic and electrical properties. The relationship between the complex crystal structures and magnetic properties are reported for LnCo2Al8 (Ln = La-Nd, Sm, Yb), CeCo2-xMnxAl8 (0 < x < 1), and Pr2Fe4-xCoxSb5 (1 ≤ x < 3). The discovery of magnetic frustration in LnCo2Al8 (Ln = Ce, Nd) and complex magnetic ordering coupled with large positive magnetoresistance of up to 150% and 60% at 200 K with relatively low field of H = 1 T in Pr2Fe4-xCoxSb5 (x ≈ 2 and 2.5) is also reported. The demand of new inorganic solid materials as scaffolds for the engineering of bone tissue has led to the synthesis of calcium magnesium silicates such as, diopside (CaMgSi2O6), akermanite (Ca2MgSi2O7), monticellite (CaMgSiO4), and merwinite (Ca3Mg(SiO4)2)) for studying dimensionality and mechanical properties. This dissertation highlights the synergism of solid state chemistry at the interface of condensed matter physics and biological engineering. The discovery of compounds with tunable magnetic, electrical, and mechanical properties will be described herein.

I. Synthesis Of Ascarosides For Chemical Biology Studies In Caenorhabditis Elegans, Ii. A Photochemical Approach To Delavayine, And Iii. Remote Hydroxylation By Radical Translocation And Polar Crossover, Kyle Allen Hollister

LSU Doctoral Dissertations

The foci of this dissertation are the synthesis of analogs for chemical biology studies, synthetic chemistry method development (with an emphasis on photochemistry), and the application of these methods toward total synthesis. Chapter 1 outlines the synthesis of an array of pheromone analogs that are derivatives of the dideoxy sugar ascarylose. Referred to as ascarosides, such compounds have recently been shown to influence important biological processes in the model organism Caenorhabditis elegans. C. elegans secretes ascarosides into its environment, where the compounds then act as signaling molecules by providing information on factors like population density. Chapter 2 describes the biological …

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 …

Heavy Flavor Interactions And Spectroscopy From Lattice Quantum Chromodynamics, Zachary S. Brown

Dissertations, Theses, and Masters Projects

In the present work, spectroscopy and interactions of hadrons containing heavy quarks is investigated. In particular, a focus is placed on properties of exotic heavy hadronic states, including doubly and triply heavy baryons and doubly heavy tetraquark states. The framework in which these calculations are carried out is provided by lattice quantum chromodynamics, a discrete formulation of the modern theory of the strong interaction. The main body of the thesis had two main project focuses. For the first project, an extensive calculation of the mass spectrum of doubly and triply heavy baryons including both charm and bottom quarks is carried …

Scientific Software Communities [Guest Editor Introduction], Andy Terrel, Michael Tobis, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

Guest editor introduction

Heartbeat Location Assistance For Electrocardiograms, Sarah Bass

EWU Masters Thesis Collection

"The electrocardiogram (ECG) is the main source of heartbeat analysis throughout the medical community, due to the distinctive appearance of the QRS complex at the time of each beat. There are other signals that also exhibit distinctive patterns at the time of each heartbeat; however, the ECG is still the most prevalently used. Analyzing the ECG alone can be problematic because ECG data can be noisy. The noise often makes it appear as if the heartbeat is missing or that multiple beats occurred in quick succession. This research will analyze the association between a variety of signals and the ECG, …

A Systematic Study On Explicit-State Non-Zenoness Checking For Timed Automata, Ting Wang, Jun Sun, Xinyu Wang, Yang Liu, Yuanjie Si, Jin Song Dong, Xiaohu Yang, Xiaohong Li

Research Collection School Of Computing and Information Systems

Zeno runs, where infinitely many actions occur within finite time, may arise in Timed Automata models. Zeno runs are not feasible in reality and must be pruned during system verification. Thus it is necessary to check whether a run is Zeno or not so as to avoid presenting Zeno runs as counterexamples during model checking. Existing approaches on non-Zenoness checking include either introducing an additional clock in the Timed Automata models or additional accepting states in the zone graphs. In addition, there are approaches proposed for alternative timed modeling languages, which could be generalized to Timed Automata. In this work, …

The Role Of Intermembrane Space Redox Factors In Glutathione Metabolism And Intracellular Redox Equilibrium, Hatice Kubra Ozer

Theses and Dissertations

The mitochondrial intermembrane space (IMS) is a unique subcellular compartment that houses key thiol-dependent redox pathways such as protein transport, mitochondrial respiration, and detoxification of ROS (reactive oxygen species). These pathways are all dependent on cysteine-rich proteins, thus maintaining thiol-disulfide balance in this organelle is crucial for cellular functions. An IMS protein import pathway called the Mia40-Erv1 disulfide relay system uses disulfide bond formation for the import and retention of substrate proteins in the IMS. Erv1 is also suggested to be involved in maturation of cytosolic Fe-S cluster proteins and regulation of iron homeostasis in S. cerevisiae. However, these studies …

Charged-To-Neutral Correlation At Forward Rapidity In Au + Au Collisions At √S(Nn)=200 Gev, L. Adamczyk, J. K. Adkins, G. Agakishiev, A. A. Aggarwal, Z. Ahammed, I. Alekseev, S. Bültmann

Physics Faculty Publications

Event-by-event fluctuations of the multiplicities of inclusive charged particles and photons at forward rapidity in Au + Au collisions at √s(NN) = 200 GeV have been studied. The dominant contribution to such fluctuations is expected to come from correlated production of charged and neutral pions. We search for evidence of dynamical fluctuations of different physical origins. Observables constructed out of moments of multiplicities are used as measures of fluctuations. Mixed events and model calculations are used as base lines. Results are compared to the dynamical net-charge fluctuations measured in the same acceptance. A nonzero statistically significant signal of dynamical fluctuations …

Measurement Of Parity-Violating Asymmetry In Electron-Deuteron Inelastic Scattering, D. Wang, K. Pan, R. Subedi, Z. Ahmed, K. Allada, S. Golge, C. E. Hyde

Physics Faculty Publications

The parity-violating asymmetries between a longitudinally polarized electron beam and an unpolarized deuterium target have been measured recently. The measurement covered two kinematic points in the deep-inelastic scattering region and five in the nucleon resonance region. We provide here details of the experimental setup, data analysis, and results on all asymmetry measurements including parity-violating electron asymmetries and those of inclusive pion production and beam-normal asymmetries. The parity-violating deep-inelastic asymmetries were used to extract the electron-quark weak effective couplings, and the resonance asymmetries provided the first evidence for quark-hadron duality in electroweak observables. These electron asymmetries and their interpretation were published …

Impact Of Spatial Aliasing On Sea-Ice Thickness Measurements, Cathleen Geiger, Hans-Reinhard Müller, Jesse P. Samluk, E Rachel Bernstein, Jacqueline Richter-Menge

Dartmouth Scholarship

We explore spatial aliasing of non-Gaussian distributions of sea-ice thickness. Using a heuristic model and >1000 measurements, we show how different instrument footprint sizes and shapes can cluster thickness distributions into artificial modes, thereby distorting frequency distribution, making it difficult to compare and communicate information across spatial scales. This problem has not been dealt with systematically in sea ice until now, largely because it appears to incur no significant change in integrated thickness which often serves as a volume proxy. Concomitantly, demands are increasing for thickness distribution as a resource for modeling, monitoring and forecasting air–sea fluxes and growing human …

Gene Expression Changes Reflect Clinical Response In A Placebo-Controlled Randomized Trial Of Abatacept In Patients With Diffuse Cutaneous Systemic Sclerosis, Eliza F. Chakravarty, Viktor Martyanov, David Fiorentino, Tammara A. Wood, David J. Haddon, Justin A. Jarrell, Paul Utz, Mark Genovese, Michael Whitfield, Lorinda Chung

Dartmouth Scholarship

Systemic sclerosis is an autoimmune disease characterized by inflammation and fibrosis of the skin and internal organs. We sought to assess the clinical and molecular effects associated with response to intravenous abatacept in patients with diffuse cutaneous systemic.

The Action Cycle/Structural Context Framework: A Fisheries Application, D. G. Webster

Dartmouth Scholarship

There is a growing consensus that environmental governance is a wicked problem that requires understanding of the many linkages and feedbacks between human and natural systems. Here, I propose an action cycle/structural context (AC/SC) framework that is based on the concept of responsive governance, in which individuals and decision makers respond to problems rather than working to prevent them. By linking agency and structure, the AC/SC framework points out two key problems in the realm of environmental governance: the profit disconnect, whereby economic signals of environmental harm are dampened by endogenous or exogenous forces, and the power disconnect, whereby those …

Predicting Variability Of Basal Scour And Quantifying Vertical Connectivity For Channel-Belt Reservoirs Using Observations From The Holocene Mississippi River And Channel-Belt, Neal Alexandrowicz

Earth & Environmental Sciences Dissertations

Assessment of potential for draining unpenetrated but closely stacked channel-belt reservoirs from an existing belt penetration depends upon an understanding of the methods of and the likelihood for connectivity between otherwise isolated reservoirs. Knowledge of both the variability in scour depth beneath a channel-belt and the distribution of channel-belt lithofacies is critical for making such assessments, yet is very poorly understood. In order to evaluate these two properties, a collection of 314 driller’s records, 245 cross section points, and over 300 hand-augered boreholes along a 75 mile stretch of an active Mississippi River meander belt were reviewed, along with a …

Spectrally Accurate Quadratures For Evaluation Of Layer Potentials Close To The Boundary For The 2d Stokes And Laplace Equations, Alex Barnett, Bowei Wu, Shravan Veerapaneni

Dartmouth Scholarship

Dense particulate flow simulations using integral equation methods demand accurate evaluation of Stokes layer potentials on arbitrarily close interfaces. In this paper, we generalize techniques for close evaluation of Laplace double-layer potentials in [J. Helsing and R. Ojala, J. Comput. Phys., 227 (2008), pp. 2899--2921]. We create a “globally compensated” trapezoid rule quadrature for the Laplace single-layer potential on the interior and exterior of smooth curves. This exploits a complex representation, a product quadrature (in the style of Kress) for the sawtooth function, careful attention to branch cuts, and second-kind barycentric-type formulae for Cauchy integrals and their derivatives. Upon …