Physical Sciences and Mathematics Commons^™

Investigations Into The Fluorescent Covalent Labeling Of Biomolecules Utilizing Rhodamine Dyes, Electrophilic Leaving Groups And Mrna Display., Susan D. Selaya

Theses and Dissertations

The discovery of a method by which proteins of interest can selectively be labeled with a probe of choice intracellularly is a longstanding goal in chemical biology research. Conventional labeling techniques have utilized large domain tags but despite the development of small labeling molecules there have been no short peptide sequences known to covalently label a small molecule without the aid of an enzymatic process or metal chelation. We aimed to find a sequence of nucleophilic peptides that reacted covalently and specifically with electrophilic small labeling molecules using mRNA display. Our goal was to show that an electrophilic small labeling …

Exploring The Asymmetric Environment Of Various Chiral Catalysts Using A Modified Ion-Trap Mass Spectrometer: Towards The Development Of A Rapid Chiral Catalyst Screening Method, Cary M. Davis

Theses and Dissertations

Since the tragedy of the drug Thalidomide® in the late 1950 to early 1960’s, chirality has been recognized as an important aspect that must be controlled in the drug development process in the pharmaceutical industry. Since then, there has been a considerable movement towards single enantiomer drugs. This demand has presented many challenges for the synthetic organic chemist. Chiral catalysts offer one solution to this problem, as they afford the unique ability to preferentially synthesize one enantiomer. Unfortunately, the design of new chiral catalysts is often empirical, with luck and trial and error necessary due to factors that govern enantioselectivity. …

Magnetic Properties Of Hematite (Α-Fe2o3) Nanorods, Samar A. Ghopry

Theses and Dissertations

At this study three samples of hematite nanorods were deposited on the silicon substrates with different varieties of glancing angle deposition techniques. One sample (S1) was prepared by using thermal deposition with partially ionized beam (PIB) and substrate rotation. The second sample (S2) was synthesized by using thermal deposition with PIB and no substrate rotation. The third sample (S3) was obtained by using E-beam deposition, PIB and rotating substrate. In addition, one sample of magnetite nanorods (S4) has been prepared in order to compare the magnetic properties of the two different iron oxides. S4 was prepared by using thermal deposition …

Using Structural Analysis To Investigate The Function Of Suppressor Of Ikk-Epsilon (Sike), Sean W. Mckinley

Theses and Dissertations

The innate immune system provides the body’s first line of defense against pathogenic challenge through pathogen recognition and initiation of the immune response. Among the various cellular mechanisms of pathogen recognition in mammals, Toll-like receptor 3 (TLR3) recognizes viral dsRNA. Stimulation of TLR3 signaling pathway leads to transcription of pro-inflammatory cytokines and type-1 Interferons. Suppressor of IKKε (SIKE) interacts with two kinases in the signaling pathway, IKKε and TANK binding kinase 1 (TBK1), inhibiting the transcription of type I interferons. Recently, the Bell Laboratory discovered that SIKE blocks TBK1-mediated activation of type I interferons by acting as a high affinity, …

Hydrological Influences On Ecological Zonation In A Salt Marsh Tidal Creek Basin: Crab Haul Creek, South Carolina, Usa, Elizabeth Madsen

Theses and Dissertations

Ecological zones in a salt marsh are controlled by many factors, including hydroperiod, elevation, soil salinity, groundwater flow, competition, and nutrient/oxygen availability. The primary driving factor(s) are still debated, but most models of zonation consider elevation or hydroperiod as the key factor. This project is designed to gather high-resolution aerial images from a helium balloon kite (Helikite) to improve our understanding of the influence of hydroperiod on zonation. The Helikite was used to capture aerial photographs of Crab Haul Creek Basin, the most landward salt marsh basin in North Inlet, South Carolina. Near-IR photographs were taken from 75-100m altitude to …

Turán Problems On Non-Uniform Hypergraphs, Jeremy Travis Johnston

Theses and Dissertations

A non-uniform hypergraph H = (V, E) consists of a vertex set V and an edge set E ⊆ 2 V; the edges in E are not required to all have the same cardinality. The set of all cardinalities of edges in H is denoted by R(H), the set of edge types. For a fixed hypergraph H, the Turán density π(H) is defined to be the maximum Lubell value of a graph G (in the limit) which is H-free and such that R(G) ⊆ R(H). The Lubell function, is the expected number of edges in G hit by a random …

Timewalk Correction Analysis With Fadcs, Saptaparnee Chaudhuri

Theses and Dissertations

The upgraded CLAS12 (12 GeV) detector is built around a six-coil toroidal magnet that divides the active detection area into six azimuthal sectors. The Forward Time-of-Flight system (FTOF) is a major component of the CLAS 12 detector. It is used to measure the time-of-flight of the charged particles emerging from the interaction of the probing particle and the target. In each of the six sectors of the CLAS12, the FTOF system is comprised of three arrays of counters referred to as panel-1a, panel-1b, panel-2b. Panel-1b arrays consists of 62 counters each. This research focuses on the "timewalk corrections" analysis of …

Traceability Implementation In Organic Farming: Case Study, Chamomile Tea Production, Shaima Ibrahim

Theses and Dissertations

Implementing a traceability plan in an herbal production plant is a complex task. In this study an attempt to integrate food safety, quality and traceability through the different stages of the organic German Chamomile (Matricaria recutita) production chain was made. First, all the current relevant international laws, regulations and standards regarding traceability, safety and quality, with emphasis on how and why they are necessary for any food production chain, were set forward. Second, physico-chemical and microbiological analyses were run throughout the different processing stages of production, for four different Chamomile batches produced over the same season using the same farming …

Seismic Characterization Of The J-Reflector Near The Meizoseismal Area Of The 1886 Charleston Earthquake For Lithologic Constraint, Craig Cunningham

Theses and Dissertations

Investigations into the relationship between geologic structure and seismicity in and around the meizoseismal area of the 1886 Charleston earthquake have been ongoing since the 1970s. Seismic reflection profiles collected in this area display a prominent, laterally continuous, high amplitude, low frequency, two cycle reflection at ~0.7-1.2 s TWT, termed the "J" reflector, which has been correlated with Lower to Middle Jurassic tholeiitic basalt flows encountered in the Clubhouse Crossroads wells. The "J" reflector was also extended offshore onto the continental shelf. Recent reevaluation of sub Coastal Plain wells within the South Georgia Rift (SGR) Basin, including wells around the …

Web Service Transaction Correctness, Aspen Olmsted

Theses and Dissertations

In our research we investigate the problem of providing consistency, availability and durability for Web Service transactions. First, we show that the popular lazy replica update propagation method is vulnerable to loss of transactional updates in the presence of hardware failures. We propose an extension to the lazy update propagation approach to reduce the risk of data loss. Our approach is based on the "buddy" system, requiring that updates are preserved synchronously in two replicas, called buddies. The rest of the replicas are updated using lazy update propagation protocols. Our method provides a balance between durability (i.e., effects of the …

Electron Donor Contributions To Denitrification In The Elk Valley Aquifer, North Dakota, Amanda M. Krieger

Theses and Dissertations

Six denitrification tracer tests were performed over eight and a half years in in situ mesocosms (ISMs) in the Elk Valley Aquifer (EVA) in east-central North Dakota. Groundwater samples were analyzed to determine how much nitrate was lost beyond that explained by dilution of the bromide tracer. Additional losses were attributed to denitrification. The denitrification rates varied from 0.10 to 0.23 mg N/L/day for the six tests. In general, the major electron donors for denitrification are organic carbon (OC), pyrite (FeS2), and ferrous iron silicate minerals. In the EVA tracer tests, increases in sulfate indicated that the oxidation of pyrite …

The Depositional Environment And Diagenetic Effects On Sand Bodies Within The Unconventional Resource Play Of The Spearfish Formation (Triassic) In North Central North Dakota, Matthew J. Sebade

Theses and Dissertations

The Triassic Spearfish Formation in North Dakota is comprised of three members, the Belfield, Pine, and Saude Members, in ascending order. This study focuses on the Saude Member in north-central North Dakota on the eastern margin of the Williston basin. Both the upper and lower contacts of the Spearfish in the study area are unconformable. In this region, the lateral distribution of red sandstone and argillaceous siltstone lithofacies were mapped using well log data. Four sandstone bodies were identified then mapped across the region using gamma ray logs. Sandstone bodies in descending order are the A sand, B sand, water …

Next Discoveries In Neutrino Mixing: Electron Neutrino Appearance, Hongyue Duyang

Theses and Dissertations

The discovery of neutrino oscillation is a clear evidence of new physics beyond the Standard Model. Measurements of electron neutrino ($\nu_e$) and electron anti-neutrino $\bar{\nu}_{e}$ appearances are the most important channels to complete the neutrino mixing matrix. In a $ \nu_{e} $/$\bar{\nu}_{e}$ appearance experiment, a near detector (ND) is used to constrain the neutrino flux and measure the backgrounds to the signal. Backgrounds to the $ \nu_{e} $ appearance comes from Neutral Current Muon Neutrino Interactions ($\nu_{\mu}$-NC), Charged Current Muon Neutrino Interactions ($\nu_{\mu}$-CC), beam $ \nu_{e} $ events and outside backgrounds. The background components are then extrapolated to the far …

Oldtimers & Newcomers In Collective Action, Stefanie R. Chamberlain

Theses and Dissertations

Most work on groups facing collective action assumes that group membership is static, or fixed. Yet static membership is rare, with members joining and leaving groups. In this thesis, I propose to explore how the presence of newcomers to groups affects group coordination. Past research has shown an overall negative effect of newcomers on group contributions. The proposed thesis attempts to further establish the effect by determining whether newcomers, oldtimers, or both are responsible for the declining cooperation in groups. While the empirical component is focused solely on establishing who is responsible for driving down cooperation rates in dynamic groups, …

A Quantitative Analysis Of White-Tailed Deer Harvest Across States And Counties, Rebecca Lynne Cain

Theses and Dissertations

White-tailed deer (Odocoileus virginianus) have gone from locally extirpated to overabundant in many areas in the United States since the early 1900s. Ecosystems with chronically overabundant populations experience many disastrous effects resulting from the selective browsing behavior of deer. White-tailed deer are managed at the state level resulting in different management strategies, harvest data collection, and deer management goals between states. However recreational hunting is the primary tool used by wildlife agencies to control population growth. As such, it is beneficial to understand the influence each regulatory variable has on white-tailed deer harvest.

For this research, I compiled historical harvest …

Bayesian Analysis Of Continuous Curve Functions, Wen Cheng

Theses and Dissertations

We consider Bayesian analysis of continuous curve functions in 1D, 2D and 3D spaces. A fundamental feature of the analysis is that it is invariant under a simultaneous warping/re-parameterization of all target curves, as well as translation, rotation and scale of each individual if necessary. We introduce Bayesian models based on a special curve representation named Square Root Velocity Function (SRVF) introduced by Srivastava et al. (2011, IEEE PAMI). A Gaussian process model for the SRVFs of curves is proposed, and suitable prior models such as the Dirichlet distribution are employed for modeling the warping function as a cumulative distribution …

Applications Of Bayesian Nonparametrics To Reliability And Survival Data, Li Li

Theses and Dissertations

Reliability and survival data are widely encountered across many common settings. Subjects under investigation often include machines, bioassays, patients, etc.; their reliability or survival distribution, and its association with covariate processes, are commonly of interest. Within this dissertation, the first two chapters focus on reliability data where repairable systems fail and get interventions, e.g. repairs in the event process. It begins with a nonparametric test for the commonly assumed ''good as old'' assumption for minimal repair models and then a semi-parametric regression model is introduced for reliability data using Kijima's effective age. The third chapter focuses on survival data observed …

Approximate Quantum Trajectory Method For Modeling Chemical Reaction Dynamics: Application To Enzymatic Proton Transfer, James William Mazzuca

Theses and Dissertations

Molecular dynamics simulations, providing a detailed picture of the reaction mechanism, is an essential tool for theoretical and experimental chemists. In these simulations the nuclei are typically treated as classical particles, but under some conditions (low energies and temperatures, processes involving multiple electronic states) a classical description is inappropriate. Quantum effects of nuclear motion, such as tunneling and zero-point energy can play an important role in determining a reaction mechanism, yet exact quantum dynamics methods are limited to reactive systems of just 3-4 atoms. Central to this work is the development and implementations of an efficient trajectory-based methodology, in which …

Patterns And Mechanisms Of Heat Transport In The Northern Denver Basin Nebraska, South Dakota And Wyoming, Aaron T. Ochsner

Theses and Dissertations

Finite difference simulations of the hydrothermal system of the northern Denver Basin are suggestive of a correlation between anomalous heat flux and the presence of faults and structural lineaments mapped in the region. Geothermal, hydrogeological, lithological, and structural data available for the northern Denver Basin were compiled and analyzed in an effort to determine the hydrothermal mechanisms responsible for observed heat flow anomalies in the study area. Measurement of thermal conductivity was conducted for 82 solid core samples and 60 unconsolidated samples from drill cuttings, yielding a harmonic mean thermal conductivity value of 1.52 ± 0.91W m-1 K-1 for the …

Lithostratigraphic Investigation Of A Late Devonian Carbonate-Evaporite Sequence; The Duperow Formation, Williston Basin, North Dakota, Zachary P. Alcorn

Theses and Dissertations

The Duperow Formation of northwestern North Dakota is a cyclical carbonate evaporite unit deposited on a shallow marine shelf during the early part of the Late Devonian (Frasnian). The formation forms the lower part of the Jefferson Group and lithostratigraphic review permits three informal members to be recognized: lower, middle, and upper. Petrographic, lithologic, and well log examination of drill cores and thin sections allows the identification of seven lithofacies within the three members. Lithofacies include; bioclastic wackestone/packstone (LF1), stromatoporoid boundstone/floatstone (LF2), Amphipora boundstone/floatstone (LF3), peloidal wackestone (LF4), dolomitic mudstone (LF5), microbially laminated dolowackestone (LF6), and anhydrite (Lf7). Lithofacies are …

Landscape Evolution And Preservation Of Ice Over One Million Years Old Quantified With Cosmogenic Nuclides 26al, 10be, And 21ne, Ong Valley, Antarctica, Theodore C. Bibby

Theses and Dissertations

Antarctica has been glaciated for the past 35-40 million years (Denton et al., 1991) and evidence of periodic fluctuations of the Antarctic ice sheet (AIS) during the Cenozoic are recorded in the ice sheet itself, deep sea sediments, and glacial deposits on the continent (Ingólfsson, 2004). Quaternary continental records of AIS extent is limited to few locations along the Transantarctic Mountains (TAM) and coastal continental boundaries (Denton et al., 1984; Denton et al., 1989). Records of atmospheric variation over time, glacial extents, and ice sheet responses to environmental changes are required to understand modern day forces on climate and the …

Stratigraphy, Depositional Environments, And Petroleum Potential Of The Three Forks Formation -- Williston Basin, North Dakota, Richard A. Ashu

Theses and Dissertations

The hydrocarbon potential of the Three Forks Formation in North Dakota is poorly known due to limited stratigraphic, geochemical, and petrophysical data. This study presents a methodology and results of a reservoir characterization study of the stratigraphy, lithofacies distribution, petroleum potential, and paleo-environments of the Three Forks Formation in North Dakota as a potential for hydrocarbon exploration with the principal objective to evaluate the Three Forks Formation’s potential for future developments. The detailed lithology is computed by employing a probabilistic interpretation approach calibrated with lab results and five major lithofacies of the Three Forks Formation in North Dakota, which display …

Quantifying Nutrient Cycling And Fate Within An Abandoned Feedlot And Adjacent Wetlands, Prosper Prosper Gbolo

Theses and Dissertations

Feedlot operations over the years have increased revenue and boosted economies of states and countries, but these operations have resulted in elevated concentrations of nutrients in soils, surface water, and groundwater. Feedlot operations generate large quantities of manure and other waste, which when not managed properly can result in environmental problems.

It is hypothesized that nitrogen can cause a short-term contamination of soils and groundwater beneath abandoned feedlots, but phosphorus can cause both short- and long term contamination, especially in well-drained carbonate and iron-rich soils associated with Concentrated Animal Feeding Operations. It is also hypothesized that a spectral vegetation index …

Characterization, Diagenesis, And Geocellular Modeling Of Winnipegosis Formation Pinnacle Reefs In The Williston Basin, North Dakota, Nicholas W. Bosshart

Theses and Dissertations

The Middle Devonian Winnipegosis Formation of the North Dakota Williston Basin contains pinnacle reef structures which have been targeted in the past for hydrocarbon production. These reefs have not been proven to hold economically important primary recoverable reserves, and are now being analyzed for potential CO₂ EOR and storage applications.

During this study multiple sizes of Winnipegosis Formation pinnacle reef geocellular models were constructed utilizing data from North Dakota Winnipegosis pinnacle reefs wells, cores, and thin sections. These models were then simulated for CO₂ injectivity.

Initial results show that Winnipegosis pinnacle reefs smaller than 1.5 miles in diameter are likely …

Elemental Chemostratigraphy Of The Three Forks Formation, Williston Basin, North Dakota, Brian R. Murphy

Theses and Dissertations

The Three Forks Formation of the Williston Basin in northwestern North Dakota is an Upper Devonian stratigraphic unit unconformably overlain by the Bakken Formation. It consists principally of dolostone, shale and anhydrite. The Three Forks is a productive tight oil resource play, which in recent years has been increasingly targeted and developed as part of the unconventional Bakken Petroleum System. Core analysis via energy dispersive x-ray fluorescence (ED-XRF) is a non-destructive, high-resolution chemostratigraphic data collection method that has been used here to produce concentration logs which reflect both lithologic heterogeneity and paleoredox conditions for the Three Forks Formation. These geochemical …