Physical Sciences and Mathematics Commons^™

Long-Range Pcr Amplification Of Dna By Dna Polymerase Iii Holoenzyme From Thermus Thermophilus, Wendy Ribble, Shawn D. Kane, James M. Bullard

Chemistry Faculty Publications and Presentations

DNA replication in bacteria is accomplished by a multicomponent replicase, the DNA polymerase III holoenzyme (pol III HE). The three essential components of the pol III HE are the α polymerase, the β sliding clamp processivity factor, and the DnaX clamp-loader complex. We report here the assembly of the functional holoenzyme from Thermus thermophilus (Tth), an extreme thermophile. The minimal holoenzyme capable of DNA synthesis consists of α, β and DnaX ( and γ), and components of the clamp-loader complex. The proteins were each cloned and expressed in a native form. Each component of the system was purified extensively. The …

Gamma-Radiation Induced Redox Reactions And Colloidal Formation Of Chromium And Cobalt Oxide Nanoparticles, Leena M. Alrehaily

Electronic Thesis and Dissertation Repository

The main goal of this thesis research is to develop a mechanistic understanding of radiation-induced chromium oxide and cobalt oxide nanoparticle formation in aqueous solutions containing initially dissolved metal ions. When exposed to ionizing radiation, water decomposes to form a range of chemically reactive radical and molecular products. This redox agents can readily change the oxidation state of dissolved metal ions. The solubility of a transition metal ion can vary by several orders of magnitude depending on its oxidation state and the solution pH. Thus, reactions that can alter the oxidation state of a dissolved ion can lead to the …

Use Of Research Aircraft Data To Validate Mesoscale Model Forecasts, Travis Swaggerty, Melanie Wetzel, Dorothea Ivanova

Aviation / Aeronautics / Aerospace International Research Conference

A NSF funded Student Training in Airborne Research and Technology (START) two-week deployment of the University of Wyoming King Air (UWKA) research aircraft was conducted at Embry-Riddle Aeronautical University (ERAU) in Prescott, Arizona during late March and early April 2014. Some of the goals of this program were to build knowledge on airborne atmospheric research for undergraduate students across multiple departments and to collect a valuable set of aircraft data for atmospheric model validation. Data collection for 10 research flights is available for mesoscale model case study validation.

This project utilizes the Weather Research and Forecasting mesoscale model (WRF), version …

Improvement In Pilot Training For Aircraft Icing Conditions, Cody Denver, Melanie A. Wetzel

Aviation / Aeronautics / Aerospace International Research Conference

One of the most dangerous atmospheric hazards in aviation is aircraft icing. Ice can build on aircraft surfaces, causing decreases in thrust and lift while increasing drag and weight. These effects can be detrimental to any aircraft's ability to successfully remain in flight. Improvement in pilot knowledge of and response to icing conditions can be attained through use of specific meteorological forecast products, completion of interactive training modules, and understanding of cloud physical processes gained through the analysis of aircraft measurement case studies. This poster presents a strategy for enhancing the training of professional pilots in meteorological conditions which cause …

Microcontrollers In The Aviation Classroom, Padraig Houlahan

Aviation / Aeronautics / Aerospace International Research Conference

Modern commercial aircraft are increasingly dependent on digital technologies that detect sensor data and pilot control movements, interpret them, and then issue appropriate control signals to remote motors that move control surfaces. Because such technologies are innately complex, it would appear there is an unacceptably large academic burden on introducing them into the undergraduate pilot's curriculum .

However, in recent years there has been an explosion of interest in using micro-controllers in academic teaching (high-school and undergraduate levels) and in hobby applications, resulting in a large, online, freely available knowledgebase of techniques and solutions. Here, I demonstrate how easy it …

Aviation Security Impacts Of Meteorological And Climatic Disruption, Melanie Wetzel

Aviation / Aeronautics / Aerospace International Research Conference

Commercial and military flight operations are frequently imperiled or disrupted by meteorological conditions. Severe weather events and climate-related factors create aviation security impacts on airport siting and reliability, human safety, economic stability, military defense strategy, aircraft routing and computer systems vulnerability. Climate trends have been associated with increased frequency of storm surge incursions at coastal airports, intense snowfall accumulations, runway closures due to rainstorm runoff, extended periods of fog/stratus restrictions and severe-weather related risk from lightning, hail and icing. The economic and safety impacts of these events are being incorporated into long-term planning by the U.S. Department of Defense (DoD), …

Statistical Variation Of Diverse Light Emission Measurements From Bisphenol/Amine Epoxy Under Energetic Electron Bombardment, Justin Christensen

Physics Capstone Projects

Dielectric materials subjected to energetic electron fluxes can emit light in several forms. We have observed three distinct types of emissions: (i) short-duration (<1 ms), high-intensity electrostatic discharge (ESD) or “arc” events; (ii) intermediate-duration, high-intensity events which begin with a bright arc followed by an exponential decay of intensity (~10 to 100 s decay constant), termed “flares”; and (iii) long-duration, low-intensity emission, or cathodoluminescence, that continues as long as the electron flux is on. These events were studied for bulk samples of bisphenol/amine epoxy, using an electron gun with varying current densities (0.3 to 5 nA/cm2) and energies (12 to 40 keV) in a high vacuum chamber. Light emitted from the samples was measured with a high-sensitivity visible to near-infrared video camera. Results of the spatial and temporal extent for each type of event are presented as well as a discussion of how absolute spectral radiance and rates for each type of event are dependent on incident electron current density, energy, and power density and on material type, temperature, and thickness. Applications of this research to spacecraft charging and light emissions are discussed.

Statistical Variation Of Diverse Light Emission Measurements From Bisphenol/Amine Epoxy Under Energetic Electron Bombardment, Justin Christensen

Senior Theses and Projects

No abstract provided.

On Static And Dynamic Partitioning Behavior Of Large-Scale Networks, Zhongmei Yao, Derek Leonard, Xiaoming Wang, Dmitri Loguinov

Zhongmei Yao

In this paper, we analyze the problem of network disconnection in the context of large-scale P2P networks and understand how both static and dynamic patterns of node failure affect the resilience of such graphs. We start by applying classical results from random graph theory to show that a large variety of deterministic and random P2P graphs almost surely (i.e., with probability 1 − o(1)) remain connected under random failure if and only if they have no isolated nodes. This simple, yet powerful, result subsequently allows us to derive in closed-form the probability that a P2P network develops isolated nodes, and …

Residual-Based Measurement Of Peer And Link Lifetimes In Gnutella Networks, Xiaoming Wang, Zhongmei Yao, Dmitri Loguinov

Zhongmei Yao

Existing methods of measuring lifetimes in P2P systems usually rely on the so-called create-based method (CBM), which divides a given observation window into two halves and samples users "created" in the first half every Delta time units until they die or the observation period ends. Despite its frequent use, this approach has no rigorous accuracy or overhead analysis in the literature. To shed more light on its performance, we flrst derive a model for CBM and show that small window size or large Delta may lead to highly inaccurate lifetime distributions. We then show that create-based sampling exhibits an inherent …

On Node Isolation Under Churn In Unstructured P2p Networks With Heavy-Tailed Lifetimes, Zhongmei Yao, Xiaoming Wang, Dmitri Loguinov

Zhongmei Yao

Previous analytical studies [12], [18] of unstructured P2P resilience have assumed exponential user lifetimes and only considered age-independent neighbor replacement. In this paper, we overcome these limitations by introducing a general node-isolation model for heavy-tailed user lifetimes and arbitrary neighbor-selection algorithms. Using this model, we analyze two age-biased neighbor-selection strategies and show that they significantly improve the residual lifetimes of chosen users, which dramatically reduces the probability of user isolation and graph partitioning compared to uniform selection of neighbors. In fact, the second strategy based on random walks on age-weighted graphs demonstrates that for lifetimes with infinite variance, the system …

Modeling Heterogeneous User Churn And Local Resilience Of Unstructured P2p Networks, Zhongmei Yao, Derek Leonard, Dmitri Loguinov, Xiaoming Wang

Zhongmei Yao

Previous analytical results on the resilience of unstructured P2P systems have not explicitly modeled heterogeneity of user churn (i.e., difference in online behavior) or the impact of in-degree on system resilience. To overcome these limitations, we introduce a generic model of heterogeneous user churn, derive the distribution of the various metrics observed in prior experimental studies (e.g., lifetime distribution of joining users, joint distribution of session time of alive peers, and residual lifetime of a randomly selected user), derive several closed-form results on the transient behavior of in-degree, and eventually obtain the joint in/out degree isolation probability as a simple …

Link Lifetimes And Randomized Neighbor Selection In Dhts, Zhongmei Yao, Dmitri Loguinov

Zhongmei Yao

Several models of user churn, resilience, and link lifetime have recently appeared in the literature [12], [13], [34], [35]; however, these results do not directly apply to classical Distributed Hash Tables (DHTs) in which neighbor replacement occurs not only when current users die, but also when new user arrive into the system, and where replacement choices are often restricted to the successor of the failed zone in the DHT space. To understand neighbor churn in such networks, this paper proposes a simple, yet accurate, model for capturing link dynamics in structured P2P systems and obtains the distribution of link lifetimes …

Residual-Based Estimation Of Peer And Link Lifetimes In P2p Networks, Xiaoming Wang, Zhongmei Yao, Dmitri Loguinov

Zhongmei Yao

Existing methods of measuring lifetimes in P2P systems usually rely on the so-called Create-BasedMethod (CBM), which divides a given observation window into two halves and samples users ldquocreatedrdquo in the first half every Delta time units until they die or the observation period ends. Despite its frequent use, this approach has no rigorous accuracy or overhead analysis in the literature. To shed more light on its performance, we first derive a model for CBM and show that small window size or large Delta may lead to highly inaccurate lifetime distributions. We then show that create-based sampling exhibits an inherent tradeoff …

Robust Lifetime Measurement In Large-Scale P2p Systems With Non-Stationary Arrivals, Xiaoming Wang, Zhongmei Yao, Yueping Zhang, Dmitri Loguinov

Zhongmei Yao

Characterizing user churn has become an important topic in studying P2P networks, both in theoretical analysis and system design. Recent work has shown that direct sampling of user lifetimes may lead to certain bias (arising from missed peers and round-off inconsistencies) and proposed a technique that estimates lifetimes based on sampled residuals. In this paper, however, we show that under non-stationary arrivals, which are often present in real systems, residual-based sampling does not correctly reconstruct user lifetimes and suffers a varying degree of bias, which in some cases makes estimation completely impossible. We overcome this problem using two contributions: a …

Stochastic Analysis Of Horizontal Ip Scanning, Derek Leonard, Zhongmei Yao, Xiaoming Wang, Dmitri Loguinov

Zhongmei Yao

Intrusion Detection Systems (IDS) have become ubiquitous in the defense against virus outbreaks, malicious exploits of OS vulnerabilities, and botnet proliferation. As attackers frequently rely on host scanning for reconnaissance leading to penetration, IDS is often tasked with detecting scans and preventing them. However, it is currently unknown how likely an IDS is to detect a given Internet-wide scan pattern and whether there exist sufficiently fast scan techniques that can remain virtually undetectable at large-scale. To address these questions, we propose a simple analytical model for the window-expiration rules of popular IDS tools (i.e., Snort and Bro) and utilize a …

In-Degree Dynamics Of Large-Scale P2p Systems, Zhongmei Yao, Daren B. H. Cline, Dmitri Loguinov

Zhongmei Yao

This paper builds a complete modeling framework for understanding user churn and in-degree dynamics in unstructured P2P systems in which each user can be viewed as a stationary alternating renewal process. While the classical Poisson result on the superposition of n stationary renewal processes for n→∞ requires that each point process become sparser as n increases, it is often difficult to rigorously show this condition in practice. In this paper, we first prove that despite user heterogeneity and non-Poisson arrival dynamics, a superposition of edge-arrival processes to a live user under uniform selection converges to a Poisson process when …

Automatically Discovering The Number Of Clusters In Web Page Datasets, Zhongmei Yao

Zhongmei Yao

Clustering is well-suited for Web mining by automatically organizing Web pages into categories, each of which contains Web pages having similar contents. However, one problem in clustering is the lack of general methods to automatically determine the number of categories or clusters. For the Web domain in particular, currently there is no such method suitable for Web page clustering. In an attempt to address this problem, we discover a constant factor that characterizes the Web domain, based on which we propose a new method for automatically determining the number of clusters in Web page data sets. We discover that the …

Node Isolation Model And Age-Based Neighbor Selection In Unstructured P2p Networks, Zhongmei Yao, Derek Leonard, Dmitri Loguinov

Zhongmei Yao

Previous analytical studies of unstructured P2P resilience have assumed exponential user lifetimes and only considered age-independent neighbor replacement. In this paper, we overcome these limitations by introducing a general node-isolation model for heavy-tailed user lifetimes and arbitrary neighbor-selection algorithms. Using this model, we analyze two age-biased neighbor-selection strategies and show that they significantly improve the residual lifetimes of chosen users, which dramatically reduces the probability of user isolation and graph partitioning compared with uniform selection of neighbors. In fact, the second strategy based on random walks on age-proportional graphs demonstrates that, for lifetimes with infinite variance, the system monotonically increases …

Λλ Correlation Function In Au+Au Collisions At √SNn=200  Gev, J. Kevin Adkins, Renee Fatemi, Suvarna Ramachandran, L. Adamczyk, G. Agakishiev, M. M. Aggarwal, Z. Ahammed, I. Alekseev, J. Alford, C. D. Anson, A. Aparin, D. Arkhipkin, E. C. Aschenauer

Physics and Astronomy Faculty Publications

We present ΛΛ correlation measurements in heavy-ion collisions for Au+Au collisions at √^S_NN=200  GeV using the STAR experiment at the Relativistic Heavy-Ion Collider. The Lednický-Lyuboshitz analytical model has been used to fit the data to obtain a source size, a scattering length and an effective range. Implications of the measurement of the ΛΛ correlation function and interaction parameters for dihyperon searches are discussed.

Probing The Inverted Classroom: A Study Of Teaching And Learning Outcomes In Engineering And Mathematics, Nancy K. Lape, Rachel Levy, Darryl Yong

All HMC Faculty Publications and Research

Flipped classrooms have started to become commonplace on university campuses. Despite the growing number of flipped courses, however, quantitative information on their effectiveness remains sparse. Active learning is a mode of instruction that focuses the responsibility of learning on learners. Multiple studies have shown that active learning leads to better student outcomes. Given that instructors in flipped classrooms are generally able to create more opportunities for students to apply or practice course material, we hypothesized that students in a flipped classroom would exhibit more learning compared to students in an unflipped class. This case study describes our research comparing …

Identification And Characterization Of N-Acyltransferase Enzymes That Are Involved In The Biosynthesis Of Fatty Acid Amides, Daniel Robert Dempsey

USF Tampa Graduate Theses and Dissertations

Fatty acid amides are an emerging family of bioactive lipids that consists of N-acylethanolamines, N-acylarylalkylamides, N-acylglycines, N-acyl amino acids, N-monoacylpolyamides, and primary fatty acid amides. Short chain fatty acid amides are products of inactivated biogenic amines such as dopamine, histamine, octopamine, and serotonin, whereas long chain fatty acid amides have been implicated in a number of physiological process such as the perception and inhibition of chronic pain through binding to their specific receptors. The most famous; therefore, the most studied long chain fatty acid amide is anandamide or also known as N-arachidonylethanolamine. The biosynthesis …

Multiple-Time Step Ab Initio Molecular Dynamics Based On Two-Electron Integral Screening, Shervin Fatehi, Ryan P. Steele

Chemistry Faculty Publications and Presentations

A multiple-timestep ab initio molecular dynamics scheme based on varying the two-electron integral screening method used in Hartree–Fock or density functional theory calculations is presented. Although screening is motivated by numerical considerations, it is also related to separations in the length- and timescales characterizing forces in a molecular system: Loose thresholds are sufficient to describe fast motions over short distances, while tight thresholds may be employed for larger length scales and longer times, leading to a practical acceleration of ab initio molecular dynamics simulations. Standard screening approaches can lead, however, to significant discontinuities in (and inconsistencies between) the energy and …

Web Conferencing For Business, David Laratta, Yves Mekongo

Mathematics and Computer Science Capstones

Many companies are investing to offer their workforce the best collaboration and web conferencing products they can afford. Many Information Technology scholars believe that efficient collaboration technologies for all are no longer a nice to have but a must have (M2 Presswire, 2014). To that effect, there is a dilemma many corporations and leaders face today when it comes to online collaboration and in which products to invest; Wayne Mayson cited above, claims that many leaders are failing to exploit mobile communications and collaboration tools despite their emergence and their growing accessibility in the market place. The results from this …

Some Covariance Inequalities For Non-Monotonic Functions With Applications To Mean-Variance Indiference Curves And Bank Hedging, Martin Egozcue

Martin Egozcue

No abstract provided.

Applying Multiple Imputation For External Calibration To Propensty Score Analysis, Yenny Webb-Vargas, Kara E. Rudolph, D. Lenis, Peter Murakami, Elizabeth A. Stuart

Johns Hopkins University, Dept. of Biostatistics Working Papers

Although covariate measurement error is likely the norm rather than the exception, methods for handling covariate measurement error in propensity score methods have not been widely investigated. We consider a multiple imputation-based approach that uses an external calibration sample with information on the true and mismeasured covariates, Multiple Imputation for External Calibration (MI-EC), to correct for the measurement error, and investigate its performance using simulation studies. As expected, using the covariate measured with error leads to bias in the treatment effect estimate. In contrast, the MI-EC method can eliminate almost all the bias. We confirm that the outcome must be …

Estimation Of Daily Air Temperature Based On Modis Land Surface Temperature Products Over The Corn Belt In The Us, Linglin Zeng, Brian D. Wardlow, Tsegaye Tadesse, Jie Shan, Michael J. Hayes, Deren Li, Daxiang Xiang

Drought Mitigation Center: Faculty Publications

Air temperature (Ta) is a key input in a wide range of agroclimatic applications. Moderate Resolution Imaging Spectroradiometer (MODIS) Ts (Land Surface Temperature (LST)) products are widely used to estimate daily Ta. However, only daytime LST (Ts-day) or nighttime LST (Ts-night) data have been used to estimate Tmax/Tmin (daily maximum or minimum air temperature), respectively. The relationship between Tmax and Ts-night, and the one between Tmin and Ts-day has not been studied. In this study, both the ability of Ts-night data to estimate Tmax and the ability of Ts-day data to estimate Tmin were tested and studied in the Corn …

Peat Formation Concentrates Arsenic Within Sediment Deposits Of The Mekong Delta, Jason W. Stuckey, Michael V. Schaefer, Benjamin D. Kocar, Jessica Dittmar, Juan Lezama Pacheco, Shawn G. Benner, Scott Fendorf

Geosciences Faculty Publications and Presentations

Mekong River Delta sediment bears arsenic that is released to groundwater under anaerobic conditions over the past several thousand years. The oxidation state, speciation, and distribution of arsenic and the associated iron bearing phases are crucial determinants of As reactivity in sediments. Peat from buried mangrove swamps in particular may be an important host, source, or sink of arsenic in the Mekong Delta. The total concentration, speciation, and reactivity of arsenic and iron were examined in sediments in a Mekong Delta wetland by X-ray fluorescence spectrometry (XRF), X-ray absorption spectroscopy (XAS), and selective chemical extractions. Total solid-phase arsenic concentrations in …

Nodal To Nodeless Superconducting Energy-Gap Structure Change Concomitant With Fermi-Surface Reconstruction In The Heavy-Fermion Compound Cecoin₅, Hyunsoo Kim, M. A. Tanatar, R. Flint, C. Petrovic, Rongwei Hu, B. D. White, I. K. Lum, M. B. Maple, R. Prozorov

Physics Faculty Research & Creative Works

The London penetration depth λ(T) was measured in single crystals of Ce_1-xR_xCoIn₅, R = La, Nd, and Yb down to T_min ≈ 50mK (T_c/T_min ∼ 50) using a tunnel-diode resonator. In the cleanest samples Δλ(T) is best described by the power law Δλ(T) α Tⁿ, with n ∼ 1, consistent with the existence of line nodes in the superconducting gap. Substitutions of Ce with La, Nd, and Yb lead to similar monotonic suppressions of Tc; however, the effects on Δλ(T) differ. While La and Nd substitution leads to …

Estimation Of Daily Air Temperature Based On Modis Land Surface Temperature Products Over The Corn Belt In The Us, Linglin Zeng, Brian D. Wardlow, Tsegaye Tadesse, Jie Shan, Michael Hayes, Deren Li, Daxiang Xiang

Drought Mitigation Center: Faculty Publications

Air temperature (Ta) is a key input in a wide range of agroclimatic applications. Moderate Resolution Imaging Spectroradiometer (MODIS) Ts (Land Surface Temperature (LST)) products are widely used to estimate daily Ta. However, only daytime LST (Ts-day) or nighttime LST (Ts-night) data have been used to estimate Tmax/Tmin (daily maximum or minimum air temperature), respectively. The relationship between Tmax and Ts-night, and the one between Tmin and Ts-day has not been studied. In this study, both the ability of Ts-night data to estimate Tmax and the ability of Ts-day data to estimate Tmin were tested and studied in the Corn …