Physical Sciences and Mathematics Commons^™

A Compartmentalized Approach To The Assembly Of Physical Maps, Serdar Bozdag, Timothy J. Close, Stefano Lonardi

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background: Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint data. Results: We propose a novel compartmentalized method for the assembly of high quality physical maps from fingerprinted clones. The knowledge of genetic markers enables us to group clones into clusters so that clones in the same cluster are more likely to overlap. For each cluster of clones, a local physical map is first …

Dendrites, Topological Graphs, And 2-Dominance, Paul Bankston

Mathematics, Statistics and Computer Science Faculty Research and Publications

For each positive ordinal α, the reflexive and transitive binary relation of α-dominance between compacta was first defined in our paper [Mapping properties of co-existentially closed continua, Houston J. Math., 31 (2005), 1047-1063] using the ultracopower construction. Here we consider the important special case α =2, and show that any Peano compactum 2-dominated by a dendrite is itself a dendrite (with the same being true for topological graphs and trees). We also characterize the topological graphs that 2-dominate arcs (resp., simple closed curves) as those that have cut points of order 2 (resp., those that are not trees).

Corporate Voting, Paul H. Edelman, Robert B. Thompson

Vanderbilt Law School Faculty Publications

Discussion of shareholder voting frequently begins against a background of the democratic expectations and justifications present in decision-making in the public sphere. Directors are assumed to be agents of the shareholders in much the same way that public officers are representatives of citizens. Recent debates about majority voting and shareholder nomination of directors illustrate this pattern. Yet the corporate process differs in significant ways, partly because the market for shares permits a form of intensity voting and lets markets mediate the outcome in a way that would be foreign to the public setting and partly because the shareholders' role is …

A Practical Solution To The Reference Class Problem, Edward K. Cheng

Vanderbilt Law School Faculty Publications

The "reference class problem" is a serious challenge to the use of statistical evidence that arguably arises every day in wide variety of cases, including toxic torts, property valuation, and even drug smuggling. At its core, it observes that statistical inferences depend critically on how people, events, or things are classified. As there is (purportedly) no principle for privileging certain categories over others, statistics become manipulable, undermining the very objectivity and certainty that make statistical evidence valuable and attractive to legal actors. In this paper, I propose a practical solution to the reference class problem by drawing on model selection …

Law, Statistics, And The Reference Class Problem, Edward K. Cheng

Vanderbilt Law School Faculty Publications

Statistical data are powerful, if not crucial, pieces of evidence in the courtroom. Whether one is trying to demonstrate the rarity of a DNA profile, estimate the value of damaged property, or determine the likelihood that a criminal defendant will recidivate, statistics often have an important role to play. Statistics, however, raise a number of serious challenges for the legal system, including concerns that they are difficult to understand, are given too much deference from juries, or are easily manipulated by the parties' experts. In this preview piece, I address one of these challenges, known as the "reference class problem," …

State Of The River Report For The Lower St. Johns River Basin, Florida: Water Quality, Fisheries, Aquatic Life, And Contaminants 2009, Environmental Protection Board, City Of Jacksonville, University Of North Florida, Jacksonville University

State of the River Report

No abstract provided.

Arabidopsis Thaliana Glx2-1 Contains A Dinuclear Metal Binding Site, But Is Not A Glyoxalase 2, Pattraranee Limphong, Michael W. Crowder, Brian Bennett, Christopher A. Makaroff

Physics Faculty Research and Publications

In an effort to probe the structure and function of a predicted mitochondrial glyoxalase 2, GLX2-1, from Arabidopsis thaliana, GLX2-1 was cloned, overexpressed, purified and characterized using metal analyses, kinetics, and UV–visible, EPR, and ¹H-NMR spectroscopies. The purified enzyme was purple and contained substoichiometric amounts of iron and zinc; however, metal-binding studies reveal that GLX2-1 can bind nearly two equivalents of either iron or zinc and that the most stable analogue of GLX2-1 is the iron-containing form. UV–visible spectra of the purified enzyme suggest the presence of Fe(II) in the protein, but the Fe(II) can be oxidized over …

Existence Of Infinitely Many Distinct Solutions To The Quasi-Relativistic Hartree-Fock Equations, Mattias Enstedt, Michael Melgaard

Articles

We establish existence of infinitely many distinct solutions to the semilinear elliptic Hartree-Fock equations for N-electron Coulomb systems with quasirelativistic kinetic energy −α−2Δxn α−4 − α−2 for the nth electron. Moreover, we prove existence of a ground state. The results are valid under the hypotheses that the total charge Ztot of K nuclei is greater than N − 1 and that Ztot is smaller than a critical charge Zc. The proofs are based on a new application of the Fang-Ghoussoub critical point approach to multiple solutions on a noncompact Riemannian manifold, in combination with density operator techniques.

Isolation And Dependency Resolution Of Presentation, Processing And Persistence, Mehrab Monjur

Master's Theses (2009 -)

For business application development it is important to isolate programming efforts of the concerns: Presentation, Processing and Persistence. Development of each of these concerns has an independent thinking process and requires somewhat different programming languages and development tools. In order to isolate the concerns, we provide passages between the concerns and control the flow of execution by following essentially three rules: 1. Presentation and Processing are coroutines, 2. Processing is finished before Presentation can begin to show output, and 3. Persistence is a subsystem of Processing. We explain how these rules come to existence, and what the implications are in …

Antivortex Dynamics In Magnetic Nanostripes, Andrew Kunz, Eric C. Breitbach, Andy J. Smith

Physics Faculty Research and Publications

In a thin magnetic nanostripe, an antivortex nucleates inside a moving domain wall when driven by an in-plane magnetic field greater than the so-called Walker field. The nucleated antivortex must cross the width of the nanostripe before the domain wall can propagate again, leading to low average domain wall speeds. A large out-of-plane magnetic field, applied perpendicularly to the plane of the nanostripe, inhibits the nucleation of the antivortex leading to fast domain wall speeds for all in-plane driving fields. We present micromagnetic simulation results relating the antivortex dynamics to the strength of the out-of-plane field. An asymmetry in the …

Molecular Modeling Of Para-Benzyne And A Series Of Push-Pull [14]-Pyridoannulenes, Evan B. Wang

Honors Theses

Molecular modeling is vital for gaining insight into experimental results and discovering molecular properties not yet characterized by experiment. Depending on the type of molecule under investigation, certain methods will yield more accurate and revealing answers. In the first project, a state-averaged, multireference complete active space (CAS) approach was used for the determination of the vertical excitation energies of valence and Rydberg states of para-benzyne. Orbitals were generated with a 10- and 32-state averaged multiconfigurational self consistent field (MCSCF) approach. Electron correlation was included using multireference configuration interaction with singles and doubles (MR-CISD), including Pople correction for size extensivity (MR-CISD+Q), …

On-Road Motor Vehicle Emissions Including Nh3, So2 And No2, Donald H. Stedman, Gary A. Bishop, Allison Peddle

Fuel Efficiency Automobile Test Publications

No abstract provided.

Molecular Structures And Pulsed Discharge Emission Studies Of Volatile Organic Compound Derivatives, Ashley Osthoff

Masters Theses

No abstract provided.

Electrochemical And Spectroscopic Characterization Of A Polypyridyl Ru(Ii) Complex Containing A Fused Alloxazine, Waynie Wilson Olaprath

Masters Theses

No abstract provided.

Liposomes Recruit Ipac To The Shigella Flexneri Type Iii Secretion Apparatus Needle As A Final Step In Secretion Induction, C. R. Epler, Nicholas E. Dickenson, A. J. Olive, W. L. Picking, W. D. Picking

Chemistry and Biochemistry Faculty Publications

Shigella flexneri contact with enterocytes induces a burst of protein secretion via its type III secretion apparatus (TTSA) as an initial step in cellular invasion. We have previously reported that IpaD is positioned at the TTSA needle tip (M. Espina et al., Infect. Immuno. 74:4391-4400, 2006). From this position, IpaD senses small molecules in the environment to control the presentation of IpaB to the needle tip. This step occurs without type III secretion induction or IpaC recruitment to the S. flexneri surface. IpaC is then transported to the S. flexneri surface when target cell lipids are added, and this event …

Integrated Water Resources Management And Modeling At Multiple Spatial Scales In Jordan, David E. Rosenberg

Civil and Environmental Engineering Faculty Publications

Water shortages from intermittent public supplies are a major and expanding problem in the Hashemite Kingdom of Jordan. Yet individual users, utility managers, and government officials can improve access or cope with shortages in many ways. New supplies, more efficient use of existing resources, long-term investments to expand infrastructure and reduce leakage, and short-term measures to flexibly transfer, ration, or curtail some uses represent several different approaches for management. This paper reviews three separate systems analysis that use stochastic optimization with recourse. Analysis for individual residential users, the water utility serving 2.2 million residents in the capital Amman, and the …

Modeling Integrated Decisions For A Municipal Water System With Recourse And Uncertainties: Amman, Jordan, David E. Rosenberg, Jay Lund

Civil and Environmental Engineering Faculty Publications

Stochastic mixed-integer optimization is used to identify a portfolio of long- and short-term supply and conservation actions for a municipal water system to cost-effectively accommodate a distribution of water shortages. Alternative robust, grey-number, and best/worst case formulations systematically explore implications of uncertainties in action costs, life spans, water volumes gained or saved, shortage levels, and shortage probabilities. A detailed example for Amman, Jordan considers 23 potential actions. Results show: (1) remarkable consistency occurs across the different modeling approaches. (2) Conserving water—reducing leakage and targeting select customers to install water efficient appliances—plays an important and growing role over time. (3) A …

The Effects Of Model Misspecification On Linear Regression Coefficients As Applicable To Solar And Linear Terms, Troy A. Wynn, Vincent B. Wickwar

Reports

Determining atmospheric solar response from data is typically done by fitting a linear model to the data using a least squares approximation. These models typically include a solar proxy that follows the 11 year solar intensity variation, as well as a linear cooling trend. In this paper it is argued that such a regression model is flawed in that the atmospheric solar response might be out of phase with the solar input. And if so, the phase difference between solar input and atmospheric solar response can significantly bias the linear regression coefficient and attenuate the solar coefficient. This result is …

Fault Formation In Porous Sedimentary Rocks At High Strain Rates, Wendy R.O. Key

Canyonlands Research Bibliography

No abstract provided.

Convection: The Likely Source Of The Medium-Scale Gravity Waves Observed In The Oh Airglow Layer Near Brasilia, Brazil, During The Spreadfex Campaign, Sharon L. Vadas, Michael J. Taylor, Pierre-Dominique Pautet, P. A. Stamus, David C. Fritts, H. L. Liu, F. T. São Sabbos, V. T. Batista, H. Takahashi, V. T. Rampinelli

Publications

Six medium-scale gravity waves (GWs) with horizontal wavelengths of λH=60–160 km were detected on four nights by Taylor et al. (2009) in the OH airglow layer near Brasilia, at 15° S, 47° W, during the Spread F Experiment (SpreadFEx) in Brazil in 2005. We reverse and forward ray trace these GWs to the tropopause and into the thermosphere using a ray trace model which includes thermospheric dissipation. We identify the convective plumes, convective clusters, and convective regions which may have generated these GWs. We find that deep convection is the highly likely source of four of these GWs. We pinpoint …

Infinite-Randomness Quantum Critical Points Induced By Dissipation, Thomas Vojta, Chetan Kotabage, Jose A. Hoyos

Physics Faculty Research & Creative Works

We develop a strong-disorder renormalization group to study quantum phase transitions with continuous O(N) symmetry order parameters under the influence of both quenched disorder and dissipation. For Ohmic dissipation, as realized in Hertz's theory of the itinerant antiferromagnetic transition or in the superconductor-metal transition in nanowires, we find the transition to be governed by an exotic infinite-randomness fixed point in the same universality class as the (dissipationless) random transverse-field Ising model. We determine the critical behavior and calculate key observables at the transition and in the associated quantum Griffiths phase. We also briefly discuss the cases of super-Ohmic and sub-Ohmic …

Review: On Quantum Yang-Baxter Coherent Algebra Sheaves, Gizem Karaali

Pomona Faculty Publications and Research

No abstract provided.

Design Of Novel Anticancer Drugs Utilizing Busulfan For Optimizing Pharmacological Properties And Pattern Recognition Techniques For Elucidation Of Clinical Efficacy, Ronald Bartzatt

Chemistry Faculty Publications

Chronic myelogenous leukemia (CML) is a disorder in which an excessive number of blood stem cells develop into the white blood cell group called granulocytes. The anticancer drug Busulfan is a cell cycle non-specific alkylating agent which is utilized to maintain white blood cell counts below 15000 cells/microliter. The side effects induced by busulfan are significant and affirms the intimation for new drug constructs. Fifteen analogous compounds were generated from the molecular structure of busulfan . These compounds retain the double methanesulfonate functional groups descriptive of this class of alkylating anticancer drugs. However, the carbon chain substituent separating the methanesulfonate …

Determination Of Azeotropy, Kyle Cogswell

Undergraduate Journal of Mathematical Modeling: One + Two

The ultimate goal of this paper is the determination of an azeotrope within a methanol-acetone system. An azeotrope is the point in a chemical system at which coexisting compositions of vapor and liquid phases are equal. The importance of this point lies in the fact that azeotropes are undesirable; they prevent one from completely separating a mixture through distillation. This state can occur over a range of temperatures and for the purposes of this paper there is only one azeotrope for each given temperature. All azeotropes occur at relative extrema in pressure. By finding these extrema, we find the mole …

Detecting Edges, Sam Maniscalo

Undergraduate Journal of Mathematical Modeling: One + Two

In human vision the first level of processing is edge detection. Edges are determined by the transitions from dark points to bright points in an image. For this paper, we consider an edge profile model representing a boundary or edge in an image. From this model we can determine the strength of the edge, the width of the edge, and either the transition from dark to bright to dark or the transition from bright to dark to bright. Our first step was to take the given edge profile and determine the type of edge that is represented and the characteristics …

Reconstruction Of Brooksville Ridge Cave Temperatures From Speleothem Samples, Amor Elder

Undergraduate Journal of Mathematical Modeling: One + Two

A problem was proposed to use an adjusted version of Dorale's speleothem delta function to model the temperature fluctuations in the Brooksville Ridge Cave from the Medieval Warm Period to the present. The temperature values reconstructed by the model can be compared to the known temperature trend during the same selected time period. If the results matched the trend, it indicates that the cave's temperature was the dominant influence. If not, a different variable was the main influence of the cave.

Using δ¹⁸O values gathered from a speleothem, past temperatures of the cave were modeled. Results show that …

Arsenic And Growth Of Amphistegina Gibbosa, Elise Keister

Undergraduate Journal of Mathematical Modeling: One + Two

A laboratory tested various concentrations of arsenic on the growth of foraminifera and recorded their findings. Upon examination, the plotted probability density function for each of these trials resembled a similar shape. The plots were then characterized in a general model composed of linear segments. Using calculus, statistics such as the expected value, variance and standard deviation were calculated to interpret the collected data. The statistics revealed that arsenic limits the growth of ocean life.

Robotics Potential Fields, Jordi Lucero

Undergraduate Journal of Mathematical Modeling: One + Two

This problem was to calculate the path a robot would take to navigate an obstacle field and get to its goal. Three obstacles were given as negative potential fields which the robot avoided, and a goal was given a positive potential field that attracted the robot. The robot decided each step based on its distance, angle, and influence from every object. After each step, the robot recalculated and determined its next step until it reached its goal. The robot's calculations and steps were simulated with Microsoft Excel.

Calculating Power Of A Co2 Compressor, Jennifer Wedebrock

Undergraduate Journal of Mathematical Modeling: One + Two

In this project the goal is to find the power of a CO₂ compressor used in a process of storing CO₂ underground. Although the compressor is not 100% efficient and does not exist under ideal conditions, the power can first be calculated as if it were under ideal conditions by calculating its enthalpy and entropy. Residual terms are then added to both the enthalpy and the entropy to account for the behavior of CO₂ under non-ideal conditions. Since the sum of the change in entropy under ideal conditions and the residual terms for entropy is zero, a …

Call Forecasting For Inbound Call Center, Peter Vinje

Undergraduate Journal of Mathematical Modeling: One + Two

In a scenario of inbound call center customer service, the ability to forecast calls is a key element and advantage. By forecasting the correct number of calls a company can predict staffing needs, meet service level requirements, improve customer satisfaction, and benefit from many other optimizations. This project will show how elementary statistics can be used to predict calls for a specific company, forecast the rate at which calls are increasing/decreasing, and determine if the calls may stop at some point.