Physical Sciences and Mathematics Commons^™

Refactoring Tools: Fitness For Purpose, Emerson Murphy-Hill, Andrew P. Black

Computer Science Faculty Publications and Presentations

Refactoring tools can improve the speed and accuracy with which we create and maintain software -- but only if they are used. In practice, tools are not used as much as they could be: this seems to be because sometimes they do not align with the refactoring tactic preferred by the majority of programmers, a tactic we call floss refactoring. We propose five principles that characterize successful floss refactoring tools -- principles that can help programmers to choose the most appropriate refactoring tools and also help toolsmiths to design tools that fit the programmer's purpose.

The Cis-Δ2,3-Double Bond Of Phoslactomycins Is Generated By A Post-Pks Tailoring Enzyme, Nadaraj Palaniappan, Mamoun M. Alhamadsheh, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

The antifungal phoslactomycins (PLM A-F), produced by Streptomyes sp HK803, are structurally unusual in that three of their four double bonds are in the cis form (Δ^12,13, Δ^14,15, Δ^2,3). The PLM polyketide synthase (PKS) has the predicted dehydratase catalytic domain in modules 1,2 and 5 required for establishing two of these cis double bonds (Δ^12,13Δ^14,15), as well as the only trans Δ^6,7double bond. By contrast, the formation of the cis Δ^2,3 in the unsaturated lactone moiety of PLMs has presented an enigma because the predicted dehydratase domain …

Traffic Analysis Of Udp-Based Flows In Ourmon, Jim Binkley, Divya Parekh

Computer Science Faculty Publications and Presentations

We present a custom UDP flow tuple with an IP address key and a set of simple related statistical attributes. Attributes are used to calculate a per host metric called the UDP work weight which roughly measures the amount of network noise caused by a host. The work weight is used to produce a near real-time sorted top N report for UDP host tuples. We also present a derived attribute based on an algorithm called the UDP guesstimator. The UDP guesstimator roughly classifies port report hosts into various traffic categories including security threats (DOS/scanning) or P2P hosts based on high …

Reconstructing Images As Piecewise Smooth Functions, Ralf Juengling

Computer Science Faculty Publications and Presentations

Leclerc’s approach to image reconstruction consists of finding the shortest description of the data (an image) as a model (reconstruction) plus noise [5]. The approach poses two design problems: 1. Define an appropriate description language for image models and noise, 2. Derive an objective function and conceive an optimization algorithm that finds good local minima. Leclerc proposed to model images as piecewise low order polynomials and to describe models in terms of region boundaries (discontinuity set) and polynomial coefficients.

In this report I describe Leclerc’s methodology, and, adopting his image model and description language, derive an objective function within this …

An Embarrassment Of Riches: The Enzymology Of Rna Modification, Dirk Iwata-Reuyl

Chemistry Faculty Publications and Presentations

The maturation of transfer RNA (tRNA) involves extensive chemical modification of the constituent nucleosides and results in the introduction of significant chemical diversity to tRNA. Many of the pathways to these modified nucleosides are characterized by chemically complex transformations, some of which are unprecedented in other areas of biology. To illustrate the scope of the field, recent progress in understanding the enzymology leading to the formation of two distinct classes of modified nucleosides, the thiouridines and queuosine, a 7-deazaguanosine, is reviewed. In particular, recent data validating the involvement of several proposed intermediates in the formation of thiouridines are discussed, including …

Patterns Of Aspect-Oriented Design, Black P. Andrew, James Noble, David J. Pearce, Arno Scmidmeir

Computer Science Faculty Publications and Presentations

Aspect-oriented programming languages are becoming commonplace, and programmers are accumulating experience in building and maintaining aspect-oriented systems. This paper addresses how the use of these languages affects program design: how aspect-oriented languages change the design space, which designs should be emulated and which avoided, and the strengths and weaknesses of particular kinds of design. We identify five patterns of aspect-oriented design: Spectator, Regulator, Patch, Extension, and Heterarchical Design. For each pattern, we describe the problem it solves, show how aspect-oriented language features are used in the pattern, give characteristic examples of the pattern’s use, and assess its benefits and liabilities. …

Electrical Detection Of The Temperature Induced Melting Transition Of A Dna Hairpin Covalently Attached To Gold Interdigitated Microelectrodes, Greg P. Brewood, Yaswanth Rangineni, Daniel J. Fish, Ashwini Bhandiwad, David R. Evans, Raj Solanki, Albert S. Benight

Chemistry Faculty Publications and Presentations

The temperature induced melting transition of a self-complementary DNA strand covalently attached at the 5' end to the surface of a gold interdigitated microelectrode (GIME) was monitored in a novel, label-free, manner. The structural state of the hairpin was assessed by measuring four different electronic properties of the GIME (capacitance, impedance, dissipation factor and phase angle) as a function of temperature from 25 degrees C to 80 degrees C. Consistent changes in all four electronic properties of the GIME were observed over this temperature range, and attributed to the transition of the attached single-stranded DNA (ssDNA) from an intramolecular, folded …

Chiral Recognition Of Amino Acids By Use Of A Fluorescent Resorcinarene, Gerald I. Richard, Hadi M. Marwani, Shan Jiang, Sayo O. Fakayode, Mark Lowry, Robert M. Strongin, Isiah M. Warner

Chemistry Faculty Publications and Presentations

The spectroscopic properties of a chiral boronic acid based resorcinarene macrocycle employed for chiral analysis were investigated. Specifically, the emission and excitation characteristics of tetraarylboronate resorcinarene macrocycle (TBRM) and its quantum yield were evaluated. The chiral selector TBRM was investigated as a chiral reagent for the enantiomeric discrimination of amino acids using steady-state fluorescence spectroscopy. Chiral recognition of amino acids in the presence of the macrocycle was based on diastereomeric complexes. Results demonstrated that TBRM had better chiral discrimination ability for lysine as compared to the other amino acids. Partial least squares regression modeling (PLS-1) of spectral data for macrocycle-lysine …

Unsymmetric Aryl–Alkyl Disulfide Growth Inhibitors Of Methicillin-Resistant Staphylococcus Aureus And Bacillus Anthracis, Edward Turos, Kevin D. Revell, Praveen Ramaraju, Danielle A. Gergeres, Kerriann Greenhalgh, Ashley Young, Nalini Sathyanarayan, Sonja Dickey, Daniel Lim, Mamoun M. Alhamadsheh, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

This study describes the antibacterial properties of synthetically-produced mixed aryl alkyl disulfide compounds as a means to control the growth of Staphylococcus aureus and Bacillus anthracis. Some of these compounds exerted strong in vitro bioactivity. Our results indicate that among the twelve different aryl substituents examined, nitrophenyl derivatives provide the strongest antibiotic activities. This may be the result of electronic activation of the arylthio moiety as a leaving group for nucleophilic attack on the disulfide bond. Small alkyl residues on the other sulfur provide the best activity as well, which for different bacteria appears to be somewhat dependent on …

Synthesis And Characterization Of Novel Chiral Ionic Liquids And Investigation Of Their Enantiomeric Recognition Properties, David K. Bwambok, Hadi M. Marwani, Vivian E. Fernand, Sayo O. Fakayode, Mark Lowry, Ioan Negulescu, Robert M. Strongin, Isiah M. Warner

Chemistry Faculty Publications and Presentations

We report the synthesis and characterization of amino acid ester based chiral ionic liquids, derived from L- and D-alanine tert butyl ester chloride. The synthesis was accomplished via an anion metathesis reaction between commercially available L- and D-alanine tert butyl ester chloride using a variety of counterions such as lithium bis (trifluoromethane) sulfonimide, silver nitrate, silver lactate, and silver tetrafluoroborate. Both enantiomeric forms were obtained as confirmed by bands of opposite sign in the circular dichroism spectra. The L- and D-alanine tert butyl ester bis (trifluoromethane) sulfonimide were obtained as liquids at room temperature and intriguingly exhibited the highest thermal …

Multigrid Convergence For Second Order Elliptic Problems With Smooth Complex Coefficients, Jay Gopalakrishnan, Joseph E. Pasciak

Mathematics and Statistics Faculty Publications and Presentations

The finite element method when applied to a second order partial differential equation in divergence form can generate operators that are neither Hermitian nor definite when the coefficient function is complex valued. For such problems, under a uniqueness assumption, we prove the continuous dependence of the exact solution and its finite element approximations on data provided that the coefficients are smooth and uniformly bounded away from zero. Then we show that a multigrid algorithm converges once the coarse mesh size is smaller than some fixed number, providing an efficient solver for computing discrete approximations. Numerical experiments, while confirming the theory, …

Polynomial Extension Operators. Part I, Leszek Demkowicz, Jay Gopalakrishnan, Joachim Schöberl

Mathematics and Statistics Faculty Publications and Presentations

In this series of papers, we construct operators that extend certain given functions on the boundary of a tetrahedron into the interior of the tetrahedron, with continuity properties in appropriate Sobolev norms. These extensions are novel in that they have certain polynomial preservation properties important in the analysis of high order finite elements. This part of the series is devoted to introducing our new technique for constructing the extensions, and its application to the case of polynomial extensions from H^½(∂K) into H¹(K), for any tetrahedron K.

A Mixed Method For Axisymmetric Div-Curl Systems, Dylan M. Copeland, Jay Gopalakrishnan, Joseph E. Pasciak

Mathematics and Statistics Faculty Publications and Presentations

We present a mixed method for a three-dimensional axisymmetric div-curl system reduced to a two-dimensional computational domain via cylindrical coordinates. We show that when the meridian axisymmetric Maxwell problem is approximated by a mixed method using the lowest order Nédélec elements (for the vector variable) and linear elements (for the Lagrange multiplier), one obtains optimal error estimates in certain weighted Sobolev norms. The main ingredient of the analysis is a sequence of projectors in the weighted norms satisfying some commutativity properties.

Quantifying Twentieth Century Glacier Change In The Sierra Nevada, California, Hassan J. Basagic

Dissertations and Theses

Numerous small alpine glaciers occupy the high elevation regions of the central and southern Siena Nevada, California. These glaciers change size in response to variations in climate and are therefore important indicators of climate change. An inventory based on USGS topographic maps (l :24,000) revealed 1719 glaciers and perennial snow and ice features for a total area of 39.l5 ±7.52 km². The number of 'true' glaciers, versus non-moving ice, is estimated to be 118, covering 15.87 ± 1.69 Km². All glaciers were located on north to northeast aspects, at elevations >3000 m. Historical photographs, geologic evidence, …