Physical Sciences and Mathematics Commons^™

Modeling Correlated Main-Chain Motions In Proteins For Flexible Molecular Recognition., Maria Zavodsky, Ming Lei, M. Thorpe, Anthony Day, Leslie Kuhn

Anthony Roy Day

We describe a new method for modeling protein and ligand main-chain flexibility, and show its ability to model flexible molecular recognition. The goal is to sample the full conformational space, including large-scale motions that typically cannot be reached in molecular dynamics simulations due to the computational intensity, as well as conformations that have not been observed yet by crystallography or NMR. A secondary goal is to assess the degree of flexibility consistent with protein–ligand recognition. Flexibility analysis of the target protein is performed using the graph-theoretic algorithm FIRST, which also identifies coupled networks of covalent and noncovalent bonds within the …

An Entrepreneur's Dilemma : To Swot Or Not To Swot, A. Desai Chaanakya, Arcot Desai Narasimhalu

Arcot Desai NARASIMHALU

This work presents an updated and revised model for evaluating companies using a 'snapshot' analysis. Historically, the SWOT model has been the preferred analysis tool, but with an increasing number of entrepreneurs faced with a non-mature market, a new tool must be developed for accurate analysis.

Knowledge Discovery From Multispectral Satellite Images, Arun D. Kulkarni

Arun Kulkarni

Wavelet Estimation Of Partially Linear Models, Xiao-Wen Chang, Leming Qu

Leming Qu

A wavelet approach is presented for estimating a partially linear model (PLM). We find an estimator of the PLM by minimizing the square of the l₂ norm of the residual vector while penalizing the l₁ norm of the wavelet coefficients of the nonparametric component. This approach, an extension of the wavelet approach for nonparametric regression problems, avoids the restrictive smoothness requirements for the nonparametric function of the traditional smoothing approaches for PLM, such as smoothing spline, kernel and piecewise polynomial methods. To solve the optimization problem, an efficient descent algorithm with an exact line search is presented. Simulation …

Constraining The Exhumation And Burial History Of The Safod Pilot Hole With Apatite Fission Track And (U-Th)/He Thermochronometry, Ann Blythe, M D’Alessio, R Bürgmann

Ann Blythe

[1] The San Andreas Fault Observatory at Depth (SAFOD) pilot hole traverses the upper 2 km of a site 1.8 km west of the San Andreas fault (SAF) near Parkfield, California. In order to evaluate the burial and exhumation history of the site and its relationship to the kinematics and mechanics of the SAF, we use 15 apatite fission-track (FT) and 5 (U-Th)/He analyses from pilot hole samples to document their thermal history. Sample ages decrease with depth: FT and (U-Th)/He ages range from ∼60 and ∼31 Ma, respectively, in the upper 800 m of the hole to ∼3 and …

Investigation Of New Chelation Ion Chromatography Procedure To Determine The Surface Composition Of Powdered Metal Oxide Samples In The Solid State., B. Peebles, Michael Setter

Michael P. Setter

Numerous tests have been conducted on the feasibility of characterizing the surfaces of metal oxide powders using HPLC. An in-line filter housing was modified to serve as a sample chamber to replace the sample loop. A gradient pump was used to gradually increase eluent acidity to find the conditions at which the surface of a metal oxide powder began to dissolve. The theoretical masses of surface monolayers of metal oxide powders were compared with the experimentally determined masses of dissolved material thought to be from the surface to test whether surface and bulk dissolution phenomena in acidic conditions are separable …

Waiting To Inhale: The Demographics Of Toxic Air Release Facilities In 21st-Century California, Manuel Pastor, James Sadd, Rachel Morello-Frosch

James Sadd

We examine the spatial distribution of toxic air releases and residential demographics in California using 2000 Census data and coeval information from the Federal Toxic Release Inventory for evidence of disproportionate exposure. Methods. We use spatial analysis using GIS, and multivariate regression analysis, including ordered and multinomial logit regressions, in our study. Results. Analytical results suggest a pattern of disproportionate exposure based on race, with the disparity most severe for Latinos, which holds in a series of multivariate regressions, including attempts to test for varying levels of pollution risk and to control for spatial dependence. Conclusions. The study corroborates earlier …

Prediction Of Radiation Pneumonitis By Dose-Volume Histogram Parameters In Lung Cancer--A Systematic Review, George Rodrigues, Michael Lock, David D'Souza, Edward Yu, Jake Van Dyk

Edward Yu

BACKGROUND AND PURPOSE: To perform a systematic review of the predictive ability of various dose-volume histogram (DVH) parameters (V(dose), mean lung dose (MLD), and normal tissue complication probability (NTCP)) in the incidence of radiation pneumonitis (RP) caused by external-beam radiation therapy. METHODS AND MATERIALS: Studies assessing the relationship between CT-based DVH reduction parameters and RP rate in radically treated lung cancer were eligible for the review. Synonyms for RP, lung cancer, DVH and its associated parameters (NTCP, V(20), V(30), MLD) were combined in a search strategy involving electronic databases, secondary reference searching, and consultation with experts. Individual or group data …

Conduction Band Splitting And Transport Properties Of Bi2se3., J. Navrátil, J. Horák, T. Plecháček, S. Kamba, P. LošŤÁK, Jeffrey Dyck, W. Chen, C. Uher

Jeffrey Dyck

Detailed transport studies of single crystals of Bi2Se3 were made in the temperature range of 2–300K, and the data were analyzed in terms of a model consisting of two groups of electrons—a centrosymmetrical lower conduction band and an upper conduction band located away from the Γ-point. Very good agreement with the experimental data is obtained assuming the electrons are scattered on acoustic phonons and ionized impurities. A rather strong influence of the latter mechanism is attributed to a large number of charged selenium vacancies in Bi2Se3. The fitted transport parameters were used to calculate the electronic portion of the thermal …

Infrared Depletion Spectroscopy Of Aniline–Toluene Cluster: The Investigation Of The Red Shifts Of The Nh2 Stretching Vibrations Of Aniline–Aromatic Clusters, Naveed Piracha, F. Ito, T. Nakanaga

Naveed K. Piracha

The infrared spectra of the NH2 stretching vibrations of aniline–toluene cluster and corresponding cluster cation have been measured by the infrared depletion method. The NH2 stretching vibrations of aniline–toluene cluster were observed at 3393 and 3468 cm−1. The red shifts from the corresponding bands of aniline monomer are 29 and 40 cm−1, respectively, for the NH2 symmetric and anti-symmetric stretching vibrations. The magnitudes of the red shifts are similar to those of other aniline–aromatic clusters. The structure of this cluster has been found to be a sandwich type, that is, the two aromatic rings are parallel in the cluster and …

Cubic : Bulk Thermoelectric Materials With High Figure Of Merit, Kuei Hsu, Sim Loo, Fu Guo, Wei Chen, Jeffrey Dyck, Cterid Uher, Tim Hogan, E. Polychroniadis, Mercouri Kanatzidis

Jeffrey Dyck

The conversion of heat to electricity by thermoelectric devices may play a key role in the future for energy production and utilization. However, in order to meet that role, more efficient thermoelectric materials are needed that are suitable for high-temperature applications. We show that the material system may be suitable for this purpose. With m = 10 and 18 and doped appropriately, n-type semiconductors can be produced that exhibit a high thermoelectric figure of merit of ~2.2 at 800 kelvin. In the temperature range 600 to 900 kelvin, the material is expected to outperform all reported bulk thermoelectrics, thereby earmarking …

Diethylaluminum Chloride Mediated Vinylsilane Synthesis: Comparison Of Different Solvent Systems., Man Lung Kwan, Merle Battiste, Megan Macala, Sylvia Aybar, Nicholas James, Joseph Haoui

Man Lung Desmond Kwan

Aromatic ketones were converted to one-carbon elongated-vinylsilanes in a convenient one-pot operation via the Peterson protocol. Reactions were conducted in two different solvents for comparison: pentane and triethylamine. Results indicate that triethylamine appeared to be a more suitable solvent for such a transformation producing vinylsilanes with great chemo- and stereo-selectivity than pentane.

Solvent-Free Conversion Of Alpha-Naphthaldehyde To 1-Naphthoic Acid And 1-Naphthalenemethanol: Application Of The Cannizzaro Reaction, John Esteb, Keith Gligorich, Stacy O'Reilly, Jeremy Richter

John Esteb

The Cannizzaro reaction is routinely covered in organic textbooks, but owing to the shortage of suitable procedures for the undergraduate teaching laboratory, this reaction is seldom performed in a first-year organic chemistry class. In this experiment, powdered potassium hydroxide and α-naphthaldehyde are heated under solvent-free conditions to produce 1-naphthoic acid and 1-naphthalenemethanol in 86% and 79% yields, respectively. The solvent-free nature of this procedure greatly reduces the quantity of waste generated by students relative to the typical solvent-based method of preparation. Note:Link is to the article in a subscription database available to users affiliated with Butler University. Appropriate login information …

Quantum Mysteries Revisited Again, Padmanabhan Aravind

Padmanabhan K. Aravind

This paper describes a device, consisting of a central source and two widely separated detectors with six switch settings each, that provides a simple gedanken demonstration of the non-classical correlations that are the subject of Bell’s theorem without relying on either statistical effects or the occurrence of rare events. The mechanism underlying the operation of the device is revealed for readers with a knowledge of quantum mechanics.

Microwave Thawing Of Cylinders., Tim Marchant

Tim Marchant

Microwave thawing of a cylinder is examined. The electromagnetic field is governed by Maxwell's equations, where the electrical conductivity and the thermal absorptivity are both assumed to depend on temperature. The forced heat equation governs the absorption and diffusion of heat where convective heating occurs at the surface of the cylinder, while the Stefan condition governs the position of the moving phase boundary. A semi-analytical model, which consists of ordinary differential equations, is developed using the Galerkin method. Semi-analytical solutions are found for the temperature, the electric-field amplitude in the cylinder and the position of the moving boundary. Two examples, …

Asymptotic Solitons For A Third-Order Kortweg-De Vries Equation, Tim Marchant

Tim Marchant

Solitary wave interaction for a higher-order version of the Korteweg–de Vries (KdV) equation is considered. The equation is obtained by retaining third-order terms in the perturbation expansion, where for the KdV equation only first-order terms are retained. The third-order KdV equation can be asymptotically transformed to the KdV equation, if the third-order coefficients satisfy a certain algebraic relationship. The third-order two-soliton solution is derived using the transformation. The third-order phase shift corrections are found and it is shown that the collision is asymptotically elastic. The interaction of two third-order solitary waves is also considered numerically. Examples of an elastic and …

Pseudospectral Iterated Method For Differential Equations With Delay Terms, Jodi Mead, Barbara Zubik-Kowal

Jodi Mead

New efficient numerical methods for hyperbolic and parabolic partial differential equations with delay terms are investigated. These equations model a development of cancer cells in human bodies. Our goal is to study numerical methods which can be applied in a parallel computing environment. We apply our new numerical method to the delay partial differential equations and analyse the error of the method. Numerical experiments confirm our theoretical results.

Model Development Techniques And Evaluation Methods For Prediction And Classification Of Consumer Risk In The Credit Industry, Jennifer Priestley, Satish Nargundkar

Jennifer L. Priestley

In this chapter, we examine and compare the most prevalent modeling techniques in the credit industry, Linear Discriminant Analysis, Logistic Analysis and the emerging technique of Neural Network modeling. K-S Tests and Classification Rates are typically used in the industry to measure the success in predictive classification. We examine those two methods and a third, ROC Curves, to determine if the method of evaluation has an influence on the perceived performance of the modeling technique. We found that each modeling technique has its own strengths, and a determination of the “best” depends upon the evaluation method utilized and the costs …

Cautionary Comments (Author Response), John Esteb, Anne Wilson

John Esteb

Reply to concerns about a safety factor in the paper, “A Solvent-Free Oxidation of Alcohols in an Organic Laboratory."

Note:Link is to the article in a subscription database available to users affiliated with Butler University. Appropriate login information will be required for access. Users not affiliated with Butler University should contact their local librarian for assistance in locating a copy of this article.

Semi-Analytical Solutions For One - And Two-Dimensional Pellet Problems., Tim Marchant

Tim Marchant

The problem of heat and mass transfer within a porous catalytic pellet in which an irreversible first–order exothermic reaction occurs is a much–studied problem in chemical–reactor engineering. The system is described by two coupled reaction–diffusion equations for the temperature and the degree of reactant conversion. The Galerkin method is used to obtain a semi–analytical model for the pellet problem with both one– and two–dimensional slab geometries. This involves approximating the spatial structure of the temperature and reactant–conversion profiles in the pellet using trial functions. The semi–analytical model is obtained by averaging the governing partial differential equations. As the Arrhenius law …

Structural Correction Of Paleomagnetic Vectors Dispersed About Two Fold Axes And Application To The Duke Island (Alaska) Ultramafic Complex, Scott Bogue, C. Sherman Gromme

Scott Bogue

A new analysis of paleomagnetic data from the mid-Cretaceous (∼110 Ma) ultramafic complex at Duke Island (southeast Alaska) supports large poleward transport of the Insular superterrane relative to North America consistent with the Baja British Columbia hypothesis. Previous paleomagnetic work has shown that the characteristic remanence of the ultramafic complex predates kilometer-scale deformation of the very well developed cumulate layering but that the layering was not horizontal everywhere before the folding. It is possible, however, to estimate paleohorizontal for the Duke Island ultramafic complex because the postremanence deformation of the intrusion occurred about two well-defined and spatially separate fold axes. …

Simple Epoxide Formation For The Organic Laboratory Using Oxone, John Esteb

John Esteb

We present an epoxide formation experiment for a second-semester organic chemistry laboratory. This oxidation utilizes Oxone, a commercially available oxidizing agent, in the industrially relevant process of epoxide formation. The oxidant performing the oxidation is dimethyldioxirane, which is formed in situ. This experiment demonstrates a simple synthesis of an epoxide and formation of a secondary oxidizing agent.

Note:Link is to the article in a subscription database available to users affiliated with Butler University. Appropriate login information will be required for access. Users not affiliated with Butler University should contact their local librarian for assistance in locating a copy of …

Rapid Two-Dimensional Optical Spectroscopy Through Acousto-Optic Pulse Shaping, W. Wagner, Peifang Tian, L. Chunqiang, J. Semmlow, Warren Warren

Peifang Tian

No abstract provided.

When Indexing Equals Compression: Experiments With Compressing Suffix Arrays And Applications, Roberto Grossi, Ankur Gupta, Jeffrey Vitter

Ankur Gupta

Cubic Autocatalysis With Michaelis - Menten Kinetics: Semi-Analytical Solutions For The Reaction - Diffusion Cell, Tim Marchant

Tim Marchant

Cubic-autocatalysis with Michaelis–Menten decay is considered in a one-dimensional reaction–diffusion cell. The boundaries of the reactor allow diffusion into the cell from external reservoirs, which contain fixed concentrations of the reactant and catalyst. The Galerkin method is used to obtain a semi-analytical model consisting of ordinary differential equations. This involves using trial functions to approximate the spatial structure of the reactant and autocatalyst concentrations in the reactor. The semi-analytical model is then obtained from the governing partial differential equations by averaging. The semi-analytical model allows steady-state concentration profiles and bifurcation diagrams to be obtained as the solution to sets of …

Hermitian, Hermitian R-Symmetric, And Hermitian R-Skew Symmetric Procrustes Problems, William F. Trench

William F. Trench

No abstract provided.

An Elementary Note On Asymptotic Properties Of Toeplitz And Multilevel Toeplitz Matrices, William F. Trench

William F. Trench

No abstract provided.

Characterization And Properties Of Matrices With Generalized Symmetry Or Skew Symmetry, William F. Trench

William F. Trench

No abstract provided.