Digital Commons Network^™

Potential Energy Surfaces For Small Alcohol Dimers I: Methanol And Ethanol, Richard L. Rowley, Tapani A. Pakkanen, Christopher M. Tracy

Faculty Publications

Potential energy landscapes for homogeneous dimers of methanol and ethanol were calculated using counterpoise (CP) corrected energies at the MP2/6-311+G(2df,2pd) level. The landscapes were sampled at approximately 15 dimer separation distances for different relative monomer geometries, or routes, given in terms of a relative monomer yaw, pitch, and roll and the spherical angles between the monomer centers (taken as the C atom attached to the O). The 19 different routes studied for methanol and the 22 routes examined for ethanol include 607 CP corrected energies. Both landscapes can be adequately represented by site-site, pairwise-additive models, suitable for use in molecular …

Quantum Nature Of The Big Bang: Improved Dynamics, Abhay Ashtekar, Tomasz Pawlowski, Parampreet Singh

Faculty Publications

An improved Hamiltonian constraint operator is introduced in loop quantum cosmology. Quantum dynamics of the spatially flat, isotropic model with a massless scalar field is then studied in detail using analytical and numerical methods. The scalar field continues to serve as "emergent time", the big bang is again replaced by a quantum bounce, and quantum evolution remains deterministic across the deep Planck regime. However, while with the Hamiltonian constraint used so far in loop quantum cosmology the quantum bounce can occur even at low matter densities, with the new Hamiltonian constraint it occurs only at a Planck-scale density. Thus, the …

"God Is A God Who Bears": Bonhoeffer For A Flat World, Gary M. Simpson

Faculty Publications

This is one of a series of articles in Word & World commemorating the 100th birthday of Dietrich Bonhoeffer. Bonhoeffer learned in his own time of crisis that “only the suffering God can help.” As God bears us in Christ, we are given the possibility of bearing the burdens of our brothers and sisters.

Taxing Development: The Law And Economics Of Traffic Impact Fees, John B. Estill, Benjamin Powell, Edward Stringham

Faculty Publications

No abstract provided.

Modeling Of Bathymetry-Locked Residual Eddies In Well-Mixed Tidal Channels With Arbitrary Depth Variations, Chunyan Li

Faculty Publications

The concept of the in-out-type exchange flow in estuaries only applies to situations with significant freshwater discharge and/or elongated channels with relatively simple variations in depth and coastline along the channel. In waterways with complex bottom topography, the in-out-type exchange flows may be replaced by residual eddies that are locked to bathymetry. This paper develops an analytic model for such tidally induced residual eddies. The model allows arbitrary depth variations in both along- and across-channel directions. The model produces residual eddies locked to bathymetry features, similar to observations in Wassaw Sound using a ship-mounted ADCP. Analysis indicates that for problems …

Liberty Of Ecological Conscience, Aaron Lercher

Faculty Publications

Our concern for nonhuman nature can be justified in terms of a human right to liberty of ecological conscience. This right is analogous to the right to religious liberty, and is equally worthy of recognition as that fundamental liberty. The liberty of ecological conscience, like religious liberty, is a negative right against interference. Each ecological conscience supports a claim to protection of the parts of nonhuman nature that are current or potential sites of its active pursuit of natural value. If we acknowledge the fallibility of each conscience in its pursuit of genuine natural value, a policy of indefinitely extensive …

York County Court Of Common Pleas, Jury Utilization And Representation Assessment, Paula Hannaford-Agor

Faculty Publications

In May 2006, the York County Office of Court Administration requested that the National Center for State Courts (NCSC) assess its jury management and utilization practices and make recommendations for improvement. The impetus for this request came from concerns both within the Office of Court Administration and from the Administrative Office of the Pennsylvania Courts that existing jury management practices make inefficient use of jurors, imposing excessive and unnecessary costs on the court and on the citizens who report for jury service. The York County Office of Court Administration also expressed concern that its jury pool may not adequately reflect …

Monoreflections Of Archimedean ℓ-Groups, Regular Σ-Frames And Regular Lindelöf Frames, A. W. Hager, J. J. Madden

Faculty Publications

We prove that in the category of Archimedean lattice-ordered groups with weak unit there is no homomorphism-closed monoreflection strictly between the strongest essential monoreflection (the so-called "closure under countable composition") and the strongest monoreflection (the epicompletion). It follows that in the category of regular σ-frames, the only non-trivial monoreflective subcategory that is hereditary with respect to closed quotients consists of the boolean σ-algebras. Also, in the category of regular Lindelöf locales, there is only one non-trivial closed-hereditary epi-coreflection. The proof hinges on an elementary lemma about the kinds of discontinuities that are exhibited by the elements of a composition-closed l-group …

Support Properties And Holmgren's Uniqueness Theorem For Differential Operators With Hyperplane Singularities, Gestur Ólafsson, Angela Pasquale

Faculty Publications

Let W be a finite Coxeter group acting linearly on Rn. In this article we study the support properties of a W-invariant partial differential operator D on Rn with real analytic coefficients. Our assumption is that the principal symbol of D has a special form, related to the root system corresponding to W. In particular the zeros of the principal symbol are supposed to be located on hyperplanes fixed by reflections in W. We show that conv (supp D f) = conv (supp f) holds for all compactly supported smooth functions f so that conv (supp f) is W-invariant. The …

Estimation Of The Rigid-Body Motion From Three-Dimensional Images Using A Generalized Center-Of-Mass Points Approach, B. Feng, P. P. Bruyant, P. H. Pretorius, R. D. Beach, H. C. Gifford, J. Dey, M. A. Gennert, M. A. King

Faculty Publications

We present an analytical method for the estimation of rigid-body motion in sets of three-dimensional (3-D) SPECT and PET slices. This method utilizes mathematically defined generalized center-of-mass points in images, requiring no segmentation. It can be applied to compensation of the rigid-body motion in both SPECT and PET, once a series of 3-D tomographic images are available. We generalized the formula for the center-of-mass to obtain a family of points comoving with the object's rigid-body motion. From the family of possible points we chose the best three points which resulted in the minimum root-mean-square difference between images as the generalized …

Assessment Of Pws System Effects On The Random Selection Of Jurors And The Demographic Characteristics Of The Jury Poll In The Superior Court Of Arizona, Maricopa County, Paula Hannaford-Agor, G. Thomas Munsterman

Faculty Publications

In July 2006, the Superior Court of Arizona, Maricopa County (Superior Court), contracted with the National Center for State Courts (NCSC) to review its jury management system. The Superior Court specifically requested that the NCSC Center for Jury Studies determine whether its Proximity Weighted Summoning (PWS) System randomly selects jurors from the master jury list for the county; whether the PWS System systematically excludes any identifiable group or population; and the effect of the PWS System on the demographic characteristics of jurors reporting at the various courthouse facilities in Maricopa County. The Superior Court also requested that the NCSC describe …

Large Grain Size Stochastic Optimization Alignment, Hyrum Carroll, Mark J. Clement, Perry Ridge, Dan Sneddon, Quinn O. Snell

Faculty Publications

DNA sequence alignment is a critical step in identifying homology between organisms. The most widely used alignment program, ClustalW, is known to suffer from the local minima problem, where suboptimal guide trees produce incorrect gap insertions. The optimization alignment approach, has been shown to be effective in combining alignment and phylogenetic search in order to avoid the problems associated with poor guide trees. The optimization alignment algorithm operates at a small grain size, aligning each tree found, wasting time producing multiple sequence alignments for suboptimal trees. This research develops and analyzes a large grain size algorithm for optimization alignment that …

Steganalysis Embedding Percentage Determination With Learning Vector Quantization, Benjamin M. Rodriguez, Gilbert L. Peterson, Kenneth W. Bauer, Sos S. Agaian

Faculty Publications

Steganography (stego) is used primarily when the very existence of a communication signal is to be kept covert. Detecting the presence of stego is a very difficult problem which is made even more difficult when the embedding technique is not known. This article presents an investigation of the process and necessary considerations inherent in the development of a new method applied for the detection of hidden data within digital images. We demonstrate the effectiveness of learning vector quantization (LVQ) as a clustering technique which assists in discerning clean or non-stego images from anomalous or stego images. This comparison is conducted …

Open Source, Openness, And Higher Education, David Wiley

Faculty Publications

With the growth of open source software and other related trends, a culture of openness is advancing from the edges of society to the core of academic culture. In this article I provide an overview of how the expansion of open source software in culture at large has affected the world of education, describe how the greater use of open source software in education has unfolded hand-in-hand with the development of open course content and open access research, and argue that this more comprehensive shift towards "openness" in academic practice is not only a positive trend, but a necessary one …

Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell

Faculty Publications

Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching to explore the effects of varying the gap open and gap extension penalties for three nuclear ribosomal data sets. Particular attention is given to optimal phylogeny scores for 200 alignments of a range of gap open and gap extension penalties and their respective …

Pharmacogenomics: Analyzing Snps In The Cyp2d6 Gene Using Amino Acid Properties, Wesley A. Beckstead, Mark J. Clement, Mark Ebbert, David Mcclellan, Timothy O'Connor

Faculty Publications

Each year people suffer from complications of adverse drug reactions, but with pharmacogenomics there is hope to prevent thousands of these people from suffering or dying needlessly. The CYP2D6 gene is responsible for metabolizing a large portion of these drugs. Because of the gene’s importance, various approaches have been taken to analyze CYP2D6 and single nucleotide polymorphisms (SNPs) throughout its sequence. This study introduces a novel method to analyze the effects of SNPs on encoded protein complexes by focusing on the biochemical properties of each nonsynonymous substitution using the program TreeSAAP. We apply this technique to SNPs found in the …

A Nd Isotopic Study Of Southern Sourced Waters And Indonesian Throughflow At Intermediate Depths In The Cenozoic Indian Ocean, Ellen E. Martin, Howie Scher

Faculty Publications

We present Nd isotopic data for fossil fish teeth recovered from the past 40 m.y. at ODP Site 757, currentlylocated at 1650m water depth on the Ninetyeast Ridge in the Indian Ocean. Although Site 757 sits in a regionstrongly influenced by weathering inputs from the Himalayas and volcanic inputs from the Indonesian arc, the pattern of Nd isotopic variations does not appear to respond to these potential sources of Nd. Instead, secular variations correlate to changes in the composition of intermediate to deep water masses bathing thesite and circulation patterns in the Indian Ocean. From ~40 to 10 Ma, eNd …

A Fourier Transformation Based Method To Mine Peptide Space For Antimicrobial Activity, Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, Mohamed O. Elasri, Youping Deng

Faculty Publications

Background

Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every living organism, it is possible to discover new candidate peptides using the available genomic and proteomic data. High throughput computational techniques could also be used to virtually scan the entire peptide space for discovering out new candidate antimicrobial peptides.

Result

We have identified a unique indexing method based on biologically distinct characteristic features of known antimicrobial peptides. Analysis of the entries in the antimicrobial peptide databases, based on our indexing method, using Fourier transformation …

Geometric Phase For N -Level Systems Through Unitary Integration, D. B. Uskov, A. R.P. Rau

Faculty Publications

Geometric phases are important in quantum physics and are now central to fault-tolerant quantum computation. For spin 1a•2, the Bloch sphere S2, together with a U(1) phase, provides a complete SU(2) description. We generalize to N -level systems and SU (N) in terms of a 2 (Na 1) -dimensional base space and reduction to a (Na 1) -level problem, paralleling closely the two-dimensional case. This iteratively solves the time evolution of an N -level system and gives (Na 1) geometric phases explicitly. A complete analytical construction of an S4 Bloch-like sphere for two qubits is given for the Spin(5) or …

Mesostructured Silica Chemically Doped With RuIi As A Superior Optical Oxygen Sensor, Bingfu Lei, Bin Li, Haoran Zhang, Shaozhe Lu, Zhuhong Zheng, Wenlian Li, Yue Wang

Faculty Publications

Novel oxygen sensors consisting of a [Ru(bpy)2phen]2+ (bpy: 2,2′-bipyridyl, phen: phenathroline) portion covalently grafted to a mesostructured silica-based network are prepared in situ via a sol-gel approach with the help of cetyltrimethylammonium-bromide (CTAB) surfactant. 1,10-Phenanthroline covalently grafted to 3-(triethoxysilyl)propyl isocyanate is used as not only the sol-gel precursor but also as the second ligand of the Ru(bpy)2d2 · 2H2O complex to prepare the sol-gel-derived mesostructured silicates for an oxygen sensor. For comparison purposes, the oxygen sensors in which [Ru(bpy)2phen]Q2 is conventionally physically incorporated into the matrix are also prepared. Elemental analysis, NMR, Fourier transform IR, UV-vis electronic absorption, luminescence-intensity quenching …

Multiplatform Genome-Wide Identification And Modeling Of Functional Human Estrogen Receptor Binding Sites, Chin-Yo Lin, Vinsensius B. Vega, Koon Siew Lai, Li Say Kong, Min Xie, Xiaodi Su, Huey Fang The, Jane S. Thomsen, Ai Li Yeo, Wing Kin Sung, Guillaume Bourque, Edison T. Liu

Faculty Publications

Transcription factor binding sites (TFBS) impart specificity to cellular transcriptional responses and have largely been defined by consensus motifs derived from a handful of validated sites. The low specificity of the computational predictions of TFBSs has been attributed to ubiquity of the motifs and the relaxed sequence requirements for binding. We posited that the inadequacy is due to limited input of empirically verified sites, and demonstrated a multiplatform approach to constructing a robust model. Results: Using the TFBS for the estrogen receptor (ER)alpha (estrogen response element [ERE]) as a model system, we extracted EREs from multiple molecular and genomic platforms …

Sar Imaging And Hydrodynamic Analysis Of Ocean Bottom Topographic Waves, Quanan Zheng, Li Li, Xiaogang Guo, Yong Ge, Dayong Zhu, Chunyan Li

Faculty Publications

The satellite synthetic aperture radar (SAR) images display wave-like patterns of the ocean bottom topographic features at the south outlet of Taiwan Strait (TS). Field measurements indicate that the most TS water body is vertically stratified. However, SAR imaging models available were developed for homogeneous waters. Hence explaining SAR imaging mechanisms of bottom features in a stratified ocean is beyond the scope of those models. In order to explore these mechanisms and to determine the quantitative relations between the SAR imagery and the bottom features, a two-dimensional, three-layer ocean model with sinusoidal bottom topographic features is developed. Analytical solutions and …

Absorption Properties Of A Porous Organic Crystalline Apohost Formed By A Self-Assembled Bis-Urea Macrocycle, Mahender B. Dewal, Michael W. Lufaso, Andrew D. Hughes, Stevan A. Samuel, Perry J. Pellechia, Linda S. Shimizu

Faculty Publications

We report herein the characterization and binding properties of a microporous crystalline host formed by the self assembly of a bis-urea macrocycle 1. Bis-urea macrocycle 1 has been designed to crystallize into stacked hollow columns. The self-assembly process is guided primarily by hydrogen bonding and aromatic stacking interactions that yield crystals of filled host 1âacetic acid (AcOH). The AcOH guests are bound in the cylindrical cavities of the crystal. The guest AcOH can be removed by heating to form a stable crystalline apohost 1. Apohost 1 displays a type I gas adsorption isotherm with CO₂ that is consistent with …

Tc-99m Pyrophosphate Imaging Of Poloxamer-Treated Electroporated Skeletal Muscle In An In Vivo Rat Model, Kenneth L. Matthews, John N. Aarsvold, Robert A. Mintzer, Chin Tu Chen, Raphael C. Lee

Faculty Publications

Objective: This study investigates whether 99mTc pyrophosphate (PYP) imaging provides a quantitative non-invasive assessment of the extent of electroporation injury, and of the effect of poloxamer in vivo on electroporated skeletal muscle. Methods: High-voltage electrical shock was used to produce electroporation injury in an anesthetized rat's hind limb. In each experiment, the injured limb was treated intravenously by either poloxamer-188, dextran, or saline, and subsequently imaged with 99mTc PYP. The radiotracer's temporal behavior among the experimental groups was compared using curve fitting of time-activity curves from the dynamic image data. Results: The washout kinetics of 99mTc PYP changed in proportion …

Tc-99m Pyrophosphate Imaging Of Poloxamer-Treated Electroporated Skeletal Muscle In An In Vivo Rat Model, Kenneth L. Matthews, John N. Aarsvold, Robert A. Mintzer, Chin Tu Chen, Raphael C. Lee

Faculty Publications

Objective: This study investigates whether 99mTc pyrophosphate (PYP) imaging provides a quantitative non-invasive assessment of the extent of electroporation injury, and of the effect of poloxamer in vivo on electroporated skeletal muscle. Methods: High-voltage electrical shock was used to produce electroporation injury in an anesthetized rat's hind limb. In each experiment, the injured limb was treated intravenously by either poloxamer-188, dextran, or saline, and subsequently imaged with 99mTc PYP. The radiotracer's temporal behavior among the experimental groups was compared using curve fitting of time-activity curves from the dynamic image data. Results: The washout kinetics of 99mTc PYP changed in proportion …

Higher-Rank Wavelet Transforms, Ridgelet Transforms, And Radon Transforms On The Space Of Matrices, Gestur Ólafsson, Elena Ournycheva, Boris Rubin

Faculty Publications

Let Mn, m be the space of real n × m matrices which can be identified with the Euclidean space Rn m. We introduce continuous wavelet transforms on Mn, m with a multivalued scaling parameter represented by a positive definite symmetric matrix. These transforms agree with the polar decomposition on Mn, m and coincide with classical ones in the rank-one case m = 1. We prove an analog of Calderón's reproducing formula for L2-functions and obtain explicit inversion formulas for the Riesz potentials and Radon transforms on Mn, m. We also introduce continuous ridgelet transforms associated to matrix planes in …

Further Results On Active Magnetic Bearing Control With Input Saturation, F. Mazenc, M. S. De Queiroz, M. Malisoff, F. Gao

Faculty Publications

We study the low-bias stabilization of active magnetic bearings (AMBs) subject to voltage saturation based on a recently proposed model for the AMB switching mode of operation. Using a forwarding-like approach, we construct a stabilizing controller of arbitrarily small amplitude and a control-Lyapunov function for the AMB dynamics. We illustrate our construction using a numerical example. © 2006 IEEE.

Introduction: Self-Organization In Nonequilibrium Chemical Systems, Irving R. Epstein, John A. Pojman, Oliver Steinbock

Faculty Publications

The field of self-organization in nonequilibrium chemical systems comprises the study of dynamical phenomena in chemically reacting systems far from equilibrium. Systematic exploration of this area began with investigations of the temporal behavior of the Belousov-Zhabotinsky oscillating reaction, discovered accidentally in the former Soviet Union in the 1950s. The field soon advanced into chemical waves in excitable media and propagating fronts. With the systematic design of oscillating reactions in the 1980s and the discovery of Turing patterns in the 1990s, the scope of these studies expanded dramatically. The articles in this Focus Issue provide an overview of the development and …

Pair Production From Nuclear Collisions And Cosmic Ray Transport, John W. Norbury

Faculty Publications

Modern cosmic ray transport codes, that are capable of use for a variety of applications, need to include all significant atomic, nuclear and particle reactions at a variety of energies. Lepton pair production from nucleus-nucleus collisions has not been included in transport codes to date. Using the methods of Baur, Bertulani and Baron, the present report provides estimates of electron positron pair production cross sections for nuclei and energies relevant to cosmic ray transport. It is shown that the cross sections are large compared to other typical processes such as single neutron removal due to strong or electromagnetic interactions. Therefore, …

Induction Of Characters And Finite P-Groups, Edith Adan-Bante

Faculty Publications

Let G be a finite p-group, where p is an odd prime number, H be a subgroup of G and θ ∈ Irr(H) be an irreducible character of H. Assume also that | G : H | = p². Then the character θ^G of G induce by θ is either a multiple of an irreducible character of G, or has at least ^p+1/₂ distinct irreducible constituents.