Digital Commons Network^™

Inflation, Quantum Fields, And Cmb Anisotropies, Iván Agulló, José Navarro-Salas, Gonzalo J. Olmo, Leonard Parker

Faculty Publications

Inflationary cosmology has proven to be the most successful at predicting the properties of the anisotropies observed in the cosmic microwave background (CMB). In this essay we show that quantum field renormalization significantly influences the generation of primordial perturbations and hence the expected measurable imprint of cosmological inflation on the CMB. However, the new predictions remain in agreement with observation, and in fact favor the simplest forms of inflation. In the near future, observations of the influence of gravitational waves from the early universe on the CMB will test our new predictions. © 2009 World Scientific Publishing Company.

Theory Of Thermal Conductivity In Extended-S State Superconductors: Application To Ferropnictides, V. Mishra, A. Vorontsov, P. J. Hirschfeld, I. Vekhter

Faculty Publications

Within a two-band model for the recently discovered ferropnictide materials, we calculate the thermal conductivity assuming general superconducting states of A1g (" s -wave") symmetry, considering both currently popular isotropic "sign-changing" s states and states with strong anisotropy, including those which manifest nodes or deep minima of the order parameter. We consider both intraband and interband disorder scattering effects, and show that in situations where a low-temperature linear- T term exists in the thermal conductivity, it is not always "universal" as in d -wave superconductors. We discuss the conditions under which such a term can disappear, as well as how …

Auger Decay In Krypton Induced By Attosecond Pulse Trains And Twin Pulses, Christian Buth, Kenneth J. Schafer

Faculty Publications

Using attoscience, we study the electron correlations responsible for Auger decay in krypton atoms. The Auger decay is induced by a pulse train or a twin pulse composed of subpulses of attosecond duration. During the Auger decay an optical dressing laser may be present. Interference effects between the ejected Auger electron wave packets are predicted.

Bloch Sphere-Like Construction Of Su(3) Hamiltonians Using Unitary Integration, Sai Vinjanampathy, A. R.P. Rau

Faculty Publications

The Bloch sphere is a familiar and useful geometrical picture of the time evolution of a single spin or a quantal two-level system. The analogous geometrical picture for three-level systems is presented with several applications. The relevant SU(3) group and su(3) algebra are eight-dimensional objects and are realized in our picture as two four-dimensional manifolds that describe the time evolution operator. The first, called the base manifold, is the counterpart of the S2 Bloch sphere, whereas the second, called the fiber, generalizes the single U(1) phase of a single spin. Now four dimensional, it breaks down further into smaller objects …

Erratum: All-Sky Search For Periodic Gravitational Waves In Ligo S4 Data (Physical Review D (2008) 77 (022001)), B. Abbott, R. Abbott, R. Adhikari, J. Agresti, P. Ajith, B. Allen, R. Amin, S. B. Anderson, W. G. Anderson, M. Arain, M. Araya, H. Armandula, M. Ashley, S. Aston, P. Aufmuth, C. Aulbert, S. Babak, S. Ballmer, H. Bantilan, B. C. Barish, C. Barker, D. Barker, B. Barr, P. Barriga, M. A. Barton, K. Bayer, K. Belczynski, J. Betzwieser, P. T. Beyersdorf, B. Bhawal, I. A. Bilenko, G. Billingsley, R. Biswas

Faculty Publications

No abstract provided.

Monte Carlo Simulation Of The Neutron Spectral Fluence And Dose Equivalent For Use In Shielding A Proton Therapy Vault, Yuanshui Zheng, Wayne Newhauser, Eric Klein, Daniel Low

Faculty Publications

Neutron production is of principal concern when designing proton therapy vault shielding. Conventionally, neutron calculations are based on analytical methods, which do not accurately consider beam shaping components and nozzle shielding. The goal of this study was to calculate, using Monte Carlo modeling, the neutron spectral fluence and neutron dose equivalent generated by a realistic proton therapy nozzle and evaluate how these data could be used in shielding calculations. We modeled a contemporary passive scattering proton therapy nozzle in detail with the MCNPX simulation code. The neutron spectral fluence and dose equivalent at various locations in the treatment room were …

Reply To Zimmerman Et Al.: The Space Of Single Domain Protein Structures Is Continuous And Highly Connected, Jeffrey Skolnick, Michal Brylinski, Seung Yup Lee

Faculty Publications

No abstract provided.

Near-Infrared Fluorescent Nanogumbos For Biomedical Imaging, David K. Bwambok, Bilal El-Zahab, Santhosh K. Challa, Min Li, Lin Chandler, Gary A. Baker, Isiah M. Warner

Faculty Publications

Herein, we report on near-infrared (NIR) fluorescent nanoparticles generated from an emergent class of materials we refer to as a Group of Uniform Materials Based on Organic Salts (GUMBOS). GUMBOS are largely frozen ionic liquids, although the concept is more general and is also easily applied to solid ionic materials with melting points in excess of 100 °C. Nanoparticles based on GUMBOS (nanoGUMBOS) derived from a NIR fluorophore are prepared using a reprecipitation method and evaluated for in vivo fluorescence imaging. Due to their uniformity, single-step preparation, and composite nature, nanoGUMBOS help to resolve issues with dye leakage problems innate …

The Creation And Use Of Open Educational Resources In Christian Higher Education, John L. Hilton Iii, David Wiley

Faculty Publications

A significant movement in education concerns the use of open educational resources (OERs). By “open” it is generally meant that the resource is freely available to others to reuse in different contexts. These resources could include books, lesson plans, syllabi, slide shows, etc. There are several examples of individuals and institutions providing open educational resources; this openness is also specifically manifest in the field of religious education. I discuss different levels in which OERs can be “open” and the implications of these levels when creating OERs. Common motivations and obstacles to creating OERs are discussed. A particularly significant issue regarding …

Measurement Of The Inclusive Isolated Prompt Photon Cross Section In Pp̄ Collisions At S=1.96tev Using The Cdf Detector, T. Aaltonen, J. Adelman, B. Álvarez González, S. Amerio, D. Amidei, A. Anastassov, A. Annovi, J. Antos, G. Apollinari, A. Apresyan, T. Arisawa, A. Artikov, J. Asaadi, W. Ashmanskas, A. Attal, A. Aurisano, F. Azfar, W. Badgett, A. Barbaro-Galtieri, V. E. Barnes, B. A. Barnett, P. Barria, P. Bartos, G. Bauer, P. H. Beauchemin, F. Bedeschi, D. Beecher, S. Behari

Faculty Publications

A measurement of the cross section for the inclusive production of isolated photons by the CDF experiment at the Fermilab Tevatron collider is presented. The measurement covers the pseudorapidity region |ηγ|<1.0 and the transverse energy range ETγ>30GeV and is based on 2.5fb-1 of integrated luminosity. The sample is almost a factor of 7 larger than those used for recent published results and extends the ETγ coverage by 100 GeV. The result agrees with next-to-leading order perturbative QCD calculations within uncertainties over the range 50

Meditation On Wendell Berry’S The Gift Of Good Land, Steven C. Bouma-Prediger

Faculty Publications

No abstract provided.

The Executive Pay Drama: From Comedy To Tragedy, David J. Cherrington

Faculty Publications

Over the past century, an interesting play has been performed in the United States called Executive Pay, Starring Your Local CEO. The play opened as a comedy, with executive bonuses and stock options rising at ridiculous rates compared to the pay of factory workers, teachers, and engineers. The performance didn’t get a lot of laughs, but people would smile and shake their heads as if the surprise of ever-escalating pay was an amusing disclosure. During economic downturns there were fewer smiles, and some outspoken critics were remarkably blunt in labeling executive pay practices as “enormous,” “immoral,” and “outrageous.” The title …

Selective Complexation And Reactivity Of Metallic Nitride And Oxometallic Fullerenes With Lewis Acids And Use As An Effective Purification Method, Steven Stevenson, Mary A. Mackey, Jane E. Pickens, Melissa A. Stuart, Bridget S. Confait, J. Paige Phillips

Faculty Publications

Metallic nitride fullerenes (MNFs) and oxometallic fullerenes (OMFs) react quickly with an array of Lewis acids. Empty-cage fullerenes are largely unreactive under conditions used in this study. The reactivity order is Sc₄O₂@I_h-C₈₀ > Sc₃N@C₇₈ > Sc₃N@C₆₈ > Sc₃N@D_5h-C₈₀ > Sc₃N@I_h-C₈₀. Manipulations of Lewis acids, molar ratios, and kinetic differences within the family of OMF and MNF metallofullerenes are demonstrated in a selective precipitation scheme, which can be used either alone for purifying Sc₃N@I_{h …}

A Comparison Of The Wellbeing Of Orphans And Abandoned Children Ages 6–12 In Institutional And Community-Based Care Settings In 5 Less Wealthy Nations, Kathryn Whetten, Jan Ostermann, Rachel A. Whetten, Brian W. Pence, Karen O'Donnell, Lynne C. Messer, Nathan M. Thielman, The Positive Outcomes For Orphans (Pofo) Research Team

Faculty Publications

Background

Leaders are struggling to care for the estimated 143,000,000 orphans and millions more abandoned children worldwide. Global policy makers are advocating that institution-living orphans and abandoned children (OAC) be moved as quickly as possible to a residential family setting and that institutional care be used as a last resort. This analysis tests the hypothesis that institutional care for OAC aged 6–12 is associated with worse health and wellbeing than community residential care using conservative two-tail tests.

Methodology

The Positive Outcomes for Orphans (POFO) study employed two-stage random sampling survey methodology in 6 sites across 5 countries to identify 1,357 …

Deliberation Versus Dispute: The Impact Of Argumentative Discourse Goals On Learning And Reasoning In The Science Classroom, Mark Felton, Merce Garcia-Mila, Sandra Gilabert

Faculty Publications

Researchers in science education have converged on the view that argumentation can be an effective intervention for promoting knowledge construction in science classrooms.However, the impact of such interventions may be mediated by individuals’ task goals while arguing. In argumentative discourse, one can distinguish two overlapping but distinct kinds of activity: dispute and deliberation. In dispute the goal is to defend a conclusion by undermining alternatives, whereas in deliberation the goal is to arrive at a conclusion by contrasting alternatives. In this study, we examine the impact of these discourse goals on both content learning and argument quality in science.

Asymptotic Falloff Of Local Waveform Measurements In Numerical Relativity, Denis Pollney, Christian Reisswig, Nils Dorband, Erik Schnetter, Peter Diener

Faculty Publications

We examine current numerical relativity computations of gravitational waves, which typically determine the asymptotic waves at infinity by extrapolation from finite (small) radii. Using simulations of a black hole binary with accurate wave extraction at r=1000M, we show that extrapolations from the near zone are self-consistent in approximating measurements at this radius, although with a somewhat reduced accuracy. We verify that ψ4 is the dominant asymptotic contribution to the gravitational energy (as required by the peeling theorem) but point out that gauge effects may complicate the interpretation of the other Weyl components. © 2009 The American Physical Society.

Phylogeny Of The Macaques (Cercopithecidae: Macaca) Based On Alu Elements, Jing Li, Kyudong Han, Jinchuan Xing, Heui Soo Kim, Jeffrey Rogers, Oliver A. Ryder, Todd Disotell, Bisong Yue, Mark A. Batzer

Faculty Publications

Genus Macaca (Cercopithecidae: Papionini) is one of the most successful primate radiations. Despite previous studies on morphology and mitochondrial DNA analysis, a number of issues regarding the details of macaque evolution remain unsolved. Alu elements are a class of non-autonomous retroposons belonging to short interspersed elements that are specific to the primate lineage. Because retroposon insertions show very little homoplasy, and because the ancestral state (absence of the SINE) is known, Alu elements are useful genetic markers and have been utilized for analyzing primate phylogenentic relationships and human population genetic relationships. Using PCR display methodology, 298 new Alu insertions have …

Internal Priming: An Opportunistic Pathway For L1 And Alu Retrotransposition In Hominins, Deepa Srikanta, Shurjo K. Sen, Erin M. Conlin, Mark A. Batzer

Faculty Publications

Retrotransposons, specifically Alu and L1 elements, have been especially successful in their expansion throughout primate genomes. While most of these elements integrate through an endonuclease-mediated process termed target primed reverse transcription, a minority integrate using alternative methods. Here we present evidence for one such mechanism, which we term internal priming and demonstrate that loci integrating through this mechanism are qualitatively different from "classical" insertions. Previous examples of this mechanism are limited to cell culture assays, which show that reverse transcription can initiate upstream of the 3′ poly-A tail during retrotransposon integration. To detect whether this mechanism occurs in vivo as …

Measured Optical Constants Of Copper From 10 Nm To 35 Nm, David D. Allred, Nicole Brimhall, Nicholas Herrick, Justin Peatross, R. Steven Turley, Michael Ware

Faculty Publications

We use laser high-order harmonics and a polarization-ratioreflectance technique to determine the optical constants of copper and oxidized copper in the wavelength range 10-35 nm. This measurement resolves previously conflicting data sets, where disagreement on optical constants of copper in the extreme ultraviolet most likely arises from inadvertent oxidation of samples before measurement.

Enhance Diamond Coating Adhesion By Oriented Interlayer Microcracking, Habio Guo, Xingcheng Xiao, Yue Qi, Zhi-Hui Xu, Xiaodong Li

Faculty Publications

In this paper, we report a microcrack toughening mechanism for enhancing the adhesion of diamondcoating. The oriented microcracks were formed within the TiC interlayer to dissipate strain energy and accommodate deformation via the crack opening-closing mechanism, thus enhancing the coating/substrate interfacial toughness. The delamination of diamondcoating was effectively prevented when the parallel microcracks were confined within the interlayer and arrested at interfaces of coating/interlayer/substrate. Density functional theory calculations revealed that the highly anisotropicfracture strength of the TiC phase energetically favors crack initiation and propagation along (100) planes only, which are 54.7° away from the interface. These microcracks are constrained inside …

Applied Climate-Change Analysis: The Climate Wizard Tool, Evan H. Girvetz, Chris Zganjar, George T. Raber, Edwin P. Maurer, Peter Kareiva, Joshua J. Lawler

Faculty Publications

Background: Although the message of "global climate change'' is catalyzing international action, it is local and regional changes that directly affect people and ecosystems and are of immediate concern to scientists, managers, and policy makers. A major barrier preventing informed climate-change adaptation planning is the difficulty accessing, analyzing, and interpreting climate-change information. To address this problem, we developed a powerful, yet easy to use, web-based tool called Climate Wizard (http://ClimateWizard.org) that provides non-climate specialists with simple analyses and innovative graphical depictions for conveying how climate has and is projected to change within specific geographic areas throughout the world. Methodology/Principal Findings: …

Feature Selection And Classification Of Maqc-Ii Breast Cancer And Multiple Myeloma Microarray Gene Expression Data, Qingzhong Liu, Andrew H. Sung, Zhongxue Chen, Jianzhong Liu, Xudong Huang, Youping Deng

Faculty Publications

Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging. In the task of analyzing microarray data for the purpose of, e.g., predicting gene-disease association, feature selection is very important because it provides a way to handle the high dimensionality by exploiting information redundancy induced by associations among genetic markers. Judicious feature selection in microarray data analysis can result in significant reduction of cost while maintaining or improving the classification or prediction accuracy of learning machines that are employed to sort …

Environmental Dna Sequencing Primers For Eutardigrades And Bdelloid Rotifers, Byron J. Adams, Jeremy Whiting, Elizabeth K. Costello, Kristen R. Freeman, Andrew P. Martin, Michael S. Robeson, Steve K. Schmidt

Faculty Publications

Background: The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. The lack of consistent morphological information and the extreme abundance of these classes makes morphological identification of rare, or even common cryptic taxa a large and unwieldy task. This limits the ability to perform large-scale surveys of the diversity of these organisms. Here we demonstrate a culture-independent molecular survey approach that enables the generation of large amounts of eutardigrade and bdelloid rotifer sequence data directly …

Nonsingular Ekpyrotic/Cyclic Model In Loop Quantum Cosmology, Thomas Cailleteau, Parampreet Singh, Kevin Vandersloot

Faculty Publications

We study the role of nonperturbative quantum gravity effects in the ekpyrotic/cyclic model using the effective framework of loop quantum cosmology in the presence of anisotropies. We show that quantum geometric modifications to the dynamical equations near the Planck scale as understood in the quantization of Bianchi-I spacetime in loop quantum cosmology lead to the resolution of classical singularity and result in a nonsingular transition of the Universe from the contracting to the expanding branch. In the Planck regime, the Universe undergoes multiple small bounces and the anisotropic shear remains bounded throughout the evolution. A novel feature, which is absent …

Strong Field Double Ionization Of H2: Insights From Nonlinear Dynamics, F. Mauger, C. Chandre, T. Uzer

Faculty Publications

The uncorrelated ("sequential") and correlated ("nonsequential") double ionization of the H2 molecule in strong laser pulses is investigated using tools of nonlinear dynamics. We focus on the phase-space dynamics of this system, specifically by finding the dynamical structures that regulate these ionization processes. The emerging picture complements the recollision scenario by clarifying the distinct roles played by the recolliding and core electrons. Our analysis leads to verifiable predictions of the intensities where qualitative changes in ionization occur. We also show how these findings depend on the internuclear distance. © 2009 Elsevier B.V. All rights reserved.

Detrital U-Pb Zircon Dating Of Lower Ordovician Syn-Arc-Continent Collision Conglomerates In The Irish Caledonides, Peter D. Clift, Andrew Carter, Amy E. Draut, Hoang Van Long, David M. Chew, Hans A. Schouten

Faculty Publications

The Early Ordovician Grampian Orogeny in the British Isles represents a classic example of collision between an oceanic island arc and a passive continental margin, starting around 480 Ma. The South Mayo Trough in western Ireland preserves a complete and well-dated sedimentary record of arc collision. We sampled sandstones and conglomerates from the Rosroe, Maumtrasna and Derryveeny Formations in order to assess erosion rates and patterns during and after arc collision. U-Pb dating of zircons reveals a provenance dominated by erosion from the upper levels of the Dalradian Supergroup (Southern Highland and Argyll Groups), with up to 20% influx from …

Rfx2 Is A Candidate Downstream Amplifier Of A-Myb Regulation In Mouse Spermatogenesis, Gary C. Horvath, Malathi K. Kistler, Wilson Stephen Kistler

Faculty Publications

Background: Mammalian spermatogenesis involves formation of haploid cells from the male germline and then a complex morphological transformation to generate motile sperm. Focusing on meiotic prophase, some tissue-specific transcription factors are known (A-MYB) or suspected (RFX2) to play important roles in modulating gene expression in pachytene spermatocytes. The current work was initiated to identify both downstream and upstream regulatory connections for Rfx2.

Results: Searches of pachytene up-regulated genes identified high affinity RFX binding sites (X boxes) in promoter regions of several new genes: Adam5, Pdcl2, and Spag6. We confirmed a strong promoter-region X-box for Alf, a germ cell-specific variant of …

Fused Visible And Infrared Video For Use In Wilderness Search And Rescue, Dennis Eggett, Michael A. Goodrich, Bryan S. Morse, Nathan Rasmussen

Faculty Publications

Mini Unmanned Aerial Vehicles (mUAVs) have the potential to assist Wilderness Search and Rescue groups by providing a bird’s eye view of the search area. This paper proposes a method for augmenting visible-spectrum searching with infrared sensing in order to make use of thermal search clues. It details a method for combining the color and heat information from these two modalities into a single fused display to reduce needed screen space for remote field use. To align the video frames for fusion, a method for simultaneously pre-calibrating the intrinsic and extrinsic parameters of the cameras and their mount using a …

Precise Calibration Of Ligo Test Mass Actuators Using Photon Radiation Pressure, E. Goetz, P. Kalmus, S. Erickson, R. L. Savage, G. Gonzalez, K. Kawabe, M. Landry, S. Marka, B. O'Reilly, K. Riles, D. Sigg, P. Willems

Faculty Publications

Precise calibration of kilometer-scale interferometric gravitational wave detectors is crucial for source localization and waveform reconstruction. A technique that uses the radiation pressure of a power-modulated auxiliary laser to induce calibrated displacements of one of the ∼10 kg arm cavity mirrors, a so-called photon calibrator, has been demonstrated previously and has recently been implemented on the LIGO detectors. In this paper, we discuss the inherent precision and accuracy of the LIGO photon calibrators and several improvements that have been developed to reduce the estimated voice coil actuator calibration uncertainties to less than 2% (1σ). These improvements include accounting for rotation-induced …

A Tale Of Two Functions: Enzymatic Activity And Translational Repression By Carboxyltransferase, Glen Meades, Brian K. Benson, Anne Grove, Grover L. Waldrop

Faculty Publications

Acetyl-CoA Carboxylase catalyzes the first committed step in fatty acid synthesis. Escherichia coli acetyl-CoA carboxylase is composed of biotin carboxylase, carboxyltransferase and biotin carboxyl carrier protein functions. The accA and accD genes that code for the α- and β-subunits, respectively, are not in an operon, yet yield an α2β2 carboxyltransferase. Here, we report that carboxyltransferase regulates its own translation by binding the mRNA encoding its subunits. This interaction is mediated by a zinc finger on the β-subunit; mutation of the four cysteines to alanine diminished nucleic acid binding and catalytic activity. Carboxyltransferase binds the coding regions of both subunit mRNAs …