Physical Sciences and Mathematics Commons^™

Association Studies For Sequencing Data With Functional Analysis Of Variance, Olga A. Vsevolozhskaya, Mark C. Greenwood, Changshuai Wei, Qing Lu

Olga A. Vsevolozhskaya

The rapid development of next generation sequencing technologies and accompanying reduction in cost produce an increasing number of single nucleotide polymorphisms (SNPs) that can be identified across the genome. Analyzing high-dimensional genomic data is a challenge and requires development of new statistical methods. We propose to use the functional analysis of variance (FANOVA) to perform inference for sequencing data. FANOVA is used to test for differences in functional means of k groups over time. We suggest using FANOVA to test for a significant difference among SNPs between levels of a phenotype, such as the presence or absence of a disease. …

Is Security Sustainable?, Jeremy W. Crampton

Geography Faculty Publications

No abstract provided.

The Redshift And Mass Dependence On The Formation Of The Hubble Sequence At Z > 1 From Candels/Uds, Alice Mortlock, Christopher J. Conselice, William G. Hartley, Jamie R. Ownsworth, Caterina Lani, Asa F. L. Bluck, Omar Almaini, Kenneth Duncan, Arjen Van Der Wel, Anton M. Koekemoer, Avishai Dekel, Romeel Davé, Harry C. Ferguson, Duilia F. De Mello, Jeffrey A. Newman, Sandra M. Faber, Norman A. Grogin, Dalibor D. Kocevski, Kamson Lai

Physics and Astronomy Faculty Publications

In this paper we present a detailed study of the structures and morphologies of a sample of 1188 massive galaxies with M_* ≥ 10¹⁰ M_⊙between redshifts z = 1 and 3 within the Ultra Deep Survey (UDS) region of the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS) field. Using this sample we determine how galaxy structure and morphology evolve with time, and investigate the nature of galaxy structure at high redshift. We visually classify our sample into discs, ellipticals and peculiar systems and correct for redshift effects on these classifications through simulations. We find significant …

Interstellar H2O Masers From J Shocks, David Hollenbach, Moshe Elitzur, Christopher F. Mckee

Physics and Astronomy Faculty Publications

We present a model in which the 22 GHz H₂O masers observed in star-forming regions occur behind shocks propagating in dense regions (preshock density n ₀ ~ 10⁶-10⁸ cm^–3). We focus on high-velocity (v_s ≳ 30 km s^–1) dissociative J shocks in which the heat of H₂ re-formation maintains a large column of ~300-400 K gas; at these temperatures the chemistry drives a considerable fraction of the oxygen not in CO to form H₂O. The H₂O column densities, the hydrogen densities, and the warm …

The Importance Of Major Mergers In The Build Up Of Stellar Mass In Brightest Cluster Galaxies At Z = 1, C. Lidman, G. Iacobuta, A. E. Bauer, L. F. Barrientos, P. Cerulo, W. J. Couch, L. Delaye, R. Demarco, E. Ellingson, A. J. Faloon, D. Gilbank, M. Huertas-Company, S. Mei, J. Meyers, A. Muzzin, A. Noble, J. Nantais, A. Rettura, P. Rosati, R. Sánchez-Janssen, V. Strazzullo, T. M. A. Webb, G. Wilson, Renbin Yan, H. K. C. Yee

Physics and Astronomy Faculty Publications

Recent independent results from numerical simulations and observations have shown that brightest cluster galaxies (BCGs) have increased their stellar mass by a factor of almost 2 between z ∼ 0.9 and z ∼ 0.2. The numerical simulations further suggest that more than half this mass is accreted through major mergers. Using a sample of 18 distant galaxy clusters with over 600 spectroscopically confirmed cluster members between them, we search for observational evidence that major mergers do play a significant role. We find a major merger rate of 0.38 ± 0.14 mergers per Gyr at z ∼ 1. While the uncertainties, …

Tuning The JEff = 1/2 Insulating State Via Electron Doping And Pressure In The Double-Layered Iridate Sr3Ir2O7, L. Li, P. P. Kong, Tongfei Qi, C. Q. Jin, Shujuan Yuan, Lance E. Delong, P. Schlottmann, Gang Cao

Physics and Astronomy Faculty Publications

Sr₃Ir₂O₇ exhibits a novel J_eff = 1/2 insulating state that features a splitting between J_eff = 1/2 and 3/2 bands due to spin-orbit interaction. We report a metal-insulator transition in Sr3Ir2O7 via either dilute electron doping (La³⁺ for Sr²⁺) or application of high pressure up to 35 GPa. Our study of single-crystal Sr₃Ir₂O₇ and (Sr_1−xLa_x)₃Ir₂O₇ reveals that application of high hydrostatic pressure P leads to a drastic reduction in the electrical resistivity by as much …

Comparative Feedstock Analysis In Setaria Viridis L. As A Model For C4 Bioenergy Grasses And Panicoid Crop Species, Carloalberto Petti, Andrew Shearer, Mizuki Tateno, Mathew J. Ruwaya, Sue E. Nokes, Tom Brutnell, Seth Debolt

Horticulture Faculty Publications

Second generation feedstocks for bioethanol will likely include a sizable proportion of perennial C4 grasses, principally in the Panicoideae clade. The Panicoideae contain agronomically important annual grasses including Zea mays L. (maize), Sorghum bicolor (L.) Moench (sorghum), and Saccharum officinarum L. (sugar cane) as well as promising second generation perennial feedstocks including Miscanthus × giganteus and Panicum virgatum L. (switchgrass). The underlying complexity of these polyploid grass genomes is a major limitation for their direct manipulation and thus driving a need for rapidly cycling comparative model. Setaria viridis (green millet) is a rapid cycling C4 panicoid grass with a relatively …

Polypeptides, Systems, And Methods Useful For Detecting Glucose, Sylvia Daunert, Kendrick Turner, Smita Joel, Laura Rowe

Chemistry Faculty Patents

The presently-disclosed subject matter provides biosensors for detecting molecules of interest. The biosensors include a polypeptide capable of selectively-binding glucose, wherein the polypeptide molecule is selected from: an unnatural analogue of wild type glucose binding protein; a fragment of wild type glucose binding protein; and an unnatural analogue fragment of wild type glucose binding protein.

Influence Of Media Composition On The Growth Rate Of Chlorella Vulgaris And Scenedesmus Acutus Utilized For Co2 Mitigation, Czarena L. Crofcheck, Xinyi E, Aubrey Shea, Michael D. Montross, Mark Crocker, Rodney Andrews

Biosystems and Agricultural Engineering Faculty Publications

Atmospheric carbon dioxide levels have increased since the industrial revolution due to increasing combustion of fossil fuels. One possible CO₂ mitigation strategy is the use of microalgae for mitigation of CO₂. This paper focuses on the influence of media composition on the growth rate of two microalgae strains, Chlorella vulgaris and Scenedesmus actus. A KNO₃ based medium was found to work better for Chlorella, while a urea based equivalent worked better for Scenedesmus. The urea based media investigated here resulted in growth similar to that found with previously reported KNO₃ based media. …

Single-Step Electrochemical Functionalization Of Double-Walled Carbon Nanotube (Dwcnt) Membranes And The Demonstration Of Ionic Rectification, Xin Zhan, Ji Wu, Zhiqiang Chen, Bruce J. Hinds

Chemistry Faculty Publications

Carbon nanotube (CNT) membranes allow the mimicking of natural ion channels for applications in drug delivery and chemical separation. Double-walled carbon nanotube membranes were simply functionalized with dye in a single step instead of the previous two-step functionalization. Non-faradic electrochemical impedance spectra indicated that the functionalized gatekeeper by single-step modification can be actuated to mimic the protein channel under bias. This functional chemistry was proven by a highly efficient ion rectification, wherein the highest experimental rectification factor of ferricyanide was up to 14.4. One-step functionalization by electrooxidation of amine provides a simple and promising functionalization chemistry for the application of …

2,2',5',6-Tetrachloro-4-[(1S)-1-Methylpropoxy]Biphenyl, Hans-Joachim Lehmler, Huimin Wu, Sean Parkin

Chemistry Faculty Publications

In the title molecule, C₁₆H₁₄Cl₄O, the dihedral angle between the least-square planes of the benzene rings is 84.40 (7)°. No unusual intermolecular interactions are present.

Coupled Flow Field Simulations Of Charring Ablators With Nonequilibrium Surface Chemistry, Hicham Alkandry, Iain D. Boyd, Alexandre Martin

Mechanical Engineering Faculty Publications

This paper describes the coupling of a Navier-Stokes solver to a material response code to simulate nonequilibrium gas-surface interactions. The Navier-Stokes solver used in this study is LeMANS, which is a three-dimensional computational fluid dynamics code that can simulate hypersonic reacting flows including thermo-chemical nonequilibrium effects. The material response code employed in this study is MOPAR, which uses the one-dimensional control volume nite-element method to model heat conduction and pyrolysis gas behavior. This coupling is demonstrated using a test case based on the Stardust sample return capsule. Coupled simulations are performed at three different trajectory conditions. The effects of the …

Volume Averaged Modeling Of The Oxidation Of Porous Carbon Fiber Material, Alexandre Martin

Mechanical Engineering Faculty Publications

Charring ablators remain the premium choice for space exploration missions that involve atmospheric re-entry. This type of ablative material is composed of a carbon matrix, usually made of fibers, which is then impregnated with a resin. During re-entry, the high heat flux produced by convective heating causes the material to chemically react. First, the resin pyrolyzes, and is vaporized into a gas that travels through the material, and is eventually ejected at the surface. Then, as the temperature rises, the surface of the porous matrix recess through ablative processes. For re-entry conditions typical of space exploration missions, this is mainly …

Flow-Tube Oxidation Experiments On The Carbon Preform Of Pica, Francesco Panerai, Alexandre Martin, Nagi N. Mansour, Steven A. Sepka, Jean Lachaud

Mechanical Engineering Faculty Publications

Oxidation experiments on the carbon preform of a phenolic-impregnated carbon ablator were performed in the NASA Ames ow-tube reactor facility, at temperatures between 700 and 1300 K, under dry air gas at pressures between 103 and 104 Pa. Mass loss, volumetric recession and density changes were measured at different test conditions. An analysis of the diffusion/reaction competition within the porous material, based on the Thiele number, allowed us to identify low temperature and low pressure conditions to be dominated by in-depth volume oxidation. Experiments above 1000 K were found at transition conditions, where diffusion and reaction occur at similar scales. …

Multi-Dimensional Modeling Pyrolysis Gas Flow Inside Charring Ablators, Haoyue Weng, Alexandre Martin

Mechanical Engineering Faculty Publications

Using an ablative thermal/material response code, the importance of three-dimensionality for modeling ablative test-article is addressed. In particular, the simulation of the pyrolysis gas flow inside a porous material is presented, using two different geometries. The effects of allowing the gas to flow out of the side wall are especially highlighted. Results show that the flow inside the test-article is complex, and that the 0D or 1D assumption made in most Material Response (MR) codes might not be valid for certain geometries.

Estimations Of The Magnetic Field Strength In The Torus Of Ic 5063 Using Near-Infrared Polarimetry, E. Lopez-Rodriguez, C. Packham, S. Young, Moshe Elitzur, N. A. Levenson, R. E. Mason, C. Ramos Almeida, A. Alonso-Herrero, T. J. Jones, E. Perlman

Physics and Astronomy Faculty Publications

An optically and geometrically thick torus obscures the central engine of active galactic nuclei (AGN) from some lines of sight. From a magnetohydrodynamical framework, the torus can be considered to be a particular region of clouds surrounding the central engine where the clouds are dusty and optically thick. In this framework, the magnetic field plays an important role in the creation, morphology and evolution of the torus. If the dust grains within the clouds are assumed to be aligned by paramagnetic alignment, then the ratio of the intrinsic polarization and visual extinction, P(per cent)/A_v, is a …

The X-Ray Properties Of Optically Selected Clusters Of Galaxies, A. K. Hicks, G. W. Pratt, M. Donahue, E. Ellingson, M. Gladders, H. Böhringer, H. K. C. Yee, Renbin Yan, J. H. Croston, D. G. Gilbank

Physics and Astronomy Faculty Publications

We present the results of Chandra and Suzaku X-ray observations of nine moderate-redshift (0.16 < z < 0.42) clusters discovered via the Red-sequence Cluster Survey (RCS). Surface brightness profiles are fitted to β-models, gas masses are determined, integrated spectra are extracted within R₂₅₀₀, and X-ray temperatures and luminosities are inferred. TheL_X–T_X relationship expected from self-similar evolution is tested by comparing this sample to our previous X-ray investigation of nine high-redshift (0.6 < z < 1.0) optically selected clusters. We find that optically selected clusters are systematically less luminous than X-ray selected clusters of similar X-ray temperature at both moderate and high z. We are unable to constrain evolution in the L_X–T_X relation with these data, but find it consistent with no evolution, within relatively large uncertainties. To investigate selection effects, we compare the X-ray properties of our sample to those of clusters in the …

Topography-Guided Spreading And Drying Of 6,13-Bis(Triisopropylsilylethynyl)-Pentacene Solution On A Polymer Insulator For The Field-Effect Mobility Enhancement, Chang-Min Keum, Jin-Hyuk Bae, Min-Hoi Kim, Hea-Lim Park, Marcia M. Payne, John E. Anthony, Sin-Doo Lee

Chemistry Faculty Publications

We report on the enhancement of the field-effect mobility of solution-processed 6,13-bis(triisopropylsilylethynyl)-pentacene (TIPS-pentacene) by unidirectional topography (UT) of an inkjet-printed polymer insulator. The UT leads to anisotropic spreading and drying of the TIPS-pentacene droplet and enables to spontaneously develop the ordered structures during the solvent evaporation. The mobility of the UT-dictated TIPS-pentacene film (0.202 ± 0.012 cm²/Vs) is found to increase by more than a factor of two compared to that of the isotropic case (0.090 ± 0.032 cm²/Vs). The structural arrangement of the TIPS-pentacene molecules in relation to the mobility enhancement is described within an …

Studies Of Ngc 6720 With Calibrated Hst/Wfc3 Emission-Line Filter Images. Iii. Tangential Motions Using Astrodrizzle Images, C. R. O'Dell, Gary J. Ferland, W. J. Henney, M. Peimbert

Physics and Astronomy Faculty Publications

We have been able to compare with astrometric precision AstroDrizzle processed images of NGC 6720 (the Ring Nebula) made using two cameras on the Hubble Space Telescope. The time difference of the observations was 12.925 yr. This large time base allowed the determination of tangential velocities of features within this classic planetary nebula. Individual features were measured in [N II] images as were the dark knots seen in silhouette against background nebular [O III] emission. An image magnification and matching technique was also used to test the accuracy of the usual assumption of homologous expansion. We found that homologous …

Spin Switching And Magnetization Reversal In Single-Crystal Ndfeo3, Shujuan Yuan, W. Ren, F. Hong, Y. B. Wang, J. C. Zhang, L. Bellaiche, Gang Cao

Physics and Astronomy Faculty Publications

We report an experimental and computational study of single-crystal NdFeO₃, which features two inequivalent magnetic sublattices, namely, Fe and Nd sublattices that are coupled in an antiparallel fashion. This paper reveals that a strong interaction between 3d and 4f electrons of the two sublattices along with a spin-lattice coupling drives an extremely interesting magnetic state that is highly sensitive to the orientation and history of weak magnetic field. The following phenomena are particularly remarkable: (1) sharply contrasting magnetization M(T) along the a and c axes; (2) a first-order spin switching along the a …

5,5'-Dichloro-2,2'-Dimethoxybiphenyl, Hans-Joachim Lehmler, Huimin Wu, Sean Parkin

Chemistry Faculty Publications

In the title molecule, C₁₄H₁₂Cl₂O₂, the dihedral angle between the least-square planes of the benzene rings is 62.17 (6)°. Both methoxy groups are slightly out of the plane of the benzene rings to which they are attached, making dihedral angles of 4.22 (18) and 18.82 (16)°.

Method Of Ameliorating Oxidative Stress And Supplementing The Diet, Boyd E. Haley, Niladrl Narayan Gupta

Chemistry Faculty Patents

A method of supplementing a diet and ameliorating oxidative stress in a mammal includes administering a pharmaceutically effective amount of lipid soluble, hydrophobic active compounds having a chemical structure . . .

To see the remainder of this abstract, please download this patent.

Magnetic And Crystal Structures Of Sr2Iro4: A Neutron Diffraction Study, Feng Ye, Songxue Chi, Bryan C. Chakoumakos, Jaime A. Fernandez-Baca, Tongfei Qi, Gang Cao

Center for Advanced Materials Faculty Publications

We report a single-crystal neutron diffraction study of the layered Sr₂IrO₄. This work unambiguously determines the magnetic structure of the system and reveals that the spin orientation rigidly tracks the staggered rotation of the IrO₆ octahedra in Sr₂IrO₄. The long-range antiferromagnetic order has a canted spin configuration with an ordered moment of 0.208(3) μ_B/Ir site within the basal plane; a detailed examination of the spin canting yields 0.202(3) and 0.049(2) μ_B/site for the a axis and the b axis, respectively. It is intriguing that forbidden nuclear reflections …

Classification And Analysis Of Emission-Line Galaxies Using Mean Field Independent Component Analysis, James T. Allen, Paul C. Hewett, Chris T. Richardson, Gary J. Ferland, Jack A. Baldwin

Physics and Astronomy Faculty Publications

We present an analysis of the optical spectra of narrow emission-line galaxies, based on mean field independent component analysis (MFICA), a blind source separation technique. Samples of galaxies were drawn from the Sloan Digital Sky Survey (SDSS) and used to generate compact sets of ‘continuum’ and ‘emission-line’ component spectra. These components can be linearly combined to reconstruct the observed spectra of a wider sample of galaxies. Only 10 components – five continuum and five emission line – are required to produce accurate reconstructions of essentially all narrow emission-line galaxies to a very high degree of accuracy; the median absolute deviations …

Strongly Localized Magnetization Modes In Permalloy Antidot Lattices, J. Sklenar, V. S. Bhat, Lance E. De Long, O. Heinonen, J. B. Ketterson

Physics and Astronomy Faculty Publications

Antidot lattices (ADLs) patterned into soft magnetic thin films exhibit rich ferromagnetic resonance (FMR) spectra corresponding to many different magnetization modes. One of the predicted modes is highly localized at the edges of the antidots; this mode is difficult to detect experimentally. Here we present FMR data for a permalloy thin film patterned into a square array of square antidots. Comparison of these data with micromagnetic simulations permits identification of several edge modes. Our simulations also reveal the effect of the antidot shape on the mode dispersion.

Suppression Of Dielectronic Recombination Due To Finite Density Effects, D. Nikolić, T. W. Gorczyca, K. T. Korista, Gary J. Ferland, N. R. Badnell

Physics and Astronomy Faculty Publications

We have developed a general model for determining density-dependent effective dielectronic recombination (DR) rate coefficients in order to explore finite-density effects on the ionization balance of plasmas. Our model consists of multiplying by a suppression factor those highly-accurate total zero-density DR rate coefficients which have been produced from state-of-the-art theoretical calculations and which have been benchmarked by experiment. The suppression factor is based upon earlier detailed collision-radiative calculations which were made for a wide range of ions at various densities and temperatures, but used a simplified treatment of DR. A general suppression formula is then developed as a function of …

Erratum: 'Improved He I Emissivities In The Case B Approximation', R. L. Porter, Gary J. Ferland, P. J. Storey, M. J. Detisch

Physics and Astronomy Faculty Publications

No abstract provided.

Tuning Electronic Structure Via Exipatial Strain In Sr2Iro4 Thin Films, J. Nichols, Jsaminka Terzic, Emily Geraldine Bittle, Oleksandr B. Korneta, Lance E. De Long, Joseph Brill, Gang Cao, Sung S. Ambrose Seo

Physics and Astronomy Faculty Publications

We have synthesized epitaxial Sr₂IrO₄ thin-films on various substrates and studied their electronic structure as a function of lattice-strain. Under tensile (compressive) strain, increased (decreased) Ir-O-Ir bond-angle is expected to result in increased (decreased) electronic bandwidth. However, we have observed that the two optical absorption peaks near 0.5 eV and 1.0 eV are shifted to higher (lower) energies under tensile (compressive) strain, indicating that the electronic-correlation energy is also affected by in-plane lattice-strain. The effective tuning of electronic structure under lattice-modification provides an important insight into the physics driven by the coexisting strong spin-orbit coupling and electronic …

Expanded Iron Uta Spectra—Probing The Thermal Stability Limits In Agn Clouds, Gary J. Ferland, R. Kisielius, F. P. Keenan, P. A. M. Van Hoof, V. Jonauskas, Matt L. Lykins, R. L. Porter, R. J. R. Williams

Physics and Astronomy Faculty Publications

The Fe unresolved transition arrays (UTAs) produce prominent features in the ~15-17 Å wavelength range in the spectra of active galactic nuclei (AGNs). Here, we present new calculations of the energies and oscillator strengths of inner-shell lines from Fe XIV, Fe XV, and Fe XVI. These are crucial ions since they are dominant at inflection points in the gas thermal stability curve, and UTA excitation followed by autoionization is an important ionization mechanism for these species. We incorporate these, and data reported in previous papers, into the plasma simulation code Cloudy. This updated physics is subsequently employed to reconsider the …

3,4',5-Trichlorobiphenyl-4-Yl 2,2,2-Trichloroethyl Sulfate, Hans-Joachim Lehmler, Xianran He, Michael W. Duffel, Sean Parkin

Chemistry Faculty Publications

Crystals of the title compound, C₁₄H₈Cl₆O₄S, are twinned by inversion, with unequal components [0.85 (3):0.15 (3)]. The asymmetric unit contains two independent molecules that are related by a pseudo-inversion center. The C_ar-O [1.393 (9) and 1.397 (9) Å] and ester S-O bond lengths [1.600 (5) and 1.590 (5) Å] of both molecules are comparable to the structurally related 2,3,5,5-trichlorobiphenyl-4-yl 2,2,2-trichloroethyl sulfate. The dihedral angles between the benzene rings in the two molecules are 37.8 (2) and 35.0 (2)°.