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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Optical Variability of ICRF3 Quasars in the Pan-STARRS 3Pi Survey with Functional Principal Component Analysis

We make use of individual (epoch) detection data from the Pan-STARRS “3π” survey for 2863 optical ICRF3 counterparts in the five wavelength bands g, r, i, z, and y, published as part of the Data Release 2. A dedicated method based on the Functional Principal Component Analysis is developed for these sparse and irregularly sampled data. With certain regularization and normalization constraints, it allows us to obtain uniform and compatible estimates of the variability amplitudes and average magnitudes between the passbands and objects. We find that the starting assumption of affinity of the light curves for a given object at different wavelengths is violated for several percent of the sample. The distributions of rms variability amplitudes are strongly skewed toward small values, peaking at ∼0.1 mag with tails stretching to 2 mag. Statistically, the lowest variability is found for the r band and the largest for the reddest y band. A small “brighter-redder” effect is present, with amplitudes in y greater than amplitudes in g in 57% of the sample. The variability versus redshift dependence shows a strong decline with z toward redshift 3, which we interpret as the time dilation of the dominant time frequencies. The colors of radio-loud ICRF3 quasars are correlated with redshift in a complicated, wavy pattern governed by the emergence of brightest emission lines within the five passbands.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Functional Principal Component Analysis of Radio–Optical Reference Frame Tie

The Gaia optical reference frame is intrinsically undefined with respect to global orientation and spin, so it needs to be anchored in the radio-based International Celestial Reference Frame (ICRF) to provide a referenced and quasi-inertial celestial coordinate system. The link between the two fundamental frames is realized through two samples of distant extragalactic sources, mostly active galactic nuclei and quasars, but only the smaller sample of radio-loud ICRF sources with optical counterparts is available to determine the mutual orientation. The robustness of this link can be mathematically formulated in the framework of functional principal component analysis using a set of vector spherical harmonics to represent the differences in celestial positions of the common objects. The weakest eigenvectors are computed, which describe the greatest deficiency of the link. The deficient or poorly determined terms are specific vector fields on the sphere that carry the largest errors of absolute astrometry using Gaia in reference to the ICRF. This analysis provides guidelines for the future development of the ICRF maximizing the accuracy of the link over the entire celestial sphere. A measure of the robustness of a least-squares solution, which can be applied to any linear model fitting problem, is introduced to help discriminate between reference frame tie models of different degrees.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Photon wave function formalism for analysis of Mach–Zehnder interferometer and sum-frequency generation

Biakynicki-Birula introduced a photon wave function similar to the matter wave function that satisfies the Schrödinger equation. Its second quantization form can be applied to investigate nonlinear optics at nearly full quantum level. In this paper, we applied the photon wave function formalism to analyze both linear optical processes in the well-known Mach–Zehnder interferometer and nonlinear optical processes for sum-frequency generation in dispersive and lossless medium. Results by photon wave function formalism agree with the well-established Maxwell treatments and existing experimental verifications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Elastic functional principal component regression

We study regression using functional predictors in situations where these functions contains both phase and amplitude variability. In other words, the functions are misaligned due to errors in time measurements, and these errors can significantly degrade both model estimation and prediction performance. The current techniques either ignore the phase variability, or handle it via preprocessing, that is, use an off–the–shelf technique for functional alignment and phase removal. We develop a functional principal component regression model which has a comprehensive approach in handling phase and amplitude variability. The model utilizes a mathematical representation of the data known as the square–root slope function. These functions preserve the L 2 norm under warping and are ideally suited for simultaneous estimation of regression and warping parameters. Furthermore, using both simulated and real–world data sets, we demonstrate our approach and evaluate its prediction performance relative to current models. In addition, we propose an extension to functional logistic and multinomial logistic regression.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Infrared and Raman spectroscopy of α-ZrW 2 O 8 : A comprehensive density functional perturbation theory and experimental study

We report that cubic zirconium tungstate (α-ZrW 2 O 8 ), a well-known negative thermal expansion material, has been investigated within the framework of density functional perturbation theory (DFPT), combined with experimental characterization to assess and validate computational results. Using combined Fourier transform infrared measurements and DFPT calculations, new and extensive assignments were made for the far-infrared (<400 cm -1 ) spectrum of α-ZrW 2 O 8 . Lastly, a systematic comparison of DFPT-simulated infrared, Raman, and phonon density-of-state spectra with Fourier transform far-/mid-infrared and Raman data collected in this study, as well as with available inelastic neutron scattering measurements, shows the superior accuracy of the PBEsol exchange-correlation functional over standard PBE calculations for studying the spectroscopic properties of this material.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Analysis of Variance of Functional Data (F-ANOVA) [Slides]

Goals: What is Analysis of Variance (ANOVA); Extending Analysis of Variance to Function Data (F-ANOVA); The role of stochastic processes in F-ANOVA; One and Two Sample Problems for F-ANOVA; One-Way F-ANOVA.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Wavelet analysis of MR functional data from the cerebellum

The main goal of this project was to create a computer algorithm based on wavelet analysis of BOLD signals, which automatically diagnosed ADHD using information from resting state MR experiments. Male right handed volunteers (infants with ages between 7 and 11 years old) were studied and compared with age matched controls. Wavelet analysis, which is a mathematical tool used to decompose time series into elementary constituents and detect hidden information, was applied here to the BOLD signal obtained from the cerebellum 8 region of all our volunteers. Statistical differences between the values of the a parameters of wavelet analysis was found and showed significant differences (p<0.02) between groups. This difference might help in the future to distinguish healthy from ADHD patients and therefore diagnose ADHD.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Symmetry-mode analysis for local structure investigations using pair distribution function data

Symmetry-adapted distortion modes provide a natural way of describing distorted structures derived from higher-symmetry parent phases. Structural refinements using symmetry-mode amplitudes as fit variables have been used for at least ten years in Rietveld refinements of the average crystal structure from diffraction data; more recently, this approach has also been used for investigations of the local structure using real-space pair distribution function (PDF) data. Here, the value of performing symmetry-mode fits to PDF data is further demonstrated through the successful application of this method to two topical materials: TiSe2, where a subtle but long-range structural distortion driven by the formation of a charge-density wave is detected, and MnTe, where a large but highly localized structural distortion is characterized in terms of symmetry-lowering displacements of the Te atoms. Here, the analysis is performed using fully open-source code within the DiffPy framework via two packages developed for this work: isopydistort, which provides a scriptable interface to the ISODISTORT web application for group theoretical calculations, and isopytools, which converts the ISODISTORT output into a DiffPy-compatible format for subsequent fitting and analysis. These developments expand the potential impact of symmetry-adapted PDF analysis by enabling high-throughput analysis and removing the need for any commercial software.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Configuration mixing of angular-momentum-projected triaxial relativistic mean-field wave functions. II. Microscopic analysis of low-lying states in magnesium isotopes

The recently developed structure model that uses the generator coordinate method to perform configuration mixing of angular-momentum projected wave functions, generated by constrained self-consistent relativistic mean-field calculations for triaxial shapes (3DAMP+GCM), is applied in a systematic study of ground states and low-energy collective states in the even-even magnesium isotopes {sup 20-40}Mg. Results obtained using a relativistic point-coupling nucleon-nucleon effective interaction in the particle-hole channel and a density-independent {delta} interaction in the pairing channel are compared to data and with previous axial 1DAMP+GCM calculations, both with a relativistic density functional and the nonrelativistic Gogny force. The effects of the inclusion of triaxial degrees of freedom on the low-energy spectra and E2 transitions of magnesium isotopes are examined.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Synthetic Access to a Framework-Stabilized and Fully Sulfided Analogue of an Anderson Polyoxometalate that is Catalytically Competent for Reduction Reactions

Polyoxometalates (POMs) featuring 7, 12, 18, or more redox-accessible transition metal ions are ubiquitous as selective catalysts, especially for oxidation reactions. The corresponding synthetic and catalytic chemistry of stable, discrete, capping-ligand-free polythiometalates (PTMs), which could be especially attractive for reduction reactions, is much less well developed. Among the challenges are the propensity of PTMs to agglomerate and the tendency for agglomeration to block reactant access of catalyst active sites. Nevertheless, the pervasive presence of transition metal sulfur clusters metalloenzymes or cofactors that catalyze reduction reactions and the justifiable proliferation of studies of two-dimensional (2D) metal-chalcogenides as reduction catalysts point to the promise of well-defined and controllable PTMs as reduction catalysts. Here, we report the fabrication of agglomeration-immune, reactant-accessible, capping-ligand-free Co II Mo 6 IV S 24 n– clusters as periodic arrays in a water-stable, hierarchically porous Zr-metal–organic framework (MOF; NU1K) by first installing a disk-like Anderson polyoxometalate, Co III Mo 6 VI O 24 m– , in size-matched micropores where the siting is established via difference electron density (DED) X-ray diffraction (XRD) experiments. Flowing H 2 S, while heating, reduces molybdenum(VI) ions to Mo(IV) and quantitatively replaces oxygen anions with sulfur anions (S 2– , HS – , S 2 2– ). DED maps show that MOF-templated POM-to-PTM conversion leaves clusters individually isolated in open-channel-connected micropores. Importantly, the structure of the immobilized cluster as determined, in part, by X-ray photoelectron spectroscopy (XPS), X-ray absorption fine structure (XAFS) analysis, and pair distribution function (PDF) analysis of total X-ray scattering agrees well with the theoretically simulated structure. PTM@MOF displays both electrocatalytic and photocatalytic competency for hydrogen evolution. Nevertheless, the initially installed PTM appears to be a precatalyst, gaining competency only after the loss of ~3 to 6 sulfurs and exposure to hydride-forming metal ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Room temperature analysis of dielectric function of ZnO-based thin film on fused quartz substrate

A set of sample consist of pure ZnO and Cu-doped ZnO film were grown on fused-quartz substrates using pulsed laser deposition (PLD) technique. Here, we report room temperature spectroscopic ellipsometry analysis (covering energy range of 0.5 to 6.3 eV) of pure ZnO film and Cu doped ZnO film at 8 in at. %. The thickness of pure ZnO and Cu-doped ZnO film using in this study is about 350 nm. To extract the dielectric function of ZnO thin film, multilayer modeling is performed which takes into account reflections at each interface through Fresnel coefficients. This method based on Drude-Lorentz models that connect with Kramers-Kronig relations. The best fitting of Ψ (amplitude ratio) and Δ (phase difference) taken by SE measurement are obtained reasonably well by mean the universal fitting of three different photon incident angles. The imaginary part of dielectric function (ε{sub 2}) show the broad peak at around 3.3 eV assigned as combination of optical band energy edge with excitonic states. The exitonic states could not be observed clearly in this stage. The evolution of extracted dielectric function is observable by introducing 8% Cu as indicated by decreasing of excitonic intensity. This result indicates the screening of excitonic state. This study will bring us to have a good undestanding for the role of Cu impurities for ZnO thin films.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Comparative analysis of the functional properties of human and mouse ferroportin

Ferroportin (Fpn)—expressed at the plasma membrane of macrophages, enterocytes, and hepatocytes—mediates the transfer of cellular iron into the blood plasma. Under the control of the iron-regulatory hormone hepcidin, Fpn serves a critical role in systemic iron homeostasis. Although we have previously characterized human Fpn, a great deal of research in iron homeostasis and disorders uses mouse models. By way of example, the flatiron mouse, a model of classical ferroportin disease, bears the mutation H32R in Fpn and is characterized by systemic iron deficiency and macrophage iron retention. The flatiron mouse also appears to exhibit a manganese phenotype, raising the possibility that mouse Fpn serves a role in manganese metabolism. At odds with this observation, we have found that human Fpn does not transport manganese, so we considered the possibility that a species difference could explain this discrepancy. We tested the hypothesis that mouse but not human Fpn can transport manganese and performed a comparative analysis of mouse and human Fpn. We examined the functional properties of human Fpn, mouse Fpn, and mutant mouse Fpn by using radiotracer assays in RNA-injected Xenopus oocytes. We found that neither mouse nor human Fpn transports manganese. Mouse and human Fpn share identical properties with respect to substrate profile, calcium dependence, optimal pH, and hepcidin sensitivity. We have also demonstrated that Fpn is not an ATPase pump. Our findings validate the use of mouse models of ferroportin function in iron homeostasis and disease.

Cell Biology↗
DOE OSTI2016

Density functional theory + U analysis of the electronic structure and defect chemistry of LSCF (La 0.5 Sr 0.5 Co 0.25 Fe 0.75 O 3-δ )

Reducing operating temperatures is a key step in making solid oxide fuel cell (SOFC) technology viable. A promising strategy for accomplishing this goal is employing mixed ion–electron conducting (MIEC) cathodes. La 1-x Sr x Co 1-y Fe y O 3-δ (LSCF) is the most widely employed MIEC cathode material; however, rational optimization of the composition of LSCF requires fundamental insight linking its electronic structure to its defect chemistry. To provide the necessary insight, density functional theory plus U (DFT+U) calculations are used to investigate the electronic structure of LSCF (xSr = 0.50, yCo = 0.25). The DFT+U calculations show that LSCF has a significantly different electronic structure than La 1-x Sr x FeO 3 because of the addition of cobalt, but that minimal electronic structure differences exist between La 0.5 Sr 0.5 Co 0.25 Fe 0.75 O 3 and La 0.5 Sr 0.5 Co 0.5 Fe 0.5 O 3 . The oxygen vacancy (V$-\atop{o}$) formation energy (ΔEf,vac) is calculated for V$-\atop{o}$ residing in different local environments within La 0.5 Sr 0.5 Co 0.25 Fe 0.75 O 3 . These results show that Co-V$-\atop{o}$-Co configurations have the highest ΔEf,vac, while Co-V$-\atop{o}$-Fe have the lowest ΔEf,vac and may act as traps for V$-\atop{o}$. We conclude that compositions with more Fe than Co are preferred because the additional Co-V$-\atop{o}$-Co sites would lead to higher overall ΔEf,vac (and lower V$-\atop{o}$ concentrations), while the trapping strength of the Image Co-V$-\atop{o}$-Fe sites is relatively weak (~0.3 eV).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Functional and structural analysis of a highly-expressed Yersinia pestis small RNA following infection of cultured macrophages

Non-coding small RNAs (sRNAs) are found in practically all bacterial genomes and play important roles in regulating gene expression to impact bacterial metabolism, growth, and virulence. We performed transcriptomics analysis to identify sRNAs that are differentially expressed in Yersinia pestis that invaded the human macrophage cell line THP-1, compared to pathogens that remained extracellular in the presence of host. Using ultra high-throughput sequencing, we identified 37 novel and 143 previously known sRNAs in Y. pestis . In particular, the sRNA Ysr170 was highly expressed in intracellular Yersinia and exhibited a log2 fold change ~3.6 higher levels compared to extracellular bacteria. We found that knock-down of Ysr170 expression attenuated infection efficiency in cell culture and growth rate in response to different stressors. In addition, we applied selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to determine the secondary structure of Ysr170 and observed structural changes resulting from interactions with the aminoglycoside antibiotic gentamycin and the RNA chaperone Hfq. Interestingly, gentamicin stabilized helix 4 of Ysr170, which structurally resembles the native gentamicin 16S ribosomal binding site. Lastly, we modeled the tertiary structure of Ysr170 binding to gentamycin using RNA motif modeling. Integration of these experimental and structural methods can provide further insight into the design of small molecules that can inhibit function of sRNAs required for pathogen virulence.

59 BASIC BIOLOGICAL SCIENCES↗