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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Electronic Structure and Optical Properties of Cu 2 ZnGeSe 4 . First-Principles Calculations and Vacuum-Ultraviolet Spectroscopic Ellipsometric Studies

Cu 2 ZnGeSe 4 is of interest for the development of next-generation thin-film photovoltaic technologies. To understand its electronic structure and related fundamental optical properties, we perform first-principles calculations for three structural variations: kesterite, stannite, and primitive-mixed CuAu phases. The calculated data are compared with the room-temperature dielectric functionϵ=ϵ1+iϵ2 spectrum of polycrystalline Cu 2 ZnGeSe 4 determined by vacuum-ultraviolet spectroscopic ellipsometry in the photon-energy range of 0.7 to 9.0 eV. Ellipsometric data are modeled with the sum of eight Tauc-Lorentz oscillators, and the best-fit model yields the band-gap and Tauc-gap energies of 1.25 and 1.19 eV, respectively. A comparison of overall peak shapes and relative intensities between experimental spectra and the calculated ϵ data for three structural variations suggests that the sample may not have a pure (ordered) kesterite phase. We found that the complex refractive index N=n+ik, normal-incidence reflectivity R, and absorption coefficients α are calculated from the modeled ϵ spectrum, which are also compared with those of Cu 2 ZnSnSe 4 . The spectral features for Cu 2 ZnGeSe 4 appear to be weaker and broader than those for Cu 2 ZnSnSe 4 , which is possibly due to more structural imperfections presented in Cu 2 ZnGeSe 4 than Cu 2 ZnSnSe 4 .

14 SOLAR ENERGY↗
DOE OSTI2020

Measurement of atom resolvability in cryo-EM maps with Q-scores

Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Here, assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong

Abstract Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare, and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among 5 locations and found they achieve close to the same levels of accuracy as Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also implemented a method of uncertainty quantification called conformalized quantile regression that we demonstrate has similar patterns of sensitivity to model misspecification as Bayesian highest posterior density (HPD) and greatly overlap with HPDs, but have lower precision (more conservative). Finally, we trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of region-specific epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster after training. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models.

Evolutionary Biology↗
DOE OSTI2020

Combined Neyman–Pearson chi-square: An improved approximation to the Poisson-likelihood chi-square

We describe an approximation to the widely-used Poisson-likelihood chi-square using a linear combination of Neyman’s and Pearson’s chi-squares, namely “combined Neyman–Pearson chi-square” ($X^2_{CNP}$). Through analytical derivations and toy model simulations, we show that leads to a significantly smaller bias on the best-fit model parameters compared to those using either Neyman’s or Pearson’s chi-square. When the computational cost of using the Poisson-likelihood chi-square is high, $X^2_{CNP}$ provides a good alternative given its natural connection to the covariance matrix formalism.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Cosmological implications of baryon acoustic oscillation measurements

Here, we derive constraints on cosmological parameters and tests of dark energy models from the combination of baryon acoustic oscillation (BAO) measurements with cosmic microwave background (CMB) data and a recent reanalysis of Type Ia supernova (SN) data. Particularly, we take advantage of high-precision BAO measurements from galaxy clustering and the Lyman-α forest (LyaF) in the SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS). Treating the BAO scale as an uncalibrated standard ruler, BAO data alone yield a high confidence detection of dark energy; in combination with the CMB angular acoustic scale they further imply a nearly flat universe. Adding the CMB-calibrated physical scale of the sound horizon, the combination of BAO and SN data into an “inverse distance ladder” yields a measurement of H 0 =67.3±1.1 km s -1 Mpc -1 , with 1.7% precision. This measurement assumes standard prerecombination physics but is insensitive to assumptions about dark energy or space curvature, so agreement with CMB-based estimates that assume a flat ΛCDM cosmology is an important corroboration of this minimal cosmological model. For constant dark energy (Λ), our BAO+SN+CMB combination yields matter density Ω m =0.301±0.008 and curvature Ω k =-0.003±0.003. When we allow more general forms of evolving dark energy, the BAO+SN+CMB parameter constraints are always consistent with flat ΛCDM values at ≈1σ. And while the overall χ 2 of model fits is satisfactory, the LyaF BAO measurements are in moderate (2–2.5σ) tension with model predictions. Models with early dark energy that tracks the dominant energy component at high redshift remain consistent with our expansion history constraints, and they yield a higher H 0 and lower matter clustering amplitude, improving agreement with some low redshift observations. Expansion history alone yields an upper limit on the summed mass of neutrino species, Σm ν <0.56 eV (95% confidence), improving to Σm ν <0.25 eV if we include the lensing signal in the Planck CMB power spectrum. In a flat ΛCDM model that allows extra relativistic species, our data combination yields N eff =3.43±0.26; while the LyaF BAO data prefer higher Neff when excluding galaxy BAO, the galaxy BAO alone favor N eff ≈3. Finally, when structure growth is extrapolated forward from the CMB to low redshift, standard dark energy models constrained by our data predict a level of matter clustering that is high compared to most, but not all, observational estimates.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Monte Carlo Study of Imaging Plate Response to Laser-Driven Aluminum Ion Beams

We measured the response of BAS-TR imaging plate (IP) to energetic aluminum ions up to 222 MeV, and compared it with predictions from a Monte Carlo simulation code using two different IP response models. Energetic aluminum ions were produced with an intense laser pulse, and the response was evaluated from cross-calibration between CR-39 track detector and IP energy spectrometer. For the first time, we obtained the response function of the BAS-TR IP for aluminum ions with a kinetic energy as high as 222 MeV. On close examination of the two IP response models, we confirm that the exponential model fits our experimental data better. Moreover, we find that the IP sensitivity in the exponential model is nearly constant in this energy range, suggesting that the response function can be determined even with little experimental data.

Won, Junho↗
DOE OSTI2016

ESTIMATING THE RADIUS OF THE CONVECTIVE CORE OF MAIN-SEQUENCE STARS FROM OBSERVED OSCILLATION FREQUENCIES

The determination of the size of the convective core of main-sequence stars is usually dependent on the construction of models of stars. Here we introduce a method to estimate the radius of the convective core of main-sequence stars with masses between about 1.1 and 1.5 M {sub ⊙} from observed frequencies of low-degree p -modes. A formula is proposed to achieve the estimation. The values of the radius of the convective core of four known stars are successfully estimated by the formula. The radius of the convective core of KIC 9812850 estimated by the formula is 0.140 ± 0.028 R {sub ⊙}. In order to confirm this prediction, a grid of evolutionary models was computed. The value of the convective-core radius of the best-fit model of KIC 9812850 is 0.149 R {sub ⊙}, which is in good agreement with that estimated by the formula from observed frequencies. The formula aids in understanding the interior structure of stars directly from observed frequencies. The understanding is not dependent on the construction of models.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

SUPERMASSIVE BLACK HOLES AND THEIR HOST SPHEROIDS. I. DISASSEMBLING GALAXIES

Several recent studies have performed galaxy decompositions to investigate correlations between the black hole mass and various properties of the host spheroid, but they have not converged on the same conclusions. This is because their models for the same galaxy were often significantly different and not consistent with each other in terms of fitted components. Using 3.6 μm Spitzer imagery, which is a superb tracer of the stellar mass (superior to the K band), we have performed state-of-the-art multicomponent decompositions for 66 galaxies with directly measured black hole masses. Our sample is the largest to date and, unlike previous studies, contains a large number (17) of spiral galaxies with low black hole masses. We paid careful attention to the image mosaicking, sky subtraction, and masking of contaminating sources. After a scrupulous inspection of the galaxy photometry (through isophotal analysis and unsharp masking) and—for the first time—2D kinematics, we were able to account for spheroids; large-scale, intermediate-scale, and nuclear disks; bars; rings; spiral arms; halos; extended or unresolved nuclear sources; and partially depleted cores. For each individual galaxy, we compared our best-fit model with previous studies, explained the discrepancies, and identified the optimal decomposition. Moreover, we have independently performed one-dimensional (1D) and two-dimensional (2D) decompositions and concluded that, at least when modeling large, nearby galaxies, 1D techniques have more advantages than 2D techniques. Finally, we developed a prescription to estimate the uncertainties on the 1D best-fit parameters for the 66 spheroids that takes into account systematic errors, unlike popular 2D codes that only consider statistical errors.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Implementation of Stochastic Gradient Descent in an Automated Glow Peak Identification Software for Multiple Thermoluminescent Dosimeter Types

A glow-curve analysis code was previously developed in C++ to analyze thermoluminescent dosimeter glow curves using automated peak detection while applying a first-order kinetics model. A newer version of this code was implemented to improve the automated peak detection and curve fitting models. The Stochastic Gradient Descent Algorithm was introduced to replace the prior approach of taking first and second-order derivatives for peak detection. Additionally, early stopping mechanisms were invoked to improve the previously used Levenberg-Marquardt Algorithm employed for curve fitting. The two software versions were compared through glow curve analysis of different thermoluminescent dosimeter materials and calculation of the corresponding figures of merit. Altogether improvements were shown, namely an increase in the number of peaks detected and a reduction of the mean figure of merit by approximately 46%.

137Cs↗
DOE OSTI2016

SU-D-204-05: Fitting Four NTCP Models to Treatment Outcome Data of Salivary Glands Recorded Six Months After Radiation Therapy for Head and Neck Tumors

Purpose: To estimate the radiobiological parameters of four popular NTCP models that describe the dose-response relations of salivary glands to the severity of patient reported dry mouth 6 months post chemo-radiotherapy. To identify the glands, which best correlate with the manifestation of those clinical endpoints. Finally, to evaluate the goodness-of-fit of the NTCP models. Methods: Forty-three patients were treated on a prospective multiinstitutional phase II study for oropharyngeal squamous cell carcinoma. All the patients received 60 Gy IMRT and they reported symptoms using the novel patient reported outcome version of the CTCAE. We derived the individual patient dosimetric data of the parotid and submandibular glands (SMG) as separate structures as well as combinations. The Lyman-Kutcher-Burman (LKB), Relative Seriality (RS), Logit and Relative Logit (RL) NTCP models were used to fit the patients data. The fitting of the different models was assessed through the area under the receiver operating characteristic curve (AUC) and the Odds Ratio methods. Results: The AUC values were highest for the contralateral parotid for Grade ≥ 2 (0.762 for the LKB, RS, Logit and 0.753 for the RL). For the salivary glands the AUC values were: 0.725 for the LKB, RS, Logit and 0.721 for the RL. For the contralateral SMG the AUC values were: 0.721 for LKB, 0.714 for Logit and 0.712 for RS and RL. The Odds Ratio for the contralateral parotid was 5.8 (1.3–25.5) for all the four NTCP models for the radiobiological dose threshold of 21Gy. Conclusion: It was shown that all the examined NTCP models could fit the clinical data well with very similar accuracy. The contralateral parotid gland appears to correlated best with the clinical endpoints of severe/very severe dry mouth. An EQD2Gy dose of 21Gy appears to be a safe threshold to be used as a constraint in treatment planning.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Planck 2015 results: XVIII. Background geometry and topology of the Universe

We report that maps of cosmic microwave background (CMB) temperature and polarization from the 2015 release of Planck data provide the highestquality full-sky view of the surface of last scattering available to date. This enables us to detect possible departures from a globally isotropic cosmology. We present the first searches using CMB polarization for correlations induced by a possible non-trivial topology with a fundamental domain that intersects, or nearly intersects, the last-scattering surface (at comoving distance χ rec ), both via a direct scan for matched circular patterns at the intersections and by an optimal likelihood calculation for specific topologies. We specialize to flat spaces with cubic toroidal (T3) and slab (T1) topologies, finding that explicit searches for the latter are sensitive to other topologies with antipodal symmetry. These searches yield no detection of a compact topology with a scale below the diameter of the last-scattering surface. The limits on the radius R i of the largest sphere inscribed in the fundamental domain (at log-likelihood ratio ΔlnL > -5 relative to a simply-connected flat Planck best-fit model) are: R i > 0.97 χ rec for the T3 cubic torus; and R i > 0.56 χ rec for the T1 slab. The limit for the T3 cubic torus from the matched-circles search is numerically equivalent, R i > 0.97 χ rec at 99% confidence level from polarization data alone. We also perform a Bayesian search for an anisotropic global Bianchi VII h geometry. In the non-physical setting, where the Bianchi cosmology is decoupled from the standard cosmology, Planck temperature data favour the inclusion of a Bianchi component with a Bayes factor of at least 2.3 units of log-evidence. However, the cosmological parameters that generate this pattern are in strong disagreement with those found from CMB anisotropy data alone. Fitting the induced polarization pattern for this model to the Planck data requires an amplitude of -0.10 ± 0.04 compared to the value of + 1 if the model were to be correct. In the physically motivated setting, where the Bianchi parameters are coupled and fitted simultaneously with the standard cosmological parameters, we find no evidence for a Bianchi VII h cosmology and constrain the vorticity of such models to (ω/H) 0 < 7.6 × 10 -10 (95% CL).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Long-Term Effects of Humidity on Stainless Steel Pitting in Sea Salt Exposures

Ground 304 stainless steel (SS) samples were exposed to sea salt particles at 35 °C and two relative humidity (RH) levels for durations ranging from 1 week to 2 years. For all exposure times, pit number density and total pit volume at 40% RH were observed to be considerably greater than those at 76% RH. Statistical analysis of distributions of pit populations for both RH conditions showed that pit number density and total pit volume increased rapidly at first but slowed as exposure time increased. Cross-hatched features were observed in the 40% RH pits while ellipsoidal, faceted pits were observed at 76% RH. Optical profilometry indicated that most pits were not hemispherical. X-ray tomography provided evidence of undercutting and fissures. Piecewise curve fitting modeled the 40% RH data closely, predicting that corrosion damage would eventually plateau. However, a similar treatment of the 76% RH data suggested that corrosion damage would continuously increase, which implied that the piecewise power-law fit was limited in its ability to model atmospheric corrosion generally. Based on these observations, the operative mechanisms determining long-term corrosion behavior were hypothesized to be different depending on the RH of exposure.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Data-Driven Selection of Tessellation Models Describing Polycrystalline Microstructures

Tessellation models have proven to be useful for the geometric description of grain microstructures in polycrystalline materials. With the use of a suitable tessellation model, the complex morphology of grains can be represented by a small number of parameters assigned to each grain, which not only entails a significant reduction in complexity, but also facilitates the investigation of certain geometric features of the microstructure. However, for a given set of microstructural data, the choice of a particular geometric model is traditionally based on researcher intuition. The model should provide a sufficiently good approximation to the data, while keeping the number of parameters small. In this paper, we discuss general aspects of the process of model selection and suggest several criteria for selecting an appropriate candidate from a certain set of tessellation models. The choice of candidate represents a trade-off between accuracy and complexity of the model. Here, the selected model is used solely to approximate given data samples, but it also provides guidance for developing stochastic tessellation models and generating virtual microstructures. Model fitting is carried out by simulated annealing, applied in a consistent manner to twelve different tessellation models.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

MAGIC gamma-ray and multi-frequency observations of flat spectrum radio quasar PKS 1510-089 in early 2012

Aims. We report amongst more than fifty blazars detected in very high energy (VHE, E> 100 GeV) γ rays, only three belong to the subclass of flat spectrum radio quasars (FSRQs). The detection of FSRQs in the VHE range is challenging, mainly because of their soft spectra in the GeV-TeV regime. MAGIC observed PKS 1510-089 (z = 0.36) starting 2012 February 3 until April 3 during a high activity state in the high energy (HE, E> 100 MeV) γ-ray band observed by AGILE and Fermi. MAGIC observations result in the detection of a source with significance of 6.0 standard deviations (σ). We study the multi-frequency behaviour of the source at the epoch of MAGIC observation, collecting quasi-simultaneous data at radio and optical (GASP-WEBT and F-Gamma collaborations, REM, Steward, Perkins, Liverpool, OVRO, and VLBA telescopes), X-ray (Swift satellite), and HE γ-ray frequencies. Methods. We study the VHE γ-ray emission, together with the multi-frequency light curves, 43 GHz radio maps, and spectral energy distribution (SED) of the source. The quasi-simultaneous multi-frequency SED from the millimetre radio band to VHE γ rays is modelled with a one-zone inverse Compton model. We study two different origins of the seed photons for the inverse Compton scattering, namely the infrared torus and a slow sheath surrounding the jet around the Very Long Baseline Array (VLBA) core. Results. We find that the VHE γ-ray emission detected from PKS 1510-089 in 2012 February-April agrees with the previous VHE observations of the source from 2009 March-April. We find no statistically significant variability during the MAGIC observations on daily, weekly, or monthly time scales, while the other two known VHE FSRQs (3C 279 and PKS 1222+216) have shown daily scale to sub-hour variability. The γ-ray SED combining AGILE, Fermi and MAGIC data joins smoothly and shows no hint of a break. The multi-frequency light curves suggest a common origin for the millimetre radio and HE γ-ray emission, and the HE γ-ray flaring starts when the new component is ejected from the 43 GHz VLBA core and the studied SED models fit the data well. However, the fast HE γ-ray variability requires that within the modelled large emitting region, more compact regions must exist. Lastly, we suggest that these observed signatures would be most naturally explained by a turbulent plasma flowing at a relativistic speed down the jet and crossing a standing conical shock.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

A study of defect structures in Fe-alloyed ZnO: Morphology, magnetism, and hyperfine interactions

In order to study the effect of Fe cation substitution on the local structure, defect formation, and hyperfine interactions in ZnO, Mössbauer spectroscopy measurements of the microwave processed Zn 1 - x Fe x O (x = 0.05, 0.10, 0.15, and 0.20) nanoparticles, together with ab initio calculations, were performed. Complementary information on the distribution of particle size and morphology, as well as magnetic properties, were obtained by X-ray diffraction, transmission electron microscopy, and squid-magnetometry. The selected model for analyzing the Mössbauer spectra of our samples is a distribution of quadrupole splittings. The fitting model with two Lorentz doublets was rejected due to its failure to include larger doublets. The Fe 3 + ions do not yield magnetic ordering in the samples at room temperature. The results from first-principles calculations confirm that the major component of the Mössbauer spectra corresponds to the Fe-alloyed ZnO with Zn vacancy in the next nearest neighbor environment. The magnetic measurements are consistent with the description of the distribution of iron ions over the randomly formed clusters in the ZnO host lattice. While at room temperature all the samples are paramagnetic, magnetic interactions cause a transition into a cluster spin-glass state at low temperatures. © 2019 Author(s).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

MODELING THE RESOLVED DISK AROUND THE CLASS 0 PROTOSTAR L1527

We present high-resolution sub/millimeter interferometric imaging of the Class 0 protostar L1527 IRS (IRAS 04368+2557) at {lambda} = 870 {mu}m and 3.4 mm from the Submillimeter Array and Combined Array for Research in Millimeter Astronomy. We detect the signature of an edge-on disk surrounding the protostar with an observed diameter of 180 AU in the sub/millimeter images. The mass of the disk is estimated to be 0.007 M{sub Sun }, assuming optically thin, isothermal dust emission. The millimeter spectral index is observed to be quite shallow at all the spatial scales probed: {alpha} {approx} 2, implying a dust opacity spectral index {beta} {approx} 0. We model the emission from the disk and surrounding envelope using Monte Carlo radiative transfer codes, simultaneously fitting the sub/millimeter visibility amplitudes, sub/millimeter images, resolved L' image, spectral energy distribution, and mid-infrared spectrum. The best-fitting model has a disk radius of R = 125 AU, is highly flared (H{proportional_to}R {sup 1.3}), has a radial density profile {rho}{proportional_to}R {sup -2.5}, and has a mass of 0.0075 M{sub Sun }. The scale height at 100 AU is 48 AU, about a factor of two greater than vertical hydrostatic equilibrium. The resolved millimeter observations indicate that disks may grow rapidly throughout the Class 0 phase. The mass and radius of the young disk around L1527 are comparable to disks around pre-main-sequence stars; however, the disk is considerably more vertically extended, possibly due to a combination of lower protostellar mass, infall onto the disk upper layers, and little settling of {approx}1 {mu}m-sized dust grains.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

NGC 7457: evidence for merger-driven cylindrical rotation in disc galaxies

ABSTRACT We construct Schwarzschild orbit-based models of NGC 7457, known as a peculiar low-mass lenticular galaxy. Our best-fitting model successfully retrieves most of the unusual kinematics behaviours of this galaxy, in which, the orbital distribution of stars is dominated by warm and hot orbits. The reconstructed surface brightness of the hot component matches fairly well the photometric bulge and the reconstructed LOSVD map of this component shows clear rotation around the major photometric axis of the galaxy. In the absence of a dominant cold component, the outer part of our model is dominated by warm orbits, representing an exponential thick disc. Our orbital analysis also confirms the existence of a counter-rotating orbital substructure in the very centre, reported in previous observational studies. By comparing our model with a variety of simulation studies, and considering the stellar kinematics and populations properties of this galaxy, we suggest that the thick disc is most likely a dynamically heated structure, formed through the interactions and accretion of satellite(s) with near-polar initial inclination. We also suggest a merger-driven process as the most plausible scenario to explain the observed and dynamically modelled properties of the bulge of NGC 7457. We conclude that both the high level of cylindrical rotation and unusually low velocity dispersion reported for the NGC 7457 have most likely external origins. Therefore, NGC 7457 could be considered as a candidate for merger-driven cylindrical rotation in the absence of a strong bar in disc galaxies.

Molaeinezhad, A.↗