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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

A new streaked soft x-ray imager for the National Ignition Facility

Here, a new streaked soft x-ray imager has been designed for use on high energy-density (HED) physics experiments at the National Ignition Facility based at the Lawrence Livermore National Laboratory. This streaked imager uses a slit aperture, single shallow angle reflection from a nickel mirror, and soft x-ray filtering to, when coupled to one of the NIF’s x-ray streak cameras, record a 4× magnification, one-dimensional image of an x-ray source with a spatial resolution of less than 90 μm. The energy band pass produced depends upon the filter material used; for the first qualification shots, vanadium and silver-on-titanium filters were used to gate on photon energy ranges of approximately 300–510 eV and 200–400 eV, respectively. A two-channel version of the snout is available for x-ray sources up to 1 mm and a single-channel is available for larger sources up to 3 mm. Both the one and two-channel variants have been qualified on quartz wire and HED physics target shots.

42 ENGINEERING↗
DOE OSTI2016

X-ray optics testing beamline 1-BM at the advanced photon source

Beamline 1-BM at the APS has been reconfigured in part for testing of synchrotron optics with both monochromatic and white beams. Operational since 2013, it was reconfigured to accommodate users of the APS as well as users from other DOE facilities. Energies between 6 and 28 keV are available. The beamline was reconfigured to remove two large mirrors and to provide a 100 mm wide monochromatic beam at 54 m from the source. In addition a custom white beam shutter was implemented for topography exposures as short as 65 millisec over the full available horizontal width. Primary agendas include both white beam and monochromatic beam topography, Talbot grating interferometry, and tests of focusing optics. K-B mirrors, MLLs, and FZPs have been characterized. Measurements of the spatial coherence lengths on the beamline were obtained with Talbot interferometry. Topography data has been reported.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

The Generality of the GUGA MRCI Approach in COLUMBUS for Treating Complex Quantum Chemistry

The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Quasiclassical sampling and Wigner sampling of initial vibrational coordinates and momenta for polyatomic molecules in Monte Carlo molecular dynamics simulations

In a quasiclassical trajectory simulation, the vibrational modes are initialised with quantised vibrational energies, but vibrational phases are sampled by Monte Carlo. This requires an algorithm to assign coordinates and momenta to the various atoms. In this work, we present two methods for implementing this for nonrotating polyatomic molecules, namely, fixed-energy vibrational-state-selected initial conditions and thermal initial conditions. We also present a method for initiating classical trajectories with a ground-state Wigner distribution. These vibrational treatments are sufficient to initialise trajectories for unimolecular processes, and we also show how they can be applied to simulate bimolecular collision processes. The treatments of unimolecular and bimolecular collision processes are available in two Python codes called wigner_state_selected.py and bimolecular_collision.py, respectively, which will generate initial condition files that are recognisable by the SHARC and SHARC-MN computer programs for dynamics calculations. Both codes are available as standalone programs, as well as being included in SHARC-MN, and they will be included in future versions of SHARC. Here, the methods implemented in these codes are mostly also available in the ANT computer program, and those that are not available in ANT will be incorporated in future versions of ANT.

Wigner distribution↗
DOE OSTI2014

Optical spectroscopic observations of blazars and γ-ray blazar candidates in the Sloan digital sky survey data release nine

We present an analysis of the optical spectra available in the Sloan Digital Sky Survey data release nine (SDSS DR9) for the blazars listed in the ROMA-BZCAT and for the γ-ray blazar candidates selected according to their IR colors. First, we adopt a statistical approach based on Monte Carlo simulations to find the optical counterparts of the blazars listed in the ROMA-BZCAT catalog. Then, we crossmatched the SDSS spectroscopic catalog with our selected samples of blazars and γ-ray blazar candidates, searching for those with optical spectra available to classify our blazar-like sources and, whenever possible, to confirm their redshifts. Our main objectives are to determine the classification of uncertain blazars listed in the ROMA-BZCAT and to discover new gamma-ray blazars. For the ROMA-BZCAT sources, we investigated a sample of 84 blazars, confirming the classification for 20 of them and obtaining 18 new redshift estimates. For the γ-ray blazars, indicated as potential counterparts of unassociated Fermi sources or with uncertain nature, we established the blazar-like nature of 8 out of the 27 sources analyzed and confirmed 14 classifications.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

DISSECTING PHOTOMETRIC REDSHIFT FOR ACTIVE GALACTIC NUCLEUS USING XMM- AND CHANDRA-COSMOS SAMPLES

In this paper, we release accurate photometric redshifts for 1692 counterparts to Chandra sources in the central square degree of the Cosmic Evolution Survey (COSMOS) field. The availability of a large training set of spectroscopic redshifts that extends to faint magnitudes enabled photometric redshifts comparable to the highest quality results presently available for normal galaxies. We demonstrate that morphologically extended, faint X-ray sources without optical variability are more accurately described by a library of normal galaxies (corrected for emission lines) than by active galactic nucleus (AGN) dominated templates, even if these sources have AGN-like X-ray luminosities. Preselecting the library on the bases of the source properties allowed us to reach an accuracy {sigma}{sub {Delta}z/(1+z{sub s{sub p{sub e{sub c)}}}}}{approx}0.015 with a fraction of outliers of 5.8% for the entire Chandra-COSMOS sample. In addition, we release revised photometric redshifts for the 1735 optical counterparts of the XMM-detected sources over the entire 2 deg{sup 2} of COSMOS. For 248 sources, our updated photometric redshift differs from the previous release by {Delta}z > 0.2. These changes are predominantly due to the inclusion of newly available deep H-band photometry (H{sub AB} = 24 mag). We illustrate once again the importance of a spectroscopic training sample and how an assumption about the nature of a source together, with the number and the depth of the available bands, influences the accuracy of the photometric redshifts determined for AGN. These considerations should be kept in mind when defining the observational strategies of upcoming large surveys targeting AGNs, such as eROSITA at X-ray energies and the Australian Square Kilometre Array Pathfinder Evolutionary Map of the Universe in the radio band.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

PG 1553+113: FIVE YEARS OF OBSERVATIONS WITH MAGIC

We present the results of five years (2005-2009) of MAGIC observations of the BL Lac object PG 1553+113 at very high energies (VHEs; E > 100 GeV). Power-law fits of the individual years are compatible with a steady mean photon index {Gamma} = 4.27 {+-} 0.14. In the last three years of data, the flux level above 150 GeV shows a clear variability (probability of constant flux < 0.001%). The flux variations are modest, lying in the range from 4% to 11% of the Crab Nebula flux. Simultaneous optical data also show only modest variability that seems to be correlated with VHE gamma-ray variability. We also performed a temporal analysis of (all available) simultaneous Fermi/Large Area Telescope data of PG 1553+113 above 1 GeV, which reveals hints of variability in the 2008-2009 sample. Finally, we present a combination of the mean spectrum measured at VHEs with archival data available for other wavelengths. The mean spectral energy distribution can be modeled with a one-zone synchrotron self-Compton model, which gives the main physical parameters governing the VHE emission in the blazar jet.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

EXTRAGALACTIC BACKGROUND LIGHT FROM HIERARCHICAL GALAXY FORMATION: GAMMA-RAY ATTENUATION UP TO THE EPOCH OF COSMIC REIONIZATION AND THE FIRST STARS

We present a new model of the extragalactic background light (EBL) and corresponding {gamma}{gamma} opacity for intergalactic gamma-ray absorption from z = 0 up to z = 10, based on a semi-analytical model of hierarchical galaxy formation that reproduces key observed properties of galaxies at various redshifts. Including the potential contribution from Population III stars and following the cosmic reionization history in a simplified way, the model is also broadly consistent with available data concerning reionization, particularly the Thomson scattering optical depth constraints from Wilkinson Microwave Anisotropy Probe (WMAP). In comparison with previous EBL studies up to z {approx} 3-5, our predicted {gamma}{gamma} opacity is in general agreement for observed gamma-ray energy below 400/(1 + z) GeV, whereas it is a factor of {approx}2 lower above this energy because of a correspondingly lower cosmic star formation rate, even though the observed ultraviolet (UV) luminosity is well reproduced by virtue of our improved treatment of dust obscuration and direct estimation of star formation rate. The horizon energy at which the gamma-ray opacity is unity does not evolve strongly beyond z {approx} 4 and approaches {approx}20 GeV. The contribution of Population III stars is a minor fraction of the EBL at z = 0, and is also difficult to distinguish through gamma-ray absorption in high-z objects, even at the highest levels allowed by the WMAP constraints. Nevertheless, the attenuation due to Population II stars should be observable in high-z gamma-ray sources by telescopes such as Fermi or the Cherenkov Telescope Array and provide a valuable probe of the evolving EBL in the rest-frame UV. The detailed results of our model are publicly available in numerical form at http://www.slac.stanford.edu/{approx}yinoue/Download.html.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

PHOTOMETRY AND PHOTOMETRIC REDSHIFT CATALOGS FOR THE LOCKMAN HOLE DEEP FIELD

We present broadband photometry and photometric redshifts for 187,611 sources located in {approx}0.5 deg{sup 2} in the Lockman Hole area. The catalog includes 388 X-ray-detected sources identified with the very deep XMM-Newton observations available for an area of 0.2 deg{sup 2}. The source detection was performed on the R{sub c}-, z'-, and B-band images and the available photometry is spanning from the far-ultraviolet to the mid-infrared, reaching in the best-case scenario 21 bands. Astrometry corrections and photometric cross-calibrations over the entire data set allowed the computation of accurate photometric redshifts. Special treatment is undertaken for the X-ray sources, the majority of which are active galactic nuclei (AGNs). For normal galaxies, comparing the photometric redshifts to the 253 available spectroscopic redshifts, we achieve an accuracy of {sigma}{sub {Delta}z/(1+z)} = 0.036, with 12.6% outliers. For the X-ray-detected sources, compared to 115 spectroscopic redshifts, the accuracy is {sigma}{sub {Delta}z/(1+z)} = 0.069, with 18.3% outliers, where the outliers are defined as sources with |z{sub phot} - z{sub spec}| > 0.15 Multiplication-Sign (1 + z{sub spec}). These results are a significant improvement over the previously available photometric redshifts for normal galaxies in the Lockman Hole, while it is the first time that photometric redshifts are computed and made public for AGNs for this field.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

3D-HST WFC3-SELECTED PHOTOMETRIC CATALOGS IN THE FIVE CANDELS/3D-HST FIELDS: PHOTOMETRY, PHOTOMETRIC REDSHIFTS, AND STELLAR MASSES

The 3D-HST and CANDELS programs have provided WFC3 and ACS spectroscopy and photometry over ≈900 arcmin{sup 2} in five fields: AEGIS, COSMOS, GOODS-North, GOODS-South, and the UKIDSS UDS field. All these fields have a wealth of publicly available imaging data sets in addition to the Hubble Space Telescope (HST) data, which makes it possible to construct the spectral energy distributions (SEDs) of objects over a wide wavelength range. In this paper we describe a photometric analysis of the CANDELS and 3D-HST HST imaging and the ancillary imaging data at wavelengths 0.3-8 μm. Objects were selected in the WFC3 near-IR bands, and their SEDs were determined by carefully taking the effects of the point-spread function in each observation into account. A total of 147 distinct imaging data sets were used in the analysis. The photometry is made available in the form of six catalogs: one for each field, as well as a master catalog containing all objects in the entire survey. We also provide derived data products: photometric redshifts, determined with the EAZY code, and stellar population parameters determined with the FAST code. We make all the imaging data that were used in the analysis available, including our reductions of the WFC3 imaging in all five fields. 3D-HST is a spectroscopic survey with the WFC3 and ACS grisms, and the photometric catalogs presented here constitute a necessary first step in the analysis of these grism data. All the data presented in this paper are available through the 3D-HST Web site (http://3dhst.research.yale.edu)

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

A model for dark matter, naturalness and a complete gauge unification

We consider dark matter in a minimal extension of the Standard Model (SM) which breaks electroweak symmetry dynamically and leads to a complete unification of the SM and technicolor coupling constants. The unification scale is determined to be M{sub U}≈2.2×10{sup 15} GeV and the unified coupling α{sub U}≈0.0304. Moreover, unification strongly suggest that the technicolor sector of the model must become strong at the scale of O(TeV). The model also contains a tightly constrained sector of mixing neutral fields stabilized by a discrete symmetry. We find the lightest of these states can be DM with a mass in the range m{sub DM}≈30–800 GeV. We find a large set of parameters that satisfy all available constraints from colliders and from dark matter search experiments. However, most of the available parameter space is within the reach of the next generation of DM search experiments. The model is also sensitive to a modest improvement in the measurement of the precision electroweak parameters.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Identifying the theory of dark matter with direct detection

Identifying the true theory of dark matter depends crucially on accurately characterizing interactions of dark matter (DM) with other species. In the context of DM direct detection, we present a study of the prospects for correctly identifying the low-energy effective DM-nucleus scattering operators connected to UV-complete models of DM-quark interactions. We take a census of plausible UV-complete interaction models with different low-energy leading-order DM-nuclear responses. For each model (corresponding to different spin–, momentum–, and velocity-dependent responses), we create a large number of realizations of recoil-energy spectra, and use Bayesian methods to investigate the probability that experiments will be able to select the correct scattering model within a broad set of competing scattering hypotheses. We conclude that agnostic analysis of a strong signal (such as Generation-2 would see if cross sections are just below the current limits) seen on xenon and germanium experiments is likely to correctly identify momentum dependence of the dominant response, ruling out models with either “heavy” or “light” mediators, and enabling downselection of allowed models. However, a unique determination of the correct UV completion will critically depend on the availability of measurements from a wider variety of nuclear targets, including iodine or fluorine. We investigate how model-selection prospects depend on the energy window available for the analysis. In addition, we discuss accuracy of the DM particle mass determination under a wide variety of scattering models, and investigate impact of the specific types of particle-physics uncertainties on prospects for model selection.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Characterizing the Lyα forest flux probability distribution function using Legendre polynomials

The Lyman-α forest is a highly non-linear field with considerable information available in the data beyond the power spectrum. The flux probability distribution function (PDF) has been used as a successful probe of small-scale physics. In this paper we argue that measuring coefficients of the Legendre polynomial expansion of the PDF offers several advantages over measuring the binned values as is commonly done. In particular, the n -th Legendre coefficient can be expressed as a linear combination of the first n moments, allowing these coefficients to be measured in the presence of noise and allowing a clear route for marginalisation over mean flux. Moreover, in the presence of noise, our numerical work shows that a finite number of coefficients are well measured with a very sharp transition into noise dominance. This compresses the available information into a small number of well-measured quantities. In conclusion, we find that the amount of recoverable information is a very non-linear function of spectral noise that strongly favors fewer quasars measured at better signal to noise.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM)

Abstract Motivation Many recent advancements in single-molecule localization microscopy exploit the stochastic photoswitching of fluorophores to reveal complex cellular structures beyond the classical diffraction limit. However, this same stochasticity makes counting the number of molecules to high precision extremely challenging, preventing key insight into the cellular structures and processes under observation. Results Modelling the photoswitching behaviour of a fluorophore as an unobserved continuous time Markov process transitioning between a single fluorescent and multiple dark states, and fully mitigating for missed blinks and false positives, we present a method for computing the exact probability distribution for the number of observed localizations from a single photoswitching fluorophore. This is then extended to provide the probability distribution for the number of localizations in a direct stochastic optical reconstruction microscopy experiment involving an arbitrary number of molecules. We demonstrate that when training data are available to estimate photoswitching rates, the unknown number of molecules can be accurately recovered from the posterior mode of the number of molecules given the number of localizations. Finally, we demonstrate the method on experimental data by quantifying the number of adapter protein linker for activation of T cells on the cell surface of the T-cell immunological synapse. Availability and implementation Software and data available at https://github.com/lp1611/mol_count_dstorm. Supplementary information Supplementary data are available at Bioinformatics online.

Patel, Lekha↗
DOE OSTI2021

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

Abstract Motivation Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task. Results We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D. Availability and implementation Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

Abstract Motivation Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue–residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue–residue contacts in homodimers from residue–residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue–residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features. Results Tested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset and CASP-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.10% and 33.50% respectively at 6 Å contact threshold, which is substantially better than DeepHomo and DNCON2_inter and similar to Glinter. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs well, even though its accuracy is lower than using true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers. Availability and implementation The source code of DRCon is available at https://github.com/jianlin-cheng/DRCon. The datasets are available at https://zenodo.org/record/5998532#.YgF70vXMKsB. Supplementary information Supplementary data are available at Bioinformatics online.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties

Abstract Motivation BISCAP is a state-of-the-art tool for automatically characterizing biofilm images obtained from Optical Coherence Tomography. Limited availability of other software tools is reported in the field. BISCAP’s first version processes 2D images only. Processing 3D images is a problem of greater scientific relevance since it deals with the entire structure of biofilms instead of their 2D slices. Results Building on the image-processing principles and algorithms proposed earlier for 2D images, these were adapted to the 3D case, and a more general implementation of BISCAP was developed. The primary goal concerns the extension of the initial methodology to incorporate the depth axis in 3D images; multiple improvements were also made to boost computational performance. The calculation of structural properties and visual outputs was extended to offer new insights into the 3D structure of biofilms. BISCAP was tested using 3D images of biofilms with different morphologies, consistently delivering accurate characterizations of 3D structures in a few minutes using standard laptop machines. Low user dependency is required for image analysis. Availability and implementation BISCAP is available from https://github.com/diogonarciso/BISCAP. All images used in the tutorials and the validation examples are available from https://web.fe.up.pt/∼fgm/biscap3d.

Narciso, Diogo A. C. (ORCID:0000000227767477)↗
DOE OSTI2024

Information-incorporated gene network construction with FDR control

Abstract Motivation Large-scale gene expression studies allow gene network construction to uncover associations among genes. To study direct associations among genes, partial correlation-based networks are preferred over marginal correlations. However, FDR control for partial correlation-based network construction is not well-studied. In addition, currently available partial correlation-based methods cannot take existing biological knowledge to help network construction while controlling FDR. Results In this paper, we propose a method called Partial Correlation Graph with Information Incorporation (PCGII). PCGII estimates partial correlations between each pair of genes by regularized node-wise regression that can incorporate prior knowledge while controlling the effects of all other genes. It handles high-dimensional data where the number of genes can be much larger than the sample size and controls FDR at the same time. We compare PCGII with several existing approaches through extensive simulation studies and demonstrate that PCGII has better FDR control and higher power. We apply PCGII to a plant gene expression dataset where it recovers confirmed regulatory relationships and a hub node, as well as several direct associations that shed light on potential functional relationships in the system. We also introduce a method to supplement observed data with a pseudogene to apply PCGII when no prior information is available, which also allows checking FDR control and power for real data analysis. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PCGII.

59 BASIC BIOLOGICAL SCIENCES↗