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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

ScalaBLAST 2.0: Rapid and robust BLAST calculations on multiprocessor systems

BLAST remains one of the most widely used tools in computational biology. The rate at which new sequence data is available continues to grow exponentially, driving the emergence of new fields of biological research. At the same time multicore systems and conventional clusters are more accessible. ScalaBLAST has been designed to run on conventional multiprocessor systems with an eye to extreme parallelism, enabling parallel BLAST calculations using over 16,000 processing cores with a portable, robust, fault-resilient design. ScalaBLAST 2.0 source code can be freely downloaded from http://omics.pnl.gov/software/ScalaBLAST.php.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2016

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra

Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a “bird’s eye view” of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem. Results: We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry data sets showed that TopMG outperformed existing methods in identifying complex proteoforms.

Dynamic Programming↗
DOE OSTI2019

Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa)

Abstract Background Anthozoa, Endocnidozoa, and Medusozoa are the 3 major clades of Cnidaria. Medusozoa is further divided into 4 clades, Hydrozoa, Staurozoa, Cubozoa, and Scyphozoa—the latter 3 lineages make up the clade Acraspeda. Acraspeda encompasses extraordinary diversity in terms of life history, numerous nuisance species, taxa with complex eyes rivaling other animals, and some of the most venomous organisms on the planet. Genomes have recently become available within Scyphozoa and Cubozoa, but there are currently no published genomes within Staurozoa and Cubozoa. Findings Here we present 3 new draft genomes of Calvadosia cruxmelitensis (Staurozoa), Alatina alata (Cubozoa), and Cassiopea xamachana (Scyphozoa) for which we provide a preliminary orthology analysis that includes an inventory of their respective venom-related genes. Additionally, we identify synteny between POU and Hox genes that had previously been reported in a hydrozoan, suggesting this linkage is highly conserved, possibly dating back to at least the last common ancestor of Medusozoa, yet likely independent of vertebrate POU-Hox linkages. Conclusions These draft genomes provide a valuable resource for studying the evolutionary history and biology of these extraordinary animals, and for identifying genomic features underlying venom, vision, and life history traits in Acraspeda.

Ohdera, Aki↗
DOE OSTI2021

Detection of the Metabolic Response to Drought Stress Using Hyperspectral Reflectance

Drought is the most important limitation on crop yield. Understanding and detecting drought stress in crops is vital for improving water use efficiency through effective breeding and management. Leaf reflectance spectroscopy offers a rapid, non-destructive alternative to traditional techniques for measuring plant traits involved in a drought response. We measured drought stress in six glasshouse-grown agronomic species using physiological, biochemical and spectral data. In contrast to physiological traits, leaf metabolite concentrations revealed drought stress before it was visible to the naked eye. We used full-spectrum leaf reflectance data to predict metabolite concentrations using partial least-squares regression, with validation R2 values of 0.49 to 0.87. We show for the first time that spectroscopy may be used for the quantitative estimation of proline and abscisic acid, demonstrating the first use of hyperspectral data to detect a phytohormone. We used linear discriminant analysis and partial least squares discriminant analysis to differentiate between droughted and watered plants based on measured traits (accuracy: 71%) and raw spectral data (66%). Finally, we validated our glasshouse-developed models in an independent field trial. We demonstrate that spectroscopy can detect drought stress via underlying biochemical changes, before visual differences occur, representing a powerful advance for measuring limitations on yield.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Wobbly discs – corrugations seen in the dust lanes of edge-on galaxies

ABSTRACT We report the detection of small-scale bending waves, also known as corrugations, in the dust lanes of five nearby edge-on disc galaxies. This phenomenon, where the disc mid-plane bends to become wavy, just as in warps but on a smaller scale, is seen here for the first time, in the dust lanes running across the discs. Because they are seen in absorption, this feature must be present in the dust disc in the outskirts of these galaxies. We enhance the visibility of these features using unsharp masking, trace the dust mid-plane across the disc, measure the corrugation amplitude by eye and the corrugation wavelength using Fourier analysis. The corrugation amplitude is found to be in the range of 70–300pc and the wavelengths lie between 1 and 5 kpc. In this limited sample, we find that the amplitude of the corrugations tends to be larger for lower mass galaxies, whereas the wavelength of corrugation does not seem to depend on the mass of host galaxies. Linear stability analysis is performed to find out the dynamical state of these dust discs. Based on WKB analysis, we find that the dust corrugations in about half of our sample are stable. Further analysis, on a larger sample would be useful to strengthen the above results.

Narayan, Chaitra A.↗
DOE OSTI2020

The Atacama Cosmology Telescope: a CMB lensing mass map over 2100 square degrees of sky and its cross-correlation with BOSS-CMASS galaxies

In this work, we construct cosmic microwave background lensing mass maps using data from the 2014 and 2015 seasons of observations with the Atacama Cosmology Telescope (ACT). These maps cover 2100 square degrees of sky and overlap with a wide variety of optical surveys. The maps are signal dominated on large scales and have fidelity such that their correlation with the cosmic infrared background is clearly visible by eye. We also create lensing maps with thermal Sunyaev-Zel’dovich contamination removed using a novel cleaning procedure that only slightly degrades the lensing signal-to-noise ratio. The cross-spectrum between the cleaned lensing map and the BOSS CMASS galaxy sample is detected at 10σ significance, with an amplitude of A = 1.02 ± 0.10 relative to the Planck best-fitting Lambda cold dark matter cosmological model with fiducial linear galaxy bias. Our measurement lays the foundation for lensing cross-correlation science with current ACT data and beyond.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

A redefinition of the halo boundary leads to a simple yet accurate halo model of large-scale structure

ABSTRACT We present a model for the halo–mass correlation function that explicitly incorporates halo exclusion and allows for a redefinition of the halo boundary in a flexible way. We assume that haloes trace mass in a way that can be described using a single scale-independent bias parameter. However, our model exhibits scale-dependent biasing due to the impact of halo-exclusion, the use of a ‘soft’ (i.e. not infinitely sharp) halo boundary, and differences in the one halo term contributions to ξhm and ξmm. These features naturally lead us to a redefinition of the halo boundary that lies at the ‘by eye’ transition radius from the one-halo to the two-halo term in the halo–mass correlation function. When adopting our proposed definition, our model succeeds in describing the halo–mass correlation function with $\approx 2{{\ \rm per\ cent}}$ residuals over the radial range 0.1 h−1 Mpc < r < 80 h−1 Mpc, and for halo masses in the range 1013 h−1 M⊙ < M < 1015 h−1 M⊙. Our proposed halo boundary is related to the splashback radius by a roughly constant multiplicative factor. Taking the 87 percentile as reference we find rt/Rsp ≈ 1.3. Surprisingly, our proposed definition results in halo abundances that are well described by the Press–Schechter mass function with δsc = 1.449 ± 0.004. The clustering bias parameter is offset from the standard background-split prediction by $\approx 10{{\ \rm per\ cent}}\!-\!15{{\ \rm per\ cent}}$. This level of agreement is comparable to that achieved with more standard halo definitions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Pushing automated morphological classifications to their limits with the Dark Energy Survey

ABSTRACT We present morphological classifications of ∼27 million galaxies from the Dark Energy Survey (DES) Data Release 1 (DR1) using a supervised deep learning algorithm. The classification scheme separates: (a) early-type galaxies (ETGs) from late-type galaxies (LTGs); and (b) face-on galaxies from edge-on. Our convolutional neural networks (CNNs) are trained on a small subset of DES objects with previously known classifications. These typically have mr ≲ 17.7 mag; we model fainter objects to mr < 21.5 mag by simulating what the brighter objects with well-determined classifications would look like if they were at higher redshifts. The CNNs reach 97 per cent accuracy to mr < 21.5 on their training sets, suggesting that they are able to recover features more accurately than the human eye. We then used the trained CNNs to classify the vast majority of the other DES images. The final catalogue comprises five independent CNN predictions for each classification scheme, helping to determine if the CNN predictions are robust or not. We obtain secure classifications for ∼87 per cent and 73 per cent of the catalogue for the ETG versus LTG and edge-on versus face-on models, respectively. Combining the two classifications (a) and (b) helps to increase the purity of the ETG sample and to identify edge-on lenticular galaxies (as ETGs with high ellipticity). Where a comparison is possible, our classifications correlate very well with Sérsic index (n), ellipticity (ϵ), and spectral type, even for the fainter galaxies. This is the largest multiband catalogue of automated galaxy morphologies to date.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

B/PS bulges in DESI Legacy edge-on galaxies – I. Sample building

ABSTRACT We present the biggest up-to-date sample of edge-on galaxies with boxy/peanut-shaped (B/PS) bulges and X-structures. The sample was prepared using images from the Dark Energy Spectroscopic Instrument (DESI) Legacy catalogue and contains about 2000 galaxies. To find suitable candidates in catalogue, we made the assumption that the residues (original images minus model) of galaxies with B/PS bulges should exhibit a characteristic X-shape. Galaxies with such features were selected by eye and then used as input data for a neural network training, which was applied to a bigger sample of edge-on galaxies. Using the available data and the photometric models from the literature, we investigated the observational and statistical properties of the sample created. Comparing the B/D ratios for galaxies with and without B/PS bulges, we found that the B/D ratio for galaxies from our sample is statistically higher, with typical values in the range ≈0.2–0.5 depending on the decomposition procedure. We studied how the opening angles φ of the X-structure and the length of its rays are distributed in the formed sample and found them to be consistent with previous measurements and predictions from N-body models, e.g. $\varphi \gtrsim 25{^\circ }$, but measured here for a much larger number of galaxies. We found a sharp increase in the B/PS bulge fraction for stellar masses log M⋆ ≳ 10.4, but for edge-on galaxies, which complements the results of previous works. The sample can be used in future work to test various bar models and their relationship with B/PS bulges, as well as to study their stability and evolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

Long-term monitoring of PKS 0537-441 with Fermi-LAT and multiwavelength observations

Here, we report on multiwavelength observations of the blazar PKS 0537-441 (z = 0.896) obtained from microwaves through γ-rays by Submillimeter Array, Rapid Eye Mounting, Automatic Telescope for Optical Monitoring (ATOM), Swift and Fermi mostly during 2008 August–2010 April. Strong variability has been observed in γ-rays, with two major flaring episodes (2009 July and 2010 March) and a harder-when-brighter behaviour, quite common for flat spectrum radio quasars and low-synchrotron-peaked BL Lacertae objects (BL Lacs), in 2010 March. In the same way, the spectral energy distribution (SED) of the source cannot be modelled by a simple synchrotron self-Compton model, as opposed to many BL Lacs, but the addition of an external Compton component of seed photons from a dust torus is needed. The 230 GHz light curve showed an increase simultaneous with the γ-ray one, indicating co-spatiality of the mm and γ-ray emission region likely at large distance from the central engine. The low, average, and high activity SED of the source could be fit changing only the electron distribution parameters, but two breaks in the electron distribution are necessary. The ensuing extra spectral break, located at near-infrared (NIR)–optical frequencies, together with that in γ-rays seem to indicate a common origin, most likely due to an intrinsic feature in the underlying electron distribution. An overall correlation between the γ-ray band with the R band and K band has been observed with no significant time lag. On the other hand, when inspecting the light curves on short time-scales some differences are evident. In particular, flaring activity has been detected in NIR and optical bands with no evident γ-ray counterparts in 2009 September and November. Moderate variability has been observed in X-rays with no correlation between flux and photon index. Finally, an increase of the detected X-ray flux with no counterpart at the other wavelengths has been observed in 2008 October, suggesting once more a complex correlation between the emission at different energy bands.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Simulations of radiative turbulent mixing layers

ABSTRACT Radiative turbulent mixing layers should be ubiquitous in multi-phase gas with shear flow. They are a potentially attractive explanation for the high ions such as O vi seen in high-velocity clouds and the circumgalactic medium (CGM) of galaxies. We perform 3D magnetohydrohynamics (MHD) simulations with non-equilibrium (NEI) and photoionization modelling, with an eye towards testing simple analytic models. Even purely hydrodynamic collisional ionization equilibrium (CIE) calculations have column densities much lower than observations. Characteristic inflow and turbulent velocities are much less than the shear velocity, and the layer width $h \propto t_{\mathrm{cool}}^{1/2}$ rather than h ∝ tcool. Column densities are not independent of density or metallicity as analytic scalings predict, and show surprisingly weak dependence on shear velocity and density contrast. Radiative cooling, rather than Kelvin–Helmholtz instability, appears paramount in determining the saturated state. Low pressure due to fast cooling both seeds turbulence and sets the entrainment rate of hot gas, whose enthalpy flux, along with turbulent dissipation, energizes the layer. Regardless of initial geometry, magnetic fields are amplified and stabilize the mixing layer via magnetic tension, producing almost laminar flow and depressing column densities. NEI effects can boost column densities by factors of a few. Suppression of cooling by NEI or photoionization can, in principle, also increase O vi column densities, but, in practice, is unimportant for CGM conditions. To explain observations, sightlines must pierce hundreds or thousands of mixing layers, which may be plausible if the CGM exists as a ‘fog’ of tiny cloudlets.

Ji (季索清), Suoqing↗
DOE OSTI2019

Investigating the multiwavelength behaviour of the flat spectrum radio quasar CTA 102 during 2013–2017

ABSTRACT We present a multiwavelength study of the flat-spectrum radio quasar CTA 102 during 2013–2017. We use radio-to-optical data obtained by the Whole Earth Blazar Telescope, 15 GHz data from the Owens Valley Radio Observatory, 91 and 103 GHz data from the Atacama Large Millimeter Array, near-infrared data from the Rapid Eye Monitor telescope, as well as data from the Swift (optical-UV and X-rays) and Fermi (γ-rays) satellites to study flux and spectral variability and the correlation between flux changes at different wavelengths. Unprecedented γ-ray flaring activity was observed during 2016 November–2017 February, with four major outbursts. A peak flux of (2158 ± 63) × 10−8 ph cm−2 s−1, corresponding to a luminosity of (2.2 ± 0.1) × 1050 erg s−1, was reached on 2016 December 28. These four γ-ray outbursts have corresponding events in the near-infrared, optical, and UV bands, with the peaks observed at the same time. A general agreement between X-ray and γ-ray activity is found. The γ-ray flux variations show a general, strong correlation with the optical ones with no time lag between the two bands and a comparable variability amplitude. This γ-ray/optical relationship is in agreement with the geometrical model that has successfully explained the low-energy flux and spectral behaviour, suggesting that the long-term flux variations are mainly due to changes in the Doppler factor produced by variations of the viewing angle of the emitting regions. The difference in behaviour between radio and higher energy emission would be ascribed to different viewing angles of the jet regions producing their emission.

D’Ammando, F.↗
DOE OSTI2019

Kinetic ‘jets’ from fast-moving pulsars

Abstract Some fast-moving pulsars, such as the Guitar and the Lighthouse, exhibit asymmetric non-thermal emission features that extend well beyond their ram pressure confined pulsar wind nebulae (PWNe). Based on our 3D relativistic simulations, we analytically explain these features as kinetically streaming pulsar wind particles that escaped into the interstellar medium (ISM) due to reconnection between the PWN and ISM magnetic fields. The structure of the reconnecting magnetic fields at the incoming and outgoing regions produces highly asymmetric magnetic bottles therefore and result in asymmetric extended features. For the features to become visible, the ISM magnetic field should be sufficiently high, BISM > 10 $\mu$G. We also discuss archival observations of PWNe displaying evidence of kinetic jets: the Dragonfly PWN (PSR J2021 + 3651), G327.1–1.1, and MSH 11–62, the latter two of which exhibit symmetric ‘snail eyes’ morphologies. We suggest that in those cases the pulsar is moving along the ambient magnetic field in a frisbee-type configuration.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Genome-Wide Characterization of Arabian Peninsula Populations: Shedding Light on the History of a Fundamental Bridge between Continents

Abstract The Arabian Peninsula (AP) was an important crossroad between Africa, Asia, and Europe, being the cradle of the structure defining these main human population groups, and a continuing path for their admixture. The screening of 741,000 variants in 420 Arabians and 80 Iranians allowed us to quantify the dominant sub-Saharan African admixture in the west of the peninsula, whereas South Asian and Levantine/European influence was stronger in the east, leading to a rift between western and eastern sides of the Peninsula. Dating of the admixture events indicated that Indian Ocean slave trade and Islamization periods were important moments in the genetic makeup of the region. The western–eastern axis was also observable in terms of positive selection of diversity conferring lactose tolerance, with the West AP developing local adaptation and the East AP acquiring the derived allele selected in European populations and existing in South Asia. African selected malaria resistance through the DARC gene was enriched in all Arabian genomes, especially in the western part. Clear European influences associated with skin and eye color were equally frequent across the Peninsula.

Fernandes, Veronica↗
DOE OSTI2021

Regioselectivity mechanism of the Thunbergia alata Δ 6 -16:0-acyl carrier protein desaturase

Plant plastidial acyl–acyl carrier protein (ACP) desaturases are a soluble class of diiron-containing enzymes that are distinct from the diiron-containing integral membrane desaturases found in plants and other organisms. The archetype of this class is the stearoyl-ACP desaturase which converts stearoyl-ACP into oleoyl (18:1Δ 9 cis )-ACP. Several variants expressing distinct regioselectivity have been described including a Δ 6 -16:0-ACP desaturase from black-eyed Susan vine ( Thunbergia alata ). We solved a crystal structure of the T. alata desaturase at 2.05 Å resolution. Using molecular dynamics (MD) simulations, we identified a low-energy complex between 16:0-ACP and the desaturase that would position C6 and C7 of the acyl chain adjacent to the diiron active site. The model complex was used to identify mutant variants that could convert the T. alata Δ 6 desaturase to Δ 9 regioselectivity. Additional modeling between ACP and the mutant variants confirmed the predicted regioselectivity. Furthermore, to validate the in-silico predictions, we synthesized two variants of the T. alata desaturase and analyzed their reaction products using gas chromatography-coupled mass spectrometry. Assay results confirmed that mutants designed to convert T. alata Δ 6 to Δ 9 selectivity exhibited the predicted changes. In complementary experiments, variants of the castor desaturase designed to convert Δ 9 to Δ 6 selectivity lost some of their Δ9 desaturation ability and gained the ability to desaturate at the Δ 6 position. The computational workflow for revealing the mechanistic understanding of regioselectivity presented herein lays a foundation for designing acyl-ACP desaturases with novel selectivities to increase the diversity of monoenes available for bioproduct applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2010

Personal Dose Equivalent Conversion Coefficients For Photons To 1 GEV

The personal dose equivalent, H{sub p}(d), is the quantity recommended by the International Commission on Radiation Units and Measurements (ICRU) to be used as an approximation of the protection quantity Effective Dose when performing personal dosemeter calibrations. The personal dose equivalent can be defined for any location and depth within the body. Typically, the location of interest is the trunk where personal dosemeters are usually worn and in this instance a suitable approximation is a 30 cm X 30 cm X 15 cm slab-type phantom. For this condition the personal dose equivalent is denoted as H{sub p,slab}(d) and the depths, d, are taken to be 0.007 cm for non-penetrating and 1 cm for penetrating radiation. In operational radiation protection a third depth, 0.3 cm, is used to approximate the dose to the lens of the eye. A number of conversion coefficients for photons are available for incident energies up to several MeV, however, data to higher energies are limited. In this work conversion coefficients up to 1 GeV have been calculated for H{sub p,slab}(10) and H{sub p,slab}(3) using both the kerma approximation and by tracking secondary charged particles. For H{sub p}(0.07) the conversion coefficients were calculated, but only to 10 MeV due to computational limitations. Additionally, conversions from air kerma to H{sub p,slab}(d) have been determined and are reported. The conversion coefficients were determined for discrete incident energies, but analytical fits of the coefficients over the energy range are provided. Since the inclusion of air can influence the production of secondary charged particles incident on the face of the phantom conversion coefficients have been determined both in vacuo and with the source and slab immersed within a sphere in air. The conversion coefficients for the personal dose equivalent are compared to the appropriate protection quantity, calculated according to the recommendations of the latest International Commission on Radiological Protection (ICRP) guidance.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Atomic photoionization by multiple temporal pairs of slits

In this work, we study interactions between multiple temporal pairs of slits in coherent control of photoionization of S-state atoms using a pulse train of N+1 pairs evenly delayed in time by τ, in which the two pulses in a pair with a delay τ0 are counter-rotating circularly polarized. For interacting two double-slit experiments, while Ramsey interference between two identical Archimedean spirals yields pairs of principal spirals, interference of two spirals with opposite handedness does not lead to spirals, but instead to crocodile-eye-like patterns with nictares. For more than two interacting experiments, the resulting patterns turn out just to be those two reference patterns modulated by different kinds of N-dependent time-energy Fraunhofer functions exhibiting diffraction-grating-like patterns.

74 ATOMIC AND MOLECULAR PHYSICS↗