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All sourcesNASA NTRSDOE OSTI
NASA NTRS2006

Herschel and the Molecular Universe

Over the next decade, space-based missions will open up the universe to high spatial and spectral resolution studies at infrared and submillimeter wavelengths. This will allow us to study, in much greater detail, the composition and the origin and evolution of molecules in space. Moreover, molecular transitions in these spectral ranges provide a sensitive probe of the dynamics and the physical and chemical conditions in a wide range of objects at scales ranging from budding planetary systems to galactic and extragalactic sizes. Hence, these missions provide us with the tools to study key astrophysical and astrochemical processes involved in the formation and evolution of planets, stars, and galaxies. These new missions can be expected to lead to the detection of many thousands of new spectral features. Identification, analysis and interpretation of these features in terms of the physical and chemical characteristics of the astronomical sources will require detailed astronomical modeling tools supported by laboratory measurements and theoretical studies of chemical reactions and collisional excitation rates on species of astrophysical relevance. These data will have to be made easily accessible to the scientific community through web-based data archives. In this paper, we will review the Herschel mission and its expected impact on our understanding of the molecular universe.

Tielens, A. G. G. M.↗
NASA NTRS2006

The Swift/BAT Hard X-Ray Survey

The BAT instrument on Swift is a wide field (70 deg. '100 deg.) coded aperture instrument with a CdZnTe detector array sensitive to energies of 14-200 keV. Each day, the BAT survey typically covers 60% of the sky to a detection limit of 30 millicrab. BAT makes hard X-ray light curves of similar sensitivity and coverage to the X-ray light curves from XTE/ASM, but in an energy range where sources show remarkably different behavior. Integrating the BAT data produces an all sky map with a source detection limit at 15 months of a few 10(exp -11) ergs per square centimeter per second, depending on the exposure. This is the first uniform all-sky survey at energies high enough to be unaffected by absorption since HEAO 1 in 1977-8. BAT has detected greater than 200 AGN and greater than 180 galactic sources. At high galactic latitudes, the BAT sources are usually easy to identify, but many are heavily absorbed and there are a few quite surprising identifications. The BAT selected galaxies can be used to calculate LogN/LogS and the luminosity function for AGN which are complete and free from common systematics. Several crucial parameters for understanding the cosmic hard x-ray background are now determined.

Tueller, Jack↗
DOE OSTI2014

A Multi-Contact, Low Capacitance HPGe Detector for High Rate Gamma Spectroscopy

The detection, identification and non-destructive assay of special nuclear materials and nuclear fission by-products are critically important activities in support of nuclear non-proliferation programs. Both national and international nuclear safeguard agencies recognize that current accounting methods for spent nuclear fuel are inadequate from a safeguards perspective. Radiation detection and analysis by gamma-ray spectroscopy is a key tool in this field, but no instrument exists that can deliver the required performance (energy resolution and detection sensitivity) in the presence of very high background count rates encountered in the nuclear safeguards arena. The work of this project addresses this critical need by developing a unique gamma-ray detector based on high purity germanium that has the previously unachievable property of operating in the 1 million counts-per-second range while achieving state-of-the-art energy resolution necessary to identify and analyze the isotopes of interest. The technical approach was to design and fabricate a germanium detector with multiple segmented electrodes coupled to multi-channel high rate spectroscopy electronics. Dividing the germanium detector’s signal electrode into smaller sections offers two advantages; firstly, the energy resolution of the detector is potentially improved, and secondly, the detector is able to operate at higher count rates. The design challenges included the following; determining the optimum electrode configuration to meet the stringent energy resolution and count rate requirements; determining the electronic noise (and therefore energy resolution) of the completed system after multiple signals are recombined; designing the germanium crystal housing and vacuum cryostat; and customizing electronics to perform the signal recombination function in real time. In this phase I work, commercial off-the-shelf electrostatic modeling software was used to develop the segmented germanium crystal geometry, which underwent several iterations before an optimal electrode configuration was found. The model was tested and validated against real-world measurements with existing germanium detectors. Extensive modeling of electronic noise was conducted using established formulae, and real-world measurements were performed on candidate front-end electronic components. This initial work proved the feasibility of the design with respect to expected high count rate and energy resolution performance. Phase I also delivered the mechanical design of the detector housing and vacuum cryostat to be built in Phase II. Finally, a Monte Carlo simulation was created to show the response of the complete design to a Cs-137 source. This development presents a significant advance for nuclear safeguards instrumentation with increased speed and accuracy of detection and identification of special nuclear materials. Other significant applications are foreseen for a gamma-ray detector that delivers high energy resolution (1keV FWHM noise) at high count rate (1 Mcps), especially in the areas of physics research and materials analysis.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2013

CHANDRA VIEW OF THE WARM-HOT INTERGALACTIC MEDIUM TOWARD 1ES 1553+113: ABSORPTION-LINE DETECTIONS AND IDENTIFICATIONS. I

We present the first results from our pilot 500 ks Chandra Low Energy Transmission Grating Large Program observation of the soft X-ray brightest source in the z {approx}> 0.4 sky, the blazar 1ES 1553+113, aimed to secure the first uncontroversial detections of the missing baryons in the X-rays. We identify a total of 11 possible absorption lines, with single-line statistical significances between 2.2{sigma} and 4.1{sigma}. Six of these lines are detected at high single-line statistical significance (3.6 {<=} {sigma} {<=} 4.1), while the remaining five are regarded as marginal detections in association with either other X-ray lines detected at higher significance and/or far-ultraviolet (FUV) signposts. Three of these lines are consistent with metal absorption at z {approx_equal} 0, and we identify them with Galactic O I and C II. The remaining eight lines may be imprinted by intervening absorbers and are all consistent with being high-ionization counterparts of FUV H I and/or O VI intergalactic medium signposts. In particular, five of these eight possible intervening absorption lines (single-line statistical significances of 4.1{sigma}, 4.1{sigma}, 3.9{sigma}, 3.8{sigma}, and 2.7{sigma}), are identified as C V and C VI K{alpha} absorbers belonging to three WHIM systems at z{sub X} = 0.312, z{sub X} = 0.237, and (z{sub X} ) = 0.133, which also produce broad H I (and O VI for the z{sub X} = 0.312 system) absorption in the FUV. For two of these systems (z{sub X} = 0.312 and 0.237), the Chandra X-ray data led the a posteriori discovery of physically consistent broad H I associations in the FUV (for the third system the opposite applies), so confirming the power of the X-ray-FUV synergy for WHIM studies. The true statistical significances of these three X-ray absorption systems, after properly accounting for the number of redshift trials, are 5.8{sigma} (z{sub X} = 0.312; 6.3{sigma} if the low-significance O V and C V K{beta} associations are considered), 3.9{sigma} (z{sub X} = 0.237), and 3.8{sigma} ((z{sub X} ) = 0.133), respectively.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Identification of two mechanisms for current production in a biharmonic flashing electron ratchet

Ratchets rectify the motion of randomly moving particles, which are driven by isotropic sources of energy such as thermal and chemical energy, without applying a net, time-averaged force between source and drain. We describe the behavior of a damped electron, modeled by a quantum Lindblad master equation, within a flashing ratchet (a one-dimensional potential that oscillates between a flat surface and a periodic asymmetric surface). By investigating the complete space of all biharmonic potential shapes and a large range of oscillation frequencies, two modes of ratchet operation, differentiated by their oscillation frequencies (relative to the rate of electron relaxation), are identified. Slow-oscillating, strong friction ratchets operate by a classical, overdamped mechanism. In fast-oscillating, weak friction ratchets, current is primarily produced when the frequency of the oscillating potential is resonant with the beating of the electron wave function in the potential well. The shape of the ratchet potential determines the direction of the current (and, in some cases, straightforwardly accounts for current reversals), but the maximum achievable current at any shape is controlled by the degree of friction applied to the electron.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

High Throughput Ambient Mass Spectrometric Approach to Species Identification and Classification from Chemical Fingerprint Signatures

A high throughput method for species identification and classification through chemometric processing of direct analysis in real time (DART) mass spectrometry-derived fingerprint signatures has been developed. The method entails introduction of samples to the open air space between the DART ion source and the mass spectrometer inlet, with the entire observed mass spectral fingerprint subjected to unsupervised hierarchical clustering processing. Moreover, a range of both polar and non-polar chemotypes are instantaneously detected. The result is identification and species level classification based on the entire DART-MS spectrum. In this paper, we illustrate how the method can be used to: (1) distinguish between endangered woods regulated by the Convention for the International Trade of Endangered Flora and Fauna (CITES) treaty; (2) assess the origin and by extension the properties of biodiesel feedstocks; (3) determine insect species from analysis of puparial casings; (4) distinguish between psychoactive plants products; and (5) differentiate between Eucalyptus species. An advantage of the hierarchical clustering approach to processing of the DART-MS derived fingerprint is that it shows both similarities and differences between species based on their chemotypes. Furthermore, full knowledge of the identities of the constituents contained within the small molecule profile of analyzed samples is not required.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2004

A Detection of the Same Hot Plasma in the Corona: During a CME and Later at Ulysses

We show direct evidence for the same very hot plasma being detected remotely from SOHO in the corona and subsequently, at Ulysses in the solar wind. This is, to our knowledge, the first time that such an unambiguous identification has been made in the case of hot plasma. This detection complements studies correlating other plasma and field properties observed to the properties measured at the source in the corona. This observation takes advantage of a SOHO-Sun-Ulysses quadrature, during which the Sun-Ulysses included angle is $90^\circ$ and it is possible to observe with Ulysses instruments the same plasma that has previously been remotely observed with SOHO instruments in the corona on the limb of the Sun. The identification builds on an existing base of separate SOHO and interplanetary detections of hot plasma. SOHO/UVCS has found evidence for very hot coronal plasma in current sheets in the aftermath of CMEs in the [Fe XVIII] $\lambda$ \AA\ line, implying a temperature on the order of $6\times 10(exp 6)$ K. This temperature is unusually high even for active regions, but is compatible with the high temperature predicted in current sheets. In the solar wind, ACE data from early 1998 to middle 2000 revealed high frozen-in Fe charge state in many cases to be present in interplanetary plasma.

Suess, S. T.↗
DOE OSTI2016

ALMA spectroscopic survey in the Hubble Ultra Deep Field: survey description

We present the rationale for and the observational description of ASPECS: the ALMA SPECtroscopic Survey in the Hubble Ultra-Deep Field (UDF), the cosmological deep field that has the deepest multi-wavelength data available. Our overarching goal is to obtain an unbiased census of molecular gas and dust continuum emission in high-redshift (z > 0.5) galaxies. The ∼1′ region covered within the UDF was chosen to overlap with the deepest available imaging from the Hubble Space Telescope. Our ALMA observations consist of full frequency scans in band 3 (84–115 GHz) and band 6 (212–272 GHz) at approximately uniform line sensitivity (L{sub CO}{sup ′} ∼ 2 × 10{sup 9} K km s{sup −1} pc{sup 2}), and continuum noise levels of 3.8 μJy beam{sup −1} and 12.7 μJy beam{sup −1}, respectively. The molecular surveys cover the different rotational transitions of the CO molecule, leading to essentially full redshift coverage. The [C ii] emission line is also covered at redshifts 6.0<z<8.0. We present a customized algorithm to identify line candidates in the molecular line scans and quantify our ability to recover artificial sources from our data. Based on whether multiple CO lines are detected, and whether optical spectroscopic redshifts as well as optical counterparts exist, we constrain the most likely line identification. We report 10 (11) CO line candidates in the 3 mm (1 mm) band, and our statistical analysis shows that <4 of these (in each band) are likely spurious. Less than one-third of the total CO flux in the low-J CO line candidates are from sources that are not associated with an optical/NIR counterpart. We also present continuum maps of both the band 3 and band 6 observations. The data presented here form the basis of a number of dedicated studies that are presented in subsequent papers.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Molecular identification of wines using in situ liquid SIMS and PCA analysis

Composition analysis in wine is gaining increasing attention because it can provide information about the wine quality, source, and nutrition. In this work, in situ liquid secondary ion mass spectrometry (SIMS) was applied to 14 representative wines, including six wines manufactured by a manufacturer in Washington State, United States, four Cabernet Sauvignon wines, and four Chardonnay wines from other different manufacturers and locations. In situ liquid SIMS has the unique advantage of simultaneously examining both organic and inorganic compositions from liquid samples. Principal component analysis (PCA) of SIMS spectra showed that red and white wines can be clearly differentiated according to their aromatic and oxygen-contained organic species. Furthermore, the identities of different wines, especially the same variety of wines, can be enforced with a combination of both organic and inorganic species. Meanwhile, in situ liquid SIMS is sample-friendly, so liquid samples can be directly analyzed without any prior sample dilution or separation. Taken together, we demonstrate the great potential of in situ liquid SIMS in applications related to the molecular investigation of various liquid samples in food science.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics and exposomics studies is to fully characterize the small molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversi-ty present within the metabolome and exposome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials (“standards”), which are not available for most molecules. Computational quantum chemis-try methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alter-native route for building reference libraries, i.e., in silico libraries for “standards-free” identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solu-tion. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectros-copy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics and exposomics studies. We expect this review will inspire researchers in the field of small molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

Metabolism↗
NASA NTRS2019

NASA GIBS and Worldview: Leveraging FOSS for NASA Earth Science Data Visualizations

The NASA Global Imagery Browse Services (GIBS) and Worldview interactive mapping site leverage scientific and community best practices, open source software, and public standards to provide a scalable, compliant, and authoritative source for NASA Earth Observing System (EOS) Earth science data visualizations. GIBS and Worldview allow end users to easily and quickly interact with more than 800 full resolution pre-generated raster- and vector-based visualizations. This interactive discovery approach relies on visual observation and identification of phenomena that are not as simply identified otherwise. This eLightning presentation will exhibit the broad set of capabilities and visualization layers made possible through the GIBS and Worldview open source software. Specific dependencies on, and contributions to, open source software will be highlighted. Additionally, opportunities for future improvements for better interoperability and reuse through open source software will be discussed.

NASA Global Imagery Browse Services (GIBS)↗
DOE OSTI2024

Isotopic gamma lines for identification of shielding materials

Identifying the constituting materials of concealed objects is crucial in a wide range of sectors, such as medical imaging, geophysics, nonproliferation, national security investigations, and so on. Existing methods face limitations, particularly when multiple materials are involved or when there are challenges posed by scattered radiation and large areal mass. Here we introduce a novel brute-force statistical approach for material identification using high spectral resolution detectors, such as HPGe. The method relies upon updated semianalytic formulae for computing uncollided flux from source of gamma radiation, shielded by a sequence of nested spherical or cylindrical materials. These semianalytical formulae make possible rapid flux estimation for material characterization via combinatorial search through all possible combinations of materials, using a high-resolution HPGe counting detector. An important prerequisite for the method is that the geometry of the objects is known (for example, from X-ray radiography). We demonstrate the viability of this material characterization technique in several use cases with both simulated and experimental data in spherical geometry.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2018

Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples

One of the greatest challenges for mass spectrometry (MS)-based proteomics is the limited ability to analyze small samples. Here we investigate the relative contributions of liquid chromatography (LC), MS instrumentation and data analysis methods with the aim of improving proteome coverage for sample sizes ranging from 0.5 ng to 50 ng. We show that the LC separations utilizing 30-µm-i.d. columns increase signal intensity by >3-fold relative to those using 75-µm-i.d. columns, leading to 32% increase in peptide identifications. The Orbitrap Fusion Lumos mass spectrometer significantly boosted both sensitivity and sequencing speed relative to earlier generation Orbitraps (e.g., LTQ-Orbitrap), leading to a ~3× increase in peptide identifications and 1.7× increase in identified protein groups for 2 ng tryptic digests of bacterial lysate. The Match Between Runs algorithm of open-source MaxQuant software further increased proteome coverage by ~ 95% for 0.5 ng samples and by ~42% for 2 ng samples. The present platform is capable of identifying >3000 protein groups from tryptic digestion of cell lysates equivalent to 50 HeLa cells and 100 THP-1 cells (~10 ng total proteins), respectively, and >950 proteins from subnanogram bacterial and archaeal cell lysates. The present ultrasensitive LC-MS platform is expected to enable deep proteome coverage for subnanogram samples, including single mammalian cells.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

The identification of extreme asymptotic giant branch stars and red supergiants in M33 with 24 μm variability

We present the first detection of 24 μm variability in 24 sources in the Local Group galaxy M33. These results are based on 4 epochs of Multiband Imaging Photometer for Spitzer observations, which are irregularly spaced over ∼750 days. We find that these sources are constrained exclusively to the Holmberg radius of the galaxy, which increases their chances of being members of M33. We have constructed spectral energy distributions (SEDs) ranging from the optical to the submillimeter to investigate the nature of these objects. We find that 23 of our objects are most likely heavily self-obscured, evolved stars, while the remaining source is the Giant H ii region, NGC 604. We believe that the observed variability is the intrinsic variability of the central star reprocessed through their circumstellar dust shells. Radiative transfer modeling was carried out to determine their likely chemical composition, luminosity, and dust production rate (DPR). As a sample, our modeling has determined an average luminosity of (3.8±0.9)×10{sup 4} L{sub ⊙} and a total DPR of (2.3±0.1)×10{sup −5} M{sub ⊙} yr{sup −1}. Most of the sources, given the high DPRs and short wavelength obscuration, are likely extreme asymptotic giant branch (XAGB) stars. Five of the sources are found to have luminosities above the classical AGB limit (M{sub bol} <−7.1 mag, L > 54,000 L{sub ⊙}), which classifies them as probable red supergiants (RSGs). Almost all of the sources are classified as oxygen-rich. As also seen in the LMC, a significant fraction of the dust in M33 is produced by a handful of XAGB and RSG stars.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1980

Monitoring and control requirement definition study for Dispersed Storage and Generation (DSG). Volume 4, appendix C: Identification from utility visits of present and future approaches to integration of DSG into distribution networks

Visits to four utilities concerned with the use of DSG power sources on their distribution networks yielded useful impressions of present and future approaches to the integration of DSGs into electrical distribution network. Different approaches to future utility systems with DSG are beginning to take shape. The new DSG sources will be in decentralized locations with some measure of centralized control. The utilities have yet to establish firmly the communication and control means or their organization. For the present, the means for integrating the DSGs and their associated monitoring and control equipment into a unified system have not been decided.

Source record↗
DOE OSTI2022

A stilbene–strontium iodide based radioxenon detection system for monitoring nuclear explosions

Atmospheric measurement of noble gases has been extensively used for monitoring clandestine nuclear weapon explosions for many years. The ratios of four xenon isotopes of interest ( 131 mXe, 133 mXe, 133 Xe, and 135 Xe) help in discriminating regular reactor operations from nuclear tests. A new coincidence-based detection system using stilbene and strontium iodide [SrI 2 (Eu)] for electron and photon detection respectively was developed at Oregon State University to address some of the challenges of the radioxenon systems deployed in the field such as memory effect, and poor energy resolution. Silicon photomultipliers (SiPMs) were used for sensing optical photons from all scintillation media. Real-time coincidence identification was achieved using the eight-channel digital pulse processor. The detection system was evaluated using lab check sources and Oregon State TRIGA reactor irradiated radioxenon samples. A 48-hour background coincidence spectrum was collected yielding a coincidence count rate and background rejection rate of 0.0174 ± 0.0003 counts per second (cps) and 98.9% respectively. The minimum detectable concentration (MDC) of the system was evaluated to be 0.11 ± 0.01, 0.13 ± 0.02, 0.20 ± 0.02, and 0.73 ± 0.08 for 131 mXe, 133 mXe, 133 Xe, and 135 Xe respectively. The memory effect of the detection system was found to be 0.069 ± 0.015%, which is almost a 70-fold reduction compared to traditional plastic scintillators. Here, the detection elements, custom-designed electronics, and the detector response to radioxenon are detailed in this work.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Large Scale Comparative Visualisation of Regulatory Networks with TRNDiff

The advent of Next Generation Sequencing (NGS) technologies has seen explosive growth in genomic datasets, and dense coverage of related organisms, supporting study of subtle, strain-specific variations as a determinant of function. Such data collections present fresh and complex challenges for bioinformatics, those of comparing models of complex relationships across hundreds and even thousands of sequences. Transcriptional Regulatory Network (TRN) structures document the influence of regulatory proteins called Transcription Factors (TFs) on associated Target Genes (TGs). TRNs are routinely inferred from model systems or iterative search, and analysis at these scales requires simultaneous displays of multiple networks well beyond those of existing network visualisation tools [1]. In this paper we describe TRNDiff, an open source system supporting the comparative analysis and visualization of TRNs (and similarly structured data) from many genomes, allowing rapid identification of functional variations within species. The approach is demonstrated through a small scale multiple TRN analysis of the Fur iron-uptake system of Yersinia, suggesting a number of candidate virulence factors; and through a larger study exploiting integration with the RegPrecise database (http://regprecise.lbl.gov; [2]) - a collection of hundreds of manually curated and predicted transcription factor regulons drawn from across the entire spectrum of prokaryotic organisms.

Bioinformatics, Visualisation, Transcription, Regu↗
DOE OSTI2017

A metabolic pathway for catabolizing levulinic acid in bacteria

Microorganisms can catabolize a wide range of organic compounds and therefore have the potential to perform many industrially relevant bioconversions. One barrier to realizing the potential of biorefining strategies lies in our incomplete knowledge of metabolic pathways, including those that can be used to assimilate naturally abundant or easily generated feedstocks. For instance, levulinic acid (LA) is a carbon source that is readily obtainable as a dehydration product of lignocellulosic biomass and can serve as the sole carbon source for some bacteria. Yet, the genetics and structure of LA catabolism have remained unknown. Here, we report the identification and characterization of a seven-gene operon that enables LA catabolism in Pseudomonas putida KT2440. When the pathway was reconstituted with purified proteins, we observed the formation of four acyl-CoA intermediates, including a unique 4-phosphovaleryl-CoA and the previously observed 3-hydroxyvaleryl-CoA product. Using adaptive evolution, we obtained a mutant of Escherichia coli LS5218 with functional deletions of fadE and atoC that was capable of robust growth on LA when it expressed the five enzymes from the P. putida operon. Here, this discovery will enable more efficient use of biomass hydrolysates and metabolic engineering to develop bioconversions using LA as a feedstock.

59 BASIC BIOLOGICAL SCIENCES↗