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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics

Abstract Summary Although advances in untargeted metabolomics have made it possible to gather data on thousands of cellular metabolites in parallel, identification of novel metabolites from these datasets remains challenging. To address this need, Metabolic in silico Network Expansions (MINEs) were developed. A MINE is an expansion of known biochemistry which can be used as a list of potential structures for unannotated metabolomics peaks. Here, we present MINE 2.0, which utilizes a new set of biochemical transformation rules that covers 93% of MetaCyc reactions (compared to 25% in MINE 1.0). This results in a 17-fold increase in database size and a 40% increase in MINE database compounds matching unannotated peaks from an untargeted metabolomics dataset. MINE 2.0 is thus a significant improvement to this community resource. Availability and implementation The MINE 2.0 website can be accessed at https://minedatabase.ci.northwestern.edu. The MINE 2.0 web API documentation can be accessed at https://mine-api.readthedocs.io/en/latest/. The data and code underlying this article are available in the MINE-2.0-Paper repository at https://github.com/tyo-nu/MINE-2.0-Paper. MINE 2.0 source code can be accessed at https://github.com/tyo-nu/MINE-Database (MINE construction), https://github.com/tyo-nu/MINE-Server (backend web API) and https://github.com/tyo-nu/MINE-app (web app). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Optical properties of Peaked Spectrum radio sources

ABSTRACT In this work, we study the optical properties of compact radio sources selected from the literature in order to determine the impact of the radio-jet in their circumnuclear environment. Our sample includes 58 Compact Steep Spectrum (CSS) and GigaHertz Peaked Spectrum (GPS) and 14 Megahertz-Peaked spectrum (MPS) radio sources located at z ≤ 1. The radio luminosity (LR) of the sample varies between Log LR ∼ 23.2 and 27.7 W Hz−1. We obtained optical spectra for all sources from SDSS-DR12 and performed a stellar population synthesis using the starlight code. We derived stellar masses (M⋆), ages 〈t⋆〉, star formation rates (SFR), metallicities 〈Z⋆〉 and internal reddening AV for all young AGNs of our sample. A visual inspection of the SDSS images was made to assign a morphological class for each source. Our results indicate that the sample is dominated by intermediate to old stellar populations and there is no strong correlation between optical and radio properties of these sources. Also, we found that young AGNs can be hosted by elliptical, spiral and interacting galaxies, confirming recent findings. When comparing the optical properties of CSS/GPS and MPS sources, we do not find any significant difference. Finally, the Mid-Infrared WISE colours analysis suggests that the compact radio sources defined as powerful AGNs are, in general, gas-rich systems.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

H i 21-cm absorption in radio-loud AGN with double-peaked [O iii ] emission

ABSTRACT Different physical processes in galaxy evolution, such as galaxy mergers that lead to coalescence of dual Active Galactic Nuclei (AGN) and outflows emanating from the narrow line region, can leave their imprint on the optical spectra of AGN in the form of double-peaked narrow emission lines. To investigate the neutral gas in the centres of such AGN, we have conducted a pilot survey of H i 21-cm absorption, using the upgraded Giant Metrewave Radio Telescope (uGMRT), in radio-loud AGN whose optical spectra show double-peaked [O iii] emission lines at z ≤ 0.4 (median z ≈ 0.14). Among the eight sources for which we could obtain clean spectra, we detect H i 21-cm absorption in three sources (detection rate of $38^{+36}_{-20}$ per cent) and find tentative indication of absorption in two other sources. The detection rate of H i 21-cm absorption is tentatively higher for the systems that show signatures of interaction or tidal disturbance (≳ 50 per cent) in the ground-based optical images than that for the systems that appear single and undisturbed (≈25 per cent). This is consistent with the high incidence of H i 21-cm absorption observed in z ≤ 0.2 galaxy mergers. Higher spatial resolution spectroscopy is required to confirm the origin of the H i absorbing gas, i.e. either gas infalling on to the radio-loud AGN, outflowing gas ejected by the AGN, or gas in rotation on the galactic-scale or circumnuclear discs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

A VLBA-uGMRT search for candidate binary black holes: study of six X-shaped radio galaxies with double-peaked emission lines

ABSTRACT Identifying methods to discover dual active galactic nucleus (AGN) has proven to be challenging. Several indirect tracers have been explored in the literature, including X/S-shaped radio morphologies and double-peaked (DP) emission lines in the optical spectra. However, the detection rates of confirmed dual AGN candidates from the individual methods remain extremely small. We search for binary black holes (BBH) in a sample of six sources that exhibit both X-shaped radio morphology and DP emission lines using the Very Long Baseline Array (VLBA). Three out of the six sources show dual VLBA compact components, making them strong candidates for BBH sources. In addition, we present deep uGMRT images revealing the exquisite details of the X-shaped wings in three sources. We present a detailed precession modeling analysis of these sources. The black hole separations estimated from the simplistic geodetic precession model are incompatible with those estimated from emission line offsets and the VLBA separations. However, precession induced by a non-coplanar secondary black hole is a feasible mechanism for explaining the observed X-shaped radio morphologies and the black hole separations estimated from other methods. The black hole separations estimated from the double-peaked emission lines agree well with the VLBA compact component separations. Future multifrequency VLBA observations will be critical in ruling out or confirming the BBH scenario in the three galaxies with dual component detections.

Sebastian, Biny (ORCID:0000000184286525)↗
DOE OSTI2021

Experimental demonstration of coupled multi-peak Bragg coherent diffraction imaging with genetic algorithms

Bragg coherent diffraction imaging has the potential to provide significant insight into the structure-properties relationship for crystalline materials by imaging, with nanoscale resolution, three-dimensional strain fields within individual grains and nanoparticles. The capability of present-day synchrotrons to locate and measure a multiplicity of Bragg reflections from a single grain makes it possible to recover the full strain tensor with nanometer resolution. Recent methods for coupling reconstructions from several peaks to determine the strain tensor have been developed and applied to synthetic data, but have not been applied to experimental data. Here, using a coupled genetic reconstruction algorithm, we reconstruct an experimental data set and demonstrate improvements in the ability to resolve vector-valued displacement fields internal to the particle as compared to what is achieved with a noncoupled approach. The coupled approach developed in this work was also validated on simulated data sets. In both simulated and experimental data, reconstructions from our coupled Bragg peak algorithm show improvements over the noncoupled independent reconstruction method of 5% in terms of accuracy and 53% in terms of consistency.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Spin-carrier coupling induced ferromagnetism and giant resistivity peak in EuCd 2 P 2

EuCd 2 P 2 is notable for its unconventional transport: upon cooling the metallic resistivity changes slope and begins to increase, ultimately 100-fold, before returning to its metallic value. Surprisingly, this giant peak occurs at 18 K, well above the Néel temperature (T N ) of 11.5 K. Here, using a suite of sensitive probes of magnetism, including resonant x-ray scattering and magneto-optical polarimetry, we have discovered that ferromagnetic order onsets above T N in the temperature range of the resistivity peak. The observation of inverted hysteresis in this regime shows that ferromagnetism is promoted by coupling of localized spins and itinerant carriers. The resulting carrier localization is confirmed by optical conductivity measurements.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Searching for the origin of the rare-earth peak with precision mass measurements across Ce–Eu isotopic chains

A nuclear mass survey of rare-earth isotopes has been conducted with the Canadian Penning Trap mass spectrometer using the most neutron-rich nuclei thus far extracted from the CARIBU facility. Here, we present a collection of 12 nuclear masses determined with a precision of ≤ 10 keV/c 2 for Z = 58-63 nuclei near N = 100. Independently, a detailed study exploring the role of nuclear masses in the formation of the r-process rare-earth abundance peak has been performed. Employing a Markov chain Monte Carlo (MCMC) technique, mass predictions of lanthanide isotopes have been made which uniquely reproduce the observed solar abundances near A = 164 under three distinct astrophysical outflow conditions. We demonstrate that the mass surface trends thus far mapped out by our measurements are most consistent with MCMC mass predictions given an r process that forms the rare-earth peak during an extended (n, γ) ⇌ (γ, n) equilibrium.

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

Insights on the peak in the speed of sound of ultradense matter

In this work we investigate the minimal physical requirements needed for generating a speed of sound that surpasses its asymptotic conformal limit. It is shown that a peak in the speed of sound of homogeneous matter naturally emerges in the transition from a phase with broken chiral symmetry to one with a gapped Fermi surface. We argue that this could be relevant for understanding the peak in the speed of sound displayed by some of the current models for cold ultradense matter. A minimal model implementation of this mechanism is presented, based on the spontaneous breakdown of an approximate particle-antiparticle symmetry, and its thermodynamic properties are determined.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Coordination of Energy Storage and Distributed Generation for Voltage Control and Peak-valley Filling

The increasing penetration of distributed energy resources (DERs) in distribution network (DN) poses challenges on voltage control. In addition, the growing integration of DERs also reshapes the traditional load profile. To comprehensively address the voltage control and peak-valley filling in DN, this paper proposes a model predictive control (MPC) based optimization framework. The proposed method can achieve coordinated voltage control and peak-valley filling by adjusting the reactive power output from distributed generations (DGs) and the charging/discharging of energy storage systems (ESS). The performance of the proposed method is demonstrated by simulations on a modified IEEE-123 bus system.

Zhang, Zhengfa [University of Tennessee, Knoxville↗
DOE OSTI2023

Insufficient reporting of x-ray photoelectron spectroscopy instrumental and peak fitting parameters (metadata) in the scientific literature

This study was motivated by earlier observations. It is a systematic examination of the adequacy of reporting of information (metadata) necessary to understand x-ray photoelectron spectroscopy (XPS) data collection and data analysis in the scientific literature. The information for this study was obtained from papers published in three high-quality journals over a six-month period in 2019 and throughout 2021. Each paper was evaluated to determine whether the authors had reported (percentages of the papers properly providing the information are given in parentheses) the spectrometer (66%), fitting software (15%), x-ray source (40%), pass energy (10%), spot size (5%), synthetic peak shapes in fits (10%), backgrounds in fits (10%), whether the XPS data are shown in the main body of the paper or in the supporting information (or both), and whether fitted or unfitted spectra were shown (80% of published spectra are fit). The Shirley background is the most widely used background in XPS peak fitting. The Al Kα source is the most widely used x-ray source for XPS data collection. CASAXPS is the most widely used fitting program for XPS data analysis. Further, there is good agreement between the results gathered during the two years of our survey. There are some hints the situation may be improving. This study also provides a list of the information/parameters that should be reported when XPS is performed.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Demonstration of a 1 TW peak power, joule-level ultrashort Tm:YLF laser

Here we report on the demonstration of a diode-pumped, Tm:YLF-based, chirped pulse amplification laser system operating at λ ≈ 1.9 µm that produces amplified pulse energies exceeding 1.5 J using a single 8-pass power amplifier. The amplified pulses are subsequently compressed to sub-300 fs durations by a diffraction grating pair, producing record >1 TW peak power pulses. To the best of our knowledge, this is the highest peak power demonstrated for any solid-state, near-2 µm laser architecture and illustrates the potential of Tm:YLF for the next generation of high-power, diode-pumped ultrashort lasers.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Nonlinear refraction and absorption properties of optical materials for high-peak-power long-wave-infrared lasers

Optical materials transparent in the CO 2 laser wavelength range have been evaluated regarding their suitability for components in ultrashort-pulse (≤ a few ps), high-peak-power (≥ a few TW) long-wave infrared (LWIR) lasers. We provide values for the nonlinear refractive index ( n 2 ) for seventeen materials, and onsets for nonlinear absorption for eleven materials. Characterizations were performed using a 2 ps laser pulse at λ =9.2 μ m. This paper methodically presents the newly acquired data in conjunction with existing literature on linear optical properties, establishing it as a comprehensive reference for designing high-peak-power LWIR laser systems.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance

For many species, vision is one of the most important sensory modalities for mediating essential tasks that include navigation, predation and foraging, predator avoidance, and numerous social behaviors. The vertebrate visual process begins when photons of the light interact with rod and cone photoreceptors that are present in the neural retina. Vertebrate visual photopigments are housed within these photoreceptor cells and are sensitive to a wide range of wavelengths that peak within the light spectrum, the latter of which is a function of the type of chromophore used and how it interacts with specific amino acid residues found within the opsin protein sequence. Minor differences in the amino acid sequences of the opsins are known to lead to large differences in the spectral peak of absorbance (i.e. the λ max value). In our prior studies, we developed a new approach that combined homology modeling and molecular dynamics simulations to gather structural information associated with chromophore conformation, then used it to generate statistical models for the accurate prediction of λ max values for photopigments derived from Rh1 and Rh2 amino acid sequences. In the present study, we test our novel approach to predict the λ max of phylogenetically distant Sws2 cone opsins. To build a model that can predict the λ max using our approach presented in our prior studies, we selected a spectrally-diverse set of 11 teleost Sws2 photopigments for which both amino acid sequence information and experimentally measured λ max values are known. The final first-order regression model, consisting of three terms associated with chromophore conformation, was sufficient to predict the λ max of Sws2 photopigments with high accuracy. This study further highlights the breadth of our approach in reliably predicting λ max values of Sws2 cone photopigments, evolutionary-more distant from template bovine RH1, and provided mechanistic insights into the role of known spectral tuning sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

AmeriFlux US-CPF Cameron Peak

This is the AmeriFlux version of the carbon flux data for the site US-CPF Cameron Peak. Site Description - This site was established in 2021 in the wake of the Cameron Peak fire, the largest wildfire in Colorado to date. The site is situated at 3,100m elevation on a ~0.5km^2 flat ridgetop within the burn zone between Sawmill Creek and Chambers Lake. The site, populated by lodgepole pine, subalpine fir and Engelmann spruce, burned heavily in fall 2020. The tower consists of one level of construction scaffolding with instruments mounted at 4.3m height.

Frank, John [US Forest Service, Rocky Mountain Res↗
DOE OSTI2024

Conventional single-gap $s-$wave superconductivity and hidden peak effect in single crystals of Mo$_8$Ga$_{41}$ superconductor

London and Campbell penetration depths were measured in single crystals of the endohedral gallide cluster superconductor, Mo _8 8 Ga _41 41 . The full temperature range superfluid density, \rho_s(T) ρ s ( T ) , is consistent with the clean isotropic s- s − wave weak-coupling BCS theory without any signs of the second gap or strong coupling. The temperature dependence of the Campbell length is hysteretic between zero-field cooling (ZFC) and field-cooling (FC) protocols, indicating an anharmonic vortex pinning potential. The field dependence of the effective critical current density, j_{c}(H) j c ( H ) , reveals an unusual result. While in the ZFC protocol, j_{c}(H) j c ( H ) is monotonically suppressed by the magnetic field, it exhibits a profound “hidden” peak effect in the FC protocol, that is, without a vortex density gradient. We suggest a possible novel mechanism for such a peak effect, which involves both static and dynamic aspects of vortex pinning.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Filtration Performance Results: Sierra Peaks Material No. 4

Sandia National Laboratories (SNL) assessed the filtration performance of materials from Sierra Peaks to identify alternatives which may perform similarly to materials used in FDA-approved N95 respirators. This work is meant to characterize the aerosol performance of materials to give Sierra Peaks information for them to determine if they elect to submit masks made using these materials for follow-on N95 certification testing at an accredited facility. The R&D testbed used is a large-scale filtration system designed to test commercial filter boxes. System modifications were performed to simulate, where possible, parameters defined by the National Institute for Occupational Safety and Health (NIOSH) for certification of filter materials for N95 respirators (NIOSH 2019). The system is a pull-through design. Air enters through a Laminar Flow Element (LFE) and the volumetric flow is measured based on the pressure drop across the LFE. Pressure is measured via a Pressure Transducer (PT). The air then passes through a High Efficiency Particulate Air (HEPA) filter to purge the air of ambient airborne particulates. Test aerosol is injected into the flow shortly after and mixing is induced via a coarse mesh. The airflow is allowed to fully develop prior to arriving at the test section. The aerosol then passes through the test material mounted in a box in the test section. Pressure drop across the test article is measured and aerosol sampling probes measure the aerosol concentrations upstream and downstream of the sample. The air passes through a second HEPA filter prior to being exhausted to ambient by a blower. A Topas aerosol generator is used to produce the test aerosol from Sodium Chloride (NaC1) dissolved in deionized (DI) water. Generated aerosol passes through a heated mixing chamber and a desiccant dryer to produce nanosized solid-state particulates. A dilution loop allows for the aerosol concentration to be regulated. The aerosol sampling probes upstream and downstream of the test section are aligned with the flow path. These are ducted directly to the aerosol sizing and counting instruments. A Laser Aerosol Spectrometer (LAS) was used for data collection in the original configuration of the system and was also used for initial testing in this project. Because the lower measurement range for the LAS is 90 nanometers (nm), the LAS was switched out for a more complicated Scanning Mobility Particle Sizer (SMPS) spectrometer system. The SMPS is comprised of an Electrostatic Classifier (EC), Differential Mobility Analyzer (DMA), and a Condensation Particle Counter (CPC). This enabled data collection at 75 nm, the particle size called out in the NIOSH guidelines.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Non-visual analysis of miniaturized melt wire arrays for in-pile measurement of peak irradiation temperature

As a part of the in-pile instrumentation program, the Idaho National Laboratory (INL) has established in-house capabilities to fabricate and test new advanced manufactured printed sensors for measurement of peak temperature inside the harsh environment of a nuclear test reactor. Although nuclear test reactors may use standard methods that can provide real-time temperature information, such as thermocouples, the need for feedthroughs for real-time measurements greatly increases the cost of the experiment. Some experiments also present the problem of limited space available for instrumentation. To address this need, INL is working to improve temperature detection options for such applications. The lab is developing advanced manufactured melt wire arrays to determine peak temperatures in experiments with limited space. Furthermore, capabilities to print multiple melt wires with different melting properties on a single miniaturized unit is being established. Recent results and knowledge from this ongoing work have made it possible to develop unique temperature sensors that can accomplish user specific temperature ranges inside the harsh environments experienced during radiation testing.

36 MATERIALS SCIENCE↗
DOE OSTI2021

National Lightning Detection Network: Summary of Strike Peak Currents

Over the years 2006 through 2017, the National Lightning Detection Network (NLDN) mea- sured about 880 million lightning ground strikes in the continental United States. About 5.5% of these strikes had positive initial peak current. We examine the extreme quantiles of positive and negative peak current. For example, the 99% quantile indicates that 99 out of 100 strokes are less than the quantile. Noting that the estimation of the 99% quantile, e.g., depends on the area and time period under consideration, we examined the e ects of location and time period (both seasonally and yearly) on the determination of 99% quantiles. In the appendices, we detail the uncertainty quanti cation procedure and summarize strikes in January 2016.

47 OTHER INSTRUMENTATION↗