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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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

MEMOTE for standardized genome-scale metabolic model testing

Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organism’s metabolism under different conditions. State-of-the-art genome-scale metabolic models (GEMs) can include thousands of metabolites and reactions that are assigned to subcellular locations. Gene–protein–reaction (GPR) rules and annotations using database information can add meta-information to GEMs. GEMs with metadata can be built using standard reconstruction protocols, and guidelines have been put in place for tracking provenance and enabling interoperability, but a standardized means of quality control for GEMs is lacking. Here we report a community effort to develop a test suite named MEMOTE (for metabolic model tests) to assess GEM quality.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses

Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Experimental confirmation of the standard magnetorotational instability mechanism with a spring-mass analogue

Abstract The magnetorotational instability (MRI) has long been considered a plausibly ubiquitous mechanism to destabilize otherwise stable Keplerian flows to support radially outward transport of angular momentum. Such an efficient transport process would allow fast accretion in astrophysical objects such as stars and black holes to release copious kinetic energy that powers many of the most luminous sources in the universe. But the standard MRI under a purely vertical magnetic field has heretofore never been directly measured despite numerous efforts over more than a decade. Here we report an unambiguous laboratory demonstration of the spring-mass analogue to the standard MRI by comparing motion of a spring-tethered ball within different rotating flows. The experiment corroborates the theory: efficient outward angular momentum transport manifests only for cases with a weak spring in quasi-Keperian flow. Our experimental method accomplishes this in a new way, thereby connecting solid and fluid mechanics to plasma astrophysics.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Antimicrobial properties of nanostructured surfaces – demonstrating the need for a standard testing methodology

Bioinspired nanostructured materials that exhibit antimicrobial properties are being synthesized and tested at increasing rates for use in healthcare, manufacturing processes, and diagnostics. Although progress has been made in improving and understanding their bactericidal activity, arguably, the biggest problem currently in the field is the lack of a standard testing methodology that allows for optimal characterization and better comparison of emerging nanostructures. In this work, we examine two forms of nanostructured silicon that vary in their ability to kill certain bacterial species due to different physical mechanisms and derive guidelines for the comparative testing. We perform a comprehensive evaluation of methodologies used extensively in the field (e.g., colony counting and live dead analysis) and the novel application of high-throughput flow cytometry. The data reveal how the techniques are complementary but not always directly equivalent or correlative. Therefore, comparison of results obtained using different methodologies on different materials can be grossly misleading. We report significant variations in bactericidal efficiencies depending on experimental environments (medium type, etc.) and methodologies employed. In addition, we demonstrate how cytometry is yet another powerful complementary tool that can aid the mechanistic understanding of antimicrobial activities of rough surfaces. Besides standardization for comparison, ultimately, evaluation methods need to consider anticipated applications. Then and only then can the true potential (or limitation) of a novel material be determined for its suitability for advancement in a particular field of use.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Evolving data standards for cryo-EM structures

Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of a broad spectrum of biological specimens from molecules to cells. Anticipating this progress in the early 2000s, an international collaboration of scientists with expertise in both cryo-EM and structure data archiving was established (EMDataResource, previously known as EMDataBank). The major goals of the collaboration have been twofold: to develop the necessary infrastructure for archiving cryo-EM-derived density maps and models, and to promote development of cryo-EM structure validation standards. We describe how cryo-EM data archiving and validation have been developed and jointly coordinated for the Electron Microscopy Data Bank and Protein Data Bank archives over the past two decades, as well as the impact of evolving technology on data standards. Just as for X-ray crystallography and nuclear magnetic resonance, engaging the scientific community via workshops and challenging activities has played a central role in developing recommendations and requirements for the cryo-EM structure data archives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Creation of the first Russian time and frequency standard on a fountain of ultracold rubidium atoms

Technical specific features of the first Russian rubidium frequency standard of a fountain type are described, which are distinct from those of abroad analogues. Test results of separate systems and the metrological characteristics of the standard are presented. The achievable output frequency instability is 4 × 10{sup −16} per measurement interval of 24 hours and 1 × 10{sup −16} per 16 days. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Acousto-optic modulators for a controlled frequency shift of light beams in optical and microwave cold-atom frequency standards

A series of specialised acousto-optic modulators/frequency shifters based on paratellurite (TeO{sub 2}) single crystals is developed for systems of laser cooling and frequency stabilisation of laser sources in optical and microwave frequency standards based on cold strontium, rubidium and caesium atoms. The methods of calculation and optimisation of the main parameters of acousto-optic modulators are considered; their basic technical characteristics are experimentally investigated in the spectral range of optical radiation 460 – 900 nm and in the frequency shift range of 5 – 400 MHz. The modulators have a high diffraction efficiency, low power consumption and the ability to work with linearly and randomly polarised optical radiation. (frequency standards)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Testing the Standard Model at the Precision Frontier with the Q weak Experiment

The standard model of particle physics (SM) has been wildly successful describing the strong, electromagnetic, and weak forces between visible matter. Despite this success, there is a host of phenomena it fails to describe, including neutrino oscillations, gravity, dark matter, and baryon asymmetry. Something is missing—the theory is not complete. This conviction has compelled physicists to develop ever-more-stringent tests in the hope of finding cracks in the SM that could point to where the beyond-the-standard-model (BSM) physics might lie. Direct searches at high-energy colliders have yielded no evidence for some of the most intriguing possibilities, like supersymmetry, and have not been able to shed much light on where to look next.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Performance based approaches in standards and regulations for smart ventilation in residential buildings: a summary review

As ventilation systems become more sophisticated (or ‘smart’) standards and regulations are changing to accommodate their use. A key smart ventilation concept is to use controls to ventilate more at times it provides either an energy or IAQ advantage (or both) and less when it provides a disadvantage. This paper discusses the favorable contexts that exist in many countries, with regulations and standards proposing ‘performance-based approaches’ that both enable and reward smart ventilation. The paper gives an overview of such approaches from five countries. The common thread in all these methods is the use of metrics for the exposure to an indoor generated parameter (usually CO 2 ), and condensation risk. As the result, demand-control ventilation strategies (DCV) are widely and easily available on the market, with more than 20–30 systems available in some countries.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Study of VUV radiation of hybrid and standard X-pinches on KING electric discharge facility

The radiative characteristics of standard and hybrid X-pinches are studied in VUV range on the small-size KING electric discharge facility (200 kA, 190 ns, 45 kV) for the same initial conditions. In this work, studies were performed for different X-pinch materials. A comparative analysis of the VUV spectra was performed and the output energy of soft x-rays and VUV radiation was measured for standard and hybrid X-pinches.

bright spot↗
DOE OSTI2022

Dispersive interactions between standard and Dirac materials and the role of dimensionality

The van der Waals (vdW) interaction plays a prominent role between neutral objects at separations where short ranged chemical forces are negligible. This type of dispersive coupling is determined by the interplay between geometry and response properties of the materials making up the objects. Here, we investigate the vdW interaction between 1D, 2D, and 3D standard and Dirac materials within the Random Phase Approximation, which takes into account collective excitations originating from the electronic Coulomb potential. A comprehensive understanding of characteristic functionalities and scaling laws are obtained for systems with parabolic energy dispersion (standard materials) and crossing linear bands (Dirac materials). By comparing the quantum mechanical and thermal limits the onset of thermal fluctuations in the vdW interaction is discussed showing that thermal effects are significantly pronounced at smaller scales in reduced dimensions.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Abstract Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Standardized naming of microbiome samples in Genomes OnLine Database

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Standardizing reverberation-measured Mg II time-lag quasars, by using the radius–luminosity relation, and constraining cosmological model parameters

ABSTRACT We use 78 reverberation-measured Mg II time-lag quasars (QSOs) in the redshift range 0.0033 ≤ z ≤ 1.89 to constrain cosmological parameters in six different cosmological models. The basis of our method is the use of the radius–luminosity or R−L relation to standardize these 78 Mg II QSOs. In each cosmological model, we simultaneously determine R−L relation and cosmological model parameters, thus avoiding the circularity problem. We find that the R−L relation parameter values are independent of the cosmological model used in the analysis, thus, establishing that current Mg II QSOs are standardizable candles. Cosmological constraints obtained using these QSOs are significantly weaker than, but consistent with, those obtained from a joint analysis of baryon acoustic oscillation (BAO) observations and Hubble parameter [H(z)] measurements. So, we also analyse these QSOs in conjunction with the BAO + H(z) data and find cosmological constraints consistent with the standard spatially flat ΛCDM model as well as with mild dark energy dynamics and a little spatial curvature. A larger sample of higher quality reverberation-measured QSOs should have a smaller intrinsic dispersion and so should provide tighter constraints on cosmological parameters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Aspects of the Domain-Wall Standard Model

Abstract In the “Domain-Wall Standard Model,” all the Standard Model (SM) fields are localized in certain domains in a non-compact 5D space-time. While the SM is realized as a 4D effective theory at low energies, the model involves Kaluza–Klein (KK) modes of the SM particles. In this paper we introduce two simple solvable examples which lead to domain-wall configurations for the SM particles and their KK-modes. Based on the examples, we address a variety of phenomenologies of the Domain-Wall SM, such as the KK-mode gauge boson phenomenology at the Large Hadron Collider (LHC), the effect of the KK-mode SM fermions on Higgs boson phenomenology, and the KK-mode fermion search at the LHC with its decay into a corresponding SM fermion and a Nambu–Goldstone boson associated with a spontaneous breaking of the translational invariance in the 5th dimension. We also propose a simple unified picture of localizing all the SM fields.

Physics↗
DOE OSTI2023

Proposed minimal standards for description of methanogenic archaea

Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA–DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.

Microbiology↗
DOE OSTI2026

Searches for CE ν NS and physics beyond the standard model using Skipper-CCDs at CONNIE

The Coherent Neutrino-Nucleus Interaction Experiment (CONNIE) aims to detect the coherent scattering ( CE ν NS ) of reactor antineutrinos off silicon nuclei using thick fully depleted high-resistivity silicon CCDs. Two Skipper-CCD sensors with subelectron readout noise capability were installed at the experiment next to the Angra-2 reactor in 2021, making CONNIE the first experiment to employ Skipper-CCDs for reactor neutrino detection. We report on the performance of the Skipper-CCDs, the new data processing, data quality, and event selection for CE ν NS interactions, which enable CONNIE to reach a record low detection threshold of 15 eV. The data were collected over 300 days in 2021–2022 and correspond to exposures of 14.9 g-days with the reactor-on and 3.5 g-days with the reactor-off. The difference between the reactor-on and off event rates shows no excess and yields upper limits for the neutrino interaction rates, comparable with previous CONNIE limits from standard CCDs and higher exposures. Searches for new neutrino interactions beyond the Standard Model improve the previous CONNIE limit on a simplified model with light vector mediators. A first dark matter (DM) search by diurnal modulation by CONNIE obtains the best limits on the DM-electron scattering cross section by a surface-level experiment. These promising results, obtained using a very small-mass sensor, illustrate the potential of Skipper-CCDs to probe rare neutrino interactions and motivate the plans to increase the detector mass in the near future.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Linear point and sound horizon as purely geometric standard rulers

The baryon acoustic oscillations feature (BAO) imprinted in the clustering correlation function is known to furnish us cosmic distance determinations that are independent of the cosmological-background model and the primordial perturbation parameters. These measurements can be accomplished rigorously by means of the purely geometric BAO methods. To date two different purely geometric BAO approaches have been proposed. The first exploits the linear-point standard ruler. The second, called correlation-function model-fitting, exploits the sound-horizon standard ruler. A key difference between them is that, when estimated from clustering data, the linear point makes use of a cosmological-model-independent procedure to extract the ratio of the ruler to the cosmic distance, while the correlation-function model-fitting relies on a phenomenological cosmological model for the correlation function. Nevertheless the two rulers need to be precisely defined independently of any specific observable (e.g., the BAO). We define the linear point and sound horizon and we fully characterize and compare the two rulers’ cosmological-parameter dependence. We find that they are both geometrical (i.e., independent of the primordial cosmological parameters) within the required accuracy, and that they have the same parameter dependence for a wide range of parameter values. We estimate the rulers’ best-fit values and errors, given the cosmological constraints obtained by the Planck Satellite team from their measurements of the cosmic microwave background temperature and polarization anisotropies. We do this for three different cosmological models encompassed by the purely geometric BAO methods. In each case we find that the relative errors of the two rulers coincide and they are insensitive to the assumed cosmological model. Interestingly both the linear point and the sound horizon shift by 0.5σ when we do not fix the spatial geometry to be flat in Λ CDM. Finally, this points toward a sensitivity of the rulers to different cosmological models when they are estimated from the cosmic microwave background.

79 ASTRONOMY AND ASTROPHYSICS↗