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All sourcesNASA NTRSDOE OSTI
NASA NTRS2021

Harmonized Emissions Component (HEMCO) 3.0 as a Versatile Emissions Component for Atmospheric Models: Application in the GEOS-Chem, NASA GEOS, WRF-GC, CESM2, NOAA GEFS-Aerosol, and NOAA UFS Models

Emissions are a central component of atmospheric chemistry models. The Harmonized Emissions Component (HEMCO) is a software component for computing emissions from a user-selected ensemble of emission inventories and algorithms. It allows users to re-grid, combine, overwrite, subset, and scale emissions from different inventories through a configuration file and with no change to the model source code. The configuration file also maps emissions to model species with appropriate units. HEMCO can operate in offline stand-alone mode, but more importantly it provides an online facility for models to compute emissions at runtime. HEMCO complies with the Earth System Modeling Framework (ESMF) for portability across models. We present a new version here, HEMCO 3.0, that features an improved three-layer architecture to facilitate implementation into any atmospheric model and improved capability for calculating emissions at any model resolution including multiscale and unstructured grids. The three-layer architecture of HEMCO 3.0 includes (1) the Data Input Layer that reads the configuration file and accesses the HEMCO library of emission inventories and other environmental data, (2) the HEMCO Core that computes emissions on the user-selected HEMCO grid, and (3) the Model Interface Layer that re-grids (if needed) and serves the data to the atmospheric model and also serves model data to the HEMCO Core for computing emissions dependent on model state (such as from dust or vegetation). The HEMCO Core is common to the implementation in all models, while the Data Input Layer and the Model Interface Layer are adaptable to the model environment. Default versions of the Data Input Layer and Model Interface Layer enable straightforward implementation of HEMCO in any simple model architecture, and options are available to disable features such as re-gridding that may be done by independent couplers in more complex architectures. The HEMCO library of emission inventories and algorithms is continuously enriched through user contributions so that new inventories can be immediately shared across models. HEMCO can also serve as a general data broker for models to process input data not only for emissions but for any gridded environmental datasets. We describe existing implementations of HEMCO 3.0 in (1) the GEOS-Chem “Classic” chemical transport model with shared-memory infrastructure, (2) the high-performance GEOS-Chem (GCHP) model with distributed-memory architecture, (3) the NASA GEOS Earth System Model (GEOS ESM), (4) the Weather Research and Forecasting model with GEOS-Chem (WRF-GC), (5) the Community Earth System Model Version 2 (CESM2), and (6) the NOAA Global Ensemble Forecast System – Aerosols (GEFS-Aerosols), as well as the planned implementation in the NOAA Unified Forecast System (UFS). Implementation of HEMCO in CESM2 contributes to the Multi-Scale Infrastructure for Chemistry and Aerosols (MUSICA) by providing a common emissions infrastructure to support different simulations of atmospheric chemistry across scales.

Haipeng Lin↗
NASA NTRS1975

Uranian methane abundance, rotational temperature, and effective pressure from the 6800 A band

Measurements of the methane absorption features at 6800 A in two spectrograms of Uranus have been analyzed on the working hypothesis that the features are the R branch of the 5 mu(3) rotation-vibration overtone. Internal and external consistencies in temperature calculations from the measurements give increased confidence that the band identification and rotational-quantum-number assignments to band members are correct. Parametric fitting of synthetic reflecting-layer and homogeneous scattering-layer spectra to the spectrograms is attempted. The best-fit methane abundances, taken with recent estimates of the molecular hydrogen abundance, correspond to an average C:H ratio between 1.5 and 25 times larger than the solar ratio. Even greater enrichment of the C:H ratio may occur below the visible cloud boundary. High spectroscopic resolution of the present data permits direct measurement of the methane line halfwidth in Uranus's spectrum. The halfwidth corresponds to an effective pressure greater than 3 atm, depending on the mixture of atmospheric gases. Pressure in this range, at the methane rotational temperature of between 93 and 100 K, is inconsistent with current Uranus atmosphere models having solar elemental-abundance ratios. It is consistent with models which are considerably enriched in 'heavier' constituents.

Bergstralh, J. T.↗
DOE OSTI2023

3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism

The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (Danio rerio), respond to toxicant exposure. Recently, the development of 3' RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3' RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data. Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3' or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3' and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes. These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3' RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.

3’ RNA-seq↗
DOE OSTI2023

Neutron calorimeter development at fission and fusion pulsed neutron sources

A neutron calorimeter fielded in pulsed neutron irradiation experiments at the National Ignition Facility (NIF) and White Sands Missile Range Fast Burst Reactor (WSMR FBR) is described, and results are provided and discussed. The calorimeter is modular in design to allow fielding of various neutron absorber materials and thicknesses, as well as use at both fission and fusion sources, all of which has been done. Neutron calorimeters designed for fission sources have been fielded at fusion sources as well, but these instances are not documented in available literature—making this work novel. The functional calorimeter consists of a neutron absorber and two sheathed, grounded thermocouples secured within a subassembly made of thermally insulating materials. This subassembly is placed into a sealed vessel for material and facility safety considerations. The device was fielded at NIF in four polar-direct-drive exploding pusher shots and eleven WSMR FBR pulses. Calorimeter data from NIF experiments show a discernable thermal response accredited to neutron heating within the first 10 s, but the data are dominated by noise from ambient X-ray heating after time = 10 s post-pulse. This response is highly consistent between shots and linearly related to incident neutron fluence and neutron absorber thickness. A temperature rise of 1.1E-2 K/(10 13 neutrons/cm 2 ) per millimeter of absorber thickness was determined for both 0.4 mm and 1 mm thick depleted uranium absorbers with linear best fit R 2 of 0.97 and 0.98 for each thickness and y-axis offsets of 8.8E-3 and 1.3E-2, respectively. WSMR FBR experiment data show a temperature rise of 6.2E-2 K/(10 13 neutrons/cm 2 ) with linear best fit R 2 of 0.14 and y-axis offset of 7.6E-3 for a calorimeter with a 1 mm thick enriched boron carbide ( 10 B 4 C) absorber, though it must be noted that device-to-device variability is significant at both facilities. So these data are also affected by noise on a similar timescale as at NIF, though the noise is significantly lesser in magnitude but oscillatory.

42 ENGINEERING↗
DOE OSTI2025

IER 516: Zirconium Test Assembly CED Phase-1: Preliminary Experiment Design

IER-516, Zirconium Test Assembly (ZTA), is a campaign to design, execute, and document a series of high-fidelity critical benchmark experiments to validate current and future zirconium (Zr) and zirconium hydride (ZrH x ) nuclear data evaluations. ZTA is a collaborative project between Los Alamos National Laboratory and the French Autoritè de Sûretè Nuclèaire et de Radioprotection. The experiments will be fueled with highly enriched uranium (HEU), and utilize the Comet critical assembly machine at the National Criticality Experiments Research Center. A total of ten preliminary critical experiments were designed and optimized for Zr and ZrHx nuclear data sensitivities using the MCNP-Particle Swarm Optimization methodology in the thermal, epithermal, intermediate, and fast neutron energy regions.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Metals and methylotrophy: Via global gene expression studies

A number of minerals, such as copper, cobalt, and rare earth elements (REE), are essential modulators of microbial one-carbon metabolism. This chapter provides an overview of the gene expression study design and analysis protocols for uncovering REE-induced changes in methylotrophic bacteria. By interrogating relationships and differences in total gene expression induced by mineral micronutrients, a deeper understanding of gene regulation at a systems scale can be gained. With careful design and execution of RNA-sequencing experiments, thorough processing and assessment of read quality can be utilized to assess and adjust for possible biases. Here, by ensuring only quality data are utilized in downstream processes, differential gene expression, overrepresented analyses, and gene-set enrichment analyses provide reliable and reproducible representation of pathways and functions which are being affected by changes in environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Californium-252 production at the High Flux Isotope Reactor - II: Comparison between the highly enriched uranium and a proposed low-enriched uranium core

This is the second paper on a 252 Cf production study performed in support of efforts to convert the High Flux Isotope Reactor (HFIR) from highly enriched uranium (HEU) to low-enriched uranium (LEU) fuel. The first paper primarily focuses on validating computational tools and nuclear data. This companion paper evaluates another critical aspect: the 252 Cf production capability with a proposed LEU core. HFIR must maintain its world-class performance and missions following conversion and because 252 Cf is a vital, multipurpose neutron-emitting radioisotope, the ability to efficiently produce 252 Cf must be preserved. In this study, the HFIRCON transport and depletion tool, several nuclear data libraries, and Campaign 78 data were used to compute 252 Cf production, sensitivity, and safety metrics. Further, results indicate the 252 Cf production and production rates are slightly higher with a 95MW th LEU core compared with those obtained with the 85MW th HEU core. Additionally, the target peak fission rate densities, discharge cumulative fission densities, and heat deposition rates with the LEU core are within a few percent of those calculated with the HEU core. The findings suggest HFIR’s 252 Cf production capability can be effectively maintained with an LEU core without adversely affecting the safety metrics.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2023

Protein-based approach for high-purity Sc, Y, and grouped lanthanide separation

Rare earth elements (REEs: Sc, Y, La- Lu) are irreplaceable components in many clean energy and consumer technologies. However, the extraction and subsequent separation of individual REEs from ore-based feedstocks remains a significant economic and environmental challenge. Here in this work, we investigated the intra-REE separation potential of lanmodulin (LanM), a natural protein from Methylorubrum extorquens that has emerged as a sustainable potential alternative to conventional solvent extraction-based separation. By determining the intra-REE selectivity of immobilized LanM and systematically testing pH-based and small chelator-based (i.e., citrate and malonate) desorption processes, we established the framework and methodology for achieving select individual and grouped REE separations from a mixed REE feedstock. We show that Sc forms the tightest complex with LanM among REEs but can be readily and selectively desorbed using malonate to generate high-purity Sc (>99 % purity, >99 % yield) in a single adsorption/desorption cycle. We further show that the intrinsic REE selectivity of LanM is sufficient to achieve heavy REE (HREE) separation from light and middle REEs (L-MREEs), yielding an yttrium-enriched product. This separation effect is further magnified by pairing LanM’s unique M-LREE preference with a HREE-preferring chelator in the desorption process, which enriches HREE and MREE fractions relative to low value, abundant La/Ce. Finally, by combining pH- and citrate-based desorption processes in a two-cycle separation scheme, we demonstrate the generation of fractions highly enriched in Y, Gd-Lu, Pr-Eu, and La-Ce. Collectively, these data support the application of a LanM-based approach for achieving impactful REE separations from mixed REE feedstocks.

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

Computationally restoring the potency of a clinical antibody against Omicron

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs and revealed how quickly viral escape can curtail effective options. When the SARS-CoV-2 Omicron variant emerged in 2021, many antibody drug products lost potency, including Evusheld and its constituent, cilgavimab. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign and renew the efficacy of COV2-2130 against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and subsequent variants of concern, and provides protection in vivo against the strains tested: WA1/2020, BA.1.1 and BA.5. Deep mutational scanning of tens of thousands of pseudovirus variants reveals that 2130-1-0114-112 improves broad potency without increasing escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Our computational approach does not require experimental iterations or pre-existing binding data, thus enabling rapid response strategies to address escape variants or lessen escape vulnerabilities.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Charge trapping correction and energy performance of the Majorana Demonstrator

P-type point contact (PPC) high-purity germanium detectors are an important technology in astroparticle and nuclear physics due to their superb energy resolution, low noise, and pulse shape discrimination capabilities. Analysis of data from the Majorana Demonstrator, a neutrinoless double-β decay experiment deploying PPC detectors enriched in 76 Ge, has led to several novel improvements in the analysis of PPC signals. Here, in this work we discuss charge trapping in PPC detectors and its effect on energy resolution. Small dislocations or impurities in the crystal lattice result in trapping of charge carriers from an ionization event of interest, attenuating the signal, and degrading the measured energy. We present a modified digital pole-zero correction to the signal energy estimation that counters the effects of charge trapping and improves the energy resolution of the Majorana Demonstrator by approximately 30 % to around 2.4 keV full width at half-maximum at 2039 keV, the 76 Ge Q value. An alternative approach achieving similar resolution enhancement is also presented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Spatially Resolved Characterisation of Low Mass Fraction Uranium Glass Working Reference Materials

Here, we present the results of a study to generate reference glasses that reflect an environment analogous to historic nuclear fallout samples of interest for post-detonation nuclear forensics. The glasses were generated by melting and then quenching SiO 2 , Al 2 O 3 and CaCO 3 powders. Two suites of glasses with three distinct U isotopic ratios were successfully made with enrichments in the 235 U isotope (~ natural [0.72%], ~ 53% and 94%), but the bulk elemental data showed heterogeneity (~ 10% RSD) with U mass fractions ranging from 331.47 to 373.63 μg g -1 . Spatially resolved U isotopic measurements were performed using three mass spectrometry techniques (secondary ion mass spectrometry-single stage accelerator mass spectrometry [SIMS-SSAMS], large geometry [LG] - SIMS, and laser ablation-inductively coupled plasma-mass spectrometry [LA-ICP-MS]) across five National Laboratories. The results showed good agreement with the bulk U isotopic data for the low, medium, and high U mass fractions. We conclude that despite elemental heterogeneity, these samples can serve as useful working reference materials for spatially resolved nuclear fallout analyses, as well as for other related spatially resolved analyses.

36 MATERIALS SCIENCE↗
NASA NTRS1974

Surface properties of the Orgueil meteorite - Implications for the early history of solar system volatiles

The Kr and H2O adsorption properties of Orgueil were studied. Dehydration by stepwise calcination produced a tenfold change in its B.E.T. surface area, which increased to 120 and then fell to 40 square meters per gram. Water exchangeability was measured by water regain from lab air between calcination cycles. Dehydration at room temperature showed that Orgueil contained 6 per cent by weight of water adsorbed on free surfaces. These results are consistent with an identification of Orgueil as montmorillonite, although chemical data conflict with this. High D/H ratios in CI carbonaceous chondrites may result from D enrichment in OH- groups during equilibration of dispersed phyllosilicate dust with preplanetary nebula gas at temperatures much less than 0 C.

Fanale, F. P.↗
NASA NTRS1984

Mantle-derived Archaean monzodiorites and trachyandesites

Geochemical data on monzodiorites and trachyandesites from the Rainy Lake area in Ontario which are strongly enriched in large-ion lithophile elements (LILE) are presented. It is concluded that they are derived by direct melting of the mantle at depths of less than 50 km in either anhydrous or hydrous conditions. Their rare earth element abundances and initial Nd-143/Nd-144 ratios suggest that their mantle sources were enriched in LILE shortly before melting. The monzodiorites-trachyandesites and their granodioritic derivatives may comprise up to 20 percent of the exposed igneous rocks in the Rainy Lake region and Vermilion District. If these rocks are as abundant in other Archaean terranes, a significant part of the early continental crust could have formed by direct melting of LILE-enriched mantle.

Shirey, S. B.↗
NASA NTRS1987

Spectral characteristics and the extent of paleosols of the Palouse formation

Three spectral models defining the spatial distribution of soil areas by levels of amorphous iron, organic carbon, and the ratio of amorphous iron to organic carbon were developed and field verification studies were conducted. The models used particular Thematic Mapper band ratios selected by statistical correlation with soil chemical data. The ability of the models to indicate erosion severity and to differentiate between iron enriched and carbonate paleosols is discussed. In addition, the effect of vegetation cover on paleosols is addressed.

Frazier, B. E.↗
NASA NTRS1991

Leaching behavior of microtektite glass compositions in sea water and the effect of precipitation on glass leaching

The present study attempts to account for the slow corrosion rates of microtektite glass in nature by comparing the leach rates of synthetic microtektite glass samples in deionized water and in sea-water, respectively. In order to obtain systematic data about leachant composition effects, leach tests were also carried out with synthetic leachant compositions enriched with respect to silica or depleted with respect to certain major components of sea-water (Mg, Ca).

Source record↗
NASA NTRSDate not supplied

High School Citizen Scientists Use AI/ML to Predict Intra-Ocular Pressure From Gene Expression Data for Spaceflown Mice

Artificial Intelligence (AI) and Machine Learning (ML) have increasingly become pivotal in biological and biomedical research, largely due to the culture of open data sharing and its associated benefits. The methodologies inherent in AI/ML are particularly adept at identifying and forecasting biological phenotypes from the vast amounts of data generated by next-generation sequencing technologies. These techniques offer substantial promise for advancing research in space biosciences and for the development of automated systems for monitoring space health. Nevertheless, there are crucial aspects to consider when training, validating, and testing machine learning models in both biological research and clinical contexts. It is essential that Open Science principles, including data sharing and the availability of open-source code, are complemented by high-quality, publicly accessible training resources. These resources should focus on best practices and include modules based on real-world scientific cases and data to ensure that future AI/ML practitioners gain practical experience with genuine problems. Addressing this knowledge gap, we have designed, developed, and delivered both interactive and self-paced training programs for citizen scientists worldwide, enabling them to utilize AI/ML for space biology research. This initiative was made possible through generous funding from a Transformation to Open Science Training grant. The interactive training sessions, conducted this summer, utilized AI/ML techniques to analyze data from the Open Science Data Repository, specifically targeting the effects of spaceflight on ocular structure and function. The dataset OSD-583, from the Rodent Research 9 mission, provides experimental data detailing the ocular responses of mice subjected to a 35-day spaceflight, compared with ground control counterparts. Using OSD-583 as observational data, our summer training participants applied AI/ML methods to predict intraocular pressure from RNA-seq data and identify the genes most predictive of the observed responses. Further analysis through pathway enrichment and gene set enrichment revealed that these genes are involved in molecular and cellular processes contributing to retinal degeneration.

James Casaletto↗
DOE OSTI2021

Metals and methylotrophy: Via global gene expression studies

A number of minerals, such as copper, cobalt, and rare earth elements (REE), are essential modulators of microbial one carbon metabolism. This chapter provides an overview of the gene expression study design and analysis protocols for uncovering REE-induced changes in methylotrophic bacteria. By interrogating relationships and differences in total gene expression induced by mineral micronutrients, a deeper understanding of gene regulation at a systems scale can be gained. With careful design and execution of RNA-sequencing experiments, thorough processing and assessment of read quality can be utilized to assess and adjust for possible biases. By ensuring only quality data are utilized in downstream processes, differential gene expression, overrepresented analyses, and gene-set enrichment analyses provide reliable and reproducible representation of pathways and functions which are being affected by changes in environmental conditions.

Johnson, Zachary J.↗
DOE OSTI2021

Uranium integral fission product yields for a spectrally-shaped 14.1 MeV neutron source at the National Ignition Facility

This paper describes the experimental results for an energy tuning assembly created to modify the National Ignition Facility deuterium–tritium fusion neutron source into a notional thermonuclear and prompt fission neutron spectrum, which has applications in integral measurements, nuclear data benchmarks, and radiation effects on microelectronics. The Monte Carlo neutron transport utilized MCNP5 to estimate the ETA-modified fluence using the ENDF-B/VIII.0 and IRDFF-II continuous energy nuclear data libraries, and SCALE Sampler was used to estimate the systematic nuclear data covariance using ENDF-B/VII.1 and IRDFF-II in a 252-group structure. The experiment fielded eight activation foils and a highly enriched uranium sample. This provided fifteen reaction channels that were used in a forward-fit comparison to the modeled results and to unfold the neutron spectrum using STAYSL. Gamma-ray spectrometry was performed on the activation and highly enriched uranium foils, and the reduced Χ 2 between the modeled and experimental values was 1.21. The results from the STAYSL unfold, reduced Χ 2 = 1.62, indicated that the modeled neutron spectrum was achieved and the systematic nuclear data uncertainty associated with the neutron transport and activation product cross sections was representative of the experiment. Integral cumulative fission product yield data were collected for 37 mass chains with a combination of gamma-ray spectrometry and radiochemical analysis. Fission product analysis was generally in agreement with two models using a semi-empirical fit and the General Observables of Fission code, with the exception of mass chains 88, 109, 111, 112, 113, 129, 139, 142, 144, 151, and 156.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗