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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Ion-Specific Effects in Carboxylate Binding Sites

Specific ion binding by carboxylates (-COO–) is a broadly important topic because -COO– is one of the most common functional groups coordinated to metal ions in metalloproteins and synthetic polymers. We apply quantum chemical methods and the quasi-chemical free-energy theory to investigate how variations in the number of -COO – ligands in a binding site determine ion-binding preferences. We study a series of monovalent (Li + , Na + , K + , Cs + ) and divalent (Zn 2+ , Ca 2+ ) ions relevant to experimental work on ion channels and ionomers. Of two competing hypotheses, our results support the ligand field strength hypothesis and follow the reverse Hofmeister series for ion solvation and ion transfer from aqueous solution to binding sites with the preferred number of ligands. New insight arises from the finding that ion-binding sequences can be manipulated and even reversed just by constraining the number of carboxylate ligands in the binding sites. Our results help clarify the discrepancy in ion association between molecular ligands in aqueous solutions and ionomers, and their chemical analogues in ion-channel binding sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Solute concentrations influence microbial methanogenesis in coal-bearing strata of the Cherokee basin, USA

In this study, microorganisms have contributed significantly to subsurface energy resources by converting organic matter in hydrocarbon reservoirs into methane, the main component of natural gas. In this study, we consider environmental controls on microbial populations in coal-bearing strata of the Cherokee basin, an unconventional natural gas resource in southeast Kansas, USA. Pennsylvanian-age strata in the basin contain numerous thin (0.4–1.1 m) coalbeds with marginal thermal maturities (0.5–0.7% R o ) that are interbedded with shale and sandstone. We collected gas, water, and microbe samples from 16 commercial coalbed methane wells for geochemical and microbiological analysis. The water samples were Na–Cl type with total dissolved solids (TDS) content ranging from 34.9 to 91.3 g L –1 . Gas dryness values [C 1 /(C 2 + C 3 )] averaged 2640 and carbon and hydrogen isotope ratios of methane differed from those of carbon dioxide and water, respectively, by an average of 65 and 183‰. These values are thought to be consistent with gas that formed primarily by hydrogenotrophic methanogenesis. Results from cultivation assays and taxonomic analysis of 16S rRNA genes agree with the geochemical results. Cultivable methanogens were present in every sample tested, methanogen sequences dominate the archaeal community in each sample (avg 91%), and few archaeal sequences (avg 4.2%) were classified within Methanosarcinales , an order of methanogens known to contain methylotrophic methanogens. Although hydrogenotrophs appear dominant, geochemical and microbial analyses both indicate that the proportion of methane generated by acetoclastic methanogens increases with the solute content of formation water, a trend that is contrary to existing conceptual models. Consistent with this trend, beta diversity analyses show that archaeal diversity significantly correlates with formation water solute content. In contrast, bacterial diversity more strongly correlates with location than solute content, possibly as a result of spatial variation in the thermal maturity of the coalbeds.

03 NATURAL GAS↗
DOE OSTI2023

National Prevalence of Caprine Prion Protein Genetic Variability at Codons 146, 211, and 222 in Goat Herds in the United States

Scrapie is a neurodegenerative disease that impacts sheep and goats, characterized by gradual and progressive changes in neurological function. Recent research shows that the scrapie incubation period is significantly influenced by specific variations in amino acids within the prion protein gene (PRNP). The objective of this study was to estimate the national prevalence of caprine PRNP genetic variability at codons 146, 211, and 222 in goat populations across the United States. A total of 3052 blood, ear tissue, and brain tissue samples were collected from goats from 50 states. The participating states were categorized into four Veterinary Service (VS) district regions. The samples underwent DNA extraction, and the PRNP variants corresponding to codons 146, 211, and 222 were amplified and sequenced. The analysis of PRNP variants, when compared to the PRNP reference sequence, revealed seven alleles in twelve genotypes. The homozygous 146NN, 211RR, and 222QQ alleles, which have been linked to an increased risk of scrapie, were found to be the most prevalent among all the goats. The heterozygous 222QK, 211RQ, 146SD, 146ND, and 146NS alleles and the homozygous 222KK, 146SS, and 146DD alleles, known to be associated with reduced scrapie susceptibility and a prolonged incubation period after experimental challenge, were found in 1.098% (222QK), 2.33% (211RQ), 0.58% (146SD), 3.13% (146ND), 20.68% (146NS), 0.005% (222KK), 3.31% (146SS), and 0.67% (146DD) of goats, respectively. The 222QK allele was found most frequently in goats tested from the east (VS District 1, 1.59%) and southwest (VS District 4, 1.08%) regions, whereas the 211RQ allele was found most often in goats tested from the Midwest (VS District 2, 8.03%) and east (VS District 1, 6.53%) regions. The 146NS allele was found most frequently in goats tested from the northwest (VS District 3, 29.02%) and southwest (VS District 4, 20.69%) regions. Our results showed that the prevalence of less susceptible genotypes at PRNP codon 146 may be sufficient to use genetic susceptibility testing in some herds. This may reduce the number of goats removed as part of a herd clean-up plan and may promote the selective breeding goats for less susceptible alleles in high-risk herds at the national level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1981

Software metrics: The quantitative impact of four factors on work rates experienced during software development

A model of a software development process is described. The software development process is seen to consist of a sequence of activities, such as 'program design' and 'module development' (or coding). A manpower estimate is made by multiplying code size by the rates (man months per thousand lines of code) for each of the activities relevant to the particular case of interest and summing up the results. The effect of four objectively determinable factors (organization, software product type, computer type, and code type) on productivity values for each of nine principal software development activities was assessed. Four factors were identified which account for 39% of the observed productivity variation.

Gaffney, J. E., Jr.↗
NASA NTRS2011

Toward Realistic Dynamics of Rotating Orbital Debris, and Implications for Lightcurve Interpretation

Optical observations of rotating space debris near GEO contain important information on size, shape, composition, and rotational states, but these aspects are difficult to extract due to data limitations and the high number of degrees of freedom in the modeling process. For tri-axial rigid debris objects created by satellite fragmentations, the most likely initial rotation state has a large component of initial angular velocity directed along the intermediate axis of inertia, leading to large angular reorientations of the body on the timescale of the rotation period. This lends some support to the simplest possible interpretation of light curves -- that they represent sets of random orientations of the objects of study. However, effects of internal friction and solar radiation are likely to cause significant modification of rotation states within a time as short as a few orbital periods. In order to examine the rotational dynamics of debris objects under the influences of these effects, a set of seven first-order coupled equations of motion were assembled in state form: three are Euler equations describing the rates of change of the components of angular velocity in the body frame, and four describe the rates of change of the components of the unit quaternion. Quaternions are a four-dimensional extension of complex numbers that form a seamless, singularity-free representation of body orientation on S3. The Euler equations contain explicit terms describing torque from solar radiation in terms of spherical harmonics, and terms representing effects of a prescribed rate of internal friction. Numerical integrations of these equations of motion are being performed, and results will be presented. Initial tests show that internal friction without solar radiation torque leads to rotation about the maximum principal axis of inertia, as required, and solar radiation torque is expected to lead to spin-up of objects. Because the axis of maximum rotational inertia tends to be roughly coincident with the normal to the largest projected cross-sectional area, internal friction is expected to lead to reduced variation of light curve amplitudes at a given phase angle, but a large dependence of the same on phase angle. At a given phase angle, databases are generated which contain reflected intensities for comprehensive sets of equally-likely orientations, represented as unit quaternions. When projected onto three dimensions (S2) and color-coded by intensity, the set is depicted as points within a solid, semi-transparent unit sphere, within which all possible reflected intensities for an object at a given phase angle may be inspected simultaneously. Rotational sequences are represented by trajectories through the sphere. Databases are generated for each of a set of phase angles separately, forming a comprehensive dataset of reflected intensities spanning all object orientations and solar phase angles. Symmetries in the problem suggest that preferred rotation states are likely, defined relative to the object-sun direction in inertial space and relative to the maximum principal axis of inertia in the body coordinate system. Such rotation states may greatly simplify the problem of light curve interpretation by reducing the number of degrees of freedom in the problem.

Ojakangas, Gregory W.↗
DOE OSTI2019

A Knowledge Graph Approach for the Secondary Use of Cancer Registry Data

Population-based central cancer registries collect valuable structured and unstructured data primarily for cancer surveillance and research, enhancing insights into clinical features associated with cancer occurrence, cancer treatment, and cancer outcomes to guide interventions which reduce the cancer burden. Cancer registries primarily collect data on (1) cancer type (case or tumor); (2) patient demographics such as age, gender, and residential address at time of diagnosis; (3) planned first course of treatment; and (4) date of last contact, vital status, and cause of death. Cancer registry data is dynamic, structured data, which is extracted from many unstructured sources such as electronic healthcare records, and consolidated for reporting and other purposes. While available advanced analytic tools such as SEER*Stat have the ability to build SAS queries, we, however, explore an innovative knowledge graph approach to organizing cancer registry data for advanced analytics and visualization, which has unique advantages over approaches of existing tools. This innovative knowledge graph approach semantically enriches the data and easily enables linkage with third-party data, which can better explain variation in outcomes. We have developed a prototype knowledge graph based on data from the Louisiana Tumor Registry and other publicly available datasets including Behavioral Risk Factor Surveillance System, Clinical Trials, DBpedia, GeoNames, Rural-Urban Continuum Codes, and Semantic MEDLINE. The resource description framework (RDF) data model was selected to represent our knowledge graph, which contains more than 25 billion triples and is ~4TB in storage size. To exhibit the benefits of the knowledge graph approach, we used scenario specific queries, which find the relationships between cancer treatment sequences and outcomes. To illustrate its ease of use in iterative analysis, the knowledge graph was linked to external datasets for performing complex queries across multiple datasets. In addition, we used knowledge graphs to identify data discrepancies and to handle schema changes. Finally, we visualized the knowledge graph to discover data patterns. Our results demonstrate this graph-based solution enables cancer researchers to execute complex queries and more easily perform iterative analyses to improve understanding of cancer registry data. In the future, we would like to use high-performance computing (HPC) resources for faster-generating hypotheses with clinical potential from our knowledge graph.

Hasan, S M Shamimul↗
DOE OSTI2022

Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Navigating the maze: the impact of configurability in bioinformatics software

The bioinformatics software domain contains thousands of applications for automating tasks such as the pairwise alignment of DNA sequences, building and reasoning about metabolic models or simulating growth of an organism. Its end users range from sophisticated developers to those with little computational experience. In response to their needs, developers provide many options to customize the way their algorithms are tuned. Yet there is little or no automated help for the user in determining the consequences or impact of the options they choose. In this paper we describe our experience working with configurable bioinformatics tools. We find limited documentation and help for combining and selecting options along with variation in both functionality and performance. We also find previously undetected faults. We summarize our findings with a set of lessons learned, and present a roadmap for creating automated techniques to interact with bioinformatics software. We believe these will generalize to other types of scientific software.

McDevitt, Mikaela Cashman↗
NASA NTRS1978

Mechanics of failure of composite materials

Composite materials are both inhomogeneous and anisotropic. Both of these characteristics affect the internal stress distributions since inhomogeneity involves variations in both strength and stiffness. The fracture mechanics of nonuniform materials are considered, taking into account the effect of nonuniformity on stress distributions near the crack tip, predicted yield zones in nonuniform and uniform materials, and the fracture of a center-notched unidirectional specimen. The mechanics of failure of laminated materials is discussed. It is found that the development of damage in a laminate with increasing load and, possibly, increasing numbers of cycles of loading is peculiar to the laminate in question, i.e., the material system, the stacking sequence, and the geometry. Approaches for monitoring damage development are also described.

Reifsnider, K. L.↗
DOE OSTI2016

Unification of [FeFe]-hydrogenases into three structural and functional groups

[FeFe]-hydrogenases (Hyd) are structurally diverse enzymes that catalyze the reversible oxidation of hydrogen (H 2 ). Recent biochemical data demonstrate new functional roles for these enzymes, including those that function in electron bifurcation where an exergonic reaction is coupled with an endergonic reaction to drive the reversible oxidation/production of H 2 . To identify the structural determinants that underpin differences in enzyme functionality, a total of 714 homologous sequences of the catalytic subunit, HydA, were compiled. Bioinformatics approaches informed by biochemical data were then used to characterize differences in inferred quaternary structure, HydA active site protein environment, accessory iron-sulfur clusters in HydA, and regulatory proteins encoded in HydA gene neighborhoods. HydA homologs were clustered into one of three classification groups, Group 1 (G1), Group 2 (G2), and Group 3 (G3). G1 enzymes were predicted to be monomeric while those in G2 and G3 were predicted to be multimeric and include HydB, HydC (G2/G3) and HydD (G3) subunits. Variation in the HydA active site and accessory iron-sulfur clusters did not vary by group type. Group-specific regulatory genes were identified in the gene neighborhoods of both G2 and G3 Hyd. Analyses of purified G2 and G3 enzymes by mass spectrometry strongly suggests that they are post-translationally modified by phosphorylation. In conclusion, these results suggest that bifurcation capability is dictated primarily by the presence of both HydB and HydC in Hyd complexes, rather than by variation in HydA.

09 BIOMASS FUELS↗
DOE OSTI2023

Internal gravity waves in massive stars: II. Frequency analysis across stellar mass

Stars that are over 1.6 solar masses are generally known to possess convective cores and radiative envelopes, which allows for the propagation of outwardly travelling internal gravity waves (IGWs). Here, we study the generation and propagation of IGWs in such stars using two-dimensional, fully non-linear hydrodynamical simulations with realistic stellar reference states from the one-dimensional stellar evolution code, Modules for Stellar Astrophysics. Compared to previous similar works, this study utilises radius-dependent thermal diffusivity profiles for five different stellar masses at the middle of the main sequence: 3 M ⊙ , 5 M ⊙ , 7 M ⊙ , 10 M ⊙ , and 13 M ⊙ . From the simulations, we find that the surface perturbations are larger for higher masses, but no noticeable trends are observed for the frequency slopes with different stellar masses. The slopes are also similar to the results from previous works. We compared our simulation results with stellar photometric data from a recent survey and we found that for frequency intervals above 8 μHz, there is a good agreement between the temperature frequency slopes from the simulations and the surface brightness variations of these observed stars. This indicates that the brightness variations are caused by core-generated IGWs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Differences in substrate use linked to divergent carbon flow during litter decomposition

ABSTRACT Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Galaxy populations in massive galaxy clusters to $z$ = 1.1: Color distribution, concentration, halo occupation number and red sequence fraction

We study the galaxy populations in 74 Sunyaev–Zeldovich effect selected clusters from the South Pole Telescope survey, which have been imaged in the science verification phase of the Dark Energy Survey. The sample extends up to z ~ 1.1 with 4 × 10 14 M⊙ ≤ M200 ≤ 3 × 10 15 M⊙. Using the band containing the 4000 Å break and its redward neighbour, we study the colour–magnitude distributions of cluster galaxies to ~m* + 2, finding that: (1)The intrinsic rest frame g – r colour width of the red sequence (RS) population is ~0.03 out to z ~ 0.85 with a preference for an increase to ~0.07 at z = 1, and (2) the prominence of the RS declines beyond z ~ 0.6. The spatial distribution of cluster galaxies is well described by the NFW profile out to 4R200 with a concentration of c g = 3.59$+0.20\atop{–0.18}$, 5.37$+0.27\atop{-0.24}$ and 1.38$+0.21\atop{-0.19}$ for the full, the RS and the blue non-RS populations, respectively, but with ~40 per cent to 55 per cent cluster to cluster variation and no statistically significant redshift or mass trends. The number of galaxies within the virial region N200 exhibits a mass trend indicating that the number of galaxies per unit total mass is lower in the most massive clusters, and shows no significant redshift trend. The RS fraction within R200 is (68 ± 3) per cent at z = 0.46, varies from ~55 per cent at z = 1 to ~80 per cent at z = 0.1 and exhibits intrinsic variation among clusters of ~14 per cent. Finally, we discuss a model that suggests that the observed redshift trend in RS fraction favours a transformation time-scale for infalling field galaxies to become RS galaxies of 2–3 Gyr.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1973

Lunar atmospheric composition experiment

On the Apollo 17 mission, a miniature mass spectrometer, called the lunar atmospheric composition experiment (LACE), was carried to the moon as part of the Apollo lunar surface experiments package (ALSEP) to study the composition of and variation in the lunar atmosphere. The instrument was successfully deployed in the Taurus-Littrow valley with its entrance aperture oriented upward to intercept and measure the downward flux of gases at the lunar surface. Initial activation of the LACE instrument occurred on December 27, 1972, approximately 50 hr after sunset, and operation continued throughout the first lunar night. Sunrise brought a high background gas level and necessitated discontinuing operation during lunar daytime except for a brief check near noon. Near sunset, operation was resumed and continued throughout the night. This sequence was repeated for the second and third lunations.

J. H. Hoffman↗
NASA NTRS1991

Parameter estimation in space systems using recurrent neural networks

The identification of time-varying parameters encountered in space systems is addressed, using artificial neural systems. A hybrid feedforward/feedback neural network, namely a recurrent multilayer perception, is used as the model structure in the nonlinear system identification. The feedforward portion of the network architecture provides its well-known interpolation property, while through recurrency and cross-talk, the local information feedback enables representation of temporal variations in the system nonlinearities. The standard back-propagation-learning algorithm is modified and it is used for both the off-line and on-line supervised training of the proposed hybrid network. The performance of recurrent multilayer perceptron networks in identifying parameters of nonlinear dynamic systems is investigated by estimating the mass properties of a representative large spacecraft. The changes in the spacecraft inertia are predicted using a trained neural network, during two configurations corresponding to the early and late stages of the spacecraft on-orbit assembly sequence. The proposed on-line mass properties estimation capability offers encouraging results, though, further research is warranted for training and testing the predictive capabilities of these networks beyond nominal spacecraft operations.

Parlos, Alexander G.↗
NASA NTRS1993

A survey for rapid variability among early main-sequence A stars

A survey of nonpeculiar early (A0-A5) main-sequence A stars for rapid, low-amplitude variability is presented. The survey is also an independent test of the main-sequence mass-loss theory proposed by Willson et al. (1986). All observations were gathered with the University of Wisconsin Two-Star Photometer. Several period-searching methods are used to analyze time series of differential-photometric data. This instrument coupled with a computerized high-speed data collection system was used with small telescopes at Pine Bluff Observatory and Table Mountain Observatory. Several period-search methods are used to analyze time series of differential-photometric data. This instrument and data-reduction technique allow millimagnitude light variations to be detected. The survey also discovered several low-amplitude Delta Sct stars, all of which are in or blueward of the recognized instability strip.

Schutt, Randy L.↗