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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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DOE OSTI2023

Continental United States climate projections based on thermodynamic modification of historical weather

Abstract Regional climate models can be used to examine how past weather events might unfold under different climate conditions by simulating analogue versions of those events with modified thermodynamic conditions (i.e., warming signals). Here, we apply this approach by dynamically downscaling a 40-year sequence of past weather from 1980–2019 driven by atmospheric re-analysis, and then repeating this 40-year sequence a total of 8 times using a range of time-evolving thermodynamic warming signals that follow 4 80-year future warming trajectories from 2020–2099. Warming signals follow two emission scenarios (SSP585 and SSP245) and are derived from two groups of global climate models based on whether they exhibit relatively high or low climate sensitivity. The resulting dataset, which contains 25 hourly and over 200 3-hourly variables at 12 km spatial resolution, can be used to examine a plausible range of future climate conditions in direct reference to previously observed weather and enables a systematic exploration of the ways in which thermodynamic change influences the characteristics of historical extreme events.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2012

Sodium Fast Reactor Safety and Licensing Research Plan – Volume II

Expert panels comprised of subject matter experts identified at the U.S. National Laboratories (SNL, ANL, INL, ORNL, LBL, and BNL), universities (University of Wisconsin and Ohio State University), international agencies (IRSN, CEA, JAEA, KAERI, and JRC-IE) and private consultation companies (Radiation Effects Consulting) were assembled to perform a gap analysis for sodium fast reactor licensing. Expert-opinion elicitation was performed to qualitatively assess the current state of sodium fast reactor technologies. Five independent gap analyses were performed resulting in the following topical reports: (1) Accident Initiators and Sequences (i.e., Initiators/Sequences Technology Gap Analysis), (2) Sodium Technology Phenomena (i.e., Advanced Burner Reactor Sodium Technology Gap Analysis), (3) Fuels and Materials (i.e., Sodium Fast Reactor Fuels and Materials: Research Needs), (4) Source Term Characterization (i.e., Advanced Sodium Fast Reactor Accident Source Terms: Research Needs), and (5) Computer Codes and Models (i.e., Sodium Fast Reactor Gaps Analysis of Computer Codes and Models for Accident Analysis and Reactor Safety). Volume II of the Sodium Research Plan consolidates the five gap analysis reports produced by each expert panel, wherein the importance of the identified phenomena and necessities of further experimental research and code development were addressed. The findings from these five reports comprised the basis for the analysis in Sodium Fast Reactor Research Plan Volume I.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2021

Improved Microbial Community Characterization of 16S rRNA via Metagenome Hybridization Capture Enrichment

Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic methods sample more genomic regions with fewer sequence acquisition biases, but are much more expensive (even with moderate sequencing depth) and computationally challenging. Here, we develop a set of 16S rRNA sequence capture baits that offer a potential middle ground with the advantages from both approaches for investigating microbial communities. These baits cover the diversity of all 16S rRNA sequences available in the Greengenes (v. 13.5) database, with no sequence having <78% sequence identity to at least one bait for all segments of 16S. The use of our baits provide comparable results to 16S amplicon libraries and shotgun metagenomic libraries when assigning taxonomic units from 16S sequences within the metagenomic reads. We demonstrate that 16S rRNA capture baits can be used on a range of microbial samples (i.e., mock communities and rodent fecal samples) to increase the proportion of 16S rRNA sequences (average > 400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely due in part to the extent and curation of the reference databases considered. Thus, enriching existing aliquots of shotgun metagenomic libraries and obtaining modest numbers of reads from them offers an efficient orthogonal method for assessment of bacterial community composition.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Regulatory Treatment of Low Frequency External Events under a Risk-Informed Performance-Based Licensing Pathway

Significant efforts are underway to develop and implement a risk-informed performance-based licensing framework for advanced reactors built on the establishment of an affirmative safety case. Such approaches offer the benefits of increased flexibility regarding key design and licensing decisions based on a detailed assessment and understanding of plant risk. These methods include the comprehensive analysis of scenarios that have historically been addressed through conservative and deterministic licensing analysis approaches, such as the evaluation of event sequences at frequencies of occurrence beyond the design basis. While the detailed analysis of low frequency events provides insights that can help justify alternative treatments to past conservatism, the findings are dependent on the quality and confidence associated with the analyses. The assessment of external hazards presents a unique challenge, as their potential frequency of occurrence, especially of large magnitude events, is inherently uncertain given the long return periods in question. The current project seeks to further explore the regulatory treatment of low frequency external events as part of a risk-informed performance-based framework. The goals are to identify the benefits and challenges of such approaches for advanced reactor vendors and to aid in the development of consistent and appropriate methodologies. As part of this effort, the current report summarizes initial project findings, with a focus on the evaluation of the seismic hazard. This includes an exploration of the implementation of a risk-informed performance-based approach through an example analysis. Based on the identified challenges associated with the probabilistic treatment of low frequency event sequences, additional performance-based methods were explored as complementary tools for demonstrating regulatory compliance. The report highlights key challenges and opportunities associated with the methods and outlines recommendations and future activities to assist with their implementation.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

NASA NTRS2005

HYBRID NEURAL NETWORK AND SUPPORT VECTOR MACHINE METHOD FOR OPTIMIZATION

System and method for optimization of a design associated with a response function, using a hybrid neural net and support vector machine (NN/SVM) analysis to minimize or maximize an objective function, optionally subject to one or more constraints. As a first example, the NN/SVM analysis is applied iteratively to design of an aerodynamic component, such as an airfoil shape, where the objective function measures deviation from a target pressure distribution on the perimeter of the aerodynamic component. As a second example, the NN/SVM analysis is applied to data classification of a sequence of data points in a multidimensional space. The NN/SVM analysis is also applied to data regression.

Rai, Man Mohan↗

NASA NTRS2007

Hybrid Neural Network and Support Vector Machine Method for Optimization

Rai, Man Mohan↗

DOE OSTI2022

BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data

Bacterial microcompartments (BMCs) are protein-based organelles found across the bacterial tree of life. They consist of a shell, made of proteins that oligomerize into hexagonally and pentagonally shaped building blocks, that surrounds enzymes constituting a segment of a metabolic pathway. The proteins of the shell are unique to BMCs. They also provide selective permeability; this selectivity is dictated by the requirements of their cargo enzymes. We have recently surveyed the wealth of different BMC types and their occurrence in all available genome sequence data by analyzing and categorizing their components found in chromosomal loci using HMM (Hidden Markov Model) protein profiles. To make this a “do-it yourself” analysis for the public we have devised a webserver, BMC Caller (https://bmc-caller.prl.msu.edu), that compares user input sequences to our HMM profiles, creates a BMC locus visualization, and defines the functional type of BMC, if known. Shell proteins in the input sequence data are also classified according to our function-agnostic naming system and there are links to similar proteins in our database as well as an external link to a structure prediction website to easily generate structural models of the shell proteins, which facilitates understanding permeability properties of the shell. Additionally, the BMC Caller website contains a wealth of information on previously analyzed BMC loci with links to detailed data for each BMC protein and phylogenetic information on the BMC shell proteins. Our tools greatly facilitate BMC type identification to provide the user information about the associated organism’s metabolism and enable discovery of new BMC types by providing a reference database of all currently known examples.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1973

Summary of attitude dynamic analysis for IMP-J wire antenna spacecraft

The work is reported in the determination of acceptable deployment sequences, simulation of EFM antenna deployment, and contingency analysis for the IMP-J S/C. The spacecraft, mission profile and deployment sequences are described along with the simulation of EFM deployment and deployment failure.

Bell, L. W.↗

DOE OSTI2021

Origin and evolution of HIV-1 subtype A6

Background: HIV outbreaks in the Former Soviet Union (FSU) countries were characterized by repeated transmission of the HIV variant AFSU, which is now classified as a distinct subtype A sub-subtype called A6. The current study used phylogenetic/phylodynamic and signature mutation analyses to determine likely evolutionary relationship between subtype A6 and other subtype A sub-subtypes. Methods: For this study, an initial Maximum Likelihood phylogenetic analysis was performed using a total of 553 full-length, publicly available, reverse transcriptase sequences, from A1, A2, A3, A4, A5, and A6 sub-subtypes of subtype A. For phylogenetic clustering and signature mutation analysis, a total of 5961 and 3959 pol and env sequences, respectively, were used. Results: Phylogenetic and signature mutation analysis showed that HIV-1 sub-subtype A6 likely originated from sub-subtype A1 of African origin. A6 and A1 pol and env genes shared several signature mutations that indicate genetic similarity between the two subtypes. For A6, tMRCA dated to 1975, 15 years later than that of A1. Conclusion: The current study provides insights into the evolution and diversification of A6 in the backdrop of FSU countries and indicates that A6 in FSU countries evolved from A1 of African origin and is getting bridged outside the FSU region.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Assessing microbial community patterns under incipient soil formation from basalt

Microbial dynamics drive the biotic machinery of early soil evolution. However, integrated knowledge of microbial community establishment, functional associations, and community assembly processes in incipient soil is lacking. This study presents a novel approach of combining microbial phylogenetic profiling, functional predictions, and community assembly processes to analyze drivers of microbial community establishment in an emerging soil system. Rigorous sub-meter sampling of a basalt-soil lysimeter after two years of irrigation revealed the contrasting depth-dependent distribution patterns of soil parameters and community diversity. Phylogenetic analysis of 16S rRNA gene indicated the presence of diverse bacterial and archaeal phyla, with high relative abundance of Actinobacteria on the surface and a consistently high abundance of Proteobacteria at all depths. Predicted functional gene analysis suggested dominant autotrophy signatures, evidence of an incomplete nitrogen cycle, and predicted enzymes of iron (III) to iron (II) conversion followed by intracellular uptake, transport, and regulation. Null modeling revealed microbial community assembly predominantly governed by variable selection. The relative influence of the variable selection decreased with depth, indicating unique and relatively harsh environmental conditions near the surface and more benign conditions with depth. Additionally, high levels of dispersal influenced community composition near the center of the domain, suggesting that spatial processes interact with deterministic selection imposed by the environment. Characterizing the complexity in incipient soils can advance research insights about microbial community diversity and assembly in other incipient systems (e.g., transformation of marginal soils, or soils recovering from disturbances such as fire, erosion, intensive agricultural practices, or contamination).

Sengupta, Aditi↗

DOE OSTI2020

PhycoCosm, a comparative algal genomics resource

Abstract Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis. PhycoCosm (https://phycocosm.jgi.doe.gov) is an algal multi-omics portal, developed by the US Department of Energy Joint Genome Institute to support analysis and distribution of algal genome sequences and other ‘omics’ data. PhycoCosm provides integration of genome sequence and annotation for >100 algal genomes with available multi-omics data and interactive web-based tools to enable algal research in bioenergy and the environment, encouraging community engagement and data exchange, and fostering new sequencing projects that will further these research goals.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Computational Strategies for Scalable Genomics Analysis

The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data technologies have been explored to scale up/out current bioinformatics solutions to mine the big genomics data. In this review, we survey some of these exciting developments in the applications of parallel distributed computing and special hardware to genomics. We comment on the pros and cons of each strategy in the context of ease of development, robustness, scalability, and efficiency. Although this review is written for an audience from the genomics and bioinformatics fields, it may also be informative for the audience of computer science with interests in genomics applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Calcination products of gibbsite studied by X-ray diffraction, XPS and solid-state NMR

The changes caused by heat treatment of gibbsite powder at 300–1473 K were studied using the X-ray diffraction (XRD), X-ray photoemission (XPS) spectra and {sup 27}Al magic angle spinning nuclear magnetic resonance spectroscopy ({sup 27}Al MAS NMR). XRD analysis indicates that the transformation sequence involves the formation of κ-Al{sub 2}O{sub 3} as an intermediate phase between χ- and α-Al{sub 2}O{sub 3}. The crystallite size of χ-Al{sub 2}O{sub 3} is as small as 10 nm. XPS analysis indicates that the ratio of aluminium atoms to oxygen atoms in χ-Al{sub 2}O{sub 3} and κ-Al{sub 2}O{sub 3} increases, whereas the expected ratio is observed in α-Al{sub 2}O{sub 3}. The percentage of AlO{sub 4} units in the transition aluminas follows the same behaviour as the ratio of Al/O. - Graphical abstract: The percentage of AlO{sub 4} units in transition aluminas follows the same behaviour as the ratio of Al/O. - Highlights: • Calcination products of gibbsite studied by XRD, XPS and solid-state NMR. • The crystallite size of χ-Al{sub 2}O{sub 3} is as small as 10 nm. • The Al/O atomic ratio determined by XPS is larger than 2/3 in χ-Al{sub 2}O{sub 3} and κ-Al{sub 2}O{sub 3}. • The percentage of AlO{sub 4} in the aluminas follows the same behaviour as the Al/O atomic ratio.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2014

Preliminary Analysis of Aircraft Loss of Control Accidents: Worst Case Precursor Combinations and Temporal Sequencing

Aircraft loss of control (LOC) is a leading cause of fatal accidents across all transport airplane and operational classes, and can result from a wide spectrum of hazards, often occurring in combination. Technologies developed for LOC prevention and recovery must therefore be effective under a wide variety of conditions and uncertainties, including multiple hazards, and their validation must provide a means of assessing system effectiveness and coverage of these hazards. This requires the definition of a comprehensive set of LOC test scenarios based on accident and incident data as well as future risks. This paper defines a comprehensive set of accidents and incidents over a recent 15 year period, and presents preliminary analysis results to identify worst-case combinations of causal and contributing factors (i.e., accident precursors) and how they sequence in time. Such analyses can provide insight in developing effective solutions for LOC, and form the basis for developing test scenarios that can be used in evaluating them. Preliminary findings based on the results of this paper indicate that system failures or malfunctions, crew actions or inactions, vehicle impairment conditions, and vehicle upsets contributed the most to accidents and fatalities, followed by inclement weather or atmospheric disturbances and poor visibility. Follow-on research will include finalizing the analysis through a team consensus process, defining future risks, and developing a comprehensive set of test scenarios with correlation to the accidents, incidents, and future risks. Since enhanced engineering simulations are required for batch and piloted evaluations under realistic LOC precursor conditions, these test scenarios can also serve as a high-level requirement for defining the engineering simulation enhancements needed for generating them.

Belcastro, Christine M.↗

DOE OSTI2015

1α,25-dihydroxyvitamin D 3 stimulates human SOST gene expression and sclerostin secretion

Sclerostin, the SOST gene product, is a negative regulator of bone formation and a positive regulator of bone resorption. Here, in this study, treatment of human primary osteoblasts, including cells differentiated to an osteocyte-like stage, with 1α,25-dihydroxyvitaminD 3 (1,25D) resulted in the dose-dependent increased expression of SOST mRNA. A similar effect was observed in human trabecular bone samples cultured ex vivo, and in osteocyte-like cultures of differentiated SAOS2 cells. Treatment of SAOS2 cells with 1,25D resulted in the production and secretion of sclerostin protein. In silico analysis of the human SOST gene revealed a single putative DR3-type vitamin D response element (VDRE) at position -6216 bp upstream of the transcription start site (TSS). This sequence was confirmed to have strong VDRE activity by luciferase reporter assays and electrophoretic mobility shift analysis (EMSA). Sequence substitution in the VDR/RXR half-sites abolished VDRE reporter activity and binding of nuclear proteins. A 6.3 kb fragment of the human proximal SOST promoter demonstrated responsiveness to 1,25D. The addition of the evolutionary conserved region 5 (ECR5), a known bone specific enhancer region, ahead of the 6.3 kb fragment increased basal promoter activity but did not increase 1,25D responsiveness. Site-specific mutagenesis abolished the responsiveness of the 6.3 kb promoter to 1,25D. We conclude that 1,25D is a direct regulator of human SOST gene and sclerostin protein expression, extending the pathways of control of sclerostin expression. At least some of this responsiveness is mediated by the identified classical VDRE however the nature of the transcriptional regulation by 1,25D warrants further investigation.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2017

Mid-L/D Lifting Body Entry Demise Analysis

The mid-lift-to-drag ratio (mid-L/D) lifting body is a fully autonomous spacecraft under design at NASA for enabling a rapid return of scientific payloads from the International Space Station (ISS). For contingency planning and risk assessment for the Earth-return trajectory, an entry demise analysis was performed to examine three potential failure scenarios: (1) nominal entry interface conditions with loss of control, (2) controlled entry at maximum flight path angle, and (3) controlled entry at minimum flight path angle. The objectives of the analysis were to predict the spacecraft breakup sequence and timeline, determine debris survival, and calculate the debris dispersion footprint. Sensitivity analysis was also performed to determine the effect of the initial pitch rate on the spacecraft stability and breakup during the entry. This report describes the mid-L/D lifting body and presents the results of the entry demise and sensitivity analyses.

Ling, Lisa↗

NASA NTRS2017

Analysis of in Vitro Evolution Reveals the Underlying Distribution of Catalytic Activity Among Random Sequences

The emergence of catalytic RNA is believed to have been a key event during the origin of life. Understanding how catalytic activity is distributed across random sequences is fundamental to estimating the probability that catalytic sequences would emerge. Here, we analyze the in vitro evolution of triphosphorylating ribozymes and translate their fitnesses into absolute estimates of catalytic activity for hundreds of ribozyme families. The analysis efficiently identified highly active ribozymes and estimated catalytic activity with good accuracy. The evolutionary dynamics follow Fisher’s Fundamental Theorem of Natural Selection and a corollary, permitting retrospective inference of the distribution of fitness and activity in the random sequence pool for the first time. The frequency distribution of rate constants appears to be log-normal, with a surprisingly steep dropoff at higher activity, consistent with a mechanism for the emergence of activity as the product of many independent contributions.

Abe Pressman↗

DOE OSTI2019

Microseismic Focal Mechanisms and Implications for Changes in Stress during the 2014 Newberry EGS Stimulation

We adapt the relative polarity method from Shelly et al. (2016) to compute focal mechanisms for microearthquakes associated with the 2014 hydroshearing stimulation at the Newberry volcano geothermal site. We focus the analysis on events relocated by Aguiar and Myers (2018), who report that six event clusters predominantly comprise the 2014 sequence. Data quality allows focal mechanism analysis for four of the six event clusters. We use Hardebeck and Shearer (2002, 2003; hereafter HASH) to compute focal mechanisms based on first–motion polarities and S/P amplitude ratios. We manually determine P– and S–wave polarities for a well–recorded reference event in each cluster, then use waveform cross correlation to determine whether recordings of other events in the cluster are the same or reversed polarity at each network station. Here, most waveform polarities are consistent with the affiliated reference event, indicating similar focal mechanisms within each cluster. The deeper clusters are east–west–striking normal faults, whereas the shallower clusters, close to the top of the open–hole section of the borehole, are strike slip with east–west motion. Regional studies and prestimulation borehole breakouts find the maximum stress direction is vertical and maximum horizontal stress is approximately north–south. Fault geometry and focal mechanisms of microseismicity during the stimulation suggest that increased pressure from fluid injection predominantly caused changes in horizontal stress, consistent with predictions from numerical studies of stress change caused by fluid injection. At shallow depths, where previous studies suggest the difference between vertical and horizontal stress is lowest, injection appears to have rotated the direction of maximum stress from vertical to horizontal, resulting in strike–slip motion. At greater depth, vertical stress continued to be the dominant direction during the stimulation, but fault orientation indicates either reactivation of pre–existing fractures or rotation of the direction of maximum horizontal stress from approximately north–south to east–west.

15 GEOTHERMAL ENERGY↗