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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 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

LabVIEW Task Manager v. 1.10.0

LabVIEW Task Manager is a debugging tool for use during code development in the National Instruments (NI) LabVIEW® IDE. While providing a dynamic & big-picture view of running code, an expandable/collapsible tree diagram displays detailed information (both static and dynamic) on all VIs in memory, belonging to a selected project/target. It allows for interacting with single or multiple selected VIs at a time, providing significant benefits while troubleshooting, and has the following features: Look & Feel similar to Windows® Task Manager; Selection of project/target; Lists all VIs in memory, grouped by class/library; Searches for and enumerates clones in memory; DropIn VI for including dynamically referenced clones (Clone Beacon); 'Refresh Now' (F5) re-reads all VIs in memory and adds new ones to the tree; Displays VI name, owning class/library, state, path, data size & code size; Displays VI FP Behavior, Reentrant?, Reentrancy Type, Paused? & Highlight?; Sort by any column, including by library name; Filter by item types vi, ctl, and vit/ctt; Filter out vi.lib and global VIs; Tracking of, and ability to toggle, execution highlighting on multiple selected VIs; Tracking of paused VIs with ability to Pause/Resume/TogglePause multiple selected VIs; DropIn VI for pausing on a condition; If a clone initiates a pause, a different pause symbol is used for all clones of that same reentrant original VI; Select multiple VIs and open or close their FPs or BDs; Double Click a VI from the tree to bring the BD (first choice) or FP to front, if already open; and Select multiple top-level VIs and Abort them.

Vargo, TimothyD.↗
DOE OSTI2018

Cabana

Physics simulations that use particles in their algorithms are ubiquitous on modern high performance computers. Cabana is a C++ library for developing particle-based simulations on heterogeneous high performance computing platforms. Cabana provides general data structures and algorithms for common particle operations in a way that is both performant and portable on HPC systems. This includes particle data structure allocatable and configurable on GPU and CPU architectures, and threaded and distributed algorithms for sorting particles, halo exchanges, neighbor list generation, and other basic particle operations.

Slattery, StuartR↗
DOE OSTI2020

Image Search for Scientific Data (camBIR) v1.0

camBIR is the CAMERA based image retrieval, a software that takes several different kinds of imagery, such as 2 dimensional images, both scientific as well as non scientific. camBIR is specially designed for training different kinds of Deep Convolutional Neural Network, including new Deep Learning architectures, such as ResNet, Inception-ResNet, NasNet, DenseNet…. It can be used to automate the classification, sort and rank of X-ray imagery such as microCT, GISAXS, GIWAXS, SAXS and WAXS.

Ushizima, Daniela↗
DOE OSTI2013

extendFromReads

This package assists in genome assembly. extendFromReads takes as input a set of Illumina (eg, MiSeq) DNA sequencing reads, a query seed sequence and a direction to extend the seed. The algorithm collects all seed-- ]matching reads (flipping reverse-- ]orientation hits), trims off the seed and additional sequence in the other direction, sorts the remaining sequences alphabetically, and prints them aligned without gaps from the point of seed trimming. This produces a visual display distinguishing the flanks of multi- ]copy seeds. A companion script hitMates.pl collects the mates of seed-- ]hi]ng reads, whose alignment reveals longer extensions from the seed. The collect/trim/sort strategy was made iterative and scaled up in the script denovo.pl, for de novo contig assembly. An index is pre-- ]built using indexReads.pl that for each unique 21-- ]mer found in all the reads, records its gfate h of extension (whether extendable, blocked by low coverage, or blocked by branching after a duplicated sequence) and other characteristics. Importantly, denovo.pl records all branchings that follow a branching contig endpoint, providing contig- ]extension information

Williams, KellyP.↗
DOE OSTI2021

Explainable Neural Architecture Search (XNAS)

Code for the paper Learning Interpretable Models Through Multi-Objective Neural Architecture Search by Zachariah Carmichael, Tim Moon, and Sam Ade Jacobs. Monumental advances in deep learning have led to unprecedented achievements across a multitude of domains. While the performance of deep neural networks is indubitable, the architectural design and interpretability of such models are nontrivial. Research has been introduced to automate the design of neural network architectures through neural architecture search (NAS). Recent progress has made these methods more pragmatic by exploiting distributed computation and novel optimization algorithms. However, there is little work in optimizing architectures for interpretability. To this end, we propose a multiobjective distributed NAS framework that optimizes for both task performance and introspection. We leverage the non-dominated sorting genetic algorithm (NSGA-II) and explainable AI (XAI) techniques to reward architectures that can be better comprehended by humans. The framework is evaluated on several image classification datasets. We demonstrate that jointly optimizing for introspection ability and task error leads to more disentangled architectures that perform within tolerable error.

Carmichael, ZachariahJ↗
DOE OSTI2019

ErrFilter

ErrFilter is a tool that allows an analyst to explore data by defining simple Boolean filters on data. The tool also allows the user to sort the results by any attribute. The user sees both the distribution of filtered data as well as selected examples. The tool was designed to be applied generally to multivariate data associated with machine learning models.

Arendt, Dustin↗
DOE OSTI2024

ninterp: N-dimensional interpolation Rust crate [SWR-25-25]

The ninterp crate provides multivariate interpolation over a regular, sorted, nonrepeating grid of any dimensionality. A variety of interpolation strategies are implemented, however more are likely to be added. Extrapolation beyond the range of the supplied coordinates is supported for 1-D linear interpolators, using the slope of the nearby points. There are hard-coded interpolators for lower dimensionalities (up to N = 3) for better runtime performance. All interpolation is handled through instances of the Interpolator enum, with the selected tuple variant containing relevant data. Interpolation is executed by calling Interpolator::interpolate.

Carow, Kyle↗
DOE OSTI2026

Multithreaded copy ('cp')

This is a modification to 'cp' and 'mv' commands to make them multi-threaded. Simple benchmarks showed that multi-threading could reduce the time to copy a large Linux source directory by over 2x. The 'cp' and 'mv' utilities are part of the existing Coreutils (https://www.gnu.org/software/coreutils/) software package that get installed on all Linux distros. Changes: * Add '-j|--parallel ' flags to 'cp' and 'mv'. This allows the utilities to recursively copy regular files in directories in parallel. This does NOT parallelize multiple single file copies to a destination (like 'cp file2 file2 file3 dst/'). Along with this, add in new 'CP_NUM_THREADS' and 'MV_NUM_THREADS' environment variables to set the number of threads. This can be useful when you want to enable parallelism by default in /etc/profile. The maximum number of threads is internally capped to the number of CPUs. * Add a '-j' flag to 'sort' to complement its existing '--parallel' flag. This is only done for consistency with 'cp' and 'mv'. * Add test cases for the new flags. Also, run each 'cp' and 'mv' test both in single-threaded and multithreaded modes for extra coverage.

Hutter, AnthonyJ [Lawrence Livermore National Labo↗
DOE OSTI2018

Multiscale Atmospheric Overturning of the Indian Summer Monsoon as Seen through Isentropic Analysis

This study investigates multiscale atmospheric overturning during the 2009 Indian summer monsoon (ISM) using a cloud-permitting numerical model. The isentropic analysis technique adopted here sorts vertical mass fluxes in terms of the equivalent potential temperature of air parcels, which is capable of delineating the atmospheric overturning between ascending air parcels with high entropy and subsiding air parcels with low entropy. The monsoonal overturning is further decomposed into contributions from three characteristic scales: the basinwide ascent over the Indian monsoon domain, the regional-scale overturning associated with synoptic and mesoscale systems, and the convective-scale overturning. Results show that the convective-scale component dominates the upward mass transport in the lower troposphere while the region-scale component plays an important role by deepening the monsoonal overturning. The spatial variability of the convective-scale overturning is analyzed, showing intense convection over the Western Ghats and the Bay of Bengal while the deepest overturning is localized over northern India and the Himalayan foothills. The equivalent potential temperature in convective updrafts is higher over land than over the ocean or coastal regions. There is also substantial variability in the atmospheric overturning associated with the intraseasonal variability. The upward mass and energy transport increase considerably during the active phases of the ISM. A clear northeastward propagation in the peak isentropic vertical mass and energy transport over different characteristic regions can be found during the ISM, which corresponds to the intraseasonal oscillations of the ISM. Altogether, this study further demonstrates the utility of the isentropic analysis technique to characterize the spatiotemporal variations of convective activities in complex atmospheric flows.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Precipitation and Moisture in Four Leading CMIP5 Models: Biases across Large-Scale Circulation Regimes and Their Attribution to Dynamic and Thermodynamic Factors

As key variables in general circulation models, precipitation and moisture in four leading models from CMIP5 (phase 5 of the Coupled Model Intercomparison Project) are analyzed, with a focus on four tropical oceanic regions. It is found that precipitation in these models is overestimated in most areas. However, moisture bias has large intermodel differences. The model biases in precipitation and moisture are further examined in conjunction with large-scale circulation by regime-sorting analysis. Results show that all models consistently overestimate the frequency of occurrence of strong upward motion regimes and peak descending regimes of 500-hPa vertical velocity $ω500$. In a given $ω500$ regime, models produce too much precipitation compared to observation and reanalysis. But for moisture, their biases differ from model to model and also from level to level. Furthermore, error causes are revealed through decomposing contribution biases into dynamic and thermodynamic components. For precipitation, the contribution errors in strong upward motion regimes are attributed to the overly frequent $ω500$. In the weak upward motion regime, the biases in the dependence of precipitation on $ω500$ and the $ω500$ probability density function (PDF) make comparable contributions, but often of opposite signs. On the other hand, the biases in column-integrated water vapor contribution are mainly due to errors in the frequency of occurrence of $ω500$, while thermodynamic components contribute little. These findings suggest that errors in the frequency of $ω500$ occurrence are a significant cause of biases in the precipitation and moisture simulation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Changes in Frequency of Large Precipitation Accumulations over Land in a Warming Climate from the CESM Large Ensemble: The Roles of Moisture, Circulation, and Duration

Projected changes in the frequency of major precipitation accumulations (hundreds of millimeters), integrated over rainfall events, over land in the late twenty-first century are analyzed in the Community Earth System Model (CESM) Large Ensemble, based on the RCP8.5 scenario. Accumulation sizes are sorted by the local average recurrence interval (ARI), ranging from 0.1 to 100 years, for the current and projected late-twenty-first-century climates separately. For all ARIs, the frequency of exceedance of the given accumulation size increases in the future climate almost everywhere, especially for the largest accumulations, with the 100-yr accumulation becoming about 3 times more frequent, averaged over the global land area. The moisture budget allows the impacts of individual factors—moisture, circulation, and event duration—to be isolated. In the tropics, both moisture and circulation cause large future increases, enhancing the 100-yr accumulation by 23% and 13% (average over tropical land), and are individually responsible for making the current-climate 100-yr accumulation 2.7 times and 1.8 times more frequent, but effects of shorter durations slightly offset these effects. In the midlatitudes, large accumulations become about 5% longer in duration, but are predominantly controlled by enhanced moisture, with the 100-yr accumulation (land average) becoming 2.4 times more frequent, and 2.2 times more frequent due to moisture increases alone. In some monsoon-affected regions, the 100-yr accumulation becomes more than 5 times as frequent, where circulation changes are the most impactful factor. These projections indicate that changing duration of events is a relatively minor effect on changing accumulations, their future enhancement being dominated by enhanced intensity (the combination of moisture and circulation).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Substitution or Shared Utilization? Intrahousehold Vehicle Use in Mixed-Powertrain Households

While previous research has focused heavily on understanding the factors deriving alternative fuel vehicle adoption rates, there remains a significant gap in understanding how households distribute mileage across different powertrains. This study utilizes data from the 2022 Next Generation National Household Travel Survey to investigate vehicle miles traveled within a sample of 150 plug-in electric vehicle (PEV)-owning households (in which at least one battery electric vehicle is present), characterizing how different powertrains are integrated into daily mobility. Leveraging a Seemingly Unrelated Regression (SUR) framework the study jointly models the utilization of PEVs, hybrid electric vehicles (HEV), and internal combustion engine vehicles (ICEVs) while accounting for household-level substitution effects. The results provide evidence of an asymmetric substitution effect. In households with mixed-powertrain configurations, the ICEV captures a substantially higher share of household miles (compared with the PEV), acting as a utility sponge. Conversely, the model identifies specific socioeconomic and geographic cohorts that prioritize PEV as the primary household workhorse, indicating a systematic sorting effect. Although the sample size limits broader generalizability, these findings suggest that PEVs are used for frequent, specific routine-intensive roles, whereas the ICEV remains a specialized utility vehicle. These insights highlight distinct intrahousehold vehicle use behaviors that are often obscured by aggregate fleetwide statistics.

25 ENERGY STORAGE↗
DOE OSTI2013

Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes

Background: Single cell genomics has revolutionized microbial sequencing, but complete coverage of genomes in complex microbiomes is imperfect due to enormous variation in organismal abundance and amplification bias. Empirical methods that complement rapidly improving bioinformatic tools will improve characterization of microbiomes and facilitate better genome coverage for low abundance microbes. Methods: We describe a new approach to sequencing individual species from microbiomes that combines antibody phage display against intact bacteria with fluorescence activated cell sorting (FACS). Single chain (scFv) antibodies are selected using phage display against a bacteria or microbial community, resulting in species-specific antibodies that can be used in FACS for relative quantification of an organism in a community, as well as enrichment or depletion prior to genome sequencing. Results: We selected antibodies against Lactobacillus acidophilus and demonstrate a FACS-based approach for identification and enrichment of the organism from both laboratory-cultured and commercially derived bacterial mixtures. The ability to selectively enrich for L. acidophilus when it is present at a very low abundance (<0.2%) leads to complete (>99.8%) de novo genome coverage whereas the standard single-cell sequencing approach is incomplete (<68%). We show that specific antibodies can be selected against L. acidophilus when the monoculture is used as antigen as well as when a community of 10 closely related species is used demonstrating that in principal antibodies can be generated against individual organisms within microbial communities. Conclusions: The approach presented here demonstrates that phage-selected antibodies against bacteria enable identification, enrichment of rare species, and depletion of abundant organisms making it tractable to virtually any microbe or microbial community. Combining antibody specificity with FACS provides a new approach for characterizing and manipulating microbial communities prior to genome sequencing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

A rapid live-cell ELISA for characterizing antibodies against cell surface antigens of Chlamydomonas reinhardtii and its use in isolating algae from natural environments with related cell wall components

Background: Cell walls are essential for most bacteria, archaea, fungi, algae and land plants to provide shape, structural integrity and protection from numerous biotic and abiotic environmental factors. In the case of eukaryotic algae, relatively little is known of the composition, structure or mechanisms of assembly of cell walls in individual species or between species and how these differences enable algae to inhabit a great diversity of environments. In this paper we describe the use of camelid antibody fragments (VHHs) and a streamlined ELISA assay as powerful new tools for obtaining mono-specific reagents for detecting individual algal cell wall components and for isolating algae that share a particular cell surface component. Results: To develop new microalgal bioprospecting tools to aid in the search of environmental samples for algae that share similar cell wall and cell surface components, we have produced single-chain camelid antibodies raised against cell surface components of the single-cell alga, Chlamydomonas reinhardtii. We have cloned the variable-region domains (VHHs) from the camelid heavy-chain-only antibodies and overproduced tagged versions of these monoclonal-like antibodies in E. coli. Using these VHHs, we have developed an accurate, facile, low cost ELISA that uses live cells as a source of antigens in their native conformation and that requires less than 90 minutes to perform. This ELISA technique was demonstrated to be as accurate as standard ELISAs that employ proteins from cell lysates and that generally require >24 hours to complete. Among the cloned VHHs, VHH B11, exhibited the highest affinity (EC50 < 1 nM) for the C. reinhardtii cell surface. The live-cell ELISA procedure was employed to detect algae sharing cell surface components with C. reinhardtii in water samples from natural environments. In addition, mCherry-tagged VHH B11 was used along with fluorescence activated cell sorting (FACS) to select individual axenic isolates of presumed wild relatives of C. reinhardtii and other Chlorphyceae from the same environmental samples. Conclusions: Camelid antibody VHH domains provide a highly specific tool for detection of individual cell wall components of algae and for allowing the selection of algae that share a particular cell surface molecule from diverse ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron

Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development. Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data. We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Single-cell proteomics of Arabidopsis leaf mesophyll reveals dynamic protein responses to water-deficit stress

Background The application of single-cell omics tools to biological systems can provide unique insights into diverse cellular populations and their heterogeneous responses to internal and external perturbations. Thus far, most single-cell studies in plant systems have been limited to RNA-sequencing approaches, which only provide indirect readouts of cellular functions. Results Here, we present a single-cell proteomics workflow for plant cells that integrates tape-sandwich protoplasting, piezoelectric cell sorting, nanoPOTS sample preparation, and ion mobility-based MS data acquisition method for label-free single-cell proteomics analysis of Arabidopsis leaf mesophyll cells. From a single leaf protoplast, over 3,000 proteins were quantified with high precision. The workflow is demonstrated to identify stress associated changes in protein abundance by analyzing 117 protoplasts from well-watered and water-deficit stressed plants. Additionally, we describe a new approach for constructing covarying protein networks at the single-cell level and demonstrate how single-cell protein covariation analysis can reveal previously unrecognized protein functions while also capturing stress-induced changes in protein–protein dynamics. Conclusions The label-free scProteomic approach presented here represents a significant advance through the demonstration of a facile protoplast isolation method combined with deep and precise proteomic coverage of Arabidopsis leaf mesophyll cell types. We believe this study will serve as an informative reference to future plant scProteomic investigations.

Arabidopsis↗
DOE OSTI2014

Systematically programmed adaptive evolution reveals potential role of carbon and nitrogen pathways during lipid accumulation in Chlamydomonas reinhardtii

Background: The concept of adaptive evolution implies underlying genetic mutations conferring a selective advantage to an organism under particular environmental conditions. Thus, a flow cytometry-based strategy was used to study the adaptive evolution in Chlamydomonas reinhardtii wild-type strain CC124 and starchless mutant sta6-1 cells, with respect to lipid metabolism under nitrogen-(N) depleted and -replete conditions. Results: The successive sorting and regeneration of the top 25,000 high-lipid content cells of CC124 and sta6-1, combined with nitrogen starvation, led to the generation of a new population with an improved lipid content when compared to the original populations (approximately 175% and 50% lipid increase in sta6-1 and CC124, respectively). During the adaptive evolution period, the major fatty acid components observed in cells were C16:0, C16:1, C18:0, and C18:1-3, and elemental analysis revealed that cellular carbon to nitrogen ratio increased at the end of adaptive evolution period In order to gain an insight into highly stimulated intracellular lipid accumulation in CC124 and sta6-1 resulting from the adaptive evolution, proteomics analyses of newly generated artificial high-lipid content populations were performed. Functional classifications showed the heightened regulation of the major chlorophyll enzymes, and the enzymes involved in carbon fixation and uptake, including chlorophyll-ab-binding proteins and Rubisco activase. The key control protein (periplasmic L-amino acid oxidase (LAO1)) of carbon-nitrogen integration was specifically overexpressed. Glutathione-S-transferases and esterase, the enzymes involved in lipid-metabolism and lipid-body associated proteins, were also induced during adaptive evolution. Conclusions: Adaptive evolution results demonstrate the potential role of photosynthesis in terms of carbon partitioning, flux, and fixation and carbon-nitrogen metabolism during lipid accumulation in microalgae. This strategy can be used as a new tool to develop C. reinhardtii strains and other microalgal strains with desired phenotypes such as high lipid accumulation.

09 BIOMASS FUELS↗
DOE OSTI2019

A finalized determinant for complete lignocellulose enzymatic saccharification potential to maximize bioethanol production in bioenergy Miscanthus

Miscanthus is a leading bioenergy crop with enormous lignocellulose production potential for biofuels and chemicals. However, lignocellulose recalcitrance leads to biomass process difficulty for an efficient bioethanol production. Hence, it becomes essential to identify the integrative impact of lignocellulose recalcitrant factors on cellulose accessibility for biomass enzymatic hydrolysis. In this study, we analyzed four typical pairs of Miscanthus accessions that showed distinct cell wall compositions and sorted out three major factors that affected biomass saccharification for maximum bioethanol production. Among the three optimal (i.e., liquid hot water, H 2 SO 4 and NaOH) pretreatments performed, mild alkali pretreatment (4% NaOH at 50 °C) led to almost complete biomass saccharification when 1% Tween-80 was co-supplied into enzymatic hydrolysis in the desirable Miscanthus accessions. Consequently, the highest bioethanol yields were obtained at 19% (% dry matter) from yeast fermentation, with much higher sugar–ethanol conversion rates by 94–98%, compared to the other Miscanthus species subjected to stronger pretreatments as reported in previous studies. By comparison, three optimized pretreatments distinctively extracted wall polymers and specifically altered polymer features and inter-linkage styles, but the alkali pretreatment caused much increased biomass porosity than that of the other pretreatments. Based on integrative analyses, excellent equations were generated to precisely estimate hexoses and ethanol yields under various pretreatments and a hypothetical model was proposed to outline an integrative impact on biomass saccharification and bioethanol production subjective to a predominate factor (CR stain) of biomass porosity and four additional minor factors (DY stain, cellulose DP, hemicellulose X/A, lignin G-monomer). Using four pairs of Miscanthus samples with distinct cell wall composition and varied biomass saccharification, this study has determined three main factors of lignocellulose recalcitrance that could be significantly reduced for much-increased biomass porosity upon optimal pretreatments. It has also established a novel standard that should be applicable to judge any types of biomass process technology for high biofuel production in distinct lignocellulose substrates. Hence, this study provides a potential strategy for precise genetic modification of lignocellulose in all bioenergy crops.

09 BIOMASS FUELS↗