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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 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta

Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergent subspecies. Here, we delineate the evolutionary processes driving the genetic diversity and population differentiation in this species. Using whole-genome re-sequencing data from 517 B. stricta accessions, we identify four genetic groups that diverged around 30-180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence ( d XY ), and lower relative divergence ( F ST ) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome, we also find regions with both high F ST and d XY among the groups, termed F ST -islands. Population genetic signatures indicate that F ST -islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms. Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Object storage model for CMS data

In CMS, data access and management is organized around the data-tier model: a static definition of what subset of event information is available in a particular dataset, realized as a collection of files. In previous work, we have proposed a novel data management model that obviates the need for data tiers by exploding files into individual event data product objects. In this work, we estimate the potential savings in data volume based on user analysis patterns.

Smith, Nick↗
DOE OSTI2020

Combining Mass Spectrometry of Picoliter Samples with a Multicompartment Electrodynamic Trap for Probing the Chemistry of Droplet Arrays

Single droplet levitation provides contactless access to the microphysical and chemical properties of micrometer-sized samples. Most applications of droplet levitation to chemical and biological systems use nondestructive optical techniques to probe droplet properties. To provide improved chemical specificity, we coupled a multicompartment quadrupole electrodynamic trap (QET) with single droplet mass spectrometry. Our QET continuously traps a monodisperse droplet population (tens to hundreds of droplets) and allows for the simultaneous sizing of a single droplet using its Mie scattering pattern. Single droplets are subsequently ejected into the ionization region of an ambient pressure inlet mass spectrometer. We optimized two complementary soft ionization techniques for picoliter aqueous droplets: (1) paper spray (PS) ionization and (2) thermal desorption glow discharge (TDGD) ionization. Both techniques detect oxygenated organic acids in single droplets, with signal-to-noise ratios >100 and detection limits on the order of 10 pg. Sensitivity and reproducibility across single droplets are driven by the droplet deposition location and spray stability in PS-MS and the ionization region humidity and analyte evaporation rate in TDGD-MS. Importantly, the analyte evaporation rate can control the TDGD-MS quantitative capability because high evaporation rates result in significant ion suppression. Additionally, this effect is mitigated by optimizing the vaporization temperature, droplet size range, and analyte volatility. We demonstrate quantitative and reproducible measurements with a droplet internal standard (<10% RSD) and compare the sensitivity of PS-MS and TDGD-MS. Finally, we demonstrate the application of QET-MS to the study of heterogeneous chemical kinetics with the reaction of gas phase O 3 and aqueous maleic acid droplets.

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

Using research networks to create the comprehensive datasets needed to assess nutrient availability as a key determinant of terrestrial carbon cycling

A wide range of research shows that nutrient availability strongly influences terrestrial carbon (C) cycling and shapes ecosystem responses to environmental changes and hence terrestrial feedbacks to climate. Nonetheless, our understanding of nutrient controls remains far from complete and poorly quantified, at least partly due to a lack of informative, comparable, and accessible datasets at regional-to-global scales. A growing research infrastructure of multi-site networks are providing valuable data on C fluxes and stocks and are monitoring their responses to global environmental change and measuring responses to experimental treatments. These networks thus provide an opportunity for improving our understanding of C-nutrient cycle interactions and our ability to model them. However, coherent information on how nutrient cycling interacts with observed C cycle patterns is still generally lacking. Here, we argue that complementing available C-cycle measurements from monitoring and experimental sites with data characterizing nutrient availability will greatly enhance their power and will improve our capacity to forecast future trajectories of terrestrial C cycling and climate. Therefore, we propose a set of complementary measurements that are relatively easy to conduct routinely at any site or experiment and that, in combination with C cycle observations, can provide a robust characterization of the effects of nutrient availability across sites. In addition, we discuss the power of different observable variables for informing the formulation of models and constraining their predictions. Most widely available measurements of nutrient availability often do not align well with current modelling needs. This highlights the importance to foster the interaction between the empirical and modelling communities for setting future research priorities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

NuclPred v1

This tool takes a genome assembly as input and predicts per-site nucleosome occupancy as output. Trained on physical maps of nucleosome binding preferences across the fungal kingdom, NuclPred can be applied broadly across fungi (and other eukaryotes). This breadth, combined with its accuracy, means it could have both basic and applied biological implications, for example in understanding eukaryotic gene regulation and genetic engineering. Almost universally across eukaryotes, nucleosomes - each wrapping ~150 base pairs of DNA - serve to package DNA inside the nucleus, with major consequences on DNA access, gene activity and DNA integration. NuclPred was generated using a supervised deep learning approach combining convolutional and recurrent neural networks to take DNA features (nucleotides, GC content and structural information) as input, then use that information to predict the physical attractiveness DNA sequences might have for forming nucleosomes. With this information at hand, researchers can design more efficient CRISPR constructs, explore the interplay between DNA signatures and other regulators impact nucleosome locations, predict expression patterns, etc. This tool will be published as part of a manuscript currently under revision at iScience (draft attached).

Mondo, Stephen↗
NASA NTRS2004

SAMZ: Satellite-Derived Management Zones

The term "satellite-derived management zones" (SAMZ) denotes agricultural management zones that are subdivisions of large fields and that are derived from images of the fields acquired by instruments aboard Earth orbiting satellites during approximately the past 15 years. "SAMZ" also denotes the methodology and the software that implements the methodology for creating such zones. The SAMZ approach is one of several products of continuing efforts to realize a concept of precision agriculture, which involves optimal variations in seeding, in application of chemicals, and in irrigation, plus decisions to farm or not to farm certain portions of fields, all in an effort to maximize profitability in view of spatial and temporal variations in the growth and health of crops and in the chemical and physical conditions of soils. As used here, "management zone" signifies, more precisely, a subdivision of a field within which the crop production behavior is regarded as homogeneous. From the perspective of precision agriculture, management zones are the smallest subdivisions between which the seeding, application of chemicals, and other management parameters are to be varied. In the SAMZ approach, the main sources of data are the archives of satellite imagery that have been collected over the years for diverse purposes. One of the main advantages afforded by the SAMZ approach is that the data in these archives can be reused for purposes of precision agriculture at low cost. De facto, these archives contain information on all sources of variability within a field, including weather, crop types, crop management, soil types, and water drainage patterns. The SAMZ methodology involves the establishment of a Web-based interface based on an algorithm that generates management zones automatically and quickly from archival satellite image data in response to requests from farmers. A farmer can make a request by either uploading data describing a field boundary to the Web site or else drawing the boundary on a reference image. Hence, a farmer can start to engage in precision farming shortly after gaining access to the Web site, without need for incurring the high costs of conventional precision-agriculture data-collection practices that include collecting soil samples, mapping electrical conductivity of soil, and compiling multi-year crop-yield data. Given the boundary of a field, a SAMZ server computes the zones within the field in a three-stage process. In the first stage, a vector-valued image of the field is constructed by assembling, from the archives, the equivalent of a stack of the available images of the field (see figure). In the second stage, the vector-valued image is analyzed by use of a wavelet transform that detects spatial variations considered significant for precision farming while suppressing small-scale heterogeneities that are regarded as insignificant. In the third stage, a segmentation algorithm assembles the zones from smaller regions that have been identified in the wavelet analysis.

Source record↗
NASA NTRS2005

Satellite-Derived Management Zones

The term "satellite-derived management zones" (SAMZ) denotes agricultural management zones that are subdivisions of large fields and that are derived from images of the fields acquired by instruments aboard Earth-orbiting satellites during approximately the past 15 years. "SAMZ" also denotes the methodology and the software that implements the methodology for creating such zones. The SAMZ approach is one of several products of continuing efforts to realize a concept of precision agriculture, which involves optimal variations in seeding, in application of chemicals, and in irrigation, plus decisions to farm or not to farm certain portions of fields, all in an effort to maximize profitability in view of spatial and temporal variations in the growth and health of crops, and in the chemical and physical conditions of soils. As used here, "management zone" signifies, more precisely, a subdivision of a field within which the crop-production behavior is regarded as homogeneous. From the perspective of precision agriculture, management zones are the smallest subdivisions between which the seeding, application of chemicals, and other management parameters are to be varied. In the SAMZ approach, the main sources of data are the archives of satellite imagery that have been collected over the years for diverse purposes. One of the main advantages afforded by the SAMZ approach is that the data in these archives can be reused for purposes of precision agriculture at low cost. De facto, these archives contain information on all sources of variability within a field, including weather, crop types, crop management, soil types, and water drainage patterns. The SAMZ methodology involves the establishment of a Web-based interface based on an algorithm that generates management zones automatically and quickly from archival satellite image data in response to requests from farmers. A farmer can make a request by either uploading data describing a field boundary to the Web site or else drawing the boundary on a reference image. Hence, a farmer can start to engage in precision farming shortly after gaining access to the Web site, without the need for incurring the high costs of conventional precision-agriculture data-collection practices that include collecting soil samples, mapping electrical conductivity of soil, and compiling multiyear crop-yield data. Given the boundary of a field, a SAMZ server computes the zones within the field in a three-stage process. In the first stage, a vector-valued image of the field is constructed by assembling, from the archives, the equivalent of a stack of the available images of the field (see figure). In the second stage, the vector-valued image is analyzed by use of a wavelet transform that detects spatial variations considered significant for precision farming while suppressing small-scale heterogeneities that are regarded as insignificant. In the third stage, a segmentation algorithm assembles the zones from smaller regions that have been identified in the wavelet analysis.

Lepoutre, Damien↗
DOE OSTI2019

Experimental and 3D Micromechanical Analysis of Stress–Strain Behavior and Damage Initiation in Dual-Phase Steels

In the recent decade, dual-phase steel has been used extensively in the industry due to its high strength and formability. In this paper, deformation pattern and mechanical behavior of DP steel are predicted using the 2D and 3D representative volume element (RVE) and finite elements method. Also, the obtained results were compared with the experimental SEM images. The experiments are performed in three stages to obtain the stress–strain curve and failure pattern in the specimens with the different state of stress distribution at the test sections. In the 3D state of stress, the state of applied stress to the RVE is obtained from macro-modeling of the test specimens and this model was analyzed using the finite element method. Furthermore, the effects of volume fraction and mesh size in 3D simulation on the stress–strain behavior are investigated. Metallography and SEM images are also used to access the failure mechanism at the microscale. It is shown that the martensite particles remain almost in their original form and their deformations are very small for the specimens with the thickness-to-width ratio of 0.8 (3D state of stress). This phenomenon is completely different from those obtained for smaller thickness-to-width ratio that the martensite particles were pulled and its length was increased. On the other hand, SEM images show that voids are located in the phase boundaries. According to the experimental and numerical results, although the main factor in the formation and growth of 2D voids is shear stress, in the 3D state of stress, the voids grow in spherical form due to the existence of large hydrostatic stresses.

36 MATERIALS SCIENCE↗
DOE OSTI2023

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Development of a Generalized Residual Stress Inversion Technique

Residual stress is a common result of manufacturing processes, but it is one that is often overlooked in design and qualification activities. There are many reasons for this oversight, such as lack of observable indicators and difficulty in measurement. Traditional relaxation-based measurement methods use some type of material removal to cause surface displacements, which can then be used to solve for the residual stresses relieved by the removal. While widely used, these methods may offer only individual stress components or may be limited by part or cut geometry requirements. Diffraction-based methods, such as X-ray or neutron, offer non-destructive results but require access to a radiation source. With the goal of producing a more flexible solution, this LDRD developed a generalized residual stress inversion technique that can recover residual stresses released by all traction components on a cut surface, with much greater freedom in part geometry and cut location. The developed method has been successfully demonstrated on both synthetic and experimental data. The project also investigated dislocation density quantification using nonlinear ultrasound, residual stress measurement using Electronic Speckle Pattern Interferometry Hole Drilling, and validation of residual stress predictions in Additive Manufacturing process models.

42 ENGINEERING↗
NASA NTRS1993

Features in the spectra of gamma-ray bursts

Gravitational lensing of cosmological gamma-ray bursts by objects in the mass range about 10 exp 17 to 10 exp 20 g (femtolensing) may introduce complicated interference patterns that might be interpreted as absorption or emission lines in the bursts' spectra. This phenomenon, if detected, may be used as a unique probe of dark matter in the universe. The BATSE spectral data should allow one to detect such spectral features or to put significant upper limits on the cosmic density of a dark matter component that may be in the femtolensing range. Software to generate theoretical spectra has been developed, and it is accessible over the computer network with anonymous ftp.

Stanek, Krzysztof Z.↗
NASA NTRS2010

Optical Characterization of a Multipoint Lean Direct Injector for Gas Turbine Combustors: Velocity and Fuel Drop Size Measurements

Performance of a multipoint, lean direct injection (MP-LDI) strategy for low emission aero-propulsion systems has been tested in a Jet-A fueled, lean flame tube combustion rig. Operating conditions for the series of tests included inlet air temperatures between 672 and 828 K, pressures between 1034 and 1379 kPa and total equivalence ratios between 0.41 and 0.45, resulting in equilibrium flame temperatures approaching 1800 K. Ranges of operation were selected to represent the spectrum of subsonic and supersonic flight conditions projected for the next-generation of commercial aircraft. This document reports laser-based measurements of in situ fuel velocities and fuel drop sizes for the NASA 9-point LDI hardware arranged in a 3 3 square grid configuration. Data obtained represent a region of the flame tube combustor with optical access that extends 38.1-mm downstream of the fuel injection site. All data were obtained within reacting flows, without particle seeding. Two diagnostic methods were employed to evaluate the resulting flow path. Three-component velocity fields have been captured using phase Doppler interferometry (PDI), and two-component velocity distributions using planar particle image velocimetry (PIV). Data from these techniques have also offered insight into fuel drop size and distribution, fuel injector spray angle and pattern, turbulence intensity, degree of vaporization and extent of reaction. This research serves to characterize operation of the baseline NASA 9- point LDI strategy for potential use in future gas-turbine combustor applications. An additional motive is the compilation of a comprehensive database to facilitate understanding of combustor fuel injector aerodynamics and fuel vaporization processes, which in turn may be used to validate computational fluid dynamics codes, such as the National Combustor Code (NCC), among others.

Heath, Christopher M.↗
DOE OSTI2018

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence–absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Inferring Strength of Tantalum from Hydrodynamic Instability Recovery Experiments

Hydrodynamic instability experiments allow access to material properties at extreme conditions, where strain rates exceed 105 s -1 and pressures reach 100 GPa. Current hydrodynamic instability experimental methods require in-flight radiography to image the instability growth at high pressure and high strain rate, limiting the facilities where these experiments can be performed. An alternate approach, recovering the sample after loading, allows measurement of the instability growth with profilometry. Tantalum samples were manufactured with different 2D and 3D initial perturbation patterns and dynamically compressed by a blast wave generated by laser ablation. The samples were recovered from peak pressures between 30 and 120 GPa and strain rates on the order of 107 s -1 , providing a record of the growth of the perturbations due to hydrodynamic instability. These records are useful validation points for hydrocode simulations using models of material strength at high strain rate. Recovered tantalum samples were analyzed, providing an estimate of the strength of the material at high pressure and strain rate.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging

Mass spectrometry imaging (MSI) has primarily been applied in localizing biomolecules within biological matrices. Although well-suited, the application of MSI for comparing thousands of spatially defined spotted samples has been limited. One reason for this is a lack of suitable and accessible data processing tools for the analysis of large arrayed MSI sample sets. In this paper, the OpenMSI Arrayed Analysis Toolkit (OMAAT) is a software package that addresses the challenges of analyzing spatially defined samples in MSI data sets. OMAAT is written in Python and is integrated with OpenMSI (http://openmsi.nersc.gov), a platform for storing, sharing, and analyzing MSI data. By using a web-based python notebook (Jupyter), OMAAT is accessible to anyone without programming experience yet allows experienced users to leverage all features. OMAAT was evaluated by analyzing an MSI data set of a high-throughput glycoside hydrolase activity screen comprising 384 samples arrayed onto a NIMS surface at a 450 μm spacing, decreasing analysis time >100-fold while maintaining robust spot-finding. The utility of OMAAT was demonstrated for screening metabolic activities of different sized soil particles, including hydrolysis of sugars, revealing a pattern of size dependent activities. Finally, these results introduce OMAAT as an effective toolkit for analyzing spatially defined samples in MSI. OMAAT runs on all major operating systems, and the source code can be obtained from the following GitHub repository: https://github.com/biorack/omaat.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Specific modulation of the root immune system by a community of commensal bacteria

Significance In natural environments, plants establish intimate interactions with a wide diversity of microbes. It is unknown, however, how microbiota composed of commensal bacteria colonize roots in the face of a sophisticated plant immune system that evolved to recognize microbial-associated molecular patterns. We investigate the interaction between plant immune system function and the root microbiota. We report that root-associated commensal bacteria actively suppress the host immune response in the context of a community. Suppressors and nonsuppressors co-occur in the root microbiome and the presence of the former can enhance the colonization ability of the latter. We highlight the role of a specific sector of the plant immune system and its suppression in gating microbial access to the roots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

A Work-Efficient Parallel Sparse Matrix-Sparse Vector Multiplication Algorithm

We design and develop a work-efficient multithreaded algorithm for sparse matrix-sparse vector multiplication (SpMSpV) where the matrix, the input vector, and the output vector are all sparse. SpMSpV is an important primitive in the emerging GraphBLAS standard and is the workhorse of many graph algorithms including breadth-first search, bipartite graph matching, and maximal independent set. As thread counts increase, existing multithreaded SpMSpV algorithms can spend more time accessing the sparse matrix data structure than doing arithmetic. Our shared-memory parallel SpMSpV algorithm is work efficient in the sense that its total work is proportional to the number of arithmetic operations required. The key insight is to avoid each thread individually scan the list of matrix columns. Our algorithm is simple to implement and operates on existing column-based sparse matrix formats. It performs well on diverse matrices and vectors with heterogeneous sparsity patterns. A high-performance implementation of the algorithm attains up to 15x speedup on a 24-core Intel Ivy Bridge processor and up to 49x speedup on a 64-core Intel KNL manycore processor. In contrast to implementations of existing algorithms, the performance of our algorithm is sustained on a variety of different input types include matrices representing scale-free and high-diameter graphs.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1990

Antenna Beam Coverage Concepts

The strawman Personal Access Satellite System (PASS) design calls for the use of a CONUS beam for transmission between the supplier and the satellite and for fixed beams for transmission between the basic personal terminal and the satellite. The satellite uses a 3 m main reflector for transmission at 20 GHz and a 2 m main reflector for reception at 30 GHz. There are several types of spot beams under consideration for the PASS system besides fixed beams. The beam pattern of a CONUS coverage switched beam is shown along with that of a scanning beam. A switched beam refers to one in which the signal from the satellite is connected alternatively to various feed horns. Scanning beams are taken to mean beams whose footprints are moved between contiguous regions in the beam's coverage area. The advantages and disadvantages of switched and/or scanning beams relative to fixed beams. The consequences of using switched/scanning in lieu of fixed beams in the PASS design and attempts are made to evaluate the listed advantages and disadvantages. Two uses of switched/scanning beams are examined. To illustrate the implications of switched beams use on PASS system design, operation at two beam scan rates is explored.

Estabrook, Polly↗