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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

In–context promoter bashing of the Sorghum bicolor gene models functionally annotated as bundle sheath cell preferred expressing phosphoenolpyruvate carboxykinase and alanine aminotransferase

In-context promoter bashing via genome editing is a route to identify and characterize critical regulatory regions that govern expression of genes of interest. The outcomes of in-context promoter bashing can be used to inform editing strategies to modulate the expression of selected gene models in a desired fashion. Here, we employed in-context promoter bashing to characterize the proximal upstream regulatory regions of sorghum genes encoding phosphoenolpyruvate carboxykinase bundle sheath (SbPEPCK.BS, SbiTx430.01G455400) and alanine aminotransferase bundle sheath (SbAlaAT.BS, SbiTx430.02G006600), two proteins involved in the PCK C 4 pathway. Characterized germinal edits within the targeted regions upstream of these two genes ranged in size from 138 up to 1790 bp. A 138 bp within the SbPEPCK.BS upstream region and a 1643 bp element within the SbAlaAT.BS upstream region were determined to be important for maintenance of transcription levels. No change in development or various physiological parameters was observed in characterized lineages carrying promoter edits. However, significant changes in seed reserves and a reduction in 100-seed weight were consistently observed, under both greenhouse and field environments, in plants carrying an edit in the promoter of SbPEPCK.BS gene, which were significantly reduced in transcript accumulation for this gene.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Supplementary table, figures and DNA sequences of sorghum gene models SbiRTx430.01G455400 and SbiRTx.02G006600 that feature primers, gRNAs and indels created

In-context promoter bashing via genome editing is a route to identify and characterize critical regulatory regions that govern expression of genes of interest. The outcomes of in-context promoter bashing can be used to inform editing strategies to modulate the expression of selected gene models in a desired fashion. Here we employed in-context promoter bashing to characterize the proximal upstream regulatory regions of sorghum genes encoding phosphoenolpyruvate carboxykinase (Sb.PEPCK.BS, SbiTx430.01G455400) and alanine aminotransferase (SbiTx430.02G006600, SbAlaAT.BS), two proteins involved in the PCK C4 pathway. Characterized germinal edits within the targeted regions upstream of these two genes ranged in size from 138 bp up to 1790 bp. A 138 bp within the Sb.PEPCK.BS upstream region and a 1643 bp element within the Sb.AlaAT.BS upstream region were determined to be important for maintenance of transcription levels. No change in development or various physiological parameters was observed in characterized lineages carrying promoter edits. However, significant changes in seed reserves and a reduction in 100 seed weight were consistently observed, under both greenhouse and field environments, in plants carrying an edit in the promoter of Sb.PEPCK.BS gene were significantly reduced in transcript accumulation for this gene.

Quach, Truyen [Center for Plant Science Innovation↗
NASA NTRS2024

Brillouin Asymmetric Spatial Heterodyne Oceanographic Lidar Receiver for Profiling Temperature, Salinity, and Sound Velocity

A lidar receiver employing a proposed Brillouin asymmetric spatial heterodyne (BASH) spectrometer to measure depth resolved profiles of near surface ocean temperature, salinity, and sound velocity from aircraft is conceptualized. A BASH spectrometer can have high throughput, can be designed for any wavelength and, importantly, can be field widened, allowing accurate, high spectral resolution of the Brillouin spectrum within diffuse scatter from depth. Temperature and salinity are measured independently with no assumptions about one or the other and the measurements are unbiased by the presence of particulate or elastic scatter. A sensitivity analysis and lidar simulations show the expected performance.

John A Smith↗
DOE OSTI2024

Automating Log Synthesis and Visualization with Python and Splunk

The goal of this project is to automate log analysis by utilizing Splunk, Bash, and Python together. Simplifying the monitoring and analysis of network traffic was the main goal. In order to accomplish this, a Bash script was created to use 'tcpdump' to automate network sniffing. It also included a 24-hour file rotation mechanism to effectively manage the pcap files that were generated. After that, a Python script was written to read these pcap files and retrieve pertinent data about network traffic. After processing the collected data, Splunk is used to summarize the important metrics and visualize said information with relevant graphs.

99 GENERAL AND MISCELLANEOUS↗
NASA NTRS1987

Star formation and spiral structure in M81

High resolution digitized images of M81 in the radio continuum, H alpha, H I, and I band are used to see how well various density wave models agree in detail with observations. It was found that the observed width of the nonthermal radio arms favors a cloudy version of a density wave model. The radial distribution of the set of giant radio H II regions disagrees with the simple expression of Shu and Visser for star formation by a density wave. The observed displacements of the giant radio H II regions from the spiral velocity shock indicate that some revisions in the details of the ballistic particle model of Leisawitz and Bash are necessary.

Kaufman, Michele↗
NASA NTRS1987

Giant H II regions in M81

H-alpha and VLA radio continuum observations at wavelengths of 6 and 20 cm are used to study the distribution of extinction and the distribution of giant radio H II regions along the spiral arms in M81. The radial distribution of visual extinction Av in the plane of M81 shows no trend, with an upper limit 0.1 mag/kpc for the radial extinction gradient and a mean Av of 1.1 + or - 0.4 mag. Nearly all the giant radio H II regions lie along the spiral arms or the inner H I ring. The radial distribution of the set of giant radio H II regions exhibits a strong maximum at a galactocentric distance R roughly 300 arcsec. Unless molecular hydrogen in M81 is also concentrated near R roughly 300 arcsec, the data disagree with Visser's (1980) model for star formation associated with a density wave. Some suggestions are made about how to change the ballistic particle model of Leisawitz and Bash to agree with the observed radial distribution of giant radio H II regions.

Kaufman, Michele↗
NASA NTRS2014

Integration and Testing of LCS Software

Kennedy Space Center is in the midst of developing a command and control system for the launch of the next generation manned space vehicle. The Space Launch System (SLS) will launch using the new Spaceport Command and Control System (SCCS). As a member of the Software Integration and Test (SWIT) Team, command scripts, and bash scripts were written to assist in integration and testing of the Launch Control System (LCS), which is a component of SCCS. The short term and midterm tasks are for the most part completed. The long term tasks if time permits will require a presentation and demonstration.

Command Script↗
DOE OSTI2024

HTESP (High-throughput electronic structure package): A package for high-throughput ab initio calculations

High-throughput ab initio calculations are the indispensable parts of data-driven discovery of new materials with desirable properties, as reflected in the establishment of several online material databases. The accumulation of extensive theoretical data through computations enables data-driven discovery by constructing machine learning and artificial intelligence models to predict novel compounds and forecast their properties. Efficient usage and extraction of data from these existing online material databases can accelerate the next stage materials discovery that targets different and more advanced properties, such as electron–phonon coupling for phonon-mediated superconductivity. However, extracting data from these databases, generating tailored input files for different ab initio calculations, performing such calculations, and analyzing new results can be demanding tasks. Here, in this work, we introduce a software package named “HTESP” (High-Throughput Electronic Structure Package) written in Python and Bash languages, which automates the entire workflow including data extraction, input file generation, calculation submission, result collection and plotting. Our HTESP will help speed up future computational materials discovery processes.

36 MATERIALS SCIENCE↗
DOE OSTI2024

High-throughput electronic structure package

We introduce HTESP (High-Throughput Electronic Structure Package), an automated tool designed for high-throughput ab initio calculations. HTESP simplifies the entire workflow, including data extraction, input files generation, calculation submission, result collection, and plotting. The package is implemented in Python and Bash languages. In this paper, we provide detailed information about the package, its installation process and some illustrative examples to demonstrate its usage. Additionally, the package includes comprehensive online documentation on input parameters and tutorials to assist users.

Nepal, NirajK↗
DOE OSTI2024

Nodeman: A Node Management Tool For Hpc Clusters

NodeMan is a command line tool to manage nodes in an HPC cluster. At it's core, it is an extensible framework composed of bash scripting and GNU parallel. HPC System Administrator will find it useful in that it encapsulates desired functions and allows them to be assembled in a way familiar to administrators - through pipes. In fact, NodeMan functions can work with common command line tools as long as they use stdin/stdout. System Administrators can construct moderately complex logic and filtering on a compact command line that would normally require a substantial shell script. In the spirit of clush and pdsh, it is able to run commands remotely on nodes. Additionally, NodeMan is more flexible. For example, it can interact with IPMI and naturally processes node lists for orchestrating different tools. The library of useful pre-built functions is growing. System administrators can easily create new functions and make it their own.

Serr, ScottM↗
DOE OSTI2025

JGI-Trichoderma v1.0

There is a series of Python and bash scripts to parse genomics datasets used to evaluate the coevolution of gene families and the feature importance of gene families using an SVM classifier. - Cover analysis: takes a list of single-copy genes in a set of genomes, aligns and builds the gene trees to determine if two gene families have a signature of covariation with one another. It parses the files to run phykit cover script described here: https://jlsteenwyk.com/PhyKIT/usage/index.html - SVM-classifier: This Python script is an SVM-based genomic classifier designed for biological data analysis. It combines machine learning with feature selection to identify important genomic markers and classify biological samples. Core Functionality: The script uses Support Vector Machines from scikit-learn to classify genomic data, incorporating SelectKBest for automated feature selection and leave-one-out cross-validation for performance assessment. It operates in multiple modes: feature ranking, optimal combination discovery, and sample prediction. Primary Applications: Genomic sample classification and biomarker discovery Feature importance analysis in high-dimensional biological datasets Prediction of sample categories based on genomic profiles Research applications requiring robust classification of biological data Key Advantages: High-dimensional handling: SVMs excel with genomic data's typical high feature-to-sample ratios Integrated feature selection: Reduces noise and computational overhead while identifying key markers Probability estimation: Provides confidence scores essential for biological interpretation Validation robustness: Leave-one-out cross-validation ensures reliable performance metrics Operational flexibility: Multiple analysis modes support different research phases from exploration to prediction

Stecca Steindorff, Andrei [Lawrence Berkeley Natio↗
DOE OSTI2026

wastewater_virus

This repo contains software used to clean and assemble high-throughput sequencing data containing viruses. The input is raw illumina sequencing reads and the output is a database of high-quality viral genomes. The specific application is to wastewater viral concentrates but it is not restricted to that sample type. The software is composed of Nextflow workflows and a set of custom Python and bash scripts that call publicly available bioinformatics tools to accomplish obvious tasks in data analysis in a high performance computing environment. For detailed information, please see the repo's README file.

Kantor, Rose [Lawrence Livermore National Laborato↗
DOE OSTI2026

CodeScribe Agent

SF-26-086 CodeScribe introduces a structured, multi-stage pipeline that combines deterministic program analysis with LLM-powered translation to enable incremental, testable Fortran-to-C++ migration. First, `code-scribe index` traverses the project directory tree and produces `scribe.yaml` metadata files recording all modules, subroutines, and functions at each level, giving the LLM accurate structural context instead of a hallucinated codebase model. Second, `code-scribe draft` performs the deterministic portion of translation — converting Fortran types to C++ equivalents, replacing `use` statements with `#include` and `using namespace` directives, and detecting constructs requiring special handling — while embedding`scribe-prompt` annotations that guide the LLM through non-trivial cases such as statement-function-to-lambda conversions and `extern "C"` wrapper generation. Third, `code-scribe translate` applies project-specific TOML-based few-shot prompt templates and submits the composed prompt to a pluggable LLM backend (OpenAI, Anthropic, Argonne ARGO, any OpenAI-compatible endpoint, or local Hugging Face checkpoints), producing a C++ source file, a header, and a Fortran-C++ interface file for each translated routine so the codebase compiles and runs correctly throughout the migration. Beyond translation, CodeScribe includes a tool-using coding agent (`code-scribe agent`) with read, bash, edit, and write capabilities, and a bounded loop mode (`code-scribe loop`) that runs repeated stateless agent sessions over a task file with restricted tool access — enabling sustained, auditable software development workflows for broader scientific computing tasks.

Dhruv, Akash [Argonne National Laboratory (ANL), A↗
DOE OSTI2026

Data From: "Warming and snow loss increase reliance on old groundwater in a Colorado River headwater"

This repository contains the data and code associated with the paper titled "Warming and snow loss increase reliance on old groundwater in a Colorado River headwater," published in Nature Geoscience, 2026. This study seeks to answer how various ages of groundwater interact with mountainous streamflow in mountainous headwaters such as the East River. It includes various model-data processing scripts, primarily for ParFlow-CLM analysis of simulated water years 2015-2021, and two numerical warming experiments (+2.5 and +4.0 degrees C), including run scripts, forcing scripts, and post-processing, as well as comparison to observation datasets, detailed below. This data requires the use of R (.r, .rmd), Python (.py), Jupyter Notebook or Jupyter Lab (.ipynb), ParFLOW-CLM, EcoSLIM. Further information on the use of all file formats mentioned below (e.g. .tff. .nc) are provided within the associated scripts and directory where the files are located. Contents & Usage ASO/: ​​Contains the bash and python scripts used to convert airborne snow observatory (ASO) data (ASO, 2023) in various data formats (georeferenced tiff file, NetCDF, UTM, and to latitude/longitude) then regrided to the ParFlow equivalent grid. Output data are in regrid_regll_data.zip and subsequently visualized and analyzed in plot_and_compare.py for Supplementary Figures A14 and A15. The wksht_ASO_comparison.xlsx spreadsheet is used to calculate the data for Supplementary Figure A16. EcoSLIM/: Contains the scripts and input files to run the EcoSLIM particle tracking simulations (/run_scripts) and the post-processing python script (/plot_scripts/eco_agedist_plots.ipynb). Jasechko et al./: Contains the jupyter notebook (Extract_Elevation.ipynb) to determine the outlet elevations of the 260 watersheds used in Jasechko et al. (2016), and the corresponding table, Table_S1_Watersheds_alt.csv. Used to create Supplementary Information Figure A2. PLM_Wells/: Contains the QA/QC-ed groundwater level time series of the PLM-1 and PLM-6 Monitoring Wells from Faybishenko et al. (2023), reformatted to water years used for Supplementary Figures A19 and and A20. ParFlow/: Contains the input files and run scripts to run ParFlow-CLM (/run_scripts), the python and tool command language (Tcl) scripts to create and distribute the ParFlow forcing simulation files (/forcing), and various scripts and intermediary files to analyze the model outputs (/post_process). SQUIRE/: Contains the processing scripts and intermediary files for the Surface QUantitatIve pRecipitation Estimation (SQUIRE) data (Grover, 2023) used to generate Supplementary Figure A18. USGS_Streamflow/: Contains the raw and gap-filled United States Geological Survey streamflow data (U.S. Geological Survey, 2026) used at the Almont station (site number 09112500). Gap-filling is performed in the R script with data from the Taylor station (site number 09110000). (/USGS_09112500_EAST_RIVER_AT_ALMONT_GAP_FILLED/code_almont_streamflow_gap_fill.Rmd). discharge/: Contains the gap-filled discharge data at the Watershed Function SFA East River pumphouse site (Newcomer et al., 2022) used to generate Supplementary Figure A13 and to compute hourly Nash-Sutcliffe model efficiency coefficients (NSE) in Table A4. snotel_and_flux_tower/: Contains the snow telemetry data (U.S. Department of Agriculture, 2024) from the Butte (site ID 380) and Schofield (site ID 737) stations, reformatted by water year, accessed with the snotelr R package. Used to create Supplementary Figure A17. Also contains the flux tower observational data (FluxTower_Pumphouse_ESS-DIVE.ET_only.h.txt) from Ryken et al. (2022) and sap flux transpiration data (MaxB_Transpiration_5Sites.daily_sums.h.txt) from Ryken (2021), used to create Supplementary Figures A22 and A23, respectively. Raw EcoSLIM model outputs are in excess of 24TB, and are stored on National Energy Research Scientific Computing Center (NERSC) and publicly available via the external link provided in the paper.

atmospheric warming↗
NASA NTRS1989

Commentary on interstellar matter associated with 18 open clusters

Information supplementary to that contained in Section 4 of an article entitled, A CO Survey of Regions Around 34 Open Clusters, (Leisawitz, Bash, and Thaddeus) published in the Astrophysical Journal Supplement Series, Volume 70, Number 4, August 1989 is summarized. The information presented here, which describes the interstellar environments of young clusters and some cluster physical characteristics, comes from observations published in the astronomical literature and the author's carbon monoxide (CO) emission line survey, and may help clarify our understanding of the interaction of massive stars with the interstellar medium.

Leisawitz, David↗
NASA NTRS1997

Temporal, Spatial, and Diurnal Patterns in Avian Activity at the Shuttle Landing Facility, John F. Kennedy Space Center, Florida, USA

Spatial and temporal patterns in bird abundance within the five-mile airspace at the Shuttle Landing Facility (SLF) on John F. Kennedy Space Center (KSC), Florida, USA were investigated for purposes of quantifying Bird Aircraft Strike Hazards (BASH). The airspace is surrounded by the Merritt Island National Wildlife Refuge (MINWR) which provides habitat for approximately 331 resident and migratory bird species. Potential bird strike hazards were greatest around sunrise and sunset for most avian taxonomic groups, including wading birds, most raptors, pelicans, gulls/terns, shorebirds, and passerines. Turkey Vultures and Black Vultures were identified as a primary threat to aircraft operations and were represented in 33% of the samples. Diurnal vulture activity varied seasonally with the development of air thermals in the airspace surrounding the SLF. Variation in the presence and abundance of migratory species was shown for American Robins, swallows, and several species of shorebirds. Analyses of bird activities provides for planning of avionics operations during periods of low-dsk and allows for risk minimization measures during periods of high-risk.

Larson, Vickie L.↗
NASA NTRS2013

Filament Eruptions, Jets, and Space Weather

Previously, from chromospheric H alpha and coronal X‐ray movies of the Sun's polar coronal holes, it was found that nearly all coronal jets (greater than 90%) are one or the other of two roughly equally common different kinds, different in how they erupt: standard jets and blowout jets (Yamauchi et al 2004, Apl, 605, 5ll: Moore et all 2010, Apj, 720, 757). Here, from inspection of SDO/AIA He II 304 A movies of 54 polar x-ray jets observed in Hinode/XRT movies, we report, as Moore et al (2010) anticipated, that (1) most standard x-ray jets (greater than 80%) show no ejected plasma that is cool enough (T is less than or approximately 10(exp 5K) to be seen in the He II 304 A movies; (2) nearly all blownout X-ray jets (greater than 90%) show obvious ejection of such cool plasma; (3) whereas when cool plasma is ejected in standard X-ray jets, it shows no lateral expansion, the cool plasma ejected in blowout X-ray jets shows strong lateral expansion; and (4) in many blowout X-ray jets, the cool plasma ejection displays the erupting-magnetic-rope form of clasic filament eruptions and is thereby seen to be a miniature filament eruption. The XRT movies also showed most blowout X-ray jets to be larger and brighter, and hence to apparently have more energy, than most standard X-ray jets. These observations (1) confirm the dichotomy of coronal jets, (2) agree with the Shibata model for standard jets, and (3) support the conclusion of Moore et al (2010) that in blowout jets the magnetic-arch base of the jet erupts in the manner of the much larger magnetic arcades in which the core field, the field rooted along the arcade's polarity inversion line, is sheared and twisted (sigmoid), often carries a cool‐plasma filament, and erupts to blowout the arcade, producing a CME. From Hinode/SOT Ca II movies of the polar limb, Sterling et al (2010, ApJ, 714, L1) found that chromospheric Type‐II spicules show a dichotomy of eruption dynamics similar to that found here for the cool‐plasma component of coronal X‐ray jets. This favors the idea that Type‐II spicules are miniature counterparts of coronal X‐ray jets. In Moore et al (2011, ApJ, 731, L18), we pointed out that if Type‐II spicules are magnetic eruptions that work like coronal X‐ray jets, they carry an area‐averaged mechanical energy flux of approximately 7x10)(exp 5) erg cm(exp -2) s(exp-1) into the corona in the form of MHD waves and jet outflow, enough to power the heating of the global corona and solar wind. On this basis, from our observations of mini‐filament eruptions in blowout X‐ray jets, we infer that magnetic explosions of the type that have erupting filaments in them are the main engines of both (1) the steady solar wind and (2) the CMEs that produce the most severe space weather by blasting out through the corona and solar wind, making solar energetic particle storms, and bashing the Earth's magnetosphere. We conclude that in focusing on prominences and filament eruptions, Einar had his eye on the main bet for understanding what powers all space weather, both the extreme and the normal.

Moore, Ronald↗
NASA NTRSDate not supplied

Trajectory Simulation Using Multi Model Monte Carlo with Python (MXMCPy)

EDL (Entry, Descent and Landing) is the process from a vehicle approaching a surface to landing on it, such as a Mars rover approaching the planet before landing. POST2 (Program to Optimize Simulated Trajectories 2) is Langley’s primary EDL simulation tool and is used NASA-wide for simulations. POST2 can generate highly accurate results by running a precise, but time consuming, Monte Carlo (MC) simulation hundreds or thousands of times. Though POST2 can produce highly accurate results, it can take unrealistic time spans to generate these results, which has created a need to speed up the simulations. The new NASA software MXMCPy offers various ways to speed up the simulations while getting just as precise results. Instead of running high-precision POST2 simulations many times for traditional MC, MXMCPy can run fewer high-precision POST2 simulations and many less precise POST2 simulations and merge the results. MXMCPy contains 30+ different methods which will each suggest different allocations between model precision levels, which result in results of varying precision based on the POST2 simulation. I created Python and Bash code to automate the 5 steps of MXMCPy’s application to POST2. I also tested the precision of traditional Monte Carlo simulations to MXMCPy aided simulations and found that MXMCPy can achieve substantially more precise solutions at the same computer runtime. I learned Test Driven Development (TDD), a software programming workflow which involves writing computer-automated tests before writing the code which is being tested. These tests are ran every time the code is changed and they can find glitches in the code much quicker than a human can. This programming workflow saved me a lot of time because the automated tests could tell me exactly where the code had stopped working. I plan on using this software development method for future academic and professional software projects. I have greatly enjoyed my work at NASA, so I have been applying to NASA internships and Pathways positions. In addition, I plan on applying what I have learned about Test Driven Development to my computer science courses next semester

James Warner↗