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At least 145 records · Page 8

A novel method may reveal bulk metallic glass compressive ductility trends in high data rate nanoindentation

Recent methods allow novel amorphous alloy compositions to be rapidly manufactured at small scale; however, obtaining materials properties such as compressive ductility from these smaller specimens has remained a challenge. Here, we suggest a potential high-throughput nanoindentation method that may be able to rapidly characterize the relative compressive ductility between these alloys based on their serration characteristics. The properties of emergent serrations, when interpreted in a simple micromechanical stress relaxation model, may order these materials by their compressive plastic strain to failure. These results are consistent with the ordering obtained from compressed specimens as well as with model simulations, suggesting that this model may be broadly useful for interpreting compressive ductility from nanoindentation serrations. After it is validated on more materials, this new method will match the rapid pace of amorphous alloy development, thus allowing metallic glass properties to be fine-tuned for each application prior to scale prototyping.

36 MATERIALS SCIENCE↗

3D Continuous Forcing Dataset from 3D Constrained Variational Analysis at SGP

The continuous 3D large-scale forcing (VARANAL3D) data set derived from 3D constrained variational analysis (3DCVA) extends the conventional constrained variational analysis method by incorporating multiple sub-columns within the analysis domain. This advancement introduces spatial variability into the large-scale forcing fields, thereby enriching the data set’s applicability. The VARANAL3D data set spans from 2004 to 2018 and covers a region of 5˚×4.5˚ domain around the ARM SGP site. The analysis domain is divided into 10×9 sub-columns with 0.5˚ resolution. The 3D large-scale forcing data provides necessary variables to drive and evaluate single-column models (SCM), cloud-resolving models (CRM) ,and large-eddy simulations (LES), as well as information for testing model sensitivity to spatial variability of the large-scale forcing data, facilitating more rigorous testing and refinement of physical processes in SCM/CRM/LES.

54 ENVIRONMENTAL SCIENCES↗

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗

Chlamydomonas reinhardtii responses to Fe-excess, Fe-deficiency, and Fe-limitation in either photoautotrophic or mixotrophic growth

A systems level analysis of Chlamydomonas reinhardtii grown photoautotrophically or mixotrophically with a reduced carbon source, acetate, under four different defined Fe stages of Fe-replete, Fe-deficient, Fe-limited, or Fe-excess. Samples were digested with trypsin, labeled with TMT 10-Plex, then analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline. [doi:10.25345/C5707X12X] [dataset license: CC0 1.0 Universal (CC0 1.0)]

59 BASIC BIOLOGICAL SCIENCES↗

Human Primary Airway Epithelium +/- Macrophages Response to HCoV-229E Infection Transcriptomics (ACS-DP3)

The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-299E) infection. Sample data was obtained for mock and infected (MOI 3) primary human airway epithelial cells with and without macrophages and grown in air-liquid interface conditions. Sample data was acquired using an Illumina Hi-Seq 4000 sequencer system and further processed for RNA sequencing (RNA-Seq) expression analysis.

59 BASIC BIOLOGICAL SCIENCES↗

CROCUS Air Quality Data at Argonne National Laboratory Prairie Site

The AQT (Vaisala AQT530) instrument provides observations on meteorological conditions, including particulate matter (PM2.5, PM10), gas species concentrations (NO, NO2, O3, CO), and environment temperature and moisture. These measurements are critical for understanding air quality. These measurements are useful for understanding changes in aerosol properties, air quality research, and comparing to model experiments especially in urban environments. These measurements are collected at the Argonne Testbed for Multiscale Observational Science (ATMOS), a prairie field site at Argonne National Laboratory in Lemont, Illinois. Data is available in the netCDF data format, we encourage data users review documentation through Project Pythia to understand how to work with netCDF data https://foundations.projectpythia.org/core/data-formats/netcdf-cf.html. Each file contains one day's worth of data (24 hours, starting at 0000 UTC). The data is aggregated into daily frequency to make it easier to process multiple days, and compress the higher-resolution fields. File naming convention includes the project (CROCUS), location (atmos), data level (raw, a1), date (year, month, day), and hour (0000).

54 ENVIRONMENTAL SCIENCES↗

Visualization Within the Department of Energy: NREL IEEE VIS Application Spotlight

This presentation highlights the role of advanced visualization techniques at the National Renewable Energy Laboratory (NREL) in supporting cutting-edge research across diverse energy domains. From immersive analytics and uncertainty visualization to high-resolution and real-time data analysis, NREL's visualization capabilities enable scientists to explore complex datasets more effectively. These tools are critical for advancing research in materials science, renewable energy technologies, biofuels, electric vehicle infrastructure, energy efficiency - from industrial processes to entire communities - and then bringing these innovations to practice through energy systems integration. NREL's visualization tools drive innovation across renewable energy and grid modernization efforts by providing deeper insights and improving decision-making.

grid modernization↗

Data and Scripts associated with a manuscript on ecosystem responses to wildfires in the Columbia River Basin

This data package is associated with the publication “Ecosystem leaf area, gross primary production, and evapotranspiration responses to wildfire in the Columbia River Basin” submitted to Biogeosciences (Shi et al., 2024; doi: 10.22541/au.171053013.30286044/v1). In this research, data products, leaf area index (LAI), gross primary production (GPP), and evapotranspiration (ET), from the Moderate Resolution Imaging Spectroradiometer (MODIS) are used to quantify the resistance and resilience of different ecosystem types in the Columbia River Basin (CRB). A machine learning algorithm, random forest (RF), was used to examine the impacts of precipitation, vapor pressure deficit (VPD), and burn severity from Monitoring Trends in Burn Severity (MTBS) on ecosystem resilience. The data package includes the processed MODIS data products, precipitation, VPD, and burn severity in 138 fire regions in CRB and the input files for RF model training. This data package includes six folders. The MODIS products are included in three MODIS_* folders with shell scripts for data clipping and *ncl files for data processing: (1) “/MODIS_LAI_CRB”; (2) “/MODIS_GPP_CRB”; and (3) “/MODIS_ET_CRB”. All the processed data for each fire event are NetCDF formatted. The MTBS burn severity data and the shell and *ncl scripts used for data processing are in the folder named (4) “MTBS_fire”. The ERA meteorological fields and the data processing scritps are in (5) “ERA_Var_CR”. All the scripts for figure development are in the format of *ncl and in the folder (6) “paper_scripts”. See the file ending in “flmd.csv” for a list of all files contained in this data package and descriptions for each. Tabular column headers and units are described in the data dictionary file ending in “dd.csv”.

54 ENVIRONMENTAL SCIENCES↗

Accelerating Discovery of Atomistic Defects via Machine Learning

The quantification of defects such as vacancies in crystalline structures is a cornerstone of materials science research. Traditional efforts often rely on manual detection, a process that is time-intensive, prone to human error, and challenging to scale. Here we leverage machine learning (ML) methods to identify and quantify vacancies within a crystalline lattice, aiming to expedite detection while improving accuracy. Additionally, we explore the transferability of these ML techniques, identifying characteristics of atomistic imaging data that complicate this task. We show how the integration of ML can drive innovation, providing a powerful tool that will play an increasingly crucial role in the future of materials science.

2D materials↗

Spatially Resolved Raman Spectroscopic Investigation of Uranyl Fluoride: A Case Study in the Importance of Instrument Optimization

Raman spectroscopy is an emerging technique for rapid and nondestructive analysis of nuclear materials for forensic and nonproliferation applications as it is a powerful tool for distinguishing multiple chemical forms of materials with similar stoichiometries. Recent developments in spectroscopic software have enabled rapid data collection with high-speed Raman spectroscopic mapping capabilities. However, some uranium-rich materials are susceptible to degradation in humid air and/or laser-induced phase transformations. To mitigate environmental or measurement-related sample degradation of potential samples of interest, we have taken a systematic approach to define optimized data collection parameters for high-throughput measurements of uranyl fluoride (UO 2 F 2 ), which is an important intermediate material in the nuclear fuel cycle. First, we systematically describe the influence of optical magnification (5× to 100×), laser power, and exposure time on obtained signal for identical particles of UO 2 F 2 and find that at low laser power and exposure times, comparable signal is obtained regardless of optical magnification. Second, we ensure sample integrity during data collection, and third, collect spectroscopic maps that employ optimized parameters to reduce the time required to obtain spatially resolved spectroscopic information. Reductions of 90% and 99% in measurement times are discussed as they relate to differences in resolving spectroscopic features of particles in identical mapping areas. Finally, during this work, we found that additional data processing options were needed and thus developed a customized Python script for importing, processing, analyzing, and visualizing Raman spectroscopic map data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Development of Accelerated High Temperature Mechanical Testing Techniques

The Advanced Materials and Manufacturing Technologies (AMMT) Program focuses on advancing materials and manufacturing techniques for nuclear energy applications, particularly in the qualification of materials for high-temperature structural use. This report presents work on refining the creep testing of small specimen geometries. Efforts include the development of a new specimen geometry for sub-sized specimens, which were subjected to uniaxial creep tests. The results contribute to the understanding of material behavior under stress at elevated temperatures and offer potential improvements in creep data collection methods. These findings support ongoing advancements in material qualification processes essential for nuclear reactor applications.

36 MATERIALS SCIENCE↗

The GREEN ‘omics of Nutrient Feedbacks to Soil Warming

The GREEN ‘omics of Nutrient Feedbacks in Soil project advanced the DOE Biological and Environmental Research (BER) mission by developing and applying isotope-enabled ’omics tools to understand how soil microbes regulate carbon and nutrient cycling. Guided by the Growth Rate, growth Efficiency, and stoichiometry of Essential Nutrients (GREEN ’omics) framework, the project aimed to build a predictive, systems-level understanding of microbial traits that control ecosystem biogeochemistry. In a collaboration among Northern Arizona University (lead), West Virginia University, Lawrence Livermore National Laboratory, and Pacific Northwest National Laboratory, we combined quantitative stable isotope probing (qSIP), Chip-SIP, NanoSIMS, and genome-resolved metagenomics across long-term experiments in Arctic, boreal, temperate, and tropical ecosystems. The project produced three key outcomes: 1) We showed that community-weighted temperature sensitivities of bacterial growth (Q10) can predict ecosystem-scale soil respiration responses across diverse soils. 2) We provided the first in situ evidence for density-dependent population dynamics in soil bacteria and demonstrated that nutrient additions intensify competition, concentrating carbon use into fewer taxa. 3) We improved and extended isotope-enabled ’omics methods by quantifying qSIP measurement error to guide experimental design and coupling SIP with genome-resolved metagenomics to reveal cross-kingdom interactions among bacteria, fungi, and viruses. Together, these results show that a small number of microbial traits and taxa exert disproportionate control over soil carbon and nutrient cycling, providing critical data and methods to improve representation of microbial processes in Earth system models.

54 ENVIRONMENTAL SCIENCES↗

Evaluating the Effectiveness of Retrieval-Augmented Large Language Models in Scientific Document Reasoning

Despite the dramatic progress in Large Language Model (LLM) development, LLMs often provide seemingly plausible but not factual information, often referred as hallucinations. Retrieval-augmented LLMs provide a non-parametric approach to solve these issues by retrieving relevant information from external data sources and augment the training process. These models helps to trace evidence from an externally provided knowledge base allowing the model predictions to be better interpreted and verified. In this work, we critically evaluate these models in their ability to perform in scientific document reasoning tasks. To this end, we tuned multiple such model variants with science-focused instructions and evaluated them on a scientific document reasoning benchmark for the usefulness of the retrieved document passages. Our findings suggest that models justify predictions in science tasks with fabricated evidence and leveraging scientific corpus as pretraining data does not alleviate the risk of evidence fabrication.

• Artificial intelligence (AI) / machine learning ↗

Computational Modeling of Atmospheric Processes at Texas Southern University

Texas Southern University (TSU) is strengthening its research program in atmospheric chemistry and physics with a climate science emphasis by leveraging partnerships with the U.S. Department of Energy’s Atmospheric Radiation Measurement (ARM) Facility, Brookhaven National Laboratory (BNL), and the Tracking Aerosol Convection Interactions ExpeRiment (TRACER). This RDPP-supported program focuses on secondary organic aerosols (SOAs) and reactive atmospheric species that influence cloud formation, precipitation processes, and radiative forcing. SOAs play a critical role in cloud microphysics and Earth’s energy balance, yet the chemical and physical mechanisms governing SOA–cloud interactions remain a significant source of uncertainty in predictive climate models. Through computational modeling, observational data analysis, and national laboratory collaboration, this program develops a skilled cohort of students trained in atmospheric science, environmental data analysis, and climate-relevant modeling. These research experiences build technical competencies that are transferable to careers in government laboratories, academia, and industry. By engaging students from historically underrepresented communities in high-impact climate research, TSU expands participation in the atmospheric sciences workforce while contributing meaningful scientific insights to DOE-supported ARM research activities. This partnership strengthens national capacity in climate science and supports the development of the next generation of atmospheric researchers.

54 ENVIRONMENTAL SCIENCES↗

CROCUS Urban Canyons - Space Science and Engineering Center (SPARC) Doppler lidar data

This is the netCDF format output from the Halo Photonics Streamline XR Doppler lidar that was deployed next to the Space Science and Engineering Center (SPARC) trailer at the University of Illnois-Chicago greenhouse parking lot during CROCUS Urban Canyons. The purpose of collecting this dataset is to provide vertical and horizontal wind profiles for studying the characteristics of turbulence over the urban canyon of Chicago. This data contains the radial velocity, intensity, and backscatter from the vertical profile, range height indicator, and sector scans that were performed over both Intensive Operating Period 1 and 2 of CROCUS Urban Canyons. There are four different types of files: * The Range Height Indicator (RHI) files contain scans that are along a constant azimuth, spanning the entire hemisphere of elevation values above the surface. * The Velocity Azimuth Display (VAD) files contain the raw radial velocity data from the 6-beam, 60 degree scans. * The User1 files contain stacked Plan Position Indicator scans over a 45 degree quadrant over downtown Chicago. * The Stare files contain vertically pointing scans. These are standard netCDF files that can be opened using xarray. The VAD scans can be processed from their raw radial velocities to horizontal wind speeds with the Atmospheric data Community Toolkit (https://arm-doe.github.io/ACT/).

EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC WINDS↗

Enhancing Discoverability and Management of Atmospheric Data at Scale: Solutions from the ARM Data Center

The Atmospheric Radiation Measurement (ARM) is a multi-laboratory and multi-institutional U.S. Department of Energy (DOE) Office of Science National User Facility. The ARM Data Center (ADC), located at Oak Ridge National Laboratory, collects, archives, and shares vast atmospheric data crucial for climate research. The ADC manages over 7 PB of data from 460 instruments worldwide, processing it into more than 11,000 diverse data products using the Network Common Data Form (NetCDF) for machine-independent accessibility. The primary challenge addressed in this paper is the efficient management and distribution of vast and diverse datasets essential for the climate research community, enhancing accessibility through advanced tools like Data Discovery. The ADC has developed advanced infrastructure and software architecture to handle the continuous influx of heterogeneous data to enhance data discoverability, resulting in increased scientific collaboration. In 2023, users from over 34 countries downloaded and utilized ARM data, resulting in 1,455 publications. The ADC’s efforts have significantly improved the discoverability and usability of atmospheric data, fostering extensive scientific research and collaboration. This paper details the solutions implemented by the ADC team for efficient data discovery and distribution, and it demonstrates ARM’s capability of staging processed data for scientific analysis.

Shah, Chirag [ORNL] (ORCID:0000000203145737)↗

Ensemble Simulations on Leadership Computing Systems

Scientific productivity can be enhanced through workflow management tools, relieving large High Performance Computing (HPC) system users from the tedious tasks of scheduling and designing the complex computational execution of scientific applications. This paper presents a study on the usage of ensemble workflow tools to accelerate science using the Summit and Frontier supercomputing systems. The research aims to connect science domain simulations using Oak Ridge Leadership Computing Facility (OLCF) supercomputing platforms with ensemble workflow methods in order to accelerate HPC-enabled discovery and boost scientific impact. We present the coupling, porting and optimization of Radical-Cybertools on three applications: Chroma, NAMD and LAMMPS. The tools augment traditional HPC monolithic runs with a pilot scheduler. Lessons-learned are discussed for physics, biology and materials science applications. We discuss intrinsic limitations of coupling and porting ensemble workflow tools to applications that run on large HPC systems. The origins of technical challenges and their solutions developed during the implementation process are discussed. Data management strategies, OLCF’s policies for ensembles, and natively supported workflow tools are also summarized.

Georgiadou, Antigoni [ORNL] (ORCID:000000020977631↗