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Results for “reproducible science”

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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis

Abstract Background Many organizations face challenges in managing and analyzing data, especially when relevant datasets arise from multiple sources and methods. Analyzing heterogeneous datasets and additional derived data requires rigorous tracking of their interrelationships and provenance. This task has long been a Grand Challenge of data science and has more recently been formalized in the FAIR principles: that all data objects be Findable, Accessible, Interoperable, and Reusable, both for machines and for people. Adherence to these principles is necessary for proper stewardship of information, for testing regulatory compliance, for measuring the efficiency of processes, and for facilitating reuse of data-analytical frameworks. Findings We present the Contextual Ontology-based Repository Analysis Library (CORAL), a platform that greatly facilitates adherence to all 4 of the FAIR principles, including the especially difficult challenge of making heterogeneous datasets Interoperable and Reusable across all parts of a large, long-lasting organization. To achieve this, CORAL's data model requires that data generators extensively document the context for all data, and our tools maintain that context throughout the entire analysis pipeline. CORAL also features a web interface for data generators to upload and explore data, as well as a Jupyter notebook interface for data analysts, both backed by a common API. Conclusions CORAL enables organizations to build FAIR data types on the fly as they are needed, avoiding the expense of bespoke data modeling. CORAL provides a uniquely powerful platform to enable integrative cross-dataset analyses, generating deeper insights than are possible using traditional analysis tools.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Metastability of stratified magnetohydrostatic equilibria and their relaxation

Motivated by explosive releases of energy in fusion, space and astrophysical plasmas, we consider the nonlinear stability of stratified magnetohydrodynamic equilibria against two-dimensional interchanges of straight magnetic-flux tubes. We demonstrate that, even within this restricted class of dynamics, the linear stability of an equilibrium does not guarantee its nonlinear stability: equilibria can be metastable. We show that the minimum-energy state accessible to a metastable equilibrium under non-diffusive two-dimensional dynamics can be found by solving a combinatorial optimisation problem. These minimum-energy states are, to good approximation, the final states reached by our simulations of destabilised metastable equilibria for which turbulent mixing is suppressed by viscosity. To predict the result of fully turbulent relaxation, we construct a statistical mechanical theory based on the maximisation of Boltzmann's mixing entropy. This theory is analogous to the Lynden-Bell statistical mechanics of collisionless stellar systems and plasma, and to the Robert–Sommeria–Miller theory of two-dimensional vortex turbulence. Our theory reproduces well the results of our numerical simulations for sufficiently large perturbations to the metastable equilibrium.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Annual Mean Arctic Amplification 1970–2020: Observed and Simulated by CMIP6 Climate Models

While the annual mean Arctic Amplification (AA) index varied between two and three during the 1970–2000 period, it reached values exceeding four during the first two decades of the 21st century. The AA did not change in a continuous fashion but rather in two sharp increases around 1986 and 1999. During those steps the mean global surface air temperature trend remained almost constant, while the Arctic trend increased. Although the “best” CMIP6 models reproduce the increasing trend of the AA in 1980s they do not capture the sharply increasing trend of the AA after 1999 including its rapid step-like increase. We propose that the first sharp AA increase around 1986 is due to external forcing, while the second step close to 1999 is due to internal climate variability, which models cannot reproduce in the observed time.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Molecular mechanisms underlying host-induced gene silencing

Abstract Host-induced gene silencing (HIGS) refers to the silencing of genes in pathogens and pests by expressing homologous double-stranded RNAs (dsRNA) or artificial microRNAs (amiRNAs) in the host plant. The discovery of such trans-kingdom RNA silencing has enabled the development of RNA interference-based approaches for controlling diverse crop pathogens and pests. Although HIGS is a promising strategy, the mechanisms by which these regulatory RNAs translocate from plants to pathogens, and how they induce gene silencing in pathogens, are poorly understood. This lack of understanding has led to large variability in the efficacy of various HIGS treatments. This variability is likely due to multiple factors, such as the ability of the target pathogen or pest to take up and/or process RNA from the host, the specific genes and target sequences selected in the pathogen or pest for silencing, and where, when, and how the dsRNAs or amiRNAs are produced and translocated. In this review, we summarize what is currently known about the molecular mechanisms underlying HIGS, identify key unanswered questions, and explore strategies for improving the efficacy and reproducibility of HIGS treatments in the control of crop diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Community Based Data of Potentiometric Titration of Iron Oxides: Ferrihydrite (HFO), Goethite, Hematite, Magnetite

This data release includes experimental data of potentiometric titration for iron oxides. The data in the provided .csv files is not our own experimental data but have been compiled from the multiple literature sources. The master database is L-SCIE (LLNL Surface Complexation/Ion Exchange) database, and the provided .csv files are extracted data from L-SCIE. The .csv files were obtained by using the Lawrence Livermore National Laboratory Surface Complexation Database Converter (SCDC) code written in the R programming language (free licensing available at https://ipo.llnl.gov/technologies/software/llnl-surface-complexation-database-converter-scdc).The released data was used for developing a comprehensive community data-driven surface complexation modeling (SCM) framework for simulating potentiometric titration of mineral surfaces. Compiled community data for ferrihydrite, goethite, hematite, and magnetite are fit to produce representative protolysis constants that can reproduce potentiometric titration data collected from multiple literature sources.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Simulation of Electron-Proton Scattering Events by a Feature-Augmented and Transformed Generative Adversarial Network (FAT-GAN)

We apply generative adversarial network (GAN) technology to build an event generator that simulates particle production in electron-proton scattering that is free of theoretical assumptions about underlying particle dynamics. The difficulty of efficiently training a GAN event simulator lies in learning the complicated patterns of the distributions of the particles physical properties. We develop a GAN that selects a set of transformed features from particle momenta that can be generated easily by the generator, and uses these to produce a set of augmented features that improve the sensitivity of the discriminator. The new Feature-Augmented and Transformed GAN (FAT-GAN) is able to faithfully reproduce the distribution of final state electron momenta in inclusive electron scattering, without the need for input derived from domain-based theoretical assumptions. The developed technology can play a significant role in boosting the science of existing and future accelerator facilities, such as the Electron-Ion Collider.

Alanazi, Yasir↗
DOE OSTI2022

Uncertainty Quantification for a Multi-phase Carbon Equation of State Model

Many physics models have tunable parameters that are calibrated by matching the model output to experimental or calculated data. However, given that calibration data often contain uncertainty and that different model parameter sets might result in a very similar simulated output for a finite calibration data set, it is advantageous to provide an ensemble of parameter sets that are consistent with the calibration data. Uncertainty quantification (UQ) provides a means to generate such an ensemble in a statistically rigorous fashion. In this work, we perform UQ for a multi-phase equation of state (EOS) model for carbon containing the diamond, graphite, and liquid phases. We use a Bayesian framework for the UQ and introduce a novel strategy for including phase diagram information in the calibration. The method is highly general and accurately reproduces the calibration data without any material-specific prior knowledge of the EOS model parameters.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Geometry-complete perceptron networks for 3D molecular graphs

Abstract Motivation The field of geometric deep learning has recently had a profound impact on several scientific domains such as protein structure prediction and design, leading to methodological advancements within and outside of the realm of traditional machine learning. Within this spirit, in this work, we introduce GCPNet, a new chirality-aware SE(3)-equivariant graph neural network designed for representation learning of 3D biomolecular graphs. We show that GCPNet, unlike previous representation learning methods for 3D biomolecules, is widely applicable to a variety of invariant or equivariant node-level, edge-level, and graph-level tasks on biomolecular structures while being able to (1) learn important chiral properties of 3D molecules and (2) detect external force fields. Results Across four distinct molecular-geometric tasks, we demonstrate that GCPNet’s predictions (1) for protein–ligand binding affinity achieve a statistically significant correlation of 0.608, more than 5%, greater than current state-of-the-art methods; (2) for protein structure ranking achieve statistically significant target-local and dataset-global correlations of 0.616 and 0.871, respectively; (3) for Newtownian many-body systems modeling achieve a task-averaged mean squared error less than 0.01, more than 15% better than current methods; and (4) for molecular chirality recognition achieve a state-of-the-art prediction accuracy of 98.7%, better than any other machine learning method to date. Availability and implementation The source code, data, and instructions to train new models or reproduce our results are freely available at https://github.com/BioinfoMachineLearning/GCPNet.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dataset for 'Stream Temperature Predictions for River Basin Management in the Pacific Northwest and Mid-Atlantic Regions Using Machine Learning', Water 2022

This data package presents forcing data, model code, and model output for classical machine learning models that predict monthly stream water temperature as presented in the manuscript ‘Stream Temperature Predictions for River Basin Management in the Pacific Northwest and Mid-Atlantic Regions Using Machine Learning’, Water (Weierbach et al., 2022). Specifically, for input forcing datasets we include two files each generated using the BASIN-3D data integration tool (Varadharajan et al., 2022) for stations in the Pacific Northwest and Mid Atlantic Hydrologic regions. Model code (written in python with the use of jupyter notebooks) includes codes for data preprocessing, training Multiple Linear Regression, Support Vector Regression, and Extreme Gradient Boosted Tree models, and additional notebooks for analysis of model output. We include specific model output files which represent modeling configurations presented in the manuscript also presented in an hdf5 format. Together, these data make up the workflow for predictions across three scenarios (single station, regional, and predictions in unmonitored basins) presented in the manuscript and allow for reproducibility of modeling procedures.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Materials data science using CRADLE: A distributed, data-centric approach

Abstract There is a paradigm shift towards data-centric AI, where model efficacy relies on quality, unified data. The common research analytics and data lifecycle environment (CRADLE™) is an infrastructure and framework that supports a data-centric paradigm and materials data science at scale through heterogeneous data management, elastic scaling, and accessible interfaces. We demonstrate CRADLE’s capabilities through five materials science studies: phase identification in X-ray diffraction, defect segmentation in X-ray computed tomography, polymer crystallization analysis in atomic force microscopy, feature extraction from additive manufacturing, and geospatial data fusion. CRADLE catalyzes scalable, reproducible insights to transform how data is captured, stored, and analyzed. Graphical abstract

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Detection of innate immune response modulating impurities (IIRMI) in therapeutic peptides and proteins: Impact of excipients

Unintended immunogenicity can affect the safety and efficacy of therapeutic proteins and peptides, so accurate assessments of immunogenicity risk can aid in the selection, development, and regulation of biologics. Product- and process- related impurities can act as adjuvants that activate the local or systemic innate immune response increasing the likelihood of product immunogenicity. Thus, assessing whether products have innate immune response modulating impurities (IIRMI) is a key component of immunogenicity risk assessments. Identifying trace levels of individual IIRMI can be difficult and testing individually for all potential impurities is not feasible. Therefore, to mitigate the risk, cell-based assays that use human blood cells or monocyte-macrophage reporter cell lines are being developed to detect minute quantities of impurities capable of eliciting innate immune activation. As these are cell-based assays, there is concern that excipients could blunt the cell responses, masking the presence of immunogenic IIRMI. Here, we explore the impact of frequently used excipients (non-ionic detergents, sugars, amino acids, bulking agents) on the sensitivity of reporter cell lines (THP-1- and RAW-Blue cells) and fresh human blood cells to detect purified TLR agonists as model IIRMI. We show that while excipients do not modulate the innate immune response elicited by TLR agonists in vivo, they can impact on the sensitivity of cell-based IIRMI assays. Reduced sensitivity to detect LPS, FSL-1, and other model IIRMI was also evident when testing 3 different recombinant drug products, product A (a representative mAb), B (a representative growth factor), C (a representative peptide), and their corresponding formulations. These results indicate that product formulations need to be considered when developing and validating cell-based assays for assessing clinically relevant levels of IIRMI in therapeutic proteins. Optimization of reporter cells, culture conditions and drug product concentration appear to be critical to minimize the impact of excipients and attain sensitive and reproducible assays.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Qualification and Quantification of Porosity at the Top of the Fuel Pins in Metallic Fuels Using Image Processing

Approximately 130,000 metal fuel pins were irradiated in the Experimental Breeder Reactor II (EBR-II) during its 30 years of operation to develop and characterize existing and prospective fuels. For many of the metal fuel irradiation experiments, neutron radiography imaging was performed to characterize fuel behavior, such as fuel axial expansion. While several fuel expansion results obtained from neutron radiography imaging have been published, the analysis of neutron radiography for the purpose of describing statistical properties of porous matter formed on top of the fuel pins, also referred to as fluff in previous publications, is significantly less represented in the literature with just a single paper so far. This study aims to validate and augment results reported in previous publications using automated image processing. The paper describes the statistical properties of the porous matter in terms of nine parameters derived from radiography images and correlates those parameters with such fuel properties as composition, expansion, temperature, and burnup. The reported results are based on 1097 fuel pins of eight different fuel compositions. For three major fuel types, U-10Zr, U-8Pu-10Zr, and U-19Pu-10Zr, a clear negative correlation is found between the Pu content and five parameters describing the amount of porous matter generated. The parameters describing granularity properties, however, showed either negative correlation or nonlinear dependency from fuel composition. The parameters describing the amount showed a positive correlation with fuel axial expansion, while granularity parameters showed a negative correlation with axial expansion. The dependency on cladding temperature was found to be weak. A positive correlation is demonstrated for volume parameters and fuel burnup. In general, reported results confirm and validate findings published in previous studies using a much larger number of pins and automated processing techniques, which easily lend themselves to reproducibility, thus avoiding subjective bias.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Enhancing Cluster Identification in Atom Probe Tomography Data Using Transfer Learning

Atom probe tomography (APT) has enabled the direct visualization of solute clusters, providing valuable insights into material structures. This clustering is crucial for understanding the nanoscale composition and behavior of materials, which can significantly influence their mechanical and physical properties. However, the widely used clustering methods in the APT community face challenges such as subjective parametric selection and limited applicability, particularly in dealing with overlapping clusters, nested clusters, and artifacts across different scales, such as precipitates and dislocations. To address these challenges, we present a framework based on density-based cluster analysis that aims to be less dependent on user input, reproducible, and robust.

Density-based clustering↗
NASA NTRSDate not supplied

Standardizing Algorithm Documentation For Improved Scientific Data Understanding: The Algorithm Publication Tool Prototype

Algorithm Theoretical Basis Documents (ATBDs) are documents which accompany Earth observation data products generated from algorithms. While ATBDs are essential to scientific reproducibility, these key documents are not standardized and are often difficult to find. In this paper, we present the prototype Algorithm Publication Tool (APT), a cloud-based ATBD authoring and editing tool for NASA’s Earth science data systems. A standardized ATBD information model is also described as well as lessons learned from developing the prototype tool.

Kaylin Bugbee↗
DOE OSTI2025

A high-throughput experimentation platform for data-driven discovery in electrochemistry

Automating electrochemical analyses combined with artificial intelligence is poised to accelerate discoveries in renewable energy sciences and technologies. This study presents an automated high-throughput electrochemical characterization (AHTech) platform as a cost-effective and versatile tool for rapidly assessing liquid analytes. The Python-controlled platform combines a liquid handling robot, potentiostat, and customizable microelectrode bundles for diverse, reproducible electrochemical measurements in microtiter plates, minimizing chemical consumption and manual effort. To showcase the capability of AHTech, we screened a library of 180 small molecules as electrolyte additives for aqueous zinc metal batteries, generating data for training machine learning models to predict Coulombic efficiencies. Key molecular features governing additive performance were elucidated using Shapley Additive exPlanations and Spearman’s correlation, pinpointing high-performance candidates like cis-4-hydroxy-d-proline, which achieved an average Coulombic efficiency of 99.52% over 200 cycles. The workflow established herein is highly adaptable, offering a powerful framework for accelerating the exploration and optimization of extensive chemical spaces across diverse energy storage and conversion fields.

Lin, Dian-Zhao [Johns Hopkins University, Baltimor↗
NASA NTRSDate not supplied

Open Science Approach to Analyze Climate-Crop Relationships in the US Leveraging GES DISC and Galaxy Workflows

Understanding the intricate relationship between climate variability and agricultural production is crucial for ensuring food security. This study investigates the impact of climate parameters, such as temperature, precipitation, and soil moisture, on major US crop yields. Adopting an open science approach, the study analyzes the impact of climate on agricultural production in the United States. The Galaxy workflow engine serves as the primary tool for integrating climate data from the Goddard Earth Sciences Data and Information Services Center (GES DISC), retrieved via the Giovanni system, with yield statistics from the United States Department of Agriculture’s National Agricultural Statistics Service (USDA NASS). Extensions for reading, preprocessing, and analyzing external data have been developed, enabling the creation of workflows within the Galaxy platform. The development of a reproducible workflow allows for the calculation of seasonal climate averages, which are then assessed for their correlation with crop yields. This methodology ensures the replicability of the research, promoting transparency and collaboration in the scientific community. Correlational and regression analyses have been applied to different sub-zones and crops. The findings from this research offer valuable insights into the relationship between climate parameters and crop yields. These insights contribute to a deeper understanding of climate-crop relationships, providing a solid foundation for informed decision-making in the agricultural sector. The high correlation values indicate a significant relationship between climate parameters and crop yields, underscoring the importance of considering climate factors in agricultural planning and policymaking. This research also exemplifies the power of open science in advancing our understanding of complex environmental and agricultural phenomena. By leveraging open data and services, it provides a robust and replicable framework for future studies in this critical field.

Open science↗
DOE OSTI2020

Matching Crystal Structures Atom-to-Atom

Finding an optimal match between two different crystal structures underpins many important materials science problems, including describing solid-solid phase transitions and developing models for interface and grain boundary structures. Here, we formulate the matching of crystals as an optimization problem where the goal is to find the alignment and the atom-to-atom map that minimize a given cost function such as the Euclidean distance between the atoms. We construct an algorithm that directly solves this problem for large finite portions of the crystals and retrieves the periodicity of the match subsequently. We demonstrate its capacity to describe transformation pathways between known polymorphs and to reproduce experimentally realized structures of semi-coherent interfaces. Additionally, from our findings, we define a rigorous metric for measuring distances between crystal structures that can be used to properly quantify their geometric (Euclidean) closeness.

36 MATERIALS SCIENCE↗