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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 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Transport Simulations on Scanning Transmission Electron Microscope Images of Nanoporous Shale

Digital rock physics is an often-mentioned approach to better understand and model transport processes occurring in tight nanoporous media including the organic and inorganic matrix of shale. Workflows integrating nanometer-scale image data and pore-scale simulations are relatively undeveloped, however. In this paper, a workflow is demonstrated progressing from sample acquisition and preparation, to image acquisition by Scanning Transmission Electron Microscopy (STEM) tomography, to volumetric reconstruction to pore-space discretization to numerical simulation of pore-scale transport. Key aspects of the workflow include (i) STEM tomography in high angle annular dark field (HAADF) mode to image three-dimensional pore networks in µm-sized samples with nanometer resolution and (ii) lattice Boltzmann method (LBM) simulations to describe gas flow in slip, transitional, and Knudsen diffusion regimes. It is shown that STEM tomography with nanoscale resolution yields excellent representation of the size and connectivity of organic nanopore networks. In turn, pore-scale simulation on such networks contributes to understanding of transport and storage properties of nanoporous shale. Interestingly, flow occurs primarily along pore networks with pore dimensions on the order of tens of nanometers. Smaller pores do not form percolating pathways in the sample volume imaged. Apparent gas permeability in the range of 10−19 to 10−16 m2 is computed.

42 ENGINEERING↗
DOE OSTI2022

Toward designing effective exascale scientific computing workflows: experiences and best practices

Many fields within scientific computing have embraced advances in big-data analysis and machine learning, which often requires the deployment of large, distributed and complicated workflows that may combine training neural networks, performing simulations, running inference, and performing database queries and data analysis in asynchronous, parallel and pipelined execution frameworks. Such a shift has brought into focus the need for scalable, efficient workflow management solutions with reproducibility, error and provenance handling, traceability, and checkpoint-restart capabilities, among other needs. Here, we discuss challenges and best-practices for deploying exascale-generation computational science workflows on resources at the Oak Ridge Leadership Computing Facility (OLCF). We present our experiences with large-scale deployment of distributed workflows on the Summit supercomputer, including for bioinformatics and computational biophysics, materials science, and deep learning model optimization. We also present problems and solutions created by working within a Python-centric software base on traditional HPC systems, and discuss steps that will be required before the convergence of HPC, AI, and data science can be fully realized. Our results point to a wealth of exciting new possibilities for harnessing this convergence to tackle new scientific challenges.

Coletti, Mark↗
DOE OSTI2023

polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies

Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) continuous long reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies made from CLR data. PolishCLR can be initiated from several input options that extend best practices to suboptimal cases. It also provides re-entry points throughout several key processes, including identifying duplicate haplotypes in purge_dups, allowing a break for scaffolding if data are available, and throughout multiple rounds of polishing and evaluation with Arrow and FreeBayes. PolishCLR is containerized and publicly available for the greater assembly community as a tool to complete assemblies from existing, error-prone long-read data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Model-based Reconstruction for Single Particle Cryo-Electron Microscopy

Single particle cryo-electron microscopy is a vital tool for 3D characterization of protein structures. A typical workflow involves acquiring projection images of a collection of randomly oriented particles, picking and classifying individual particle projections by orientation, and finally using the individual particle projections to reconstruct a 3D map of the electron density profile. The reconstruction is challenging because of the low signal-to-noise ratio of the data, the unknown orientation of the particles, and the sparsity of data especially when dealing with flexible proteins where there may not be sufficient data corresponding to each class to obtain an accurate reconstruction using standard algorithms. In this paper we present a model-based image reconstruction technique that uses a regularized cost function to reconstruct the 3D density map by assuming known orientations for the particles. Our method casts the reconstruction as minimizing a cost function involving a novel forward model term that accounts for the contrast transfer function of the microscope, the orientation of the particles and the center of rotation offsets. We combine the forward model term with a regularizer that enforces desirable properties in the volume to be reconstructed. Using simulated data, we demonstrate how our method can significantly improve upon the typically used approach.

Venkatakrishnan, Singanallur↗
DOE OSTI2023

Combined Data and Deep Learning Model Uncertainties: An Application to the Measurement of Solid Fuel Regression Rate

In complex physical process characterization, such as the measurement of the regression rate for solid hybrid rocket fuels, where both the observation data and the model used have uncertainties originating from multiple sources, combining these in a systematic way for quantities of interest (QoI) remains a challenge. In this paper, we present a forward propagation uncertainty quantification (UQ) process to produce a probabilistic distribution for the observed regression rate r. We characterized two input data uncertainty sources from the experiment (the distortion from the camera U c and the non-zero-angle fuel placement U Y ), the prediction and model form uncertainty from the deep neural network (U m ), as well as the variability from the manually segmented images used for training it (U s ). Here, we conducted seven case studies on combinations of these uncertainty sources with the model form uncertainty. The main contribution of this paper is the investigation and inclusion of the experimental image data uncertainties involved, and how to include them in a workflow when the QoI is the result of multiple sequential processes.

42 ENGINEERING↗
DOE OSTI2026

3D seismic imaging of a fracture damage zone controlling reservoir compartmentalization at the Raft River EGS using multi-azimuth walkaway VSP

Accurate imaging of steeply dipping fracture zones in crystalline enhanced geothermal systems (EGS) is critical for constraining permeability architecture and guiding stimulation design. However, such structures remain poorly resolved by conventional surface seismic methods. We present a fully three-dimensional (3D) elastic-waveform inversion-migration workflow applied to multi-azimuth walkaway vertical seismic profiling (VSP) data acquired in a deviated borehole at the Raft River EGS. The workflow integrates first-arrival traveltime tomography, multi-scale elastic waveform inversion (EWI), and elastic least-squares reverse-time migration (ELSRTM) to recover high-resolution compressional-and shear-wave velocity models and to image structural discontinuities in the crystalline basement. The results reveal a laterally continuous low-velocity anomaly, with shear-wave velocity reductions of 25-30%, consistent with fractureinduced mechanical weakening. Two steeply dipping discontinuities bound a 50-80 m wide fracture damage zone. Independent constraints from microseismic clustering and geochemical compartmentalization corroborate the geometry and structural significance of this feature. Synthetic modeling further confirms that structures of this scale are resolvable (~30 m). These findings indicate that the Narrows structure is a distributed fracture damage zone rather than a discrete fault plane. By resolving fracture-zone geometry at the tens-of-meters scale using a single borehole, this workflow provides a practical and transferable approach for improving structural characterization, reducing uncertainty in permeability architecture, and supporting reservoir modeling and stimulation design in fractured crystalline EGS reservoirs.

58 GEOSCIENCES↗
DOE OSTI2020

An open source analysis framework for large-scale building energy modeling

Full integration of building energy modelling into the design and retrofit process has long been a goal of building scientists and practitioners. However, significant barriers still exist. Among them are the lack of available: (1) configurable technology stacks for performing both small- and large-scale analyses, (2) different classes of algorithms compatible with common design workflows, and (3) analysis tools for effectively visualizing large-scale simulation results. This article discusses the OpenStudio® Analysis Framework: a scalable analysis framework for building energy modelling that was developed to overcome the three barriers listed above. The framework is open-source and scalable to facilitate wider adoption and has a clearly defined application programming interface upon which other applications can be built. It runs on high-performance computing systems, within cloud infrastructure, and on laptops, and uses a common workflow to enable different classes of algorithms. Lessons learned from previous development efforts are also discussed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Short-Term Probabilistic Solar Forecasting via Reinforcement Learning over ECMWF

In this paper, we present an innovative reinforcement learning approach for short-term solar forecasting, leveraging data from the European Centre for Medium-Range Weather Forecasts (ECMWF). The methodology begins with the application of the System Advisor Model (SAM) to transform various ECMWF numerical weather prediction members into predictive photovoltaic power generation. To enhance the precision of deterministic forecasting, we introduce a dynamic model selection algorithm based on Q-learning. This algorithm dynamically identifies and utilizes the most accurate ensemble member for forecasting purposes. Furthermore, we employ a support vector regression surrogate model with a Gaussian distribution to generate probabilistic forecasts, providing a holistic view of solar energy generation uncertainty. To expedite the training process and make it more practical for real-world applications, we integrate a rolling update workflow. This innovative workflow reduces the training period from months to a mere 19 days, making our method highly efficient. Numerical results of the case study show that in comparison to benchmark models, the proposed method improves the deterministic and probabilistic solar forecasting accuracy by up to 40.84% and 48.42%, respectively.

ensemble forecasting↗
DOE OSTI2024

Augmenting the Structural Dynamics Workflow to Reduce Development Times

The success of future systems development at Los Alamos National Laboratory (LANL) depends, in part, on the ability to make informed decisions quickly. This is particularly true when asked to perform structural-mechanical analyses across many design alternatives. To help reduce development time, techniques in reduced-order finite-element modeling (FEM), pretest predictions, and FEM-test correlation and updating were demonstrated in the fiscal year (FY) 23 Technology and Demonstration Project (TED): Augmenting the Structural Dynamics Workflow to Reduce Development Times. This report expands on the TED project final report, LA-UR-34022.

42 ENGINEERING↗
DOE OSTI2025

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0

Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable comparative analysis, predictive modeling, and data integration across bioinformatics platforms. While professional biocuration is resource-intensive and usually limited to institutional settings, community-driven approaches can mobilize large-scale annotation of specialized datasets and are more resilient to disruptions in scientific funding. Here, we present a model for community-powered curation applied to the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Through a framework of workflows for metadata capture, annotation validation, and contributor coordination, the MIBiG 4.0 initiative recruited 267 scientists across 178 institutions from 33 countries, volunteering an estimated 4000 h of work. These efforts expanded the MIBiG repository by 22% and enhanced its usability in downstream molecular data analyses in comparative genomic analyses, natural product discovery, and machine learning applications. We provide strategies and actionable lessons for adopting this model, supporting the sustainability of curated bioinformatics resources central to nucleic acid research and related fields.

biocuration↗
DOE OSTI2026

OCHRE

OCHRE™ uses a variety of input data sources to run time-series simulations. Building models can be taken from the ResStock™ database or generated using the Building Energy Optimization Tool (BEopt™) or other OpenStudio-HPXML workflows. EV charging profiles can be taken from datasets used in NLR's 2030 National Charging Network project. Weather data can be taken from the National Solar Radiation Database or EnergyPlus® weather files. There are no public datasets with OCHRE outputs at this time. However, a recent project dataset on water heater and EV demand flexibility can be requested. OCHRE is a Python-based energy modeling tool designed to model flexible loads in residential buildings. OCHRE includes detailed models and controls for flexible devices including HVAC equipment, water heaters, EVs, solar PV, and batteries. It is designed to run in co-simulation with custom controllers, aggregators, and grid models.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

helios: An R package to process heating and cooling degrees for GCAM

helios is an open-source R package that estimates population-weighted heating and cooling degree-hours (HDH and CDH) and degree-days (HDD and CDD) at various temporal (e.g., energy dispatch segments, monthly, yearly) and spatial scales (e.g., U.S. states, global political regions, countries). The degree hour and degree day outputs from helios are used to inform electricity demand load in the Global Change Analysis Model (GCAM) as well as in GCAM-USA (which is the version of GCAM with U.S. state-level details). helios uses a workflow with four steps: processing raw data; calculating heating and cooling degrees; visualizing performance diagnostics; and outputing results in various formats. There are two sources of widely-used climate data compatible with helios: (1) hourly climate data with 12-km resolution that are dynamically downscaled with the Weather Research and Forecasting (WRF) model and projected using a thermal global warming (TGW) approach; and (2) daily climate data with 0.5-degree resolution from the Coupled Model Intercomparison Project (CMIP) that is bias-adjusted and statistical downscaled by the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP). In summary, helios is a model that standardizes methodology of heating and cooling degrees-hours and degree-days using publicly available data and advance the understanding of the impact of spatial and temporal temperature variability on building energy services.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Dataset for "Evaluating Deep Learning Approaches for Predictions in Unmonitored Basins with Continental-scale Stream Temperature Models" Willard et al. (2024)

This data release provides all data and code used in the paper " "Evaluating Deep Learning Approaches for Predictions in Unmonitored Basins with Continental-scale Stream Temperature Models" Willard et al. (2024)" to model stream temperature, evaluate, and assess results. The associated manuscript explores current open questions in prediction in ungauged and unmonitored basins concerning top-down versus bottom-up approaches, tradeoffs between data available and input requirements, and the appropriate representation of catchment attributes as inputs to deep learning models. Modeling was done primarily with long short-term memory (LSTM) models, and stream site coverage spans 1362 locations across the conterminous United States. The data is organized into these items items:Code repository and data for the paper " "Evaluating Deep Learning Approaches for Predictions in Unmonitored Basins with Continental-scale Stream Temperature Models" Willard et al. (2024)".Code: stream_temp_ml_regionalization.zip contains the code repositoryData to run the code: - data_dir.zip -- contains all files that should be moved to the "DATA_DIR" variable defined in the "set_env_vars.sh" script in the code repository- metadata_dir.zip -- contains all files that should be moved to the "METADATA_DIR" variable defined in the "set_env_vars.sh" script in the code repository- error_analysis_attribute_and_groundwater_dir.zip - workflows for the extended error analysis by stream attribute and groundwater influenceData produced by the code and used in the paper:- outputs_dir.zip - contains model output and results (outputs_dir/results), model weights (outputs_dir/models), and all other outputs used for the paper including feature importances.To cite this code, please use the following BibTeX or MLA entries:bibtex:@misc{willard2024streamdata, author = {Jared Willard and Fabio Ciulla and Helen Weierbach and Vipin Kumar and Charuleka Varadharajan}, title = {Dataset for "Evaluating Deep Learning Approaches for Predictions in Unmonitored Basins with Continental-scale Stream Temperature Models"}, year = {2024}, doi = {10.15485/2448016}, publisher = {ESS-DIVE Repository}, url = {https://doi.org/10.15485/2448016}}MLA: Willard, Jared, et al. Dataset for "Evaluating Deep Learning Approaches for Predictions in Unmonitored Basins with Continental-scale Stream Temperature Models". 2024. ESS-DIVE Repository, doi:10.15485/2448016.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Hierarchical Reinforcement Learning of a Short-Range Bond-Order Potential for Silica: Analytic Embedding of Coordination with Classical Efficiency

Reinforcement learning (RL) has recently emerged as a data-efficient strategy to parametrize short-range interatomic potentials. Building on our past RL optimization of pairwise silica models, we extend the framework to a bond-order (Tersoff-type) potential that provides an analytic embedding of local coordination through a three-body term. A hierarchical RL workflow combining continuous-action Monte Carlo Tree Search and property-based rewards efficiently explores the 26-dimensional parameter space, sequentially optimizing lattice parameters, densities, angles, and cohesive energies of 21 silica polymorphs. The resulting models, Q-Tersoff and ML-Tersoff, reproduce the energetic ordering of low-energy phases and capture the angular correlations and amorphous structure factors of silica with improved fidelity over pairwise force fields, while remaining orders of magnitude faster than high-dimensional machine-learned potentials. Both models underperform for elastic constants and high-energy frameworks, delineating the limits of the current analytic form. The approach establishes a general and interpretable route to angle-aware, short-range potentials that bridge physics-based and machine-learned descriptions of silicate materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Supporting Nuclear Energy Research with MLOps

Artificial intelligence (AI) and machine learning (ML) have been shown to be increasingly helpful tools in a growing number of use-cases relevant to scientific research, despite significant software-related obstacles. There exist large technical costs to setting up, using, and maintaining AI/ML models in production. This often prevents researchers from utilizing these models in their work. The growing field of machine learning operations (MLOps) aims to automate much of the AI/ML life cycle while increasing access to these models. This paper presents our initial work in creating a nuclear energy MLOps platform for use by researchers at Idaho National Laboratory (INL) and aims to reduce the barriers of using AI/ML in scientific research. We hope to promote the integration of the latest AI/ML technologies into researchers' workflows and create more opportunity for scientific innovation. In this paper we discuss how our MLOps efforts aim to increase usage and the impact of AI/ML models created by engineers. We also present several use-cases that are currently integrated. Finally, we evaluate the maturity of our project as well as our plans for future functionality.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Ingrained: An Automated Framework for Fusing Atomic-Scale Image Simulations into Experiments

To fully leverage the power of image simulation to corroborate and explain patterns and structures in atomic resolution microscopy, an initial correspondence between the simulation and experimental image must be established at the outset of further high accuracy simulations or calculations. Furthermore, if simulation is to be used in context of highly automated processes or high-throughput optimization, the process of finding this correspondence itself must be automated. In this work, "ingrained," an open-source automation framework which solves for this correspondence and fuses atomic resolution image simulations into the experimental images to which they correspond, is introduced. Here, the overall "ingrained" workflow, focusing on its application to interface structure approximations, and the development of an experimentally rationalized forward model for scanning tunneling microscopy simulation are described.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Combining Deep Learning and scatterControl for High-Throughput X-ray CT Based Non-Destructive Characterization of Large-Scale Casted Metallic Components

X-ray computed tomography (XCT) is essential for nondestructive evaluation and quality control of large-scale metal components. XCT imaging, however, faces significant challenges from metal artifacts, particularly those caused by Compton scattering, which degrade image quality and obscure critical details. Hardware-based solutions (e.g. scatterControl) offer advancements by intercepting scattered photons and reducing artifacts, but they can be time-consuming and require additional processing. Here, we propose modifying and leveraging a novel deep learning (DL) framework, Simurgh, to enhance and accelerate scatter correction in XCT. By combining scatterControl with DL-based artifact removal, we demonstrate significant reduction in scan time while producing high-quality reconstructions. Through extensive evaluation on industrial XCT data, we show that our methods reduce scan time by up to more than 10 x while preserving flaw detectability. Quantitative analysis across multiple segmentation techniques confirms that Simurgh-based reconstructions consistently outperform traditional Feldkamp-Davis-Kress, model-based iterative reconstruction, and commercial DL models in both pixel-level and task-specific evaluations, enabling scalable, high-throughput XCT workflows for characterization of large scale components in applications such as casting and metal additive manufacturing.

Complex metal parts↗
DOE OSTI2022

SBbadger: biochemical reaction networks with definable degree distributions

Abstract Motivation An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis. Results In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software. Availability and implementation SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗