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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Data for "Efficient Mutagenesis and Genotyping of Maize Inbreds Using Biolistics, Multiplex CRISPR/Cas9 Editing, and Indel-Selective PCR"

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present an approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to Type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel-Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The ‘end to end’ pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

gene editing↗
DOE OSTI2024

Intro to HPC Bootcamp: Engaging New Communities Through Energy Justice Projects

The U.S. Department of Energy (DOE) is a long-standing leader in research and development of high-performance computing (HPC) in the pursuit of science. However, we face daunting challenges in fostering a robust and diverse HPC workforce. Basic HPC is not typically taught at early stages of students' academic careers, and the capacity and knowledge of HPC at many institutions are limited. Even so, such topics are prerequisites for advanced training programs, internships, graduate school, and ultimately for careers in HPC. To help address this challenge, as part of the DOE Exascale Computing Project's Broadening Participation Initiative, we recently launched the Introduction to HPC Training and Workforce Pipeline Program to provide accessible introductory material on HPC, scalable AI, and analytics. We describe the Intro to HPC Bootcamp, an immersive program designed to engage students from underrepresented groups as they learn foundational HPC skills. Here, the program takes a novel approach to HPC training by turning the traditional curriculum upside down. Instead of focusing on technology and its applications, the bootcamp focuses on energy justice to motivate the training of HPC skills through project-based pedagogy and real-life science stories. Additionally, the bootcamp prepares students for internships and future careers at DOE labs. The first bootcamp, hosted by the advanced computing facilities at Argonne, Lawrence Berkeley, and Oak Ridge National Labs and organized by Sustainable Horizons Institute, took place in August 2023.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2022

Optimal high-throughput virtual screening pipeline for efficient selection of redox-active organic materials

As global interest in renewable energy continues to increase, there has been a pressing need for developing novel energy storage devices based on organic electrode materials that can overcome the shortcomings of the current lithium-ion batteries. One critical challenge for this quest is to find materials whose redox potential (RP) meets specific design targets. In this study, we propose a computational framework for addressing this challenge through the effective design and optimal operation of a high-throughput virtual screening (HTVS) pipeline that enables rapid screening of organic materials that satisfy the desired criteria. Starting from a high-fidelity model for estimating the RP of a given material, we show how a set of surrogate models with different accuracy and complexity may be designed to construct a highly accurate and efficient HTVS pipeline. We demonstrate that the proposed HTVS pipeline construction and operation strategies substantially enhance the overall screening throughput.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Helium recovery system at IB3a

The increasing need for optimal and sustainable use of cryogenic resources to support Fermilab’s scientific mission has highlighted the necessity of improving the Laboratory’s helium management practices. An assessment of cryogenic test facilities identified the Technical Division’s Industrial Building 3a (IB3A) as a key site requiring upgrades to integrate a helium recovery system. The IB3A facility is essential for characterizing and testing superconductors, cables, and coils for various R&D projects, including the US High-Luminosity LHC Accelerator Upgrade Project (AUP), Mu2e, and other external collaborations. Currently, the facility relies on 500 L helium Dewars and vents the vaporized helium directly into the atmosphere, leading to significant helium loss. Given the non-renewable nature of helium, recovering and reusing this resource is critical for the sustainability of Fermilab’s operations. To address this challenge, a project has been initiated to connect IB3A to an existing helium purification station and refrigeration system located in another building via a dedicated pipeline pass over the roof of several buildings. This solution will enable the efficient capture of vented helium, its transfer to the purification station, and subsequent liquefaction for reuse in future operations. The project includes a detailed design phase, specifying the pipeline route, flow control mechanisms, and integration with the existing cryogenic infrastructure, followed by phased implementation and commissioning. By implementing this pipeline connection and upgrading IB3A, Fermilab aims to significantly reduce helium waste, lower operational costs, and align with its commitment to sustainability. This initiative provides a model for resource-efficient cryogenic operations and reinforces the Laboratory’s capacity to support its science mission for the long term.

Porwisiak, D. [Fermilab]↗
DOE OSTI2026

REDI – Readiness Engine for Data Integration

The Readiness Engine for Data Integration (REDI) is an open-source framework for automating, standardizing, and assessing the process of preparing scientific data for AI training. REDI implements a five-stage pipeline (ingest, preprocess, transform, structure, output) with per-stage provenance instrumentation via Flowcept, domain-aware transformation logic (PII anonymization, regridding, graph encoding, and more), and built-in readiness assessment and validation modes. REDI has been evaluated across climate, proteomics, materials science, and nuclear fusion datasets, demonstrating near-ideal parallel scaling to 100 nodes on OLCF's Frontier system. REDI is deployable as an agent-callable skill in coding environments such as Claude Code and OpenAI Codex, and is complemented by SetGo for FAIR compliance and catalog publication.

Brewer, Wesley [Oak Ridge National Laboratory (ORN↗
DOE OSTI2023

In-depth analysis on parallel processing patterns for high-performance Dataframes

The Data Science domain has expanded monumentally in both research and industry communities during the past decade, predominantly owing to the Big Data revolution. Artificial Intelligence (AI) and Machine Learning (ML) are bringing more complexities to data engineering applications, which are now integrated into data processing pipelines to process terabytes of data. Typically, a significant amount of time is spent on data preprocessing in these pipelines, and hence improving its efficiency directly impacts the overall pipeline performance. The community has recently embraced the concept of Dataframes as the de-facto data structure for data representation and manipulation. However, the most widely used serial Dataframes today (R, pandas) experience performance limitations while working on even moderately large data sets. We believe that there is plenty of room for improvement by taking a look at this problem from a high-performance computing point of view. In a prior publication, we presented a set of parallel processing patterns for distributed dataframe operators and the reference runtime implementation, Cylon. In this paper, we are expanding on the initial concept by introducing a cost model for evaluating the said patterns. Furthermore, we evaluate the performance of Cylon on the ORNL Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

First detection of the BAO signal from early DESI data

We present the first detection of the baryon acoustic oscillations (BAOs) signal obtained using unblinded data collected during the initial 2 months of operations of the Stage-IV ground-based Dark Energy Spectroscopic Instrument (DESI). From a selected sample of 261 291 luminous red galaxies spanning the redshift interval 0.4 < z < 1.1 and covering 1651 square degrees with a 57.9 per cent completeness level, we report a ∼5σ level BAO detection and the measurement of the BAO location at a precision of 1.7 per cent. Using a bright galaxy sample of 109 523 galaxies in the redshift range 0.1 < z < 0.5, over 3677 square degrees with a 50.0 per cent completeness, we also detect the BAO feature at ∼3σ significance with a 2.6 per cent precision. These first BAO measurements represent an important milestone, acting as a quality control on the optimal performance of the complex robotically actuated, fibre-fed DESI spectrograph, as well as an early validation of the DESI spectroscopic pipeline and data management system. Based on these first promising results, we forecast that DESI is on target to achieve a high-significance BAO detection at sub-per cent precision with the completed 5-yr survey data, meeting the top-level science requirements on BAO measurements. This exquisite level of precision will set new standards in cosmology and confirm DESI as the most competitive BAO experiment for the remainder of this decade.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Using Large Language Models to help customers monitor global threat data

Large Language Models have proven adept at answering general knowledge questions. To make these generative AI tools useful to our mission customers for monitoring global threats, the data sciences team at Sandia is utilizing retrieval augmented generation (RAG) techniques to customize these models with local data. The local data we use consists of data such as research articles and patent abstracts that we've collected over the last several years using automated pipelines.

Herzer, John Andrew [Sandia National Laboratories ↗
DOE OSTI2020

Viral Annotation Pipeline in KBase

This data analysis workflow demonstrates how to process a metagenome to identify viruses using VirSorter. Then, provides taxonomic classification using vConTACT2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Quantitative cross-species translators of cardiac myocyte electrophysiology: Model training, experimental validation, and applications

Animal experimentation is key in the evaluation of cardiac efficacy and safety of novel therapeutic compounds. However, interspecies differences in the mechanisms regulating excitation-contraction coupling can limit the translation of experimental findings from animal models to human physiology and undermine the assessment of drugs’ efficacy and safety. Here, we built a suite of translators for quantitatively mapping electrophysiological responses in ventricular myocytes across species. We trained these statistical operators using a broad dataset obtained by simulating populations of our biophysically detailed computational models of action potential and Ca 2+ transient in mouse, rabbit, and human. We then tested our translators against experimental data describing the response to stimuli, such as ion channel block, change in beating rate, and β-adrenergic challenge. We demonstrate that this approach is well suited to predicting the effects of perturbations across different species or experimental conditions and suggest its integration into mechanistic studies and drug development pipelines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Machine learning pipeline to predict defect behavior in metallic alloy systems

The interaction between defect and solute atoms is critical to the thermodynamic and kinetic behavior of metallic alloys under exposure to high-energy radiation, causing irradiation damage in materials. Radiation can generate non-equilibrium concentrations of point defects such as vacancies and interstitials. The excess point defects not only accelerate diffusional processes such as precipitation that cause radiation embrittlement, but also change the pathway of phase transformations, including nucleation processes. Understanding these defect behaviors is complicated by the challenge and complexity of addressing each possible local and discrete distribution of environments and chemical interactions around targeted defects-solute or solute-solute complexes. To resolve the challenge, machine learning regression techniques have emerged as powerful tools that can train and construct an energy model to accurately describe the chemical interactions of solutes and defects. In Fiscal Year 2022, the work focused on the workflow development and demonstration using machine learning regression, density functional theory, cluster expansion, and Monte Carlo simulation to predict the effects of ternary solute elements (e.g., aluminum and molybdenum) and point defects on the Cr-rich $\alpha^{\prime}$ precipitation in multicomponent FeCr model alloys. The computational outcomes include the prediction of the ternary phase diagram, vacancy formation energy for different compositions, and the effect of vacancies on the nucleation of Cr-rich clusters. The simulations predict a pronounced change of Cr solubility in bcc Fe by the addition of Al and the rejection of Al atoms from $\alpha^{\prime}$ precipitates. Additionally, the simulations show the formation of Cr-vacancy clusters as the initial nuclei for stable nucleation and growth of $\alpha^{\prime}$ particles. The results demonstrate important outcomes and applications of using machine learning pipeline to study model or commercial alloys with multicomponent solute species and point defects.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

The Last Journey. I. An Extreme-scale Simulation on the Mira Supercomputer

The Last Journey is a large-volume, gravity-only, cosmological N-body simulation evolving more than 1.24 trillion particles in a periodic box with a side length of 5.025 Gpc. It was implemented using the HACC simulation and analysis framework on the BG/Q system Mira. The cosmological parameters are chosen to be consistent with the results from the Planck satellite. A range of analysis tools have been run in situ to enable a diverse set of science projects and, at the same time, keep the resulting data amount manageable. Analysis outputs have been generated starting at redshift z ~ 10 to allow for construction of synthetic galaxy catalogs using a semianalytic modeling approach in postprocessing. As part of our in situ analysis pipeline, we employ a new method for tracking halo substructures, introducing the concept of subhalo cores. The production of multiwavelength synthetic sky maps is facilitated by generating particle light cones in situ, also beginning at z ~ 10. We provide an overview of the simulation setup and generated data products; a first set of analysis results is presented. A subset of the data is publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Hypergraph Analytics of Domain Name System Relationships

We report on the use of novel mathematical methods in hypergraph analytice over a large quantity of DNS data. Hypergraphs generalize graphs, as used in network science, to better model complex multiway relations in cyber data. Specifically, casting DNS data from Georgia Tech's ActiveDNS repository as hypergraphs allows us to fully represent the interactions between {\em collections} of domains and IP addresses. To facilitate large-scale analytics, we fielded an analytical pipeline of two capabilities. HyperNetX (HNX) is a Python package for the exploration and visualization of hypergraphs, acting as a frontend. For the backend, the Chapel HyperGraph Library (CHGL) is a library for high performance hypergraph analytics written in the exascale programming language Chapel. CHGL was used to process gigascale DNS data, performing compute-intensive calculations for data reduction and segmentation. Identified portions are then sent to HNX for both exploratory analysis and knowledge discovery targeting known tactics, techniques, and procedures.

Joslyn, Cliff A.↗
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

A Joint Roman Space Telescope and Rubin Observatory Synthetic Wide-Field Imaging Survey

We present and validate 20 deg(2) of overlapping synthetic imaging surveys representing the full depth of the Nancy Grace Roman Space Telescope High-Latitude Imaging Survey (HLIS) and 5 yr of observations of the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST). The two synthetic surveys are summarized, with reference to the existing 300 deg(2) of LSST simulated imaging produced as part of Dark Energy Science Collaboration (DESC) Data Challenge 2 (DC2). Both synthetic surveys observe the same simulated DESC DC2 universe. For the synthetic Roman survey, we simulate for the first time fully chromatic images along with the detailed physics of the Sensor Chip Assemblies derived from lab measurements using the flight detectors. The simulated imaging and resulting pixel-level measurements of photometric properties of objects span a wavelength range of similar to 0.3-2.0 mu m. We also describe updates to the Roman simulation pipeline, changes in how astrophysical objects are simulated relative to the original DC2 simulations, and the resulting simulated Roman data products. We use these simulations to explore the relative fraction of unrecognized blends in LSST images, finding that 20-30 per cent of objects identified in LSST images with i-band magnitudes brighter than 25 can be identified as multiple objects in Roman images. These simulations provide a unique testing ground for the development and validation of joint pixel-level analysis techniques of ground- and space-based imaging data sets in the second half of the 2020s - in particular the case of joint Roman-LSST analyses.

gravitational lensing↗
DOE OSTI2021

The effect of protein mutations on drug binding suggests ensuing personalised drug selection

The advent of personalised medicine promises a deeper understanding of mechanisms and therefore therapies. However, the connection between genomic sequences and clinical treatments is often unclear. We studied 50 breast cancer patients belonging to a population-cohort in the state of Qatar. From Sanger sequencing, we identified several new deleterious mutations in the estrogen receptor 1 gene (ESR1). The effect of these mutations on drug treatment in the protein target encoded by ESR1, namely the estrogen receptor, was achieved via rapid and accurate protein–ligand binding affinity interaction studies which were performed for the selected drugs and the natural ligand estrogen. Four nonsynonymous mutations in the ligand-binding domain were subjected to molecular dynamics simulation using absolute and relative binding free energy methods, leading to the ranking of the efficacy of six selected drugs for patients with the mutations. Our study shows that a personalised clinical decision system can be created by integrating an individual patient’s genomic data at the molecular level within a computational pipeline which ranks the efficacy of binding of particular drugs to variant proteins.

59 BASIC BIOLOGICAL SCIENCES↗