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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection

Mycobacterium tuberculosis is one of the most consequential human bacterial pathogens, posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its ability to adapt its transcriptional response to environmental stresses through its transcriptional regulatory network (TRN). While many studies have sought to characterize specific portions of the M. tuberculosis TRN, and some studies have performed system-level analysis, few have been able to provide a network-based model of the TRN that also provides the relative shifts in transcriptional regulator activity triggered by changing environments. Here, we compiled a compendium of nearly 650 publicly available, high quality M. tuberculosis RNA-sequencing data sets and applied an unsupervised machine learning method to obtain a quantitative, top-down TRN. It consists of 80 independently modulated gene sets known as “iModulons,” 41 of which correspond to known regulons. These iModulons explain 61% of the variance in the organism’s transcriptional response. We show that iModulons (i) reveal the function of poorly characterized regulons, (ii) describe the transcriptional shifts that occur during environmental changes such as shifting carbon sources, oxidative stress, and infection events, and (iii) identify intrinsic clusters of regulons that link several important metabolic systems, including lipid, cholesterol, and sulfur metabolism. This transcriptome-wide analysis of the M. tuberculosis TRN informs future research on effective ways to study and manipulate its transcriptional regulation and presents a knowledge-enhanced database of all published high-quality RNA-seq data for this organism to date.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Mapping the soil microbiome functions shaping wetland methane emissions

Accounting for only 8% of Earth’s land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.

MAG↗
DOE OSTI2024

Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440

ABSTRACT There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules (“functional modules”), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida . Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

09 BIOMASS FUELS↗
DOE OSTI2025

Moltensaltpropnet

MoltenSaltPropnet is a physics-informed machine learning framework that aims to predict the thermophysical properties of molten fluoride and chloride salt mixtures, which are crucial for the design and safety of Generation IV molten salt reactors. The code processes data from the Molten-Salt Thermal Properties Database (MSTDB-TP) and the Janz compendium, converting critically evaluated correlations into fast, differentiable surrogate models for density, viscosity, thermal conductivity, and heat capacity across 448 distinct salt systems. The implementation consists of several key components: 1. Data Curation: The code parses and cleans the raw data, normalizing elemental mole fractions and extracting relevant regression coefficients for various thermophysical properties. 2. Feature Engineering: It generates fixed-length numerical descriptors that encapsulate the composition and temperature, incorporating polynomial interaction terms and dimensionality-reduction techniques to optimize model performance. 3. Coefficient Learning: Four different machine learning architectures are employed: a deep residual network (ResNet), a Kolmogorov–Arnold network (KAN), a sparsity-inducing neural network (SNN), and classical regression models. Each model learns to predict coefficients that define the temperature-dependent correlations for the thermophysical properties. 4. Property Reconstruction: The predicted coefficients are used to compute temperature-dependent property values, ensuring positivity and monotonic trends through a composite loss function that enforces physical constraints. 5. User Interface: An open-source web application enables users to filter the database, train task-specific models, and visualize the results, allowing for rapid exploration of candidate salt mixtures. MoltenSaltPropnet bridges the gap between limited experimental data and high-fidelity reactor simulations, providing a powerful tool for researchers in the field of molten salt reactors and advanced nuclear energy systems.

Retamales, Mauricio Eduardo Tano [Idaho National L↗
DOE OSTI2026

NuMaCo

The Nuclear Material and Composition (NuMaCo) server is a web-based platform for storing, managing, and serving material composition data. It includes the SCALE Standard Composition Library and the PNNL Compendium, along with their associated references and uncertainty data. NuMaCo also provides tools to generate, compare, and validate material input definitions for both SCALE and MCNP.

Skutnik, Steve (000000016441135X)↗
DOE OSTI2021

Gene co-expression network analysis in zebrafish reveals chemical class specific modules

Zebrafish is a popular animal model used for high-throughput screening of chemical hazards, however, investigations of transcriptomic mechanisms of toxicity are still needed. Here, our goal was to identify genes and biological pathways that Aryl Hydrocarbon Receptor 2 (AHR2) Activators and flame retardant chemicals (FRCs) alter in developing zebrafish. Taking advantage of a compendium of phenotypically-anchored RNA sequencing data collected from 48-h post fertilization (hpf) zebrafish, we inferred a co-expression network that grouped genes based on their transcriptional response. Genes responding to the FRCs and AHR2 Activators localized to distinct regions of the network, with FRCs inducing a broader response related to neurobehavior. AHR2 Activators centered in one region related to chemical stress responses. We also discovered several highly co-expressed genes in this module, including cyp1a, and we subsequently show that these genes are definitively within the AHR2 signaling pathway. Systematic removal of the two chemical types from the data, and analysis of network changes identified neurogenesis associated with FRCs, and regulation of vascular development associated with both chemical classes. We also identified highly connected genes responding specifically to each class that are potential biomarkers of exposure. Overall, we created the first zebrafish chemical-specific gene co-expression network illuminating how chemicals alter the transcriptome relative to each other. In addition to our conclusions regarding FRCs and AHR2 Activators, our network can be leveraged by other studies investigating chemical mechanisms of toxicity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Knowledge Beacons: Web services for data harvesting of distributed biomedical knowledge

The continually expanding distributed global compendium of biomedical knowledge is diffuse, heterogeneous and huge, posing a serious challenge for biomedical researchers in knowledge harvesting: accessing, compiling, integrating and interpreting data, information and knowledge. In order to accelerate research towards effective medical treatments and optimizing health, it is critical that efficient and automated tools for identifying key research concepts and their experimentally discovered interrelationships are developed. As an activity within the feasibility phase of a project called “Translator” (https://ncats.nih.gov/translator) funded by the National Center for Advancing Translational Sciences (NCATS) to develop a biomedical science knowledge management platform, we designed a Representational State Transfer (REST) web services Application Programming Interface (API) specification, which we call a Knowledge Beacon. Knowledge Beacons provide a standardized basic API for the discovery of concepts, their relationships and associated supporting evidence from distributed online repositories of biomedical knowledge. This specification also enforces the annotation of knowledge concepts and statements to the NCATS endorsed the Biolink Model data model and semantic encoding standards (https://biolink.github.io/biolink-model/). Implementation of this API on top of diverse knowledge sources potentially enables their uniform integration behind client software which will facilitate research access and integration of biomedical knowledge.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2026

Optical Vibrational Spectroscopic Investigation of Natural and Synthetic Analogs of Uranyl Oxyhydroxyhydrate Minerals

Uranyl oxy-hydroxy-hydrate minerals are common alteration products of uraninite (UO2+x) which is chemically and structurally analogous to uranium dioxide nuclear fuel. Therefore, structural and spectroscopic investigations of these alteration minerals and their analogous anthropogenic counterparts can provide insight into the environmental behavior of nuclear fuel cycle materials. Previously, we compiled available vibrational spectroscopic data for uranyl minerals in the Compendium of Uranium Raman and Infrared Experimental Spectra (CURIES) and found that only 37% of known uranyl oxy-hydroxy-hydrate minerals had spectra readily available in the literature and existing databases for inclusion therein. Furthermore, no available infrared spectra for this mineral group were included in CURIES. To expand our understanding of the spectroscopic features of uranyl oxy-hydroxy-hydrates and the structural origins thereof, we collected, and now include in CURIES, Raman and infrared spectra for an additional 12 uranyl hydroxide phases. To better understand the impact of structural and compositional variations of these phases on their spectroscopic features, we compare Raman spectra of different anion sheet topological groups and of analogous phases hosting different counter cations. We identify spectroscopic variations related to differences in equatorial bonding and structural changes as a result of cation substitution. We also prepare a uranyl hydroxide phase via hydrolysis of uranyl fluoride (UO2F2) as an analog of hydrolysis reactions that occur in nuclear fuel cycle materials; and we find that the alteration product of UO2F2, despite chemical and structural similarities to uranyl oxy-hydroxy-hydrate minerals, is readily distinguishable from related mineral phases using Raman spectroscopy. In this work, we provide new insights into the structural origins of spectroscopic features in uranyl oxy-hydroxy-hydrate minerals, improve the average Raman spectrum for this group of minerals, and thereby improve capabilities for identifying these mineral species and related anthropogenic phases using Raman spectroscopy.

Barth, Brodie [ORNL] (ORCID:0000000256142601)↗
DOE OSTI2020

Transportation Energy Data Book: Edition 38

The Transportation Energy Data Book: Edition 38 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available via the Internet. This edition of the Data Book has 13 chapters which focus on various aspects of the transportation industry. Chapter 1 - focuses on petroleum; Chapter 2 - energy; Chapter 3 - highway vehicles; Chapter 4 - light vehicles; Chapter 5 - heavy vehicles; Chapter 6 - alternative fuel vehicles; Chapter 7 - transit and shared mobility; Chapter 8 - fleet vehicles; Chapter 9 - household vehicles; Chapter 10 - nonhighway modes; Chapter 11 - transportation and the economy; Chapter 12 - greenhouse gas emissions; and Chapter 13 - criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and energy tables and figures with electricity generation and distribution taken into account. A glossary of terms is also included for the reader’s convenience.

02 PETROLEUM↗
DOE OSTI2021

Transportation Energy Data Book: Edition 39

The Transportation Energy Data Book: Edition 39 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available via the Internet (tedb.ornl.gov).This edition of the Data Book has 13 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 – energy; Chapter 3 – highway vehicles; Chapter 4 – light vehicles; Chapter 5 – heavy vehicles; Chapter 6 – alternative fuel vehicles; Chapter 7 – transit and other shared mobility; Chapter 8 – fleet vehicles; Chapter 9 – household vehicles; Chapter 10 – nonhighway modes; Chapter 11 – transportation and the economy; Chapter 12 – greenhouse gas emissions; and Chapter 13 – criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and energy tables with electricity generation and distribution. A glossary of terms is also included for the reader’s convenience.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

Transportation Energy Data Book (Edition 40)

The Transportation Energy Data Book: Edition 40 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available via the Internet (tedb.ornl.gov).This edition of the Data Book has 13 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 – energy; Chapter 3 – highway vehicles; Chapter 4 – light vehicles; Chapter 5 – heavy vehicles; Chapter 6 – alternative fuel vehicles; Chapter 7 – transit and other shared mobility; Chapter 8 – fleet vehicles; Chapter 9 – household vehicles; Chapter 10 – nonhighway modes; Chapter 11 – transportation and the economy; Chapter 12 – greenhouse gas emissions; and Chapter 13 – criteria pollutant emissions. The sources used represent the latest available data. There are also two appendices which include detailed source information for some tables and measures of conversion. A glossary of terms is also included for the reader’s convenience.

02 PETROLEUM↗
DOE OSTI2020

Status of the Atlas of Neutron Resonances [Slides]

The Atlas of Neutron Resonances is the most comprehensive compilation of neutron resonances, thermal cross sections, resonance integrals and Maxwellian averaged cross sections generally available. For decades, the Atlas was carefully curated and maintained by Dr. Said Mughabghab who sadly passed on during the summer of 2018 after publishing the 2018 edition of the Atlas . We are continuing the development of this important compendium. To a large extent, the Atlas book is generated from a series of text files given in a single purpose domain-specific format. Therefore, we developed a software API and began the systematic assessment of the Atlas files. With this work past, we are now focusing on new efforts to expand the quality and scope of the Atlas . Current and recently completed projects include a cross comparison of the Atlas bibliography with Nuclear Science References and the EXFOR data library, a better determination of average resonance parameters, and using machine learning to assess the correctness of the spin group assignments of resonances tabulated in the Atlas .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

MCNP ® Code Version 6.3.0 Verification & Validation Testing

This report describes the verification and validation testing performed on MCNP ® code version 6.3.0. The purpose of this report is to act as a compendium of test suite descriptions and results. Accordingly the document is divided into two parts. Part I (this part) describes each test suite in the following sections. Part II provides the results of testing each suite and comparisons to experimental and/or alternative computational results, as appropriate.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Volume 6: Experiment Facility Spectrum Tailoring (HFIR Futures – Enhanced Capabilities Series)

In-core irradiation experiment research, such as materials and fuels irradiation research and radioisotope production, is one of the primary missions of Oak Ridge National Laboratory’s (ORNL) versatile High Flux Isotope Reactor (HFIR). In support of the HFIR-Sustaining and Enhancing Neutron Science (SENSe) Initiative, a technically diverse group of ORNL irradiation research subject matter experts formed the Spectrum Tailoring Working Group, with the goal of developing a compendium of experiment facility concepts to enhance irradiation experiment conditions via neutron spectrum tailoring capabilities. The purpose of this report is to document the concepts developed in FY22 and the associated scientific justifications, identify potential facility sponsors, and estimate costs and schedules for each concept. This report documents the efforts performed in FY22, which may continue in FY23 or later pending the direction of the HFIR-SENSe Initiative and the interested sponsors.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2023

Performance Assessment Maintenance Plan for the Active Low-Level Burial Ground Trenches 31, 34, and 94 at the Hanford Site

This report documents the maintenance plan for the Hanford Site 200 West Area Active Low-Level Burial Ground Trenches 31 and 34 and 200 East Area Active Trench 94 performance assessment (PA). The PA maintenance plan is one of several supporting documents that are compendiums to the active trenches (Trenches 31, 34, and 94) PA as required in DOE O 435.1, Radioactive Waste Management . The PA is documented in DOE/RL-2021-26, Performance Assessment of Active Trenches in 200 East and West Low-Level Burial Grounds at the Hanford Site . This plan follows the requirements and outline specified in the applicable U.S. Department of Energy (DOE) standard used for developing documents supporting DOE-STD-5002-2017, Disposal Authorization Statement and Tank Closure Documentation . This maintenance plan summarizes the following major activities DOE plans to conduct to maintain the Trenches 31, 34, and 94 PA: Monitoring; Research and development; Planned reviews and analyses; Revisions of Trenches 31, 34, and 94 PA. The planned research and development activities relate to evaluating the key assumptions, including evaluating conceptual model assumptions and parameter value assumptions used in the PA. The planned research and development activities include those that are designed to track the release mechanisms for Category 1, Category 3, and uranium billet waste sources, as well as continued characterization and related modeling of the natural environment in the Central Plateau of the Hanford Site. In addition, the planned research and development activities include focused testing and evaluation of engineered and natural materials to reduce the uncertainty in the conceptual models and parameter values used in the PA. All key and secondary issues identified during the review of the PA by the Low-Level Waste Disposal Facility Federal Review Group have been resolved prior to finalization of the PA. There are no outstanding issues.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Update on Activities Related to the Library of Graphite Microstructures

This report provides an overview and update of the ongoing efforts to create a comprehensive library of microstructures for nuclear graphite and carbon-based materials under consideration for nuclear applications. The library includes data on microstructural characterization of unirradiated graphite materials, a guide to the techniques used to analyze graphite (which complements the ASME guidelines and ASTM standards), a summary of characterization data for neutron-irradiated or oxidized material, and a compendium of microstructural information for carbon-based materials. These efforts are being conducted at various length scales for the filler and binder phases in graphite to better understand graphite’s local structure and property relationships. This report is a follow-up to the previous milestone report titled Report on initial development of a database of nuclear graphite characteristics based on microstructural characterization, ORNL/TM/-2023/2992, published in July 2023.The effort to develop the library of microstructures supports the US Department of Energy Office of Advanced Reactor Technologies program objectives of aiding the material selection, licensing, management, and core assessments of a graphite core by documenting the unirradiated microstructure of relevant grades or characterizing the microstructure’s evolution under the reactor environment. Additionally, this project aims to provide (1) information and guidelines for the characterizing of graphite and (2) a protocol to assess a nuclear graphite grade.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Establishing and Maintaining Engagement for a Distributional Equity Analysis [Slides]

The Distributional Equity Analysis (DEA) is an analytical framework that allows for the evaluation of the distributional equity of utility resource investments in combination with benefit-cost analysis. This guide serves as a resource for organizations to develop an engagement strategy for a DEA that is accessible, inclusive, and grounded in community interests. It is organized by the guiding principles of engagement for a DEA, summarized in the figure on the right, and offers a compendium of resources for further support and learning.

24 POWER TRANSMISSION AND DISTRIBUTION↗