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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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13 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

The Gene Ontology knowledgebase in 2026

Abstract The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgebase is regularly updated and improved. We describe here the major updates that have been made in the past 3 years. The ontology and annotations have been expanded and revised, particularly in several areas of biology: cellular metabolism, multi-organism interactions (e.g. host-pathogen), extracellular matrix proteins, chromatin remodeling (e.g. the “histone code”), and noncoding RNA functions. We have released version 2 of a comprehensive set of integrated, reviewed annotations for human genes, which we call the “functionome.” We have also dramatically increased the number of GO-CAM models, with over 1500 models of metabolic and signaling pathways, primarily in human, mouse, budding and fission yeast, and fruit fly. Finally, we discuss our current recommendations and future prospects of AI in the use and development of GO.

Aleksander, Suzi A (ORCID:0000000167872901)↗
DOE OSTI2024

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Abstract BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

Liu, Tiqing↗
DOE OSTI2024

Path Forward: Materials Data Modernization for ASME Codes and Standards in the Artificial Intelligence Era

Development of the ASME Materials Properties Database was initiated in the early 2010s to support the ASME Codes and Standards. As information technologies advance at an accelerated pace with the artificial intelligence era on the horizon, the ASME Materials Properties Database must be further modernized from a database to a knowledgebase to ride the wave of digital information revolution and effectively support the ASME Codes and Standards in the new era. This paper is intended to provide an overview of the ASME Materials Properties Database and discuss a roadmap for its future development to facilitate understanding of and participation from different sectors of the Codes and Standards community. Further, it first reviews the basic concepts of data, information, knowledge, database, and database system as well as the pros and cons in different types of data management and then discusses the path forward for a desired evolution of the database into a self-explanatory and machine-readable knowledgebase that is consistent with human cognitive processes for the Codes and Standards development and, furthermore, provides resources for data processing and analysis to reach an eventual goal of streamlining the Codes and Standards development from the initial inquiry, throughout data submission, analysis, …, to Codes and Standards rule establishment for final publication.

36 MATERIALS SCIENCE↗
DOE OSTI2025

General Biology 2 Sugar Beet Lab - Spring 24

This module uses the Department of Energy Systems Biology Knowledgebase (KBase) platform to explore topics such as genome assembly, metagenomics, and phylogenomics. Here students will use sequences from DNA that they collected to compare the metagenomes of microbial communities from the rhizosphere of plants grown in fertilized vs. unfertilized soils. Using these data students will evaluate the impact of fertilizer on these communities and how these microbial communities influence soil health and plant growth.

Schirmer, Aaron [Northeastern Illinois University,↗
DOE OSTI2026

Finding the missing pieces: filling gaps that impede the translation of omics data into models

High-throughput omics technologies such as DNA sequencing have made the sequencing and computational assembly of microbial genomes recovered from the environment relatively routine. Computational inference of the protein products encoded by these genomes, and the associated biochemical functions, should enable the accurate prediction and modeling of microbial metabolism, organismal interactions, and ecosystem processes. However, a lack of scalable, probabilistic protein annotation tools limits the full potential of modeling for understanding the metabolism and biogeochemical cycles of microbial communities. Our approach to improve inference of protein annotations and metabolic models relied on learning from and emulating expert manual curation, leveraging software engineering and data science best practices to scale up the throughput and accuracy of annotations and metabolic model construction, building software to objectively evaluate different annotation strategies, and more closely linking the protein annotation and metabolic model inference process. Outcomes of this research include several improved or new computational tools, including DRAM (Distilled and Refined Annotation of Metabolism) for annotating microbial genomes with protein function and metabolic traits, CAMPER (Curated Annotations for Microbial Polyphenol Enzymes and Reactions) for annotating key polyphenol metabolisms, EC-Bench for comprehensive and unbiased benchmarking of annotation tools, and several apps available via the DOE Systems Biology Knowledgebase (KBase) for building genome-scale metabolic models. We demonstrate that these tools allow us to scalably annotate and understand thousands of genomes for microbial communities from a variety of systems and test cases, including rivers, thawing permafrost, and gut microbiomes. All of these computational tools are available as open-source software, with most broadly and easily accessible to the scientific community via KBase apps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

General Biology 2 Sugar Beet Lab - SU2025 - Final

This module uses the Department of Energy Systems Biology Knowledgebase (KBase) platform to explore topics such as genome assembly, metagenomics, and phylogenomics. Here students will use sequences from DNA that they collected to compare the metagenomes of microbial communities from the rhizosphere of plants grown in fertilized vs. unfertilized soils. Using these data students will evaluate the impact of fertilizer on these communities and how these microbial communities influence soil health and plant growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Soil metagenomics umbrella narrative

Implementing accessible, authentic research experiences in introductory courses is challenging, particularly at institutions serving diverse student populations. To address this gap, we developed and deployed a Course-based Undergraduate Research Experience (CURE) focused on plant-microbe interactions in General Biology II at Northeastern Illinois University (NEIU), a minority-serving institution with a diverse student body. Students grew sugar beets (Beta vulgaris), extracted DNA from the rhizoplane, and used the Department of Energy Systems Biology Knowledgebase (KBase) for bioinformatic analysis to compare microbial relative abundance in fertilized versus unfertilized soil. Over five semesters, the CURE engaged 103 students and leveraged the intuitive KBase platform to make complex sequencing data accessible. Pre/post-course survey data revealed significant increases in student self-assessed research skills, including the ability to explain results and determine the types of data to collect. Furthermore, students reported significant gains in confidence related to experimental design and hypothesis development, alongside a strong increase in familiarity with KBase. Informal faculty feedback indicated high student engagement and appreciation for the real-world connections (e.g. food systems, agriculture, and health). This scalable, low-cost model effectively integrates data science tools into the foundational curriculum, demonstrating a potent strategy for boosting research skills and broadening participation in authentic scientific inquiry among diverse undergraduate students.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Elucidating the corrosion mechanism of Ni-based superalloys in the presence of uranium-containing chloride molten salt

The United States Department of Energy (DOE) is committed to the advancement of nuclear reactor technology through initiatives such as the Advanced Reactor Development Program (ARDP), in an effort to diversify the United States energy portfolio towards more sustainable energy options. The ARDP includes demonstration by industry partners of molten chloride fast reactors (MCFRs). Construction of MCFRs requires qualified nuclear structural materials. Unfortunately, there are no current materials that are fully qualified by the Nuclear Regulatory Commission for the construction of molten salt reactors, including MCFRs. Adapting current structural material qualifications requires expansion of our current knowledgebase on the property-performance relationships regarding corrosion performance. In this investigation, we assess microstructural changes in a Ni-based superalloy after exposure to a UCl3¬-containing chloride salt eutectic mixture through a correlated multi-modal approach combining several advanced characterization techniques, including scanning electron microscopy/focused ion beam (SEM/FIB) and transmission electron microscopy (TEM). SEM/FIB analysis will illustrate changes in elemental composition, microstructure, and isotopic information acquired from energy x-ray dispersive spectroscopy (EDS), electron backscatter diffraction (EBSD), and secondary ion mass spectroscopy (SIMS), respectively. This information will then aid in identifying localized regions to elucidate the corrosion mechanism with TEM through a combination of electron diffraction, electron energy loss spectroscopy (EELS), and additional EDS. The findings from this investigation will further expand our assessment of the corrosion performance of structural materials in molten salt chloride systems, aiding to developing fully qualified materials for construction of MCFRs.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Elucidating the corrosion mechanism of commercial Ni-based superalloys in UCl3 containing-chloride molten salt systems

Elucidating the role of UCl3 in the corrosion mechanism of Ni-based superalloys exposed to chloride molten salts Trishelle Copeland-Johnson1, Michael Woods1, Ruchi Gakhar1, Daniel J. Murray1, Guoping Cao1, Lingfeng He1 1Idaho National Laboratory, Idaho Falls, ID, United States The United States Department of Energy (DOE) aims to diversify the domestic energy portfolio towards more sustainable options, including implementation of molten salt reactor (MSR) technology. Chloride molten salts have been investigated as an appropriate MSR coolant and fuel because their relatively inexpensive, abundant, and exhibit favorable thermophysical properties. However, the corrosivity of chloride molten salts have not been extensively studied, especially with the inclusion of actinide products, such as UCl3. Accordingly, the development of nuclear structural materials with excellent corrosion performance is critical to the successful implementation of MSRs, particularly from a mechanistic perspective. In this investigation, we attempt to elucidate the interfacial corrosion mechanism between Ni-based structural materials, such as Inconel 617, and UCl3-containing salt systems through a multi-modal advanced characterization approach, including electron microscopy techniques. The findings from this investigation will expand the knowledgebase of chloride molten salt corrosion of MSR structural materials for strategic property-to-performance design.

36 - MATERIALS SCIENCE↗
DOE OSTI2024

Multi-Modal Characterization of Interfacial Corrosion of Ni-based Alloys in Chloride-based Molten Salts

The United States Department of Energy (DOE) is committed to the advancement of nuclear reactor technology through initiatives such as the Advanced Reactor Development Program (ARDP), to diversify the United States energy portfolio towards more sustainable energy options. The ARDP includes demonstration by industry partners of molten salt fast reactors (MSRs). Construction of molten salt reactor technology requires qualified nuclear structural materials. Unfortunately, there are no current materials that meet current qualification requirements dictated by the Nuclear Regulatory Commission for construction of MSRs. Adapting current structural material qualifications requires expansion of our current knowledgebase on corrosion performance. In this investigation, we assess microstructural changes in a Ni-based superalloy after exposure to a chloride-containing salt system through a correlated multi-modal approach combining several advanced characterization techniques. Namely we will highlight the impact of grain boundary phenomena at the onset of corrosion attack, including the role of intergranular crack propagation and development of internal corrosion products. The findings from this investigation will further expand our assessment of the corrosion performance of structural materials being investigated for construction of MSR components.

36 - MATERIALS SCIENCE↗
DOE OSTI2025

Seven soil endospore forming bacteria from campus woodland fragments

We isolated 7 endospore forming bacteria from campus woodland and sequenced their genomes using Illumina NextSeq. We share the draft genome assemblies for strains Bacillus wiedmanii_SC129, Bacillus pseudomycoides_SC131, Bacillus pumilis_SC133, Peribacillus butanolivorans_SC135, Bacillus thuringiensis_SC136, Priestia megaterium_SC138, and Bacillus wiedmanii_SC141. Draft genomes are between 3645032-5969865 bp and 34.8-41.2 % GC.

59 BASIC BIOLOGICAL SCIENCES↗