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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 OSTI2023

K-RET: knowledgeable biomedical relation extraction system

Abstract Motivation Relation extraction (RE) is a crucial process to deal with the amount of text published daily, e.g. to find missing associations in a database. RE is a text mining task for which the state-of-the-art approaches use bidirectional encoders, namely, BERT. However, state-of-the-art performance may be limited by the lack of efficient external knowledge injection approaches, with a larger impact in the biomedical area given the widespread usage and high quality of biomedical ontologies. This knowledge can propel these systems forward by aiding them in predicting more explainable biomedical associations. With this in mind, we developed K-RET, a novel, knowledgeable biomedical RE system that, for the first time, injects knowledge by handling different types of associations, multiple sources and where to apply it, and multi-token entities. Results We tested K-RET on three independent and open-access corpora (DDI, BC5CDR, and PGR) using four biomedical ontologies handling different entities. K-RET improved state-of-the-art results by 2.68% on average, with the DDI Corpus yielding the most significant boost in performance, from 79.30% to 87.19% in F-measure, representing a P-value of 2.91×10−12. Availability and implementation https://github.com/lasigeBioTM/K-RET.

Sousa, Diana F. (ORCID:0000000305979273)↗
DOE OSTI2024

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Abstract FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The impact of curation errors in the PDBBind Database on machine learning predictions of protein–protein binding affinity

The PDBBind database has been widely utilized for the computational prediction of protein–protein binding affinities. While the accuracy of the PDBBind-curated equilibrium dissociation constants (K D ) has been reported for the protein–ligand subset of the PDBBind database, the curation accuracy has not been reported for the protein–protein subset. Here, we present a detailed manual analysis for the subset of PDBBind records with PubMed Central Open Access primary publications and find that ~19% of these records had K D values that were not supported by their primary publications. The impact of these putative curation errors on the machine learning-based prediction of K D from experimental protein–protein 3D structures was evaluated and correcting the curation errors improved the Pearson correlation coefficient between measured and random forest-predicted log 10 (K D ) values by ~8 percentage points. This finding underscores the importance of dataset accuracy for computational modelling and highlights the need for more stringent curation processes when extracting information from the scientific literature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs

Abstract T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

NP-MRD: the Natural Products Magnetic Resonance Database

The Natural Products Magnetic Resonance Database (NP-MRD) is a comprehensive, freely available electronic resource for the deposition, distribution, searching and retrieval of nuclear magnetic resonance (NMR) data on natural products, metabolites and other biologically derived chemicals. NMR spectroscopy has long been viewed as the ‘gold standard’ for the structure determination of novel natural products and novel metabolites. NMR is also widely used in natural product dereplication and the characterization of biofluid mixtures (metabolomics). All of these NMR applications require large collections of high quality, well-annotated, referential NMR spectra of pure compounds. Unfortunately, referential NMR spectral collections for natural products are quite limited. It is because of the critical need for dedicated, open access natural product NMR resources that the NP-MRD was funded by the National Institute of Health (NIH). Since its launch in 2020, the NP-MRD has grown quickly to become the world's largest repository for NMR data on natural products and other biological substances. It currently contains both structural and NMR data for nearly 41,000 natural product compounds from >7400 different living species. All structural, spectroscopic and descriptive data in the NP-MRD is interactively viewable, searchable and fully downloadable in multiple formats. Extensive hyperlinks to other databases of relevance are also provided. The NP-MRD also supports community deposition of NMR assignments and NMR spectra (1D and 2D) of natural products and related meta-data. The deposition system performs extensive data enrichment, automated data format conversion and spectral/assignment evaluation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

PSInet: a new global water potential network

Abstract Given the pressing challenges posed by climate change, it is crucial to develop a deeper understanding of the impacts of escalating drought and heat stress on terrestrial ecosystems and the vital services they offer. Soil and plant water potential play a pivotal role in governing the dynamics of water within ecosystems and exert direct control over plant function and mortality risk during periods of ecological stress. However, existing observations of water potential suffer from significant limitations, including their sporadic and discontinuous nature, inconsistent representation of relevant spatio-temporal scales and numerous methodological challenges. These limitations hinder the comprehensive and synthetic research needed to enhance our conceptual understanding and predictive models of plant function and survival under limited moisture availability. In this article, we present PSInet (PSI—for the Greek letter Ψ used to denote water potential), a novel collaborative network of researchers and data, designed to bridge the current critical information gap in water potential data. The primary objectives of PSInet are as follows. (i) Establishing the first openly accessible global database for time series of plant and soil water potential measurements, while providing important linkages with other relevant observation networks. (ii) Fostering an inclusive and diverse collaborative environment for all scientists studying water potential in various stages of their careers. (iii) Standardizing methodologies, processing and interpretation of water potential data through the engagement of a global community of scientists, facilitated by the dissemination of standardized protocols, best practices and early career training opportunities. (iv) Facilitating the use of the PSInet database for synthesizing knowledge and addressing prominent gaps in our understanding of plants’ physiological responses to various environmental stressors. The PSInet initiative is integral to meeting the fundamental research challenge of discerning which plant species will thrive and which will be vulnerable in a world undergoing rapid warming and increasing aridification.

Forestry↗
DOE OSTI2021

Genome Assembly and Transcriptome of Colletotrichum sublineola CsGL1, a New Resource to Study Anthracnose Disease in Sorghum

Colletotrichum species are globally distributed and well known as members of a destructive phytopathogenic genus, causing the anthracnose disease in a wide variety of crops and fruits. Colletotrichum sublineola is the causal agent of the anthracnose disease in sorghum, causing losses of up to 50% in yield. Here, we used PacBio sequencing combined with RNA-seq to generate a chromosome-level assembly and annotation of the Colletotrichum sublineola strain CsGL1. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Biochemistry & Molecular Biology↗
DOE OSTI2021

Diazotrophic Bacteria and Their Mechanisms to Interact and Benefit Cereals

Plant-growth-promoting bacteria (PGPB) stimulate plant growth through diverse mechanisms. In addition to biological nitrogen fixation, diazotrophic PGPB can improve nutrient uptake efficiency from the soil, produce and release phytohormones to the host, and confer resistance against pathogens. The genetic determinants that drive the success of biological nitrogen fixation in nonlegume plants are understudied. These determinants include recognition and signaling pathways, bacterial colonization, and genotype specificity between host and bacteria. This review presents recent discoveries of how nitrogen-fixing PGPB interact with cereals and promote plant growth. We suggest adopting an experimental model system, such as the Setaria–diazotrophic bacteria association, as a reliable way to better understand the associated mechanisms and, ultimately, increase the use of PGPB inoculants for sustainable agriculture. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Biochemistry & Molecular Biology↗
DOE OSTI2022

Quantitative Resistance Loci to Southern Rust Mapped in a Temperate Maize Diversity Panel

Southern rust is a severe foliar disease of maize (Zea mays) resulting from infection with the obligate biotrophic fungus Puccinia polysora. This disease reduces photosynthetic productivity, which in turn reduces yields, with the greatest yield losses (up to 50%) associated with earlier onset infections. P. polysora urediniospores overwinter only in tropical and subtropical regions but cause outbreaks when environmental conditions favor initial infection. Increased temperatures and humidity during the growing season combined with an increased frequency of moderate winters are likely to increase the frequency of severe southern rust outbreaks in the U.S. Corn Belt. In summer 2020, a severe outbreak of southern rust was observed in eastern Nebraska, United States. We scored a replicated maize association panel planted in Lincoln, NE for disease severity and found that disease incidence and severity showed significant variation among maize genotypes. Genome-wide association studies identified four loci associated with significant quantitative variation in disease severity. These loci were associated with candidate genes with plausible links to quantitative disease resistance. A transcriptome-wide association study identified additional genes associated with disease severity. Together, these results indicate that substantial diversity in resistance to southern rust exists among current temperate-adapted maize germplasm, including several candidate loci that may explain the observed variation in resistance to southern rust. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Plant Sciences↗
DOE OSTI2021

Infrared surface phonon nanospectroscopy of an interacting dielectric-particle–dielectric-substrate dimer using fast electrons

Refinements in energy monochromation and aberration correction in state-of-the-art scanning transmission electron microscopes has opened access to the far infrared regime for spectroscopic characterization at the nanoscale. At these low energies, the dielectric environment, such as a dielectric slab adjacent to the target specimen, may no longer play a passive role in the spectrum. Instead, the environment may itself host resonances that mix with those of the target and complicate interpretation of its spectral responses. This article explores a theoretical description of the coupling between the collective vibrational surface modes of a dielectric particle and dielectric slab of varying thickness for the purpose of elucidating the interacting phononic excitations in dielectric materials typical of inelastic electron scattering measurements in the infrared. Dynamical coordinates and a governing Hamiltonian are rigorously defined in the quasistatic limit to account for phonon mode mixing and forcing by an aloof electron probe, which travels along a grazing trajectory, parallel to the dielectric slab. As the spectral window of interrogation by fast electron probes has been extended down to thermal energies with unprecedented meV energy resolution, theoretical models like that presented herein are crucial for accurate interpretation of experimental data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Approaching PetaVolts per Meter Plasmonics Using Structured Semiconductors

A newly uncovered class of plasmons in the strongly excited limit opens access to unprecedented Petavolts per meter electromagnetic fields with wide-ranging, transformative impact. Unlike conventional plasmons, such plasmons are constituted by non-perturbative, large-amplitude oscillations of the ultradense, delocalized free electron Fermi gas inherent in conductive media. Here structured semiconductors doped to have an appropriate conduction electron density are introduced to tune the properties of the Fermi gas for matched excitation of large-amplitude plasmons using readily available electron beams which enables immediate experimental validation. Specifically, an electrostatic, surface “crunch-in” plasmon is collisionlessly excited by the beam launched inside a tube. Strong excitation due to matching results in relativistic oscillations of the electron gas and unravels unique phenomena. Relativistically induced ballistic electron transport comes about due to relativistic multifold increase in the mean free path and also leads to unconventional heat deposition beyond Ohm’s law. This explains the absence of observed damage or solid-plasma formation in past experiments on conductive samples interacting with electron bunches shorter than 10-13 seconds. Furthermore, relativistic momentum leads to copious tunneling of electron gas across the surface, which then crunches inside the tube. Relativistic effects along with large, localized electron density variations underlying these modes necessitate kinetic approach to theoretical and computational modeling. Kinetic model presented here demonstrates experimental viability of observing tens of gigavolts per meter plasmonic fields excited by matching readily available electron beams to plasmons in semiconductors with 1018cm-3 free electron density, and paves the way for Petavolts per meter plasmonics.

42 ENGINEERING↗
DOE OSTI2025

Material Needs and Measurement Challenges for Advanced Semiconductor Packaging: Understanding the Soft Side of Science

This Perspective builds upon insights from the National Institute of Standards and Technology (NIST)-organized workshop, “Materials and Metrology Needs for Advanced Semiconductor Packaging Strategies,” held at the 35th annual Electronics Packaging Symposium in Binghamton, NY, on September 5, 2024. It outlines critical challenges and opportunities related to polymer-based “soft” materials in advanced semiconductor packaging, with emphasis on polymer science, measurement science (metrology), and the strategic development of Research-Grade Test Materials (RGTMs). These efforts, led by the NIST CHIPS team, aim to advance the fundamental understanding of structure-property-processing relationships, promote standardized guidelines and innovative methods for material characterization, and accelerate the development, qualification, and adoption of next-generation packaging materials. The Perspective also distills key insights from the panel discussion with industry experts, emphasizing the need for close collaboration among materials scientists, process engineers, and metrology experts to enable a holistic strategy, further highlighting the importance of cross-sector partnerships among industry, academia, and government to address pressing challenges in packaging materials and processes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Thermal Runaway of Li-Ion Cells: How Internal Dynamics, Mass Ejection, and Heat Vary with Cell Geometry and Abuse Type

Thermal runaway of lithium-ion batteries can involve various types of failure mechanisms each with their own unique characteristics. Using fractional thermal runaway calorimetry and high-speed radiography, the response of three different geometries of cylindrical cell (18650, 21700, and D-cell) to different abuse mechanisms (thermal, internal short circuiting, and nail penetration) are quantified and statistically examined. Correlations between the geometry of cells and their thermal behavior are identified, such as increasing heat output per amp-hour (kJ Ah −1 ) of cells with increasing cell diameter during nail penetration. High-speed radiography reveals that the rate of thermal runaway propagation within cells is generally highest for nail penetration where there is a relative increase in rate of propagation with increasing diameter, compared to thermal or internal short-circuiting abuse. For a given cell model tested under the same conditions, a distribution of heat output is observed with a trend of increasing heat output with increased mass ejection. Finally, internal temperature measurements using thermocouples embedded in the penetrating nail are shown to be unreliable thus demonstrating the need for care when using thermocouples where the temperature is rapidly changing. All data used in this manuscript are open access through the NREL and NASA Battery Failure Databank.

25 ENERGY STORAGE↗
DOE OSTI2022

BattPhase—A Convergent, Non-Oscillatory, Efficient Algorithm and Code for Predicting Shape Changes in Lithium Metal Batteries Using Phase-Field Models: Part I. Secondary Current Distribution

Electrochemical models at different scales and varying levels of complexity have been used in the literature to study the evolution of the anode surface in lithium metal batteries. This includes continuum, mesoscale (phase-field approaches), and multiscale models. Thermodynamics-based equations have been used to study phase changes in lithium batteries using phase-field approaches. However, grid convergence studies and the effect of additional parameters needed to simulate these models are not well-documented in the literature. In this paper, using a motivating example of a moving boundary model in one- and two-dimensions, we show how one can formulate phase-field models, implement algorithms for the same and analyze the results. An open-access code with no restrictions is provided as well. This article concludes with some thoughts on the computational efficiency of phase-field models for simulating dendritic growth.

25 ENERGY STORAGE↗
DOE OSTI2020

NLR Engage™: A Calliope Web Environment for Collaborative Energy Systems Modeling and Planning [SWR-20-16]

NLR Engage™ is a free, open-access energy system planning tool that allows multiple users/stakeholders to develop and collaborate on capacity expansion models. The tool, developed at the National Laboratory of the Rockies (NLR), provides a collaborative and easy-to-use interface built on Calliope, a multi-scale energy systems modeling framework. Visit the NLR hosted webtool at https://engage.nlr.gov/en/login/?next=/en/

Harris, Tom↗
DOE OSTI2022

Combined Thermal-Water Microgrid Model

SAND2022-3874 O The Combined Thermal-Water Microgrid Model is a set of three models combined with controls algorithms for a Water Thermal Storage (WTS), Ground Source Heat Pump (GSHP), and Thermal Bridge Loop (TBL) that serves a residential neighborhood. The model allows a parametric investigation of volume of water storage versus number of ground heat exchanger bore-holes versus seasonal energy efficiency measures. The code is being released as open source so that the entire study can be replicated per an open access journal publication. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Villa, Daniel↗
DOE OSTI2026

polars-dovmed (dovmed) v0.1.0

polars-dovmed is a python package for text search and extraction from NCBI's PubMed Central Open Access subset. It is powered by the polars dataframe library and leverages modern file formats (parquet) to efficiently scan public literature.

Roux, Simon [Lawrence Berkeley National Laboratory↗