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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

Chemical structure↗
DOE OSTI2022

Electronic and Spintronic Open-Shell Macromolecules, Quo Vadis ?

Open-shell macromolecules (i.e., polymers containing radical sites either along their backbones or at the pendant sites of repeat units) have attracted significant attention owing to their intriguing chemical and physical (e.g., redox, optoelectronic, and magnetic) properties, and they have been proposed and/or implemented in a wide range of potential applications (e.g., energy storage devices, electronic systems, and spintronic modules). These successes span multiple disciplines that range from advanced macromolecular chemistry through nanoscale structural characterization and on to next-generation solid-state physics and the associated devices. In turn, this has allowed different scientific communities to expand the palette of radical-containing polymers relatively quickly. However, critical gaps remain on many fronts, especially regarding the elucidation of key structure–property–function relationships that govern the underlying electrochemical, optoelectronic, and spin phenomena in these materials systems. Here, we highlight vital developments in the history of open-shell macromolecules to explain the current state of the art in the field. Moreover, we provide a critical review of the successes and bring forward open opportunities that, if solved, could propel this class of materials in a meaningful manner. Finally, we provide an outlook to address where it seems most likely that open-shell macromolecules will go in the coming years. Furthermore, our considered view is that the future of radical-containing polymers is extremely bright and the addition of talented researchers with diverse skills to the field will allow these materials and their end-use devices to have a positive impact on the global science and technology enterprise in a relatively rapid manner.

36 MATERIALS SCIENCE↗
DOE OSTI2019

The Atmospheric River Tracking Method Intercomparison Project (ARTMIP): Quantifying Uncertainties in Atmospheric River Climatology

Atmospheric rivers (ARs) are now widely known for their association with high-impact weather events and long-term water supply in many regions. Researchers within the scientific community have developed numerous methods to identify and track of ARs—a necessary step for analyses on gridded data sets, and objective attribution of impacts to ARs. These different methods have been developed to answer specific research questions and hence use different criteria (e.g., geometry, threshold values of key variables, and time dependence). Furthermore, these methods are often employed using different reanalysis data sets, time periods, and regions of interest. The goal of the Atmospheric River Tracking Method Intercomparison Project (ARTMIP) is to understand and quantify uncertainties in AR science that arise due to differences in these methods. This paper presents results for key AR-related metrics based on 20+ different AR identification and tracking methods applied to Modern-Era Retrospective Analysis for Research and Applications Version 2 reanalysis data from January 1980 through June 2017. We show that AR frequency, duration, and seasonality exhibit a wide range of results, while the meridional distribution of these metrics along selected coastal (but not interior) transects are quite similar across methods. Furthermore, methods are grouped into criteria-based clusters, within which the range of results is reduced. AR case studies and an evaluation of individual method deviation from an all-method mean highlight advantages/disadvantages of certain approaches. For example, methods with less (more) restrictive criteria identify more (less) ARs and AR-related impacts. Finally, this paper concludes with a discussion and recommendations for those conducting AR-related research to consider.

Rutz, Jonathan J.↗
DOE OSTI2020

Medium Energy Electron Flux in Earth's Outer Radiation Belt (MERLIN): A Machine Learning Model

The radiation belts of the Earth, filled with energetic electrons, comprise complex and dynamic systems that pose a significant threat to satellite operation. While various models of electron flux both for low and relativistic energies have been developed, the behavior of medium energy (120–600 keV) electrons, especially in the MEO region, remains poorly quantified. At these energies, electrons are driven by both convective and diffusive transport, and their prediction usually requires sophisticated 4D modeling codes. In this paper, we present an alternative approach using the Light Gradient Boosting (LightGBM) machine learning algorithm. The Medium Energy electRon fLux In Earth's outer radiatioN belt (MERLIN) model takes as input the satellite position, a combination of geomagnetic indices and solar wind parameters including the time history of velocity, and does not use persistence. MERLIN is trained on >15 years of the GPS electron flux data and tested on more than 1.5 years of measurements. Tenfold cross validation yields that the model predicts the MEO radiation environment well, both in terms of dynamics and amplitudes o f flux. Evaluation on the test set shows high correlation between the predicted and observed electron flux (0.8) and low values of absolute error. The MERLIN model can have wide space weather applications, providing information for the scientific community in the form of radiation belts reconstructions, as well as industry for satellite mission design, nowcast of the MEO environment, and surface charging analysis.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Integrated, Coordinated, Open, and Networked (ICON) Science to Advance the Geosciences: Introduction and Synthesis of a Special Collection of Commentary Articles

Abstract The sciences struggle to integrate across disciplines, coordinate across data generation and modeling activities, produce connected open data, and build strong networks to engage stakeholders within and beyond the scientific community. The American Geophysical Union (AGU) is divided into 25 sections intended to encompass the breadth of the geosciences. Here, we introduce a special collection of commentary articles spanning 19 AGU sections on challenges and opportunities associated with the use of ICON science principles. These principles focus on research intentionally designed to be Integrated, Coordinated, Open, and Networked (ICON) with the goal of maximizing mutual benefit (among stakeholders) and cross‐system transferability of science outcomes. This article (a) summarizes the ICON principles; (b) discusses the crowdsourced approach to creating the collection; (c) explores insights from across the articles; and (d) proposes steps forward. There were common themes among the commentary articles, including broad agreement that the benefits of using ICON principles outweigh the costs, but that using ICON principles has important risks that need to be understood and mitigated. It was also clear that the ICON principles are not monolithic or static, but should instead be considered a heuristic tool that can and should be modified to meet changing needs. As a whole, the collection is intended as a resource for scientists pursuing ICON science and represents an important inflection point in which the geosciences community has come together to offer insights into ICON principles as a unified approach for improving how science is done across the geosciences and beyond.

Goldman, A. E.↗
DOE OSTI2022

Volcanology, Geochemistry, and Petrology Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science

This article is composed of a commentary about the state of Integrated, Coordinated, Open, and Networked (ICON) principles in Volcanology, Geochemistry, and Petrology (VGP), and discussion on the opportunities and challenges of adopting them. VGP encompasses a broad field that addresses volcanic, magmatic, hydrothermal, geomicrobial systems; process investigations that span the physical, geochemical and biological realms, including planetary geology; and one that is extensively supported by state-of-the-art research facilities. We suggest that an open, inclusive, collaborative and evolving model of an international coordinated network is critical to answering the most pressing challenges in VGP. In this commentary piece, we begin to discuss the elements of, challenges to, and path forward in developing such a model. For this team, ICON means collaboration, equitable access to data for the entire scientific community, and forging of partnerships that potentially contribute to more innovative ways of coordinating and sharing research. It also means bringing more equity to science, by implementing effective measures which consider access to funding, analytical equipment, resources, and mentors. More importantly, ICON to us means having important conversations around what we value in the advancement of science, perhaps exploring outside the idea of meritocracy and evaluating what individual traits can contribute to science outside what has traditionally been considered the norm.

58 GEOSCIENCES↗
DOE OSTI2023

60 Years and Beyond of Reviews of Geophysics

Reviews of Geophysics is an AGU journal, first established in February 1963. It is a hybrid open access invitation-only journal that publishes comprehensive review articles across various disciplines within the Earth and Space Sciences. The selection criteria are rigorous and many submissions are declined without review. The journal is the highest ranked in the fields of Geochemistry and Geophysics, with a high Journal Impact Factor (JIF 2021 = 24.9), which is indicative of its high visibility and influence within the scientific community. The journal's published review papers, beyond a mere summary of literature, provide crucial context for current work, and establish the framework for comprehensive understanding of research progress, challenges, and interconnections between different communities, so that research may be appreciated by a broad audience. Finally, we emphasize the importance of publishing studies that provide a comprehensive overview and synthesis of the current state of knowledge in a field, especially in the case of geophysics, where knowledge is rapidly developing, increasing and becoming more specialized.

58 GEOSCIENCES↗
DOE OSTI2025

Early Career Perspectives to Broaden the Scope of Critical Zone Science

Abstract Critical Zone (CZ) scientists have advanced understanding of Earth's surface through process‐based research that quantifies water, energy, and mass fluxes in predominantly undisturbed systems. However, the CZ is being increasingly altered by humans through climate and land use change. Expanding the scope of CZ science to include both human‐ and non‐human controls on the CZ is important for understanding anthropogenic impacts to Earth's surface processes and ecosystem services. Here, we share perspectives from predominantly U.S.‐based, early career CZ scientists centered around broadening the scope of CZ science to focus on societally relevant science through a transdisciplinary science framework. We call for increased training on transdisciplinary methods and collaboration opportunities across disciplines and with stakeholders to foster a scientific community that values transdisciplinary science alongside physical science. Here, we build on existing transdisciplinary research frameworks by highlighting the need for institutional support to include and educate graduate students throughout the research processes. We also call for graduate‐student‐led initiatives to increase their own exposure to transdisciplinary science through activities such as transdisciplinary‐focused seminars and symposiums, volunteering with local conservation groups, and participating in internships outside academia.

Warix, Sara [University of Utah Department of Geol↗
DOE OSTI2025

Mesoscale Cellular Convection Detection and Classification Using Convolutional Neural Networks: Insights From Long-Term Observations at ARM Eastern North Atlantic Site

Marine boundary layer clouds are crucial in Earth's climate system. They frequently manifest as closed or open cell mesoscale cellular convection (MCC). MCC clouds are challenging to represent accurately in current climate models, highlighting the need for detailed observational data sets and in-depth analyses. This study utilizes over 8 years of observations from the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) User Facility Eastern North Atlantic (ENA) site at Graciosa Island, Azores, to investigate these clouds. We first apply a convolutional neural network with a U-Net architecture to classify open and closed cells, marking the first application of such an approach for automatically detecting MCC patterns from ground-based radar measurements. This method addresses some observational gaps in satellite data related to low temporal resolution, nighttime challenges, and limited vertical structure capture. The analysis of the MCC cases shows clear differences between closed and open MCCs: Closed MCC clouds are characterized by lower cloud tops and bases, shallower cloud geometrical depth, weaker horizontal wind speeds, stronger atmospheric stability, and a more homogeneous liquid water path than open MCCs. Finally, we demonstrate two potential applications of our radar-based MCC classifications: (a) facilitating the investigation of aerosol-cloud interactions and (b) exploring meteorological factors along with MCC's evolution by integrating satellite imagery and back-trajectory analysis. The identified MCC cases offer a valuable resource for the scientific community to study MCC processes further and improve climate model accuracy.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The P132H mutation in the main protease of Omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition

The ongoing SARS-CoV-2 pandemic continues to be a significant threat to global health. First reported in November 2021, the Omicron variant (B.1.1.529) is more transmissible and can evade immunity better than previous SARS-CoV-2 variants, fueling an unprecedented surge in cases. To produce functional proteins from its polyprotein, SARS-CoV-2 relies on the cysteine proteases Nsp3/papain-like protease (PL pro ) and Nsp5/main protease (M pro )/3C-like protease to cleave at three and more than 11 sites, respectively. Therefore, M pro and PL pro inhibitors are considered to be one of the most promising SARS-CoV-2 antivirals. On December 22, 2021, the Food and Drug Administration (FDA) issued an Emergency Use Authorization (EUA) for PAXLOVID, a ritonavir-boosted formulation of nirmatrelvir. Nirmatrelvir is a first-in-class orally bioavailable SARS-CoV-2 M pro inhibitor. Thus, the scientific community must vigilantly monitor potential mechanisms of drug resistance, especially because SARS-CoV-2 is naïve to M pro inhibitors. Mutations have been well identified in variants to this point. Notably, Omicron M pro (OM pro ) harbors a single mutation—P132H. Here, we characterized the enzymatic activity, drug inhibition, and structure of OM pro while evaluating the past and future implications of M pro mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Future changes in the trading of virtual water

Water stressed regions rely heavily on the import of water-intensive goods to offset insufficient food production driven by socioeconomic and environmental factors. The water embedded in these traded commodities, virtual water, has received increasing interest in the scientific community. However, comprehensive future projections of virtual water trading remain absent. Here we show, for the first time, changes over the 21st century in the amount of various water types required to meet international agricultural demands. Accounting for evolution in socioeconomic and climatic conditions, we estimate future interregional virtual water trading and find trading of renewable water sources may triple by 2100 while nonrenewable groundwater trading may at least double. Basins in North America, and the La Plata and Nile Rivers are found to contribute extensively to virtual water exports, while much of Africa, India, and the Middle East relies heavily on virtual water imports by the end of the century.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Heterogenous electromediated depolymerization of highly crystalline polyoxymethylene

Abstract Post-consumer plastic waste in the environment has driven the scientific community to develop deconstruction methods that yield valued substances from these synthetic macromolecules. Electrocatalysis is a well-established method for achieving challenging transformations in small molecule synthesis. Here we present the first electro-chemical depolymerization of polyoxymethylene—a highly crystalline engineering thermoplastic (Delrin®)—into its repolymerizable monomer, formaldehyde/1,3,5-trioxane, under ambient conditions. We investigate this electrochemical deconstruction by employing solvent screening, cyclic voltammetry, divided cell studies, electrolysis with redox mediators, small molecule model studies, and control experiments. Our findings determine that the reaction proceeds via a heterogeneous electro-mediated acid depolymerization mechanism. The bifunctional role of the co-solvent 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) is also revealed. This study demonstrates the potential of electromediated depolymerization serving as an important role in sustainable chemistry by merging the concepts of renewable energy and circular plastic economy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Storylines for unprecedented heatwaves based on ensemble boosting

Recent temperature extremes have shattered previously observed records, reaching intensities that were inconceivable before the events. Could the possibility of an event with such unprecedented intensity as the 2021 Pacific Northwest heatwave have been foreseen, based on climate model information available before the event? Could the scientific community have quantified its potential intensity based on the current generation of climate models? Here, we demonstrate how an ensemble boosting approach can be used to generate physically plausible storylines of a heatwave hotter than observed in the Pacific Northwest. We also show that heatwaves of much greater intensities than ever observed are possible in other locations like the Greater Chicago and Paris regions. In order to establish confidence in storylines of ‘black swan’-type events, different lines of evidence need to be combined along with process understanding to make this information robust and actionable for stakeholders.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Ferroelectricity in hafnia controlled via surface electrochemical state

Ferroelectricity in binary oxides including hafnia and zirconia has riveted the attention of the scientific community due to the highly unconventional physical mechanisms and the potential for the integration of these materials into semiconductor workflows. Over the last decade, it has been argued that behaviours such as wake-up phenomena and an extreme sensitivity to electrode and processing conditions suggest that ferroelectricity in these materials is strongly influenced by other factors, including electrochemical boundary conditions and strain. Here we argue that the properties of these materials emerge due to the interplay between the bulk competition between ferroelectric and structural instabilities, similar to that in classical antiferroelectrics, coupled with non-local screening mediated by the finite density of states at surfaces and internal interfaces. Via the decoupling of electrochemical and electrostatic controls, realized via environmental and ultra-high vacuum piezoresponse force microscopy, we show that these materials demonstrate a rich spectrum of ferroic behaviours including partial-pressure-induced and temperature-induced transitions between ferroelectric and antiferroelectric behaviours. In conclusion, these behaviours are consistent with an antiferroionic model and suggest strategies for hafnia-based device optimization.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Roadmap for naming uncultivated Archaea and Bacteria

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Perspectives on ENCODE

The Encyclopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression. The project has been extended to model organisms, particularly the mouse. Finally, in the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Expanded encyclopaedias of DNA elements in the human and mouse genomes

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A compendium of human gene functions derived from evolutionary modelling

A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating a structured body of information about gene functions, which now includes experimental findings reported in more than 175,000 publications for human genes and genes in experimentally tractable model organisms 1,2 . Here, we describe the results of a large, international effort to integrate all of these findings to create a representation of human gene functions that is as complete and accurate as possible. Specifically, we apply an expert-curated, explicit evolutionary modelling approach to all human protein-coding genes. This approach integrates available experimental information across families of related genes into models that reconstruct the gain and loss of functional characteristics over evolutionary time. The models and the resulting set of 68,667 integrated gene functions cover approximately 82% of human protein-coding genes. The functional repertoire reveals a marked preponderance of molecular regulatory functions, and the models provide insights into the evolutionary origins of human gene functions. We show that our set of descriptions of functions can improve the widely used genomic technique of Gene Ontology enrichment analysis. The experimental evidence for each functional characteristic is recorded, thereby enabling the scientific community to help review and improve the resource, which we have made publicly available.

59 BASIC BIOLOGICAL SCIENCES↗