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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 19 records

Roadmap on thermodynamics and thermal metamaterials

Thermal metamaterials represent a transformative paradigm in modern physics, synergizing thermodynamic principles with metamaterial engineering to master heat flow at will. As next-generation technologies demand multi-scale thermal control, this field urgently requires systematic frameworks to unify its multidisciplinary advances. Curated through a global collaboration involving over 50 specialists across 25 subdisciplines, this review primarily summarizes two decades of advancements, ranging from theoretical breakthroughs to functional implementations. The review reveals groundbreaking innovations in heat manipulation through the exploration of both classical and non-classical transport regimes, topological thermal control mechanisms, and quantum-informed phonon engineering strategies. By bridging physical insights like non-Hermitian thermal dynamics and valleytronic phonon transport with cutting-edge applications, we demonstrate paradigm-shifting capabilities: environment-adaptive thermal cloaks, AI-optimized metamaterials, and nonlinear thermal circuits enabling heat-based computation. Experimental milestones include 3D thermal null media with reconfigurable invisibility and thermal designs breaking classical conductivity limits. Here, this collaborative effort establishes an indispensable roadmap for physicists, highlighting pathways to quantum thermal management, entropy-controlled energy systems, and topological devices. As thermal metamaterials transition from laboratory marvels to technological cornerstones, this work provides the foundational lexicon and design principles for the coming era of intelligent thermal matter.

heat conduction control↗

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗

National Virtual Biotechnology Laboratory: Report on Rapid R&D Solutions to the COVID-19 Crisis

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply short ages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. Within months, NVBL teams produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment (PPE), creating nearly 1,000 new jobs. They used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported U.S. Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDC), and U.S. Department of Defense (DoD) efforts to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. NVBL teams also studied how to control indoor virus movement to minimize uptake and protect human health. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development (R&D) solutions. As the fight against COVID continues, sustained efforts are needed to confront this pandemic as well as future threats. Examples include: 1) Establishing “supply chains on demand” to meet emergency production needs by leveraging the materials and manufacturing expertise of DOE national laboratories and developing advances in electronics, sensing, robotics, and automation capabilities; 2) Improving the speed and robustness of drug discovery by integrating experimental platforms with DOE’s computational and experimental user facilities, which provide unique resources to support the discovery of high-potential therapeutic agents; 3) Protecting public, environmental, and animal health by developing new testing protocols and instrumentation adaptable to diverse sample types (both physiological and environmental) to quickly detect a wide range of pathogens and monitor other biorisks; 4) Supporting near-real-time data needs of decision-makers at the local, regional, state, and national levels by advancing data curation, analysis, and modeling using artificial intelligence and new data science tools for managing and evaluating large diverse datasets; 5) Harnessing DOE’s expertise in environmental modeling to design rooms and air handling for offices, classrooms, restaurants, and other structures to minimize biorisk transmissions. Going forward, NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, the Office of Science will continue to be an integral component of agency wide efforts to prepare for and respond to biorisks and other crises.

42 ENGINEERING↗

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

Abstract Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI’s ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.

60 APPLIED LIFE SCIENCES↗

Fusion Imaging and Virtual Navigation to Guide Percutaneous Thermal Ablation of Hepatocellular Carcinoma: A Review of the Literature

As medical imaging advancements have improved the detectability of hepatocellular carcinoma (HCC) in early stages, the approach to percutaneous thermal ablation for curative treatment has concomitantly advanced. Although many centers are adopting cross-sectional imaging to guide percutaneous ablation, the majority of procedures are still performed under ultrasound (US) guidance worldwide. Challenges to ultrasound guidance may present due to relatively poor resolution particularly with small or isoechoic lesions, or due to intervening structures such as the bowel or diaphragm that obstruct lesional visualization. Fusion imaging (FI) systems have been employed to address these challenges. By merging or synchronizing the real-time images from US with a previously obtained cross-sectional study, FI mitigates the inherent limitations of each individual imaging modality and expands procedural feasibility and technical outcomes. This manuscript reviews the current literature on the use of FI during percutaneous thermal ablation of HCC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Community Requirements Meta-Analysis: Characterizing Needs and Opportunities for HPDF

This High Performance Data Facility (HPDF) Project is creating a new scientific user facility to provide advanced infrastructure for data-intensive science, supporting the DOE’s Office of Science (SC) community. HPDF’s mission is to enable and accelerate scientific discovery by delivering state-of-the-art data management infrastructure, capabilities, and tools. This meta-analysis examines the needs of the breadth of the SC community, captured in publicly available community reports or mission documents. The meta-analysis identifies and provides initial characterization of fifteen core requirements for the HPDF Project team to consider during the conceptual design phase. The fifteen requirements illustrate how scientific work among SC communities requires modern, seamless user experiences across the ASCR Ecosystem to advance the use of large volumes of heterogeneous data. The scientific community requires support for the missing middle of compute between local and HPC to interactively and collaboratively use growing datasets. Data producers and end users will benefit from enhanced data catalogs and portals that improve data access through advanced search of well curated data. The fifteen requirements are examined here organized across five themes for discussion. Examples in each theme illustrate the array of scientific needs that convey the important role that the fully realized and operational High Performance Data Facility will be able to play as an integral part of the evolving ASCR Ecosystem. Our amalgamated data tables from ESnet reports demonstrate ranges to the volumes of data HPDF must be concerned with, but limitations are inherent to this meta-analysis (see Key Challenges & Limitations). Feedback and validation of these requirements along with additional details and emergent community requirements will be gathered through user research and design activities.

97 MATHEMATICS AND COMPUTING↗

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. Furthermore, we observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

97 MATHEMATICS AND COMPUTING↗

GraphAide: Advanced Graph-Assisted Query and Reasoning System

Curating knowledge from multiple siloed sources that contain both structured and unstructured data is a major challenge in many real-world applications. Pattern matching and querying represent fundamental tasks in modern data analytics that leverage this curated knowledge. The development of such applications necessitates overcoming several research challenges, including data extraction, named entity recognition, data modeling, and designing query interfaces. Moreover, the explainability of these functionalities is critical for their broader adoption. The emergence of Large Language Models (LLMs) has accelerated the development lifecycle of new capabilities. Nonetheless, there is an ongoing need for domain-specific tools tailored to user activities. The creation of digital assistants has gained considerable traction in recent years, with LLMs offering a promising avenue to develop such assistants utilizing domain-specific knowledge and assumptions. In this context, we introduce an advanced query and reasoning system, GraphAide, which constructs a knowledge graph (KG) from diverse sources and allows to query and reason over the resulting KG. GraphAide harnesses both the KG and LLMs to rapidly develop domain-specific digital assistants. It integrates design patterns from retrieval augmented generation (RAG) and the semantic web to create an agentic LLM application. GraphAide underscores the potential for streamlined and efficient development of specialized digital assistants, thereby enhancing their applicability across various domains.

Purohit, Sumit [BATTELLE (PACIFIC NW LAB)] (ORCID:↗

A Cast of Thousands: How the IDEAS Productivity Project Has Advanced Software Productivity and Sustainability

Computational and data-enabled science and engineering are revolutionizing advances throughout science and society, at all scales of computing. For example, teams in the U.S. Department of Energy’s Exascale Computing Project have been tackling new frontiers in modeling, simulation, and analysis by exploiting unprecedented exascale computing capabilities—building an advanced software ecosystem that supports next-generation applications and addresses disruptive changes in computer architectures. However, concerns are growing about the productivity of the developers of scientific software. Members of the Interoperable Design of Extreme-scale Application Software project serve as catalysts to address these challenges through fostering software communities, incubating and curating methodologies and resources, and disseminating knowledge to advance developer productivity and software sustainability. This article discusses how these synergistic activities are advancing scientific discovery—mitigating technical risks by building a firmer foundation for reproducible, sustainable science at all scales of computing, from laptops to clusters to exascale and beyond.

97 MATHEMATICS AND COMPUTING↗

WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.

59 BASIC BIOLOGICAL SCIENCES↗

A Neural Network Approach to Predict Gibbs Free Energy of Ternary Solid Solutions

Here, we present a data-centric deep learning (DL) approach using neural networks (NNs) to predict the thermodynamics of ternary solid solutions. We explore how NNs can be trained with a dataset of Gibbs free energies computed from a CALPHAD database to predict ternary systems as a function of composition and temperature. We have chosen the energetics of the FCC solid solution phase in 226 binaries consisting of 23 elements at 11 different temperatures to demonstrate the feasibility. The number of binary data points included in the present study is 102,000. We select six ternaries to augment the binary dataset to investigate their influence on the NN prediction accuracy. We examine the sensitivity of data sampling on the prediction accuracy of NNs over selected ternary systems. It is anticipated that the current DL workflow can be further elevated by integrating advanced descriptors beyond the elemental composition and more curated training datasets to improve prediction accuracy and applicability.

42 ENGINEERING↗

Editorial: Predicting near-earth space environment: new perspective and capabilities in the AI age

Editorial on the Research Topic Predicting near-earth space environment: new perspective and capabilities in the AI age The near-Earth space environment is not only an operational hazard for space missions, but also a scientific laboratory for advancing our understanding and prediction of space plasma populations. This Research Topic is organized around three interconnected themes: observational datasets, machine-learning (ML) model development, and the discovery of new physical insights through those models. Its primary goal is to highlight the emerging capabilities in space environment prediction that are enabled, or will be enabled, by integrating advanced techniques—including AI/ML methods—with long-term curated datasets.

58 GEOSCIENCES↗

Physics-informed graph neural networks for predicting cetane number with systematic data quality analysis

Designing alternative fuels for advanced compression ignition engines necessitates a predictive model for cetane number (CN). In this study, the physics-informed graph neural networks are introduced for a reliable CN prediction by considering molecular features pertinent to the physical properties of molecules that affect CN. The reliability of measured data is another key factor to consider for improving the predictive model. Various experimental instruments for measuring CN exist, including standard and non-standard methods. In this regard, a systematic data quality analysis was carried out for the total 630 CNs collected from literature and new measurements in this study using Advanced Fuel Ignition Delay Analyzer (AFIDA). The results from this data curation process were reflected in the model by imposing lower sample weights on the data coming from less reliable measurement techniques. This approach effectively maximized the prediction accuracy while incorporating data from all available sources. Using the sample weights decreased the mean absolute error (MAE) up to 0.8 CN units. The accuracy was also improved by introducing the CN-related physical properties (the number of hydrogen bond donors and acceptors); the test set MAE is 5.74 and 7.01 for the model with and without such properties, respectively. Investigating molecular structural effects on CN was also carried out to gain chemical insights into factors used to design new fuel candidates. The dimensionality reduction analysis of feature vectors showed a clear clustering in terms of functional groups and CN and the structural effect derived from the model was consistent with the physicochemical insights. Finally, this physics-informed model and data curation would be helpful for accurate CN prediction and inform rational fuel design.

97 MATHEMATICS AND COMPUTING↗

LLM Generation of Online Courses from a Curated Set of Documents in the Nuclear Safeguards Domain

A multidisciplinary team at Argonne National Laboratory explores the application of advanced technologies to enhance knowledge transfer and retention within the nuclear safeguards domain. Specifically, it examines the feasibility of leveraging secure large language models (LLMs) to streamline the creation of e-learning modules for the U.S. National Nuclear Security Administration (NNSA) Office of International Nuclear Safeguards (NA-241). The initiative addresses the critical need for preserving institutional memory and accelerating skill development amidst the imminent retirement of senior professionals in the field in addition to supporting good knowledge management practices. The project integrates instructional design theory with cutting-edge AI technologies to transform curated document sets from the Safeguards Knowledge Repository (SKR) into modular online courses. By automating the generation of learning objectives and instructional content, the effort aims to reduce manual effort while maintaining high-quality educational outcomes. A limited measure of human supervision, however, ensures accuracy, relevance, and alignment with NNSA’s strategic priorities. Key findings highlight the potential of AI-assisted course generation to support safeguards professionals by creating structured, interactive learning experiences. The report underscores the importance of SME validation to address limitations in AI-generated content, such as terminology errors and gaps in coverage. Recommendations include adopting a structured workflow combining LLM acceleration with expert oversight to ensure accuracy, usability, and alignment with learner needs. This work demonstrates Argonne’s commitment to advancing national security and scientific excellence through innovative knowledge management solutions.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

NOUS: Construction and Querying of Dynamic Knowledge Graphs

The ability to construct domain specific knowledge graphs (KG) and perform question-answering or hypothesis generation is a trans- formative capability. Despite their value, automated construction of knowledge graphs remains an expensive technical challenge that is beyond the reach for most enterprises and academic institutions. We propose an end-to-end framework for developing custom knowl- edge graph driven analytics for arbitrary application domains. The uniqueness of our system lies A) in its combination of curated KGs along with knowledge extracted from unstructured text, B) support for advanced trending and explanatory questions on a dynamic KG, and C) the ability to answer queries where the answer is embedded across multiple data sources.

Choudhury, Sutanay↗

Deep Learning Models Augment Analyst Decisions for Event Discrimination

Long-term seismic monitoring networks are well positioned to leverage advances in machine learning because of the abundance of labeled training data that curated event catalogs provide. In this study, we explore the use of Convolutional and Recurrent Neural Networks to accomplish discrimination of explosive and tectonic sources for local distances. Using a 5-year event catalog generated by the University of Utah Seismograph Stations we train models to produce automated event labels using 90 s event spectrograms from 3-component and single-channel sensors. Both network architectures are able to replicate analyst labels above 98%. Most commonly, model error is the result of label error (70% of cases). Accounting for mislabeled events (~1% of the catalog) model accuracy for both models increases to above 99%. Finally, classification accuracy remains above 98% for shallow tectonic events, indicating that spectral characteristics controlled by event depth do not play a dominant role in event discrimination.

58 GEOSCIENCES↗

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗

Should Multidisciplinary Treatment Differ for Esophageal Adenocarcinoma Versus Esophageal Squamous Cell Cancer?

Current treatment of locally advanced esophageal cancers (ECs) centres on a multimodal approach regardless of histology. While surgery remains the mainstay of curative intent therapy, its implementation alone results in suboptimal outcomes, which have improved significantly with the increased utilization of induction regimens comprising of concurrent chemoradiation (CRT) or chemotherapy alone followed by surgery. Due in large part to the positive results of the CROSS trial, neoadjuvant CRT has become the predominant standard applied in the West. However, the bulk of the data published to date suggests that a more nuanced approach to the management of locally advanced EC is required with respect to the application of radiation, which related to the differential sensitivity of esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (SCC) to radiation. While the latter demonstrates excellent radiosensitivity, which has translated into improved survival outcomes, the same cannot be said for patients with EAC who may be subject to greater toxicity without any benefit. Herein, the differential effectiveness of CRT in patients with EAC versus SCC is highlighted, with a focus on the randomized evidence to date.

62 RADIOLOGY AND NUCLEAR MEDICINE↗