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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

An ontology-based knowledge graph for representing interactions involving RNA molecules

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to each patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are constantly produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph (KG) encompassing biological knowledge about RNAs gathered from more than 60 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Efficient online quantum circuit learning with no upfront training

Optimization is a promising candidate for studying the utility of variational quantum algorithms (VQAs). However, evaluating cost functions using quantum hardware introduces runtime overheads that limit exploration. Surrogate-based methods can reduce calls to a quantum computer, yet existing approaches require hyperparameter pre-training and have been tested only on small problems. Here, we show that surrogate-based methods can enable successful optimization at scale, without pre-training, by using radial basis function interpolation (RBF) to construct an adaptive, hyperparameter-free surrogate. Using the surrogate as an acquisition function drives hardware queries to the vicinity of the true optima. For 16-qubit random 3-regular Max-Cut instances with the Quantum Approximate Optimization Algorithm (QAOA), our method outperforms state-of-the-art approaches, without considering their upfront training costs. Furthermore, we successfully optimize QAOA circuits for 127-qubit random Ising models on an IBM processor using 10 4 −10 5 measurements. Strong empirical performance demonstrates the promise of automated surrogate-based learning for large-scale VQA applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

On-Demand Column Joining for High Energy Physics

As the Large Hadron Collider (LHC) transitions into the High-Luminosity LHC (HL-LHC) era, the volume of data to be processed is expected to increase significantly. The CMS Experiment currently utilizes various data formats, including AOD, MiniAOD, and NanoAOD, each with different levels of detail and storage requirements. This paper addresses the challenges of data duplication and storage inefficiencies in high-energy physics (HEP) analyses by proposing an on-demand column-joining solution. This approach aims to reduce data duplication by enabling the dynamic combination of NanoAOD data with auxiliary information from larger data tiers, such as MiniAOD. The proposed solution leverages Trino, a high-performance distributed SQL query engine, to perform efficient and scalable data joins. Benchmarks using CMS OpenData demonstrate the feasibility of this approach, showing that it can handle large datasets with low latency. Integration with the scikit-hep ecosystem and the coffea analysis framework is also discussed, highlighting the potential for seamless end-to-end data processing and analysis. Ongoing and future work focuses on expanding benchmarks, integrating ServiceX for data transformation, and exploring the use of native object storage solutions.

Manganelli, Nicholas [Northeastern U.]↗
DOE OSTI2025

Exploring scenarios for enhanced fuel compression and performance on the National Ignition Facility with machine-learning-aided design techniques

Recent fusion experiments on the National Ignition Facility (NIF) have achieved ignition, producing multi-MJ fusion yields for input laser energies of roughly 2 MJ [Abu-Shawareb et al., Phys. Rev. Lett. 132, 065102 (2024)]. Building on the success of the target designs that have achieved ignition, we explore new implosion scenarios predicted to generate significantly more compression of the dense DT ice layer and correspondingly higher yields while preserving many of the key physics characteristics of present-day ignition designs. Our main result is a novel 3-shock implosion scheme that effectively minimizes the shock-induced entropy in the dense, accelerating DT shell and maximizes the resulting fuel compression subject to a fixed leading shock strength consistent with present-day ignition experiments, which is necessary to melt the crystalline high-density carbon ablator. Compared to the first NIF experiment to fulfill Lawson's ignition criterion, shot N210808 [Abu-Shawareb et al., Phys. Rev. Lett. 129, 075001 (2022)], our design exhibits a 40% increase in simulated peak areal density (ρR) and a 5× increase in 1D fusion yield using a 4% lighter ablator and identical DT payloads. We also present a complete integrated 2D hohlraum design and laser pulse specifications capable of generating the desired 3-shock drive and maintaining control of the low-mode capsule implosion symmetry, where the increase in simulated 2D yield relative to N210808 is > 10×. This new implosion regime was discovered with help from a machine-learning-enabled capsule design optimization framework. We outline the workflow this automated tool uses to identify improved design candidates by running several rounds of capsule simulations, constructing a surrogate model mapping input variations to key physics output quantities, and querying the resulting statistical model to propose adjustments to the x-ray drive and capsule to reach a set of physics objectives prescribed by the designer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

An information-matching approach to optimal experimental design and active learning

The efficacy of mathematical models heavily depends on the quality of the training data, yet collecting sufficient data is often expensive and challenging. Many modeling applications require inferring parameters only as a means to predict other quantities of interest (QoI). Because models often contain many unidentifiable (sloppy) parameters, QoIs often depend on a relatively small number of parameter combinations. Therefore, we introduce an information-matching criterion based on the Fisher information matrix to select the most informative training data from a candidate pool. This method ensures that the selected data contain sufficient information to learn only those parameters that are needed to constrain downstream QoIs. It is formulated as a convex optimization problem, making it scalable to large models and datasets. Here, we demonstrate the effectiveness of this approach across various modeling problems in diverse scientific fields, including power systems and underwater acoustics. Finally, we use information-matching as a query function within an active learning (AL) loop for materials science applications. In all these applications, we find that a relatively small set of optimal training data can provide the necessary information for achieving precise predictions. These results are encouraging for diverse future applications, particularly AL in large machine-learning models.

Materials science↗
DOE OSTI2026

Design and performance of AI agents interfacing with an atomic layer deposition tool

In this work, we introduce the design of an atomic layer deposition (ALD) reactor augmented with an AI interface for autonomous materials synthesis. Our modular design encapsulates the particularities of the hardware behind a Python interface that communicates with the ALD control software via transmission control protocol. This interface is compatible with model context protocol interfaces used in agentic frameworks. We have integrated our tool with a simple AI agent that leverages a large language model to transform user-supplied queries into ALD processes that are then run in our reactor. Our approach uses a JavaScript object notation schema to encode ALD processes. Our experimental results show that the AI interface does not impose a significant overhead to our control software, at least within our fastest 10 ms scale. We also carried out a detailed evaluation of the agent performance using leading models in two classes of tasks: basic instruction and process discovery tasks, where the agent is presented with a target material and needs to identify the correct ALD process compatible with the reactor configuration. Despite the simplicity of our agent design, we observed that most of the advanced models excelled at the instruction tasks. However, only recent models, such as o1, o3, GPT-5, and Claude Opus 4, performed well in process discovery tasks. We also observed significant variability in the response for the hardest challenges. While the results obtained are promising, we identify areas where AI research could improve the performance of agents for ALD.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Are humans still necessary? Expanding the discussion

The rise of automation, artificial intelligence (AI), and autonomous systems raises important questions about the future role of humans and the field of human factors/ergonomics in workplaces. This paper builds on Dr. Peter Hancock’s 2023 ‘Are Humans Still Necessary?’ article published in the Ergonomics journal. Using a multi-method approach that included a debate, opinion polling, roundtable discussions, and AI queries, the current effort examined the necessity of human involvement in future work environments. Debate team members presented arguments for and against the need for human workers, considering human factors, technology, and socioeconomic factors. Observations indicate that while AI may handle routine tasks, humans will likely remain essential for complex decision making, creativity, and ethical considerations. The paper advocates for viewing workplace dynamics as collaborative human-AI partnerships rather than competition, highlighting the need for a transdisciplinary approach in which human factors/ergonomics professionals play a vital role in enhancing these relationships.

99 - GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Cataloging Legacy Data from the Tritium Systems Test Assembly Program

The Tritium Systems Test Assembly (TSTA) at Los Alamos National Laboratory, operational from 1984 to 2001, was critical in advancing fusion fuel cycle technologies, including tritium storage, gas separation, and pumping. TSTA’s contributions, particularly in safe tritium operations, have influenced subsequent fusion projects. This paper discusses the ongoing effort to digitize and catalog TSTA’s historical data to create a searchable resource for the fusion research community. While the long-term objective is to develop a relational database for structured data management, the project remains in the early phase, with current efforts focused on scanning and indexing physical documents. Initial plans for database implementations are also presented, outlining key considerations for structure, query indexing, and standardization. As digitization progresses, future discussions will refine these implantation details to ensure an efficient and comprehensive system. This initiative aims to preserve critical legacy data, enhance the design of tritium system facilities, and support the next generation of fusion energy research.

42 ENGINEERING↗
DOE OSTI2024

Training quantum neural networks using the quantum information bottleneck method

Abstract We provide in this paper a concrete method for training a quantum neural network to maximize the relevant information about a property that is transmitted through the network. This is significant because it gives an operationally well founded quantity to optimize when training autoencoders for problems where the inputs and outputs are fully quantum. We provide a rigorous algorithm for computing the value of the quantum information bottleneck quantity within error ε that requires O ( log 2 ⁡ ( 1 / ϵ ) + 1 / δ 2 ) queries to a purification of the input density operator if its spectrum is supported on { 0 } ⋃ [ δ , 1 − δ ] for δ > 0 and the kernels of the relevant density matrices are disjoint. We further provide algorithms for estimating the derivatives of the QIB function, showing that quantum neural networks can be trained efficiently using the QIB quantity given that the number of gradient steps required is polynomial.

Çatlı, Ahmet Burak (ORCID:0000000152294141)↗
DOE OSTI2025

NEAR: Neural Embeddings for Amino acid Relationships

Protein language models (PLMs) have recently demonstrated potential to supplant classical protein database search methods based on sequence alignment, but are slower than common alignment-based tools and appear to be prone to a high rate of false labeling. Here, we present NEAR, a method based on neural representation learning that is designed to improve both speed and accuracy of search for likely homologs in a large protein sequence database. NEAR’s ResNet embedding model is trained using contrastive learning guided by trusted sequence alignments. It computes per-residue embeddings for target and query protein sequences, and identifies alignment candidates with a pipeline consisting of residue-level k-NN search and a simple neighbor aggregation scheme. Tests on a benchmark consisting of trusted remote homologs and randomly shuffled decoy sequences reveal that NEAR substantially improves accuracy relative to state-of-the-art PLMs, with lower memory requirements and faster embedding and search speed. While these results suggest that the NEAR model may be useful for standalone homology detection with increased sensitivity over standard alignment-based methods, in this manuscript we focus on a more straightforward analysis of the model’s value as a high-speed pre-filter for sensitive annotation. In that context, NEAR is at least 5x faster than the pre-filter currently used in the widely-used profile hidden Markov model (pHMM) search tool HMMER3, and also outperforms the pre-filter used in our fast pHMM tool, nail.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2024

Aromatic amino acid metabolism and active transport regulation are implicated in microbial persistence in fractured shale reservoirs

Abstract Hydraulic fracturing has unlocked vast amounts of hydrocarbons trapped within unconventional shale formations. This large-scale engineering approach inadvertently introduces microorganisms into the hydrocarbon reservoir, allowing them to inhabit a new physical space and thrive in the unique biogeochemical resources present in the environment. Advancing our fundamental understanding of microbial growth and physiology in this extreme subsurface environment is critical to improving biofouling control efficacy and maximizing opportunities for beneficial natural resource exploitation. Here, we used metaproteomics and exometabolomics to investigate the biochemical mechanisms underpinning the adaptation of model bacterium Halanaerobium congolense WG10 and mixed microbial consortia enriched from shale-produced fluids to hypersalinity and very low reservoir flow rates (metabolic stress). We also queried the metabolic foundation for biofilm formation in this system, a major impediment to subsurface energy exploration. For the first time, we report that H. congolense WG10 accumulates tyrosine for osmoprotection, an indication of the flexible robustness of stress tolerance that enables its long-term persistence in fractured shale environments. We also identified aromatic amino acid synthesis and cell wall maintenance as critical to biofilm formation. Finally, regulation of transmembrane transport is key to metabolic stress adaptation in shale bacteria under very low well flow rates. These results provide unique insights that enable better management of hydraulically fractured shale systems, for more efficient and sustainable energy extraction.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2024

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Burley, Stephen K.↗
DOE OSTI2024

Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data

Abstract The Plant Metabolic Network (PMN) is a free online database of plant metabolism available at https://plantcyc.org. The latest release, PMN 16, provides metabolic databases representing >1200 metabolic pathways, 1.3 million enzymes, >8000 metabolites, >10 000 reactions and >15 000 citations for 155 plant and green algal genomes, as well as a pan-plant reference database called PlantCyc. This release contains 29 additional genomes compared with PMN 15, including species listed by the African Orphan Crop Consortium and nonflowering plant species. Furthermore, 52 new enzymes with experimentally supported function information have been included in this release. The single-species databases contain a combination of experimental information from the literature and computationally predicted information obtained through PMN’s database generation pipeline for a single species, while PlantCyc contains only experimental information but for any species within Viridiplantae. PMN is a comprehensive resource for querying, visualizing, analyzing and interpreting omics data with metabolic knowledge. It also serves as a useful and interactive tool for teaching plant metabolism.

Hawkins, Charles (ORCID:0000000312849047)↗
DOE OSTI2026

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes

Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.

Fiamenghi, Mateus B↗
DOE OSTI2025

Populus VariantDB v3.2 facilitates CRISPR and functional genomics research

The success of CRISPR genome editing studies depends critically on the precision of guide RNA (gRNA) design. Sequence polymorphisms in outcrossing tree species pose design hazards that can render CRISPR genome editing ineffective. Despite recent advances in tree genome sequencing with haplotype resolution, sequence polymorphism information remains largely inaccessible to various functional genomics research efforts. The Populus VariantDB v3.2 addresses these challenges by providing a user-friendly search engine to query sequence polymorphisms of heterozygous genomes. The database accepts short sequences, such as gRNAs and primers, as input for searching against multiple poplar genomes, including hybrids, with customizable parameters. We provide examples to showcase the utilities of VariantDB in improving the precision of gRNA or primer design. The platform-agnostic nature of the probe search design makes Populus VariantDB v3.2 a versatile tool for the rapidly evolving CRISPR field and other sequence-sensitive functional genomics applications. The database schema is expandable and can accommodate additional tree genomes to broaden its user base.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Stoichiometry dependent properties of cerium hydride: An active learning developed interatomic potential study

Cerium hydride has a variety of interesting properties, including a known lattice contraction and densification with increasing hydrogen content. However, precise stoichiometric control is not experimentally straightforward and ab initio approaches are not computationally feasible for many properties such as melting and low temperature diffusion. Therefore, we develop a machine-learned interatomic potential for cerium hydride that is valid for H to Ce ratios from 2.0 to 3.0. A query-by-committee active learning approach is used to develop the training set. Leveraging classical molecular dynamics simulations, we assess a range of properties and provide fundamental mechanisms for the trends with stoichiometry. Finally, a majority of the properties follow the trend of lattice contraction, being governed by the stronger lattice binding induced by adding octahedral atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Ansatz-Free Hamiltonian Learning with Heisenberg-Limited Scaling

Learning the unknown interactions that govern a quantum system is crucial for quantum information processing, device benchmarking, and quantum sensing. The problem, known as Hamiltonian learning, is well understood under the assumption that interactions are local, but this assumption may not hold for arbitrary Hamiltonians. Previous methods all require high-order inverse polynomial dependency with precision, unable to surpass the standard quantum limit and reach the gold-standard Heisenberg-limited scaling. Whether Heisenberg-limited Hamiltonian learning is possible without prior assumptions about the interaction structures, a challenge we term ansatz-free Hamiltonian learning , remains an open question. In this work, we present a quantum algorithm to learn arbitrary sparse Hamiltonians without any structure constraints using only black-box queries of the system’s real-time evolution and minimal digital controls to attain Heisenberg-limited scaling in estimation error. Our method is also resilient to state-preparation-and-measurement errors, enhancing its practical feasibility. We numerically demonstrate our ansatz-free protocol for learning physical Hamiltonians and validating analog quantum simulations, benchmarking our performance against the state-of-the-art Heisenberg-limited learning approach. Moreover, we establish a fundamental trade-off between total evolution time and quantum control on learning arbitrary interactions, revealing the intrinsic interplay between controllability and total evolution-time complexity for any learning algorithm. These results pave the way for further exploration into Heisenberg-limited Hamiltonian learning in complex quantum systems under minimal assumptions, potentially enabling new benchmarking and verification protocols.

machine learning↗