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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

GenomeDepot: data management system for microbial comparative genomics

Summary GenomeDepot is an open-source web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of websites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, Basic Local Alignment Search Tool (BLAST) search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools. Availability and implementation GenomeDepot is open source and distributed under the GNU General Public License via GitHub (https://github.com/aekazakov/genome-depot). GenomeDepot is implemented in Python and was tested in Ubuntu Linux. Full installation instructions and documentation are available at https://aekazakov.github.io/genome-depot/. GenomeDepot demo server is freely accessible at https://iseq.lbl.gov/demogd/.

Kazakov, Alexey [Lawrence Berkeley National Labora↗
DOE OSTI2025

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Integrating Immersive Visualization in Molten-Salt Reactor Waste Management for Experimental Design and Planning

The Molten Salt Reactor (MSR) represents a significant innovation in nuclear technology, offering several operational and safety benefits over traditional solid-fuel reactors. However, MSRs face uncertainties in waste management due to their flexible designs and variable waste compositions. To address these challenges, we propose a visualization platform that illustrates solutions and performance predictions for various waste management strategies, enhancing user experience and improving strategy and communication. Immersive visualizations are widely used in the nuclear industry for training, simulation, and safety enhancement. Our project aims to develop a visualization platform incorporating virtual reality (VR) technologies to illustrate MSR characteristics immediately following reactor shutdown. This immersive simulation will allow users to interact, explore, and understand different waste management strategies. The platform will display MSR reactor characterizations, including nuclide decay, salt solidification, and corrosion, which are crucial for assessing and selecting backend management strategies. Using the Meta Quest 3 VR headset with Unity software, our platform will provide real-scale visualizations, enabling users to experience and evaluate designs and plans as if they were physically present. This user-friendly interface will make complex data accessible and understandable for non-domain experts, aiding in decision-making for MSR waste management. Our proposed visualization workflow can be applied to other nuclear reactors, assisting in the design and planning of waste management strategies.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Immersive Scientific Visualization of Molten-Salt Reactor Waste Characteristics Using Virtual Reality

Immersive visualization is changing how we explore, communicate, and understand complex scientific systems. In nuclear energy, an area in which data are often multidimensional, time-dependent, and difficult to interpret, virtual reality (VR) represents a powerful and intuitive informational medium. This work introduces a VR-based platform that visualizes the post-shutdown behavior and waste management lifecycle of molten-salt reactors (MSRs), a next-generation reactor type with unique operational and safety characteristics. The platform, built in Unity, is streamed on the Meta Quest 3 headset. It transforms high-fidelity simulation data into an interactive, immersive experience. Users can explore time-dependent reactor characteristics such as nuclide decay, which is a key factor for evaluating reactor waste strategies. The datasets were generated using the MOOSE (Multiphysics Object-Oriented Simulation Environment) framework and then processed through ParaView scripting for smooth integration into Unity. From a visualization standpoint, the platform emphasizes spatial storytelling, temporal exploration, and user-centered interaction. Users can navigate 3D reactor geometries, slice through volumetric data, and manipulate time to observe how physical phenomena evolve. Real-scale rendering and embodied interaction make the experience feel tangible. The interface is designed to be accessible, even to those without nuclear or simulation expertise. This lowers the barrier for stakeholders, policymakers, and the general public, while still supporting expert analysis and collaborative decision-making. This work shows how immersive visualization can function as both a scientific tool and a communication interface. By integrating simulation, processing, and visualization into a cohesive workflow, we offer a scalable framework for immersive scientific storytelling. The modular design supports future extensions to other reactor types and lifecycle stages, from shutdown to long-term storage, making the platform adaptable for both research and outreach.

99 - GENERAL AND MISCELLANEOUS↗
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 OSTI2025

Visual Analytics of Crosstalk in Quantum Hardware

Crosstalk remains a major obstacle to building scalable and fault-tolerant quantum computers. Conventional diagnostic techniques-often based on numerical simulation or statistical modeling-struggle to scale with hardware complexity and offer limited interpretability. In this work, we present a visual analytics framework for diagnosing qubit crosstalk using lightweight, circuit-based models integrated with an interactive user interface. Our approach quantifies correlations between active and idle qubits under parameterized single- and twoqubit operations, enabling detection of both spatial and gateinduced crosstalk. The system incorporates qubit topology and gate performance data to support sector-based exploration and correlation mapping. This tool assists users in identifying correlated error sources, informing qubit placement strategies, and guiding noise-aware circuit design.

Chae, Junghoon [ORNL] (ORCID:0000000206016746)↗
DOE OSTI2025

Cost and Performance Baseline for Fossil Energy Plants – Volume 1: Bituminous Coal and Natural Gas to Electricity: May 2025

This presentation at EPRI's annual Generation Sector Meeting during the Advanced Generation and Carbon Capture and Storage session provides an overview of the recently published Cost and Performance Baseline for Fossil Energy Plants – Volume 1: Bituminous Coal and Natural Gas to Electricity dated May 2025. It further connects viewers with the recently released tool/dashboard, an interactive tool that allows users to manipulate six key study parameters simultaneously for each case and visualize the impact on three metrics: 1) levelized cost of electricity (LCOE), 2) cost of CO2 captured (CCC), and 3) cost of CO2 avoided (CCA).

baseline study↗
DOE OSTI2024

Machine learning visualization tool for exploring parameterized hydrodynamics

We are interested in the computational study of shock hydrodynamics, i.e. problems involving compressible solids, liquids, and gases that undergo large deformation. These problems are dynamic and nonlinear and can exhibit complex instabilities. Due to advances in high performance computing it is possible to parameterize a hydrodynamic problem and perform a computational study yielding $\mathscr{O} (TB)$ of simulation state data. We present an interactive machine learning tool that can be used to compress, browse, and interpolate these large simulation datasets. This tool allows computational scientists and researchers to quickly visualize 'what-if' situations, perform sensitivity analyses, and optimize complex hydrodynamic experiments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

A Measurement of the Pion-Energy Dependence of Muon Neutrino Charged-Current Scattering to Final States With One Charged Pion in NOvA

The study of neutrino oscillations is a main priority for particle physics as the most immediately tractable lever on physics beyond the Standard Model. In particular, more insight into violation of the combined symmetry of charge-conjugation plus parity could yield clues to the origin of matter-antimatter asymmetry, and in some theoretical frameworks the neutrino mass could give insights into dark matter. NOvA is a long-baseline accelerator neutrino experiment with both a near and far detector that seeks to measure several of the parameters of the neutrino mixing matrix, as well as carry out a broad program of additional physics. NOvA has innovated and developed a variety of techniques in the space of neutrino physics, including expanding the use of machine learning techniques in reconstruction. NOvA has also set the stage for the next generation US-based long baseline experiment, DUNE. This dissertation details the creation of a new neutrino interaction vertex reconstruction package for NOvA, which offers enormous improvements in accuracy above the previous vertexer it replaces. This is accomplished using a Convolutional Visual Network trained on large datasets of simulated events. The vertexer is validated thoroughly against data. This dissertation also presents a cross-section measurement for $\nu_\mu + N \rightarrow \mu^- + 1\pi^\pm + X$ (where X does not include additional charged pions) binned in pion kinetic energy, a challenging measurement in general and for NOvA in particular. Measurements like this provide crucial inputs for neutrino interaction models utilized by neutrino oscillation experiments. This measurement in particular is important to the energy ranges relevant for DUNE in a band not well-covered by any other experiment.

Ewart, Erin [Indiana U., Bloomington (main)]↗
DOE OSTI2024

Atomic-scale visualization of defect-induced localized vibrations in GaN

Phonon engineering is crucial for thermal management in GaN-based power devices, where phonon-defect interactions limit performance. However, detecting nanoscale phonon transport constrained by III-nitride defects is challenging due to limited spatial resolution. Here, we used advanced scanning transmission electron microscopy and electron energy loss spectroscopy to examine vibrational modes in a prismatic stacking fault in GaN. By comparing experimental results with ab initio calculations, we identified three types of defect-derived modes: localized defect modes, a confined bulk mode, and a fully extended mode. Additionally, the PSF exhibits a smaller phonon energy gap and lower acoustic sound speeds than defect-free GaN, suggesting reduced thermal conductivity. Our study elucidates the vibrational behavior of a GaN defect via advanced characterization methods and highlights properties that may affect thermal behavior.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Visualizing the impact of quenched disorder on 2D electron Wigner solids

Electron Wigner solids (WSs) provide an ideal system for understanding the competing effects of electron–electron and electron–disorder interactions, a central unsolved problem in condensed matter physics. Progress in this topic has been limited by a lack of single-defect-resolved experimental measurements as well as accurate theoretical tools to enable realistic experiment/theory comparison. Here, in this study, we overcome these limitations by combining atomically resolved scanning tunnelling microscopy (STM) with neural-quantum-state quantum Monte Carlo (NQS-QMC) simulation of disordered 2D electron WSs to discover new disorder-induced physical regimes of correlated electron behaviour. STM was used to image the electron density (n e )-dependent evolution of electron WSs in gate-tunable bilayer MoSe 2 (BL-MoSe 2 ) devices with varying long-range (n LR ) and short-range (n SR ) disorder densities. These images were compared with NQS-QMC simulations using realistic disorder maps extracted from experiment, thus allowing the roles of different disorder types to be disentangled. We identify two distinct physical regimes for disordered electron WSs that depend on n SR . For n SR ≲ n e , the WS behaviour is dominated by long-range disorder and features extensive mixed solid–liquid phases, a new type of local re-entrant melting/crystallization and prominent Friedel oscillations. By contrast, when n SR ≫ n e , these features are suppressed and a more robust amorphous WS phase emerges that persists to higher n e , highlighting the importance of short-range disorder in this regime. Our work establishes a powerful framework for studying disordered quantum solids through a combined experimental–theoretical approach.

Ge, Zhehao [University of California, Berkeley, CA↗
DOE OSTI2025

Label-free structural imaging of plant roots and microbes using third-harmonic generation microscopy

Root biology is pivotal in addressing global challenges including sustainable agriculture and climate change. However, roots have been relatively understudied among plant organs, partly due to the difficulties in imaging root structures in their natural environment. Here we used microfabricated ecosystems (EcoFABs) to establish growing environments with optical access and employed nonlinear multimodal microscopy of third-harmonic generation (THG) and three-photon fluorescence (3PF) to achieve label-free, in situ imaging of live roots and microbes at high spatiotemporal resolution. THG enabled us to observe key plant root structures including the vasculature, Casparian strips, dividing meristematic cells, and root cap cells, as well as subcellular features including nuclear envelopes, nucleoli, starch granules, and putative stress granules. THG from the cell walls of bacteria and fungi also provides label-free contrast for visualizing these microbes in the root rhizosphere. With simultaneously recorded 3PF signal, we demonstrated our ability to investigate root-microbe interactions by achieving single-bacterium tracking and subcellular imaging of fungal spores and hyphae in the rhizosphere.

Pan, Daisong [University of California, Berkeley, ↗
DOE OSTI2025

Visualizing nucleation, condensation and propagation of β-tubulin folding in chaperonin TRiC

AbstractThe folding nucleus (FN) initiates protein folding and enables an efficient folding pathway. Here we directly visualize the tubulin FN consisting of a nonnative, partially assembled Rossmann fold, in the closed chamber of human chaperonin TRiC. Chaperonin TRiC interacts with non-natively folded secondary structural elements, stabilizing the nucleus for transition into its first native domain. Through progressive folding, the unfolded sequence goes through drastic spatial arrangement in the TRiC chamber to sample the conformational space, mediated by the highly dynamic CCT tails. The observed presence of individual nonnative secondary structures first in the nonnative FN and then around the incrementally folded native domains supports the hypothesis that tubulin folding in TRiC is a hierarchical process of nucleation, condensation and propagation in cooperation with TRiC subunits.

Zhao, Yanyan (ORCID:0000000323021763)↗
DOE OSTI2024

Refining HPCToolkit for application performance analysis at exascale

As part of the US Department of Energy’s Exascale Computing Project (ECP), Rice University has been refining its HPCToolkit performance tools to better support measurement and analysis of applications executing on exascale supercomputers. To efficiently collect performance measurements of GPU-accelerated applications, HPCToolkit employs novel non-blocking data structures to communicate performance measurements between tool threads and application threads. To attribute performance information in detail to source lines, loop nests, and inlined call chains, HPCToolkit performs parallel analysis of large CPU and GPU binaries involved in the execution of an exascale application to rapidly recover mappings between machine instructions and source code. To analyze terabytes of performance measurements gathered during executions at exascale, HPCToolkit employs distributed-memory parallelism, multithreading, sparse data structures, and out-of-core streaming analysis algorithms. To support interactive exploration of profiles up to terabytes in size, HPCToolkit’s hpcviewer graphical user interface uses out-of-core methods to visualize performance data. The result of these efforts is that HPCToolkit now supports collection, analysis, and presentation of profiles and traces of GPU-accelerated applications at exascale. These improvements have enabled HPCToolkit to efficiently measure, analyze and explore terabytes of performance data for executions using as many as 64K MPI ranks and 64K GPU tiles on ORNL’s Frontier supercomputer. HPCToolkit’s support for measurement and analysis of GPU-accelerated applications has been employed to study a collection of open-science applications developed as part of ECP. This paper reports on these experiences, which provided insight into opportunities for tuning applications, strengths and weaknesses of HPCToolkit itself, as well as unexpected behaviors in executions at exascale.

Adhianto, Laksono↗
DOE OSTI2024

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

Abstract Background Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world’s best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria. Results Based on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. Conclusions We demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Visualizing the strong field–induced molecular breakup of C 60 via x-ray diffraction

Laser-driven dynamics in polyatomic molecules poses a complex many-body problem. Understanding intense light-matter interaction is crucial for steering intramolecular quantum dynamical processes. Here, we record time-resolved x-ray diffraction images of C 60 molecules during and after their interaction with intense near-infrared fields, giving direct access to structural changes of the molecules and their fragmentation in real time. Tuning the intensity of the excitation pulses, we uncover a transition from a weak-field regime of excited but stable molecules to a high-field regime dominated by Coulomb explosion. In the transition region, the molecules expand by up to 50% of their initial size within just 140 fs, with major fragmentation only setting in afterward. This work demonstrates that x-ray diffractive imaging is capable of retrieving time-resolved structural information of large molecules reshaped by intense laser fields. Laser-driven fragmentation is a first step toward observing molecular processes modified by laser fields of increasing intensity.

Schnorr, Kirsten [Paul Scherrer Inst. (PSI), Villi↗
DOE OSTI2025

Observation of Topological Spin Textures in Ferrimagnetic Mn 2 − x Zn x Sb

Ferrimagnets, which have both ferromagnetic and antiferromagnetic coupling, are attracting increased attention in the realm of spintronic devices due to advantages such as ultrafast dynamics and a suppressed skyrmion Hall effect. Thus, understanding the behavior of nontrivial spin textures in ferrimagnets is crucial; however, comprehensive reports on this topic remain limited. Here, the magnetic spin textures of ferrimagnetic Mn 2 − x Zn x Sb (x = 0.85) is explored as a function of temperature and applied magnetic field. The spin textures can be tuned to a variety of states, including stripes, skyrmion bags, and a skyrmion lattice. Chiral Néel-type magnetic structures are visualized using Lorentz transmission electron microscopy. Mn(I) ions are slightly shifted toward the Sb sites, which may be due to a strong electrostatic interaction between Mn and Sb ions. This local structural distortion breaks the inversion symmetry and introduces an effective Dzyaloshinkii–Moriya interaction. This work thus provides a pathway to use doping and heterogeneity in a ferrimagnet to control and generate chiral nontrivial spin textures.

Mn ion displacement↗
DOE OSTI2026

The 2025 Evaluation of Experimental Thermonuclear Reaction Rates (ETR25)

This work describes the formalism for estimating thermonuclear reaction rates for astrophysical applications, emphasizing modern statistical approaches such as Monte Carlo sampling and Bayesian models. We discuss related topics including the calculation of resonance energies from nuclear Q values, indirect estimates of particle partial widths, and matching of reaction rates at elevated temperatures to statistical model results. We have evaluated available experimental data on cross sections, resonance energies and strengths, partial widths, lifetimes, spin-parities, and spectroscopic factors. Based on these results, we have estimated numerical values of 78 experimental charged-particle thermonuclear reaction rates for target nuclei in the A = 2–40 mass region, for temperatures ranging from 1 MK to 10 GK. For each reaction, three rate values are provided: low, median, and high, corresponding to the 16th, 50th, and 84th percentiles, respectively, of the cumulative reaction rate probability density distribution. Additionally, we present the factor uncertainty of each rate at each temperature grid point. These results enable users to sample the reaction rate probability density in nucleosynthesis calculations, facilitating uncertainty estimates of nuclidic abundances. The rates presented here refer to their laboratory values. For use in stellar model simulations, these values need to be corrected for the effects of thermal excitations of the interacting nuclei. For each reaction, we include graphs that illustrate the fractional contributions to the overall reaction rate along with the associated uncertainty. These visuals are designed to assist both stellar modelers and nuclear experimentalists by identifying the primary sources of rate uncertain=^texttx);ty at specific stellar temperatures. A graphical comparison with earlier Monte Carlo rates is also provided.

Nuclear astrophysics↗