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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 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Modelling stellar activity with Gaussian process regression networks

ABSTRACT Stellar photospheric activity is known to limit the detection and characterization of extrasolar planets. In particular, the study of Earth-like planets around Sun-like stars requires data analysis methods that can accurately model the stellar activity phenomena affecting radial velocity (RV) measurements. Gaussian Process Regression Networks (GPRNs) offer a principled approach to the analysis of simultaneous time series, combining the structural properties of Bayesian neural networks with the non-parametric flexibility of Gaussian Processes. Using HARPS-N solar spectroscopic observations encompassing three years, we demonstrate that this framework is capable of jointly modelling RV data and traditional stellar activity indicators. Although we consider only the simplest GPRN configuration, we are able to describe the behaviour of solar RV data at least as accurately as previously published methods. We confirm the correlation between the RV and stellar activity time series reaches a maximum at separations of a few days, and find evidence of non-stationary behaviour in the time series, associated with an approaching solar activity minimum.

Camacho, J. D. (ORCID:0000000151215560)↗
DOE OSTI2022

Core of 25 F studied by the 25 F(–p) proton-removal reaction

The 9 Be( 25 F(5/2 + ), 24 O)X proton-removal reaction was studied at the NSCL using the S800 spectrometer. The experimental spectroscopic factor for the ground-state to ground-state transition indicates a substantial depletion of the proton d 5/2 strength compared to shell-model expectations, similar to the findings of an inverse-kinematics (p,2p) measurement performed at RIBF. The 25 F to 24 O ground-states overlap is considerably less than anticipated if the core nucleons behaved as rigid, doubly-magic 24 O within 25 F. We interpret the new results within the framework of the Particle-Vibration Coupling (PVC) model, of a d 5/2 proton coupled to a quadrupole phonon of an effective core. This approach provides a good description of the experimental data, requiring an effective 24 O* core with a phonon energy of ℏω 2 = 3.2 MeV and a B(E2) ≈ 2.7 W.u. – softer and more collective than a bare 24 O. Here, both the Nilsson deformed mean field and the PVC models appear to capture the properties of the effective core of 25 F, suggesting that the additional proton polarizes 24 O in such a way that it becomes either slightly deformed or a quadrupole vibrator.

20 ≤ A ≤ 38↗
DOE OSTI2021

New method for detecting fast neutrino flavor conversions in core-collapse supernova models with two-moment neutrino transport

Fast-pairwise neutrino oscillations potentially affect many aspects of core-collapse supernovae (CCSNe): the explosion mechanism, neutrino signals, and nucleosynthesis in the ejecta. This particular mode of collective neutrino oscillations has a deep connection to the angular structure of neutrinos in momentum space; for instance, the appearance of electron-neutrino lepton number (ELN) angular crossings in momentum space is a good indicator of the occurrence of flavor conversions. However, many multidimensional CCSN simulations are carried out with approximate neutrino transport (such as two-moment methods), which limits access to the angular distributions of neutrinos, i.e., inhibits ELNcrossing searches. In this paper, we develop a new method of searching for ELN crossing in these CCSN simulations. The required data is the zeroth and first angular moments of neutrinos and the matter profile, all of which are available in CCSN models with the two-moment method. One of the novelties of our new method is the use of a ray-tracing neutrino transport to determine ELNs in the direction of the stellar center. It is designed to compensate for shortcomings of the crossing searches with only two angular moments. We assess the capability of the method by carrying out a detailed comparison with results of full Boltzmann neutrino transport in 1D and 2D CCSN models. In this work, we find that the ray-tracing neutrino transport improves the accuracy of crossing searches; indeed, the appearance/disappearance of the crossings is accurately detected even in the region of forward-peaked angular distributions. The new method is computationally cheap and has the benefit of efficient parallelization; hence, it will be useful for ELN-crossing searches in any CCSN models that employ two-moment neutrino transport.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Dark matter trigger for early dark energy coincidence

Current cosmological measurements present a persistent tension in the value of the current cosmic expansion rate, the Hubble constant, as inferred from cosmic microwave background (CMB) and large-scale structure (LSS) data compared to that inferred from the classical distance ladder. Early dark energy (EDE), whose cosmological role is localized in time around the epoch of matter-radiation equality just prior to the release of the CMB photons, is designed to resolve this "Hubble tension". However, the model introduces a new coincidence problem: Why should the EDE dynamics occur near matter-radiation equality if EDE is decoupled from both matter and radiation? The resolution of this problem may lie in an early dark sector (EDS), wherein the dark matter mass is dependent on the EDE scalar field. In this work, we construct such an EDS model and show that it naturally resolves the EDE coincidence problem at the background level without any fine-tuning of the coupling to dark matter or of the initial conditions. When fitting to current cosmological data, including that from the local distance ladder, CMB, and LSS, our EDS maximum-likelihood model performs comparably to EDE for resolving the Hubble tension. However, fitting the Planck CMB data requires a specific range of initial field positions to balance the scalar field fluctuations that drive acoustic oscillations, providing testable differences with other EDE models and a platform for future model-building.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

ROI-Finder : machine learning to guide region-of-interest scanning for X-ray fluorescence microscopy

The microscopy research at the Bionanoprobe (currently at beamline 9-ID and later 2-ID after APS-U) of Argonne National Laboratory focuses on applying synchrotron X-ray fluorescence (XRF) techniques to obtain trace elemental mappings of cryogenic biological samples to gain insights about their role in critical biological activities. The elemental mappings and the morphological aspects of the biological samples, in this instance, the bacterium Escherichia coli ( E. Coli ), also serve as label-free biological fingerprints to identify E. coli cells that have been treated differently. The key limitations of achieving good identification performance are the extraction of cells from raw XRF measurements via binary conversion, definition of features, noise floor and proportion of cells treated differently in the measurement. Automating cell extraction from raw XRF measurements across different types of chemical treatment and the implementation of machine-learning models to distinguish cells from the background and their differing treatments are described. Principal components are calculated from domain knowledge specific features and clustered to distinguish healthy and poisoned cells from the background without manual annotation. The cells are ranked via fuzzy clustering to recommend regions of interest for automated experimentation. The effects of dwell time and the amount of data required on the usability of the software are also discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Pixel-Resolved Long-Context Learning for Turbulence at Exascale: Resolving Small-scale Eddies Toward the Viscous Limit

Turbulence plays a crucial role in multiphysics applications, including aerodynamics, fusion, and combustion. Accurately capturing turbulence's multiscale characteristics is essential for reliable predictions of multiphysics interactions, but remains a grand challenge even for exascale supercomputers and advanced deep learning models. The extreme-resolution data required to represent turbulence, ranging from billions to trillions of grid points, pose prohibitive computational costs for models based on architectures like vision transformers. To address this challenge, we introduce a multiscale hierarchical Turbulence Transformer that reduces sequence length from billions to a few millions and a novel RingX sequence parallelism approach that enables scalable long-context learning. We perform scaling and science runs on the Frontier supercomputer. Our approach demonstrates excellent performance up to 1.1 EFLOPS on 32,768 AMD GPUs, with a scaling efficiency of 94\%. To our knowledge, this is the first AI model for turbulence that can capture small-scale eddies down to the dissipative range in three-dimensional turbulence at high Reynolds numbers.

Yin, Junqi [ORNL] (ORCID:0000000338435520)↗
DOE OSTI2022

Nondestructive Damage Detection of Concrete With Alkali-Silica Reactions Using Coda Wave and Anomaly Detection

An anomaly detection model for early damage detection for concrete structures undergoing alkali-silica reaction (ASR) is presented. It is difficult to detect ASR initiation and early damage without a reference expansion measurement. Coda waves, or the multiply scattered portion of ultrasonic waves, have been found to be indicative of small changes in complex material such as concrete. The relationship between concrete damage and relative velocity change and decorrelation of coda waves has been studied, but a generalized model which detects when damage occurs in a concrete structure is still lacking. The presented method uses features extracted from coda waves to detect early damage in concrete structures. The model uses unsupervised learning and only requires data from undamaged structures for training. During the training process, the reconstruction error of the training data is minimized. When the data collected from damaged concrete structures is used as an input of the model, it returns high reconstruction errors that indicate the occurrence of damage in the structures. The performance of the model is validated using experimental studies and has been shown to generalize across two different ASR specimens.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

On Distributed Model-Free Reinforcement Learning Control with Stability Guarantee

Distributed learning can enable scalable and effective decision making in numerous complex cyber-physical systems such as smart transportation, robotics swarm, power systems, etc. However, the stability of the system is usually not guaranteed in most existing learning paradigms; and this limitation can hinder the wide deployment of machine learning in decision making of safety-critical systems. This paper presents a stability guaranteed distributed reinforcement learning (SGDRL) framework for interconnected linear subsystems, without knowing the subsystem models. While the learning process requires data from a peer-to-peer (p2p) communication architecture, the control implementation of each subsystem is only based on its local state. The stability of the interconnected subsystems will be ensured by a diagonally dominant eigenvalue condition, which will then be used in a model-free RL algorithm to learn the feedback control gains. The RL algorithm structure follows an off-policy iterative framework, with interleaved policy evaluation and policy update steps. We numerically validate our theoretical results by performing simulations on four interconnected sub-systems.

Mukherjee, Sayak↗
DOE OSTI2023

What's New in the NSRDB

The National Solar Radiation Database (NSRDB) provides solar resource data across the globe at a high temporal and spatial resolution. This data is primarily used in solar energy modeling. The NSRDB is updated annually for the United States and North, Central and South America and the data is currently available from 1998-2021. In 2022 the NSRDB was updated using the latest version of the underlying Physical Solar Model (PSM). This update includes improved surface albedo and gap-filling of cloud properties. The inclusion of these updates reduced the uncertainty in the data compared to previous versions of the NSRDB. The Himawari and Meteosat Indian Ocean Data Coverage (IODC) satellites were added to the Geostationary Operational Environmental Satellite (GOES) and made our coverage global. While standard data from the GOES continues to be served at an hourly 4km x 4km resolution, full resolution data has also been made available to the user. The NSRDB now contains over 200Tb of data with nearly 40Tb being added annually. We provide significant flexibility for data download depending on the amount of data required by the users. In this paper we provide an update on the current status on the NSRDB.

photovoltaic systems↗
DOE OSTI2025

Active Learning Surrogates for Integrating Electron Microscopy and Computational Insights from Simulations in Autonomous Experiments

Artificial Intelligence (AI) combined with simulations and experiments has great potential to accelerate scientific discovery across technology and pharmaceuticals. However, the gap between simulations and experiments is challenging due to disparities in time and scale, making it difficult to estimate properties like energy and electronic states from experiments, and to provide feedback based on theoretical insights.Our research addresses the challenge by developing unique deep kernel based surrogate models that learns from microscopic images, mapping structural features to energy differences from defect formation. We start with full-training using simulated images to determine optimal settings, establishing a baseline for active learning. Using these settings from the baseline, active learning is trained, and predicts structures along simulation trajectories based on uncertainty and energetic stability, thus reducing data requirements, simulation time and computational costs. The results demonstrate that the model achieves a low average error margin of approximately 0.03 meV, indicating good performance. To enhance feature extraction and reconstruction capabilities, we developed an autoencoder-decoder as additional surrogate to create latent space to capture essential features, enabling precise comparisons between simulations and experiments. The results from this model achieved a reconstruction loss of around 0.2 and accurately reconstructed molecular structures.Overall, this work advances the steering of experiments through computational simulations by employing a surrogate models that actively predicts the trajectories of structural evolution, achieving time-to-solution comparable to experimental measurements.

Saranathan, Gayathri [Hewlett-Packard]↗
DOE OSTI2024

Invariant Features for Accurate Predictions of Quantum Chemical UV-vis Spectra of Organic Molecules

Including invariance of global properties of a phys-ical system as an intrinsic feature in graph neural networks (GNNs) enhances the model's robustness and generalizability and reduces the amount of training data required to obtain a desired accuracy for predictions of these properties. Existing open source GNN libraries construct invariant features only for specific GNN architectures. This precludes the generalization of invariant features to arbitrary message passing neural network (MPNN) layers which, in turn, precludes the use of these libraries for new, user-specified predictive tasks. To address this limitation, we implement invariant MPNNs into the flexible and scalable HydraGNN architecture. HydraGNN enables a seamless switch between various MPNNs in a unified layer sequence and allows for a fair comparison between the predictive performance of different MPNNs. We trained this enhanced HydraGNN archi-tecture on the ultraviolet-visible (UV-vis) spectrum of GDB-9 molecules, a feature that describes the molecule's electronic exci-tation modes, computed with time-dependent density functional tight binding (TD-DFTB) and available open source through the GDB-9-Ex dataset. We assess the robustness (i.e., accuracy and generalizability) of the predictions obtained using different invariant MPNNs with respect to different values of the full width at half maximum (FWHM) for the Gaussian smearing of the theoretical peaks. Our numerical results show that incorporating invariance in the HydraGNN architecture significantly enhances both accuracy and generalizability in predicting UV-vis spectra of organic molecules.

Baker, Justin↗
DOE OSTI2024

$Z$-Pinch Interferometry Analysis With the Fourier-Based TNT Code

Here, we present the analysis of interferometry diagnostics with the user-friendly Talbot Numerical Tool (TNT), a Fourier-based postprocessing code that enables real-time assessment of plasma systems. TNT performance was explored with visible and infrared interferometry in pulsed-power-driven Z -pinch configurations to expand its capabilities beyond Talbot X-ray interferometry in the high-intensity laser environment. TNT enabled accurate electron density characterization of magnetically driven plasma flows and shocks through phase-retrieval methods that did not require data modification or masking. TNT demonstrated enhanced resolution, detecting below 4 % fringe shift, which corresponds to 8.7 × 10 15 cm –2 within 28 μ m, approaching the laser probing system limit. TNT was tested against a well-known interferometry analysis software, delivering an average resolving power nearly ten times better (~28 μ m versus ~ 210 μ m) when resolving plasma ablation features. TNT demonstrated higher sensitivity when probing sharp electron density gradients in supersonic shocks. A maximum electron areal density of 4.1 × 10 17 cm –2 was measured in the shocked plasma region, and a minimum electron density detection of ~ 1.0 × 10 15 cm –2 was achieved. When probing colliding plasma flows, the calculations of the effective adiabatic index and the associated errors were improved from γ* = 2.6 ± 1.6 – 1.4 ± 0.2 with TNT postprocessing, contributing valuable data for the interpretation of radiative transport. Additional applications of TNT in the characterization of pulsed-power plasmas and beyond are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Priorities, opportunities, and challenges for integrating microorganisms into Earth system models for climate change prediction

ABSTRACT Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a “top 10” list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy.

Microbiology↗
DOE OSTI2023

AMRIC: A Novel In Situ Lossy Compression Framework for Efficient I/O in Adaptive Mesh Refinement Applications

As supercomputers advance towards exascale capabilities, computational intensity increases significantly, and the volume of data requiring storage and transmission experiences exponential growth. Adaptive Mesh Refinement (AMR) has emerged as an effective solution to address these two challenges. Concurrently, error-bounded lossy compression is recognized as one of the most efficient approaches to tackle the latter issue. Despite their respective advantages, few attempts have been made to investigate how AMR and error-bounded lossy compression can function together. To this end, this study presents a novel in-situ lossy compression framework that employs the HDF5 filter to improve both I/O costs and boost compression quality for AMR applications. We implement our solution into the AMReX framework and evaluate on two real-world AMR applications, Nyx and WarpX, on the Summit supercomputer. Experiments with 512 cores demonstrate that AMRIC improves the compression ratio by 81X and the I/O performance by 39X over AMReX's original compression solution.

Wang, Daoce↗
DOE OSTI2024

OReole-FM: successes and challenges toward billion-parameter foundation models for high-resolution satellite imagery

While the pretraining of Foundation Models (FMs) for remote sensing (RS) imagery is on the rise, models remain restricted to a few hundred million parameters. Scaling models to billions of parameters has been shown to yield unprecedented benefits including emergent abilities, but requires data scaling and computing resources typically not available outside industry R&D labs. In this work, we pair high-performance computing resources including Frontier supercomputer, America's first exascale system, and high-resolution optical RS data to pretrain billion-scale FMs. Our study assesses performance of different pretrained variants of vision Transformers across image classification, semantic segmentation and object detection benchmarks, which highlight the importance of data scaling for effective model scaling. Moreover, we discuss construction of a novel TIU pretraining dataset, model initialization, with data and pretrained models intended for public release. By discussing technical challenges and details often lacking in the related literature, this work is intended to offer best practices to the geospatial community toward efficient training and benchmarking of larger FMs.

Ambrozio Dias, Philipe↗
DOE OSTI2026

ChatMPI: LLM-Driven MPI Code Generation for HPC Workloads

The Message Passing Interface (MPI) standard plays a crucial role in enabling scientific applications for parallel computing and is an essential component in high-performance computing (HPC). However, implementing MPI code manually—especially applying a proper domain decomposition and communication pattern—is a challenging and error-prone task. We present ChatMPI, an AI assistant for MPI parallelization of sequential C codes. In our analysis, we focus on testing six essential HPC workloads, which are based on Basic Linear Algebra Subprograms levels 1, 2, and 3 as well as sparse, stencil, and iterative operations. We analyze the process of creating ChatMPI by using the ChatHPC library. This lightweight large language model (LLM)–based infrastructure enables HPC experts to efficiently create and supervise trustworthy AI capabilities for critical HPC software tasks. We study the data required for training (fine-tuning) ChatMPI to generate parallel codes that not only use MPI syntax correctly but also apply HPC techniques to reduce memory communication and maximize performance by using proper work decomposition. With a relatively small training dataset composed of a few dozen prompts and fewer than 15 minutes of fine-tuning on one node equipped with two NVIDIA H100 GPUs, ChatMPI elevates trustworthiness for MPI code generation of current LLMs (e.g., Code Llama, ChatGPT-4o and ChatGPT 5). Additionally, we evaluate the performance of the MPI codes generated by ChatMPI in comparison with the ones generated by ChatGPT-4o and ChatGPT-5. The codes generated by ChatMPI provide up to a 4 × boost in performance by using better problem decomposition, communication patterns, and HPC techniques (e.g., communication avoiding).

Valero Lara, Pedro [ORNL] (ORCID:0000000214794310)↗
DOE OSTI2026

FLYING SERVING: On-the-Fly Parallelism Switching for Large Language Model Serving

Production LLM serving must simultaneously deliver high throughput, low latency, and sufficient context capacity under non-stationary traffic and mixed request requirements. Data parallelism (DP) maximizes throughput by running independent replicas, while tensor parallelism (TP) reduces per-request latency and pools memory for long-context inference. However, existing serving stacks typically commit to a static parallelism configuration at deployment; adapting to bursts, priorities, or long-context requests is often disruptive and slow. We present Flying Serving, a vLLM-based system that enables online DP-TP switching without restarting engine workers. Flying Serving makes reconfiguration practical by virtualizing the state that would otherwise force data movement: (i) a zero-copy Model Weights Manager that exposes TP shard views on demand, (ii) a KV Cache Adaptor that preserves request KV state across DP/TP layouts, (iii) an eagerly initialized Communicator Pool to amortize collective setup, and (iv) a deadlock-free scheduler that coordinates safe transitions under execution skew. Across three popular LLMs and realistic serving scenarios, Flying Serving improves performance by up to 4.79 × under high load and 3.47 × under low load while supporting latency- and memory-driven requests.

Gao, Shouwei [ORNL]↗