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Results for “structure retrieval”

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
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Generative modeling enables molecular structure retrieval from Coulomb explosion imaging

Capturing the structural changes that molecules undergo during chemical reactions in real space and time is a long-standing dream and an essential prerequisite for understanding and ultimately controlling femtochemistry. A key approach to tackle this challenging task is Coulomb explosion imaging, which benefited decisively from recently emerging high-repetition-rate X-ray free-electron laser sources. With this technique, information on the molecular structure is inferred from the momentum distributions of the ions produced by the rapid Coulomb explosion of molecules. Retrieving molecular structures from these distributions poses a highly non-linear inverse problem that remains unsolved for molecules consisting of more than a few atoms. Here, we address this challenge using a diffusion-based Transformer neural network. We show that the network reconstructs unknown molecular geometries from ion-momentum distributions with a mean absolute error below one Bohr radius, which is half the length of a typical chemical bond.

Artificial Intelligence (cs.AI)↗
DOE OSTI2025

Direct structural retrieval from gas-phase ultrafast diffraction data using a genetic algorithm

Ultrafast scattering techniques such as ultrafast electron diffraction and ultrafast x-ray diffraction have been utilized to elucidate the structural dynamics, reaction intermediates, and final products in molecular reactions following photoexcitation. The time-dependent structures are typically not directly retrieved from the experimental data, but they rely on comparison with calculations. The genetic algorithm (GA), a global optimization strategy, can be used to retrieve the molecular structures directly from diffraction patterns without any theoretical input. However, the robustness of the GA with respect to real experimental conditions such as a limited momentum transfer range, noise, and artifacts has not been studied in detail. In this work, we characterize the performance of the GA with simulated data that mimic realistic experimental conditions. We have developed and implemented a variant of the GA specific to diffraction measurements which performs better in the presence of imperfect data compared to the standard implementation of the GA. We demonstrate this method with both synthetic data and experimental ultrafast electron diffraction data on the UV-induced photodissociation of trifluoroiodomethane (C⁢F 3⁡ I) molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Quantitative Structure Determination from Experimental Four-Dimensional Scanning Transmission Electron Microscopy via the Scattering Matrix

Considerable inroads have recently been made on algorithms to determine the sample potential from four-dimensional scanning transmission electron microscopy data from thick samples where multiple scattering cannot be neglected. This paper further develops the scattering matrix approach to such structure determination. Through simulation, we demonstrate how this approach can be modified to better handle partial spatial coherence, unknown probe defocus, and information from the dark field region. By combining these developments we reconstruct the electrostatic potential of a monolithic SrTiO 3 crystal showing good quantitative agreement with the expected structure.

4D STEM↗
DOE OSTI2025

An Open-source Llm Enhanced-tool Specialized In Helping Moose Related Problems And Tasks

MOOSEenger is an open-source, terminal-first chat application for the MOOSE ecosystem that couples specialized parsing of MOOSE documentation and “.i” input files with retrieval-augmented generation to deliver grounded answers about multiphysics modeling and workflows. It includes dedicated readers for MOOSE-style HTML and a pyhit-based parser that uses the MOOSE syntax tree to preserve block structure and attach retrieval metadata. A data-ingestion pipeline performs semantic chunking into atomic facts and stores them hierarchically in a local Chroma vector database that maintains parent–child relationships across documents; the system can ingest directories, individual files, and single-page web content, and it provides CRUD operations (insert, update, delete) to manage the corpus. At query time, relevant chunks are embedded, retrieved, and fused into the model context, with interactive features such as token streaming, persistent chat history, and dynamic RAG (retrieval triggered by user input or intermediate model output). Deployment is flexible: MOOSEenger runs with local Ollama models or remote Hugging Face/OpenAI backends—typically coordinating generation, lightweight tagging/summarization, and embeddings across three models—and it also supports a server mode and integration with the VS Code Continue interface.

Li, Mengnan [Idaho National Laboratory (INL), Idah↗
DOE OSTI2024

Lambda baryon production in neutrino-nucleus interactions and light signals reconstruction in the Short-Baseline Near Detector

The field of neutrino physics is nowadays entering the era of precision measurements, with new detectors capable of capturing neutrino interactions with unprecedented detail and high intensity neutrino beams. Liquid Argon Time Projection Chambers (LArTPCs) have become one of the main neutrino detection technologies, providing excellent imaging capabilities and particle identification. The Short-Baseline Near Detector (SBND) at Fermilab is a LArTPC experiment designed to capture neutrinos from the Booster Neutrino Beam (BNB). Its proximity to the beam target (110\,m) and large size (112\,ton) enable the recording of millions of neutrino interactions annually. SBND provides the highest statistics worldwide for neutrino-argon cross-section measurements, facilitating the study of rare channels like Cabibbo-suppressed quasielastic hyperon production. Specifically, this thesis focuses on neutral $\Lambda$ baryon production for which only tens of events have been observed up to date. Our work introduces a novel selection strategy leveraging LArTPC imaging capabilities to identify the distinctive decay signatures of $\Lambda$ baryons, enhancing sensitivity to this channel. Besides being a very mature technology, LArTPCs are an evolving technology. Part of the focus of the new developments lies in harnessing the potential of scintillation light signals. The Photon Detection System (PDS) in SBND has been designed to provide an efficient detection of the scintillation light, representing a major R\&D opportunity in the LArTPC community. Its design provides a high and more uniform light yield, an excellent timing resolution and an independent 3D reconstruction of the events, including the drift coordinate, using exclusively the light signals. This work presents the first comprehensive study of the SBND PDS capabilities. The new developments in the simulation and reconstruction of the light signals in SBND are presented. The whole chain is applied to accurately tag neutrino events through timing information, with a predicted resolution $\mathcal{O}$(2\,ns), and ultimately retrieve the pulse structure of the BNB.

43 PARTICLE ACCELERATORS↗
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

Projected Urban Morphology of the Los Angeles Area by the Year 2100

This dataset provides projections of urban building morphologies for the Los Angeles urban area at 30-meter spatial resolution. It contains 192 raster files that detail two primary building attributes: building footprint fractions (ranging from 0 to 1) and average building heights (ranging from 0 to 75 meters). The projections account for a wide range of future pathways, covering two Shared Socioeconomic Pathway (SSP) scenarios (SSP3 and SSP5), two population scenarios, two developed land intensification scenarios, and four distinct levels of intensification. The dataset was created using dual Generative Adversarial Networks (GANs) trained on 2015 land cover and building properties from the National Land Cover Database (NLCD) and Model America datasets. Supporting information on the dataset has been described in the LAUrbanAreaMorphologyProjections2100_README.txt file.

Pandey, Bhartendu↗
DOE OSTI2026

Agentic artificial intelligence for multistage physics experiments at a large-scale user facility particle accelerator

We present a language-model-driven agentic artificial intelligence (AI) system to autonomously execute multistage physics experiments on a production synchrotron light source. Implemented at the Advanced Light Source particle accelerator, the system translates natural language user prompts into structured execution plans that combine archive data retrieval, control-system channel resolution, automated script generation, controlled machine interaction, and analysis. In a representative machine physics task, we show that preparation time was reduced by 2 orders of magnitude relative to manual scripting even for a system expert, while operator-standard safety constraints were strictly upheld. Core architectural features, plan-first orchestration, bounded tool access, and dynamic capability selection, enable transparent, auditable execution with fully reproducible artifacts. These results establish a blueprint for the safe integration of agentic AI into accelerator experiments and demanding machine physics studies, as well as routine operations, with direct portability across accelerators worldwide and, more broadly, to other large-scale scientific infrastructures.

Accelerator/storage ring control systems↗
DOE OSTI2026

REFSafE: A RAG-Enabled Framework for Predictive Risk Analysis and Automated Safety Report Generation in Mission-Critical Environments

Operational safety in mission-critical environments requires AI systems that are accurate, interpretable, and resistant to hallucination. We present an agentic Retrieval-Augmented Generation (RAG) framework, REFSafe, for grounded hazard analysis and automated safety report generation. The system integrates Large Language Models (LLMs) with structured operational data, historical incident repositories, policy documents, and external authoritative sources. Through iterative agentic reasoning, the framework retrieves, verifies, and synthesizes evidence prior to generation, enforcing citation-backed outputs with explicit source attribution (documents, links, and prior events) to ensure traceability and trust. To mitigate hallucinations and unsupported claims, all risk assessments and forecasts are constrained to retrieved evidence, with confidence signals derived from retrieval relevance and source consistency. A transparent pipeline enables subject matter experts (SMEs) to validate predictions, and provide structured feedback, forming a continuous performance calibration loop. Preliminary deployment demonstrates improved reliability in hazard detection and safety/vulnerability report generation. This work advances trustworthy, evidence-grounded AI for predictive safety intelligence in mission-critical operations.

Das, Sanjay [ORNL] (ORCID:0009000542591915)↗
DOE OSTI2026

Cross-Domain Reasoning for Neuromorphic Model Design

Designing performant neuromorphic models requires reasoning across neuroscience, neuromorphic computing, and machine learning, making it a natural target for cross-domain hypothesis generation. Our primary contribution is a multi-corpus knowledge graph spanning all three domains, which we show substantially increases cross-domain retrieval novelty over single-corpus baselines. We additionally introduce NeuKReAct, an agentic reasoning framework that iteratively retrieves from this graph and synthesizes design hypotheses via a step-by-step blackboard architecture, enabling structured compartmentalization of design decisions. Lastly, we introduce an execution head that translates hypotheses into structured design documents and runnable code. We evaluate novelty using a combinatorial creativity metric that measures cross-domain retrieval distance across the citation graph. Our results confirm that corpus breadth is the dominant driver of novelty. Moreover, we highlight a concrete instance of the novelty-utility tradeoff within NeuKReAct, underscoring a need for joint creativity evaluation, balancing both novelty and utility.

Ramavarapu, Vikram [ORNL] (ORCID:0009000188757213)↗
DOE OSTI2026

MCNPy

SAND2026-20425O MCNPy runs and analyzes simulations from MCNP, a software that models radiation transport of neutrons and gamma rays. MCNPy uses Python to start MCNP, retrieve event data files, and convert them into graph structures for detailed analysis. It offers visualization tools, including 2D views of particle histories, making complex simulation data easier to interpret for researchers and engineers. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Nowack, Aaron [Sandia National Lab. (SNL-CA), Live↗
DOE OSTI2025

PhaseT3M: 3D imaging at 1.6 Å resolution via electron cryo-tomography with nonlinear phase retrieval

Electron cryo-tomography (cryo-ET) enables 3D imaging of complex, radiation-sensitive structures with molecular detail. However, image contrast from the interference of scattered electrons is nonlinear with atomic density and multiple scattering further complicates interpretation. These effects degrade resolution, particularly in conventional reconstruction algorithms, which assume linearity. Particle averaging can reduce such issues but is unsuitable for heterogeneous or dynamic samples ubiquitous in biology, chemistry, and materials sciences. Here, we develop a phase retrieval-based cryo-ET method, PhaseT3M. We experimentally demonstrate its application to an approximately 7 nm Co3O4 nanoparticle on an approximately 30 nm carbon substrate, achieving a maximum resolution of 1.6 Å, surpassing conventional limits using standard cryo-TEM equipment. PhaseT3M uses a multislice model for multiple scattering and Bayesian optimization for alignment and computational aberration correction, with a positivity constraint to recover ‘missing wedge’ information. Applied directly to biological particles, it enhances reconstruction quality and reduces artifacts, establishing a standard for routine 3D imaging with phase contrast.

Biophysics↗
DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗
DOE OSTI2025

Self-supervised physics-informed generative networks for phase retrieval from a single X-ray hologram

X-ray phase contrast imaging significantly improves the visualization of structures with weak or uniform absorption, broadening its applications across a wide range of scientific disciplines. Propagation-based phase contrast is particularly suitable for time- or dose-critical in vivo/in situ/operando (tomography) experiments because it requires only a single intensity measurement. However, the phase information of the wave field is lost during the measurement and must be recovered. Conventional algebraic and iterative methods often rely on specific approximations or boundary conditions that may not be met by many samples or experimental setups. In addition, they require manual tuning of reconstruction parameters by experts, making them less adaptable for complex or variable conditions. Here we present a self-learning approach for solving the inverse problem of phase retrieval in the near-field regime of Fresnel theory using a single intensity measurement (hologram). A physics-informed generative adversarial network is employed to reconstruct both the phase and absorbance of the unpropagated wave field in the sample plane from a single hologram. Unlike most state-of-the-art deep learning approaches for phase retrieval, our approach does not require paired, unpaired, or simulated training data. This significantly broadens the applicability of our approach, as acquiring or generating suitable training data remains a major challenge due to the wide variability in sample types and experimental configurations. The algorithm demonstrates robust and consistent performance across diverse imaging conditions and sample types, delivering quantitative, high-quality reconstructions for both simulated data and experimental datasets acquired at beamline P05 at PETRA III (DESY, Hamburg), operated by Helmholtz-Zentrum Hereon. Furthermore, it enables the simultaneous retrieval of both phase and absorption information.

36 MATERIALS SCIENCE↗
DOE OSTI2026

The ABCs of phase retrieval: Connecting the acronyms of scanning transmission electron microscopy

High-resolution scanning transmission electron microscopy (S/TEM) is an indispensable tool for characterizing the structure and properties of materials down to the atomic scale. Conventional S/TEM imaging, however, is limited by the phase problem, whereby the phase of the electron exit wave is lost upon detection. Recent advances in diffractive imaging and 4D-STEM have enabled a range of phase-retrieval techniques that computationally reconstruct the missing information encoded in the phase of the transmission function. These approaches offer improved dose efficiency and enhanced sensitivity to weakly scattering signals, extending quantitative imaging to beam-sensitive materials composed of light elements. In this work, we introduce the phase problem in electron microscopy and survey the diverse landscape of phase-retrieval techniques used in the field. Despite their many acronyms and algorithmic variations, these techniques share a common physical and mathematical foundation. We present a unified framework that connects these seemingly distinct methods, from parallax imaging and tilt-corrected bright-field (tcBF-STEM), to aberration-corrected bright-field (acBF-STEM), optimum bright-field (OBF-STEM) and single-sideband (SSB) ptychography, as well as first-moment integrated center of mass techniques (iCOM) and iterative ptychographic algorithms. Based on these insights, we discuss the opportunities and practical limitations of applying these methods across different materials systems, detector designs, and microscope configurations.Graphical abstractRepresentative electron microscopy configurations used for phase retrieval and diffractive imaging in S/TEM: (a) Zernike phase-contrast transmission electron microscopy (TEM), (b) small-convergence-angle four-dimensional scanning transmission electron microscopy (4D-STEM) for nanobeam-based phase reconstruction methods, and (c) large-convergence-angle 4D-STEM for ptychographic and related diffractive imaging techniques reviewed in this work.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Light storage, retrieval, and controllable interference in an atomic tripod system

Highly efficient quantum memories are essential for advancing quantum information processing technologies, including scalable quantum computing and quantum networks. We experimentally demonstrate a light storage and retrieval protocol in a tripod system using an ensemble of laser-cooled 87 Rb atoms. The tripod system, which consists of three ground states and an excited state, offers rich dynamics: its use to coherently store and retrieve a weak probe pulse in the 87 Rb 𝐹 = 1 ground-state manifold leads to the interference of two spin-wave excitations during storage time that translate to an interference in the peak intensity of the retrieved probe pulse. Our work shows that these interferences, which manifest when varying the pulse sequence or energy level structure, can be controlled experimentally by varying the storage time, optical phase, and magnetic field strength. Theoretical simulations exhibit excellent agreement with the experimental results. In conclusion, this work demonstrates the rich dynamics and versatile capabilities of atomic tripod systems for light storage and retrieval, with key advantages over conventional Λ systems, highlighting the potential of atomic tripod systems for applications in quantum information processing, quantum synchronization, and atomic memory protocols.

Coherent control↗
DOE OSTI2025

Towards philosophical reasoning with agentic LLMs: Socratic method for scientific assistance

As large language models (LLMs) become central tools in science, improving their reasoning capabilities is critical for meaningful and trustworthy applications. We introduce a Socratic agent for scientific reasoning, implemented through a structured system prompt that guides LLMs via classical principles of inquiry. Unlike typical prompt engineering or retrieval-based methods, our approach leverages definition, analogy, hypothesis elimination, and other Socratic techniques to generate more coherent, critical, and domain-aware responses. We evaluate the agent across diverse scientific domains and benchmark it on the abstraction and reasoning corpus challenge dataset, achieving 97.15% under a fixed prompting protocol and without fine-tuning or external tools. Expert evaluation shows improved reasoning depth, clarity, and adaptability over conventional LLM outputs, suggesting that structured prompting rooted in philosophical reasoning can improve the scientific utility of language models.

LLM reasoning↗
DOE OSTI2025

Enabling Robust Exoplanet Atmospheric Retrievals with Gaussian Processes

Atmospheric retrievals are essential tools for interpreting exoplanet transmission and eclipse spectra, enabling quantitative constraints on the chemical composition, aerosol properties, and thermal structure of planetary atmospheres. The James Webb Space Telescope (JWST) offers unprecedented spectral precision, resolution, and wavelength coverage, unlocking transformative insights into the formation, evolution, climate, and potential habitability of planetary systems. However, this opportunity is accompanied by challenges: modeling assumptions and unaccounted-for noise or signal sources can bias retrieval outcomes and their interpretation. To address these limitations, we introduce a Gaussian process (GP)-aided atmospheric retrieval framework that flexibly accounts for unmodeled features and correlated noise in exoplanet spectra. We validate this method on synthetic JWST observations, and show that GP-aided retrievals reduce bias in inferred abundances and better capture model–data mismatches than traditional approaches. We also introduce the concept of mean squared error to quantify the trade-off between bias and variance, arguing that this metric more accurately reflects retrieval performance than bias alone. We then reanalyze the NIRISS/SOSS JWST transmission spectrum of WASP-96 b, finding that GP-aided retrievals yield broader constraints on CO 2 and H 2 O, possibly alleviating tension between previous retrieval results and equilibrium predictions. Our GP framework provides precise and accurate constraints while highlighting regions where models fail to explain the data. As JWST matures and future facilities come online, a deeper understanding of the limitations of both data and models will be essential, and GP-enabled retrievals like the one presented here offer a principled path forward.

Rotman, Yoav [Arizona State Univ., Tempe, AZ (Unit↗