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At least 73 records · Page 4

X-ray nano-holotomography reconstruction with simultaneous probe retrieval

In conventional tomographic reconstruction, the pre-processing step includes flat-field correction, where each sample projection on the detector is divided by a reference image taken without the sample. When using coherent X-rays as a probe, this approach overlooks the phase component of the illumination field (probe), leading to artifacts in phase-retrieved projection images, which are then propagated to the reconstructed 3D sample representation. The problem intensifies in nano-holotomography with focusing optics, which, due to various imperfections creates high-frequency components in the probe function. Here, we present a new iterative reconstruction scheme for holotomography, simultaneously retrieving the complex-valued probe function. Implemented on GPUs, this algorithm results in 3D reconstruction resolving twice thinner layers in a 3D ALD standard sample measured using nano-holotomography.

Nikitin, Viktor

ORCHID: Orchestrated Retrieval-Augmented Classification of High-Risk Property with Intelligent Decision-Making

High-Risk Property (HRP) classification is critical at U.S. Department of Energy (DOE) sites, where inventories include sensitive and often dual-use equipment. Compliance must track evolving rules designated by various export control policies to make transparent and auditable decisions. Traditional expert-only workflows are time-consuming, backlog-prone, and struggle to keep pace with shifting regulatory boundaries. We propose ORCHID, a modular agentic framework for HRP classification that pairs retrieval-augmented generation (RAG) with human oversight to produce policy based outputs that can be audited. Small cooperating agents—retrieval, description refiner, classifier, validator, and feedback logger—coordinate via agent-to-agent messaging and invoke tools through the Model Context Protocol (MCP) for model-agnostic on-premise operation. The interface follows an "Item to Evidence to Decision" loop with step-by-step reasoning, on-policy citations, and append-only audit bundles (run-cards, prompts, evidence). In preliminary tests on real HRP cases, ORCHID improves accuracy and traceability over a non-agentic baseline while deferring uncertain items to Subject Matter Experts (SMEs). The demonstration shows single item submission, grounded citations, SME feedback capture, and exportable audit artifacts—illustrating a practical path to trustworthy LLM assistance in sensitive DOE compliance workflows.

Das, Sanjay [ORNL] (ORCID:0009000542591915)

Thermodynamic Profiling Through ASSIST Observations and TROPoe Retrievals

This report reviews the most relevant theoretical aspects of thermodynamic profiling techniques based on spectral observations from ASSIST-II infrared radiometers and TROPoe retrievals. The ASSIST+TROPoe system is a cutting-edge remote sensing technology deployed during the AWAKEN and WFIP3 field campaigns to estimate high-frequency profiles of temperature and humidity in the atmosphere. These profiles are highly valuable for characterizing atmospheric stratification, improving wind models, and understanding the impacts of wind plants on the climate. In this document, we discuss the operating principles of ASSIST, the physics of atmospheric infrared radiation, and the mathematical framework and capabilities of TROPoe. Sources of uncertainties in both the instrument and the retrieval method are also thoroughly addressed. This guide is designed to help users of ASSIST, TROPoe, and thermodynamic data in collecting, estimating, and applying thermodynamic profiles rigorously and scientifically.

17 WIND ENERGY

Constraining microphysical processes of warm rain formulation using advanced spectral separations, an ensemble retrieval framework and machine learning techniques

Drizzle, a common feature of marine boundary layer clouds formed through collision coalescence, plays a key role in cloud microphysics and evolution. Yet, simultaneously retrieving cloud and drizzle properties from remote-sensing observations remains challenging because drizzle droplets often dominate radar signals, masking cloud contributions. The goal of the proposed research is to provide constraints for the process of autoconversion and accretion using ARM cloud measurements. Specifically, we provide concurrent retrievals of cloud and drizzle that allows users to derive corresponding autoconversion and accretion rates.

54 ENVIRONMENTAL SCIENCES

Influences of lidar scanning parameters on wind turbine wake retrievals in complex terrain

Abstract. Scanning lidars enable the collection of spatially distributed measurements of turbine wakes and the estimation of wake properties such as magnitude, extent, and trajectory. Lidar-based characterizations, however, may be subject to distortions due to the observational system. Distortions can arise from the resolution of the measurement points across the wake, the projection of the winds onto the beam, averaging along the beam probe volume, and intervening evolution of the flow over the scan duration. Using a large-eddy simulation and simulated measurements with a virtual lidar model, we assess how scanning lidar systems may influence the properties of the retrieved wake using a case study from the Perdigão campaign. We consider three lidars performing range-height indicator sweeps in complex terrain, based on the deployments of lidars from the Danish Technical University (DTU) and German Aerospace Center (DLR) at the Perdigão site. The unwaked flow, measured by the DTU lidar, is well-captured by the lidar, even without combining data into a multi-lidar retrieval. The two DLR lidars measure a waked transect from different downwind vantage points. In the region of the wake, the observation system reacts to the smaller spatial and temporal variations of the winds, allowing more significant observation distortions to arise. While the measurements largely capture the wake structure and trajectory over its 4–5 D extent, limited spatial resolution of measurement points and volume averaging lead to a quicker loss of the two lobes in the near wake, smearing of the vertical bounds of the wake (< 30 m), wake center displacements up to 10 m, and dampening of the maximum velocity deficit by up to a third. The virtual lidar tool, coupled with simulations, provides a means for assessing measurement capabilities in advance of measurement campaigns.

17 WIND ENERGY

Large Language Model Integration for Knowledge Retrieval and Interaction for the DUNE Experiment

The Deep Underground Neutrino Experiment (DUNE) is a next-generation neutrino experiment that will generate an unprecedented volume of heterogeneous information-from documentation and technical notes to experimental data and reconstruction pipelines. Efficient knowledge retrieval and contextual understanding are increasingly critical for collaboration-wide productivity and onboarding. In this work, we present DUNE-GPT, a prototype framework that leverages large language models (LLMs) and retrieval-augmented generation (RAG) to enable natural-language querying of DUNE's internal documentation and technical resources. The system provides an intelligent interface for DUNE collaborators to interact with experiment-specific knowledge while maintaining data privacy and infrastructure compliance within Fermilab computing resources.

Rafique, A. [Argonne (main)]

FATHOMS-RAG: A Framework for the Assessment of Thinking and Observation in Multimodal Systems that use Retrieval Augmented Generation

Retrieval-augmented generation (RAG) has emerged as a promising paradigm for improving factual accuracy in large language models (LLMs). We introduce a benchmark designed to evaluate RAG pipelines as a whole, evaluating a pipelines ability to ingest several modalities of information. We present (1) a curated dataset of 93 questions designed to evaluate a pipeline's ability to ingest textual data, tables, images, multimodal data, and cross-document multimodal data; (2) a phrase-level recall metric for correctness; (3) a nearest-neighbor embedding classifier in an attempt to classify pipeline hallucinations; (4) a comparative evaluation of 2 pipelines built with open-source retrieval mechanisms and 4 closed-source foundational models; and (5) a third-party human evaluation of the alignment of our correctness and hallucination metrics. We find that closed-source pipelines significantly outperform open-source pipelines in both the correctness and halucination metrics, with a wider performance gap in questions relying on multimodal and cross-document information. We also find after a human evaluation of our correctness and hallucination metric compared with our questions and pipeline responses, average agreement was 4.62 for correctness 4.53 for hallucination detection on a 1-5 Likert scale with 5 being strongly agree with our determination.

Hildebrand, Samuel [ORNL] (ORCID:0009000465963104)

Shallow cumulus entrainment: observational retrieval, physical interpretation, and climate impacts (Final grant report)

This document constitutes a final technical report for DE-SC0020083, a research grant awarded by the US Department of Energy Office of Science, to Prof. Daniel Kirshbaum at McGill University. The original research proposal, entitled "Shallow cumulus entrainment: observational retrieval, physical interpretation, and climate impacts", defined four scientific objectives that synthesized ARM observations with turbulence-permitting large-eddy simulations (LES) to quantify and understand the process of cumulus entrainment, whereby a cumulus cloud ingests surrounding air through its lateral edges. These objectives included developing observational climatologies of cumulus bulk entrainment rate at two ARM observatories, physical interpretation of these findings using LES, quantification of the impacts of subcloud circulations on entrainment, and the climate impacts of flow-dependent entrainment variations. In the six years that have elapsed since the grant was awarded (three funded years and three no-cost annual extensions), all four of the objectives were successfully addressed. Four personnel were trained (one B.Sc., one M.Sc. to completion, five years of Ph.D. training, and 2.5 years of postdoctoral training), eight peer-reviewed articles were published in high-impact journals, and 20 presentations were delivered (three invited).

54 ENVIRONMENTAL SCIENCES

ESAC (EQ-SANS Assisting Chatbot): Application of large language models and retrieval-augmented generation for enhanced user experience at EQ-SANS

Neutron scattering experiments have played vital roles in exploring materials properties in the past decades. While user interfaces have been improved over time, neutron scattering experiments still require specific knowledge or training by an expert due to the complexity of such advanced instrumentation and the limited number of experiments each person may perform each year. This paper introduces an innovative chatbot application that leverages Large Language Models(LLM) and Retrieval-Augmented Generation (RAG) technologies to significantly enhance the user experience at the EQ-SANS, a small-angle neutron scattering instrument at the Spallation Neutron Source of Oak Ridge National Laboratory. Through a user-centric design approach, the EQ-SANS Assisting Chatbot (ESAC) serves as an interactive reference for users, thereby facilitating the use of the instrument by visiting scientists. By bridging the gap between the users of EQ-SANS and the control systems required to perform their experiments, the ESAC sets a new standard for interactive learning and support for the scientific community using large-scale scientific facilities.

97 MATHEMATICS AND COMPUTING

Aerosol Vertical Turbulent Mass Flux Retrievals Through Novel Remote Sensing Algorithm

Abstract Integrated measurements of aerosol, radiation, cloud, and turbulent transport in the planetary boundary layer (PBL) are essential for understanding and modeling climate and air quality. Here, we developed a new technique for the identification of convective turbulent regions and deriving the vertical distribution of aerosol turbulent mass fluxes within PBL. The algorithm uses retrievals from coherent Doppler lidars and a high spectral resolution lidar. The technique was applied to study particle mass fluxes over 2 months (November–December 2020) during the campaign conducted at the DOE Atmospheric Radiation Measurement Southern Great Plains (SGP) site in Lamont, Oklahoma. The algorithm developed here is capable of continuously deriving vertically resolved (curtains) aerosol mass fluxes. Our data analysis shows that at the site, the 30‐min averaged fluxes at 135 m above the surface were mainly positive (upward) at ∼1 μg m −2 s −1 , suggesting that the surface is the primary source of the particle mass supplied to the boundary layer at the SGP site. Analyses of the individual case studies have revealed that not all the derived fluxes can be linked to surface emissions. Both positive and negative values in a range of ±5 μg m −2 s −1 can be caused by convective thermals interacting between the residual layer and the mixed layer and by rotation of the horizontal wind with the height. Large erroneous negative fluxes can also be caused by drizzling/precipitating clouds. We anticipate that the application of the current technique will lead to a more realistic representation of aerosol mass budgets and bidirectional mixing rates.

54 ENVIRONMENTAL SCIENCES

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

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)

Pan-tropical daily L-band microwave land surface emissivity retrieval from GNSS-R observations

The uncertainties in microwave land surface emissivity (MLSE) measurements have long limited the use of spaceborne microwave radiometer data. As an emerging observation method, Global Navigation Satellite System Reflectometry (GNSS-R) has demonstrated great potential in several land and ocean applications. In this study, a method for obtaining daily MLSE dataset in the pan-tropical region from Cyclone GNSS (CYGNSS) observations is presented and evaluated. The CYGNSS observations are first aggregated into the Equal-Area-Scalable-Earth (EASE) 2.0 36 km grid by a combined weight function of distance, time, and signal-to-noise ratio variance. Then, the method employs a pixel-by-pixel regression algorithm to conduct the daily MLSE retrieval using reference emissivity derived from the Soil Moisture Active Passive (SMAP) brightness temperature. The CYGNSS MLSE shows good agreement with SMAP MLSE, delivering an overall root-mean-square error (RMSE) of 0.022 and 0.017 for horizontal and vertical polarization, respectively, during the training set spanning the whole year of 2018. Furthermore, on the test set from January 2019 to May 2019, the RMSE values amounted to 0.030 and 0.023 for horizontal and vertical polarization, respectively. Temperature records from the International Soil Moisture Network are employed to calculate the emissivity and for in-situ validation, which yield an RMSE of 0.034 and 0.026 for the two polarizations, respectively. The proposed algorithm provides an encouraging approach to obtain accurate daily MLSE dataset for microwave remote sensing. Compared to the SMAP MLSE, the CYGNSS MLSE has a remarkable improvement of 86% in temporal resolution, greatly complementing the existing microwave emissivity datasets.

54 ENVIRONMENTAL SCIENCES

Lost in OCR Translation? Vision-Based Approaches to Robust Document Retrieval

Code for ‘Lost in OCR Translation?’: robust document retrieval under degradation. Compares OCR-based, vision-only, and hybrid pipelines; includes SambaNova LLaMA Vision OCR, Nougat, and ViDoRe baselines. Provides QA data generation, RAG evaluation, and metrics (Levenshtein, nDCG@k, Recall@k, EM/F1) with reproducible scripts. Includes dataset guides

Bhattarai, Manish [Los Alamos National Labs]

Combined speckle- and propagation-based single shot two-dimensional phase retrieval method

Single-shot two-dimensional (2D) phase retrieval (PR) can recover the phase shift distribution within an object from a single 2D x-ray phase contrast image (XPCI). Two competing XPCI imaging modalities often used for single-shot 2D PR to recover material properties critical for predictive performance capabilities are: speckle-based (SP-XPCI) and propagation-based (PB-XPCI) XPCI imaging. However, PR from SP-XPCI and PB-XPCI images are, respectively, limited to reconstructing accurately slowly and rapidly varying features due to noise and differences in their contrast mechanisms. Herein, we consider a combined speckle- and propagation-based XPCI (SPB-XPCI) image by introducing a mask to generate a reference pattern and imaging in the near-to-holographic regime to induce intensity modulations in the image. We develop a single-shot 2D PR method for SPB-XPCI images of pure phase objects without imposing restrictions such as object support constraints. It is compared against PR methods inspired by those developed for SP-XPCI and PB-XPCI on simulated and experimental images of a thin glass shell before and during shockwave compression. Reconstructed phase maps show improvements in quantitative scores of root-mean-square error and structural similarity index measure using our proposed method.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Deep learning-based temporal deconvolution for photon time-of-flight distribution retrieval

The acquisition of the time of flight (ToF) of photons has found numerous applications in the biomedical field. Over the last decades, a few strategies have been proposed to deconvolve the temporal instrument response function (IRF) that distorts the experimental time-resolved data. However, these methods require burdensome computational strategies and regularization terms to mitigate noise contributions. Herein, we propose a deep learning model specifically to perform the deconvolution task in fluorescence lifetime imaging (FLI). The model is trained and validated with representative simulated FLI data with the goal of retrieving the true photon ToF distribution. Its performance and robustness are validated with well-controlled in vitro experiments using three time-resolved imaging modalities with markedly different temporal IRFs. The model aptitude is further established with in vivo preclinical investigation. Overall, these in vitro and in vivo validations demonstrate the flexibility and accuracy of deep learning model-based deconvolution in time-resolved FLI and diffuse optical imaging.

Pandey, Vikas (ORCID:0000000154771095)

Molecular Vision - Multimodal, multitask retrieval of molecular structure from measured signatures for reference-free compound identification

We are currently at risk of generating false conclusions based on limited methods to identify small molecules in biological systems and in chemical forensics. By definition, the chemical structures of novel small molecules have not been determined, let alone measured or synthesized. Currently, unambiguous structure determination of small molecules is constrained by the time and effort needed to isolate compounds and perform de novo structure elucidation using laboratory-based methods, significantly extending the time to inform mitigation strategies. To address this gap, we have developed a deep learning approach to directly map molecular structure to experimental signatures. We aim to unify measurement technologies employed in untargeted small molecule identification studies—such as infrared (IR) spectrometry, tandem mass spectrometry (MS/MS), ion mobility spectrometry-derived collision cross section (CCS)—through use of a multimodal, multitask deep learning architecture. Where existing methods require direct generation of information-rich spectra and/or properties, an inherently difficult task, we will simplify molecular signature-based identification by posing the problem as a recognition or retrieval task. The model is thus presented with relevant endpoints – structure and one or more molecular signatures – and need only determine whether they are semantically related. Thus, our approach offers the following advantages over existing techniques: (i) circumvents difficulties associated with direct generation of molecular signatures from structure and structure from signatures; (ii) incorporates multiple molecular signatures simultaneously, as available, to support identification; and (iii) enables rapid computation of structural embeddings toward broad coverage of known chemical space. Taken together, the approach removes the need to explicitly obtain or compute reference spectra, representing a powerful method for compound identification that requires only experimentally observed signatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Continuous Baseline Microphysical Retrieval (MICROBASE) Value-Added Product Report

This technical report describes the Continuous Baseline Microphysical Retrieval (MICROBASE) Value-Added Product (VAP) produced operationally by the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) User Facility. MICROBASE provides a continuous estimate of cloud microphysical properties at ARM fixed observatories and ARM Mobile Facility (AMF) sites. It is designed to run operationally and provide data to the ARM Data Center for scientific distribution. This technical report presents an overview of the VAP as a resource for data users and ongoing records for major updates to these products.

54 ENVIRONMENTAL SCIENCES