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At least 415 records · Page 23

Toward Intelligent Multimodal Holography for Real-Time Chemical Imaging of Dynamic Ion Separation

Molecular-level visualization of ion transport and separation dynamics in complex environments is crucial for advancing energy systems, water purification, and critical materials recovery. Achieving this requires imaging platforms that combine structural sensitivity, chemical specificity, and real-time operation. Digital off-axis holography (DOAH) provides high-throughput, label-free quantitative phase imaging but inherently lacks chemical selectivity. Integrating DOAH with complementary spectroscopic channels such as fluorescence or hyperspectral imaging introduces the needed molecular specificity, while also creating challenges in multimodal data fusion, synchronization, and computational throughput. Artificial intelligence offers a powerful route to address these limitations by uniting physics-based reconstruction with data-driven interpretation. In this Perspective, we outline a framework for intelligent multimodal holography and demonstrate its potential using a preliminary AI-driven test case. Raw DOAH holograms of lanthanide solutions subjected to magnetic field gradients were analyzed using multi-agent AI workflows that autonomously selected reconstruction tools, extracted NMF components, and generated scientific claims consistent with true paramagnetic and diamagnetic behavior. This demonstration shows how AI-enabled reasoning can deliver real-time chemical–structural interpretation directly from raw holograms. Together, these advances define a path toward adaptive, intelligent holography platforms capable of supporting in situ chemical separations, dynamic ion transport analysis, and next-generation interfacial science.

Ricchiuti, Giovanna↗

Advanced techniques in automated high-resolution scanning transmission electron microscopy

Scanning transmission electron microscopy is a common tool used to study the atomic structure of materials. It is an inherently multimodal tool allowing for the simultaneous acquisition of multiple information channels. Despite its versatility, however, experimental workflows currently rely heavily on experienced human operators and can only acquire data from small regions of a sample at a time. Here, we demonstrate a flexible pipeline-based system for high-throughput acquisition of atomic-resolution structural data using an all-piezo sample stage applied to large-scale imaging of nanoparticles and multimodal data acquisition. As a result, the system is available as part of the user program of the Molecular Foundry at Lawrence Berkeley National Laboratory.

4D-STEM↗

Accelerating Traction Motor Optimization Design with AI Surrogate Models

The advancement of artificial intelligence systems enables the use of data-driven physics-based surrogate models to explore design spaces rapidly and deeply for engineering projects. This work presents a surrogate model workflow that accelerates electric traction motor design optimization by replacing finite element analysis (FEA) with an artificial neural network (ANN) and using this model in a genetic algorithm for design optimization. A baseline interior permanent-magnet motor is parameterized and sampled to generate FEA-labeled training data, after which a feed-forward ANN predicts key outputs (e.g., loss components and weight). The validated surrogate enables genetic-algorithm optimization and deep search over the design space without new FEA runs, producing Pareto-optimal trade-offs between weight and losses and set of optimized designs for rapid downselection of manufacturable motor designs.

Ribeiro, Pedro [ORNL] (ORCID:0009000921026641)↗

ESMs Latent Space Exploration for Uncertainty Quantification and Spatiotemporal Downscaling

This final report for DOE Award DE-SC0023044 presents advances in two key areas of climate modeling: (1) representative climate model selection and (2) Earth System Model (ESM) downscaling using hybrid AI methods. The first section introduces a reordered, three-stage workflow to select representative GCM runs that more effectively balance historical skill with ensemble spread, validated across Texas, Bihar, and New York. The second section introduces two novel super-resolution frameworks, ViSIR and ViFOR, that integrate Vision Transformers with sinusoidal and Fourier-based implicit neural representations. These models achieve state-of-the-art reconstruction accuracy for ESM variables including surface temperature and heat fluxes. The report includes detailed methodology, benchmarks, and results, demonstrating significant gains in uncertainty quantification, spatial fidelity, and scalability for climate-impact studies.

54 ENVIRONMENTAL SCIENCES↗

FY25 Theory and Simulation Performance Target: Development of an integrated modeling framework for fusion reactor design and assessment (Final Report)

This report documents the FY25 Theory and Simulation Performance Target (TSPT) of developing an integrated modeling framework for fusion reactor design and assessment (FREDA). Over Q1-Q4, new capabilities were developed across both plasma and engineering domains and demonstrated on an example representation of a Compact Advanced Tokamak with a Dual Cooled Lead Lithium blanket. This represents a first-of-a-kind demonstration of coupled core-to-wall-to-engineering for a reactor. Self-consistent CESOL workflows were applied to provide core, pedestal, and SOL prediction; new modules were developed for energetic particle stability (FAR3D) and transport (TGLF-EP) analysis; and boundary plasma modeling (SOLPS-ITER, BOUT++/Hermes-3) was expanded to evaluate wall and divertor heat fluxes and interface with engineering thermal analysis. A parameterized CAD tool, TRACER, was expanded to generate medium-fidelity divertor, blanket, and coil geometries; OpenFOAM and Diablo workflows were applied for first-wall and divertor thermal analyses with helium cooling; and reduced-order models were created for high-mass-flux divertor cooling. Magnet multiphysics capabilities were verified between Elmer, Diablo, and a new MFEM-based solver, and workflows enable stress, thermal, and neutron-fluence analysis of TF coils with neutronics-driven heating. Nuclear and blanket analysis workflows were demonstrated, including tritium breeding, transport, and CFD-informed thermo-mechanical assessment. Preliminary multi-fidelity uncertainty quantification workflows were applied to boundary modeling codes and shown to achieve variance reductions with fewer high-fidelity boundary simulations. Key findings highlight the challenges of resolving the ITEP gap to find suitable balance between wall and divertor loads, neutron heating, and practical limits of PFC cooling. Next step priorities are to develop automated workflows to check boundary code convergence and detachment, implement tighter physics-engineering CAD provenance tracking, and inclusion of plasma-material interface models for SLAG and tungsten cracking behavior. Collectively, these developments establish sophisticated capabilities for predictive, multi-fidelity, whole-device modeling that integrates plasma physics, materials, magnets, and nuclear engineering to guide pathways to viable Fusion Pilot Plant design points.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Performance and Reliability Assessment of the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) Data Advisor (ADA)

The Atmospheric Radiation Measurement (ARM) User Facility provides one of the world's largest openly accessible repositories of atmospheric observations through the ARM Data Discovery platform. Although the repository contains more than three decades of measurements collected from permanent observatories, mobile facilities, aircraft campaigns, and field experiments, identifying appropriate datasets can be challenging, particularly for new users unfamiliar with ARM instrumentation and datastream organization. To improve data accessibility, the ARM Data Center developed the ARM Data Advisor (ADA), an artificial intelligence-powered assistant designed to facilitate scientific data discovery, dataset interpretation, and user guidance. This report evaluates ADA's performance as a domain-specific scientific assistant using realistic atmospheric science workflows. The evaluation examines five key capabilities: data retrieval and curation efficiency, hallucination resistance, scientific reasoning, response to ambiguous queries, and content retention and session continuity. Representative prompts were developed to simulate typical interactions between researchers and the ARM Data Discovery platform, and ADA's responses were assessed for retrieval completeness, scientific accuracy, consistency, and practical usefulness. In these representative tests, ADA reduced the complexity of discovering and accessing ARM datasets by recommending appropriate datastreams, explaining instrumentation, interpreting metadata, and assisting with data processing workflows. ADA also exhibits strong domain knowledge of atmospheric science terminology and generally resists hallucination by acknowledging unavailable datasets and requesting clarification when appropriate. Overall, the results indicate that ADA represents a promising advancement in scientific data discovery within the ARM User Facility and has considerable potential to improve researcher productivity, particularly for new users and interdisciplinary scientists seeking efficient access to ARM observations.

Salvador, Christian [ORNL] (ORCID:0000000283287777↗

Advanced Research Directions on AI for Science, Energy, and Security: Report on Summer 2022 Workshops

Over the past decade, fundamental changes in artificial intelligence (AI)—from foundational to applied—have delivered dramatic insights across a wide breadth of U.S. Department of Energy (DOE) mission space. AI is helping to augment and improve scientific and engineering workflows (e.g., for control, design, and dramatic performance gains through surrogate models) in national security, the Office of Science, and DOE’s applied energy programs. The progress and potential for AI in DOE science was captured in the 2020 “AI for Science” report from the DOE laboratory community in collaboration with academia and industry. Specific scientific areas ready to further leverage the power of AI ranged from the scale and performance of computational models to data analysis to creating new classes of observations using computer vision. Since that report, the scale and scope of scientific AI have accelerated, revealing new, emergent properties that yield insights that go beyond enabling opportunities to being potentially transformative in the way that scientific problems are posed and solved. Thus, under the guidance of both the Office of Science (SC) and the National Nuclear Security Administration (NNSA), the DOE national laboratories organized a series of workshops in 2022 to gather input on new and rapidly emerging opportunities and challenges of scientific AI. This 2023 report is a synthesis of those workshops. The scientific community believes AI can have a foundational impact on a broad range of DOE missions, including science, energy, and national security. Further, DOE has unique capabilities that enable the community to drive progress in scientific use of AI, building on long-standing DOE strengths and investments in computation, data, and communications infrastructure, spanning the Energy Sciences Network (ESnet), the Exascale Computing Project (ECP), and integrative programs such as the NNSA Office of Defense Programs Advanced Simulation and Computing (ASC) and the SC Scientific Discovery through Advanced Computing (SciDAC) programs.

97 MATHEMATICS AND COMPUTING↗

SAGIPS: a physics-inspired scalable asynchronous generative inverse-problem solver

Abstract Solving large-scale inverse problems using deep-learning algorithms have become an essential part of modern research and industrial applications. The complexity of the underlying inverse problem may require the utilization of high performance computing systems which poses a challenge on the algorithmic design of the inverse problem solver. Most deep learning algorithms require, due to their design, custom parallelization techniques in order to be resource efficient while showing a reasonable convergence. In this paper we introduce a S calable A synchronous G enerative I nverse P roblem S olver (SAGIPS) on high-performance computing systems. We present a workflow that utilizes an asynchronous ring-allreduce algorithm to transfer the gradients of the generator network across multiple GPUs. Experiments with a scientific proxy application demonstrate that SAGIPS shows near linear weak scaling, together with a convergence quality that is comparable to traditional methods. The approach presented here allows leveraging Generative Adverserial Network across multiple GPUs, promising advancements in solving complex inverse problems at scale.

97 MATHEMATICS AND COMPUTING↗

Shaping the FutureWorkforce: Challenges and Lessons Learned in HPC Education from National Labs and Computing Centers

Workforce training at national laboratories and computing centers is essential and typically falls into two categories: foundational training for newcomers and advanced training for experienced users. Foundational topics—such as version control, build systems, and basic HPC usage—are largely transferable across institutions, while cluster-specific training varies due to differences in hardware, job schedulers, and local workflows. Training on emerging technologies is split between hardware-specific content and broadly applicable programming paradigms. Here, to reduce redundancy and increase impact, national labs, computing centers, and vendors are collaborating through initiatives like the HPC Training Working Group to share best practices, co-develop materials, and broaden outreach. These coordinated efforts aim to make HPC training more accessible, scalable, and consistent across the community.

HPC↗

Data for "Discovery, Characterization, and Application of Chromosomal Integration Sites in the Hyperthermophilic Archaeon Sulfolobus islandicus"

Sulfolobus islandicus , an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.

AI/ML↗

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography

A powerful and easy-to-use workflow environment has been developed at the ESRF for combining experiment control with online data analysis on synchrotron beamlines. This tool provides the possibility of automating complex experiments without the need for expertise in instrumentation control and programming, but rather by accessing defined beamline services. The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Basic Energy Sciences Exascale Requirements Review. An Office of Science review sponsored jointly by Advanced Scientific Computing Research and Basic Energy Sciences, November 3-5, 2015, Rockville, Maryland

Computers have revolutionized every aspect of our lives. Yet in science, the most tantalizing applications of computing lie just beyond our reach. The current quest to build an exascale computer with one thousand times the capability of today’s fastest machines (and more than a million times that of a laptop) will take researchers over the next horizon. The field of materials, chemical reactions, and compounds is inherently complex. Imagine millions of new materials with new functionalities waiting to be discovered — while researchers also seek to extend those materials that are known to a dizzying number of new forms. We could translate massive amounts of data from high precision experiments into new understanding through data mining and analysis. We could have at our disposal the ability to predict the properties of these materials, to follow their transformations during reactions on an atom-by-atom basis, and to discover completely new chemical pathways or physical states of matter. Extending these predictions from the nanoscale to the mesoscale, from the ultrafast world of reactions to long-time simulations to predict the lifetime performance of materials, and to the discovery of new materials and processes will have a profound impact on energy technology. In addition, discovery of new materials is vital to move computing beyond Moore’s law. To realize this vision, more than hardware is needed. New algorithms to take advantage of the increase in computing power, new programming paradigms, and new ways of mining massive data sets are needed as well. This report summarizes the opportunities and the requisite computing ecosystem needed to realize the potential before us. In addition to pursuing new and more complete physical models and theoretical frameworks, this review found that the following broadly grouped areas relevant to the U.S. Department of Energy (DOE) Office of Advanced Scientific Computing Research (ASCR) would directly affect the Basic Energy Sciences (BES) mission need. Simulation, visualization, and data analysis are crucial for advances in energy science and technology. Revolutionary mathematical, software, and algorithm developments are required in all areas of BES science to take advantage of exascale computing architectures and to meet data analysis, management, and workflow needs. In partnership with ASCR, BES has an emerging and pressing need to develop new and disruptive capabilities in data science. More capable and larger high-performance computing (HPC) and data ecosystems are required to support priority research in BES. Continued success in BES research requires developing the next-generation workforce through education and training and by providing sustained career opportunities.

97 MATHEMATICS AND COMPUTING↗

Remote Sensing and Fluxes Upscaling for Real-world Impact (Workshop Report)

The "Remote Sensing and Fluxes Upscaling for Real-world Impact" workshop, held on July 9-10, 2024, at Lawrence Berkeley National Lab, was a collaborative effort led by the AmeriFlux Management Project, NEON, and the Carbon Dew Community of Practice. The event brought together over 200 registrants and approximately 100 attendees each day, including leading experts, researchers, and practitioners. The primary focus was on bridging the gap between cutting-edge research and practical applications in environmental monitoring by integrating remote sensing and flux data. Key themes included the importance of site-level measurements for validating remote sensing products, providing nature-based climate solutions, and addressing challenges such as instrument costs and the need for standardized methods. At the regional scale, discussions centered on addressing spatial heterogeneity and using high-resolution remote sensing and machine learning methods to enhance data interpretation. Global scale challenges included data consistency, gap filling, and accurate emission source identification, with opportunities for international collaboration and standardized practices to improve global carbon budget assessments. The workshop emphasized the critical need for integrating data across local, regional, and global scales through explicit scale-matching and developed a workflow for scaling flux data using "straight shot" and "explicit nesting" approaches. The event highlighted the importance of connecting scientific research with real-world applications in carbon, energy, and water management, ensuring that advancements translate into tangible societal benefits. These insights will guide future research, technology transfer, and collaboration, maximizing the potential of environmental fluxes to address real-world challenges.

97 MATHEMATICS AND COMPUTING↗

Final technical report for DE-SC00012633 AToM (Advanced Tokamak Modeling)

This final report for the AToM project documents contributions from University of California, San Diego researchers over the period of 9/1/2014 – 8/31/2017. The primary focus of these efforts was on performing validation studies of core tokamak transport models using the OMFIT framework, including development of OMFIT workflow scripts. Additional work was performed to develop tools for use of the nonlinear magnetohydrodynamics code NIMROD in OMFIT, and its use in the study of runaway electron dynamics in tokamak disruptions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

MO-E-BRC-01: Online Adaptive MR-Guided RT: Workflow and Clinical Implementation

Online adaptive radiation therapy has the potential to ensure delivery of optimal treatment to the patient by accounting for anatomical and potentially functional changes that occur from one fraction to the next and over the course of treatment. While on-line adaptive RT (ART) has been a topic of many publications, discussions, and research, it has until very recently remained largely a concept and not a practical implementation. However, recent advances in on-table imaging, use of deformable image registration for contour generation and dose tracking, faster and more efficient plan optimization, as well as fast quality assurance method has enabled the implementation of ART in the clinic in the past couple of years. The introduction of these tools into routine clinical use requires many considerations and progressive knowledge to understand how processes that have historically taken hours/days to complete can now be done in less than 30 minutes. This session will discuss considerations to perform real time contouring, planning and patient specific QA, as well as a practical workflow and the required resources. Learning Objectives: To understand the difficulties, challenges and available technologies for online adaptive RT. To understand how to implement online adaptive therapy in a clinical environment and to understand the workflow and resources required. To understand the limitations and sources of uncertainty in the online adaptive process I have research funding from ViewRay Inc. and Philips Medical Systems.; R. Kashani, I have research funding from ViewRay Inc. and Philips Medical Systems.; X. Li, Research supported by Elekta Inc.

60 APPLIED LIFE SCIENCES↗

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Background: Metagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

59 BASIC BIOLOGICAL SCIENCES↗

A2SD: Accelerating Scientific Innovation Through Autonomous Discovery Systems

The 2025 Advancing Autonomous Scientific Discovery (A2SD) workshop convened researchers from academia, national laboratories, and industry to explore the transformative role of autonomy in scientific discovery. The workshop highlighted a convergence of artificial intelligence, robotics, and computational workflows into autonomous systems capable of accelerating the scientific process. Presentations and discussions spanned autonomous experimentation, intelligent workflow orchestration, digital twins, and agent-based systems for managing complex research ecosystems. Key challenges discussed included interoperability across heterogeneous infrastructures, near real-time data management under FAIR principles, reproducibility, and the integration of human oversight. The workshop also emphasized the need for modular software interfaces, federated learning models, and education initiatives to support a next-generation scientific workforce.

Taufer, Michela [University of Tennessee, Knoxvill↗