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DOE OSTI2026

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗
DOE OSTI2026

CHESS 2025: Waveform LiDAR data from NEON AOP surveys

This dataset provides Level 1 (L1) full-waveform light detection and ranging (LiDAR) data collected for the 2025 Colorado Headwaters Ecological Spectroscopy Study (CHESS). These data were acquired to enable characterization of vegetation structure and other three-dimensional features of the land surface, and to evaluate structural changes that may have occurred between a prior LiDAR acquisition in 2018 and the 2025 overflight. Waveform LiDAR data can provide more detailed information about objects on the ground than discrete point clouds typically do, and they are often used for granular target segmentation and characterization of subcanopy vegetation. The data were acquired over three study domains in the Upper Gunnison river basin: the upper East River watershed (CRBU); Almont Triangle and Taylor Canyon (ALMO); and Upper Taylor River watershed (UPTA) between 2025-06-13 and 2025-07-15. LiDAR data were acquired using the Optech Galaxy Prime Airborne LiDAR Terrain Mapper onboard the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP). These are the primary waveform LiDAR data delivered by NEON and are provided per flightline in compressed Pulsewaves format, an open-source binary file standard. A Pulsewaves object comprises a two files: a pulse (.pls) file, which stores the geographic origin, outgoing vector, and metadata for every laser pulse emitted by the scanner, and a wave file (.wvs), which stores the sequential amplitude samples of the outgoing pulse and the returning signals. The files are published here in their compressed forms (.plz, .wvz). All waveform data were processed following the theoretical workflow described in the NEON L0-to-L1 Waveform LiDAR Algorithm Theoretical Basis Document (Krause and Goulden 2022a); however, the Pulsewaves output format differs from a legacy format described in that document. Waveform amplitude samples are recorded at 1 nanosecond intervals. All coordinates are provided in meters. Horizontal coordinates are referenced in Universal Transverse Mercator (UTM) zone 13N and the World Geodetic System (WGS) 1984 ensemble datum. Elevations are referenced to Geoid12A. Waveform data for the UPTA survey area were collected without incident and the published records are complete. However, both the ALMO and CRBU collections experienced issues that resulted in incomplete data for those areas. On collection day 2018-06-16 a hardware failure caused the waveform digitizer to lose data from the eastern edge of the ALMO site (Figure 22). The waveform data for flightlines 2–20 could not be extracted from the digitizer, and the data proved unrecoverable. As a result, a portion of the site does not have coverage with waveform data. Although no hardware failure was observed during collection over the CRBU area, final waveform files generated by vendor software contained only ~25% of the expected number of return pulses. After discovery, NEON initiated troubleshooting with the vendor. The root cause of the data ablation had not been identified at the time of publication. Additional data will be published in an update to this package if further recovery proves successful. CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgement: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2024

Blueprints for Training Information Bottlenecks for Collider Analyses

Dimensionality reduction is a crucial aspect of data analysis in high energy physics, even if accompanied by information loss. Several methods, including histogram- and kernel-based analyses, are only computationally feasible for low-dimensional data. Furthermore, simulation models used in HEP can often only be validated for low-dimensional data. We provide several blueprints for using machine learning to create low-dimensional data representations (continuous event variables and discrete classification labels) for use in signal discovery and parameter estimation tasks. We also describe how to design the learned representation to facilitate a) searches with unknown model parameters and b) validation of simulation models in data control regions.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Large language model-driven database for thermoelectric materials

Thermoelectric materials have the ability to convert waste heat into electricity, offering a valuable solution for energy harvesting. However, their widespread use is hindered by low conversion efficiency, the reliance on expensive rare earth elements, and the environmental and regulatory concerns associated with lead-based materials. A fast and cost-effective way to identify highly efficient thermoelectric materials is through data-driven methods. These approaches rely on robust and comprehensive datasets to train models. Although there are several databases on thermoelectric materials, there is still a need to collect and integrate experimental data from peer-reviewed research articles to capture diverse compositions and properties of materials. Here, in this work, we developed a comprehensive database of 7,123 thermoelectric compounds, containing key information such as chemical composition, structural detail, seebeck coefficient, electrical and thermal conductivity, power factor, and figure of merit (ZT). We used the GPTArticleExtractor workflow, powered by large language models (LLM), to extract and curate data automatically from the scientific literature published in Elsevier journals. This process enabled the creation of a structured database that addresses the challenges of manual data collection. The open access database could stimulate data-driven research and advance thermoelectric material analysis and discovery.

Database↗
DOE OSTI2026

Neural entropy-stable conservative flux form neural networks for learning hyperbolic conservation laws

We propose a neural entropy-stable conservative flux form neural network (NESCFN) for learning hyperbolic conservation laws and their associated entropy functions directly from solution trajectories, without requiring any predefined numerical discretization. While recent neural network architectures have successfully integrated classical numerical principles into learned models, most rely on prior knowledge of the governing equations or assume a fixed discretization. Our approach removes this dependency by embedding entropy-stable design principles into the learning process itself, enabling the discovery of physically consistent dynamics in a fully data-driven setting. By jointly learning both the flux function and a corresponding entropy, NESCFN promotes conservation and entropy dissipation, which is critical for long-term stability and fidelity in the system of hyperbolic conservation laws. Furthermore, numerical results demonstrate that the method achieves stability and conservation over extended time horizons and accurately captures shock propagation speeds, even without oracle access to future-time solution profiles in the training data.

Conservative flux form↗
DOE OSTI2026

Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials

Silicon carbide (SiC) divacancies are attractive candidates for spin-defect qubits possessing long coherence times and optical addressability. The high activation barriers associated with SiC defect formation and motion pose challenges for their study by first-principles molecular dynamics. In this work, we develop and deploy machine learning interatomic potentials (MLIPs) to accelerate defect dynamics simulations while retaining ab initio accuracy. We employ an active learning strategy comprising symmetry-adapted collective variable discovery and enhanced sampling to compile configurationally diverse training data, calculation of energies and forces using density functional theory (DFT), and training of an E(3)-equivariant MLIP based on the Allegro model. Here, the trained MLIP reproduces DFT-level accuracy in defect transition activation free energy barriers, enables the efficient and stable simulation of multidefect 216-atom supercells, and permits an analysis of the temperature dependence of defect thermodynamic stability and formation/annihilation kinetics to propose an optimal annealing temperature to maximally stabilize VV divacancies.

Computer simulations↗
DOE OSTI2026

Roadmap for transforming heterogeneous catalysis with artificial intelligence

Artificial intelligence (AI) is poised to transform heterogeneous catalysis, opening avenues for catalytic materials discovery. By uncovering intricate patterns in high-dimensional data, AI has been reshaping our pursuit of sustainable catalytic processes across the energy, environmental and chemical sectors. This promise, however, hinges on overcoming fundamental barriers, including limitations in data availability and quality, challenges in the generalizability and interpretability of data-augmented decisions, and the persistent gap between in silico predictions and experiments. Furthermore, we outline a forward-looking roadmap for deeply integrating AI into heterogeneous catalysis with an AI-ready data ecosystem, multimodal foundation models, and ultimately autonomous laboratories to accelerate the development of next-generation catalytic technologies via AI-empowered human–machine collaboration.

Computational methods↗
DOE OSTI2026

Integrated Direct Air Capture and H₂-Free CO₂ Valorization

This project advances fundamental understanding of a novel integrated direct air capture (DAC) and CO₂ conversion process that valorizes atmospheric CO₂ without external H₂. The research encompasses four critical components: (1) design of task-specific ionic liquids for efficient CO₂ capture under ambient conditions, (2) development of H₂-free tandem catalytic systems using ethane as a reductant, (3) advanced operando characterization to elucidate capture and conversion mechanisms, and (4) data science-driven predictive computation to accelerate material discovery. Over the project period, we developed five high-performance DAC sorbent systems—including CaO/superbase ionic liquid composites, Ni-MOF/Ionic Liquid (IL) hybrids, fluorinated covalent organic frameworks with ion-pair functional groups, defect-engineered UiO-66, and a validated kinetic model for humid-condition operation, achieving CO₂ capacities up to 1.86 mmol/g at 400 ppm with excellent cycling stability. For H₂-free conversion, we constructed atomically synergistic Zn–O–Cr binuclear catalytic sites that achieve 100% ethylene selectivity, ~9.6% ethane conversion, and 99% CO₂ utilization in equimolar co-conversion of ethane and CO₂. We further demonstrated downstream valorization pathways converting CO and C₂H₄ into polyketones and C₃ chemicals. These advances strengthen the scientific foundation for producing value-added materials from ambient CO₂.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Shift Happens: Building Robust AI Models with Domain Adaptation

Artificial Intelligence (AI) is revolutionizing physics research—from probing the large-scale structure of the Universe to modeling subatomic interactions and fundamental forces. Yet, a major challenge persists: AI models trained on simulations or old experiment / astronomical survey often perform poorly when applied to new data—exposing issues of dataset (domain) shift, model robustness, and uncertainty in predictions. This summer school session will introduce students to common challenges in applying AI across domains and present solutions based on domain adaptation—a set of techniques designed to improve model generalization under domain shift. We will cover foundational ideas, practical strategies, and current research frontiers in this area. Through examples in astrophysics, we'll explore how domain adaptation can help bridge the gap between synthetic and real-world data, improve trust in model outputs, and advance scientific discovery. The concepts discussed are broadly applicable across physics and other scientific disciplines, making this a valuable topic for anyone interested in building robust, transferable AI models for science.

Ciprijanovic, A. [Fermilab] (ORCID:000000031281719↗
DOE OSTI2025

AI in Astrophysics: Tackling Domain Shift, Model Robustness and Uncertainty

Artificial Intelligence (AI) is revolutionizing physics research from probing the large-scale structure of the Universe to modeling subatomic interactions and fundamental forces. Yet, a major challenge persists: AI models trained on simulations or old experiment / astronomical survey often perform poorly when applied to new data exposing issues of dataset (domain) shift, model robustness, and uncertainty in predictions. This talk will introduce common challenges in applying AI across domains and present solutions based on domain adaptation a set of techniques designed to improve model generalization under domain shift. We will cover foundational ideas, practical strategies, and current research frontiers in this area. Through examples in astrophysics, we'll explore how domain adaptation can help bridge the gap between synthetic and real-world data, improve trust in model outputs, and advance scientific discovery.

Ciprijanvoic, Aleksandra [Fermilab] (ORCID:0000000↗
DOE OSTI2026

A Deep Look at the Ultra-Faint Milky Way Satellite Virgo III with Rubin Observatory Data Preview 2

We analyze the ultra-faint Milky Way satellite Virgo III using data from the Vera C. Rubin Observatory Data Preview 2 (DP2). Virgo III was observed in the Rubin "Cosmic Treasure Chest" (M49) First Look field, which contains 924 visits in the u,g,r,i bands comprising ~10.5hrs of exposure time with LSSTCam. These data are considerably deeper than the majority of DP2, with a $5σ$ limiting magnitude that approaches the expected 10-year depth of LSST (~25.2-26.5mag, depending on band). We report the morphological and stellar population parameters of Virgo III measured with the maximum-likelihood-based package ugali. The depth of the Rubin imaging yields more than a factor of four increase in the number of candidate member stars ($N_* = 114^{+11}_{-11}$) relative to the Virgo III discovery results ($N_* = 25^{+5}_{-4}$), enabling significantly more precise morphological constraints. Our best-fit parameters broadly agree with previous measurements, further confirming that Virgo III has properties that are consistent with an ultra-faint dwarf galaxy ($M_V = -2.72^{+0.49}_{-0.70}$; $r_{1/2} = 53^{+10}_{-8}$) located at a heliocentric distance of $D_\odot = 151^{+8}_{-8}$. We also demonstrate that the depth and photometric quality of the DP2 data are sufficient to separate metal-poor and metal-rich stars in color-color space. We further present period estimates for the three known RR Lyrae member stars derived from the DP2 forced photometry; we use theoretical Period-Luminosity-Metallicity (PLZ) and Period-Wesenheit-Metallicity (PWZ) relations to obtain independent distance estimates. We find that our period and distance estimates are broadly consistent with previous measurements for these RR Lyrae. These results demonstrate the power of LSST data for the discovery and characterization of ultra-faint dwarf galaxies and motivate future searches for new satellites across the southern sky.

Pai, Aashay [Chicago U.; Chicago U., KICP; SkAI, C↗
DOE OSTI2026

scPlantAnnotate: an accurate and robust transformer-based model for plant cell type annotation

Accurate cell type annotation remains a major bottleneck in plant single-cell RNA sequencing (scRNA-seq), where existing tools are often adapted from animal studies and perform sub-optimally on plant data. The lack of plant-specific computational frameworks limits the construction of plant cell atlases and downstream biological discovery. We develop and evaluate scPlantAnnotate, a Transformer-based reference annotation framework tailored for plant scRNA-seq data, and benchmark it against state-of-the-art deep learning and conventional methods across multiple plant species. Species-specific scPlantAnnotate models were trained using curated datasets from Arabidopsis thaliana, Zea mays, Oryza sativa, and Glycine max. We compared scPlantAnnotate with leading baselines under both standard random-split evaluation and a more stringent leave-one-dataset-out setting, which tests robustness to completely unseen datasets and tissue types. scPlantAnnotate consistently outperforms existing approaches across all four species under random-split evaluation. In the leave-one-dataset-out setting for A. thaliana, where performance drops markedly for all methods due to strong batch effects and dataset heterogeneity, scPlantAnnotate nonetheless achieves the highest Accuracy, Macro-F1, Balanced Accuracy, and Macro-AUROC on average and ranks first on most held-out datasets. These results demonstrate improved robustness to dataset shifts, a critical yet underexplored challenge in plant scRNA-seq analysis. A freely accessible web server enables users to annotate their own datasets using pretrained models. scPlantAnnotate provides a plant-specific, Transformer-based framework for single-cell annotation that delivers state-of-the-art performance and enhanced robustness to unseen datasets. By addressing limitations of existing tools and enabling scalable reference-based annotation, scPlantAnnotate supports the development of comprehensive plant cell atlases and facilitates broader use of single-cell genomics in plant biology.

Bioinformatics↗
DOE OSTI2025

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗
DOE OSTI2025

OLCF’s Advanced Computing Ecosystem (ACE): FY25 Update for Ongoing Efforts

The advent of widespread use of artificial intelligence (AI) and machine learning (ML) models in science, coupled with fast data production rates of scientific instruments strain the traditional batch-oriented high-performance computing (HPC) environment. As scientific exploration continues to require more data and faster processing and analysis, new emerging technologies and capabilities to enable cross-facility and time-sensitive workflows are required for seamless integration of HPC and experimental facilities. The Advanced Computing Ecosystem (ACE) is a strategic initiative within the Oak Ridge Leadership Computing Facility (OLCF) established in 2024 to support the development of cutting-edge technologies to advance computational research and infrastructure at OLCF and across the Department of Energy (DOE). Several DOE initiatives are spearheading the evolution of the scientific landscape by blurring facility boundaries and connecting the user facilities to advance scientific capabilities and ensure energy dominance. The DOE Integrated Research Infrastructure (IRI) program is one example that is laying a foundation to support complex cross-facility workflows. The IRI program aims to integrate diverse computational resources, data infrastructures, and scientific instruments to facilitate collaboration and accelerate scientific discovery. The Interconnected Science Ecosystem (INTERSECT) initiative at Oak Ridge National Laboratory (ORNL) is another example that aims to revolutionize scientific research through AI-driven, interconnected autonomous laboratories and research facilities. Finally, the American Science Cloud (AmSC), recently announced in the “One Big Beautiful Bill”, aims to leverage prior infrastructure efforts of the IRI and automation and AI efforts of INTERSECT (and others) to build a federated, AI-augmented AmSC platform to unify the DOE’s computing, experimental, and data resources to catalyze scientific innovation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Basic Research Needs for Inverse Methods for Complex Systems under Uncertainty

Inverse problems, which aim to infer unknown properties of a system using experimental and observational data, are central to addressing many of the U.S. Department of Energy’s (DOE) most critical scientific and engineering challenges. Accurate, computationally efficient, and data-efficient solutions to inverse problems are essential for advancing DOE mission-critical science drivers, including analyzing data from large-scale experimental facilities, optimizing fusion reactor performance, accelerating materials discovery, enhancing geophysical imaging, improving wildfire predictions, and enabling autonomous systems and digital twins. However, these problems are becoming increasingly complex, often involving nonlinear, highdimensional, and interconnected systems and models that span multiple physics and scales, while relying on data with varying quantity, quality, and information content. Compounding these challenges is the uncertainty inherent in DOE-relevant systems, where errors in inputs, noise in data, incompleteness of data, and discrepancies between models and reality constrain the accuracy and precision of solutions. At the same time, the convergence of recent scientific computing trends—scientific machine learning, artificial intelligence, and computing advances such as exascale computing—is creating unprecedented opportunities for tackling these challenges. The cross-cutting nature of inverse problems, combined with their growing complexity and rapidly evolving data and algorithmic demands, strongly motivates the formulation of a prioritized research agenda to maximize their capabilities and impact. In response to this need, DOE’s Advanced Scientific Computing Research (ASCR) program in the Office of Science convened the Workshop on Basic Research Needs for Inverse Problems for Complex Systems Under Uncertainty in June 2025. This workshop brought together experts across disciplines to identify grand challenges and major opportunities in the field. Through collaborative discussions, the workshop defined transformative research directions aimed at addressing the mathematical, statistical, and computational challenges posed by inverse problems under uncertainty. As a result of these efforts, four priority research directions (PRDs) were identified to guide future research and development in this area. These PRDs, summarized below, represent a roadmap for advancing the foundational science and mathematics of inverse problems, enabling robust, scalable, and uncertainty-aware solutions that are critical for DOE applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Machine Learning-Enabled Image Classification for Automated Electron Microscopy

Abstract Traditionally, materials discovery has been driven more by evidence and intuition than by systematic design. However, the advent of “big data” and an exponential increase in computational power have reshaped the landscape. Today, we use simulations, artificial intelligence (AI), and machine learning (ML) to predict materials characteristics, which dramatically accelerates the discovery of novel materials. For instance, combinatorial megalibraries, where millions of distinct nanoparticles are created on a single chip, have spurred the need for automated characterization tools. This paper presents an ML model specifically developed to perform real-time binary classification of grayscale high-angle annular dark-field images of nanoparticles sourced from these megalibraries. Given the high costs associated with downstream processing errors, a primary requirement for our model was to minimize false positives while maintaining efficacy on unseen images. We elaborate on the computational challenges and our solutions, including managing memory constraints, optimizing training time, and utilizing Neural Architecture Search tools. The final model outperformed our expectations, achieving over 95% precision and a weighted F-score of more than 90% on our test data set. This paper discusses the development, challenges, and successful outcomes of this significant advancement in the application of AI and ML to materials discovery.

Materials Science↗
DOE OSTI2025

Uncovering hidden enhancers through unbiased in vivo testing

Chromatin signatures are widely used to identify tissue-specific in vivo enhancers, but their sensitivity and specificity remains unclear. Here we show that many developmental enhancers remain undetectable using currently available chromatin data. In an initial comparison of over 1200 developmental enhancers with tissue-matched chromatin data, 14% (n = 285) lacked canonical enhancer-associated chromatin signatures. To further assess the prevalence of enhancers missed by chromatin profiling approaches, we used a high-throughput transgenic enhancer assay to screen the regulatory landscapes of two key developmental genes at 5 kb resolution, spanning 1.3 Mb of mouse sequence in total. We observed that 23 of 88 (26%) in vivo enhancers discovered by this approach lacked enhancer-associated chromatin signatures in the respective tissue. Our findings suggest the existence of tens of thousands of enhancers that remain undiscovered by currently available chromatin data, underscoring the continued need for expanding resources for enhancer discovery.

Epigenomics↗
DOE OSTI2025

Experimental search for the chiral magnetic effect in relativistic heavy-ion collisions: A perspective

The chiral magnetic effect (CME) refers to generation of the electric current along a magnetic field in a chirally imbalanced system of quarks. The latter is predicted by quantum chromodynamics to arise from quark interaction with nontrivial topological fluctuations of the vacuum gluonic field. The CME has been actively searched for in relativistic heavy-ion collisions, where such gluonic field fluctuations and a strong magnetic field are believed to be present. The CME-sensitive observables are unfortunately subject to a possibly large non-CME background, and firm conclusions on a CME observation have not yet been reached. In this perspective, we review the experimental status and progress in the CME search, from the initial measurements more than a decade ago to the dedicated program of isobar collisions in 2018 and the release of the isobar blind analysis result in 2022 to intriguing hints of a possible CME signal in Au + Au collisions, and discuss future prospects of a potential CME discovery in the anticipated high-statistic Au + Au collision data at the Relativistic Heavy-Ion Collider by 2025. We hope such a perspective will help sharpening our focus on the fundamental physics of the CME and steer its experimental search.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗