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DOE OSTI2024

Deep residual networks for crystallography trained on synthetic data

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

36 MATERIALS SCIENCE↗

DOE OSTI2025

What Is the Limit of Quantification for the Minor Phase in Time-of-Flight Neutron Diffraction? A Case Study on Fe and Ni Powder Mixtures at VULCAN

A phase present in small quantities within materials may not simply serve as a secondary component; it can play a crucial role in determining the integrity, properties, and performance of the material. These minor but important phases usually draw attention in material design and processing for fundamental understanding as well as material quality control. Accurately quantifying a minor phase amid a majority phase, especially at extremely low fractions, remains a challenging task. Time-of-flight neutron diffraction, coupled with advanced pattern analysis techniques like Rietveld refinement, is a powerful tool for crystal structure identification and phase quantification. The deep penetrating capability of neutrons enables the detection and quantification of trace phases within materials. In this study, the quantification limits of time-of-flight neutron diffraction were explored using the VULCAN diffractometer at the Spallation Neutron Source, using Fe–Ni powder mixtures as a sample system. By comparing the refinement results to the known weighed values, it was determined that the reliable quantification of a minor Ni phase is achievable down to about 0.1 wt% while a Ni fraction as low as 0.02 wt% is difficult to trace. Effective control of the refinement parameters, especially the profile function parameters, are found to significantly influence the convergence of fittings and the accuracy of phase quantification.

Rietveld refinement↗

DOE OSTI2024

Accurate and Data‐Efficient Micro X‐ray Diffraction Phase Identification Using Multitask Learning: Application to Hydrothermal Fluids

Traditional analysis of highly distorted micro X‐ray diffraction (μ‐XRD) patterns from hydrothermal fluid environments is a time‐consuming process, often requiring substantial data preprocessing and labeled experimental data. Herein, the potential of deep learning with a multitask learning (MTL) architecture to overcome these limitations is demonstrated. MTL models are trained to identify phase information in μ‐XRD patterns, minimizing the need for labeled experimental data and masking preprocessing steps. Notably, MTL models show superior accuracy compared to binary classification convolutional neural networks. Additionally, introducing a tailored cross‐entropy loss function improves MTL model performance. Most significantly, MTL models tuned to analyze raw and unmasked XRD patterns achieve close performance to models analyzing preprocessed data, with minimal accuracy differences. This work indicates that advanced deep learning architectures like MTL can automate arduous data handling tasks, streamline the analysis of distorted XRD patterns, and reduce the reliance on labor‐intensive experimental datasets.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Simplex‐based model for nanoparticle grain identification in four‐dimensional scanning transmission electron microscopy data

Grain identification in polycrystalline nanoparticles, for example, determining which crystal phases are present at each spatial location, is fundamental to materials characterisation. This is particularly challenging when grains overlap extensively, as commonly occurs in four-dimensional scanning transmission electron microscopy (4D-STEM) datasets. We propose a simplex-based model (SBM) in which each simplex vertex represents the diffraction pattern (DP) of a pure grain, and the simplex edges and interior represent overlapping grains. Our SBM grain identification algorithm operates on the Bragg disk (BD) data matrix distilled from the 4D-STEM data to identify the grain membership at each scan position, together with a BD feature matrix whose columns represent the DPs for each constituent grain, which is important for identifying the crystal structure of each grain. We solve the model using a two-stage algorithm. In Stage 1, we adapt a linear mixing algorithm to estimate an initial BD feature matrix whose columns represent DPs of potentially overlapping grains. Our Stage 2 algorithm incorporates sparsity considerations to transform the initial BD feature matrix so that its columns represent DPs of pure grains. Using simulated datasets with various grain configurations, we demonstrate that SBM recovers both the BD feature matrix and membership maps more accurately than existing methods, even when a grain lacks any pure region and completely overlaps with other grains.

4D-STEM segmentation↗

DOE OSTI2024

DISSIDE: Dynamic In Silico Sample Identification for Discrete Evaluation

DISSIDE uses novel unsupervised learning to select samples that best represent the strongest a priori discrete pattern in a given data set. It further removes major outliers and "noisy" samples that do not fit discrete patterns well or represent outliers in groups below a defined n value. It then estimates the fit and strength of the a priori discrete pattern using both unconstrained and constrained methods for raw and cleaned data

LeBrun, Erick↗

DOE OSTI2020

Integrating high resolution drone imagery and forest inventory to distinguish canopy and understory trees and quantify their contributions to forest structure and dynamics

Tree growth and survival differ strongly between canopy trees (those directly exposed to overhead light), and understory trees. However, the structural complexity of many tropical forests makes it difficult to determine canopy positions. The integration of remote sensing and ground-based data enables this determination and measurements of how canopy and understory trees differ in structure and dynamics. Here we analyzed 2 cm resolution RGB imagery collected by a Remotely Piloted Aircraft System (RPAS), also known as drone, together with two decades of bi-annual tree censuses for 2 ha of old growth forest in the Central Amazon. We delineated all crowns visible in the imagery and linked each crown to a tagged stem through field work. Canopy trees constituted 40% of the 1244 inventoried trees with diameter at breast height (DBH) > 10 cm, and accounted for ~70% of aboveground carbon stocks and wood productivity. The probability of being in the canopy increased logistically with tree diameter, passing through 50% at 23.5 cm DBH. Diameter growth was on average twice as large in canopy trees as in understory trees. Growth rates were unrelated to diameter in canopy trees and positively related to diameter in understory trees, consistent with the idea that light availability increases with diameter in the understory but not the canopy. The whole stand size distribution was best fit by a Weibull distribution, whereas the separate size distributions of understory trees or canopy trees > 25 cm DBH were equally well fit by exponential and Weibull distributions, consistent with mechanistic forest models. The identification and field mapping of crowns seen in a high resolution orthomosaic revealed new patterns in the structure and dynamics of trees of canopy vs. understory at this site, demonstrating the value of traditional tree censuses with drone remote sensing.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Notice of Illegal Foreign Pesticides Entering the United States: Information Bulletin v.01

This information bulletin is intended to generate a heightened awareness of illicit pesticide importation, distribution, and use in the United States. This bulletin focuses on solid, fumigant materials which are primarily used in the production of marijuana growth and cultivation. Exposure to illicit pesticides, fumigant fumes, or residual materials may pose a public health and officer safety concern. Many illegal fumigant pesticide products have been seized and determined to consist of a mixture of several pesticides and is often in contrast with the pesticide labelling. This information bulletin is not a complete account of all illegal pesticides found in country; it serves to highlight frequently encountered materials and present patterns in product presentation, packaging, and shipment containment which are intended to aid in identification and intervention. Other varieties of illegal pesticide fumigants are known to exist, and additional variations are expected to be encountered in policing intervention. This bulletin includes information on the presentation of illegal pesticides, label review recommendations, a field reference guide, which includes example photographs of seized pesticide/fumigants and their labels, and related United States federal regulation information, including relevant tariff code information for reference.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Machine learning analysis reveals relationship between pomacentrid calls and environmental cues

Sound production rates of fishes can be used as an indicator for coral reef health, providing an opportunity to utilize long-term acoustic recordings to assess environmental change. As acoustic datasets become more common, computational techniques need to be developed to facilitate analysis of the massive data files produced by long-term monitoring. Machine learning techniques demonstrate an advantage in the identification of fish sounds over manual sampling approaches. Here we evaluated the ability of convolutional neural networks to identify and monitor call patterns for pomacentrids (damselfishes) in a tropical reef region of the western Pacific. A stationary hydrophone was deployed for 39 mo (2014-2018) in the National Park of American Samoa to continuously record the local marine acoustic environment. A neural network was trained—achieving 94% identification accuracy of pomacentrids—to demonstrate the applicability of machine learning in fish acoustics and ecology. The distribution of sound production was found to vary on diel and interannual timescales. Additionally, the distribution of sound production was correlated with wind speed, water temperature, tidal amplitude, and sound pressure level. This research has broad implications for state-of-the-art acoustic analysis and promises to be an efficient, scalable asset for ecological research, environmental monitoring, and conservation planning.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The Land–Sea Connection: Insights Into the Plant Lineage from a Green Algal Perspective

The colonization of land by plants generated opportunities for the rise of new heterotrophic life forms, including humankind. A unique event underpinned this massive change to earth ecosystems—the advent of eukaryotic green algae. Today, an abundant marine green algal group, the prasinophytes, alongside prasinodermophytes and nonmarine chlorophyte algae, is facilitating insights into plant developments. Genome-level data allow identification of conserved proteins and protein families with extensive modifications, losses, or gains and expansion patterns that connect to niche specialization and diversification. Here, we contextualize attributes according to Viridiplantae evolutionary relationships, starting with orthologous protein families, and then focusing on key elements with marked differentiation, resulting in patchy distributions across green algae and plants. We place attention on peptidoglycan biosynthesis, important for plastid division and walls; phytochrome photosensors that are master regulators in plants; and carbohydrate-active enzymes, essential to all manner of carbohydratebiotransformations. Together with advances in algal model systems, these areas are ripe for discovering molecular roles and innovations within and across plant and algal lineages.

Plant Sciences↗

DOE OSTI2026

The sweeper spectrometer for neutron invariant-mass spectroscopy at FRIB

Neutron invariant-mass spectroscopy (NIMS) is a key technique for studying unbound and weakly bound nuclei at the limits of stability. At the Facility for Rare Isotope Beams (FRIB), such measurements are performed using the Sweeper spectrometer, a large-gap, high-rigidity dipole system coupled to the MoNA-LISA neutron detector arrays. To meet the demands imposed by higher beam energies (>130 MeV/u) and the broad cocktail-beam selection available at FRIB, the spectrometer has recently been upgraded to improve particle-identification and detection performance. Upstream of the reaction target, a plastic scintillator with Silicon photomultiplier (SiPM) readout provides the global trigger and time reference, two parallel plate avalanche counters (PPACs) track the trajectories of incoming beam particles, and a silicon PIN detector measures the energy loss, ΔE, for charge (Z) identification. After the Sweeper magnet, the trajectories of the reaction products are tracked by two micro-pattern drift chambers (MPDCs), their charge (Z) is identified by a Frisch-grid ionization chamber (FG-IC), and their mass-to-charge ratio (A/Q) is deduced by time-of-flight measurement using a fast plastic scintillator read out by an array of photomultiplier tubes (PMTs). The detection system also incorporates the Modular Neutron Array (MoNA) for neutron detection and the CAESium-iodide scintillator ARray (CAESAR) for high-efficiency γ-ray measurements to enable full kinematic reconstruction. Performance was evaluated using a cocktail beam around 37 Al accelerated at E ≈ 130 MeV/u during the first FRIB campaign, demonstrating the readiness of the upgraded system for future studies of nuclei at and beyond the neutron drip line.

Particle identification methods↗

DOE OSTI2026

J -Resolved Molecular Fingerprinting by Parahydrogen Hyperpolarized Low-Field NMR

A J-resolved spectroscopy that depends on homonuclear scalar coupling in the strong-coupling regime and heteronuclear coupling in the weak regime expands complex peak patterns to a second axis. Hyperpolarization by Signal Amplification by Reversible Exchange (SABRE) enables the spectroscopy at a low magnetic field of 0.82 mT. Overlapping peaks of molecules such as 3-fluoropyridine and 3,5-difluoropyridine are resolved. Density matrix simulations of the 1 H and 19 F spins indicate a strong dependence on the signs and values of the J-coupling constants, including the homonuclear couplings that are not directly observable. The best matching peak positions and intensities predict coupling constants, including couplings between chemically equivalent nuclear spins, ranging in magnitude from 0.4 to 9.0 Hz for the two molecules. Simulations of other spin systems show unique patterns for molecules containing 1 H and 19 F or 13 C. The dependence of the J-resolved peak patterns on all coupling constants in a spin system presents a new modality for portable and inexpensive identification of molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Exploiting correlations in multi-coincidence Coulomb explosion patterns for differentiating molecular structures using machine learning

Coulomb explosion imaging (CEI) is a powerful technique for capturing the real-time motion of individual atoms during ultrafast photochemical reactions. CEI generates high-dimensional data with naturally embedded correlations that allow mapping the coordinated motion of nuclei in molecules. This enables reliable separation of competing reaction pathways and makes this approach uniquely suited for characterizing weak reaction channels. However, rich information contained in experimental CEI patterns remains largely underexploited due to challenges in visualizing correlations between multiple observables in multi-dimensional parameter space. Here we present a new approach to CEI of intermediate-sized polyatomic molecules, detecting up to eight ionic fragments in coincidence and leveraging machine-learning-based analysis to identify patterns and correlations in the resulting high-dimensional momentum-space data, enabling robust molecular structure identification and differentiation. Our approach provides high-dimensional background-free data encoding exceptionally rich structural information and establishes an automated, scalable framework for extracting insightful information from the data. As a demonstration, we apply this method to image and distinguish dichloroethylene isomers, showcasing its potential for broader applications in molecular imaging. Our results pave the way for channel-specific analysis of ultrafast structural dynamics in chemically relevant systems, particularly for disentangling mixed reaction pathways and detecting contributions from weak channels and minority species.

Chemical Physics (physics.chem-ph)↗

DOE OSTI2020

Compound Drought and Heatwaves at a Global Scale: The Role of Natural Climate Variability-Associated Synoptic Patterns and Land-Surface Energy Budget Anomalies

Compound drought and heatwave (CDHW) events have garnered much attention in recent studies. However, thus far, the identification of such events is oversimplified, and their association with natural climate variability is not fully explored. Here, we derive anomalies in the weekly self-calibrated Palmer Drought Severity Index (sc_PDSI) and daily maximum temperatures to identify CDHW events from 1982 to 2016 over 26 climate regions across the globe. Using a Poisson Generalized Linear Model (GLM), we analyze yearly occurrences of seasonal CDHW events and their association with the warm and cold phases of El Nino Southern Oscillation (ENSO), Pacific Decadal Oscillation (PDO), and North Atlantic Oscillation (NAO). ENSO exhibits robust association with CDHW events over the Southern Hemisphere during the austral summer and fall, while PDO influences their occurrences over the Western North America in the Northern Hemisphere during the boreal summer, which is supported by the composites of anomalies in the atmospheric circulations and surface energy budget. However, NAO association with CDHW events is relatively weak. The CDHW occurrence over other regions is driven by a combination of these large-scale natural forcing. Our analyses also highlight that the cooccurrence of weekly to submonthly scale anomalies in the observed temperature and precipitation may not be always aligned between the observations and the reanalysis. Therefore, caution must be exercised while explaining such observed anomalies on the basis of reanalysis-based circulations and surface energy budget. Lastly, our analyses provide a new insight towards concurrent extremes and should help foster research efforts in this area.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Identification of tau leptons using a convolutional neural network with domain adaptation

A tau lepton identification algorithm,DeepTau, based on convolutional neural network techniques, has been developed in the CMS experiment to discriminate reconstructed hadronic decays of tau leptons (τ h ) from quark or gluon jets and electrons and muons that are misreconstructed as τ h candidates. The latest version of this algorithm, v2.5, includes domain adaptation by backpropagation, a technique that reduces discrepancies between collision data and simulation in the region with the highest purity of genuine τh candidates. Additionally, a refined training workflow improves classification performance with respect to the previous version of the algorithm, with a reduction of 30–50% in the probability for quark and gluon jets to be misidentified as τ h candidates for given reconstruction and identification efficiencies. This paper presents the novel improvements introduced in theDeepTau algorithm and evaluates its performance in LHC proton-proton collision data at √(s) = 13 and 13.6 TeV collected in 2018 and 2022 with integrated luminosities of 60 and 35 fb -1 , respectively. Techniques to calibrate the performance of the τ h identification algorithm in simulation with respect to its measured performance in real data are presented, together with a subset of results among those measured for use in CMS physics analyses.

Large detector-systems performance↗

DOE OSTI2025

Direct identification of Ac and No molecules with an atom-at-a-time technique

The periodic table provides an intuitive framework for understanding chemical properties. However, its traditional patterns may break down for the heaviest elements occupying the bottom of the chart. Here, the large nuclei of actinides (Z > 88) and superheavy elements (Z ≥ 104) give rise to relativistic effects that are expected to substantially alter their chemical behaviours, potentially indicating that we have reached the end of a predictive periodic table. Relativistic effects have already been cited for the unusual chemistry of the actinides compared with those of their lanthanide counterparts. Unfortunately, it is difficult to understand the full impact of relativistic effects, as research on the later actinides and superheavy elements is scarce. Beyond fermium (Z = 100), elements need to be produced and studied one atom at a time, using accelerated ion beams and state-of-the-art experimental approaches. So far, no experiments have been capable of directly identifying produced molecular species. Here ions of actinium (Ac, Z = 89) and nobelium (No, Z = 102) were synthesized through nuclear reactions at the 88-Inch Cyclotron facility at Lawrence Berkeley National Laboratory and then exposed to trace amounts of H 2 O and N 2 . The produced molecular species were directly identified by measuring their mass-to-charge ratios using FIONA (For the Identification Of Nuclide A). These results mark the first, to our knowledge, direct identification of heavy-element molecular species using an atom-at-a-time technique and highlight the importance of such identifications in future superheavy-element chemistry experiments to deepen understanding of their chemical properties.

Pore, Jennifer L. [Lawrence Berkeley National Labo↗

DOE OSTI2021

Selecting XFEL single-particle snapshots by geometric machine learning

A promising new route for structural biology is single-particle imaging with an X-ray Free-Electron Laser (XFEL). This method has the advantage that the samples do not require crystallization and can be examined at room temperature. However, high-resolution structures can only be obtained from a sufficiently large number of diffraction patterns of individual molecules, so-called single particles. Here, we present a method that allows for efficient identification of single particles in very large XFEL datasets, operates at low signal levels, and is tolerant to background. This method uses supervised Geometric Machine Learning (GML) to extract low-dimensional feature vectors from a training dataset, fuse test datasets into the feature space of training datasets, and separate the data into binary distributions of “single particles” and “non-single particles.” As a proof of principle, we tested simulated and experimental datasets of the Coliphage PR772 virus. We created a training dataset and classified three types of test datasets: First, a noise-free simulated test dataset, which gave near perfect separation. Second, simulated test datasets that were modified to reflect different levels of photon counts and background noise. These modified datasets were used to quantify the predictive limits of our approach. Third, an experimental dataset collected at the Stanford Linear Accelerator Center. The single-particle identification for this experimental dataset was compared with previously published results and it was found that GML covers a wide photon-count range, outperforming other single-particle identification methods. Moreover, a major advantage of GML is its ability to retrieve single particles in the presence of structural variability.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Wire-cell 3D pattern recognition techniques for neutrino event reconstruction in large LArTPCs: algorithm description and quantitative evaluation with MicroBooNE simulation

Wire-Cell is a 3D event reconstruction package for liquid argon time projection chambers. Through geometry, time, and drifted charge from multiple readout wire planes, 3D space points with associated charge are reconstructed prior to the pattern recognition stage. Pattern recognition techniques, including track trajectory and dQ/dx (ionization charge per unit length) fitting, 3D neutrino vertex fitting, track and shower separation, particle-level clustering, and particle identification are then applied on these 3D space points as well as the original 2D projection measurements. A deep neural network is developed to enhance the reconstruction of the neutrino interaction vertex. Compared to traditional algorithms, the deep neural network boosts the vertex efficiency by a relative 30% for charged-current ν e interactions. Therefore, this pattern recognition achieves 80–90% reconstruction efficiencies for primary leptons, after a 65.8% (72.9%) vertex efficiency for charged-current ν e (ν μ ) interactions. Based on the resulting reconstructed particles and their kinematics, we also achieve 15-20% energy reconstruction resolutions for charged-current neutrino interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Robust Anthropogenic Signal Identified in the Seasonal Cycle of Tropospheric Temperature

Previous work identified an anthropogenic fingerprint pattern in T AC (x, t), the amplitude of the seasonal cycle of mid- to upper-tropospheric temperature (TMT), but did not explicitly consider whether fingerprint identification in satellite T AC (x, t) data could have been influenced by real-world multidecadal internal variability (MIV). Here we address this question here using large ensembles (LEs) performed with five climate models. LEs provide many different sequences of internal variability noise superimposed on an underlying forced signal. Despite differences in historical external forcings, climate sensitivity, and MIV properties of the five models, their T AC (x, t) fingerprints are similar and statistically identifiable in 239 of the 240 LE realizations of historical climate change. Comparing simulated and observed variability spectra reveals that consistent fingerprint identification is unlikely to be biased by model underestimates of observed MIV. Even in the presence of large (factor of 3–4) intermodel and inter-realization differences in the amplitude of MIV, the anthropogenic fingerprints of seasonal cycle changes are robustly identifiable in models and satellite data. This is primarily due to the fact that the distinctive, global-scale fingerprint patterns are spatially dissimilar to the smaller-scale patterns of internal T AC (x, t) variability associated with the Atlantic multidecadal oscillation and El Niño–Southern Oscillation. The robustness of the seasonal cycle detection and attribution results shown here, taken together with the evidence from idealized aquaplanet simulations, suggest that basic physical processes are dictating a common pattern of forced T AC (x, t) changes in observations and in the five LEs. The key processes involved include GHG-induced expansion of the tropics, lapse-rate changes, land surface drying, and sea ice decrease.

54 ENVIRONMENTAL SCIENCES↗