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DOE OSTI2024

Anomaly inflow, dualities, and quantum simulation of Abelian lattice gauge theories induced by measurements

Previous work [] has demonstrated that quantum simulation of Abelian lattice gauge theories (Wegner models including the toric code in a limit) in general dimensions can be achieved by local adaptive measurements on symmetry-protected topological (SPT) states with higher-form generalized global symmetries. The entanglement structure of the resource SPT state reflects the geometric structure of the gauge theory. In this work we explicitly demonstrate the anomaly inflow mechanism between the deconfining phase of the simulated gauge theory on the boundary and the SPT state in the bulk by showing that the anomalous gauge variation of the boundary state obtained by bulk measurement matches that of the bulk theory. Moreover, we construct the resource state and the measurement pattern for the measurement-based quantum simulation of a lattice gauge theory with a matter field (Fradkin-Shenker model), where a simple scheme to protect gauge invariance of the simulated state against errors is proposed. We further consider taking an overlap between the wave function of the resource state for lattice gauge theories and that of a parameterized product state, and we derive precise dualities between partition functions with insertion of defects corresponding to gauging higher-form global symmetries, as well as measurement-induced phases where states induced by a partial overlap possess different (symmetry-protected) topological orders. Measurement-assisted operators to dualize quantum Hamiltonians of lattice gauge theories and their noninvertibility are also presented. Published by the American Physical Society 2024

Okuda, Takuya↗

DOE OSTI2024

Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns

Abstract Forest trees may harbor naturally occurring exon disruptive variants (DVs) in their gene sequences, which potentially impact important ecological and economic phenotypic traits. However, the abundance and molecular regulation of these variants remain largely unexplored. Here, 24,420 DVs were identified by screening 1014Populus trichocarpafull genomes. The identified DVs were predominantly heterozygous with allelic frequencies below 5% (only 26% of DVs had frequencies greater than 5%). Using common garden‐grown trees, DVs were assessed for gene expression variation in the developing xylem, revealing that their gene expression can be significantly altered, particularly for homozygous DVs (in the range of 27%–38% of cases depending on the studied common garden). DVs were further investigated for their correlations with 13 wood quality traits, revealing that, among the 148 discovered DV associations, 15 correlated with more than one wood property and six genes had more than one DV in their coding sequences associated with wood traits. Approximately one‐third of DVs correlated with wood property variation also showed significant gene expression variation, confirming their non‐spurious impact. These findings offer potential avenues for targeted introduction of homozygous mutations using tree biotechnology, and while the exact mechanisms by which DVs may directly influence wood formation remain to be unraveled, this study lays the groundwork for further investigation.

Genetics & Heredity↗

DOE OSTI2024

Fast ion confinement in the presence of core magnetic islands in Wendelstein 7-X

The effect of magnetic islands in the core region of Wendelstein 7-X (W7-X) on fast ion confinement is explored through simulations with the BEAMS3D code. A magnetic configuration where the n/m = 5/5 island chain is shifted to r/a ~ 0.7 allows the exploration of core island physics in W7-X. The control coil system on W7-X allows the tuning of the island size either increasing the island width or decreasing it. A coupling of the BEAMS3D code to the FIELDLINES code provides a versatile mechanism for incorporating magnetic islands and stochastic regions into the BEAMS3D code. Collisionless simulations suggest that the presence of core islands degrade the confinement of passing particles in the region of the island chain. Full neutral beam simulations of W7-X show a similar behavior with confinement decreasing as the island width is increased. Comparisons between a vacuum magnetic field and low beta HINT2 simulation are made showing similar fast ion behavior. Measurements of lost fast ions in W7-X confirm this trend with the control coil suppressed island configuration showing lower losses than that with no control coils applied. Simulations of fast ion wall loads are performed suggesting no drastic change in loss pattern and a slight reduction in losses with minimized islands.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Leveraging BERT and Network-Based Attention Analysis for Identifying Treatment Milestones in EHRs

This study introduces a sophisticated data-driven framework for analyzing Electronic Health Records (EHRs) using transformer-based models to identify and disentangle overlapping treatment contexts. The framework leverages a preprocessing pipeline that transforms structured procedural codes into semantically enriched descriptive text, enabling the use of attention mechanisms to cluster medical events into treatment milestones—cohesive and distinct components of care processes. The methodology is rigorously validated using synthetic datasets derived from the MIMIC-III database, designed to simulate the heterogeneity and overlapping procedural contexts characteristic of real-world EHR scenarios. Quantitative evaluation highlights the framework’s robustness in disentangling concurrent care pathways, with attention metrics and unsupervised clustering approaches demonstrating the ability to preserve intra-context relationships while distinguishing inter-context dependencies. By addressing challenges inherent in data heterogeneity, this approach provides a foundation for uncovering complex treatment patterns, advancing clinical decision-making, and optimizing resource allocation in diverse healthcare environments.

Kim, Minsu [ORNL] (ORCID:0000000224185535)↗

DOE OSTI2025

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) Software for Depletion and Fuel Management

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) software is being developed in the Research and Test Reactor (RTR) Program at Argonne National Laboratory to meet the reactor design and analysis needs of the Conversion Program. ADDER is a flexible tool that (1) provides a depletion capability through coupling external neutronics codes with a built-in CRAM solver or external depletion code and (2) provides a user-friendly interface to perform fuel management and criticality search operations. The ADDER software is a Python 3 application written using modern software development practices subject to a compliant implementation of NQA-1 and applicable Department of Energy software quality assurance standards. This report is the user guide for the software release referred to as ADDER v1.1.0. The motivation for a software to have flexible capabilities that ADDER possesses is the need to support a wide variety of geometries that are commonly required in analysis of research and test reactors. These reactors can have complex fuel, experiment, or control material shuffling patterns that persist over several years with many fuel management and partial refueling intervals. The scale of fuel management analysis can require tracking of an inventory that is multiple times the core loading. Many reactors, both power and non-power reactors of various types, will find the features of ADDER useful to facilitate key tasks that a fuel or core design engineer must perform with the convenience of concise input and validated functionality.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) Software for Depletion and Fuel Management

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Idiomatic Correctness-Checking via Julienne in Fortran 2023

This paper presents a unified approach to unit testing and runtime assertion checking using Fortran 2023. The paper describes the support for our approach in the Julienne framework. Julienne leverages recent Fortran standards to implement object-oriented design patterns, support testing parallel programs, and implement functional programming patterns in order to craft idioms inspired by natural-language expressions. The presented idioms employ novel operators to write expressions that evaluate to a test-diagnosis object encapsulating two components: (1) the test outcome or assertion outcome and (2) an automatically generated diagnostic string. Two other novel aspects of the approach include (1) the ability to enforce assertions inside pure procedures and (2) the ability to output rich diagnostic information inside pure procedures during error termination when assertions fail. The latter capability mitigates against a reason that Fortran programmers commonly cite for not writing pure procedures: difficulty obtaining useful program output inside pure procedures when debugging code. This paper demonstrates how the adoption of the proposed idioms leads naturally to a unifying theme across two otherwise disparate technologies: unit testing and runtime assertion checking. Finally, this paper describes the usage of the Julienne testing framework for writing unit tests and assertions in the Matcha high-performance computing application and the Fiats deep learning library.

Rouson, Damian↗

DOE OSTI2025

Electron cyclotron emission measurements and modeling in optically semi-transparent plasma on the HSX stellarator

On the Helically Symmetric Experiment (HSX), electron cyclotron emission (ECE) at the second harmonic of the electron gyrofrequency is measured with a 16-channel heterodyne receiver. An ECE radiometer diagnostic has been calibrated with a broadband frequency source, allowing independent measurements of the electron temperature. The antenna pattern has a significant impact on the measurements, and modeling its effect is necessary to produce an ECE radiation temperature spectrum. Measurements, calibration results, and modeling of the ECE data are presented in this paper. At a relatively high plasma density, HSX plasmas are thermal, and the radiation temperature measured by the radiometer is in good agreement with the electron temperature measured by a Thomson scattering diagnostic. At a relatively low plasma density, the deviation from a Maxwellian distribution is large, and asymmetry in the radiation temperature profile is measured. These measurements are supported by single-pass and multi-pass ray tracing calculations of the electron cyclotron emission using the TRAVIS ray tracing code. Thermal and nonthermal electron populations exist in HSX, and the effect of these populations on the asymmetry in the measured emission is presented.

Cyclotron radiation↗

DOE OSTI2025

RingX: Scalable Parallel Attention for Long-Context Learning on HPC

The attention mechanism has become foundational for remarkable AI breakthroughs since the introduction of the Transformer, driving the demand for increasingly longer context to power frontier models such as large-scale reasoning language models and high-resolution image/video generators. However, its quadratic computational and memory complexities present substantial challenges. Current state-of-the-art parallel attention methods, such as ring attention, are widely adopted for long-context training but utilize a point-to-point communication strategy that fails to fully exploit the capabilities of modern HPC network architectures. In this work, we propose ringX, a scalable family of parallel attention methods optimized explicitly for HPC systems. By enhancing workload partitioning, refining communication patterns, and improving load balancing, ringX achieves up to 3.4 × speedup compared to conventional ring attention on the Frontier supercomputer. Optimized for both bi-directional and causal attention mechanisms, ringX demonstrates its effectiveness through training benchmarks of a Vision Transformer (ViT) on a climate dataset and a Generative Pre-Trained Transformer (GPT) model, Llama3 8B. Our method attains an end-to-end training speedup of approximately 1.5 × in both scenarios. To our knowledge, the achieved 38% model FLOPs utilization (MFU) for training Llama3 8B with a 1M-token sequence length on 4,096 GPUs represents one of the highest training efficiencies reported for long-context learning on HPC systems. Our code implementation is available at https://github.com/jqyin/ringX-attention.

Yin, Junqi [ORNL] (ORCID:0000000338435520)↗

DOE OSTI2025

Flower‐Type Organized Trade‐Wind Cumulus: A Multi‐Day Lagrangian Large Eddy Simulation Intercomparison Study

Shallow cumulus cloud fields in subtropical marine trade wind environments, particularly over the tropical Atlantic Ocean, show distinct organizational patterns. Among these, Flower‐type clouds are characterized by expansive stratiform cloud patches surrounded by regions of scattered convection. The objectives of this study were (a) to construct a case study of a time period during the EUREC 4 A/ATOMIC field campaign when Flower‐type organization was observed, (b) to evaluate the fidelity of a multi‐model ensemble of large eddy simulations of that case, and (c) to analyze the interaction between cloud and precipitation processes and mesoscale organization in the simulations. The simulations follow a quasi‐Lagrangian trajectory, allowing mesoscale features to develop over time in a domain that follows the boundary‐layer airmass. The results show a broad agreement in simulated thermodynamic properties across different LES codes, with Flower‐type cloud patches appearing within hours of each other. The consensus among models is consistent with observations made during the EUREC 4 A/ATOMIC field campaign on the specific day of interest. The cloud structure reveals three distinct peaks in the joint probability densities of cloud base and cloud top height, with the dominant peak at any given time influenced by the stage of cloud organization. The simulated cloud system evolution reveals consistent occurrence of maxima in liquid water path and rain rate before Flower reaches its maximum length scale. Targeted sensitivity tests reveal a weak relationship between Cloud Droplet Number concentration and the extent/degree/type of organization.

EUREC4A↗

DOE OSTI2024

Investigating the origin of the far-field reflection interference fringe (RIF) of microdroplets

We show that the reflection interference fringe (RIF) is formed on a screen far away from the microdroplets placed on a prism-based substrate, which have low contact angles and thin droplet heights, caused by the dual convex–concave profile of the droplet, not a pure convex profile. The geometric formulation shows that the interference fringes are caused by the optical path difference when the reflected rays from the upper convex profile at the droplet–air interface interfere with reflection from the lower concave profile at oblique angles lower than the critical angle. Analytic solutions are obtained for the droplet height and the contact angle out of the fringe number and the fringe radius in RIF from the geometric formulation. Furthermore, the ray tracing simulation is conducted using the custom-designed code. The geometric formulation and the ray tracing show excellent agreement with the experimental observation in the relation between the droplet height and the fringe number and the relation between the contact angle and the fringe radius. This study is remarkable as the droplet's dual profile cannot be easily observed with the existing techniques. However, the RIF technique can effectively verify the existence of a dual profile of the microdroplets in a simple setup. In this work, the RIF technique is successfully developed as a new optical diagnostic technique to determine the microdroplet features, such as the dual profile, the height, the contact angle, the inflection point, and the precursor film thickness, by simply measuring the RIF patterns on the far-field screen.

42 ENGINEERING↗

DOE OSTI2025

Explainable Machine Learning for Functional Data

Black-box machine learning models are recognized as useful tools for prediction applications, but the algorithmic complexity of some models causes interpretation challenges. Explainability methods have been proposed to provide insight into these models, but there is little research focused on supervised modeling with functional data inputs. We argue that, especially in applications of high consequence, it is important to explicitly model the functional dependence in a black-box analysis to not obscure or misrepresent patterns in explanations. As such, we propose the V ariable importance E xplainable E lastic S hape A nalysis (VEESA) pipeline for training supervised machine learning models with functional inputs. The pipeline is an analysis process that includes the data preprocessing, modeling, and post-hoc explanations. The preprocessing is done using elastic functional principal components analysis, which accounts for vertical and horizontal variability in functional data and, ultimately, allows for explanations in the original data space that identify the important functional variability without bias due to correlated variables. Here, we demonstrate the pipeline on two high-consequence applications: explosives classification for national security and inkjet printer identification in forensic science. The applications exhibit the VEESA pipeline’s ability to provide an understanding of the characteristics of the functional data useful for prediction. Code for implementing the pipeline is available in the veesa R package (and supplemental python code).

Elastic Shape Analysis↗

DOE OSTI2025

Ptychography at all wavelengths

Ptychography is a computational imaging technique that operates across multiple wavelength regimes, from electron (picometres) to X-ray (~0.1 nm), extreme ultraviolet (~10 nm) and visible light (micrometres). By reconstructing both amplitude and phase from diffraction patterns, ptychography enables high-resolution, quantitative imaging without conventional limitations imposed by lens-based optics. Ptychography has enabled advances across a range of scales: achieving deep-sub-angstrom resolution with electron microscopy, becoming an indispensable tool at X-ray synchrotron facilities worldwide and overcoming the trade-offs between resolution and field-of-view in optical imaging. This Primer provides a unified treatment of ptychography across these wavelength regimes. First, we discuss theoretical foundations, reconstruction algorithms, experimental considerations and wavelength-specific challenges. We then give examples of raw and processed data from various configurations and wavelengths. Next, we highlight key applications of ptychography in life sciences, materials science and industry. We also discuss data standards, open-source software implementations and best practices for ensuring reproducibility across different wavelength regimes. Finally, we consider limitations and future opportunities for ptychography. Together with accompanying datasets and code implementations, this Primer aims to serve newcomers and experienced practitioners in the field, facilitating broader adoption of ptychography across different disciplines.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Toroidal phase of post-disruption runaway electron loss to wall in presence of applied 3-D fields in DIII-D

The toroidal distribution of runaway electrons (REs) striking the centre post in DIII-D post-disruption RE final loss events is simulated utilizing the MARS-F code combined with the REORBIT module, by tracing the guiding-centre drift orbits of test REs in the presence of external (applied) plus internal (intrinsic instability) 3-D fields. To better recover the experimental results, three different equilibria with different safety factor profiles are adopted. Dominant resistive magnetohydrodynamic instabilities are found to be m/n=2/1, 3/2 and 1/1 modes (where m and n are the poloidal and toroidal mode numbers). Externally applied n=1 resonant magnetic perturbations (RMPs), with both even and odd parity configuration, are considered in each equilibrium. Locking of MHD instability to the applied RMPs is simulated by minimizing the total perturbed magnetic energy in the plasma. Here, the simulated toroidal locations, where most REs strike in the presence of an edge m/n= 2/1 instability and the n=1 RMPs in even parity, are found to agree well with experiments. Modeling also captures the measured n = 2 RE loss pattern on the wall for experiments where an edge m/n=3/2 instability is dominant instead of the m/n=2/1 mode. The key overall findings include (a) the measured global RE toroidal impact pattern in experiments can be explained by a locked resistive kink instability, (b) the toroidal phase of the locked mode is well predicted by minimizing the total perturbed magnetic energy, and (c) this edge locked mode determines the toroidal phase of the peak RE wall impact.

Bai, Xue [University of California San Diego, La J↗

DOE OSTI2025

BlueCRAB Domain Overlapping Coupling: Theory & Verification

Coupling low- and high-fidelity codes is a useful way to model complex engineering systems. Thanks to the high-fidelity code, complex phenomena can be resolved in areas of the system where this is required, yet the efficiency of the lower-fidelity code is still retained in modeling the rest of the system. This document details the theory and implementation of coupling two different thermal-hydraulic codes: the system thermal-hydraulics (STH) code System Analysis Module (SAM) and the coarse-mesh computational fluid dynamics (CFD) code Pronghorn. Both applications are included in the Comprehensive Reactor Analysis Bundle (BlueCRAB) code suite and are based on the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework. The domain overlapping (DO) coupling approach was adopted, as it offers proven advantages over more conventional domain decomposition methods. In the DO coupling, SAM provides Pronghorn with boundary conditions that depend on the system-level simulation of the entire plant. In return, the overlapping coupled SAM components–termed “surrogate components”–receive friction factors and source terms computed online based on the Pronghorn simulation. The framework is designed to be generic and enable coupling regardless of geometry and the number of inlet/outlet boundaries in the DO coupled domain. The developed method leads to consistent pressure drops, enthalpies, and scalar concentrations when comparing the coupled SAM and Pronghorn simulations. This document presents the DO coupling approach, along with two verification and two demonstration cases. The proposed problems explore different physical aspects relevant to nuclear reactor analysis, including buoyancy-driven flows, complex flow patterns, and multiple inlets and outlets. Periodically, new versions of this “BlueCRAB Domain Overlapping Coupling: Theory & Verification” report will be issued to reflect future developments and verification tests.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Data and code for Daily and Multi-Day Extreme Rainfall Analysis Under Future Climates Using Stochastic Storm Transposition and NEX-GDDP-CMIP6 Over CONUS

This data package provides inputs, codes, and outputs for a comprehensive analysis of projected changes in extreme precipitation across 10 regions of the continental United States, using 34 downscaled Earth System Models (ESMs) from the NASA Earth Exchange Global Daily Downscaled Projections, Coupled Model Intercomparison Project Phase 6 (NEX-GDDP-CMIP6) dataset. These models are part of the Coupled Model Intercomparison Project Phase 6 (CMIP6), a coordinated climate modeling framework widely used to assess climate change impacts. The analysis applies a stochastic storm transposition method to quantify changes in extreme rainfall under two Shared Socioeconomic Pathway (SSP) climate scenarios—SSP2-4.5 (moderate emissions) and SSP5-8.5 (high emissions)—compared to historical conditions (1995–2014 vs. 2081–2100). The dataset includes rainfall depth estimates for extreme events with return periods from 2 to 500 years across multiple storm durations (1, 3, and 5 days) for each of the 10 U.S. regions. Weighted ensemble statistics are derived from individual ESM performance against historical precipitation patterns, enabling robust uncertainty quantification through both sign-based and permutation-test-based model agreement assessments. Key analyses address: (1) relative changes in extreme precipitation for each climate scenario, (2) differences between SSP scenarios (SSP5-8.5 vs. SSP2-4.5), (3) contrasts between rare and frequent events, and (4) variations between multi-day and daily storm durations. The workflow produces ensemble statistics—median, 5th, 25th, 75th, and 95th percentiles—along with model agreement metrics that identify regions and event types with robust climate change signals. The dataset includes: processed rainfall depth outputs (netCDF format) from the RainyDay Python package, ESM weights from historical performance evaluation using DayMet observations, ensemble statistics across all storm dimensions, and figures summarizing key findings.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

TropiRoot 1.0: Database of tropical root characteristics across environments

Tropical ecosystems contain the world's largest biodiversity of vascular plants. Yet, our understanding of tropical functional diversity and its contribution to global diversity patterns is constrained by data availability. This discrepancy underscores an urgent need to bridge data gaps by incorporating comprehensive tropical root data into global datasets. Here, we provide a database of tropical root characteristics. This new database, TropiRoot 1.0, will be instrumental in evaluating an array of hypotheses pertaining to root functional ecology and plant biogeography, both within the tropics and relative to other global biomes. The data compilation was conducted by the TropiRoot Initiative, in partnership with the Fine-Root Ecology Database (FRED) and the Global Root Trait (GRooT) database, Colorado State University (CSU) and the Smithsonian Tropical Research Institute (STRI). Literature search and data extraction were conducted between 2020 and 2024. Literature was identified using Web of Science, Scopus, and complemented using the expert knowledge of members of TropiRoot. To provide broad environmental and geographical distributions, literature searches included root characteristics (traits) across global change drivers, natural gradients, and from different continents. We adopted FRED standardized data columns and streamlined the format to enhance accessibility for data extraction across various user groups. This optimized framework resulted in a smaller, yet comprehensive datasheet. To make the database compatible with other global root trait initiatives, column identification was standardized following the codes provided by FRED. These efforts culminated in data extracted from 104 new sources, resulting in more than 8000 rows of data (either species or community data). Most of the data in TropiRoot 1.0 include root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology, and root chemistry. This initiative represents a 30% increase in the currently available data for tropical roots in FRED. TropiRoot 1.0 contains root characteristics from 25 different countries, where seven are located in Asia, six in South America, five in Central America and the Caribbean, four in Africa, two in North America, and 1 in Oceania. Due to the volume of data, when ancillary data were available, including soil data, these data were either extracted and included in the database or its availability was recorded in an additional column. Multiple contributors checked the entries for outliers during the collation process to ensure data quality. For text-based observations, we examined all cells to ensure that their content relates to their specific categories. For numerical observations, we ordered each numerical value from least to greatest and plotted the values, checking apparent outliers against the data in their respective sources and correcting or removing incorrect or impossible values. Some data (soil and aboveground) have different columns for the same variable presented in different units, including originally published units, but root characteristics data had units converted to match those reported in FRED. By filling a gap from global databases, TropiRoot 1.0 expands our knowledge of otherwise so far underrepresented regions and our ability to assess global trends. This advancement can be used to improve tropical forest representation in vegetation models. The data are freely available and should be cited when used.

FRED↗

DOE OSTI2024

Validation of the ERO2.0 code using W7-X and JET experiments and predictions for ITER operation

Abstract The paper provides an overview of recent modelling of global material erosion and deposition in the fusion devices Wendelstein 7-X (W7-X), JET and ITER using the Monte-Carlo code ERO2.0. For validating the modelling tool in a three-dimensional environment, W7-X simulations are performed to describe carbon erosion from the graphite test divertor units, which were equipped in operational phase OP 1.2 and analysed post-mortem. Synthetic spectroscopy of carbon line emission is compared with experimental results from the divertor spectrometer measurement system, showing a good agreement in the e-folding lengths in the radial intensity profiles of carbon. In the case of metallic wall materials, earlier modelling of the Be/W environment in JET and ITER is revisited and extended with an updated set of sputtering and reflection data, as well as including the mixing model for describing the Be/W dynamics in the divertor. Motivated by recent H/D/T isotope experiments in JET, limited and diverted configuration pulses are modelled, showing the expected trend of both Be and W erosion increasing with isotope mass. For the JET diverted configuration pulses, it is shown that Be migrates predominantly to the upper part of the inner divertor where it initially leads to strong W erosion. With longer exposure time, the growth of a Be deposited layer leads to a reduction of W erosion in that region. A similar trend is observed in simulations of the ITER baseline Q = 10 scenario, however with a more symmetric Be migration pattern leading to deposition also on the outer divertor.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗