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Optimal checkpointing for adjoint multistage time-stepping schemes

Here, we consider checkpointing strategies that minimize the number of recomputations needed when performing discrete adjoint computations using multistage time-stepping schemes that require computing several substeps within one complete time step. Specifically, we propose two algorithms that can generate optimal checkpoint-ing schedules under weak assumptions. The first is an extension of the seminal Revolve algorithm adapted to multistage schemes. The second algorithm, named CAMS, is developed based on dynamic programming, and it requires the least number of recomputations when compared with other algorithms. The CAMS algorithm is made publicly available in a library with bindings to C and Python. Numerical results show that the proposed algorithms can deliver up to two times the speedup compared with that of classical Revolve. Moreover, we discuss the utilization of the CAMS library in mature scientific computing libraries and demonstrate the ease of using it in an adjoint workflow. The proposed algorithms have been adopted by the PETSc TSAdjoint library. Their performance has been demonstrated with a large-scale PDE-constrained optimization problem on a leadership-class supercomputer. This work is a significant extension of the authors' conference paper.

97 MATHEMATICS AND COMPUTING↗

Optimization of well design and CO 2 injection strategy for risk reduction in Class VI geological carbon sequestration wells

The safety and durability of Class VI wells are critical for geological carbon sequestration (GCS). However, current GCS operations face unique challenges: unlike traditional Class II wells, Class VI CO 2 injection wells operate at rates up to 100 times higher, dramatically increasing the risk of wellbore leakage and structural compromise due to severe temperature drops and associated mechanical stresses. Despite existing guidelines on material selection, there remains a substantial gap in understanding how rapid CO 2 injection rates, low surface temperatures, and variable reservoir conditions interact to threaten long-term well integrity. This study presents a comprehensive, original workflow integrating advanced analytical and numerical models for both well flow and well integrity analysis. By systematically simulating a wide range of field-relevant scenarios—including variations in injection rate, CO 2 temperature, and reservoir pressure—this work provides the first cross-validated assessment of cooling effects on wellbore. The results reveal that extreme temperature drops, up to 60 °C, can occur under high injection rates, particularly in depleted reservoirs, significantly increasing the risk of cement failure. Building on these insights, the study proposes innovative, practical well design and operational strategies, including ductile cement formulations, pre-stressing techniques, advanced insulation coatings, and proactive management of injection rates. The safety of Class VI well extends beyond simply using CO 2 resistant materials. Cement materials should possess optimal thermo-hydraulic-mechanical-chemical properties for effective performance. This work provides a scientific basis for optimizing Class VI well designs, with direct benefits for minimizing environmental risk, lowering operational costs, and enhancing the long-term reliability of GCS.

25 ENERGY STORAGE↗

Tracking Dendritic Growth in Hydrogen-Based Hematite Reduction via Computer Vision

The reduction of hematite to metallic iron using hydrogen (H2) as a reducing agent presents a promising pathway for decarbonizing steel production. In this study, we employ a combination of in situ confocal scanning laser microscopy (CSLM) and advanced computer vision techniques to quantitatively analyze dendritic growth of ferrite during H2-based reduction of iron oxide at high temperatures. A workflow integrating Watershed Image Segmentation (WIS) and Lucas-Kanade Optical Flow (LKOF) is developed to extract both global and local kinetic information from time-resolved micrograph sequences. H2 reduction experiments conducted at 1400 degrees C and 1500 degrees C demonstrate a clear correlation between temperature and reduction rate, as evidenced by accuracy of fitted Johnson-Mehl-Avrami-Kolmogorov (JMAK) parameters. Optical flow analysis further elucidates the anisotropic and branched nature of dendritic growth, providing spatially resolved velocity fields that correlate well with global transformation kinetics. The proposed methodology demonstrates strong agreement with experimental measurements and literature values, offering a robust framework for automated image-based analysis to study kinetics through microstructural evolution in the reduction of iron ore, and likely other reaction-diffusion phenomena.

08 HYDROGEN↗

CoRE MOF DB: A curated experimental metal-organic framework database with machine-learned properties for integrated material-process screening

Here, we present an updated version of the Computation-Ready, Experimental (CoRE) Metal-Organic Framework (MOF) database, which includes a curated set of computation-ready MOF crystal structures designed for high-throughput computational materials discovery. Data collection and curation procedures were improved from the previous version to enable more frequent updates in the future. Machine-learning-predicted properties, such as stability metrics and heat capacities, are included in the dataset to streamline screening activities. An updated version of MOFid was developed to provide detailed information on metal nodes, organic linkers, and topologies of an MOF structure. DDEC6 partial atomic charges of MOFs were assigned based on a machine-learning model. Gibbs ensemble Monte Carlo simulations were used to classify the hydrophobicity of MOFs. The finalized dataset was subsequently used to perform integrated material-process screening for various carbon-capture conditions using high-fidelity temperature-swing adsorption (TSA) simulations. Our workflow identified multiple MOF candidates that are predicted to outperform CALF-20 for these applications.

CoRE MOF database↗

The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation

Syntrophus aciditrophicus is a syntrophic bacterium degrading fatty and aromatic acids into acetate, CO 2 , formate, and H 2 , consumed by methanogenic archaea. The syntroph’s acyllysine modifications were analyzed with a workflow avoiding antibody enrichment, enabling unbiased global acylation profiling. Seven acyl modification types were identified, six corresponding to reactive acyl-CoA species intermediates in benzoate degradation. Benzoatedegrading enzymes were also prominent among the 60 acylated proteins. The abundant acylations and active deacylases suggest that post-translational modifications directly regulate syntrophic benzoate degradation

59 BASIC BIOLOGICAL SCIENCES↗

Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform

Conventional proteomics measures the averaged signal from mixed cell populations or bulk tissues, leading to the dilution of significant changes in subpopulations of cells that might serve as important biomarkers. Recent developments in bottom-up proteomics have enabled spatial mapping of cellular heterogeneity in tissue microenvironments. However, bottom-up proteomics cannot precisely infer the abundance changes of intact proteins, which are presented as proteoforms. Herein, we described a spatially resolved top-down proteomics (TDP) platform for proteoform identification and quantification directly on thin tissue sections. The spatial TDP platform consisted of a nanoPOTS (nanodroplet Processing in One pot for Trace Samples)-based sample preparation system and an LCM (laser capture microdissection)-based cell isolation system. We improved the nanoPOTS sample preparation by adding benzonase in the extraction buffer to enhance the coverage of nucleus proteins. Using ~200 cultured cells as model samples, the improved approach increased proteoform identifications from 493 to 700; newly identified proteoforms primarily corresponded to nuclear proteins. To demonstrate the spatial TDP platform in tissue samples, we analyzed LCM-isolated tissue voxels from rat brain cortex and hypothalamus regions. We quantified 426 proteoforms by combining identifications from TopPIC and TDPortal with the quantitation from ProMex. Several proteoforms corresponding to the same gene exhibited mixed abundance profiles between two tissue regions, suggesting potential PTM-specific spatial distributions. The spatial TDP workflow has prospects for biomarker discovery at proteoform level from small tissue sections.

59 BASIC BIOLOGICAL SCIENCES↗

A publicly available PyTorch-$\mathrm{ABAQUS}$ $\mathrm{UMAT}$ deep-learning framework for level-set plasticity

Here this paper introduces a publicly available PyTorch-ABAQUS deep-learning framework of a family of plasticity models where the yield surface is implicitly represented by a scalar-valued function. In particular, our focus is to introduce a practical framework that can be deployed for engineering analysis that employs a user-defined material subroutine (UMAT/VUMAT) for ABAQUS, which is written in FORTRAN. To accomplish this task while leveraging the back-propagation learning algorithm to speed up the neural-network training, we introduce an interface code where the weights and biases of the trained neural networks obtained via the PyTorch library can be automatically converted into a generic FORTRAN code that can be a part of the UMAT/VUMAT algorithm. To enable third-party validation, we purposely make all the data sets, source code used to train the neural-network-based constitutive models, and the trained models available in a public repository. Furthermore, the practicality of the workflow is then further tested on a dataset for anisotropic yield function to showcase the extensibility of the proposed framework. A number of representative numerical experiments are used to examine the accuracy, robustness and reproducibility of the results generated by the neural network models.

36 MATERIALS SCIENCE↗

Volumetric analysis and mesh generation of real and artificial microstructural geometries

Producing a viable finite element mesh of realistic microstructural structural geometry is a critical step in analyzing the thermo-mechanical behavior of complex multi-material composites. Advancements in imaging technology such as micro computed tomography have allowed modelers to access high resolution mesoscale geometries for direct numerical simulation. However, converting from voxel based 3D images to usable finite element meshes has been challenging. A robust method including algorithms and software scripts for generating finite element meshes from 3D imaged microstructures is presented in this paper. It includes a routine for inserting cohesive elements around material interfaces to enable modeling of interface properties including delamination and damage. The algorithms and procedures presented in this method leverage currently available software packages for processing surface based geometry into volume based meshes. In addition to converting real geometry from physical imaging systems, algorithms for producing numerically generated and statistically equivalent microstructural geometry are also included. These artificial microstructures can be a valuable resource for modelers when physical specimens do not exist or are limited in quantity: Method establishes a workflow from voxel data to viable finite element mesh including interface information, and Includes a method for synthetic geometry generation based on metrics from real microstructures.

36 MATERIALS SCIENCE↗

Cascading economic losses from port disruptions under capacity constrained multimodal freight networks

This study quantifies how throughput disruptions at major seaports cascade through capacity-constrained multimodal freight networks and interregional production systems. We couple an agent-based model (ABM) multimodal freight simulation that resolves rerouting, terminal queueing, and inventory drawdown under binding modal and facility capacities with a multiregional output loss input-output (MRIIM) model that propagates realized delivery shortfalls across regions and sectors. The framework is demonstrated for the Port of Los Angeles using Freight Analysis Framework flows and Bureau of Economic Analysis input-output accounts and is evaluated over a 52-week horizon under deterministic sector targeted shocks and stochastic disruption realizations with uncertain severity and duration. Results indicate nonlinear amplification: realized national losses concentrate in manufacturing and transportation/warehousing even when exogenous port shocks are dispersed, suggesting that congestion spillback and limited short-run substitution can dominate the initial shock allocation. We further evaluate a tabular reinforcement-learning (Q-learning) intervention layer that selects among a small set of implementable system level levers (truck-to-rail and truck-to-barge shift settings) without overriding shipper routing, finding that such interventions reduce total losses for moderate disruptions but yield diminishing returns once substitute modes approach capacity. By linking operational freight behavior to system wide impacts under uncertainty, the proposed ABM-MRIIM pipeline provides a reusable workflow for port disruption stress testing, identification of structurally critical sectors/corridors, and evaluation of resilience interventions under realistic capacity limits.

42 ENGINEERING↗

Strategy to safely enable X-ray computed tomography examination of highly radioactive tristructural isotropic nuclear fuel

Nondestructive post-irradiation examination of nuclear fuels and materials is useful in collecting data to inform commercial licensing of new nuclear concepts. This work details the planning, shielding design, and workflow of an X-ray computed tomography examination of an irradiated AGR-5/6/7 fuel compact with a dose rate of 1318 R/hr on contact from both β and ɤ-ray radiation with 120 R/hr of the dose rate coming exclusively from ɤ-rays. Post-irradiation examination of highly radioactive samples can help reduce the timeframe from conceptualization of novel nuclear concepts to their commercial implementation as not only is less time spent waiting for experiments to decay away to acceptable levels for examinations, but data from these experiments can more quickly inform model efforts and subsequent experiments. While this work represents the hottest radiological sample that has been openly transported and examined at Idaho National Laboratory’s Irradiated Materials Characterization Laboratory to date, it is anticipated that this work and its lessons learned will facilitate future examinations of similar or even more radioactive specimens.

42 - ENGINEERING↗

Segmentation method comparison for residual fiber length measurement across tiled microscopy images

Fiber length distribution (FLD), in part, governs mechanical properties in discontinuous fiber composites, yet manual measurement methods limit the high-throughput characterization needed for materials design optimization. This study compares deep learning segmentation approaches for automated FLD measurement in large-field microscopy, evaluating how method choice affects the microstructural descriptors used in structure-property-processing relationships. A critical challenge is that high-resolution microscopy images (10,000×10,000 pixels) must be tiled for deep learning analysis, fragmenting fibers at boundaries. We demonstrate that segmentation method proves crucial for measurement accuracy. For example, instance segmentation with Slicing Aided Hyper Inference (SAHI) preserves individual fiber integrity across tiles while semantic segmentation prioritizes speed. Comparing against manual measurement of extracted carbon fibers, YOLOv11-SAHI matched manual ground truth (238 μm weighted mean) with 40x speedup (4.5 vs 167 minutes per image). U-Net provides rapid quantification although it is at the cost of reduced accuracy due only reliably measuring stand-alone fibers. Our comparative analysis reveals that instance segmentation with SAHI better preserves length measurements while semantic segmentation prioritizes speed, providing empirical guidance for method selection. The characterization provides essential inputs for mechanical property prediction models and inverse design workflows, accelerating composite materials development cycles.

Additive manufacturing↗

Broadband impedance modeling and single bunch instabilities estimations of the advanced light source upgrade project

We report the Advanced Light Source Upgrade (ALS-U) is a 4th generation diffraction-limited soft x-ray radiation source, consisting of a new accumulator ring (AR) and a new storage ring (SR). In both rings coupling-impedance driven instabilities need careful evaluation to ensure meeting the machine’s high-performance goals. This paper presents the workflow followed in building the impedance models and the beam-stability analysis based on those models. We follow the commonly accepted approach of separating the resistive-wall and the geometric parts of the impedance; the former is obtained by analytical formulas, the latter by numerical electro-magnetic codes (primarily CST Studio software) with perfectly-conducting boundary conditions. Impedance budgets are established and pseudo-Green functions calculated to be used in beam dynamics studies. We also present various ways to cross-check simulation results for reliable impedance modeling. Finally, the crucial single-bunch instability current thresholds for various operation modes are determined and discussed.

07 ISOTOPE AND RADIATION SOURCES↗

A machine learning approach for particle accelerator errant beam prediction using spatial phase deviation

Particle accelerators are extremely complex systems that are expected to operate on high availability. Predicting impending failures only by utilizing data collected from diagnostic equipment already on board can help operators to avoid installing expensive sensors, unscheduled downtime and associated costs. For this purpose we explore the predictive power of Machine Learning algorithms to detect faulty beams prior to the failure. In this study, we propose a Machine Learning approach to model mapping from a pair of sensors located across the accelerator. While the model is trained to represent normal operation, we evaluate the predictive performance on known faulty beam pulses. We also investigate the model performance on unseen data through k-fold cross-validation. Then we recap the analysis with a neural architecture search and hyperparameter optimization study to fine tune our initial model. In conclusion, this paper will also introduce a sustainable framework that can standardize Machine Learning workflow applied to particle accelerators.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

The high level trigger and express data production at STAR

To meet the demands of the Beam Energy Scan phase-II (BES-II) program, the STAR experiment at the Relativistic Heavy Ion Collider (RHIC) developed a dual real-time framework consisting of a High Level Trigger (HLT) and an Express Data Production system (xProduction). The HLT operates online within the Data Acquisition (DAQ) chain on a dedicated multi-core CPU cluster with the option to offload compute-intensive kernels to Xeon Phi coprocessors. It uses parallelized algorithms, such as the Cellular Automaton (CA) Track Finder, to perform rapid tracking, vertexing, and event filtering. This allows it to select events of interest in real time and provide immediate feedback on detector and beam conditions. In contrast, the xProduction workflow runs concurrently and independently of the DAQ loop. It applies near offline-quality calibration and reconstruction within hours of data collection. The xProduction input is the express data stream, whose content can be enriched by HLT trigger/priority selections under DAQ/HLT resource constraints, and it uses the STAR calibration/conditions framework, incorporating online calibration/QA information when available. This enables early preliminary physics analysis, including the reconstruction of rare signals, such as hyperons and hypernuclei. It also provides collaboration-wide access to analysis-ready datasets. Together, the HLT and xProduction systems form a complementary architecture: the HLT performs online event selection while the xProduction chain delivers high-quality results within a short amount of time. This integrated framework has enabled the prompt reconstruction of the $^5_Λ$ He hypernucleus with high statistical significance and the efficient processing of hundreds of millions of heavy-ion collision events. In conclusion, its demonstrated scalability and robustness establish a model for future high-luminosity experiments requiring both online event filtering and rapid access to analysis-quality data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Modeling the effect of nitrogen recycling on the erosion and leakage of tungsten impurities from the SAS-VW divertor in DIII-D during nitrogen gas injection

The new SAS-VW divertor in DIII-D has tungsten-coated components to enable the study of tungsten erosion and leakage from a closed, slot-like divertor. A proposed method of actively managing the tungsten impurities is to inject low-Z impurities, such as nitrogen, into the Scrape-off-Layer (SOL) to modify the conditions in the plasma boundary and in turn manipulate both the erosion and subsequent transport of tungsten. Nitrogen injection from the SOL crown has been modeled using SOLPS-ITER to calculate the background plasma including the intrinsic carbon and the injected nitrogen impurities, and subsequently DIVIMP has been used to calculate the tungsten erosion and transport on top of the background plasma solution. This workflow has been used to model scenarios at a variety of nitrogen injection rates with different assumptions about the nitrogen recycling at the target. In the scenario modeled here, an optimal nitrogen injection rate around 3-4 x 10 20 N/s is found to reduce the amount of tungsten reaching the core by a factor of about 2.4. However, when the nitrogen recycling rate at the divertor targets is high, the nitrogen redistributes within the slot leading to increased tungsten sputtering, and the range of injection rates resulting in tungsten mitigation becomes narrower.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An expert-driven literature review of “negative” chemicals for developmental neurotoxicity (DNT) in vitro assay evaluation

To date, approximately 200 chemicals have been tested in US Environmental Protection Agency (EPA) or Organization for Economic Co-operation and Development (OECD) developmental neurotoxicity (DNT) guideline studies, leaving thousands of chemicals without traditional animal information on DNT hazard potential. To address this data gap, a battery of in vitro DNT new approach methodologies (NAMs) has been proposed. Evaluation of the performance of this battery will increase the confidence in its use to determine DNT chemical hazards. One approach to evaluate DNT NAM performance is to use a set of chemicals to evaluate sensitivity and specificity. Since a list of chemicals with potential evidence of in vivo DNT has been established, this study aims to develop a curated list of “negative” chemicals for inclusion in a “DNT NAM evaluation set”. A workflow, including a literature search followed by an expert-driven literature review, was used to systematically screen 39 chemicals for lack of DNT effect. Expert panel members evaluated the scientific robustness of relevant studies to inform chemical categorizations. Following review, the panel discussed each chemical and made categorical determinations of “Favorable”, “Not Favorable”, or “Indeterminate” reflecting acceptance, lack of suitability, or uncertainty given specific limitations and considerations, respectively. Further, the panel determined that 10, 22, and 7 chemicals met the criteria for “Favorable”, “Not Favorable”, and “Indeterminate”, for use as negatives in a DNT NAM evaluation set. Ultimately, this approach not only supports DNT NAM performance evaluation but also highlights challenges in identifying large numbers of negative DNT chemicals.

59 BASIC BIOLOGICAL SCIENCES↗

Sensitivity analysis, surrogate modeling, and optimization of pebble-bed reactors considering normal and accident conditions

This research provides a valuable tool that streamlines the optimization process while significantly increasing its accuracy. This study creates a robust framework for reactor design optimization by incorporating comprehensive modeling using the Comprehensive Reactor Analysis Bundle, or BlueCRAB, within the Multiphysics Object-Oriented Simulation Environment (MOOSE). BlueCRAB is the United States Nuclear Regulatory Commission's code suite for non-light water reactor analysis and includes the Griffin, Pronghorn, and Bison applications. This not only improves the efficiency of the optimization process but also enhances the reliability of the results. Such a tool is essential for advancing the state-of-the-art in pebble-bed reactor technology and is critical for achieving the goals of Generation IV reactors, which aim for safe, sustainable, and economically viable nuclear energy solutions. This work presents and applies this workflow on pebble-bed reactors while considering both normal and off-normal conditions. A representative gas-cooled pebble-bed reactor at equilibrium core conditions serves as the nominal design specification for normal operation and is based on previous research. The depressurized loss-of-forced-cooling accident is deployed for off-normal conditions in this work. After defining design-related parameters and quantities of interest regarding reactor safety and performance, this multiphysics model is sampled using the MOOSE stochastic tools module. The result is a comprehensive dataset of configurations, enabling sensitivity analysis and the generation of surrogate models. Subsequently, the dataset and surrogate models are employed in two optimization studies aimed at maximizing fuel utilization and economic profit while adhering to safety and operational constraints. Performing the optimization process with fuel utilization as the metric leads to an improvement of approximately 10%, compared to engineering-judgment-based nominal conditions. The optimization on economic profit leads to an estimated increase of ~300 million USD over the lifetime of the reactor.

97 MATHEMATICS AND COMPUTING↗

Versatile TRISO fuel particle modeling in Bison

Tri-structural isotropic (TRISO) fuel particles are a key component in several previous and current reactors as well as in a variety of novel nuclear reactor designs. Interest in TRISO fuel is on the rise, necessitating considerable computer modeling of TRISO fuel behavior in order to support related design and licensing activities. The Bison nuclear fuel performance code, which offers a full set of capabilities for modeling TRISO fuels, makes it easier to explore the various important aspects of TRISO fuel behavior. One key advantage of Bison is its ability to create meshes in 1D, 2D, and 3D. Users can customize these meshes for specific geometries, mesh densities, and use cases. This enables a wide variety of analyses, including thermal, structural, mass diffusion, homogenization, and statistical failure analyses. Furthermore, the meshing capability simplifies analysts’ workflows. The inherent mesh generation capability eliminates the need for separate mesh-generating software and mesh file management. Also, the fact that the meshes are customizable makes it straightforward to automate an investigation over a range of geometric parameters or mesh densities. Here, the present paper highlights the ease with which Bison may be used to create meshes for both simple and relatively complex TRISO fuel particles, and it explores the types of analyses enabled by these meshes.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗