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At least 415 records · Page 23

Examination of 3013 Containers Baseline Surface Features

The Surveillance and Monitoring Program at Los Alamos National Laboratory (LANL) was tasked with evaluating the baseline features of 3013 containers. This baseline is to be used as a basis for comparison for 3013 containers that had been packaged with corrosive plutonium materials. The LANL team evaluated an unwelded container, an unused welded container, and a welded container that had held plutonium metal without any corrosive impurities. These three containers had features with depths no larger than 6 µm and had similar depth distributions. The features observed in the baseline containers were all shallower than those seen in containers packaged with corrosive plutonium materials. This work establishes workflows for feature identification and measurement, as well as establishment of baseline data for future comparison with corroded containers.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Workflow for Process Automation of Soil Gas Results from an Automated Soil Gas-Sampling System for Application in Carbon Storage Projects

Conference presentation at Geoconvention, Calgary, Alberta, Canada, May 12–14, 2025. The Energy & Environmental Research Center (EERC) developed an automated workflow for processing soil gas measurements collected from the automated soil gas-sampling systems deployed across the project site. Raw soil gas measurements are collected from each station every 4 hours and automatically uploaded to a cloud database. The workflow begins by writing code to download the data to a workstation automatically, then the data are published to an online dashboard that visualizes the measurements in time-series plots and a process-based decision-making framework. This automated workflow accelerates the time from data acquisition to decision-making. It supports carbon storage project operators by preparing and delivering a live, standardized dataset for quick analysis and source attribution to provide assurance of containment and overall permit compliance.

02 PETROLEUM↗

The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering

The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. While early versions of SBOL focused only on the description of DNA-based components and their sub-components, SBOL can now be used to represent knowledge across multiple scales and throughout the entire synthetic biology workflow, from the specification of a single molecule or DNA fragment through to multicellular systems containing multiple interacting genetic circuits. The third major iteration of the SBOL standard, SBOL3, is an effort to streamline and simplify the underlying data model with a focus on real-world applications, based on experience from the deployment of SBOL in a variety of scientific and industrial settings. Here, we introduce the SBOL3 specification both in comparison to previous versions of SBOL and through practical examples of its use.

59 BASIC BIOLOGICAL SCIENCES↗

Workflow for Process Automation of Soil Gas Results from an Automated Soil Gas-Sampling System for Application in Carbon Storage Projects

Extended abstract for Geoconvention, Calgary, Alberta, Canada, May 12–14, 2025. The Energy & Environmental Research Center (EERC) developed an automated workflow for processing soil gas measurements collected from the automated soil gas-sampling systems deployed across the project site. Raw soil gas measurements are collected from each station every 4 hours and automatically uploaded to a cloud database. The workflow begins by writing code to download the data to a workstation automatically, then the data are published to an online dashboard that visualizes the measurements in time-series plots and a process-based decision-making framework. This automated workflow accelerates the time from data acquisition to decision-making. It supports carbon storage project operators by preparing and delivering a live, standardized dataset for quick analysis and source attribution to provide assurance of containment and overall permit compliance.

02 PETROLEUM↗

Enhancing dimensionality prediction in hybrid metal halides via feature engineering and class-imbalance mitigation

We present a machine learning (ML) framework for predicting the structural dimensionality of hybrid metal halides (HMHs), including organic-inorganic perovskites, using a combination of chemically-informed feature engineering and advanced class-imbalance handling techniques. This study is motivated by the small and highly imbalanced nature of experimentally available HMH datasets, which limits the applicability and reliability of conventional ML approaches. The dataset, consisting of 494 HMH structures, is highly imbalanced across dimensionality classes (0D, 1D, 2D, 3D), posing significant challenges to predictive modeling. To mitigate this limitation, the dataset was augmented to 1336 samples using the synthetic minority oversampling technique, enabling improved learning of underrepresented dimensionality classes while preserving chemically meaningful feature relationships. We developed interaction-based descriptors designed to capture coupled steric and polarity effects relevant to dimensionality prediction, which are not readily captured by standard single-parameter or composition-only descriptors. These descriptors are integrated into a multi-stage workflow combining feature selection, ensemble stacking, and performance optimization. Our approach significantly improves F1-scores for underrepresented classes, achieving robust cross-validation performance across all dimensionalities. This work demonstrates a generalizable strategy for extracting reliable and interpretable structure–dimensionality relationships from limited experimental data, enabling pre-synthesis screening of organic cations and providing a practical blueprint for small-data ML in hybrid materials systems.

36 MATERIALS SCIENCE↗

Simulation tools, first results and experimental status of the MURAVES experiment

The MUon RAdiography of VESuvius (MURAVES) project aims at the study of Mt. Vesuvius, an active and hazardous volcano near Naples, Italy, with the use of muons freely and abundantly produced by cosmic rays. In particular, the MURAVES experiment intends to perform muographic imaging of the internal structure of the summit of Mt. Vesuvius. The challenging measurement of the rock density distribution in its summit by muography, in conjunction with data from other geophysical techniques, can help model possible eruption dynamics. The MURAVES apparatus consists of an array of three independent and identical muon trackers, with a total sensitive area of 3 square meters. In each tracker, a sequence of 4 XY tracking planes made of plastic scintillators is complemented by a 60 cm thick lead wall inserted between the two downstream planes to improve rejection of background from low energy muons. The apparatus is currently acquiring data. This paper presents preliminary results from the analysis of the first data samples acquired with trackers pointing towards Mt. Vesuvius, including the first relative measurement of the density projection of two flanks of the volcano at three different altitudes; we also present the workflow of the simulation chain of the MURAVES experiment and its ongoing developments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics

The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates—parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗

Data supporting the manuscript "Nanometer Scale Imaging to Develop Quantitative Descriptors of Bipolar Membrane Junction Structure"

This dataset contains atomic force microscopy images associated with the manuscript "Nanometer Scale Imaging to Develop Quantitative Descriptors of Bipolar Membrane Junction Structure" by Maria Kelly, Emily R. Dunn, Ellis A. Spickermann, Josephine N. Gruber, César A. Lasalde-Ramírez, P. N. Romero Zavala, Éowyn Lucas, Ankur Gupta, Harry A. Atwater, and Wilson A. Smith. The dataset contains both raw images as well as segmented images produced by the image processing workflow described in the manuscript. A readme file and meta data file are included to provide additional details regarding the sample identity, image acquisition parameters, and file naming scheme.

36 MATERIALS SCIENCE↗

Instantiation of the Damara Tern Platform for Advanced Materials and Manufacturing Technologies (AMMT) Program Collaborative Data Management

This work package focused on deploying an instance of the Damara Tern platform to support AMMT collaborative research activities. The objectives were to provide selected AMMT collaborators with access to a shared environment for capturing operations, trackables, and associated metadata, and to implement data entry functionalities that reflect site-specific procedures. Key activities included creating configurable, schema-driven entry forms and validating the data collection process. The report details the deployment process, the platform infrastructure, and the implemented data entry workflows, providing a reference for end users and establishing a foundation for future production-scale deployments.

36 MATERIALS SCIENCE↗

Integrated Neutronics Modeling for Inertial Fusion Energy Systems: Development and Application to LD-FIRST

Lawrence Livermore National Laboratory (LLNL) is proposing a new Laser Driven Fusion Integration Research and Science Test Facility (LD-FIRST) with the goal of providing an experimental testbed for future Inertial Fusion Energy (IFE) systems. However, IFE systems require detailed and accurate multiphysics modeling to quantify material damage, thermal loading, and tritium breeding within complex chamber environments. This article presents the first step in an integrated multiphysics framework that couples meshed CAD-based geometry within Monte Carlo neutronic simulations to enable high-fidelity analysis of IFE chamber concepts, with future coupling to external codes. The neutronics workflow utilizes OpenMC and its third-party capability to use CAD-based geometries through DAGMC and tally on unstructured meshes with Libmesh to evaluate neutron transport behavior, geometric fidelity, and material performance under reactor-relevant conditions. The use of tailored tallies on unstructured meshes in this framework allows direct transfer without interpolating to CFD simulation tools. Two IFE chambers were evaluated, both conceived by LLNL: HYLIFE-II and Laser IFE (LIFE). This work produced high-fidelity conformal surface and volumetric meshes of the HYLIFE-II and LIFE chambers with mapped spatial insight into material damage, thermal loading, and tritium breeding. The HYLIFE-II model was built utilizing available resources and used as a test case to verify that the neutronics framework can handle complex geometries. The LIFE chamber CAD was provided by LLNL and was the main focus of this work. This work analyzes multiple ternary alloy breeding materials for the LIFE chamber, across different 6 Li enrichments to produce data relevant to the LD-FIRST project. This work also investigates the level of model fidelity for the LIFE chamber, and results show that inclusion of detailed first wall and coolant structures increased the predicted tritium breeding ratio (TBR) by ~30%, highlighting the sensitivity of tritium breeding and the need for a high-fidelity simulation framework for IFE chambers. These developments provide a scalable toolset for the design and optimization of next-generation IFE chambers, forming a solid foundation for future coupled multiphysics analysis.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Abstract Background Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. Results Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies. Conclusions Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.

59 BASIC BIOLOGICAL SCIENCES↗

Fast Semi-automated Filtration Method for Non-targeted LC-QTOF Data of Aged Nitroplasticizer Samples

A full dataset of aged nitroplasticizer (NP) is composed of more than 2000 unique mass-to-charges (m/z) when combining the non-targeted data obtained from both positive and negative electrospray ionization modes in time-of-flight mass spectrometry. Therefore, manual processing of these data often takes days, weeks, or even months to scrutinize for mechanistic insights. To effectively extract meaningful signals that represent vital degradation intermediates in the early NP degradation mechanism, a semi-automated postprocessing workflow for data filtering, tailored to the aging experiment of NP, has been developed. The automated portion of this workflow is written in a Python code (using pandas, numpy, and matplotlib libraries), which removes more than 65% of potential false signals within seconds via four threshold-based adjustable filters: signal sensitivity, coefficient of variation, number of measurements, and retention time variability. As for the manual portion, a pattern-based inspection method is employed to reduce another 23% or more false positives, which greatly simplifies data visualization and results in less than 3% of potential candidate m/z needing in-depth data interpretation. As a positive control, known compounds are verified. Using this semi-automated data reduction method, the amount of time required is reduced to a matter of hours for data filtering in the non-targeted datasets of aged NP, which saves more time and effort for compound identification.

36 MATERIALS SCIENCE↗

Learning continuous scattering length density profiles from neutron reflectivities using convolutional neural networks

Interpreting neutron reflectivity (NR) data using ad hoc multi-layer models and physics-based models provides information about spatially resolved neutron scattering length density (NSLD) profiles. Recent improvements in data acquisition systems have allowed acquiring thousands of NR curves in a couple of hours, which has led to a need for automated data analysis tools to interpret NR measurements in real-time. Here, we present a machine learning analysis workflow that uses a series of models, based on a convolutional neural network (CNN), to learn the relation between the NSLDs and the NRs, and subsequently produce continuous NSLD profiles directly from NRs. The usefulness of our CNN-based models is demonstrated by constructing NSLDs from NRs of several films containing homopolymer polyzwitterions and diblock copolymers mixed with different types of salts. Comparisons of the NSLDs with those constructed using ad hoc multi-layer models reveal a very good agreement, suggesting the potential of CNN-based models for real-time automated data analysis of NRs.

36 MATERIALS SCIENCE↗

Improving deep learning performance for predicting large-scale geological ${{CO}_{2}}$ sequestration modeling through feature coarsening

Physics-based reservoir simulation for fluid flow in porous media is a numerical simulation method to predict the temporal-spatial patterns of state variables (e.g. pressure p) in porous media, and usually requires prohibitively high computational expense due to its non-linearity and the large number of degrees of freedom (DoF). This work describes a deep learning (DL) workflow to predict the pressure evolution as fluid flows in large-scale 3-dimensional(3D) heterogeneous porous media. In particular, we develop an efficient feature coarsening technique to extract the most representative information and perform the training and prediction of DL at the coarse scale, and further recover the resolution at the fine scale by spatial interpolation. We validate the DL approach to predict pressure field against physics-based simulation data for a field-scale 3D geologic CO 2 sequestration reservoir model. We evaluate the impact of feature coarsening on DL performance, and observe that the feature coarsening not only decreases the training time by >74% and reduces the memory consumption by >75%, but also maintains temporal error 0.63% on average. Besides, the DL workflow provides predictive efficiency with 1406 times speedup compared to physics-based numerical simulation. The key findings from this research significantly improve the training and prediction efficiency of deep learning model to deal with large-scale heterogeneous reservoir models, and thus it can also be further applied to accelerate workflows of history matching and reservoir optimization for close-loop reservoir management.

58 GEOSCIENCES↗

A workflow for segmenting soil and plant X-ray computed tomography images with deep learning in Google’s Colaboratory

X-ray micro-computed tomography (X-ray μCT) has enabled the characterization of the properties and processes that take place in plants and soils at the micron scale. Despite the widespread use of this advanced technique, major limitations in both hardware and software limit the speed and accuracy of image processing and data analysis. Recent advances in machine learning, specifically the application of convolutional neural networks to image analysis, have enabled rapid and accurate segmentation of image data. Yet, challenges remain in applying convolutional neural networks to the analysis of environmentally and agriculturally relevant images. Specifically, there is a disconnect between the computer scientists and engineers, who build these AI/ML tools, and the potential end users in agricultural research, who may be unsure of how to apply these tools in their work. Additionally, the computing resources required for training and applying deep learning models are unique, more common to computer gaming systems or graphics design work, than to traditional computational systems. To navigate these challenges, we developed a modular workflow for applying convolutional neural networks to X-ray μCT images, using low-cost resources in Google’s Colaboratory web application. Here we present the results of the workflow, illustrating how parameters can be optimized to achieve best results using example scans from walnut leaves, almond flower buds, and a soil aggregate. We expect that this framework will accelerate the adoption and use of emerging deep learning techniques within the plant and soil sciences.

59 BASIC BIOLOGICAL SCIENCES↗

Benchmarking graph neural networks for materials chemistry

Graph neural networks (GNNs) have received intense interest as a rapidly expanding class of machine learning models remarkably well-suited for materials applications. To date, a number of successful GNNs have been proposed and demonstrated for systems ranging from crystal stability to electronic property prediction and to surface chemistry and heterogeneous catalysis. However, a consistent benchmark of these models remains lacking, hindering the development and consistent evaluation of new models in the materials field. Here, we present a workflow and testing platform, MatDeepLearn, for quickly and reproducibly assessing and comparing GNNs and other machine learning models. We use this platform to optimize and evaluate a selection of top performing GNNs on several representative datasets in computational materials chemistry. From our investigations we note the importance of hyperparameter selection and find roughly similar performances for the top models once optimized. We identify several strengths in GNNs over conventional models in cases with compositionally diverse datasets and in its overall flexibility with respect to inputs, due to learned rather than defined representations. Meanwhile several weaknesses of GNNs are also observed including high data requirements, and suggestions for further improvement for applications in materials chemistry are discussed.

36 MATERIALS SCIENCE↗

Accelerating Multiscale Materials Modeling with Machine Learning

The focus of this project is to accelerate and transform the workflow of multiscale materials modeling by developing an integrated toolchain seamlessly combining DFT, SNAP, LAMMPS, (shown in Figure 1-1) and a machine-learning (ML) model that will more efficiently extract information from a smaller set of first-principles calculations. Our ML model enables us to accelerate first-principles data generation by interpolating existing high fidelity data, and extend the simulation scale by extrapolating high fidelity data (10 2 atoms) to the mesoscale (10 4 atoms). It encodes the underlying physics of atomic interactions on the microscopic scale by adapting a variety of ML techniques such as deep neural networks (DNNs), and graph neural networks (GNNs). We developed a new surrogate model for density functional theory using deep neural networks. The developed ML surrogate is demonstrated in a workflow to generate accurate band energies, total energies, and density of the 298K and 933K Aluminum systems. Furthermore, the models can be used to predict the quantities of interest for systems with more number of atoms than the training data set. We have demonstrated that the ML model can be used to compute the quantities of interest for systems with 100,000 Al atoms. When compared with 2000 Al system the new surrogate model is as accurate as DFT, but three orders of magnitude faster. We also explored optimal experimental design techniques to choose the training data and novel Graph Neural Networks to train on smaller data sets. These are promising methods that need to be explored in the future.

36 MATERIALS SCIENCE↗

Efficiently predicting pressure-composition-temperature diagrams to discover low-stability metal hydrides

Quantitatively accurate computational predictions of metal hydride thermodynamics are challenging but critical for alloy performance optimization across a multitude of technological domains, including hydrogen storage, compression, purification, and getters. Recent machine learning approaches have demonstrated great success in this area, but can potentially suffer from several shortcomings since they rely on imbalanced experimental training data and can have poor out-of-distribution (ood) test performance. Here, in this study, we circumvent such pitfalls by developing a computationally efficient, first principles-based workflow for direct prediction of metal hydride phase equilibrium, i.e., the pressure-composition-temperature (PCT) diagram. We then demonstrate its utility on predicting low stability hydrides derived from compositionally complex C14 Laves phase AB2 alloys. Specifically, we computationally predict and then experimentally validate an AB 2 alloy series (z < 0.6 for Ti 2−z Zr z CrMnFeNi) with ideal hydriding thermodynamics for a two-stage metal hydride-based compressor for pressurizing boil off from liquefied hydrogen. Importantly, this study lays the groundwork for accurate and efficient discovery/optimization of ood, low-stability hydrides for which purely data-driven approaches lack sufficient accuracy.

08 HYDROGEN↗