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At least 631 records · Page 35

A Review and Outlook on Experimental Advances and Innovations in Geological CO 2 Storage: Insights from Depleted Gas Reservoirs and Saline Aquifers

Geological storage of carbon dioxide (CO 2 ) in depleted gas reservoirs and deep saline aquifers is a key part of global decarbonization efforts. As carbon capture and storage advances toward commercial-scale deployment, the credibility and scalability of laboratory experiments are increasingly vital for guiding safe and effective field implementation. This review offers a comprehensive, cross-scale evaluation of experimental methodologies, including core flooding, high-pressure, high-temperature systems, microfluidic visualization, and emerging systems such as multilayer commingled/compartmentalized core flooding, 3D-printed micromodels, and AI-powered digital twins. These innovations are demonstrated to enhance representativeness, reproducibility, and real-time insight, thereby addressing the limitations of conventional workflows. A critical analysis of methodological gaps, such as inconsistent pressure–temperature conditions, oversimplified brine chemistry, and a lack of standardization, reveals experimental sources of scale translation errors and performance uncertainty. By comparing the unique challenges of depleted gas reservoirs (such as low water saturation and legacy well leakage) to those of saline aquifers (including pressure buildup and caprock integrity), this review identifies formation-specific priorities for experimental design. Novel contributions include a synthesis of best practices, integration strategies for model calibration, and recommendations for standardizing core handling, saturation procedures, and reporting protocols. Furthermore, this work serves as a guide for developing robust, field-relevant experimental strategies that can increase the deployment and regulatory acceptance of CO 2 storage technologies at scale.

58 GEOSCIENCES↗

LandScan HD: a high-resolution gridded ambient population methodology for the world

Unwarned population distributions accounting for routine human activities are needed to address many global human security challenges, including disasters, conflict, and infrastructure demand. LandScan High Definition (LSHD) supports this need through gridded ambient population estimates that measure average human presence between daytime and nighttime at a high spatial resolution of 3 arcseconds (approximately 90 m). Although LSHD has traditionally been produced on a country-specific basis, advances in global foundational data and computational resources now enable scaling its methodology to the world. Combining aspects of top-down and bottom-up gridded population methods, LSHD allocates subnational population totals from authoritative statistics to built-up areas based on occupancy estimates for multiple facility types (e.g., residential, commercial) and then reaggregates these estimates to a global population grid. We scale this approach by organizing the LSHD data stack into a 1° resolution tileset of vector analytic features, enabling an efficient and repeatable workflow for all countries worldwide. Examining the Philippines as an output of the global LSHD baseline dataset, we contrast unwarned and residential (WorldPop) population distributions by (1) exploring a practical application of flood risk assessment and (2) evaluating their congruence with outcomes of collective human activities (subnational CO 2 emissions). Finally, we discuss plans to address current LSHD limitations through data/modeling and uncertainty quantification improvements and provide outlook for workflow automation and extending the model to social, demographic and economic population characteristics.

Building morphology↗

Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer

With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient’s pathology based diagnosis of “poorly differentiated SqCC”. Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded lung cancer specimens, opening the way to bring powerful proteomics into the clinic. .

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Generation of random geological models using multi-randomization for machine learning

Generating high-fidelity geological models is essential for advancing machine learning (ML) methods in automated seismic interpretation. For instance, seismic images paired with corresponding fault labels are foundational for ML-based fault detection from seismic migration sections. While several open-access datasets of random geological models exist, open-source tools specifically designed to produce large volumes of such models for ML applications remain scarce. To address this gap, we present RGM (Random Geological Model), an open-source software package for efficiently generating 2D and 3D synthetic geological models tailored for ML workflows. RGM supports the creation of diverse model components, including medium property distributions (P-/S-wave velocities and density), seismic reflectivity images (i.e., synthetic migration sections), relative geological time, and discrete fault attributes such as probability, dip, strike, rake, and displacement. It also accommodates the creation of complex geological features such as salt bodies and unconformities. The model generation algorithm employs a multi-randomization strategy, yielding an effectively infinite-dimensional model space that encompasses a wide range of geological scenarios and associated seismic features. Furthermore, RGM incorporates a method to generate synthetic elastic migration images using analytical elastic reflection coefficients combined with frequency-dependent scaling. This functionality enables the creation of training datasets for ML models that leverage elastic seismic images. RGM is implemented in modern object-oriented Fortran, allowing users to flexibly control statistical parameters governing model variability. We demonstrate the capability, performance, and geological realism of the package through comprehensive 2D and 3D examples.

58 GEOSCIENCES↗

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format

Advances in mass spectrometry (MS) instrumentation, such as higher resolution, faster scan speeds, and improved sensitivity, have significantly increased the volume and complexity of data. The growing adoption of imaging and ion mobility further amplifies these challenges across MS-based omics fields, including proteomics, metabolomics, and lipidomics. While these technologies unlock new possibilities, they also present significant challenges in data management, storage, and accessibility. Existing open formats, such as the XML-based community standards mzML and imzML, struggle to meet the demands of modern MS workflows due to their large file sizes, slow data access, and limited metadata support. Vendor-specific formats, while optimized for proprietary instruments, lack interoperability, comprehensive metadata support and long-term archival reliability. This white paper lays the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multi-dimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will enable enhanced interoperability across platforms, seamless support for complex workflows including ion mobility and MS imaging, and faster data access compared to existing community formats such as mzML. Its design will ensure data is managed in compliance with regulatory standards, essential for applications such as precision medicine and chemical safety, where long-term data integrity and accessibility are critical. For vendors, mzPeak provides a streamlined, open alternative to proprietary formats, reducing the burden of regulatory compliance while aligning with the industry's push for transparency and standardization. By offering a high-performance, interoperable solution, mzPeak positions vendors to meet customer demands for sustainable data management tools which will be able to handle emerging and future data types and workflows. mzPeak aspires to become the cornerstone of MS data management, empowering researchers, vendors, and developers to innovate and collaborate more effectively.

data formats↗

Navigating Uncertainty: Challenges in Visualizing Ensemble Data and Surrogate Models for Decision Systems

Uncertainty visualization plays a critical role in transforming ensemble simulation data into actionable insights by effectively communicating various dimensions of uncertainty within a system. The emergence of artificial intelligence-driven surrogate models trained on multirun ensemble data offers a transformative opportunity to replace computationally intensive simulations with fast estimates, enabling users to explore data spaces with unprecedented depth and interactivity. However, integrating ensemble data and surrogate models into decision-making workflows and tools introduces novel challenges for uncertainty visualization. These include reconciling and clearly communicating the unique uncertainties associated with ensembles and their surrogate model estimates, and leveraging these approximations to inform actionable decisions. This work explores these challenges in the context of high-dimensional data visualization, bridging discrete datasets with their continuous representations and addressing the complexities of systems that support iterative navigation between input and output spaces. We evaluate the role of uncertainty visualization in fostering intuitive, actionable interactions and identify critical hurdles in advancing this frontier of computational simulation.

97 MATHEMATICS AND COMPUTING↗

MyCrunchGPT: A LLM Assisted Framework for Scientific Machine Learning

Scientific machine learning (SciML) has advanced recently across many different areas in computational science and engineering. Here, the objective is to integrate data and physics seamlessly without the need of employing elaborate and computationally taxing data assimilation schemes. However, preprocessing, problem formulation, code generation, postprocessing, and analysis are still time- consuming and may prevent SciML from wide applicability in industrial applications and in digital twin frameworks. Here, we integrate the various stages of SciML under the umbrella of ChatGPT, to formulate MyCrunchGPT, which plays the role of a conductor orchestrating the entire workflow of SciML based on simple prompts by the user. Specifically, we present two examples that demonstrate the potential use of MyCrunchGPT in optimizing airfoils in aerodynamics, and in obtaining flow fields in various geometries in interactive mode, with emphasis on the validation stage. To demonstrate the flow of the MyCrunchGPT, and create an infrastructure that can facilitate a broader vision, we built a web app based guided user interface, that includes options for a comprehensive summary report. The overall objective is to extend MyCrunchGPT to handle diverse problems in computational mechanics, design, optimization and controls, and general scientific computing tasks involved in SciML, hence using it as a research assistant tool but also as an educational tool. While here the examples focus on fluid mechanics, future versions will target solid mechanics and materials science, geophysics, systems biology, and bioinformatics.

97 MATHEMATICS AND COMPUTING↗

Material Science Image Analysis using Quant-CT in ImageJ

We introduce a computational analysis workflow to access properties of solid objects using nondestructive imaging techniques that rely on X-ray imaging. The goal is to process and quantify structures from material science sample cross sections. The algorithms can differentiate the porous media (high density material) from the void (background, low density media) using a Boolean classifier, so that we can extract features, such as volume, surface area, granularity spectrum, porosity, among others. Our workflow, Quant-CT, leverages several algorithms from ImageJ, such as statistical region merging and 3D object counter. It also includes schemes for bilateral filtering that use a 3D kernel, for parallel processing of sub-stacks, and for handling over-segmentation using histogram similarities. The Quant-CT supports fast user interaction, providing the ability for the user to train the algorithm via subsamples to feed its core algorithms with automated parameterization. Quant-CT plugin is currently available for testing by personnel at the Advanced Light Source and Earth Sciences Divisions and Energy Frontier Research Center (EFRC), LBNL, as part of their research on porous materials. The goal is to understand the processes in fluid-rock systems for the geologic sequestration of CO2, and to develop technology for the safe storage of CO2 in deep subsurface rock formations. We describe our implementation, and demonstrate our plugin on porous material images. This paper targets end-users, with relevant information for developers to extend its current capabilities.

97 MATHEMATICS AND COMPUTING↗

Acquire and Test IDAES Framework Components

The cooperation under the Grid Modernization Initiative and the Applied Energy Tri-Laboratory umbrellas requires mutual understanding of capabilities and a common effort to identify gaps existing in the available computational modeling and analysis tools. In this work, we report acquisition and testing of the National Energy Technology Laboratory’s Institute for the Design of Advanced Energy Systems (IDAES) framework, particularly including both electric power systems production cost model simulator Prescient as well as system optimization IDAES itself. Further, we consider the methods in which developments in Prescient and IDAES for grid-energy simulation and optimization may be included in the Framework for Optimization of ResourCes and Economics (FORCE) ecosystem that has been under collaborative development by Idaho National Laboratory, Argonne National Laboratory, and Oak Ridge National Laboratory. We propose two integration methods to introduce Prescient and IDAES into existing FORCE automated workflows. One integration involves using Prescient as a market reduced-order model and IDAES models similar to how existing Modelica models are used. The other integration involves wrapping the Prescient-IDAES dispatch optimization process with the stochastic capacity optimization workflow in FORCE.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Direct integration of atomic precision advanced manufacturing into middle-of-line silicon fabrication

Atomic precision advanced manufacturing (APAM) dopes silicon with enough carriers to change its electronic structure and can be used to create novel devices by defining metallic regions whose boundaries have single-atom abruptness. Incompatibility with the thermal and lithography process requirements for gated silicon transistor manufacturing have inhibited exploration of both how APAM can enhance CMOS performance and how transistor manufacturing steps can accelerate the discovery of new APAM device concepts. In this work, we introduce an APAM process that enables direct integration into the middle of a transistor manufacturing workflow. We show that a process that combines sputtering and annealing with a hardmask preserves a defining characteristic of APAM, a doping density far in excess of the solid solubility limit, while trading another, the atomic precision, for compatibility with manufacturing. The electrical characteristics of a chip combining a transistor with an APAM resistor show that the APAM module has only affected the transistor through the addition of a resistance and not by altering the transistor. This proof-of-concept demonstration also outlines the requirements and limitations of a unified APAM tool, which could be introduced into manufacturing environments, greatly expanding access to this technology and inspiring a new generation of devices with it.

Chemical vapor deposition↗

Automated metadata--final project report

This report summarizes the work of the Automated Metadata, Provenance Cataloging, and Navigable Interfaces: Ensuring the Usefulness of Extreme-Scale Data Project (MPO Project) funded by the United States Department of Energy (DOE), Offices of Advanced Scientific Computing Research and Fusion Energy Sciences. Initially funded for three years starting in 2012, it was extended for 6 months with additional funding. The project was a collaboration between scientists at General Atomics, Lawrence Berkley National Laboratory (LBNL), and Massachusetts Institute of Technology (MIT). The group leveraged existing computer science technology where possible, and extended or created new capabilities where required. The MPO project was able to successfully create a suite of software tools that can be used by a scientific community to automatically document their scientific workflows. These tools were integrated into workflows for fusion energy and climate research illustrating the general applicability of the project’s toolkit. Feedback was very positive on the project’s toolkit and the value of such automatic workflow documentation to the scientific endeavor.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

In-Depth Mass Spectrometry-Based Single-Cell and Nanoscale Proteomics

Leukemic stem cells are highly dynamic and heterogeneous. Analysis of leukemic stem cells at the single cell level should provide a wealth of insights that would not be possible using bulk measurements. Mass spectrometry (MS)-based proteomic workflows can quantify hundreds or thousands of proteins from a biological sample and has proven invaluable for biomedical research, but samples comprising large numbers of cells are typically required due to limited sensitivity. Recent developments in sample processing, chromatographic separations and MS instrumentation are now extending in-depth proteome profiling to single mammalian cells. We describe specific techniques that increase the sensitivity of single-cell proteomics by orders of magnitude, enabling the promise of single cell proteomics to become a reality. We anticipate such techniques could significantly advance our understanding of leukemic stem cells.

Liang, Yiran↗

Integration of Online Cross-Section Generation Capability with Depletion and Transient Solvers in Griffin

Griffin is a Multiphysics Object-Oriented Simulation Environment (MOOSE)-based reactor multiphysics analysis application jointly developed by Argonne and Idaho National Laboratories under the DOENE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. In FY25, an online crosssection generation capability based on the Self-Shielding Application Programming Interface (SSAPI) was demonstrated for TRISO-fueled reactor problems under steady-state conditions. This fiscal year, that capability was extended to support depletion and transient multiphysics calculations, enabling high-fidelity analyses that generate self-shielded cross sections on the fly from the actual evolving composition and temperature states rather than from pre-tabulated libraries. For depletion, a two-way coupling was established in which SSAPI computes compact-averaged self-shielded cross sections that the depletion solver then uses to advance the Bateman equations, with the updated compositions returned to SSAPI at each step; the depletion module was refactored to support both library-based and SSAPI-based cross sections, and additional logic was added to track daughter isotopes and to exclude minor isotopes for efficiency. For transient analysis, the SSAPI multigroup library was extended with the kinetics data required for time-dependent calculations, the Improved Quasi-Static (IQS) scheme was coupled with SSAPI, and several supporting capabilities were implemented, including a self-shielding treatment that lets control rods and drums move within a self-shielded model, which had previously been impossible and had ruled out rod- and drum-movement transients with on-the-fly cross sections altogether, a new mixing scheme for delayed-neutron precursor decay constants, a checkpoint-based restart workflow, and performance improvements such as pointwise cross-section interpolation and the bypassing of unnecessary Dancoff factor calculations. The implemented capabilities were verified against Serpent Monte Carlo solutions. For depletion, a prismatic pin-cell problem based on a Next Generation Nuclear Plant (NGNP) Very High Temperature Reactor benchmark showed excellent agreement, with eigenvalue differences within 200 pcm over the entire burnup range (up to 140 MWD/kgU) and fission-product and actinide inventories agreeing to within 0.8% and 2.5%, respectively; a heat-pipe microreactor assembly problem with a much higher fuel loading confirmed the same behavior and quantified the bias introduced when the multigroup equivalence effect is neglected. For transient analysis, a pin-cell problem with a step reactivity insertion and temperature feedback reproduced the analytically expected asymptotic power and showed close agreement between the direct and IQS solutions, and a two-dimensional microreactor core problem with control-drum rotation exercised the new moving-drum self-shielding treatment and demonstrated successful coupling of the online crosssection generation with both the direct and IQS transient methods. The capability was further exercised on a full-core pebble-bed problem, in which Griffin was coupled with the System Analysis Module (SAM) to simulate load-following operation of the gPBR with the Doppler feedback resolved at the TRISO fuel kernel temperature. These developments in Griffin provide a convenient, high-fidelity approach to cross-section generation for advanced thermal reactors with geometrically complex and highly heterogeneous configurations, including TRISO-fueled prismatic and pebble-bed systems, and support steady-state, depletion, and transient multiphysics calculations. They also enable self-shielded cross sections to be evaluated directly at the actual coupled state of the system, thereby establishing a foundation for high-fidelity, fully coupled multiphysics analysis of advanced reactors

Park, H.↗

Database and deep-learning scalability of anharmonic phonon properties by automated brute-force first-principles calculations

Understanding the anharmonic phonon properties of crystal compounds—such as phonon lifetimes and thermal conductivities—is essential for investigating and optimizing their thermal transport behaviors. These properties also impact optical, electronic, and magnetic characteristics through interactions between phonons and other quasiparticles and fields. In this study, we develop an automated first-principles workflow to calculate anharmonic phonon properties and build a comprehensive database encompassing more than 6500 inorganic compounds. Utilizing this dataset, we train a graph neural network model to predict thermal conductivity values and spectra from structural parameters, demonstrating a scaling law in which prediction accuracy improves with increasing training data size. High-throughput screening with the model enables the identification of materials exhibiting extreme thermal conductivities—both high and low. The resulting database offers valuable insights into the anharmonic behavior of phonons, thereby accelerating the design and development of advanced functional materials.

Ohnishi, Masato [University of Tokyo (Japan); Inst↗

S AP F LOWER : an automated tool for sap flow data preprocessing, gap-filling, and analysis using deep learning

Sap flow, a critical process in plant water use and ecosystem water cycles, is often measured using thermal dissipation probes (TDP) due to their ease of installation and continuous data collection. However, sap flow data frequently include noise, outliers, and gaps, creating challenges for analysis and requiring substantial manual processing. We developed S AP F LOWER , a tool that automates data preprocessing, model training, gap-filling, sapwood area scaling and modeling, and water use analysis. It integrates autocleaning, machine learning and deep learning models (e.g. random forest, Gaussian process regression, long short-term memory (LSTM), bidirectional LSTM (BiLSTM)), and efficient workflows to process sap flow data. S AP F LOWER can remove over 90% of noisy data while preserving legitimate variations and achieve high accuracy in gap-filling based on user-determined parameters. Random forest, LSTM, and BiLSTM models reduced root mean square error to 10% or less for long-term gaps. Model training and prediction can be performed efficiently within seconds. S AP F LOWER significantly enhances the efficiency and accessibility of TDP data analysis by automating complex tasks, enabling researchers without programming expertise to employ advanced techniques. Future improvements will focus on species-specific corrections for TDP and support for additional measurement methods. S AP F LOWER is openly available on GitHub (https://github.com/JiaxinWang123/SapFlower) and Zenodo (doi: 10.5281/zenodo.13665919).

ecosystem water balance↗

An Expert System to Assist Researchers with Nuclear Materials Experiment Design

The Nuclear Science User Facilities (NSUF) was created in 2007 to open National Laboratory capabilities to university, laboratory, and industry researchers. Originally founded at the Idaho National Laboratory (INL), NSUF leveraged excess capacity in the Advanced Test Reactor (ATR) and the Hot Fuel Examination Facility (HFEF) hot cells. In the eleven years since its inception, the NSUF has expanded to include most of the capabilities at the Idaho National Laboratory as well as twenty external ‘partner’ facilities. The inclusion of the partner facilities makes the NSUF the first distributed user facility, a ‘laboratory without walls.’ This paper will present recent developments in CoMET, including how the databases interconnect to create a powerful tool for NSUF users and how the Wizard is expected to change the workflow for NSUF users, staff, and partner facilities. The paper will conclude with some remarks of how CoMET demonstrates the feasibility of a broader integration of nuclear information and tools, paving the way for further collaboration and innovation following the NuKIT paradigm.

07 ISOTOPE AND RADIATION SOURCES↗

Probing flow-induced nanostructure of complex fluids in arbitrary 2D flows using a fluidic four-roll mill (FFoRM)

Abstract Engineering flow processes to direct the microscopic structure of soft materials represents a growing area of materials research. In situ small-angle neutron scattering under flow (flow-SANS) is an attractive probe of fluid microstructure under simulated processing conditions, but current capabilities require many different sample environments to fully interrogate the deformations a fluid experiences in a realistic processing flow. Inspired by recent advances in microfluidics, we present a fluidic four-roll mill (FFoRM) capable of producing tunable 2D flow fields for in situ SANS measurements, that is intended to allow characterization of complex fluid nanostructure under arbitrary complex flows within a single sample environment. Computational fluid dynamics simulations are used to design a FFoRM that produces spatially homogeneous and sufficiently strong deformation fields. Particle tracking velocimetry experiments are then used to characterize the flows produced in the FFoRM for several classes of non-Newtonian fluids. Finally, a putative FFoRM-SANS workflow is demonstrated and validated through the characterization of flow-induced orientation in a semi-dilute cellulose nanocrystal dispersion under a range of 2D deformations. These novel experiments confirm that, for steady state straining flows at moderate strain rates, the nanocrystals orient along the principal strain-rate axis, in agreement with theories for rigid, rod-like Brownian particles in a homogeneous flow.

36 MATERIALS SCIENCE↗

A combinatorially complete epistatic fitness landscape in an enzyme active site

Protein engineering often targets binding pockets or active sites which are enriched in epistasis—nonadditive interactions between amino acid substitutions—and where the combined effects of multiple single substitutions are difficult to predict. Few existing sequence-fitness datasets capture epistasis at large scale, especially for enzyme catalysis, limiting the development and assessment of model-guided enzyme engineering approaches. We present here a combinatorially complete, 160,000-variant fitness landscape across four residues in the active site of an enzyme. Assaying the native reaction of a thermostable β-subunit of tryptophan synthase (TrpB) in a nonnative environment yielded a landscape characterized by significant epistasis and many local optima. These effects prevent simulated directed evolution approaches from efficiently reaching the global optimum. There is nonetheless wide variability in the effectiveness of different directed evolution approaches, which together provide experimental benchmarks for computational and machine learning workflows. The most-fit TrpB variants contain a substitution that is nearly absent in natural TrpB sequences—a result that conservation-based predictions would not capture. Thus, although fitness prediction using evolutionary data can enrich in more-active variants, these approaches struggle to identify and differentiate among the most-active variants, even for this near-native function. Overall, this work presents a large-scale testing ground for model-guided enzyme engineering and suggests that efficient navigation of epistatic fitness landscapes can be improved by advances in both machine learning and physical modeling.

biocatalysis↗