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At least 559 records · Page 31

FAIR Ecosystems for Science at Scale

High Performance Computing (HPC) centers provide resources to users who require greater scale to “get science done”. They deploy infrastructure with singular hardware architectures, cutting-edge software environments, and stricter security measures as compared with users’ own resources. As a result, users often create and configure digital artifacts in ways that are specialized for the unique infrastructure at a given HPC center. Each user of that center will face similar challenges as they develop specialized solutions to take full advantages of the center’s resources, potentially resulting in significant duplication of effort. Much duplicated effort could be avoided, however, if users of these centers found it easier to discover others’ solutions and artifacts as well as share their own. The FAIR principles address this problem by presenting guidelines focused around metadata practices to be implemented by vaguely defined “communities”; in practice, these tend to gather by domain (e.g. bioinformatics, geosciences, agriculture). Domain-based communities can unfortunately end up functioning as silos that tend both to inhibit sharing of solutions and best practices as well as to encourage fragile and unsustainable improvised solutions in the absence of best-practice guidance. We propose that these communities pursuing “science at scale” be nurtured both individually and collectively by HPC centers so that users can take advantage of shared challenges across disciplines and potentially across HPC centers. We describe an architecture based on the EOSC-Life FAIR Workflows Collaboratory, specialized for use with and inside HPC centers such as the Oak Ridge Leadership Computing Facility (OLCF), and we speculate on user incentives to encourage adoption. We note that a focus on FAIR workflow components rather than FAIR workflows is more likely to benefit the users of HPC centers.

Wilkinson, Sean [ORNL] (ORCID:0000000214437479)↗

PyARC Status Report: New Integrations and Upgrades to the Fast Reactor Analysis Workflow Management Tool

PyARC was initially developed as an open source tool to support fast reactor analyses using the Argonne Reactor Computation (ARC) code suite as a part of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench initiative in FY17. The goal of this initiative is to provide a common user interface for model generation, real-time validation, execution, output processing, and visualization for all integrated codes. This is accomplished through the reliance on tools available in the Workbench framework and runtime environment. While initially developed to support the ARC codes, PyARC was extended in FY22 to wrap other NEAMS and non-ARC codes, including Griffin and OpenMC, in the supported other neutronics workflows, and support users in the adoption of NEAMS-supported high fidelity analysis codes. Most recently, NUBOW-3D, a recently adopted ARC code, was integrated to support reactor bowing calculations as well. Integration of these codes into the NEAMS Workbench directly benefits the advanced reactor modeling community by: • Providing a set of controlled, maintained, documented and validated scripts to generate inputs, which promotes best practices, reduces the learning curve, and facilitates project collaboration. • Improving the user experience: the Workbench interface provides assistance for building an input through auto-completion, real-time validation, document navigation, and geometry and results visualization. • Automating complex calculations and workflows for reactor analysis. • Helping users transition to using high-fidelity NEAMS codes along-side the ARC codes. In FY22, a progress report was published that described the state of each of the tools integrated into PyARC. Since then, there have been many enhancements and upgrades to the existing integrations as well as entirely new code integrations as well. This report details all new integrations and major developments in PyARC since the version 2.0.0 release highlighted in the FY22 report.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

The Artificial Scientist: in-Transit Machine Learning of Plasma Simulations

Large-scale simulations or scientific experiments produce petabytes of data per run. This poses massive challenges for I/O and storage when scientific analysis workflows are run manually offline. Unsupervised deep learning-based techniques to extract patterns and non-linear relations from these large amounts of data provide a way to build scientific understanding from raw data, reducing the need for manual pre-selection of analysis steps, but require exascale compute and memory to process the full dataset available. In this paper, we demonstrate a heterogeneous streaming workflow in which plasma simulation data is streamed directly to a Machine Learning (ML) application training a model on the simulation data in-transit, completely circumventing the capacity-constrained filesystem bottleneck. This workflow employs openPMD to provide a high level interface to describe scientific data and also uses ADIOS2, to transfer volumes of data that exceed the capabilities of the filesystem. We employ experience replay to avoid catastrophic forgetting in learning from this non-steady state process in a continual manner and adapt it to improve model convergence while learning in-transit. As a proof-of-concept, we approach the ill-posed inverse problem of predicting particle dynamics from radiation in a particle-incell (PIConGPU) simulation of the Kelvin-Helmholtz instability (KHI). We detail hardware-software co-design challenges as we scale PIConGPU to full Frontier, the Top-1 system as of June 2024 Top500 list.

Kelling, Jeffrey [Helmholtz-Zentrum Dresden Rossen↗

The InSAR Scientific Computing Environment 3.0: A Flexible Framework for NISAR Operational and User-Led Science Processing

The InSAR Scientific Computing Environment (ISCE) was first developed under the NASA Advanced Information Systems Technology as a flexible, extensible object-oriented framework for Interferometric Synthetic Aperture Radar (InSAR) processing. The ISCE framework uses Python 3 at the workflow level, controlling modules of compiled code for functional processing, and managing inputs, outputs, and other flow control services. The currently released version, called ISCE 2.1, is distributed to the research community through the Western North America InSAR Consortium under a research license. The ISCE team is working on the next generation of the code in order to prepare for the NASAISRO SAR (NISAR) mission operational processing. Innovations in this code include augmentation or conversion of the custom Python framework elements in ISCE with the Pyre framework, new workflows for interferometric and polarimetric stack processing, a more intuitive and graphically based user interface, and flow control for hybrid computing environments including CPU/GPU clusters, logging and error tracking facilities, and new more efficient computational modules that exploit graphical processor units (GPUs) when available. The ISCE 3.0 framework is designed to work in an operational environment as well as on a single user’s laptop or compute cluster, with services to discover capabilities and scale computations accordingly.

Buckley, Sean M.↗

Developing a complete AI-accelerated workflow for superconductor discovery

The quest to identify new superconducting materials with enhanced properties is hindered by the prohibitive cost of computing electron-phonon spectral functions, severely limiting the materials space that can be explored. Here, we introduce a Bootstrapped Ensemble of Equivariant Graph Neural Networks (BEE-NET), a machine-learning model trained to predict the Eliashberg spectral function and superconducting critical temperature with a mean-absolute-error of 0.87 K relative to DFT-based Allen-Dynes calculations. Intriguingly, BEE-NET achieves a true-negative-rate of 99.4%, enabling highly efficient screening for the rare property of superconductivity. Integrated into a multi-stage, AI-accelerated discovery pipeline that incorporates elemental-substitution strategies and machine-learned interatomic potentials, our workflow reduced over 1.3 million candidate structures to 741 dynamically and thermodynamically stable compounds with DFT-confirmed T c > 5 K. We report the successful synthesis and experimental confirmation of superconductivity in two of these previously unreported compounds. This study establishes a data-driven framework that integrates machine learning, quantum calculations, and experiments to systematically accelerate superconductor discovery.

Gibson, Jason B. [Quantum Formatics, Cambridge, MA↗

ppdx : Automated modeling of protein–protein interaction descriptors for use with machine learning

This paper describes ppdx, a python workflow tool that combines protein sequence alignment, homology modeling, and structural refinement, to compute a broad array of descriptors for characterizing protein–protein interactions. The descriptors can be used to predict various properties of interest, such as protein–protein binding affinities, or inhibitory concentrations (IC 50 ), using approaches that range from simple regression to more complex machine learning models. The software is highly modular. It supports different protocols for generating structures, and 95 descriptors can be currently computed. More protocols and descriptors can be easily added. The implementation is highly parallel and can fully exploit the available cores in a single workstation, or multiple nodes on a supercomputer, allowing many systems to be analyzed simultaneously. As an illustrative application, ppdx is used to parametrize a model that predicts the IC 50 of a set of antigens and a class of antibodies directed to the influenza hemagglutinin stalk.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-Energy X-ray Tomographic Analysis of Precursor Metal Powders (Ti-6Al-4V) Used for Additive Manufacturing

We utilized high-energy x-ray tomography to characterize Ti-6Al-4V metal powders (both as-received and recycled) used in powder-bed additive manufacturing process. The image processing workflow was developed to process and analyze large amount of data objectively by computer program. The distribution of size and shape of the metal particles as well as defect (mainly porosity) inside the particles was analyzed with the statistical representation and resolution in micrometer. The result revealed that circular-shaped porosity with various sizes could be embedded in the powder particles. These porosities could potentially be transferred to the 3D printed part and critically affect the mechanical performance of the component. The present study shows the effectiveness of characterizing metal powders using x-ray imaging techniques where sufficient number of particles can be sampled within tens of minutes with a minimum sample preparation and high accuracy. Clear structural differences in the as-received and recycled powders were delineated that helps in determining the feasibility of using the recycled powders.

36 MATERIALS SCIENCE↗

Reimagining metal-organic framework discovery: Integrating experiment, computation, and artificial intelligence

The traditional development of novel metal–organic frameworks (MOFs) is often hindered by challenges such as synthetic accessibility and time- and resource-intensive experimentation. High-throughput, automated experimental and computational techniques have enabled rapid chemical space exploration and theoretical MOF design. When combined with artificial intelligence (AI), these methods can be used to lead autonomous laboratories to new frontiers for MOF discovery, where these materials can be designed for a specific application, efficiently synthesized, characterized, and evaluated. Here, this perspective highlights the role of AI in advancing automated MOF synthesis and characterization, computational MOF design and screening, and the integration of these approaches within autonomous workflows to ultimately enable the MOF laboratories of the future.

Gaidimas, Madeleine A. [Northwestern University, E↗

ExaCA v2.0: A versatile, scalable, and performance portable cellular automata application for additive manufacturing solidification

The previously established ExaCA software for performance portable alloy grain structure simulation has been updated to better represent the solidification behavior during complex alloy processing conditions, such as those encountered during metal additive manufacturing (AM), and for improved performance and scalability. Here, an extension to the time–temperature history input data format and the core ExaCA algorithm to include an arbitrary number of melting and solidification events yielded improved prediction of texture for various melt pool geometries, expanding the range of AM-relevant conditions that can be accurately simulated. Improved heat transport process simulation coupling, including the creation of large raster datasets from single track time–temperature history data and in-memory coupling with the new, performance portable finite difference code Finch, were also demonstrated in example studies on the effect of multilayer AM microstructure predictions on hatch spacing and cell size, respectively. Additional new features are detailed and demonstrated, including the ability to perform simulations using various interfacial response function forms, execute simulations on state-of-the-art hardware, improved usability through post-processing versatility, and improved strong and weak scaling performance. The performance, physics, and versatility improvements demonstrated here will further enable large-scale studies on AM process–microstructure relationships that were not previously possible. Furthermore, the usability improvements and ability to run coupled AM process–microstructure simulations using the Finch-ExaCA workflow will facilitate broader use of this open-source software by the computational materials community.

36 MATERIALS SCIENCE↗

Modeling the 4D discharge of lithium-ion batteries with a multiscale time-dependent deep learning framework

The lithium-ion battery (LIB) field is moving towards the direction of investigating spatially resolved physical phenomena in the 3D porous microstructure of electrodes. These pore-scale simulations give new insights into the local dynamics of lithiation/de-lithiation and charge transport, Nevertheless, the computational time of these simulations limits the integration of these models in optimization workflows of cycling conditions or electrode manufacturing processes. Machine learning models present a way of assessing in real-time the performance of materials. While several successful techniques for replicating simulations with machine learning have been proposed, this case study presents a more demanding problem, due to the necessity of understanding the behavior of heterogeneous 3D local data, as it evolves in time: this poses both a scientific and a technical challenge. To this end, we propose an autoregressive multiscale convolutional neural network model to predict relevant quantities at the pore-scale in the solid phase: the lithium concentration (in the active material) and potential (in the active material and carbon binder). Here, these are ultimately used to reconstruct the battery discharge curve. 3D images of the electrode microstructures are the input to the network, trained with a dataset of finite element method simulations to predict the discharge behavior of the cathode side in lithium ion batteries. We propose this machine learning model as a proof-of-concept of the applicability of multiscale networks for time-dependent physics problems. The trained model exhibits very high accuracy (with errors lower than 2 %) in forecasting the discharge behavior of new unseen cathodes.

25 ENERGY STORAGE↗

PyHydroGeophysX: An extensible open-source platform for integrating hydrological models with geophysical measurements

Hydrological models and geophysical measurements are widely used tools for understanding subsurface hydrological processes relevant to water resource management, yet they typically remain disconnected due to technical barriers. We present PyHydroGeophysX, an open-source Python platform bridging this gap by providing standardized interfaces between hydrological modeling software (MODFLOW, ParFlow) and geophysical simulation tools (PyGIMLi, SimPEG). The platform implements bidirectional workflows: translating hydrological outputs into simulated geophysical responses through petrophysical models, and extracting hydrological information from geophysical inversions. Key features include bidirectional workflow modules, configurable petrophysical models, time-lapse inversion with temporal regularization, parallel computing, and mesh utilities for property transfer between geophysical and hydrological grids. The modular architecture of PyHydroGeophysX enables researchers to incorporate additional models and methods, fostering broader adoption of integrated hydrogeophysical approaches. The software is freely available on GitHub and is intended for researchers and practitioners working at the intersection of hydrology and geophysics.

Hydrogeophysics↗

Chemistry Informed Machine Learning-Based Heat Capacity Prediction of Solid Mixed Oxides

Knowing heat capacity is crucial for modeling temperature changes with the absorption and release of heat and for calculating the thermal energy storage capacity of oxide mixtures with energy applications. The current prediction methods (ab initio simulations, computational thermodynamics, and the Neumann–Kopp rule) are computationally expensive, not fully generalizable, or inaccurate. Machine learning has the potential of being fast, accurate, and generalizable, but it has been scarcely used to predict mixture properties, particularly for mixed oxides. Here, we demonstrate a method for the generalizable prediction of heat capacity of solid oxide pseudobinary mixtures using heat capacity data obtained from computational thermodynamics and descriptors from ab initio databases. Further, models trained through this workflow achieved an error (mean absolute error of 0.43 J mol –1 K –1 ) lower than the uncertainty in differential scanning calorimetry measurements, and the workflow can be extended to predict other properties derived from the Gibbs free energy and for higher-order oxide mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Application of quantitative risk assessment to address stakeholder questions in geologic carbon storage

Ambitious international greenhouse gas emissions reduction targets demand a rapid transformation to a low-carbon economy. This transformation includes the accelerated adoption of carbon dioxide (CO2) capture and storage (CCS) technology. However, as with any large-scale engineering enterprise, the widespread commercial-scale deployment of geologic carbon storage (GCS) raises important questions about technology and cost-effectiveness, safety, environmental risk, and long-term liability. Effectively assessing and managing risks and liability associated with GCS projects is a key technical need throughout the project life cycle-from site selection and permitting to monitoring design, operational risk management, and post-operational site closure. This presentation highlights recent advancements in tools for quantitative risk assessment, being developed by the National Risk Assessment Partnership (NRAP). NRAP is a multi-year, multinational laboratory research collaboration sponsored by the U.S. Department of Energy's Office of Fossil Energy and Carbon Management. Our focus will be on these tools' applications in addressing critical stakeholder questions related to supporting permitting to ensure secure and environmentally protective storage; designing effective and efficient monitoring plans; evaluating the effectiveness of remedial actions and risk management alternatives; and informing liability assessment and investment decisions. This paper will detail the key functionality of NRAP’s Open-Source Integrated Assessment Model (NRAP-Open-IAM), a computational framework for assessing leakage risk and containment assurance. This model features streamlined workflows for calculating leakage risk profiles, delineating risk-based area of review, and assessing contingency plans and post-injection site care requirements. ORION is an open-source, observation-based ensemble forecasting toolkit to help operators assess the seismic hazard at a carbon storage site. The State of Stress Analysis Tool (SOSAT), designed to assess subsurface stress conditions and evaluate geomechanical risk resulting from CO2 injection in an area of interest will also be presented. We will also introduce a prototype model to evaluate storage project costs and liability associated with risk management. The Technoeconomic and Liability Evaluation for Storage (TALES) model uses results from forecasts of leakage and induced seismicity risk to estimate the lifecycle cost of managing risk. Finally, a preliminary example of how the NRAP Risk-based Adaptive Monitoring Plan (RAMP) tool can be used to design efficient and effective site monitoring plans and estimate the detectability of fluid leakage will be provided. The relevance of these tools for addressing key stakeholder questions amidst uncertainty will be emphasized.

decision support↗

A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum

A better understanding of the genetic and metabolic mechanisms that confer stress resistance and tolerance in plants is key to engineering new crops through advanced breeding technologies. This requires a systems biology approach that builds on a genome-wide understanding of the regulation of gene expression, plant metabolism, physiology and growth. In this study, we examine the response to drought stress in Sorghum, as we leverage the tools for transcriptomics and plant metabolic modeling we have implemented at the U.S. Department of Energy Systems Biology Knowledgebase (KBase). KBase enables researchers worldwide to collaborate and advance research by allowing them to upload private or public data into the KBase Narrative Interface, empowering them to analyze this data using a rich, extensible array of computational and data-analytics tools, and allows them to securely share scientific workflows and conclusions. We demonstrate how to use the current RNA-seq tools in KBase, applicable to both plants and microbes, to assemble and quantify long transcripts and identify differentially expressed genes effectively. More specifically, we demonstrate the utility of the platform by identifying key genes that are differentially expressed during drought-stress in Sorghum bicolor, which is an important sustainable production crop plant. We then show how to use KBase tools to predict the membership of genes in metabolic pathways and examine expression data in the context of metabolic subsystems. We demonstrate the power of the platform by making the data analysis and interpretation available to the biologists in the reproducible, re-usable, point-and-click format of a KBase Narrative thus promoting FAIR (Findable, Accessible, Interoperable and Reusable) guiding principles for scientific data management and stewardship.

59 BASIC BIOLOGICAL SCIENCES↗

HEPTAPOD: Orchestrating High Energy Physics Workflows Towards Autonomous Agency

Many workflows in high-energy-physics (HEP) stand to benefit from recent advances in transformer-based large language models (LLMs). While early applications of LLMs focused on text generation and code completion, modern LLMs now support orchestrated agency: the coordinated execution of complex, multi-step tasks through tool use, structured context, and iterative reasoning. We introduce the HEP Toolkit for Agentic Planning, Orchestration, and Deployment (HEPTAPOD), an orchestration framework designed to bring this emerging paradigm to HEP pipelines. The framework enables LLMs to interface with domain-specific tools, construct and manage simulation workflows, and assist in common utility and data analysis tasks through schema-validated operations and run-card-driven configuration. To demonstrate these capabilities, we consider a representative Beyond the Standard Model (BSM) Monte Carlo validation pipeline that spans model generation, event simulation, and downstream analysis within a unified, reproducible workflow. HEPTAPOD provides a structured and auditable layer between human researchers, LLMs, and computational infrastructure, establishing a foundation for transparent, human-in-the-loop systems.

Menzo, Tony [Alabama U.; Fermilab] (ORCID:00000002↗

A robust deep learning workflow to predict multiphase flow behavior during geological C O 2 sequestration injection and Post-Injection periods

Simulation of multiphase flow in porous media is essential to manage the geologic CO 2 sequestration (GCS) process, and physics-based simulation approaches usually take prohibitively high computational cost due to the nonlinearity of the coupled physics. This paper contributes to the development and evaluation of a deep learning workflow that accurately and efficiently predicts the temporal-spatial evolution of pressure and CO 2 plumes during injection and post-injection periods of GCS operations. Based on a Fourier Neural Operator, the deep learning workflow takes input variables or features including rock properties, well operational controls and time steps, and predicts the state variables of pressure and CO 2 saturation. To further improve the predictive fidelity, separate deep learning models are trained for CO 2 injection and post-injection periods due to the difference in primary driving force of fluid flow and transport during these two phases. We also explore different combinations of features to predict the state variables. We use a realistic example of CO 2 injection and storage in a 3D heterogeneous saline aquifer, and apply the deep learning workflow that is trained from physics-based simulation data and emulate the physics process. Through this numerical experiment, we demonstrate that using two separate deep learning models to distinguish post-injection from injection period generates the most accurate prediction of pressure, and a single deep learning model of the whole GCS process including the cumulative injection volume of CO 2 as a deep learning feature, leads to the most accurate prediction of CO 2 saturation. For the post-injection period, it is key to use cumulative CO 2 injection volume to inform the deep learning models about the total carbon storage when predicting either pressure or saturation. The deep learning workflow not only provides high predictive fidelity across temporal and spatial scales, but also offers a speedup of 250 times compared to full physics reservoir simulation, and thus will be a significant predictive tool for engineers to manage the long-term process of GCS.

58 GEOSCIENCES↗

Exploration of multifidelity UQ sampling strategies for computer network applications.

Network modeling is a powerful tool to enable rapid analysis of complex systems that can be challenging to study directly using physical testing. Here, two approaches are considered: emulation and simulation. The former runs real software on virtualized hardware, while the latter mimics the behavior of network components and their interactions in software. Although emulation provides an accurate representation of physical networks, this approach alone cannot guarantee the characterization of the system under realistic operative conditions. Operative conditions for physical networks are often characterized by intrinsic variability (payload size, packet latency, etc.) or a lack of precise knowledge regarding the network configuration (bandwidth, delays, etc.); therefore uncertainty quantification (UQ) strategies should be also employed. UQ strategies require multiple evaluations of the system with a number of evaluation instances that roughly increases with the problem dimensionality, i.e., the number of uncertain parameters. It follows that a typical UQ workflow for network modeling based on emulation can easily become unattainable due to its prohibitive computational cost. In this paper, a multifidelity sampling approach is discussed and applied to network modeling problems. The main idea is to optimally fuse information coming from simulations, which are a low-fidelity version of the emulation problem of interest, in order to decrease the estimator variance. By reducing the estimator variance in a sampling approach it is usually possible to obtain more reliable statistics and therefore a more reliable system characterization. Several network problems of increasing difficulty are presented. For each of them, the performance of the multifidelity estimator is compared with respect to the single fidelity counterpart, namely, Monte Carlo sampling. For all the test problems studied in this work, the multifidelity estimator demonstrated an increased efficiency with respect to MC.

97 MATHEMATICS AND COMPUTING↗