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At least 1,261 records · Page 70

Best practices in software development for robust and reproducible geoscientific models based on insights from the Global Carbon Budget's dynamic vegetation models

Computational models play an increasingly vital role in scientific research by enabling the numerical simulation of complex processes. Such models are also fundamental in geosciences. For instance, they offer critical insights into the impacts of global change on the Earth system today and in the future. Beyond their value as research tools, models are also software products and should therefore adhere to certain established software engineering standards. However, scientists are rarely trained as software developers, which can lead to potential deficiencies in software quality like unreadable, inefficient, or erroneous code. The complexity of models, coupled with their integration into broader workflows, also often makes it challenging to reproduce results, evaluate processes, and build upon them. In this paper, we review the state and current practices of the development processes of the state-of-the-art land surface models used by the Global Carbon Budget. We combine the experience of modelers from the respective research groups with the expertise of software engineers from tech companies to outline key principles and tools for improving software quality in research. We explore four main areas: (1) model testing and validation, (2) scientific, technical, and user documentation, (3) version control, continuous integration, and code review, and (4) the portability and reproducibility of workflows. Our review reveals that while modeling communities are incorporating many best practices, significant room for improvement remains in areas such as automated testing, automated documentation, and reproducibility. Therefore, we here identify and promote essential software engineering practices, including numerous examples of practices from within the community that can serve as guidelines for other models and could help streamline processes across the entire community. We conclude with an open-source example implementation of these principles, demonstrating portable and reproducible data flows, a continuous integration setup, and web-based visualizations. This example may serve as a practical resource for model developers, users, and all scientists engaged in scientific programming.

Gregor, Konstantin [Technical Univ. of Munich (Ger↗

A rule-free workflow for the automated generation of databases from scientific literature

Abstract In recent times, transformer networks have achieved state-of-the-art performance in a wide range of natural language processing tasks. Here we present a workflow based on the fine-tuning of BERT models for different downstream tasks, which results in the automated extraction of structured information from unstructured natural language in scientific literature. Contrary to existing methods for the automated extraction of structured compound-property relations from similar sources, our workflow does not rely on the definition of intricate grammar rules. Hence, it can be adapted to a new task without requiring extensive implementation efforts and knowledge. We test our data-extraction workflow by automatically generating a database for Curie temperatures and one for band gaps. These are then compared with manually curated datasets and with those obtained with a state-of-the-art rule-based method. Furthermore, in order to showcase the practical utility of the automatically extracted data in a material-design workflow, we employ them to construct machine-learning models to predict Curie temperatures and band gaps. In general, we find that, although more noisy, automatically extracted datasets can grow fast in volume and that such volume partially compensates for the inaccuracy in downstream tasks.

36 MATERIALS SCIENCE↗

The future of self-driving laboratories: from human in the loop interactive AI to gamification

Recent developments in artificial intelligence (AI) and machine learning (ML), implemented through self-driving laboratories (SDLs), are rapidly creating unprecedented opportunities for the accelerated discovery and optimization of materials. This paper provides a joint analysis of SDLs from both academic and industry perspectives, highlighting the importance of integrating human intelligence in these systems. It discusses the necessity of careful planning in SDL design across physical, data, and workflow dimensions, including instrumental setup, experimental workflow, data management, and human–SDL interaction. The significance of integrating human input within SDLs, especially as the focus shifts from individual tools and tasks to the creation and management of complex workflows, is emphasized. The paper stresses on the crucial role of reward function design in developing forward-looking workflows and examines the interplay between hardware evolution, ML application across chemical processes, and the influence of reward systems in research. Ultimately, the article advocates for a future where SDLs blend human intuition in hypothesis formulation with AI's precision, speed, and data-handling capabilities.

97 MATHEMATICS AND COMPUTING↗

A cloud platform for atomic pair distribution function analysis: PDFitc

A cloud web platform for analysis and interpretation of atomic pair distribution function (PDF) data ( PDFitc ) is described. The platform is able to host applications for PDF analysis to help researchers study the local and nanoscale structure of nanostructured materials. The applications are designed to be powerful and easy to use and can, and will, be extended over time through community adoption and development. The currently available PDF analysis applications, structureMining, spacegroupMining and similarityMapping , are described. In the first and second the user uploads a single PDF and the application returns a list of best-fit candidate structures, and the most likely space group of the underlying structure, respectively. In the third, the user can upload a set of measured or calculated PDFs and the application returns a matrix of Pearson correlations, allowing assessment of the similarity between different data sets. structureMining is presented here as an example to show the easy-to-use workflow on PDFitc . In the future, as well as using the PDFitc applications for data analysis, it is hoped that the community will contribute their own codes and software to the platform.

97 MATHEMATICS AND COMPUTING↗

c-HAND: near real-time coastal flood mapping

The Texas Gulf Coast region contains significant centers of population, infrastructure, and economy and is threatened by intensifying tropical storms. The flooding from these tropical storms often has multiple compounding drivers. This characteristic presents a complex numerical problem where a simulation must consider multiple hydrologic forcings. While several procedures exist for addressing this problem numerically, they tend to be resource-intensive and cannot be conducted in near real-time. We extend GeoFlood, a reduced physics approach for fluvial flood forecasting, to rapidly predict coastal and compound fluvial-coastal inundation. This method is validated against a numerical ocean circulation model (ADCIRC) simulation of Hurricane Ike, a major coastal flooding event that happened on the Texas Gulf Coast in 2008. We show that the inundation map generated by coastal HAND (c-HAND) has reasonable agreement with the ADCIRC simulation while taking about 1.7% of the time currently needed to run ADCIRC on a supercomputer. While our model correctly predicts 99% of ADCIRC-inundated DEM cells, it also overpredicts inundated area by a factor of approximately 27%. We combine c-HAND with the GeoFlood framework for fluvial flood forecasting to create a compound fluvial-coastal inundation mapping workflow that can be run in near real-time. c-HAND's fast wall-clock time and low CPU requirements can support decision making by first response personnel. The method provides timely and convenient access to crucial information, such as the locations of flooded roads and inundated coastal areas.

42 ENGINEERING↗

Supporting Nuclear Energy Research with MLOps

Artificial intelligence (AI) and machine learning (ML) have been shown to be increasingly helpful tools in a growing number of use-cases relevant to scientific research, despite significant software-related obstacles. There exist large technical costs to setting up, using, and maintaining AI/ML models in production. This often prevents researchers from utilizing these models in their work. The growing field of machine learning operations (MLOps) aims to automate much of the AI/ML life cycle while increasing access to these models. This paper presents our initial work in creating a nuclear energy MLOps platform for use by researchers at Idaho National Laboratory (INL) and aims to reduce the barriers of using AI/ML in scientific research. We hope to promote the integration of the latest AI/ML technologies into researchers' workflows and create more opportunity for scientific innovation. In this paper we discuss how our MLOps efforts aim to increase usage and the impact of AI/ML models created by engineers. We also present several use-cases that are currently integrated. Finally, we evaluate the maturity of our project as well as our plans for future functionality.

97 MATHEMATICS AND COMPUTING↗

Analytical ab initio hessian from a deep learning potential for transition state optimization

Identifying transition states—saddle points on the potential energy surface connecting reactant and product minima—is central to predicting kinetic barriers and understanding chemical reaction mechanisms. In this work, we train a fully differentiable equivariant neural network potential, NewtonNet, on thousands of organic reactions and derive the analytical Hessians. By reducing the computational cost by several orders of magnitude relative to the density functional theory (DFT) ab initio source, we can afford to use the learned Hessians at every step for the saddle point optimizations. We show that the full machine learned (ML) Hessian robustly finds the transition states of 240 unseen organic reactions, even when the quality of the initial guess structures are degraded, while reducing the number of optimization steps to convergence by 2–3× compared to the quasi-Newton DFT and ML methods. All data generation, NewtonNet model, and ML transition state finding methods are available in an automated workflow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fast ion transport by sawtooth instability in the presence of ICRF-NBI synergy in JET plasmas

JET experiments have shown that the three-ion scenarios using waves in the ion cyclotron range of frequencies (ICRF) is an efficient way to build fast ion population through beam ion acceleration by radio frequency (RF) waves. Here, such a heating scheme is applied to plasmas with at least two thermal ion species. Analysis of mixed discharges with complex heating schemes requires a workflow that allows to model thermal and fast ion transport consistently. This paper is dedicated to modelling of a mixed plasma discharge with significant fraction of fast ions and contributes to development of fast ion transport models. For interpretive analysis with the TRANSP code a JET hydrogen-deuterium (HD) plasma discharge with neutral beam injection (NBI) and ICRF heating has been chosen. The task is complicated by NBI-ICRF synergy and plasma magnetohydrodynamic activity, like sawtooth crashes. D beam ions accelerated by RF waves form a high energy tail in fast ion distribution. Significant difference between the neutron rate computed by TRANSP and measured one is observed if the same diffusivity for electrons and ions is assumed. Sensitivity studies show that uncertainties in input plasma parameters and thermal ion transport models are crucial for modelling mixed plasma discharges and increased D transport is required to reach the plasma composition consistent with diagnostic measurements at the plasma edge. Fast ion redistribution by a sawtooth instability is characterised by non-resonant transport due to reconnection of magnetic field lines and resonant transport caused by resonance interaction between the instability and fast ions. With ORBIT simulations it has been shown that resonant interaction strongly affects fast ions of high energies, like beam ions accelerated by RF waves and fusion products. For the considered case, fast ion profiles simulated by ORBIT remain peaked after the sawtooth crashes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

HFIR Activity Workbook Generator (HAWK) User Guide

The HFIR Activity WorkbooK generator (HAWK) is a Python code that automates and streamlines the activity calculation of samples after irradiation in the High Flux Isotope Reactor (HFIR). HAWK’s results provide estimates of the activity and nuclide inventory of irradiated specimens before they are moved to hot cell facilities, where they undergo post-irradiation examination. The samples’ activity results guide the packing of shipping containers and inform the accountable inventories for the hot cell facilities. The toolkit was originally developed by Charles Daily, a former R&D staff member at Oak Ridge National Laboratory (ORNL). As of May 2025, HAWK is developed by the Radiation Transport & HPC Methods Group (Nuclear Energy and Fuel Cycle Division) at ORNL. Figure 1 presents HAWK’s workflow. To use HAWK, users need to: 1. Develop an Excel input workbook (i.e., XLSX extension) containing data from the experiment’s materials, irradiation history (cycles), and irradiation positions. 2. Make minor edits to an existing template JSON file (i.e., auxiliary_data.JSON) and to the Python driver. The driver sets the necessary environment variables, defines the material compositions, and ultimately calls HAWK. Once configured, HAWK runs the Oak Ridge Isotope Generation code (ORIGEN) to calculate the masses, activities, and heat load at the end of irradiation for each isotope in the specimen. ORIGEN is part of SCALE, ORNL’s in-house computational tool for performing nuclear safety and design calculations. Following this step, HAWK postprocesses the results and generates three output workbooks summarizing the activity calculations.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Adaptive workflow for simulation of RF heaters

Accurate RF (Radio Frequency) simulations of fusion systems like ITER require the definition of high-fidelity analysis geometries that include detailed antenna, reactor wall, and physics regions. Here, this paper will describe a workflow for the execution of adaptive high-performance simulations of RF fusion systems. In this workflow, the simulation input consists of a CAD model attributed with the needed analysis attributes. The analysis mesh is automatically generated and the analysis steps are executed using the time-harmonic Maxwell's equations solved using high-order Nédélec finite elements. A patch recovery-based error estimator is used to drive a conforming mesh adaptation procedure.

97 MATHEMATICS AND COMPUTING↗

3D high-fidelity automated neutronics guided optimization of fusion blanket designs

The compact Fusion Pilot Plant (FPP) is defined in the recent National Academies of Sciences, Engineering, and Medicine report as the next step of fusion energy demonstration with a $50$ MWe peak net electricity production, $Q_e$ greater than $1$, and at least $3$ hours of continuous operation. This fusion pilot plant will be a test bed enabling materials, designs, and fuel management assessment, and it will represent an engineering challenge because of its high-fusion power and compact design targets. Previous reactor data is limited to experiments operating in different design space ranges. Therefore, design iterations and assessments should rely on high-fidelity first-principle theoretical and computational models. The high-fidelity integrated modeling of the plasma is a fundamental part of fusion energy research. However, the whole device modeling is often neglected, utilizing low-fidelity, system-level analysis. Recently, the need for high-fidelity multi-physics modeling was recognized, resulting in a selection of integrated tools. Further, autonomous design optimization requires a streamlined framework that perturbs the design point, reruns the analysis, and examines the outputs. However, high-fidelity analysis requires complex geometry specification that is difficult to perturb. This work presents the parametric CAD generation tool TRACER and a new neutronic workflow. TRACER allows the perturbation of the geometry representation, creating geometry files ready for further analysis. The streamlined neutronic workflow allows efficient and accurate calculations. The two new tools coupled together were used to perform a 3D high-fidelity multi-objective, multi-input optimization of an "ARC Class" compact tokamak design. The workflow was driven by an optimization driver for full automation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Software-Defined Network for End-to-end Networked Science at the Exascale

Domain science applications and workflow processes are currently forced to view the network as an opaque infrastructure into which they inject data and hope that it emerges at the destination with an acceptable Quality of Experience. There is little ability for applications to interact with the network to exchange information, negotiate performance parameters, discover expected performance metrics, or receive status/troubleshooting information in real time. The work we presen here is motivated by a vision for a new smart network and smart application ecosystem that will provide a more deterministic and interactive environment for domain science workflows. The Software-Defined Network for End-to-end Networked Science at Exascale (SENSE) system includes a model-based architecture, implementation, and deployment which enables automated end-to-end network service instantiation across administrative domains. An intent based interface allows applications to express their high-level service requirements, an intelligent orchestrator and resource control systems allow for custom tailoring of scalability and real-time responsiveness based on individual application and infrastructure operator requirements. This allows the science applications to manage the network as a first-class schedulable resource as is the current practice for instruments, compute, and storage systems. Deployment and experiments on production networks and testbeds have validated SENSE functions and performance. Emulation based testing verified the scalability needed to support research and education infrastructures. Key contributions of this work include an architecture definition, reference implementation, and deployment. This provides the basis for further innovation of smart network services to accelerate scientific discovery in the era of big data, cloud computing, machine learning and artificial intelligence.

97 MATHEMATICS AND COMPUTING↗

Inversion of Time-Lapse Seismic Reservoir Monitoring Data Using CycleGAN: A Deep Learning-Based Approach for Estimating Dynamic Reservoir Property Changes

Carbon capture and storage is being pursued globally as a geoengineering measure for reducing the emission of anthropogenic CO 2 the atmosphere. Comprehensive monitoring, verification, and accounting programs must be established for demonstrating the safe storage of injected CO 2 . One of the most commonly deployed monitoring techniques is time-lapse seismic reservoir monitoring (also known as 4-D seismic), which involves comparing 3-D seismic survey data taken at the same study site but over different times. Analyses of 4-D seismic data volumes can help improve the quality of storage reservoir characterization, track the movement of injected CO 2 plume, and identify potential CO 2 spillover/leakage from the storage reservoirblue. However, the derivation of high-resolution CO 2 saturation maps from 4-D seismic data is a highly nonlinear and ill-posed inverse problem, often requiring significant computational effort. In this research, we apply a physics-based deep learning method to facilitate the solution of both the forward and inverse problems in seismic inversion while honoring physical constraints. A cycle generative adversarial neural network (CycleGAN) model is trained to learn the bidirectional functional mappings between the reservoir dynamic property changes and seismic attribute changes, such that both forward and inverse solutions can be obtained efficiently from the trained model. We show that our CycleGAN-based approach not only improves the reliability of 4-D seismic inversion but also expedites the quantitative interpretation. Our deep learning-based workflow is generic and can be readily used for reservoir characterization and reservoir model updates involving the use of 4-D seismic data.

58 GEOSCIENCES↗

Spatial Proteomics towards cellular Resolution

Introduction: Spatial biology is an emerging interdisciplinary field facilitating biological discoveries through the use of spatial omics technologies. Recent advancements in spatial transcriptomics, spatial genomics (e.g. genetic mutations and epigenetic marks), multiplexed immunofluorescence, and spatial metabolomics/lipidomics have enabled high-resolution spatial profiling of gene expression, genetic variation, protein expression, and metabolites/lipids profiles in tissue. These developments contribute to a deeper understanding of the spatial organization within tissue microenvironments at the molecular level. Areas covered: This report provides an overview of the untargeted, bottom-up mass spectrometry (MS)-based spatial proteomics workflow. It highlights recent progress in tissue dissection, sample processing, bioinformatics, and liquid chromatography (LC)-MS technologies that are advancing spatial proteomics toward cellular resolution. Expert opinion: The field of untargeted MS-based spatial proteomics is rapidly evolving and holds great promise. To fully realize the potential of spatial proteomics, it is critical to advance data analysis and develop automated and intelligent tissue dissection at the cellular or subcellular level, along with high-throughput LC-MS analyses of thousands of samples. In conclusion, achieving these goals will necessitate significant advancements in tissue dissection technologies, LC-MS instrumentation, and computational tools.

59 BASIC BIOLOGICAL SCIENCES↗

GPU coprocessors as a service for deep learning inference in high energy physics

In the next decade, the demands for computing in large scientific experiments are expected to grow tremendously. During the same time period, CPU performance increases will be limited. At the CERN Large Hadron Collider (LHC), these two issues will confront one another as the collider is upgraded for high luminosity running. Alternative processors such as graphics processing units (GPUs) can resolve this confrontation provided that algorithms can be sufficiently accelerated. In many cases, algorithmic speedups are found to be largest through the adoption of deep learning algorithms. We present a comprehensive exploration of the use of GPU-based hardware acceleration for deep learning inference within the data reconstruction workflow of high energy physics. We present several realistic examples and discuss a strategy for the seamless integration of coprocessors so that the LHC can maintain, if not exceed, its current performance throughout its running.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Software-defined network for end-to-end networked science at the exascale

Domain science applications and workflow processes are currently forced to view the network as an opaque infrastructure into which they inject data and hope that it emerges at the destination with an acceptable Quality of Experience. There is little ability for applications to interact with the network to exchange information, negotiate performance parameters, discover expected performance metrics, or receive status/troubleshooting information in real time. The work presented here is motivated by a vision for a new smart network and smart application ecosystem that will provide a more deterministic and interactive environment for domain science workflows. The Software-Defined Network for End-to-end Networked Science at Exascale (SENSE) system includes a model-based architecture, implementation, and deployment which enables automated end- to-end network service instantiation across administrative domains. An intent based interface allows applications to express their high-level service requirements, an intelligent orchestrator and resource control systems allow for custom tailoring of scalability and real-time responsiveness based on individual application and infrastructure operator requirements. This allows the science applications to manage the network as a first-class schedulable resource as is the current practice for instruments, compute, and storage systems. Deployment and experiments on production networks and testbeds have validated SENSE functions and performance. Emulation based testing verified the scalability needed to support research and education infrastructures. Key contributions of this work include an architecture definition, reference implementation, and deployment. This provides the basis for further innovation of smart network services to accelerate scientific discovery in the era of big data, cloud computing, machine learning and artificial intelligence.

47 OTHER INSTRUMENTATION↗

Design of an Integrated Solids Handling System to Maximize Syngas Process Reliability (Cooperative Research and Development Final Report)

The National Renewable Energy Laboratory (NREL), in partnership with Wonderful Renewable Energy (WRE) and Idaho National Laboratory (INL), plans to develop a general methodology for designing integrated biorefinery solids preprocessing, handling, and feeding systems based on the chemical, physical, and mechanical attributes of the starting biomass material. This attribute-driven approach will include detailed feedstock property measurements, iterative computational modeling, and bench-scale testing to design systems for preprocessing, handling, and reactor in-feed, up to and including the selection of the conversion reactor. The initial tests and system design will be conducted using waste material from almond and pistachio growing and production operations (shells, hulls, and wood), targeting the conversion of this material to syngas for electricity production. The methodology will then be generalized to other feedstocks. The purpose of this project is to design an integrated solids handling system to maximize the process reliability of converting almond and pistachio waste to electricity. The design methodology and workflow developed from this example will then be applied to the Feedstock Conversion Interface Consortium (FCIC) benchmark loblolly pine residues, thus demonstrating the robustness of the overall design approach and providing insight and guidance for future conversion systems. V-Grid Energy Systems was brought on as a subcontractor to provide gasifiers and labor to complete gasifier runs.

09 BIOMASS FUELS↗

Investigation of CAD-based Geometry Workflows for Multiphysics Fusion Problems Using OpenMC and MOOSE

Fusion system designs are complex and require intricate and accurate meshes to be properly modeled. In this study, we investigate the use of CAD-based geometry workflows in fusion systems multiphysics problems. A simplified tokamak was introduced and modeled in CAD using a multiphysics coupling of OpenMC Monte Carlo transport and MOOSE heat conduction. The meshed geometry was prepared using direct accelerated geometry Monte Carlo (DAGMC) for particle transport, and a volumetric mesh was also prepared to be used in MOOSE and to tally OpenMC results. Cardinal was used to run OpenMC Monte Carlo particle transport within MOOSE framework. The heat source distribution and tritium production were calculated in OpenMC. The data transfer system was used to transfer heat source and temperature distribution between OpenMC and MOOSE. Two computational studies related to mesh refinement were performed: (1) refining the DAGMC and volumetric meshes used for tallying results and solving heat conduction and (2) only refining the DAGMC particle transport mesh. The refinement of the tally mesh has a much larger effect on the runtime compared to the refinement of the DAGMC particle transport surface mesh.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗