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DOE OSTI2022

United States Nuclear Data Program Annual Report for FY2021

The US Nuclear Data Program (USNDP) Annual Report for Fiscal Year 2021 (FY21) summarizes the work of USNDP for the period of October 1, 2020 through September 30, 2021, with respect to the Work Plan for FY21 that was prepared in 2019. The Work Plan and Final Report for USNDP are prepared for the DOE Office of Science, Office of Nuclear Physics. The support for the nuclear data activity from sources outside the nuclear data program is described in the staffing table and in Appendix A. This leverage amounts to about 3.24 FTE scientific, to be compared with 25.095 FTEs at USNDP units funded by the DOE Office of Science, Office of Nuclear Physics. Since it is often difficult to separate accomplishments funded by various sources, some of the work reported in the present report was accomplished with nuclear data program support leveraged by other funding.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

United States Nuclear Data Program Annual Report for FY 23

The US Nuclear Data Program (USNDP) Annual Report for Fiscal Year 2023 (FY23) summarizes the work of USNDP for the period of October 1, 2022 through September 30, 2023, with respect to the Work Plan for FY23 that was prepared in 2022. The Work Plan and Final Report for USNDP are prepared for the DOE Office of Science, Office of Nuclear Physics. The support for the nuclear data activity from sources outside the nuclear data program is described in the staffing table and in Appendix A. This leverage amounts to about 17.4 FTE scientific, to be compared with 23.8 FTEs at USNDP units funded by the DOE Office of Science, Office of Nuclear Physics. Since it is often difficult to separate accomplishments funded by various sources, some of the work reported in the present report was accomplished with nuclear data program support leveraged by other funding.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

United States Nuclear Data Program Annual Report for Fiscal Year 2024

The US Nuclear Data Program (USNDP) Annual Report for Fiscal Year 2024 (FY24) summarizes the work of USNDP for the period of October 1, 2023 through September 30, 2024, with respect to the Work Plan for FY24 that was prepared in 2022. The Work Plan and Final Report for USNDP are prepared for the DOE Office of Science, Office of Nuclear Physics. The support for the nuclear data activity from sources outside the nuclear data program is described in the staffing table and in Appendix A. This leverage amounts to about 14.8 FTE scientific, to be compared with 13.9 FTEs at USNDP units funded by the DOE Office of Science, Office of Nuclear Physics. Since it is often difficult to separate accomplishments funded by various sources, some of the work reported in the present report was accomplished with nuclear data program support leveraged by other funding.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Discovering equations that govern experimental materials stability under environmental stress using scientific machine learning

Abstract While machine learning (ML) in experimental research has demonstrated impressive predictive capabilities, extracting fungible knowledge representations from experimental data remains an elusive task. In this manuscript, we use ML to infer the underlying differential equation (DE) from experimental data of degrading organic-inorganic methylammonium lead iodide (MAPI) perovskite thin films under environmental stressors (elevated temperature, humidity, and light). Using a sparse regression algorithm, we find that the underlying DE governing MAPI degradation across a broad temperature range of 35 to 85 °C is described minimally by a second-order polynomial. This DE corresponds to the Verhulst logistic function, which describes reaction kinetics analogous to self-propagating reactions. We examine the robustness of our conclusions to experimental variance and Gaussian noise and describe the experimental limits within which this methodology can be applied. Our study highlights the promise and challenges associated with ML-aided scientific discovery by demonstrating its application in experimental chemical and materials systems.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Scientific machine learning for modeling and simulating complex fluids

The formulation of rheological constitutive equations—models that relate internal stresses and deformations in complex fluids—is a critical step in the engineering of systems involving soft materials. While data-driven models provide accessible alternatives to expensive first-principles models and less accurate empirical models in many engineering disciplines, the development of similar models for complex fluids has lagged. The diversity of techniques for characterizing non-Newtonian fluid dynamics creates a challenge for classical machine learning approaches, which require uniformly structured training data. Consequently, early machine-learning based constitutive equations have not been portable between different deformation protocols or mechanical observables. Here, we present a data-driven framework that resolves such issues, allowing rheologists to construct learnable models that incorporate essential physical information, while remaining agnostic to details regarding particular experimental protocols or flow kinematics. These scientific machine learning models incorporate a universal approximator within a materially objective tensorial constitutive framework. By construction, these models respect physical constraints, such as frame-invariance and tensor symmetry, required by continuum mechanics. We demonstrate that this framework facilitates the rapid discovery of accurate constitutive equations from limited data and that the learned models may be used to describe more kinematically complex flows. This inherent flexibility admits the application of these “digital fluid twins” to a range of material systems and engineering problems. We illustrate this flexibility by deploying a trained model within a multidimensional computational fluid dynamics simulation—a task that is not achievable using any previously developed data-driven rheological equation of state.

Science & Technology - Other Topics↗

DOE OSTI2024

Impact of structural biology and the protein data bank on us fda new drug approvals of low molecular weight antineoplastic agents 2019–2023

Abstract Open access to three-dimensional atomic-level biostructure information from the Protein Data Bank (PDB) facilitated discovery/development of 100% of the 34 new low molecular weight, protein-targeted, antineoplastic agents approved by the US FDA 2019–2023. Analyses of PDB holdings, the scientific literature, and related documents for each drug-target combination revealed that the impact of structural biologists and public-domain 3D biostructure data was broad and substantial, ranging from understanding target biology (100% of all drug targets), to identifying a given target as likely druggable (100% of all targets), to structure-guided drug discovery (>80% of all new small-molecule drugs, made up of 50% confirmed and >30% probable cases). In addition to aggregate impact assessments, illustrative case studies are presented for six first-in-class small-molecule anti-cancer drugs, including a selective inhibitor of nuclear export targeting Exportin 1 (selinexor, Xpovio), an ATP-competitive CSF-1R receptor tyrosine kinase inhibitor (pexidartinib,Turalia), a non-ATP-competitive inhibitor of the BCR-Abl fusion protein targeting the myristoyl binding pocket within the kinase catalytic domain of Abl (asciminib, Scemblix), a covalently-acting G12C KRAS inhibitor (sotorasib, Lumakras or Lumykras), an EZH2 methyltransferase inhibitor (tazemostat, Tazverik), and an agent targeting the basic-Helix-Loop-Helix transcription factor HIF-2α (belzutifan, Welireg).

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

DLSIA: Deep Learning for Scientific Image Analysis

DLSIA (Deep Learning for Scientific Image Analysis) is a Python-based machine learning library that empowers scientists and researchers across diverse scientific domains with a range of customizable convolutional neural network (CNN) architectures for a wide variety of tasks in image analysis to be used in downstream data processing. DLSIA features easy-to-use architectures, such as autoencoders, tunable U-Nets and parameter-lean mixed-scale dense networks (MSDNets). Additionally, this article introduces sparse mixed-scale networks (SMSNets), generated using random graphs, sparse connections and dilated convolutions connecting different length scales. For verification, several DLSIA-instantiated networks and training scripts are employed in multiple applications, including inpainting for X-ray scattering data using U-Nets and MSDNets, segmenting 3D fibers in X-ray tomographic reconstructions of concrete using an ensemble of SMSNets, and leveraging autoencoder latent spaces for data compression and clustering. As experimental data continue to grow in scale and complexity, DLSIA provides accessible CNN construction and abstracts CNN complexities, allowing scientists to tailor their machine learning approaches, accelerate discoveries, foster interdisciplinary collaboration and advance research in scientific image analysis.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Geophysical borehole logging data of wells ER-GLS1, ER-GUM1, ER-PLM7, and ER-PLM8 at the East River Watershed, Colorado

The purpose of this data set is to provide a means of characterizing the bedrock variability both within a single borehole location and across the East River Watershed. The East River is part of the Watershed Function Scientific Focus Area (WFSFA) located in the Upper Colorado River Basin, United States, and all boreholes are located within Mancos shale bedrock. The data set contains geophysical borehole logging data acquired in October 2018 in boreholes ER-GUM1 (East River- Gothic Upper Montane Borehole #1) and ER-GLS1 (East River- Gothic Lower Subalpine Borehole #1), and acquired in October 2019 in boreholes ER-PLM7 (East River- Pumphouse Lower Montane Borehole #7) and ER-PLM8 (East River- Pumphouse Lower Montane Borehole #8). It contains depth, natural gamma ray emission, spectral gamma ray emission(Th, K, U), magnetic susceptibility, fluid temperature and electrical conductivity, electromagnetic (EM) induction derived rock electrical resistivity, heat pulse and spinner flow measurements to estimate groundwater flow, and Nuclear Magnetic Resonance (NMR) derived water content and hydraulic conductivity. Data for each borehole are provided as comma delimited text files. For each borehole accurate location information is provided (based on RTK GPS (Real Time Kinematic Global Positioning System) surveying). Borehole logging data were acquired using Mount Sopris borehole tools, and Vista Clara Javelin for NMR data.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

The parallelism motifs of genomic data analysis

Genomic datasets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share these data with the research community, but some of these genomic data analysis problems require large-scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high-end parallel systems today and place different requirements on programming support, software libraries and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high-performance genomics analysis, including alignment, profiling, clustering and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or ‘motifs’ that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Landscaper v1

Understanding the inner workings of machine learning models through their loss landscapes offers crucial insights into model properties, optimization dynamics, and generalizability. However, accessing these insights has traditionally required specialized mathematical expertise, limiting broader adoption. Landscaper is an open-source Python package designed to bridge this gap. Landscaper seamlessly integrates a suite of multi-dimensional loss landscape analyses with cutting-edge topological data analysis (TDA) methods. This powerful combination makes both fundamental loss landscape analysis and advanced TDA techniques accessible to the broader scientific ML community, without requiring deep pre-existing mathematical knowledge. Landscaper offers three key functionalities: * Construction: Builds detailed loss landscape representations through versatile low and high-dimensional sampling techniques. * Quantification: Applies advanced metrics, including a novel topological data analysis (TDA) based smoothness metric, enabling new perspectives on model behavior. * Visualization: Offers intuitive tools to visualize and interpret loss landscapes, providing actionable insights beyond traditional performance metrics.

Weber, Gunther [Lawrence Berkeley National Laborat↗

DOE OSTI2020

DPM: A deep learning PDE augmentation method with application to large-eddy simulation

A framework is introduced that leverages known physics to reduce overfitting in machine learning for scientific applications. The partial differential equation (PDE) that expresses the physics is augmented with a neural network that uses available data to learn a description of the corresponding unknown or unrepresented physics. Training within this combined system corrects for missing, unknown, or erroneously represented physics, including discretization errors associated with the PDE's numerical solution. For optimization of the network within the PDE, an adjoint PDE is solved to provide high-dimensional gradients, and a stochastic adjoint method (SAM) further accelerates training. Additionally, the approach is demonstrated for large-eddy simulation (LES) of turbulence. High-fidelity direct numerical simulations (DNS) of decaying isotropic turbulence provide the training data used to learn sub-filter-scale closures for the filtered Navier–Stokes equations. Out-of-sample comparisons show that the deep learning PDE method outperforms widely-used models, even for filter sizes so large that they become qualitatively incorrect. It also significantly outperforms the same neural network when a priori trained based on simple data mismatch, not accounting for the full PDE. Measures of discretization errors, which are well-known to be consequential in LES, point to the importance of the unified training formulation's design, which without modification corrects for them. For comparable accuracy, simulation runtime is significantly reduced. A relaxation of the typical discrete enforcement of the divergence-free constraint in the solver is also successful, instead allowing the DPM to approximately enforce incompressibility physics. Since the training loss function is not restricted to correspond directly to the closure to be learned, training can incorporate diverse data, including experimental data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Jackson, L., Johnson, M.B., Latrach, A., Grimes, D., Martinez, C., and Mclaughlin, J.F., 2024, Multidisciplinary geotechnical data collection, curation, and analysis for conformity with the regulatory framework for geologic carbon storage in Wyoming, USA: Geological Society of America Abstracts with Programs. Vol. 56, No. 5, 2024, doi: 10.1130/abs/2024AM-405024

Title: Multidisciplinary Geotechnical Data Collection, Curation, and Analysis for Conformity with the Regulatory Framework for Geologic Carbon Storage in Wyoming, USA. Text: Construction and operation of wells for geologic sequestration of carbon dioxide necessitate that they are permitted under the Environmental Protection Agency’s Underground Injection Control Class VI requirements. Class VI wells conform to stringent requirements to ensure long-term safety and integrity of the storage site and the protection of Underground Sources of Drinking Water. Entities pursuing Class VI permitting must provide comprehensive geologic site characterization, including regional geologic structure and stratigraphy, aquifer information, reservoir and confining unit geomechanical properties, geochemical analyses, assessment of trapping capacity and mechanisms, and a variety of other of multidisciplinary geotechnical data. The Wyoming Class VI Site Characterization Database Project is focused on developing a geologic site characterization database of geotechnical information, which has been compiled and verified from established, public databases/entities and scientific literature to expedite Class VI permitting in Sweetwater County within the Greater Green River Basin of southern Wyoming. The preliminary suite of compiled data from 14,000 wells includes 8,000 wells with logs and 7,250 wells with formation tops, ~70 wells with core data (e.g., X-Ray diffraction, petrographic, and petrophysical data), ~2,500 water analyses, ~740 seismic events data, and ~520 bottom-hole temperature measurements. Future work on—and stemming from—this project will include new core analyses, calculation and interpolation of subsurface temperature gradients, mechanical earth models, geochemical simulations, storage capacity estimation, stratigraphic column generation and correlation, and construction of subsurface maps. Finally, this work will help to inspire and facilitate subsurface data compilation and curation beyond Sweetwater County, Wyoming.

42 ENGINEERING↗

DOE OSTI2021

AI Enabled Data Quality Monitoring with Hydra

Data quality monitoring is critical to all experiments impacting the quality of any physics results. Traditionally, this is done through an alarm system, which detects low level faults, leaving higher level monitoring to human crews. Artificial Intelligence is beginning to find its way into scientific applications, but comes with difficulties, relying on the acquisition of new skill sets, either through education or acquisition, in data science. This paper will discuss the development and deployment of the Hydra monitoring system in production at Gluex. It will show how “off-the-shelf” technologies can be rapidly developed, as well as discuss what sociological hurdles must be overcome to successfully deploy such a system. Early results from production running of Hydra will also be shared as well as a future outlook for development of Hydra.

Britton, Thomas↗

DOE OSTI2023

Quantum Computing – Real-Time Data Processing from a Dilution Refrigerator

This poster presents a real-time data visualization system for monitoring and displaying data from a Bluefors control unit connected to a dilution refrigerator. The goal is to provide an aesthetically pleasing and user-friendly web-based interface that continuously updates and displays critical data such as temperature and flow rates at various points within the refrigerator. Leveraging WebSocket technology, the system establishes multiple connections to the dilution refrigerators, enabling simultaneous monitoring of several units. The interactive webpage dynamically updates the data, providing researchers and operators with instant insights into the system's performance. The system's ability to stream and visualize data in real-time enhances the understanding of the dilution refrigerator's behavior, aiding in optimizing its operation and ensuring efficient scientific experiments. The application's web-based nature makes it easily accessible from any device with internet connectivity, promoting seamless collaboration and remote monitoring capabilities. Overall, this poster offers a comprehensive solution for real-time data visualization and analysis of dilution refrigerators, catering to the needs of researchers and scientists working in low-temperature physics and quantum computing fields.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Dataset of solution-based inorganic materials synthesis procedures extracted from the scientific literature

The development of a materials synthesis route is usually based on heuristics and experience. A possible new approach would be to apply data-driven approaches to learn the patterns of synthesis from past experience and use them to predict the syntheses of novel materials. However, this route is impeded by the lack of a large-scale database of synthesis formulations. In this work, we applied advanced machine learning and natural language processing techniques to construct a dataset of 35,675 solution-based synthesis procedures extracted from the scientific literature. Each procedure contains essential synthesis information including the precursors and target materials, their quantities, and the synthesis actions and corresponding attributes. Every procedure is also augmented with the reaction formula. Through this work, we are making freely available the first large dataset of solution-based inorganic materials synthesis procedures.

36 MATERIALS SCIENCE↗

DOE OSTI2022

NREL Stratus - Enabling Workflows to Fuse Data Streams, Modeling, Simulation, and Machine Learning

Integrating cloud services into advanced computing facilities provides significant new capabilities over focusing solely on traditional high performance computing (HPC) workloads. This brings complementary capabilities as well as enabling new focused roles for HPC. They are especially potent for workflows that fuse data streams, modeling and simulation ('modsim') and machine learning. A key challenge to adopting a hybrid edge-cloud-HPC model is to align optimal capability, data, and user intent on the right resources for each step in a workflow.?The NREL Stratus service provides a basis for this: Stratus layers capabilities needed to make?cloud services accessible to a lab-based scientific community on commercial offerings, and; currently supports upwards of 200 projects ranging from IOT integration to traditional modeling and simulation. This provides a real-world inventory of scientific workflow elements. A growing knowledge base enables placing these elements appropriately between the edge, cloud, and traditional HPC. This paper outlines a vision via reference architecture and the application of that architecture in a typical workflow highlighting multiple components: sensor data intake, cleaning and transforming (edge/cloud suitable); generation of synthetic data through modsim, computationally heavy ML training and hyperparameter optimization (HPC suitable), and; inference and deployment (cloud ideal). Every step in such a workflow involves a cost-benefit analysis regarding the data movement, computational efficiency, availability, latency, and resource capabilities. The reference architecture and examples outlined allow for understanding new opportunities in the context of emerging workflows that combine IOT, cloud, and HPC to bolster scientific productivity.

AI↗

DOE OSTI2022

28 NREL Stratus - Enabling Workflows to Fuse Data Streams, Modeling, Simulation, and Machine Learning: Preprint

AI↗

DOE OSTI2023

Surface Meteorological Data from Sequim "Upstairs" PNNL Campus

Surface meteorological data (3m wind speed, wind direction, 2m air temperature, relative humidity, pressure, downwelling irradiance, total rainfall) gathered on the Sequim-PNNL campus ('upstairs'). Equipment is manufactured and calibrated by Campbell Scientific. Placement and height of sensors follows recommended guidelines of the NWS.

meteorological, meteorological data, Meteorologica↗