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DOE OSTI2024

In Situ Liquid Electron Microscope Cells Strongly Attenuate Electrochemical Behavior

In situ electrochemical Scanning Transmission Electron Microscopy (ec-S/TEM) probes the dynamics of electrochemical processes in real time and at high spatial resolution. This method utilizes microfabricated electrochemical cells, with enclosed dimensions of 800 μm wide, 800 μm long, and 1–2 μm tall, with electron-transparent silicon nitride windows. Working, counter, and reference electrodes in the configuration studied are deposited Pt with a planar surface area of about 1 μm 2 and a height of 50 nm. The cell confines the electrolyte within a 1 μm tall channel, and the microfabricated electrodes have a non-standard geometry, are coplanar, and are not front-facing. As such, standard assumptions of electrochemical experiments do not apply. COMSOL modeling was used to compare and contrast differences in electrochemical behavior between conventional experimental setups and the in situ ec-S/TEM cells. Cell height strongly affected voltammogram measurements: peak magnitudes and shifts correlate directly to cell height. Reactant concentration above the electrode quickly decreases during deposition, leading to a planar diffusion-dominated regime. The concentration gradient prioritizes particle growth along the thin edges of the electrode and not on the planar part of the electrode. Experiments done in the ec-S/TEM ex situ of a TEM verify the model’s accuracy.

Wittman, Reed M. [Oak Ridge National Laboratory (O↗

DOE OSTI2024

CROCUS Air Quality Data at Argonne National Laboratory Prairie Site

The AQT (Vaisala AQT530) instrument provides observations on meteorological conditions, including particulate matter (PM2.5, PM10), gas species concentrations (NO, NO2, O3, CO), and environment temperature and moisture. These measurements are critical for understanding air quality. These measurements are useful for understanding changes in aerosol properties, air quality research, and comparing to model experiments especially in urban environments. These measurements are collected at the Argonne Testbed for Multiscale Observational Science (ATMOS), a prairie field site at Argonne National Laboratory in Lemont, Illinois. Data is available in the netCDF data format, we encourage data users review documentation through Project Pythia to understand how to work with netCDF data https://foundations.projectpythia.org/core/data-formats/netcdf-cf.html. Each file contains one day's worth of data (24 hours, starting at 0000 UTC). The data is aggregated into daily frequency to make it easier to process multiple days, and compress the higher-resolution fields. File naming convention includes the project (CROCUS), location (atmos), data level (raw, a1), date (year, month, day), and hour (0000).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

High-Resolution Wind Resource Data Set of the Greater Puerto Rico Region

In February 2022, the U.S. Department of Energy and six national laboratories launched the Puerto Rico Grid Resilience and Transitions to 100% Renewable Energy Study (PR100). PR100 aims to provide a comprehensive analysis of possible pathways for Puerto Rico's energy future, with a goal of 100% renewable energy by 2050. As a part of the renewable energy potential assessment in this project, we developed 20 years (2001-2020) of data using a numerical weather prediction (NWP) model for onshore and offshore wind resource assessment for the Puerto Rico. The research steps in developing the long-term wind resource data sets based on the NWP model were: 1. Model wind resource based on the Weather Research and Forecasting (WRF) model. 2. Develop WRF model configurations for Puerto Rico. 3. Test WRF with 11 different physics parameterizations for planetary boundary layer (PBL). 4. Assess WRF output from the different PBL schemes against observations. 5. Select a final model configuration which can produce the modeled wind speed with sufficient accuracy. 6. Produce 20 years wind resource data sets for Puerto Rico region. In the first stage of our framework for developing wind resource data, we developed a WRF model configuration using two nested domains (9 km and 3 km) to cover Puerto Rico and U.S. Virgin Islands and downscale the ERA5 reanalysis data (0.25 degrees x 0.25 degrees; hourly interval) to a 3-km domain. For the second stage, we implemented one-year simulations focused on using 11 different PBL physics parameterizations to find a combination of WRF physics parameterizations that could provide accurately modeled wind speed for Puerto Rico. We also analyzed the sensitivity of the modeled wind speed to PBL schemes for onshore and offshore locations. The WRF output resulting from the 11 WRF experiments using different PBL parameterizations were evaluated against observations obtained from the National Data Buoy Center (NDBC) as well as at hub height for a location for which measurements were available. A final model setup selected through the validation with observational data was used to produce 20 years of data with 3-km spatial and 5-minute temporal resolution. The WRF model output was post-processed to include wind profiles and basic atmospheric variables in a format that can be easily used for downstream modeling. The 20 years of wind resource data will be made available through NREL and support the estimation of wind energy development costs for the PR100 study.

17 WIND ENERGY↗

DOE OSTI2024

Mu2e: Modeling Drift of Ionized Particles with ML

The Mu2e experiment searches for charged lepton flavor violation through muon-to-electron conversion in the field of a nucleus. The signal is a monoenergetic electron with an energy of 104.97 MeV. Its momentum is reconstructed using information from drifting ionized particles in a straw tracker detector. This project analyzes the drift of ionized particles with a deep neural network to help improve the momentum reconstruction process. The model yields a 20% improvement in resolution from a reference linear model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

HYBRD (High Resolution HYBrid Regional Downscaling) Model: Input data and Code

The HYBRD (HYBrid Regional Downscaling) model is a high-resolution urban land downscaling model that can be used to downscale intermediate urban land use and land cover (LULC) products into a high-resolution (30-meters). HYBRD uses a sequential hybrid process, combining statistical models with cellular-automata-based spatial algorithms. This repository contains all the necessary model code and inputs needed to successfully run HYBRD for Los Angeles, California. The repo also contains example outputs of each model step, except the final simulated raster outputs. Examples of simulated raster outputs for multiple scenarios for Los Angeles are available at DOI: 10.57931/2575233. Please refer to Related Works below.

Land↗

DOE OSTI2023

Process for ultra-sensitive quantification of target analytes in complex biological systems

Antibody-free processes are disclosed that provide accurate quantification of a wide variety of low-abundance target analytes in complex samples. The processes can employ high-pressure, high-resolution chromatographic separations for analyte enrichment. Intelligent selection of target fractions may be performed via on-line Selected Reaction Monitoring (SRM) or off-line rapid screening of internal standards. Quantification may be performed on individual or multiplexed fractions. Applications include analyses of, e.g., very low abundance proteins or candidate biomarkers in plasma, cell, or tissue samples without the need for affinity-specific reagents.

Shi, Tujin↗

DOE OSTI2024

Mu2e: Modeling Drift of Ionized Particles with ML

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.

42 ENGINEERING↗

DOE OSTI2024

FREDA: A Web Application for the Processing, Analysis, and Visualization of Fourier‐Transform Mass Spectrometry Data

The high-resolution measurement capability of Fourier-transform mass spectrometry (FT-MS) has made it a necessity for exploring the molecular composition of complex organic mixtures, like soil, plant, aquatic, and petroleum samples. This demand has driven a need for informatics tools to explore and analyze FT-MS data in a robust and reproducible manner. FREDA is an interactive web application developed to enable spectrometrists to format, process, and explore their FT-MS data without the need for statistical programming expertise. FREDA was built to explore outputs from a molecular identification tool, like CoreMS, and provide a suite of methods to filter data, compute chemical properties of peaks, statistically compare samples and groups of samples, conduct exploratory data analysis, and download the results with a report detailing all steps conducted. To demonstrate the utility of FREDA, an example analysis was conducted using FT-MS data from a soil microbiology study of samples collected in two different soil depths at the Sphagnum bog forest north of Grand Rapids, Minnesota. Differences between the two depths are observed using Kendrick, Gibbs free energy, and van Krevelen plots. G-tests are used to quantify a significant difference between the groups. All analyses and plotting are conducted using only the FREDA application. FREDA is an open-source and readily available web application that allows users to explore and make statistically valid conclusions about their FT-MS data. The application is available online (https://map.emsl.pnnl.gov/app/freda) with a tutorial web series (https://youtu.be/k5HLE2kNSBY?si=yB6sGoyvzxrFf5MP) and freely accessible code on Github (https://github.com/EMSL-Computing/FREDA).

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Azimuthally averaged wind and thermodynamic structures of tropical cyclones in global climate models and their sensitivity to horizontal resolution

Characteristics of tropical cyclones (TCs) in global climate models (GCMs) are known to be influenced by details of the model configurations, including horizontal resolution and parameterization schemes. Understanding model-to-model differences in TC characteristics is a prerequisite for reducing uncertainty in future TC activity projections by GCMs. This study performs a process-level examination of TC structures in eight GCM simulations that span a range of horizontal resolutions from 1° to 0.25°. A recently developed set of process-oriented diagnostics is used to examine the azimuthally averaged wind and thermodynamic structures of the GCM-simulated TCs. Results indicate that the inner-core wind structures of simulated TCs are more strongly constrained by the horizontal resolutions of the models than are the thermodynamic structures of those TCs. As expected, the structures of TC circulations become more realistic with smaller horizontal grid spacing, such that the radii of maximum wind (RMW) become smaller, and the maximum vertical velocities occur off the center. However, the RMWs are still too large, especially at higher intensities, and there are rising motions occurring at the storm centers, inconsistently with observations. The distributions of precipitation, moisture, radiative and surface turbulent heat fluxes around TCs are diverse, even across models with similar horizontal resolutions. At the same horizontal resolution, models that produce greater rainfall in the inner-core regions tend to simulate stronger TCs. Further, when TCs are weak, the radial gradient of net column radiative flux convergence is comparable to that of surface turbulent heat fluxes, emphasizing the importance of cloud-radiative feedbacks during the early developmental phases of TCs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Multimodal (Non)Linear Optical Nanoimaging and Nanospectroscopy

This article highlights recent advances in linear and nonlinear spectral nanoimaging. The described developments are motivated by the need to characterize molecular and material systems noninvasively with nanometer spatial and femtosecond temporal resolution. Indeed, the ability to image and chemically characterize heterogeneous interfaces with joint nano–femto resolution is a prerequisite to advancing our fundamental understanding of processes as diverse as heterogeneous catalysis, microbial communication, and energy flow in pristine/defect-containing low-dimensional quantum materials, to name a few. We describe pioneering work and recent demonstrations of (non)linear optical nanoimaging and nanospectroscopy, with an emphasis on high spatial resolution measurements conducted under ambient laboratory conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Redox Mechanisms and Migration Tendencies in Earth-Abundant 0.7Li 2 MnO 3 ·0.3LiFeO 2 Cathodes: Coupling Spin-Resolved X-ray Absorption Near Edge and X-ray Absorption Fine Structure Spectroscopies

We report the use of iron 1s3p resonant X-ray emission processes to conduct spin-selective, high-energy resolution fluorescence detected X-ray absorption near-edge spectroscopy (HERFD-XANES) on an iron-containing, lithium- and manganese-rich, fully earth-abundant cathode material, Li 1.3 Mn 0.5 Fe 0.2 O 2 (0.7Li 2 MnO 3 ·0.3LiFeO 2 ). Coupling this technique with conventional Mn K-edge XANES and detailed extended X-ray absorption fine structure (EXAFS) analysis from both the Mn and Fe vantage points, we gain fundamental insights into the redox processes and migration tendencies of transition metals in this cathode material at the bulk level. We show that during the first charge, Fe 3+ undergoes oxidation to form Fe 4+ prior to the activation plateau. Toward the end of activation, a significant fraction of the iron is present as tetrahedral Fe 3+ . This observation reveals that iron migration from octahedral to tetrahedral sites and iron reduction are initiated during activation. Upon first discharge from the activated state, a continuous and overlapping reduction of both Fe and Mn is observed, with Fe largely restored back as an octahedrally coordinated Fe 3+ . The manganese local environment gradually changes to a distorted cooperative Jahn–Teller Mn 3+ structure during discharge, with the clear presence of two Mn–O as well as two Mn–Mn correlation distances at 2.0 V. The significant reduction of manganese in the very first discharge is distinctly different from that seen in typical nickel-based lithium-manganese-rich materials but is similar to that observed for pure Li 2 MnO 3 . In conclusion, these findings shed light on key structure–property correlations in the cathode material and point to a causative relationship between the redox mechanisms as well as structural changes endured by the material and relatively poor performance during extended electrochemical cycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Virtual Volumetric Additive Manufacturing (VirtualVAM)

Abstract Tomographic volumetric additive manufacturing (VAM) produces arbitrary 3D geometries by exposure of a rotating volume of photopolymer resin to tomographically‐patterned illumination. This enables high speed, layer‐less printing of parts from a wide range of photopolymers not amenable to layer‐by‐layer processes. Since the entire geometry is produced at once over the course of a few seconds to minutes, molecular diffusion length scales become significant to the printing process. Understanding these molecular reaction and diffusion processes is imperative for advancing VAM to a usable technology. These processes are experimentally very difficult to monitor and measure. Herein, VirtualVAM ‐ a simulation framework for modeling the tomographic VAM process, is developed and experimentally validated. VirtualVAM simulates reaction, diffusion, and heat generation processes over the course of a print with single‐voxel resolution. From a few experimentally‐determined input parameters and a set of images for projection, VirtualVAM is able to generate a large spatio‐temporal data set for any given tomographic VAM print. Using VirtualVAM, a number of experimentally‐unattainable aspects of the VAM process are investigated such as single‐voxel conversion profiles, effect of molecular oxygen, and stopping time determination. VirtualVAM also enables the optimization of exposure patterns to further improve contrast between in‐part and out‐of‐part delivered dose.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Machine Learning and Economic Models to Enable Risk-Informed Condition Based Maintenance of a Nuclear Plant Asset

The primary objective of this research is to address challenges in the implementation of risk-informed, condition-based predictive maintenance (PdM), which reduces operating costs while still maintaining the safety and reliability of commercial nuclear power plants (NPPs). To achieve the objective, risk models are being developed by taking advantage of advancements in data analytics, deep learning, machine learning (ML), and artificial intelligence (AI). The notable outcomes presented in the report include ? Development of a ML models using heterogeneous plant process and vibration data collected at different spatial and temporal resolutions from the Salem?s CWS to diagnose a circulating water pump (CWP) failure based on salient fault signatures. The developed diagnostic models are extendable to other faults associated with CWPs and CWP motors given associated fault signatures. ? Development of a natural language processing (NLP) technique to automatically classify the WO data into different categories. The developed NLP technique was validated on independent WO data. This automates the tedious and time-consuming activity of mining and classifying WOs by subject matter experts. ? Estimation of mean time between downtime (i.e., time duration between time instances when 1 or more CWPs are not available) and developed an approach to establish reliability of CWS components using unstructured WO data along with CWS plant process data. ? Formulation of economic model based on Markov chain models. The parameters of associated with the transition rate between different states of Markov chain models were estimated using WO data. The economic model formulation and discussion captures both time-independent and time-dependent parameter variation, leading to risk-informed decision-making.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Unprecedented cloud resolution in a GPU-enabled full-physics atmospheric climate simulation on OLCF’s summit supercomputer

Clouds represent a key uncertainty in future climate projection. While explicit cloud resolution remains beyond our computational grasp for global climate, we can incorporate important cloud effects through a computational middle ground called the Multi-scale Modeling Framework (MMF), also known as Super Parameterization. This algorithmic approach embeds high-resolution Cloud Resolving Models (CRMs) to represent moist convective processes within each grid column in a Global Climate Model (GCM). The MMF code requires no parallel data transfers and provides a self-contained target for acceleration. This study investigates the performance of the Energy Exascale Earth System Model-MMF (E3SM-MMF) code on the OLCF Summit supercomputer at an unprecedented scale of simulation. Hundreds of kernels in the roughly 10K lines of code in the E3SM-MMF CRM were ported to GPUs with OpenACC directives. A high-resolution benchmark using 4600 nodes on Summit demonstrates the computational capability of the GPU-enabled E3SM-MMF code in a full physics climate simulation.

58 GEOSCIENCES↗

DOE OSTI2024

Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography

Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e - Å -2 , achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Aerosol‐Jet‐Printable Covalent Organic Framework Colloidal Inks and Temperature‐Sensitive Nanocomposite Films

Abstract With molecularly well‐defined and tailorable 2D structures, covalent organic frameworks (COFs) have emerged as leading material candidates for chemical sensing, storage, separation, and catalysis. In these contexts, the ability to directly and deterministically print COFs into arbitrary geometries will enable rapid optimization and deployment. However, previous attempts to print COFs have been restricted by low spatial resolution and/or post‐deposition polymerization that limits the range of compatible COFs. Here, these limitations are overcome with a pre‐synthesized, solution‐processable colloidal ink that enables aerosol jet printing of COFs with micron‐scale resolution. The ink formulation utilizes the low‐volatility solvent benzonitrile, which is critical to obtaining homogeneous printed COF film morphologies. This ink formulation is also compatible with other colloidal nanomaterials, thus facilitating the integration of COFs into printable nanocomposite films. As a proof‐of‐concept, boronate‐ester COFs are integrated with carbon nanotubes (CNTs) to form printable COF‐CNT nanocomposite films, in which the CNTs enhance charge transport and temperature sensing performance, ultimately resulting in high‐sensitivity temperature sensors that show electrical conductivity variation by 4 orders of magnitude between room temperature and 300 °C. Overall, this work establishes a flexible platform for COF additive manufacturing that will accelerate the incorporation of COFs into technologically significant applications.

2D materials↗

DOE OSTI2024

Spatio–Temporal Machine Learning for Regional to Continental Scale Terrestrial Hydrology

Integrated hydrologic models can simulate coupled surface and subsurface processes but are computationally expensive to run at high resolutions over large domains. Here we develop a novel deep learning model to emulate subsurface flows simulated by the integrated ParFlow–CLM model across the contiguous US. We compare convolutional neural networks like ResNet and UNet run autoregressively against our novel architecture called the Forced SpatioTemporal RNN (FSTR). The FSTR model incorporates separate encoding of initial conditions, static parameters, and meteorological forcings, which are fused in a recurrent loop to produce spatiotemporal predictions of groundwater. We evaluate the model architectures on their ability to reproduce 4D pressure heads, water table depths, and surface soil moisture over the contiguous US at 1 km resolution and daily time steps over the course of a full water year. The FSTR model shows superior performance to the baseline models, producing stable simulations that capture both seasonal and event–scale dynamics across a wide array of hydroclimatic regimes. The emulators provide over 1,000× speedup compared to the original physical model, which will enable new capabilities like uncertainty quantification and data assimilation for integrated hydrologic modeling that were not previously possible. Our results demonstrate the promise of using specialized deep learning architectures like FSTR for emulating complex process–based models without sacrificing fidelity.

54 ENVIRONMENTAL SCIENCES↗