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DOE OSTI2020

Optimal Estimation Retrievals and Their Uncertainties: What Every Atmospheric Scientist Should Know

Remote sensing instruments are heavily used to provide observations for both the operational and research communities. These sensors do not provide direct observations of the desired atmospheric variables, but instead, retrieval algorithms are necessary to convert the indirect observations into the variable of interest. It is critical to be aware of the underlying assumptions made by many retrieval algorithms, including that the retrieval problem is often ill posed and that there are various sources of uncertainty that need to be treated properly. In short, the retrieval challenge is to invert a set of noisy observations to obtain estimates of atmospheric quantities. The problem is often complicated by imperfect forward models, by imperfect prior knowledge, and by the existence of nonunique solutions. Optimal estimation (OE) is a widely used physical retrieval method that combines measurements, prior information, and the corresponding uncertainties based on Bayes’s theorem to find an optimal solution for the atmospheric state. Furthermore, OE also allows the relative contributions of the different sources of error to the uncertainty in the final retrieved atmospheric state to be understood. Here, we provide a novel Python library to illustrate the use of OE for inverse problems in the atmospheric sciences. We introduce two example problems: how to retrieve drop size distribution parameters from radar observations and how to retrieve the temperature profile from ground-based microwave sensors. Using these examples, we discuss common pitfalls, how the various error sources impact the retrieval, and how the quality of the retrieval results can be quantified.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

PNNL DataHub NIAID Program Project: Modeling Host Responses to Understand Severe Human Virus Infections, Multi-Omic Viral Dataset Catalog Collection

The National Institute of Allergy and Infectious Diseases (NIAID) "Modeling Host Responses to Understand Severe Human Virus Infections" program project was a highly integrated and comprehensive systems biology research core, funded by the National Institute of Health (U19AI106772) from 2013-06-01 to 2018-05-31, investigating the complex host response to category A, B, and C priority pathogen infections. Resulting project deliverables include an extensive comprehensive collections of linked primary and secondary transformation viral experimental infection data. Here we provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open access to viral Omics lifecycle datasets and project metadata. Using a highly integrated and multidisciplinary approach, linked primary data and metadata supporting secondary normalization datasets, provide critical information necessary for research reproducibility and long-term preservation. Enabling on-demand data access for research community consumption and developer reuse, serves to support new mechanistic insights and discoveries into host-pathogen interactions for aiding future biohazard data preparedness efforts in emergency response to global health crises involving viral infection.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Bridging the gap: Deploying AI-based Models in Real-Time Fusion Plasma Control Systems

Achieving reliable real-time control in fusion plasma experiments requires strict timing guarantees across entire control algorithms. In earlier work by Abbate et al. (2023), we demonstrated the feasibility of neural-network-based control algorithms on the DIII-D tokamak using the internally developed open-source Keras2C library for model conversion into C (Conlin et al. (2021)). However, the initial implementations relied on data buffering and branching logic outside the neural network code, causing variability in execution times. Subsequent deployments on DIII-D and KSTAR—including the RTCAKENN algorithm for kinetic profile reconstruction—proved that minimizing branching and buffering throughout the pipeline yields consistent millisecond-level cycle times under real experimental conditions (Shousha et al. (2023)). However, keeping pace with rapidly evolving AI frameworks (e.g. PyTorch) is challenging. Finally, we, therefore, propose a community-driven open-source effort to expand the tool, enabling real-time deployment across diverse systems that require strictly bounded execution times.

AI-based models↗

DOE OSTI2023

High-Resolution Near-Surface Imaging at the Basin Scale Using Dark Fiber and Distributed Acoustic Sensing: Toward Site Effect Estimation in Urban Environments

Near-surface seismic structure, particularly the shear wave velocity (V s ), can strongly affect local site response, and should be accurately estimated for ground motion prediction during seismic hazard assessment. The Imperial Valley (California), occupying the southern end of the Salton Trough, is a seismically active basin with thick surficial lacustrine sedimentary deposits. In this study, we utilize ambient noise records and local earthquake events for high-resolution near-surface characterization and site effect estimation with an unlit fiber-optic telecommunication infrastructure (dark fiber) in Imperial Valley by using the distributed acoustic sensing (DAS) technique. We apply ambient noise interferometry to retrieve coherent surface waves from DAS records, and evaluate performances of three different surface wave methods on DAS ambient noise dispersion imaging. We develop a quality control workflow to improve the dispersion measurement of noisy portions of the DAS data set by using a data selection strategy. Using the joint inversion of both the fundamental mode and higher overtones of Rayleigh waves, a high resolution two-dimensional (2D) V s structure down to 70 m depth is obtained. We successfully achieve an improved V s 30 (the time-averaged shear-wave velocity in the top 30 m) model with higher spatial-resolution and reliability compared to the existing community model for the area. We also explore the potential for utilizing DAS earthquake events for site amplification estimation. The preliminary results reveal a clear anti-correlation between the approximated site response and the V s 30 profile. In conclusion, our results indicate the potential utility of DAS deployed on dark fiber for near-surface characterization in appropriate contexts.

58 GEOSCIENCES↗

DOE OSTI2023

Analysis of Organic Electron Materials using Neutron Scattering (Final Report)

Neutron scattering is a powerful suite of measurement techniques that enable unique analysis of structure and dynamics of a wide variety of materials. Specifically, neutrons interact strongly with protons, which enables excellent contrast in light element organic materials that cannot be obtained with any other measurements. This series of three proposals focused on using inelastic neutron scattering (INS) to study the vibrations (dynamics) of the organic molecules involved in organic electronic devices. Our main goals were to demonstrate that INS is capable of elucidating new, useful, and unique knowledge about organic electronic samples that could be used to improve the function of devices or to solve outstanding problems that could not be solved using other measurement techniques. Since all of the goal involved using INS or other neutron techniques to do something “new” a large part of the effort was focused on complex data interpretation and development of modeling workflows that could be used by other members of the organic electronics community to study their materials. To facilitate the goal of making INS measurements more accessible to a broader community and for a wider range of materials, we optimized and engineered the computational workflows to be well documented, publicly available, and user friendly. The individual titles of the three sequential DOE-BES awards are: (1) Engineering doping profiles in organic semiconducting materials, (2) Measurement and modeling of molecular dopant structure and dynamics, and (3) Quantification of Dynamic Disorder in Electronic and Excitonic Organic Materials. For readability, this report is organized to highlight the progress of the research thematically. Many of the ideas started in one grant period and then spilled over into later awards and collaborative research.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Meteorological data from the Billy Bar site at the East River, Colorado

This dataset includes Quality Assessed and Quality Controlled (QA/QC) meteorological data from the Billy Bar field site in the East River Watershed, Colorado in order to inform watershed hydrobiogeochemical processes. The data includes 1-hour aligned time series of Solar Radiation, Wind Speed, Wind Direction, Air Temperature, Relative Humidity, Barometric Pressure, and Precipitation. For each parameter, the QA flags are given: 1 is for extreme (potential abnormal values), and 0 is for values in the expected range. The Rmarkdown document is a stand-alone file/notebook that preserves the text, code, and code results, as well as formatting contained in the original R script. The Data profiling report is a summary and graphical presentation of the data exploration process for data analysis and model building, so that users could focus on understanding data and extracting insights. The report provides a summary of each variable and does data profiling.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Environmental matrix and moisture are key determinants of microbial phenotypes expressed in a reduced complexity soil-analog

Soil moisture and porosity regulate microbial metabolism by influencing factors such as redox conditions, substrate availability, and soil connectivity. However, the inherent biological, chemical, and physical heterogeneity of soil complicates laboratory investigations into microbial phenotypes that mediate community metabolism. This difficulty arises from challenges in accurately representing the soil environment and in establishing a tractable microbial community that limits confounding variables. To address these challenges in our investigation of community metabolism, we use a reduced-complexity microbial consortium grown in a soil analog using a glass-bead matrix amended with chitin. Long-read and short-read metagenomes, metatranscriptomes, metaproteomes, and metabolomes were analyzed to test the effects of soil structure and moisture on chitin degradation. Our soil structure analog system greatly altered microbial expression profiles compared to the liquid-only incubations, emphasizing the importance of incorporating environmental parameters, like pores and surfaces, for understanding microbial phenotypes relevant to soil ecosystems. These changes were mainly driven by differences in overall expression of chitin-degrading Streptomyces species and stress-tolerant Ensifer. Our findings suggest that the success of Ensifer in a structured environment is likely related to its ability to repurpose carbon via the glyoxylate shunt while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits like motility, stress resistance, and biofilm formation that underlie the degradation of chitin across our treatments and inform how they may ultimately alter carbon use efficiency. Together our results demonstrate that community functions like decomposition are sensitive to environmental conditions and more complex than the multi-enzyme pathways involved in depolymerization.

Rodriguez-Ramos, Josue A↗

DOE OSTI2022

Building energy efficiency and load flexibility optimization using phase change materials under futuristic grid scenario

This work investigates the energy savings and load flexibility capacity of phase change material (PCM) integrated into building envelope under a future energy generation scenario, where 80% of the energy load comes from renewable sources. Using community-scale modeling, we first determine the net thermal storage required to fully manage the demand variability at a utility grid, and then using whole-building simulations we optimize operating parameters - such as PCM thickness, latent heat, interior setpoint profile, PCM distribution, and heat transfer coefficient - to determine the optimal conditions required for maximum energy reduction and load flexibility without compromising occupants' thermal comfort. The optimal PCM-integrated envelope proposed in this study can provide annual load flexibility up to 33.6% and annual energy savings up to 10.8% in a lightweight residential building located in Baltimore, MD. This study is relevant given the increasing contributions of renewable energy in the total energy generation mix, leading to a significant time-imbalance between peak energy demand and peak energy production. While thermal energy storage using PCM is a recognized technique, there is no known prior study dedicated to examining the thermal performance of PCM-integrated envelope under future energy generation scenarios. This study bridges the research gap by investigating a practical way to implement PCMs in the buildings and maximize the energy efficiency as well as load flexibility related benefits.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Profile observations of the Arctic atmospheric boundary layer with the BELUGA tethered balloon during MOSAiC

During the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition, the Balloon-bornE moduLar Utility for profilinG the lower Atmosphere (BELUGA) was deployed from an ice floe drifting in the Fram Strait from 29 June to 27 July 2020. The BELUGA observations aimed to characterize the cloudy Arctic atmospheric boundary layer above the sea ice using a modular setup of five instrument packages. The in situ measurements included atmospheric thermodynamic and dynamic state parameters (air temperature, humidity, pressure, and three-dimensional wind), broadband solar and terrestrial irradiance, aerosol particle microphysical properties, and cloud particle images. In total, 66 profile observations were collected during 33 balloon flights from the surface to maximum altitudes of 0.3 to 1.5 km. The profiles feature a high vertical resolution of 0.01 m to 1 m, including measurements below, inside, and above frequently occurring low-level clouds. This publication describes the balloon operations, instruments, and the obtained data set. We invite the scientific community for joint analysis and model application of the freely available data on PANGAEA.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Open Power System Datasets and Open Simulation Engines: A Survey Toward Machine Learning Applications

A major factor behind the success of machine learning (ML) models in multiple domains is the availability and accessibility of large, labeled, and well-organized datasets for training and benchmarking. In comparison, power grid datasets face three major challenges: (i) real-world data is often restricted by regulatory constraints, privacy reasons, or security concerns, making it difficult to obtain and work with; (ii) synthetic datasets, which are created to address these limitations, often have incomplete information and are released using specialized tools, making them inaccessible to the broader community; and, (iii) input-output datasets are difficult to generate through simulation for non-experts because open-source simulators are not known outside the power system community. This survey addresses these challenges by serving as an entry point to publicly available datasets and simulators for researchers venturing in this area. We review the current landscape of open-source power network data, machine models, consumer demand profiles, renewable generation data, and inverter models. We also examine open-source power system simulators, which are crucial for generating high-quality, high-fidelity power grid datasets. We aim to provide a foundation for overcoming data scarcity and advance towards a structured web of datasets and simulators to support the development of ML for power systems.

42 ENGINEERING↗

DOE OSTI2022

The dynamic nature of risk in DOE facilities in the surveillance and maintenance program–with observations for risk communications

Here, we explore three case studies of facilities at two US Department of Energy (DOE) former nuclear weapons research and production sites—the Oak Ridge National Laboratory and the Hanford site—whose risk profiles have changed during their long-term management under the DOE's surveillance and maintenance (S&M) program. These case studies provide examples of the challenges faced in communicating to external stakeholders, such as federal and state regulators, local communities surrounding the site, as well as the general public, the circumstances surrounding unexpected events or the emergence/discovery of new risk-important information at historically high-risk sites. We identify common topics of importance from these case studies and suggest a taxonomy for risk communicators to use in informing the dialogues with individuals and organizations that may not be technically oriented or fully informed on the subject matter. The taxonomy is based on technical insights from the quintessential definition of risk known as the Kaplan–Garrick “risk triplet” as well as insights from regulatory guidance documents on risk communication with external stakeholders originally developed for the commercial nuclear power industry.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2025

Initial Mobility Analysis for ORNL VA-EDH Synthetic Populations

Travel burdens are a major barrier to healthcare access among US Veteran patient populations, particularly those residing in rural areas. Spatial accessibility to points of care for US Veteran populations is commonly assessed in two ways. The first approach uses open data from the US Census to represent collective travel burdens, for example the distance between population-weighted census tract centroids and VHA points of care. The second approach uses restricted-access VHA patient data to measure travel costs (e.g., distance, time) for accessing points of care with respect to geolocated patient addresses and real or approximated transportation networks. While the advantage of the open data approach lies in its reproducibility, it has notable limitations in its tendency to infer individual travel behavior from aggregate population characteristics, a problem known as ecological fallacy. Conversely, while the patient data approach is able to account for individual travel behavior, its ability to account for localized access disparities (e.g., a neighborhood with exceptionally high transportation costs) and patient demographics is limited as protecting individual patient data requires their storage in closed systems with limited capacity for adequately modeling real-world travel patterns or for supplementing patient attributes. Additionally, the patient data approach cannot account for veterans who are not enrolled in the VHA system but who may be eligible for care. These challenges limit the ability to perform “what if” analyses on the effects of place-specific interventions on veteran populations with high access barriers to healthcare. To address these challenges, we explore the application of realistic synthetic populations to examine travel burdens and spatial accessibility issues among veteran patient populations. Synthetic populations provide a virtual, individually-resolved and cross-sectional representation of the veteran patient population that enables investigation of spatial access to points of care in ways in which aggregate data and patient data do not. First, synthetic populations allow one to directly assess how individuals access points of care, from synthesized residential locations to outpatient facilities on real-world transportation networks. Modeling access to points of care at the individual scale addresses the ecological fallacy problem associated with using aggregated census data to represent veteran populations and patterns of movement. Second, synthetic populations provide a means of completely representing an area’s veteran population using only publicly available, anonymized census microdata from the American Community Survey (ACS) to ensure the privacy of real-world individuals. Generating synthetic populations from the ACS also expands descriptive characteristics beyond what patient data typically offers to include socio-demographic, economic, housing, and mobility attributes. More detailed profiles of both VHA patient populations and veterans not enrolled in the VA system will provide a comprehensive picture of groups that may benefit from interventions or outreach. As an initial exercise for using synthetic populations to measure veteran travel burdens to VA care, we apply Oak Ridge National Laboratory’s (ORNL) UrbanPop capability to generate a series of synthetic VHA patient populations for 9 Veterans Integrated Services Networks (VISN) market areas in 9 Census Divisions across the continental United States, which are listed in Table 1. We use UrbanPop to produce synthetic populations for the VISN markets selected for each US Census Division, then assign VA outpatient clinic destinations to synthetic VHA patients based on travel about each VISN market’s road network. To demonstrate using the synthetic populations to evaluate healthcare travel burdens, we compare the time-based impedance between simulated home locations and VA outpatient clinics in each VISN market. We then perform validation exercises on the synthetic populations with respect to neighborhood (block group) demographic composition as well as patient mobility, comparing aggregate origin-destination statistics for the synthetic population to outpatient visits available in restricted patient data from the VA’s Corporate Data Warehouse (CDW) database.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

CROCUS Urban Canyons - Space Science and Engineering Center (SPARC) Doppler lidar data

This is the netCDF format output from the Halo Photonics Streamline XR Doppler lidar that was deployed next to the Space Science and Engineering Center (SPARC) trailer at the University of Illnois-Chicago greenhouse parking lot during CROCUS Urban Canyons. The purpose of collecting this dataset is to provide vertical and horizontal wind profiles for studying the characteristics of turbulence over the urban canyon of Chicago. This data contains the radial velocity, intensity, and backscatter from the vertical profile, range height indicator, and sector scans that were performed over both Intensive Operating Period 1 and 2 of CROCUS Urban Canyons. There are four different types of files: * The Range Height Indicator (RHI) files contain scans that are along a constant azimuth, spanning the entire hemisphere of elevation values above the surface. * The Velocity Azimuth Display (VAD) files contain the raw radial velocity data from the 6-beam, 60 degree scans. * The User1 files contain stacked Plan Position Indicator scans over a 45 degree quadrant over downtown Chicago. * The Stare files contain vertically pointing scans. These are standard netCDF files that can be opened using xarray. The VAD scans can be processed from their raw radial velocities to horizontal wind speeds with the Atmospheric data Community Toolkit (https://arm-doe.github.io/ACT/).

EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC WINDS↗

DOE OSTI2024

Ultrahigh-resolution mass spectrometry data associated with the manuscript “A functional microbiome catalog crowdsourced from North American rivers"

This data package is associated with the publication “A functional microbiome catalog crowdsourced from North American rivers” submitted to Nature (Borton et al., 2024); (https://www.biorxiv.org/content/10.1101/2023.07.22.550117v1). Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial determinants governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb is a publicly available resource that paves the way for watershed predictive modeling and microbiome-based management practices. This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. We identified the most cosmopolitan microbiome members, while also revealing local drivers of strain endemism across ecological dimensions. We provide the first evidence that microbial functional trait expression followed the tenets of the River Continuum Concept, suggesting the structure and function of river microbiomes is predictable. The Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) data were one of many different data types used in establishing the ecological dimensions along which different microbes were detected .This data package only contains the processed FTICR-MS data associated with this manuscript; all other data is accessible via Zenodo (https://zenodo.org/records/8173287), GitHub (https://github.com/jmikayla1991/Genome-Resolved-Open-Watersheds-database-GROWdb), KBase (https://doi.org/10.25982/109073.30/1895615), and NCBI via Bioproject PRJNA946291.This dataset consists of (1) a file-level metadata (flmd) file; (2) a data dictionary (dd) file; (3) a readme; (4) three Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) processed data files (a ‘data’ file containing peak-by-sample observations, a ‘mol’ file containing peak metadata, and a transformation profile containing transformation-by-sample observations). All files are .csv or .pdf.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

The collaborative effects of intrinsic and extrinsic impurities in low RRR SRF cavities

The superconducting radio-frequency (SRF) community has shown that introducing certain impurities into high-purity niobium can improve quality factors and accelerating gradients. We question why some impurities improve RF performance while others hinder it. The purpose of this study is to characterize the impurity profile of niobium with a low residual resistance ratio (RRR) and correlate these impurities with the RF performance of low RRR cavities so that the mechanism of impurity-based improvements can be better understood and improved upon. The combination of RF testing and material analysis reveals a microscopic picture of why low RRR cavities experience low temperature-dependent BCS resistance behavior more prominently than their high RRR counterparts. We performed surface treatments, low temperature baking and nitrogen-doping, on low RRR cavities to evaluate how the intentional addition of oxygen and nitrogen to the RF layer further improves performance through changes in the mean free path and impurity profile. The results of this study have the potential to unlock a new understanding on SRF materials and enable the next generation of SRF surface treatments.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

The Collaborative Effects of Intrinsic and Extrinsic Impurities in Low RRR SRF Cavities

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

The Collaborative Effects of Intrinsic and Extrinsic Impurities in Low RRR SRF Cavities

The SRF community has shown that introducing certain impurities into high-purity niobium can improve quality factors and accelerating gradients. We question why some impurities improve RF performance while others hinder it. The purpose of this study is to characterize the impurity profile of niobium coupons with a low residual resistance ratio (RRR) and correlate these impurities with the RF performance of low RRR cavities so that the mechanism of impurity-based improvements can be better understood and improved upon. The combination of RF testing and material analysis reveals a microscopic picture of why low RRR cavities experience low BCS resistance behavior more prominently than their high RRR counterparts. We performed surface treatments, low temperature baking and nitrogen-doping, on low RRR cavities to evaluate how the intentional addition of oxygen and nitrogen to the RF layer further improves performance through changes in the mean free path and impurity profile. Th e results of this study have the potential to unlock a new understanding on SRF materials and enable the next generation of high Q/high gradient surface treatments.

Howard, K.↗

DOE OSTI2023

The Collaborative Effects of Intrinsic and Extrinsic Impurities in Low RRR SRF Cavities

The SRF community has shown that introducing certain impurities into high-purity niobium can improve quality factors and accelerating gradients. We question why some impurities improve RF performance while others hinder it. The purpose of this study is to characterize the impurity profile of niobium coupons with a low residual resistance ratio (RRR) and correlate these impurities with the RF performance of low RRR cavities so that the mechanism of impurity-based improvements can be better understood and improved upon. The combination of RF testing and material analysis reveals a microscopic picture of why low RRR cavities experience low BCS resistance behavior more prominently than their high RRR counterparts. We performed surface treatments, low temperature baking and nitrogen-doping, on low RRR cavities to evaluate how the intentional addition of oxygen and nitrogen to the RF layer further improves performance through changes in the mean free path and impurity profile. The results of this study have the potential to unlock a new understanding on SRF materials and enable the next generation of high Q/high gradient surface treatments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗