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DOE OSTI2020

Exploring Electrocatalysis of Methane on Transition Metal Surfaces

Methane is a potent greenhouse gas because it has a heat-absorbing ability that is 20 times stronger than the better-known carbon dioxide. It is also the dominant component of nature gas (>70%). Its current greenhouse effect is only second to carbon dioxide largely because of its relatively low atmospheric concentration. Alarmingly, however, the latter has seen a 1.5-time increase since 1750, mainly due to anthropogenic livestock farming, coal and natural gas mining, and organic matter decomposing in waste landfills. Mitigating such a trend effectively and efficiently is therefore highly desirable and intensely sought for. This final technical report describes some exciting research progresses made over the last three years supported financially by the aforementioned award. The research conducted focused on exploring electrochemical direct methane to methanol (DMTM) conversion under mild conditions. The goal of research was to explore the possibility of developing potentially game-changing electrocatalysts and electrocatalysis that can convert methane directly to methanol in a most sustainable way for curbing its effect on global warming. Progress has been made in the following three directions. First, by adapting a hydrogen fuel-cell configuration that enables gaseous methane to be transported directly to the electrocatalyst surface, we have overcome the perennial difficulty in measuring activity of methane electro-oxidation at low temperature and ambient pressure that has prevented any meaningful studies of electrocatalysis of methane conversion thus far. Second, we have developed a novel and operational in situ electrochemical infrared (IR) spectral cell for studying electrocatalysis of direct methane to methanol conversion. This novel cell is also expected to alleviate the measuring difficulty caused by low solubility of methane in aqueous electrolyte and low sticking coefficient for methane adsorption onto transition metal surface. It will improve significantly the IR’s signal to noise ratio. Third, we have successfully synthesized nano-sizing copper (Cu) exchanged zeolite mordenite (Cu-ZMOR) and coated it with carbon that enabled electrochemical access to the encaged Cu ions. This opens a door to unravel the chemistry of Cu ions in catalyzing direct methane to methanol conversion under mild experimental conditions. Altogether, these progresses achieved have laid a solid foundation for further exploring electrocatalysis of direct methane to methanol conversion in general where there exists “a plenty of room” for new discoveries and developments.

03 NATURAL GAS↗

DOE OSTI2024

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗

DOE OSTI2021

Demonstrating SolarPILOT's Python API Through Heliostat Optimal Aimpoint Strategy Use Case: Preprint

SolarPILOT is a software package that generates heliostat field layouts and characterizes the optical performance of concentrating solar power (CSP) tower systems. SolarPILOT was developed by the National Renewable Energy Laboratory (NREL) as a stand-alone desktop application but has also been incorporated into NREL's System Advisor Model (SAM) in a simplified format. Prior means for user interaction with SolarPILOT have included the application's graphical interface, the SAM routines with limited configurability, and through a built-in scripting language called "LK." This paper presents a new, full-featured Python-based application programmable interface (API) for SolarPILOT, which we hereafter refer to as CoPylot. CoPylot provides access to all SolarPILOT's capabilities to generate and characterize power tower CSP systems seamlessly through Python. Supported capabilities include (i) creating and destroying a model instances with message reporting tools; (ii) accessing and setting any SolarPILOT variable including custom land boundaries for field layout; (iii) programmatically managing receiver and heliostat objects with varied attributes for systems with multiple receiver or heliostat types; (iv) generating, assigning, and modifying heliostat field layouts including the ability to set individual heliostat locations, aimpoints, soiling rates, and reflectivity levels; (v) simulating heliostat field performance; (vi) returning detailed results describing performance of individual heliostats, the aggregate field, and receiver flux; and, (vii) exporting Python-based model instances to multiple file formats. CoPylot enables Python users to perform detailed tower CSP analysis utilizing either the Hermite expansion technique (analytical) or the SolTrace ray-tracing engine. In addition to CoPylot's functionality, Python users have access to the over 100,000 open-source libraries to develop, analyze, optimize, and visualize CSP tower research.

41 EE - Solar Energy Technologies Office (EE-4S)↗

DOE OSTI2021

Improving the Accessibility and Usability of Geothermal Information with Data Lakes and Data Pipelines on the Geothermal Data Repository: Preprint

The Geothermal Data Repository (GDR) provides universal access to data and information resulting from research and development activities funded by the Department of Energy (DOE). The GDR has extended this universal access to big data through integration with data lakes developed by the Open Energy Data Initiative (OEDI). Previously, large datasets such as seismic waveform or distributed acoustic sensing (DAS) data could only be accessed by institutions with high performance data storage and compute capabilities, effectively limiting the accessibility of big data to national labs, larger universities, and major corporations. Moreover, the time and resources needed to transport big data and configure them can produce additional barriers to use. Many of the standard formats used for structured data models (also known as content models) are incapable of handling big data and can introduce additional usability problems, often requiring data to be reformatted prior to use. This paper will explore how recent integrations between the GDR and the OEDI data lake have improved the accessibility and usability of geothermal data in a big way, making the data available to a broader audience, and enabling collaborative analysis and innovation across the greater geothermal industry.

access↗

DOE OSTI2021

Improving the Accessibility and Usability of Geothermal Information with Data Lakes and Data Pipelines on the Geothermal Data Repository

access↗

DOE OSTI2020

Small-angle Neutron Scattering (SANS) Characterization of Clay- and Carbonate-rich Shale at Elevated Pressures

Unconventional oil and gas from shale formations have emerged as some of the fastest growing energy resources in the United States, providing both cleaner energy to consumers and reducing the nation’s reliance on energy imports. To properly harness these important natural resources, the nanopore structure of associated shales must be fully understood, particularly under hydraulic fracturing conditions, where they are exposed to both overburden compressive and hydrostatic fluid pressures. The current study uses small-angle neutron scattering (SANS) to characterize pore structure, including porosity, pore accessibility, and pore size distribution, in the 1–100 nm regime at elevated pressures for mineralogically distinct clay- and carbonate-rich shales from the Permian Basin. Unlike typical porosity measurement techniques, SANS is uniquely capable of characterizing both open and closed porosity, allowing measurement of how pore accessibility changes with pressure and determination of the size range of accessible versus inaccessible pores. The porosity of the clay-rich shale was 7.7%, compared to 0.51% for the carbonate-rich shale. However, only 2.6% of the nanopores in the carbonate-rich shale were inaccessible to water at 8 kPSI (55.1 MPa) compared to 7.8% for the clay-rich shale. Furthermore, our analyses indicated that the closed pores fall within distinct size ranges, likely corresponding with the chemical nature of the pore host material. These results provide valuable insight into the effects of shale petrophysical properties on hydrocarbon extraction from unconventional reservoirs.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Backbone-Photodegradable Polymers by Incorporating Acylsilane Monomers via Ring-Opening Metathesis Polymerization

Materials capable of degradation upon exposure to light hold promise in a diverse range of applications including biomedical devices and smart coatings. Despite the rapid access to macromolecules with diverse compositions and architectures enabled by ring-opening metathesis polymerization (ROMP), a general strategy to introduce facile photodegradability into these polymers is lacking. Here, we report copolymers synthesized via ROMP that can be degraded by cleaving the backbone in both solution and solid states under irradiation with a 52 W, 390 nm Kessil LED to generate heterotelechelic low-molecular-weight fragments. To the best of our knowledge, this work represents the first instance of the incorporation of acylsilanes into a polymer backbone. Mechanistic investigation of the degradation process supports the intermediacy of an α-siloxy carbene, formed via a 1,2-photo Brook rearrangement, which undergoes insertion into water followed by cleavage of the resulting hemiacetal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Integration of the NCRC Database and Other INL Databases

The Nuclear Computational Resource Center provides a portal by which industry professionals, educational staff, students, national laboratory employees, and others may request access to certain engineering software tools. As the tools provided through the Nuclear Computational Resource Center portal are not open-source and freely available, a set of approvals are necessary before access is granted. All code recipients must be associated with an institution that has a license with Idaho National Laboratory for the code requested. Information about these licenses is controlled by Idaho National Laboratory’s Technology Deployment organization and housed in a Technology Deployment database. Those requesting code access who are not citizens of the United States must also have a security plan, mandated by Idaho National Laboratory policy. Security plans are managed by the International Access Program and are stored in an International Access Program database known as IFacts. Granting access to software thus depends on information stored in the Technology Deployment database and IFacts. In the past, no connection between the Nuclear Computational Resource Center portal and these databases existed, making checking the status of license agreements and security plans time consuming and error prone. This report demonstrates that the Nuclear Computational Resource Center portal now connects to both the Technology Deployment database and IFacts, greatly improving the ease of use of the Nuclear Computational Resource Center system for administrators, which leads to a better overall experience for those requesting code access.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2021

hls4ml: An Open-Source Codesign Workflow to Empower Scientific Low-Power Machine Learning Devices

Accessible machine learning algorithms, software, and diagnostic tools for energy-efficient devices and systems are extremely valuable across a broad range of application domains. In scientific domains, real-time near-sensor processing can drastically improve experimental design and accelerate scientific discoveries. To support domain scientists, we have developed hls4ml, an open-source software-hardware codesign workflow to interpret and translate machine learning algorithms for implementation with both FPGA and ASIC technologies. We expand on previous hls4ml work by extending capabilities and techniques towards low-power implementations and increased usability: new Python APIs, quantization-aware pruning, end-to-end FPGA workflows, long pipeline kernels for low power, and new device backends include an ASIC workflow. Taken together, these and continued efforts in hls4ml will arm a new generation of domain scientists with accessible, efficient, and powerful tools for machine-learning-accelerated discovery.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Highly-scalable GPU-accelerated compressible reacting flow solver for modeling high-speed flows

Emerging supercomputing systems utilize a combination of central processing units (CPUs) and graphics processing units (GPUs) in an effort to reach exascale capabilities while minimizing the energy footprint of operating such systems. Such heterogeneous machines introduce new challenges for fluids solvers because the hardware architecture and operation of a GPU are fundamentally different from conventional CPUs. In this work, a general approach for efficient implementation of finite-volume based reacting flow solvers on such heterogeneous systems is presented. Three main challenges, namely, data access pattern, thread divergence, and thread safety, are addressed. Since compressible reacting flows require special methods to deal with chemical reactions, hyperbolic and nonlinear convection terms, and the presence of turbulence, specific algorithms that ensure GPU-based efficiency are developed. The approach is demonstrated on the widely available OpenFOAM open source software by modifying core algorithms for GPU accessibility. The scalability of the resulting solver, is demonstrated using practical test cases, including flow through a scramjet engine and the dynamics of a rotating detonation engine. Here, the solver provides near-ideal scaleup on a large number of GPUs (>3000), and extremely efficient use of the GPUs, with throughput nearly a constant even when processing a large number of control volumes.

42 ENGINEERING↗

DOE OSTI2023

Discovery of Nanoscale Electric Field‐Induced Phase Transitions in ZrO 2

Abstract The emergence of ferroelectric and antiferroelectric properties in the semiconductor industry's most prominent high‐k dielectrics, HfO 2 and ZrO 2 , is leading to technology developments unanticipated a decade ago. Yet the failure to clearly distinguish ferroelectric from antiferroelectric behavior is impeding progress. Band‐excitation piezoresponse force microscopy and molecular dynamics are used to elucidate the nanoscale electric field‐induced phase transitions present in ZrO 2 ‐based antiferroelectrics. Antiferroelectric ZrO 2 is clearly distinguished from a closely resembling pinched La‐doped HfO 2 ferroelectric. Crystalline grains in the range of 3 – 20 nm are imaged independently undergoing reversible electric field induced phase transitions. The electrically accessible nanoscale phase transitions discovered in this study open up an unprecedented paradigm for the development of new nanoelectronic devices.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Entangled Photon Correlations Allow a Continuous-Wave Laser Diode to Measure Single-Photon, Time-Resolved Fluorescence

Fluorescence lifetime experiments are a standard approach for measuring excited state dynamics and local environment effects. Here, we show that entangled photon pairs produced from a continuous-wave (CW) laser diode can replicate pulsed laser experiments without phase modulation. As a proof of principle, picosecond fluorescence lifetimes of indocyanine green are measured in multiple environments. Here, the use of entangled photons has three unique advantages. First, low power CW laser diodes and entangled photon source design lead to straightforward on-chip integration for a direct path to distributable fluorescence lifetime measurements. Second, the entangled pair wavelength is easily tuned by temperature or electric field, allowing a single source to cover octave bandwidths. Third, femtosecond temporal resolutions can be reached without requiring major advances in source technology or external phase modulation. Entangled photons could therefore provide increased accessibility to time-resolved fluorescence while also opening new scientific avenues in photosensitive and inherently quantum systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Toward More Actionable Flood‐Risk Information

Abstract The increasingly urgent need to develop knowledge and practices to manage flood risks drives innovative information design. However, experts often disagree about design practices. As a result, flood‐risk estimates can diverge, leading to different conclusions for decision‐making. Using examples of household‐scale fluvial (riverine) flood‐risk information in the United States, we assess design features and risk communication approaches that may lead to more actionable information for decision‐making. We argue that increased attention to uncertainty characterization and model diagnostics is a critical intermediate step for developing simpler approaches for designing flood‐risk information. Simpler frameworks are desirable because flood risks change over time, and simpler frameworks are less costly to update. Developing frameworks for large spatial domains require collaboration grounded in principles of open science. Finally, systematically evaluating how decision‐makers access and use information can provide new insights to guide risk communication and information design.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Structural basis of promiscuous substrate transport by Organic Cation Transporter 1

Organic Cation Transporter 1 (OCT1) plays a crucial role in hepatic metabolism by mediating the uptake of a range of metabolites and drugs. Genetic variations can alter the efficacy and safety of compounds transported by OCT1, such as those used for cardiovascular, oncological, and psychological indications. Despite its importance in drug pharmacokinetics, the substrate selectivity and underlying structural mechanisms of OCT1 remain poorly understood. Here, we present cryo-EM structures of full-length human OCT1 in the inward-open conformation, both ligand-free and drug-bound, indicating the basis for its broad substrate recognition. Comparison of our structures with those of outward-open OCTs provides molecular insight into the alternating access mechanism of OCTs. We observe that hydrophobic gates stabilize the inward-facing conformation, whereas charge neutralization in the binding pocket facilitates the release of cationic substrates. These findings provide a framework for understanding the structural basis of the promiscuity of drug binding and substrate translocation in OCT1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Surface Water Quality Data from Beaver-Impacted Streams; Trail Creek and East River, Colorado 2025

This data package contains surface water chemistry measurements collected in 2025 to evaluate how beaver damming and low-tech process-based stream restoration influence water quality and metal mobility in mountainous headwater systems of the Upper Colorado River Basin. Sampling was conducted at Trail Creek (Taylor Park watershed, Colorado), a tributary undergoing restoration through installation of low-tech process-based structures (i.e., beaver dam analogs), and at off-channel beaver ponds within the East River floodplain (East River watershed, Colorado). Samples were collected along longitudinal transects spanning upstream control reaches, beaver-influenced ponded reaches, and downstream segments. Additional samples were collected from near-surface pore waters within a beaver dam seepage face. The dataset includes concentrations of major and trace elements measured by inductively coupled plasma–mass spectrometry (ICP-MS) and inductively coupled plasma–optical emission spectrometry (ICP-OES), major anions measured by ion chromatography (IC), and dissolved organic carbon (DOC; reported as non-purgeable organic carbon, NPOC). Samples were size-fractionated at 0.45 micrometers (µm), 0.22 µm, and 0.02 µm to distinguish particulate (>0.45 µm), colloidal (0.22–0.02 µm), and dissolved (<0.02 µm) fractions. The data package consists of comma-separated value (.csv) files containing tabulated chemical concentration data, sample metadata (site identifiers, geographic coordinates, sampling dates, fraction type), and quality control flags. All files are provided in open, non-proprietary formats that can be accessed using standard data analysis software such as Microsoft Excel, R, Python, MATLAB, or other programs capable of reading .csv files. Units, detection limits, and analytical methods are documented in accompanying metadata files. The dataset is designed to support analyses of (1) how beaver impoundment and restoration structures alter elemental partitioning and transport, (2) the role of iron and organic carbon in mediating trace metal mobility, and (3) reach-scale changes in water quality across restoration gradients. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

Anions↗

DOE OSTI2023

Automated Energy-Dispersive X-ray Spectroscopy Analysis for Multi-Modal Few-Shot Learning

Scanning transmission electron microscopy (STEM) is a powerful tool that allows for the atomic-scale analysis of a materials’ structure, chemistry, and defect domains (Akers et al. 2021). The current generation of microscopes generate vast amounts of data, surpassing the limits of effective manual analysis traditionally performed by domain experts (Spurgeon et al. 2021). While recent strides in machine learning have significantly enhanced the processing of large and intricate datasets acquired through electron microscopy, the prevalent use of proprietary software packages for initial data collection poses a challenge. In many cases, these software packages act as a ‘black box’, constraining user functionality and hindering the output of data in a format that is conducive to seamless integration into machine learning models. This work addresses these challenges by adapting HyperSpy, an open-source Python library, for the analysis and quantification of raw energy dispersive spectroscopy (EDS) data acquired through STEM. The modified HyperSpy code successfully facilitates user-defined segmentation of the data, enabling the integration of atomic %, weight %, and raw EDS spectra for each segmented region into an existing few-shot machine learning model. While initial results reveal discrepancies in quantified atomic and weight percentages when compared to proprietary software, ongoing efforts aim to rectify this issue by refining the fit of the HyperSpy model to the EDS spectra. Overall, this research underscores the potential of open-source tools like HyperSpy to enhance the accessibility of analytical tools, fostering a transparent and user-friendly environment for seamlessly incorporating electron microscopy data into machine learning models.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Windowless Optical Cell Flow System

One of the goals for advanced integrated nuclear safeguards is on-line optical analysis of molten salt in molten salt reactors and electrochemical fuel reprocessing facilities. While progress has been made in the development of optical techniques that may be suitable for on-line analysis of molten salts, significant technology gaps exist with regard to integrating these analytical techniques into industrial-scale processes. One key technological hurdle is the short service life of optical window materials, which are subject to clouding and scaling during extended exposure to molten salts. To address this issue, Argonne is developing a gravity flow cell with open-apertures to support on-line optical analysis without the need for salt-wetted windows. The flow cell uses gravity flow and fluid dynamics principles to enable molten salt flow through a pipe that has holes in its wall through which salt does not flow. In FY21, an open-aperture gravity flow cell with windowless optical access to flowing salt was successfully demonstrated. Future work should include the integration of the flow cell into a sampling loop, stakeholder outreach and collaboration, integration of multiple optical analysis techniques, evaluation of the integrated methods, and analyses to determine how the various tools might fit into an integrated safeguards monitoring system of unattended near real time monitoring tools.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2026

Finding the missing pieces: filling gaps that impede the translation of omics data into models

High-throughput omics technologies such as DNA sequencing have made the sequencing and computational assembly of microbial genomes recovered from the environment relatively routine. Computational inference of the protein products encoded by these genomes, and the associated biochemical functions, should enable the accurate prediction and modeling of microbial metabolism, organismal interactions, and ecosystem processes. However, a lack of scalable, probabilistic protein annotation tools limits the full potential of modeling for understanding the metabolism and biogeochemical cycles of microbial communities. Our approach to improve inference of protein annotations and metabolic models relied on learning from and emulating expert manual curation, leveraging software engineering and data science best practices to scale up the throughput and accuracy of annotations and metabolic model construction, building software to objectively evaluate different annotation strategies, and more closely linking the protein annotation and metabolic model inference process. Outcomes of this research include several improved or new computational tools, including DRAM (Distilled and Refined Annotation of Metabolism) for annotating microbial genomes with protein function and metabolic traits, CAMPER (Curated Annotations for Microbial Polyphenol Enzymes and Reactions) for annotating key polyphenol metabolisms, EC-Bench for comprehensive and unbiased benchmarking of annotation tools, and several apps available via the DOE Systems Biology Knowledgebase (KBase) for building genome-scale metabolic models. We demonstrate that these tools allow us to scalably annotate and understand thousands of genomes for microbial communities from a variety of systems and test cases, including rivers, thawing permafrost, and gut microbiomes. All of these computational tools are available as open-source software, with most broadly and easily accessible to the scientific community via KBase apps.

59 BASIC BIOLOGICAL SCIENCES↗