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DOE OSTI2025

PPI DataHub Project Data Package: S. elongatus PCC 7942 Limited Proteolysis and Thermal Proteome Profiling Structural Proteomics (JM-PB-DP3)

The purpose of this experiment was to investigate structural alterations in proteins involved in central carbon metabolism and photosynthetic electron transfer pathways in Synechococcus elongatus PCC 7942. Sample data was obtained from S. elongatus cell lysates using three complementary mass spectrometry (MS) techniques using limited proteolysis (LiP-MS), thermal proteome profiling (TPP-MS), and redox enrichment (Redox-MS) in evaluating alterations solvent accessibility and structural stability caused by light perturbation at the molecular level. Experimentally processed sample data for LiP and TPP proteomic datasets were derived from the same cell culture stock, prepared simultaneously in parallel, and acquired by mass spectrometry. Processed datasets are openly accessible from the download button and contain secondary processed proteomic results files, computed outputs, and supporting metadata materials. Experimental samples processed for LiP-MS label-free quantification (LFQ) or TPP-MS tandem mass tag (TMT) 10-plex were acquired using a Q-Exactive HF-X mass spectrometer and processed/compiled using either MSGF+ (v2024.03.26) or PlexedPiper for proteome evaluation. Additional software supporting downstream proteomic analysis include FragPipe (v.4.0), MSFragger (v.22.1), and an adapted Microbial Isolate LiP Analysis Workflow (located at Zenodo). Processed proteomic data downloads include a sample naming key, normalized quantification results files, and processed protein annotated abundance files.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Spin-Controllable Dynamics in Defect-Engineered Carbon Nanotubes as Single Photon Emitters: Data-Driven Modeling and Computations

Quantum technologies, such as quantum computing and sensing, require efficient single-photon emission (SPE) sources that operate at room temperature in telecom wavelengths. While several materials can serve as SPE sources, no single platform meets all the criteria for efficiency, ambient operation, and scalability. Single-walled carbon nanotubes (SWCNTs) with covalently attached molecules offer a promising solution. Their SPE can be easily tuned via modifications of the SWCNT's diameter, chirality, and bonded molecules, enabling emission across near-IR to telecom wavelengths at ambient conditions. However, to fully realize the potential of SWCNTs and unlock their quantum capabilities, a deeper understanding of how structural defects from molecular adducts affect their emission and competing photoexcited processes is essential. To address this gap in our knowledge, this project combined quantum chemistry calculations with data-driven methods of cheminformatics (QSAR) and machine learning (ML). The developed computational approaches have provided several design strategies for covalent functionalization of SWCNTs to improve their optical response. The collaboration with Los Alamos National Lab (LANL) enabled direct comparison of computational and experimental data, facilitating method validation. This partnership was enhanced through access to LANL's Center for Integrated Nanotechnologies (CINT) utilizing User Facility Program and summer internships, which provided three NDSU graduate students with hands-on experience at LANL. The outcomes of this project included (1) Advancing the current stage of computational methods in accurate modeling of non-adiabatic spin-dependent photoexcited dynamics and its applicability to nanosystems consisting of thousands of atoms, realized as open-access codes linked to existing DFT-based software; (2) Establishing the relationship between the structure of adducts and SWCNTs and intrinsic excitonic and spin properties of defect states for guiding novel synthetic strategies and experimental probes of chemically functionalized SWCNTs as near-IR emitting materials; (3) Generating virtual libraries of hypothetical functionalized SWCNTs for virtual screening of their chemical structures and optical properties, leveraging new functionalities of SWCNTs; (4) Offering a unique experience for NDSU graduate students that prepared them for future scientific careers related to materials modeling and big data processing. These results were summarized in 12 published journal papers and 3 recently submitted papers. One of a key finding is that the position of defect sites on the SWCNT surface primarily drives the emission redshift (up to 100 meV), while the polarity of the defect-inducing molecules has a much smaller effect (~10 meV). However, the electron-donating or withdrawing properties of a molecule influence selecting reactivity of defect sites. These insights important for optimizing synthetic protocols for desired emissions in SWCNTs. We also revealed that the interaction between two defects at various positions on the SWCNT enhances the redshift and optical activity of states, favoring strong near-IR emission. This suggests that manipulations in defect concentrations is a promising strategy for controlling efficient emission. Mostly important, the defect position was found controllable by the spin states of photoexcited intermediates: Excited aromatic molecules form ortho defects with SWCNTs at their singlet states in the presence of oxygen, while oxygen-free conditions favor para defects via the triplet-state mechanism. Additionally, a heat-activated [2+2] cycloaddition reaction facilitates divalent defect formation with fewer bonding positions that narrows emission bands. These groundbreaking findings have been experimentally validated and significantly advance our understanding of defect chemistry in SWCNTs. Using a novel encoding technique and 3D-MoRSE descriptors, we developed highly accurate ML/QSAR models to predict both the 3D structure and optical properties of SWCNTs with chemical defects. This model enabled the creation of a virtual library of 125,556 structures, providing new insights into the relationship between SWCNT-defect structure and emission.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

The Pierre Auger Observatory open data

The Pierre Auger Collaboration has embraced the concept of open access to their research data since its foundation, with the aim of giving access to the widest possible community. A gradual process of release began as early as 2007 when 1% of the cosmic-ray data was made public, along with 100% of the space-weather information. In February 2021, a portal was released containing 10% of cosmic-ray data collected by the Pierre Auger Observatory from 2004 to 2018, during the first phase of operation of the Observatory. The Open Data Portal includes detailed documentation about the detection and reconstruction procedures, analysis codes that can be easily used and modified and, additionally, visualization tools. Since then, the Portal has been updated and extended. In 2023, a catalog of the highest-energy cosmic-ray events examined in depth has been included. A specific section dedicated to educational use has been developed with the expectation that these data will be explored by a wide and diverse community, including professional and citizen scientists, and used for educational and outreach initiatives. This paper describes the context, the spirit, and the technical implementation of the release of data by the largest cosmic-ray detector ever built and anticipates its future developments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2026

The U.S. Agrivoltaic Shading Tool: A National-Scale Interface for Modeling Light and Shade Patterns in Ten Common Agrivoltaic Configurations

Agrivoltaic systems are dual-use configurations that co-locate agriculture and photovoltaic (PV) infrastructure and require careful design to balance crop performance and energy generation. A critical element of agrivoltaic design is the spatial and temporal distribution of irradiance and shade within and around PV arrays. To support research, planning, and stakeholder decision-making, we introduce the U.S. Agrivoltaic Shading Tool, a novel web-based application that delivers high-resolution irradiance and photosynthetically active radiation (PAR) modeling for ten standardized PV configurations across the conterminous United States. The tool leverages the National Laboratory of the Rockies (NLR) System Advisor Model (SAM) to perform detailed irradiance simulations, using meteorological data from the National Solar Radiation Database (NSRDB). Outputs include seasonal, monthly, weekly, and diurnal patterns of available sunlight, amount of shade, irradiance, and PAR at ground level within agrivoltaic system footprints. For a user's selected location, these results are visualized through interactive visualizations, heatmaps, and time-series plots, designed to be accessible to both technical and non-technical users. In addition to facilitating rapid spatial exploration of agrivoltaic light environments, the tool will offer seamless integration with the InSPIRE Agrivoltaics Design and Analysis Model (ADAM). This optional workflow will allow users to port selected site and configuration parameters into a more advanced modeling environment for further customization of structural layouts, crop-system compatibility, power generation, and technoeconomic performance. Finally, to promote open science, the entire dataset will be hosted and available for open access through the OpenEI platform. By standardizing and disseminating high-quality irradiance data and design tools, the U.S. Agrivoltaic Shading Tool supports a wide range of users, including researchers, landowners, energy developers, and policymakers, in evaluating the agronomic and energetic feasibility of agrivoltaic systems across the United States.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2021

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Abstract Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A Primer on Phased Array Radar Technology for the Atmospheric Sciences

The scientific community has expressed interest in the potential of phased array radars (PARs) to observe the atmosphere with finer spatial and temporal scales. Although convergence has occurred between the meteorological and engineering communities, the need exists to increase access of PAR to meteorologists. Here, we facilitate these interdisciplinary efforts in the field of ground-based PARs for atmospheric studies. We cover high-level technical concepts and terminology for PARs as applied to studies of the atmosphere. A historical perspective is provided as context along with an overview of PAR system architectures, technical challenges, and opportunities. Envisioned scan strategies are summarized because they are distinct from traditional mechanically scanned radars and are the most advantageous for high-resolution studies of the atmosphere. Further, open access to PAR data is emphasized as a mechanism to educate the future generation of atmospheric scientists. Finally, a vision for the future of operational networks, research facilities, and expansion into complementary radar wavelengths is provided.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Arabidopsis bZIP11 Is a Susceptibility Factor During Pseudomonas syringae Infection

The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens (e.g., Xanthomonas spp.) use transcription activator-like (TAL) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pv. tomato strain DC3000 lacks TAL effectors yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Because bacteria require other nutrients in addition to sugars for efficient reproduction, we hypothesized that Pseudomonas spp. may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11-regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Biochemistry & Molecular Biology↗

DOE OSTI2024

Reference Design Cases for Floating Offshore Wind Arrays

Given the immature nature of the Floating Offshore Wind (FLOW) industry, there is a need for reference FLOW farm designs to allow researchers and technology developers to study the behavior of floating wind turbine systems, without having to design every part of those systems or without having to get access to a wide range of information that is often confidential. The International Energy Agency (IEA) Wind Task 49 is facilitating research collaboration on the integrated design of Floating Offshore Wind Arrays (FOWA), and will develop several reference FOWAs to facilitate R&D activities of the floating wind community and efficient scale change of the floating wind industry (from pilot farms to commercial ones). This paper will outline the key design considerations the task has identified for the sustainable deployment of large-scale FOWAs. The aim is to prepare a comprehensive overview of the different elements that impact the design of FOWA to support the development of best practices for FOWA design. The paper will also present three baseline reference design cases that are being prepared for shallow, intermediate and deep water sites. The final designs will be made open access including the engineering and cost inputs to accelerate further innovation, research and the deployment of FOWAs.

array layout↗

DOE OSTI2026

A Comprehensive Calibration Framework for the Northwest River Forecast Center

We present a comprehensive framework developed by the Northwest River Forecast Center for calibrating hydrologically diverse basins. The framework includes models for snow, soil moisture, routing, channel loss, and consumptive use. Data inputs include a wide range of open-access datasets for meteorology, land use, topography, and land cover. The framework uses conceptual hydrologic models to handle basins with various hydrologic regimes including rain-driven and snowmelt-dominated basins. We also develop a flexible automatic calibration system that can handle numerous unobservable model parameters in a computationally efficient manner. A single-basin automatic calibration run can typically be completed on a modern laptop in under 10 min. We found that model performance metrics for this new approach match the quality of the NWRFC's previous labor-intensive manual calibrations. The model performance also rivals that of a state-of-the-art deep learning model at a fraction of the computational cost. This framework presents a new standard for the quality of calibrations possible with lumped conceptual hydrologic models, combining careful data curation, an objective calibration framework, and expert local knowledge. In addition, we have made software packages available for the entire suite of National Weather Service River Forecast System models, including SAC-SMA, SNOW-17, and Lag-K. These modern interfaces are intended to increase accessibility and facilitate future research.

Forecasting↗

DOE OSTI2024

Three-Dimensional Ultrastructure of Arabidopsis Cotyledons Infected with Colletotrichum higginsianum

We used serial block-face scanning electron microscopy (SBF-SEM) to study the host–pathogen interface between Arabidopsis cotyledons and the hemibiotrophic fungus Colletotrichum higginsianum. By combining high-pressure freezing and freeze-substitution with SBF-SEM, followed by segmentation and reconstruction of the imaging volume using the freely accessible software IMOD, we created 3D models of the series of cytological events that occur during the Colletotrichum–Arabidopsis susceptible interaction. We found that the host cell membranes underwent massive expansion to accommodate the rapidly growing intracellular hypha. As the fungal infection proceeded from the biotrophic to the necrotrophic stage, the host cell membranes went through increasing levels of disintegration culminating in host cell death. Intriguingly, we documented autophagosomes in proximity to biotrophic hyphae using transmission electron microscopy (TEM) and a concurrent increase in autophagic flux between early to mid/late biotrophic phase of the infection process. Occasionally, we observed osmiophilic bodies in the vicinity of biotrophic hyphae using TEM only and near necrotrophic hyphae under both TEM and SBF-SEM. Overall, we established a method for obtaining serial SBF-SEM images, each with a lateral ( x-y) pixel resolution of 10 nm and an axial ( z) resolution of 40 nm, that can be reconstructed into interactive 3D models using the IMOD. Application of this method to the Colletotrichum–Arabidopsis pathosystem allowed us to more fully understand the spatial arrangement and morphological architecture of the fungal hyphae after they penetrate epidermal cells of Arabidopsis cotyledons and the cytological changes the host cell undergoes as the infection progresses toward necrotrophy. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Biochemistry & Molecular Biology↗

DOE OSTI2024

Marine Algae Industrialization Consortium (MAGIC): Combining biofuel and high-value bioproducts to meet the RFS

The Marine Algae Industrialization Consortium (MAGIC) was formed to address pressing challenges in the commercialization of microalgae as a source of biofuel. The “Marine Algae Industrialization Consortium (MAGIC): Combining biofuel and high-value bioproducts to meet the RFS” project formally addressed two US Department of Energy Bioenergy Technologies Office (BETO) goals: (1) Model the sustainable supply of 1 million metric tonnes ash free dry weight (AFDW) cultivated algal biomass and (2) Demonstrate valuable co-products produced along with biofuel intermediates to increase value of algal biomass by 30%. To achieve these goals, the project demonstrated and validated high-value co-products to drive down the cost of biofuel by increasing the value of algae “co-products” towards increasing the selling price of total algae biomass as one of the key drivers of economics and adoption. This was accomplished through five core, interdependent tasks including: (1) strain selection to identify and deliver strains for mass culture, (2) mass culture using a hybrid cultivation system and following key operating parameters for downstream applications to provide algae feedstock, (3) recovery and conversion to evaluate two alternative methods to separate dry algae biomass into oil and residuals for downstream testing, (4) product assessment to determine biofuel, aquafeed or poultry feed product efficacy using algae biomass fractions as well as to provide critical performance data for valuation and (5) commercialization to use technoeconomic and life cycle assessments (TEA/LCA) as iterative design and assessment tools including consideration of target markets, competitors, and distribution channels to guide product assessment, development and valuation. A total of 46 peer-review publications, many open-access, provide detail of much of the work carried out and the results of the tasks. Additional reports and presentations provide other technical and public engagement material. At a high level, using a variety of approaches, more than 1000 marine microalgae strains were evaluated to ultimately identify the seven winners that were down-selected to be grown in mass culture. Strain selection demonstrated that there were no ‘super strains’ and that each candidate had strengths and limitations for specific products, growth conditions or operational considerations. Mass culture growth of these seven strains at >5000 L / 29 m 2 scale found that four them were suitable for product assessment. More than 250 kg of biomass was produced across hundreds of pond runs along with thousands of cultivation entries on the growth and biomass characteristics as well as environmental parameters. In the process, dozens of standard operating procedures were generated as was custom software to process and analyze cultivation data. Recovery and conversion of algae biomass demonstrated that a hexane solvent based extraction protocol was most effective at recovering oil (biocrude) from algae and four strains were processed to produce oil and lipid extracted algae (residuals) for downstream testing. Membrane-based oil separation was less successful, but may still be applicable to other commercial applications in the future. Product testing demonstrated that algae biocrude is of high quality and hydrotreating generated numerous fractions of high quality composition for fuel and lubricate based applications. Aquafeed studies performed at a variety of scales showed that both whole and defatted (lipid extracted algae) microalgae were suitable as a feed ingredient, but that the specifics of the fed animal and biochemical composition of the algae are critical factors when determining formulation. Similarly, poultry studies on whole and defatted microalgae generally showed positive outcomes on animal growth and health, with some microalgae providing enhanced nutritional composition of the animal product. Economic and life cycle assessments covered a wide range of possible commercialization and sustainability scenarios. Replacement value, improved product value added, consumer values marketing added valuation and improved animal health were considered as alternatives for microalgae valuation. Using the open pond system, algae productivity was identified as the key driver of commercialization economics, but combination of co-products (e.g. animal feed) with biofuel production substantially increased the total selling price of algae. Modeled microalgae selling price exceeded $\$$1500/tonne and could generate competitive biofuel selling prices below $\$$5 gallon gas equivalents using realistic algal productivities. Short (process scale) and longer (decadal trends) sustainability assessments show that marine microalgae can enhance the sustainability of energy production and lead to other realized benefits in water, fertilizer and land use for other sectors (e.g. agriculture). This project successfully demonstrated all of the components of an end-to-end process from mass microalgae cultivation and dewatering, to recovery and conversion of algae biomass components, to final product demonstration and process valuation; the combined results provide a framework for future commercialization of algae based biofuels.

09 BIOMASS FUELS↗

DOE OSTI2023

Battery Charge Curve Prediction via Feature Extraction and Supervised Machine Learning

Real-time onboard state monitoring and estimation of a battery over its lifetime is indispensable for the safe and durable operation of battery-powered devices. In this study, a methodology to predict the entire constant-current cycling curve with limited input information that can be collected in a short period of time is developed. A total of 10 066 charge curves of LiNiO 2 -based batteries at a constant C-rate are collected. With the combination of a feature extraction step and a multiple linear regression step, the method can accurately predict an entire battery charge curve with an error of < 2% using only 10% of the charge curve as the input information. The method is further validated across other battery chemistries (LiCoO 2 -based) using open-access datasets. The prediction error of the charge curves for the LiCoO 2 -based battery is around 2% with only 5% of the charge curve as the input information, indicating the generalization of the developed methodology for predicting battery cycling curves. The developed method paves the way for fast onboard health status monitoring and estimation for batteries during practical applications.

25 ENERGY STORAGE↗

DOE OSTI2020

Insights from 20 years of the Molecule of the Month

For 20 years, Molecule of the Month articles have highlighted the functional stories of 3D structures found in the Protein Data Bank (PDB). The PDB is the primary archive of atomic structures of biological molecules, currently providing open access to more than 150,000 structures studied by researchers around the world. The wealth of knowledge embodied in this resource is remarkable, with structures that allow exploration of nearly any biomolecular topic, including the basic science of genetic mechanisms, mechanisms of photosynthesis and bioenergetics, and central biomedical topics like cancer therapy and the fight against infectious disease. The central motivation behind the Molecule of the Month is to provide a user-friendly introduction to this rich body of data, charting a path for users to get started with finding and exploring the many available structures. The Molecule of the Month and related materials are updated regularly at the education portal PDB-101 (http://pdb101.rcsb.org/), offering an ongoing resource for molecular biology educators and students around the world.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗

DOE OSTI2025

Changes to virus taxonomy, the international code of virus classification and nomenclature, and the ICTV statutes ratified by the International Committee on Taxonomy of Viruses (2025)

Abstract The 56th meeting of the Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) was held in Bari, Italy, in July/August, 2024, and 115 submitted taxonomy proposals were reviewed. A total of 112 were subsequently ratified by the ICTV membership. An additional 9 error correction proposals were also approved in August 2025. This article lists the taxonomy proposals that have now been incorporated into release 40 version v2 of the Master Species List ( https://ictv.global/msl ), the Virus Metadata Resource ( https://ictv.global/vmr ), and associated ICTV databases. In addition to the assignments of 1,563 new virus species, 243genera, 55 families, 11 orders, and 8 classes, there were substantial additions to higher taxonomic ranks. These include the creation of a new realm ( Singelaviria ), which is based on the recognition of a separate evolutionary origin for the hallmark capsid genes of members of the kingdom Helvetiavirae. These express capsid proteins forming a single jelly-roll fold that is structurally and evolutionarily distinct from those of members of the family Bamfordvirae , assigned to the realm Varidnaviria . Furthermore, the realm Varidnaviria underwent a major reorganization, including the addition of a new kingdom, Abadenavirae . Another notable change was the classification of the vertebrate-infecting single-stranded DNA anellovirids into a new phylum Commensaviricota (kingdom Shotokuvirae , realm Monodnaviria ). Archaeal viruses infecting the hyperthermophilic Archaeoglobi were assigned to a new phylum Calorviricota , in the kingdom Trapavirae (realm Monodnaviria ), whereas RNA viruses infecting hyperthermophilic bacteria were classified into a new phylum Artimaviricota (realm Riboviria ). In recognition of his extensive and valuable contributions to virus taxonomic developments in Study Groups and over the period of his EC membership, Stuart Siddell was honoured as a new life member of the ICTV. The ICTV has created a new strategy for disseminating information on taxonomy advances through annual open-access publication of citeable taxonomy proposal summaries from each ICTV Subcommittee. A collective total of 354 co-authors of the seven summaries were drawn from members of each Subcommittee, the EC, and a very large number of contributors from the wider virology community.

Simmonds, Peter (ORCID:0000000279644700)↗

DOE OSTI2022

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

Abstract As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

Burley, Stephen K. (ORCID:0000000224879713)↗

DOE OSTI2023

Quantifying agricultural productive use of energy load in Sub-Saharan Africa and its impact on microgrid configurations and costs

The use of advanced energy technologies for agricultural purposes—such as irrigation, refrigeration, crop processing, and egg incubation—has the potential to increase crop yield, reduce vulnerability to changing precipitation patterns, increase shelf life, strengthen income and employment opportunities in rural areas, and reduce emissions by displacing fossil fuel-based technologies. These productive uses of energy (PUE) in remote areas could potentially be powered by microgrids that additionally serve otherwise unelectrified communities, most of which are located in rural Sub-Saharan Africa. Here, in this paper, we use high-resolution geospatial data to estimate the end-use electricity demand for a range of agricultural PUE across Sub-Saharan Africa, and we share these data in an open-access mapping tool. Next, we use REopt®, a techno-economic optimization model of energy systems, to determine the cost and system sizing implications of incorporating agricultural PUE into microgrid designs in Kenya and Zambia. We estimate the upper bound of agricultural PUE demand for irrigation, milling, shelling, refrigeration, and egg incubation across Sub-Saharan to be 16.8 TWh/yr. We find that incorporating local agricultural PUE into microgrid system designs increases the required system sizing while having minimal impact on the levelized cost of energy of these systems. Our analysis is the first to demonstrate the PUE potential in the agricultural sector at a 10x10-kilometer resolution across Sub-Saharan Africa and to show, at scale, how site-specific PUE can impact the cost and sizing of microgrids that are otherwise deployed to serve local household and community load.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2023

Optimized thermodynamic properties of REE aqueous species (REE 3+ and REEOH 2+ ) and experimental database for modeling the solubility of REE phosphate minerals (monazite, xenotime, and rhabdophane) from 25 to 300 °C

Rare earth elements (REE) are critical elements found in monazite, xenotime, and hydrated REE phosphates which typically form in hydrothermal mineral deposits. Accurate predictions of the solubility of these REE phosphates and the speciation of REE in aqueous fluids are both key to understanding the controls on the transport, fractionation, and deposition of REE in natural systems. Previous monazite and xenotime solubility experiments indicate the presence of large discrepancies between experimentally derived solubility constants versus calculated solubilities by combining different data sources for the thermodynamic properties of minerals and aqueous species at hydrothermal conditions. In this study, these discrepancies were resolved by using the program GEMSFITS to optimize the standard partial molal Gibbs energy of formation (Δ f G° 298 ) of REE aqueous species (REE 3+ and REE hydroxyl complexes) at 298.15 K and 1 bar while keeping the thermodynamic properties fixed for the REE phosphates. A comprehensive experimental database was compiled using solubility data available between 25 and 300 °C. The latter permits conducting thermodynamic parameter optimization of Δ f G° 298 for REE aqueous species. Optimal matching of the rhabdophane solubility data between 25 and 100 °C requires modifying the Δ f G° 298 values of REE 3+ by 1–6 kJ/mol, whereas matching of the monazite solubility data between 100 and 300 °C requires modifying the Δ f G° 298 values of both REE 3+ and REEOH 2+ by ~15–31 kJ/mol and ~2–10 kJ/mol, respectively. For xenotime, adjustments of Δ f G° 298 values by 1–26 kJ/mol are only necessary for the REE 3+ species. The optimizations indicate that the solubility of monazite in acidic solutions is controlled by the light (L)REE 3+ species at <150 °C and the LREEOH 2+ species at >150 °C, whereas the solubility of xenotime is controlled by the heavy (H)REE 3+ species between 25 and 300 °C. Based on the optimization results, we conclude that the revised Helgeson-Kirkham-Flowers equation of state does not reliably predict the thermodynamic properties of REE 3+ , REEOH 2+ , and likely other REE hydroxyl species at hydrothermal conditions. We therefore provide an experimental database (ThermoExp_REE) as a basic framework for future updates, extensions with other ligands, and optimizations as new experimental REE data become available. As a result, the optimized thermodynamic properties of aqueous species and minerals are available open access to accurately predict the solubility of REE phosphates in fluid-rock systems.

58 GEOSCIENCES↗