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DOE OSTI2023

Affinity-matured homotypic interactions induce spectrum of PfCSP structures that influence protection from malaria infection

The generation of high-quality antibody responses to Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP), the primary surface antigen of Pf sporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth structural and functional analysis of a panel of potent antibodies encoded by the immunoglobulin heavy chain variable (IGHV) gene IGHV3-33, which is among the most prevalent and potent antibody families induced in the anti-PfCSP immune response and targets the Asn-Ala-Asn-Pro (NANP) repeat region. Cryo-electron microscopy (cryo-EM) reveals a remarkable spectrum of helical antibody-PfCSP structures stabilized by homotypic interactions between tightly packed fragments antigen binding (Fabs), many of which correlate with somatic hypermutation. We demonstrate a key role of these mutated homotypic contacts for high avidity binding to PfCSP and in protection from Pf malaria infection. Together, these data emphasize the importance of anti-homotypic affinity maturation in the frequent selection of IGHV3–33 antibodies and highlight key features underlying the potent protection of this antibody family.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Generalized Circuit Representation for a Synchronous Machine

In this letter, a generalized circuit representation for a synchronous machine is presented. This circuit represents voltage and current relationship and can be used for dynamic and harmonic analysis. A distinct feature of the circuit is the use of Laplace transform variable s , which simplifies both calculus and frame conversion. Two derivation approaches are presented. Here, the first approach starts from a steady-state circuit representation, while the second approach starts from the dq-frame dynamic model of a synchronous generator. Both arrive at the same representation.

42 ENGINEERING↗

DOE OSTI2024

A phage tail–like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria

Bacteria can repurpose their own bacteriophage viruses (phage) to kill competing bacteria. Phage-derived elements are frequently strain specific in their killing activity, although there is limited evidence that this specificity drives bacterial population dynamics. Here, in this study, we identified intact phage and their derived elements in a metapopulation of wild plant–associated Pseudomonas genomes. We discovered that the most abundant viral cluster encodes a phage remnant resembling a phage tail called a tailocin, which bacteria have co-opted to kill bacterial competitors. Each pathogenic Pseudomonas strain carries one of a few distinct tailocin variants that target the variable polysaccharides in the outer membrane of co-occurring pathogenic Pseudomonas strains. Analysis of herbarium samples from the past 170 years revealed that the same tailocin and bacterial receptor variants have persisted in Pseudomonas populations. These results suggest that tailocin genetic diversity can be mined to develop targeted “tailocin cocktails” for microbial control.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

Background: In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E. coli. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages. Results: In E. coli, the four software programs identified one of the supplementary sources of radiation (KCl) to evoke about 5 times more transcribed genes than the minus-radiation treatment (69–114 differentially expressed genes, DEGs), and so the rest of the analyses used this KCl vs “Minus” comparison. After imposing a 30-read minimum cutoff, one of the DNAStar options shared two of the three steps (mapping, normalization, and statistic) with Partek Flow (they both used median of ratios to normalize and the DESeq2 statistical package), and these two programs identified the highest number of DEGs in common with each other (53). In contrast, when the programs used different approaches in each of the three steps, between 31 and 40 DEGs were found in common. Regarding the extent of expression differences, three of the four programs gave high fold-change results (15–178 fold), but one (DNAstar’s DESeq2) resulted in more conservative fold-changes (1.5–3.5). In a parallel study comparing three qPCR commercial validation software programs, these programs also gave variable results as to which genes were significantly regulated. Similarly, the C. elegans analysis showed exaggerated fold-changes in CLC and DNAstar’s edgeR while DNAstar-D was more conservative. Conclusions: Regarding the extent of expression (fold-change), and considering the subtlety of the very low level radiation treatments, in E. coli three of the four programs gave what we consider exaggerated fold-change results (15 – 178 fold), but one (DNAstar’s DESeq2) gave more realistic fold-changes (1.5–3.5). When RT-qPCR validation comparisons to transcriptome results were carried out, they supported the more conservative DNAstar-D’s expression results. When another model organism’s (nematode) response to these radiation differences was similarly analyzed, DNAstar-D also resulted in the most conservative expression patterns. Therefore, we would propose DESeq2 (“DNAstar-D”) as an appropriate software tool for differential gene expression studies for treatments expected to give subtle transcriptome responses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Advanced High-Performance Computational Modeling of the Seismic Response of High-Hazard and/or Nuclear Facilities and Critical Infrastructure at the NNSS

New methods for predicting the amplitude and variability of ground shaking from earthquakes (and explosions) are needed for seismic hazard analysis for buildings, nuclear power plants, and critical infrastructure at the NNSS. We are comparing existing 1-D and new 3-D geophysical methods for estimating the shear-wave velocity structure in the upper 30 meters of the ground surface (Vs30), which plays a major role in ground motion amplification and seismic response of buildings. We evaluate the performance of these methodologies at the U1a Complex at the NNSS and develop simple 1-D and high-resolution 3-D Vs30 models. We then emplace these high-resolution models into a background seismic velocity model. We will collaborate with Lawrence Livermore National Laboratory (LLNL) to conduct numerical modeling of the ground shaking at the NNSS using their high-performance computing technology and state-of-the-art ground motion simulation methodology. The primary work that was completed in FY 2019 was to acquire the seismic systems and familiarize staff at the NNSS with their use. We also worked on developing a collection plan with the Device Assembly Facility (DAF) at the NNSS, but due to time constraints and other ongoing projects at the DAF, we had to use U1a as a backup. We were able to coordinate the seismic survey, and we will complete the collection of seismic data in FY 2020. Additionally, during FY 2019, we completed the geologic framework model (GFM) for the U1a Complex and modeled the Yucca fault. LLNL worked with us through FY 2019 to prepare the data files for their modeling software and tested the software for reliability. In FY 2020 we will develop the end-to-end capability so that any facility could easily be modeled and the expected shaking from a local earthquake understood. The work in FY 2020 will include building fault models from the GFM and finalizing the velocity model analysis. The final simulations will be run for multiple rupture models, and final assessments will demonstrate the seismic hazard at the U1a Complex.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Iodide uptake by forest soils is principally related to the activity of extracellular oxidases

129 I is a nuclear fission decay product of concern because of its long half-life (16 Ma) and propensity to bioaccumulate. Microorganisms impact iodine mobility in soil systems by promoting iodination (covalent binding) of soil organic matter through processes that are not fully understood. Here, we examined iodide uptake by soils collected at two depths (0–10 and 10–20 cm) from 5 deciduous and coniferous forests in Japan and the United States. Autoclaved soils, and soils amended with an enzyme inhibitor (sodium azide) or an antibacterial agent (bronopol), bound significantly less 125 I tracer (93%, 81%, 61% decrease, respectively) than the untreated control soils, confirming a microbial role in soil iodide uptake. Correlation analyses identified the strongest significant correlation between 125 I uptake and three explanatory variables, actinobacteria soil biomass ( p = 6.04E-04, 1.35E-02 for Kendall-Tau and regression analysis, respectively), soil nitrogen content ( p = 4.86E-04, 4.24E-03), and soil oxidase enzyme activity at pH 7.0 using the substrate L-DOPA ( p = 2.83E-03, 4.33E-04) and at pH 5.5 using the ABTS ( p = 5.09E-03, 3.14E-03). Together, the results suggest that extracellular oxidases, primarily of bacterial origin, are the primary catalyst for soil iodination in aerobic, surface soils of deciduous and coniferous forests, and that soil N content may be indicative of the availability of binding sites for reactive iodine species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Treatment Technology Assessment for Landfill Leachate

This presentation by NETL was given at the 2022 American Society of Mechanical Engineers conference in Pittsburgh, PA (July 18-21, 2022). The presentation gives an overview of an analysis of wastewater emissions associated with coal combustion residual leachate, including constituents present, variability according to coal type burned at the plant, national estimates of total volume of wastewater that requires treatment, and the cost to treat.

Able, Chad↗

DOE OSTI2022

Treatment Technology Assessment for Landfill Leachate (Video)

Able, Chad↗

DOE OSTI2023

Operation and Process Control Development for a Pilot-Scale Leaching and Solvent Extraction Circuit Recovering Rare Earth Elements From Coal-Based Sources

The US Department of Energy in 2010 has identified several rare earth elements as critical materials to enable clean technologies. As part of ongoing research in REEs (rare earth elements) recovery from coal sources, the University of Kentucky has designed, developed and is demonstrating a ¼ ton/hour pilot-scale processing plant to produce high-grade REEs from coal sources. Due to the need to control critical variables (e.g. pH, tank level, etc.), process control is required. To ensure adequate process control, a study was conducted on leaching and solvent extraction control to evaluate the potential of achieving low-cost REE recovery in addition to developing a process control PLC system. The overall operational design and utilization of Six Sigma methodologies is discussed. Further, the application of the controls design, both procedural and electronic for the control of process variables such as pH is discussed. Variations in output parameters were quantified as a function of time. Data trends show that the mean process variable was maintained within prescribed limits. Future work for the utilization of data analysis and integration for data-based decision-making will be discussed.

coal, rare earth elements, pilot plant, automation↗

DOE OSTI2020

DESC: A stellarator equilibrium solver

In this paper, the new code DESC is presented to solve for fixed-boundary ideal magnetohydrodynamic equilibria in stellarators. The approach directly solves the equilibrium force balance as a system of nonlinear equations in the form f(x) = 0. The independent variables x represent nested magnetic flux surfaces expressed in the inverse representation with toroidal flux coordinates, and the equations f(x) quantify equilibrium force balance errors at discrete points in real space. Discretizing with global Fourier–Zernike basis functions properly treats the magnetic axis and minimizes the number of coefficients needed to describe the flux surfaces. The pseudospectral method provides great flexibility in where the errors are evaluated, and the system of equations is efficiently solved with a Newton–Raphson iteration. Equilibria are computed and compared against VMEC for both axisymmetric and non-axisymmetric examples. The results show fast convergence rates and solutions with low errors throughout the plasma volume.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

A Data Science and Machine Learning Platform Supporting Large Particle Accelerator Control and Diagnostics Applications Final Report: SBIR Initial Phase II DE-SC0022583

The Machine Learning Data Platform (MLDP) is a product providing full-stack support for data science, Machine Learning, and Artificial Intelligence (ML/AI) applications at particle accelerator and large experimental physics facilities. It supports ML/AI applications from front-end, high-speed acquisition of heterogeneous, time-series data, through data archiving and management, to back-end analysis. The MLDP embodies a “data-science ready” platform for data analysis and ML/AI applications in diagnosis, modelling, control, and optimization of these facilities. It provides data scientists and applications a consistent, datacentric interface to archive data standardizing implementation and deployment of ML/AI algorithms to different operations configurations within the same facility, or between facilities. Being an open-source, public-domain project, the MLDP is intended for broadest possible impact by increasing accessibility and minimizing the required expertise for installation and operation. The MLDP can also be deployed at user facilities for experimental data collection, archiving, and analysis. It is capable of acquisition and archiving of heterogeneous data from experimental equipment (e.g., images, arrays, structures, etc.) along with system hardware configurations (e.g., scalars, tables), control system process variables, and any metadata required for provenance. Thus, the MLDP can manage experimental data through its entire lifecycle, from acquisition and archiving, through analysis and investigation, to release and final publication.

43 PARTICLE ACCELERATORS↗

DOE OSTI2021

Grand Challenges of Hydrologic Modeling for Food-Energy-Water Nexus Security in High Mountain Asia

Climate-influenced changes in hydrology affect water-food-energy security that may impact up to two billion people downstream of the High Mountain Asia (HMA) region. Changes in water supply affect energy, industry, transportation, and ecosystems (agriculture, fisheries) and as a result, also affect the region's social, environmental, and economic fabrics. Sustaining the highly interconnected food-energy-water nexus (FEWN) will be a fundamental and increasing challenge under a changing climate regime. High variability in topography and distribution of glaciated and snow-covered areas in the HMA region, and scarcity of high resolution (in-situ) data make it difficult to model and project climate change impacts on individual watersheds. We lack basic understanding of the spatial and temporal variations in climate, surface impurities in snow and ice such as black carbon and dust that alter surface albedo, and glacier mass balance and dynamics. These knowledge gaps create challenges in predicting where and when the impact of changes in river flow will be the most significant economically and ecologically. In response to these challenges, the United States National Aeronautics and Space Administration (NASA) established the High Mountain Asia Team (HiMAT) in 2016 to conduct research to address knowledge gaps. This paper summarizes some of the advances HiMAT made over the past 5 years, highlights the scientific challenges in improving our understanding of the hydrology of the HMA region, and introduces an integrated assessment framework to assess the impacts of climate changes on the FEWN for the HMA region. The framework, developed under a NASA HMA project, links climate models, hydrology, hydropower, fish biology, and economic analysis. The framework could be applied to develop scientific understanding of spatio-temporal variability in water availability and the resultant downstream impacts on the FEWN to support water resource management under a changing climate regime.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Modern analogs for understanding pollen-vegetation dynamics in a Mediterranean mosaic landscape (Balearic Islands, Western Mediterranean)

This paper presents the study of modern pollen analogs from the Balearic Islands. While similar studies have been largely applied to mainland areas, research focused on modern vegetation dynamics on Mediterranean islands remains very rare. In this research, we combine vegetation surveys, pollen analysis and multivariate statistics to understand landscape composition. The main objectives of are: (1) to examine pollen-vegetation relationships in relation to environmental and land-use variables; (2) to understand modern pollen representation in a mosaic landscape structure; and (3) to propose pollen indicators that characterize the primary vegetation types from the Balearic Islands to better interpret past pollen records in Mediterranean island environments. Pollen results and Redundancy Analysis (RDA) distinguish three major groups: (a) Holm oak and box formations; (b) maquis and garrigues; and (c) anthropogenic and open habitats. Landscape form, mean decadal rainfall, mean decadal temperature, fire activity, trampling, slope percentage, wet/flooded soil, saline soil, distance to agropastoral cells, gHM index, domestic herbivory presence, agropastoral use, and soil type are the major variables explaining modern pollen assemblage variation in our research. Poaceae undiff., Plantago sp., Apiaceae undiff., Cerealia-t, and Cichorieae are highly correlated to human activities but should be interpreted cautiously when occurring in low values. Quercus ilex-t, Hypericum, and Buxus are correlated to humid locations while Pistacia, Pinus, Juniperus-t, and Olea to high mean decadal temperatures. Our study indicates how pollen analysis and multivariate analysis are powerful tools for characterizing the mosaic landscape, with special focus on the main vegetation types of the Balearic Islands.

Geology↗

DOE OSTI2021

Deploying Intra-hour Uncertainty Analysis Tools to ABB’s GridView - CRADA 445

The quickly-changing generation resource mix in the US grid, with large additions of variable resources, retirements of traditional thermal generation, distributed generation and demand response, are creating new challenges on the traditional operation of both the generation and transmission systems. The ability to perform intra-hour high fidelity production cost modeling (PCM) is needed to allow grid operators and grid planners to integrate high penetration (more than 50%) of variable energy resources, and to make prompt well informed decisions in market operations and planning. In the last decade, PNNL has developed several stand-alone tools to enable grid operators and planners to understand the impact of high variable generation on their systems. These tools have been used is studies such as: (1) Evaluation the benefits of WECC balancing authorities coordination under high variable generation penetration , (2) Benefits of Energy Imbalance Market in the North West Power Pool and (3) Duke Energy and NV Energy solar integration studies. ABB’s GridView is a widely used commercial PCM tool. It is the tool used by WECC and their stakeholders to develop the WECC PCM planning model on bi-annual basis. This proposal is focused on the integrating of PNNL intra-hour uncertainty analysis tools to GridView.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Managing Solar Photovoltaic Integration in the Western United States: Power System Flexibility Requirements and Supply

As penetrations of variable renewable energy generation technologies such as wind and solar photovoltaics (PV) continue to increase across the United States, greater uncertainty and variability in the net load often lead to a concern about how power systems may adapt. Managing the system net load (i.e., load minus contribution from variable generation technologies) may become more challenging with increasing variable generation, as the magnitude and frequency of net ramps increase. However, there is inherent flexibility in power systems through the conventional generator fleet (under least-cost unit commitment and economic dispatch), less-conventional generation sources (e.g., storage, demand response, concentrating solar power with thermal energy storage), and imports and exports with neighbors. In this analysis, we create an open-source tool to analyze the flexibility of the results of a specific commercial unit commitment and economic dispatch tool (PLEXOS), but the code can be applied generically as well. The tool assesses the flexibility requirements (or demand) of a system through a net load analysis. The constraints and limitations of each generator are then considered to determine the availability (or supply) of flexibility. Then, the supply and demand of flexibility are compared to gain a more complete picture of potential flexibility concerns. We apply this open-source tool to high-penetration PV scenarios constructed for three focus regions in the western United States defined using the Resource Planning Model (RPM) capacity expansion modeling tool: RPM-OR, RPM-CO, and RPM-AZ. Generally, we find few flexibility concerns, as the western United States represents a large and interconnected power system with significant inherent flexibility. In addition, the PV scenarios we analyzed are overbuilt on capacity, leaving plenty of ramping ability on the system. We do find that for each focus region, the impact of imports on meeting ramping needs is essential. This means the PV integration in each focus region impacts the entire rest of the system. Each system has different dominant sources of flexibility. The conventional generator fleet (especially coal and gas combined-cycle technologies) as well as less-conventional sources such as storage are all shown to be important sources of flexibility. The scenarios evaluated here were designed to study the planning and operations impact of high solar penetration in each of three focus regions. However, none of the three focus regions likely will deploy PV in isolation, meaning the ability of imports and exports to provide flexibility may be considerably different in scenarios with strong PV deployment in every region. Overall, we intend that the framework we present here will be useful in future analysis of other system evolutions to identify whether and how flexibility may constrain the successful deployment of variable generation technologies.

14 SOLAR ENERGY↗

DOE OSTI2021

Developing and Testing a Novel Stochastic Ice Microphysics Parameterization for Cloud and Climate Models Using ARM Field Campaign Data (Final Progress Report)

The major goals of this project were: 1) to use field campaign measurements from DOE’s Atmospheric Radiation Measurement (ARM) program to characterize variability of important parameters describing properties of ice particles in the atmosphere; 2) based on this observational analysis, to develop a parameterization scheme for weather and climate models that stochastically varies these parameters, and implement the new scheme into a weather model called the Weather Research and Forecasting model (WRF); 3) to use WRF coupled with the new stochastic scheme to simulate ARM field campaign thunderstorm cases and analyze how accounting for this parameter variability affects the model simulations. This work was performed jointly between the National Center for Atmospheric Research, University of Oklahoma, and University of Utah. To accomplish these goals, we extended an approach previously developed to characterize the variability in the size distribution of ice particles to parameters that are explicitly represented in models (i.e., relationships between ice particle mass and size, and between particle fall velocity and size). Our project was, to our knowledge, the first to apply observationally-constrained estimates of this parameter variability describing mass-size and fall velocity-size in a modeling framework. Our results showed efficacy of the approach, evaluated using ARM observations. Similarly, to our knowledge, work in this project was the first to propose and evaluate in detail a stochastic approach for unresolved turbulent mixing in high-resolution model simulations against detailed, benchmark large eddy simulations and ARM observations. Results showed some promising behavior, particularly with increased mixing and dilution of air in thunderstorm cores with surrounding environmental air, bringing the stochastic simulations closer to the benchmark large eddy simulations; however, results were somewhat degraded using stochastic mixing compared to observations from the AMIE/DYNAMO field campaign. This project also further refined and applied a modeling methodology called “piggybacking” that can robustly separate dynamical and thermodynamic impacts of model changes, and comparison studies of different models based on cases developed from ARM observations. Finally, this project directly supported three graduate students who completed their PhDs as well as a postdoctoral research fellow.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Experimental Analysis of the Effects of Simulator Complexity on Human Performance

Human Reliability Analysis predicts accidents caused by human errors and is an important factor in Probabilistic Safety Assessment that comprehensively evaluates the safety of nuclear power plants. This study compares and analyzes the human performance of nuclear power plant operators according to the simulator complexity as part of the HRA data collection support method development project conducted by Idaho National Laboratory. This experiment was conducted by setting two types of simulators and scenarios as independent variables. The data collected by conducting the experiments in two different simulators were analyzed using an analysis of variance test and a correlation analysis, and four human performance charts were derived.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2022

Autoencoder Neural Network for chemically reacting systems

Incorporating detailed chemical kinetic models is critical for accurate simulations of reacting flows. However, detailed models involve a large number of thermochemical (TC) state variables. Solving the governing equations to evolve these TC variables becomes impractical for real-world applications. In this work, we propose an autoencoder (AE) neural network (NN)-based reduced model to accelerate such simulations. The AE NN is first trained to find a low-dimensional latent representation of the TC states. Then, the evolving state of a chemical system can be tracked by solving the equations of the latent variables instead of the original TC equations. We demonstrate the reduced model in a syngas CO/H 2 combustion system, using training data collected from canonical perfectly stirred reactors (PSRs). It is found that the AE model can reduce the dimension of the combustion system from 12 to 2 while maintaining low reconstruction error and excellent elemental mass conservation for the test dataset. In the a posteriori test, the combustion states obtained from solving the two latent equations are compared to those from solving the 12 equations of the full model. The AE reduced method is found to be able to capture the diverse combustion states on the top two branches of the S-curve well including the extinction turning point, but with higher prediction errors for states near the ignition turning point.

97 MATHEMATICS AND COMPUTING↗