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DOE OSTI2021

Anthropogenic Perturbations to the Atmospheric Molybdenum Cycle

Abstract Molybdenum (Mo) is a key cofactor in enzymes used for nitrogen (N) fixation and nitrate reduction, and the low availability of Mo can constrain N inputs, affecting ecosystem productivity. Natural atmospheric Mo aerosolization and deposition from sources such as desert dust, sea‐salt spray, and volcanoes can affect ecosystem function across long timescales, but anthropogenic activities such as combustion, motor vehicles, and agricultural dust have accelerated the natural Mo cycle. Here we combined a synthesis of global atmospheric concentration observations and modeling to identify and estimate anthropogenic sources of atmospheric Mo. To project the impact of atmospheric Mo on terrestrial ecosystems, we synthesized soil Mo data and estimated the global distribution of soil Mo using two approaches to calculate turnover times. We estimated global emissions of atmospheric Mo in aerosols (<10 μm in diameter) to be 23 Gg Mo yr −1 , with 40%–75% from anthropogenic sources. We approximated that for the top meter of soil, Mo turnover times range between 1,000 and 1,000,000 years. In some industrialized regions, anthropogenic inputs have enhanced Mo deposition 100‐fold, lowering the soil Mo turnover time considerably. Our synthesis of global observational data, modeling, and a mass balance comparison with riverine Mo exports suggest that anthropogenic activity has greatly accelerated the Mo cycle, with potential to influence N‐limited ecosystems.

Wong, Michelle Y.↗

DOE OSTI2020

Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Feasibility of raised inner strike point equilibria scenario in ITER for detritiation from beryllium co-deposits

Abstract In ITER, tritium retention primarily occurs through co-deposition with beryllium. To avoid exceeding the strict tritium inventory limit, efficient tritium recovery techniques are essential. Baking is the ITER baseline for tritium recovery, but its effectiveness in removing tritium from thick beryllium layers is limited. A raised strike point scenario is considered an alternative method for removing tritium from the ITER inner vertical divertor target by heating components via plasma flux. This paper presents SOLPS-ITER code simulations conducted under various conditions, assessing the divertor performance and tritium outgassing of the raised strike point scenario. As the strike point is raised, recycled neutrals are not efficiently baffled by the dome and scrape-off layer, significantly changing the neutral trajectory and ionization source distribution. This improves detachment accessibility but worsens core-edge compatibility compared to the baseline scenario. However, in the partially detached condition, the impact of raising the strike point, perpendicular transport, and q 95 on target heat flux is not significant, as it primarily scales with the input power. Target heat flux is translated to target surface temperature using a simplified heat transfer model that considers the 3D target monoblock geometry and active cooling condition, excluding Be layer thermal properties. For partially detached divertor conditions, the bulk tungsten monoblock surface temperature remains below the baking temperature, which is insufficient for efficient tritium outgassing under the actively cooled ITER divertor condition. However, considering the potential thermal contact resistance between the beryllium and tungsten layers, which may significantly impact temperature distribution, the temperature of the beryllium layer can be raised to a level sufficient for efficient tritium outgassing. Therefore, the raised strike point scenario can be considered as an alternative in-vessel tritium removal technique.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies

Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in bifurcating trees. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an Ancestral Recombination Graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time-signals or population bottlenecks. Further, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an Approximate Bayesian Computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally-sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Trust Model Utilization for Energy Grid Communication

The internet information that is used by the Energy Grid of Things requires both preventative security measures as well as surveillance measures. The preventative security measures include certificates, encryption, and all of the basic security protocols as defined by published standards. The surveillance measures include monitoring information flow activities and evaluating these messages for indications of potential security attacks. We describe in this paper the utilization of a Distributed Trust Model that was developed specifically for monitoring communication within an Energy Grid of Things. The goal for the Distributed Trust Models is to provide a level of aggregate trust that a Distributed Energy Resource Management System can meet its grid service obligations, as opposed to a detailed individual Distributed Energy Resources assessment.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

Structural insights into the unexpected agonism of tetracyclic antidepressants at serotonin receptors 5-HT 1e R and 5-HT 1F R

Serotonin [5-hydroxytryptamine (5-HT)] acts via 13 different receptors in humans. Of these receptor subtypes, all but 5-HT 1e R have confirmed roles in native tissue and are validated drug targets. Despite 5-HT 1e R’s therapeutic potential and plausible druggability, the mechanisms of its activation remain elusive. To illuminate 5-HT 1e R’s pharmacology in relation to the highly homologous 5-HT 1F R, we screened a library of aminergic receptor ligands at both receptors and observe 5-HT 1e R/5-HT 1F R agonism by multicyclic drugs described as pan-antagonists at 5-HT receptors. Potent agonism by tetracyclic antidepressants mianserin, setiptiline, and mirtazapine suggests a mechanism for their clinically observed antimigraine properties. Using cryo-EM and mutagenesis studies, we uncover and characterize unique agonist-like binding poses of mianserin and setiptiline at 5-HT 1e R distinct from similar drug scaffolds in inactive-state 5-HTR structures. Together with computational studies, our data suggest that these binding poses alongside receptor-specific allosteric coupling in 5-HT 1e R and 5-HT 1F R contribute to the agonist activity of these antidepressants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Climate-induced shifts in sulfate dynamics regulate anaerobic methane oxidation in a coastal wetland

Anaerobic methane oxidation (AMO) is a key microbial pathway that mitigates methane emissions in coastal wetlands, but the response of AMO to changing global climate remains poorly understood. Here, we assessed the response of AMO to climate change in a brackish coastal wetland using a 5-year field manipulation of warming and elevated carbon dioxide ( e CO 2 ). Sulfate (SO 4 2− )–dependent AMO (S-DAMO) was the predominant AMO process at our study site due to tidal inputs of SO 4 2− . However, SO 4 2− dynamics responded differently to the treatments; warming reduced SO 4 2− concentration by enhancing SO 4 2− reduction, while eCO 2 increased SO 4 2− concentration by enhancing SO 4 2− regeneration. S-DAMO rates mirrored these trends, with warming decreasing S-DAMO rates and e CO 2 stimulating them. These findings underscore the potential of climate change to alter soil AMO activities through changing SO 4 2− dynamics, highlighting the need to incorporate these processes in predictive models for more accurate representations of coastal wetland methane dynamics.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Enzyme Discovery in Anaerobic Fungi (Neocallimastigomycetes) Enables Lignocellulosic Biorefinery Innovation

Lignocellulosic biorefineries require innovative solutions to realize their full potential, and the discovery of novel lignocellulose-active enzymes could improve biorefinery deconstruction processes. Enzymatic deconstruction of plant cell walls is challenging, as noncarbohydrate linkages in hemicellulosic sidechains and lignin protect labile carbohydrates from hydrolysis.

Microbiology↗

DOE OSTI2020

Electron Transfer from Semiconductor Nanocrystals to Redox Enzymes

This review summarizes progress in understanding electron transfer from photoexcited nanocrystals to redox enzymes. The combination of the light-harvesting properties of nanocrystals and the catalytic properties of redox enzymes has emerged as a versatile platform to drive a variety of enzyme-catalyzed reactions with light. Transfer of a photoexcited charge from a nanocrystal to an enzyme is a critical first step for these reactions. This process has been studied in depth in systems that combine Cd-chalcogenide nanocrystals with hydrogenases. The two components can be assembled in close proximity to enable direct interfacial electron transfer or integrated with redox mediators to transport charges. Time-resolved spectroscopy and kinetic modeling have been used to measure the rates and efficiencies of the electron transfer. Electron transfer has been described within the framework of Marcus theory, providing insights into the factors that can be used to control the photochemical activity of these biohybrid systems. The range of potential applications and reactions that can be achieved using nanocrystal–enzyme systems is expanding, and numerous fundamental and practical questions remain to be addressed.

Chemistry↗

DOE OSTI2024

Modeling Reversible Volume Change in Automotive Battery Cells with Porous Silicon Oxide-Graphite Composite Anodes

Automotive battery manufacturers are working to improve the individual cell and overall pack design by increasing durability, performance, and range, while reducing cost, and active material volume change is a key aspect that needs to be considered during this design process. Recently, silicon oxide-graphite composite anodes are being explored to increase total anode capacity while maintaining a tolerable amount of cell level reversible volume expansion due to the relatively lower reversible volume change of the silicon oxide compared to pure battery grade or metallurgical grade silicon. To predict the blended anode response and contribution to the overall cell volume change, we integrated the mechanical behavior of the individual active materials with the multi-species, multi-reaction model to predict the state-of-lithiation of the active materials in the cell at a given potential. The resulting simulations illustrate the tradeoff in volume change between the silicon oxide and the graphite during cell operation. This type of modeling approach will allow designers to virtually consider the impact of cell level and pack level design changes on overall system mechanical performance for automotive and grid storage applications, namely that relatively small addition of silicon containing materials can drive a significant increase in the volume change at the cell level, as demonstrated by the 5 wt% addition of silicon oxide accounting for half of the overall volume change in the cell.

Garrick, Taylor R. (ORCID:0000000322518129)↗

DOE OSTI2021

Prediction of electron density and pressure profile shapes on NSTX-U using neural networks

A new model for prediction of electron density and pressure profile shapes on NSTX and NSTX-U has been developed using neural networks. The model has been trained and tested on measured profiles from experimental discharges during the first operational campaign of NSTX-U. By projecting profiles onto empirically derived basis functions, the model is able to efficiently and accurately reproduce profile shapes. In order to project the performance of the model to upcoming NSTX-U operations, a large database of profiles from the operation of NSTX is used to test performance as a function of available data. The rapid execution time of the model is well suited to the planned applications, including optimization during scenario development activities, and real-time plasma control. A potential application of the model to real-time profile estimation is demonstrated.

Boyer, Mark↗

DOE OSTI2023

Machine Learning for Cardiac Electrical Imaging

PyTorch code for cardiac electrical imaging using the 12-lead ECG. This code is associated with the paper from CINC 2022. If you use this code, please cite: Paper : https://cinc.org/2022/Program/accepted/26_Preprint.pdf Dataset : https://library.ucsd.edu/dc/object/bb29449106 The code support two tasks: Task 1: Activation Map Reconstruction from ECG Task 2: Transmembrane potential Reconstruction from ECG

Larma, MikelLandajuela↗

DOE OSTI2022

Operational Forecasting of Induced Seismicity

Operational Forecasting of Induced Seismicity (ORION) is an open-source toolkit developed as part of the US Department of Energy SMART and NRAP programs. ORION is designed to help both expert and non-expert users understand the seismic hazard at a site. This tool analyzes how the seismic hazard evolves during injection of fluid, and can be used to identify potential mitigation strategies for observed or forecasted seismic activity. ORION is built using Python, and has an optional GUI where users can easily configure model parameters, evaluate temporal and spatial forecasts, and inspect key data (seismicity, fluid injection, pressure models, etc.).

Kroll, Kayla↗

DOE OSTI2021

A Shallow-Water Model for Convective Self-Aggregation

Randomly distributed convective storms can self-aggregate in the absence of large-scale forcings. Here we present a 1D shallow-water model to study the convective self-aggregation. This model simulates the dynamics of the planetary boundary layer and represents convection as a triggered process. Once triggered, convection lasts for finite time and occupies finite length. Here we show that the model can successfully simulate self-aggregation, and that the results are robust to a wide range of parameter values. In the simulations, convection excites gravity waves. The gravity waves then form a standing wave pattern, separating the domain into convectively active and inactive regions. We analyze the available potential energy (APE) budget and show that convection generates APE, providing energy for self-aggregation. By performing dimensional analysis, we develop a scaling theory for the size of convective aggregation, which is set by the gravity wave speed, damping time scale, and number density of convective storms. This paper provides a simple modeling framework to further study convective self-aggregation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Cultivation and Use of Acidithiobacillus ferrooxidans in Tellurium Biorecovery

The use of Acidithiobacillus ferrooxidans, Thiobacillus thiooxidans, and other chemoautotrophic microbes in bioleaching have been implemented in a variety of processes.1 In industry, bioleaching has been studied for its potential to extract valuable metals from low grade ores that would otherwise be cost prohibitive to recover.2 Other applications of bioleaching include the ability of certain microbes to detoxify waste products and even heavy metal contaminated soils.3 Another potential application for such bio-oxidative microbial activity is the extraction of tellurium (Te) from mine tailings, a low-cost abundant resource. Tellurium is one of the least common elements on Earth; it is found in the planetary crust at about 1 µg/kg, a rarity most comparable to that of platinum.4 A major use of Te in the U.S. is in cadmium-telluride (CdTe) solar panels5. Te is primarily imported into the U.S. from Canada, and it is usually recovered as a byproduct of copper refining.6 Since CdTe photovoltaic (PV) cells are the most efficient, cost-effective, and environmentally friendly PV chemistry, the renewables market has seen an increased demand for CdTe PV cells causing some concerns about sustainability and the limited global availability of Te. Acidithiobacillus ferroxidans is a microorganism that can oxidize iron and sulfur to produce ferric iron and sulfuric acid, and it is possible that it could also solubilize Te from sulfidic mine tailings. In this project, different media for growth of A. ferroxidans were evaluated, and a plan for testing the ability of A. ferroxidans to leach Te from mine tailings was developed. Initial characterization of A. ferroxidans cultures grown in the presence of copper tailings suggests that conditions suitable for Te bioleaching can be established.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Wabash CarbonSAFE: Detailed Site Characterization Plan, Task 11.0, Technical Report

Wabash CarbonSAFE established that commercial-scale CO 2 storage in the Potosi Dolomite –Maquoketa Group storage complex associated with the Wabash Valley Resources (WVR) plant site near Terre Haute, IN is highly feasible. The CarbonSAFE project team performed this evaluation through extensive data acquisition and analysis including 2D seismic reflection data, wireline logs, well testing, and core/cuttings from the Wabash #1 stratigraphic test well (now plugged and abandoned). This document summarizes work detailed in separate Wabash CarbonSAFE reports and consolidates the geologic characterization, well testing, and storage complex modeling results for the Mt. Simon Sandstone and Potosi Dolomite, two distinct reservoirs characterized at the Wabash CarbonSAFE project site. The report then presents recommendations for the next steps for site characterization, identifies data gaps for future activities, and provides an overall assessment of site potential.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2022

Wabash CarbonSAFE. Final Report

This document summarizes work detailed in separate Wabash CarbonSAFE reports; the report describes the data collection efforts of the project and consolidates the geologic characterization, well testing, and storage complex modeling results for the Mt. Simon Sandstone and Potosi Dolomite, two distinct reservoirs characterized at the Wabash CarbonSAFE project site. Also presented are summaries of work to characterize the CO 2 source and infrastructure network, as well as summaries of reports analyzing stakeholder engagement options, policy, regulatory and legal considerations, and risk assessment associated with the Wabash CarbonSAFE project site. The report then presents recommendations for the next steps for site characterization, identifies data gaps for future activities, and provides an overall assessment of site potential.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗