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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Multiseriate cortical sclerenchyma enhance root penetration in compacted soils

Mechanical impedance limits soil exploration and resource capture by plant roots. We examine the role of root anatomy in regulating plant adaptation to mechanical impedance and identify a root anatomical phene in maize (Zea mays) and wheat (Triticum aestivum) associated with penetration of hard soil: Multiseriate cortical sclerenchyma (MCS). We characterize this trait and evaluate the utility of MCS for root penetration in compacted soils. Roots with MCS had a greater cell wall-to-lumen ratio and a distinct UV emission spectrum in outer cortical cells. Genome-wide association mapping revealed that MCS is heritable and genetically controlled. We identified a candidate gene associated with MCS. Across all root classes and nodal positions, maize genotypes with MCS had 13% greater root lignin concentration compared to genotypes without MCS. Genotypes without MCS formed MCS upon exogenous ethylene exposure. Genotypes with MCS had greater lignin concentration and bending strength at the root tip. In controlled environments, MCS in maize and wheat was associated improved root tensile strength and increased penetration ability in compacted soils. Maize genotypes with MCS had root systems with 22% greater depth and 49% greater shoot biomass in compacted soils in the field compared to lines without MCS. Of the lines we assessed, MCS was present in 30 to 50% of modern maize, wheat, and barley cultivars but was absent in teosinte and wild and landrace accessions of wheat and barley. MCS merits investigation as a trait for improving plant performance in maize, wheat, and other grasses under edaphic stress.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Primordial non-Gaussianity from the completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey – I: Catalogue preparation and systematic mitigation

ABSTRACT We investigate the large-scale clustering of the final spectroscopic sample of quasars from the recently completed extended Baryon Oscillation Spectroscopic Survey (eBOSS). The sample contains 343 708 objects in the redshift range 0.8 < z < 2.2 and 72 667 objects with redshifts 2.2 < z < 3.5, covering an effective area of $4699\, {\rm deg}^{2}$. We develop a neural network-based approach to mitigate spurious fluctuations in the density field caused by spatial variations in the quality of the imaging data used to select targets for follow-up spectroscopy. Simulations are used with the same angular and radial distributions as the real data to estimate covariance matrices, perform error analyses, and assess residual systematic uncertainties. We measure the mean density contrast and cross-correlations of the eBOSS quasars against maps of potential sources of imaging systematics to address algorithm effectiveness, finding that the neural network-based approach outperforms standard linear regression. Stellar density is one of the most important sources of spurious fluctuations, and a new template constructed using data from the Gaia spacecraft provides the best match to the observed quasar clustering. The end-product from this work is a new value-added quasar catalogue with the improved weights to correct for non-linear imaging systematic effects, which will be made public. Our quasar catalogue is used to measure the local-type primordial non-Gaussianity in a companion paper.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Real-time deep-learning inversion of seismic full waveform data for CO 2 saturation and uncertainty in geological carbon storage monitoring

Deep-learning inversion has recently drawn attention in geological carbon storage research due to its potential of imaging and monitoring carbon storage in real time, significantly improving efficiency and safety of carbon storage operations. We present a deep-learning full waveform inversion method that after the neural network has been trained can image CO 2 saturation and its uncertainty in real time. Our deep-learning inversion method is based on the U-Net architecture with the neural network trained on pairs of synthetic seismic data and CO 2 saturation models. Accordingly, our training establishes a mapping relationship between seismic data and CO 2 saturation models and once fully trained directly estimates CO 2 saturation as a function of subsurface location. We further quantify uncertainties of CO 2 saturation estimates using the Monte Carlo dropout method and a bootstrap aggregating method. For this proof-of-concept study, the CO 2 training models and data are derived from the Kimberlina 1.2 model, a hypothetical 3D geological carbon storage model that is constructed based on various geological and hydrological data from the Southern San Joaquin Basin, California. We perform deep-learning inversion experiments using noise-free and noisy training and test data sets and compare the results. Our modelling experiments show that (1) the deep-learning inversion can estimate 2D distributions of CO 2 fairly well even in the presence of Gaussian random noise and (2) both CO 2 saturation imaging and uncertainty quantification can be done in real time. Our results suggest that the deep-learning inversion method can serve as a robust real-time monitoring tool for geological carbon storage and/or other time-varying reservoir/aquifer properties that result from injection, extraction, and/or other subsurface transport phenomena.

58 GEOSCIENCES↗
DOE OSTI2022

Design of quantum optical experiments with logic artificial intelligence

Logic Artificial Intelligence (AI) is a subfield of AI where variables can take two defined arguments, True or False, and are arranged in clauses that follow the rules of formal logic. Several problems that span from physical systems to mathematical conjectures can be encoded into these clauses and solved by checking their satisfiability (SAT). In contrast to machine learning approaches where the results can be approximations or local minima, Logic AI delivers formal and mathematically exact solutions to those problems. In this work, we propose the use of logic AI for the design of optical quantum experiments. We show how to map into a SAT problem the experimental preparation of an arbitrary quantum state and propose a logic-based algorithm, called Klaus, to find an interpretable representation of the photonic setup that generates it. We compare the performance of Klaus with the state-of-the-art algorithm for this purpose based on continuous optimization. We also combine both logic and numeric strategies to find that the use of logic AI significantly improves the resolution of this problem, paving the path to developing more formal-based approaches in the context of quantum physics experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Microstructural Evaluation of Phase Instability in Large Bandgap Metal Halide Perovskites

The optoelectronic performance of organic–inorganic halide perovskite (OIHP)-based devices has been improved in recent years. Particularly, solar cells fabricated using mixed-cations and mixed-halides have outperformed their single-cation and single-halide counterparts. Yet, a systematic evaluation of the microstructural behavior of mixed perovskites is missing despite their known composition-dependent photoinstability. Here, we explore microstructural inhomogeneity in (FAPbI 3 ) x (MAPbBr 3 ) 1– x using advanced scanning probe microscopy techniques. In this work, contact potential difference (CPD) maps measured by Kelvin probe force microscopy show an increased fraction of grains exhibiting a low CPD with flat topography as MAPbBr 3 concentration is increased. The higher portion of low CPD contributes to asymmetric CPD distribution curves. Chemical analysis reveals these grains being rich in MA, Pb, and I. The composition-dependent phase segregation upon illumination, reflected on the emergence of a low-energy peak emission in the original photoluminescence spectra, arises from the formation of such grains with flat topology. Bias-dependent piezo-response force microscopy measurements, in these grains, further confirm vigorous ion migration and cause a hysteretic piezo-response. Our results, therefore, provide insights into the microstructural evaluation of phase segregation and ion migration in OIHPs pointing toward process optimization as a mean to further enhance their optoelectronic performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Magnetic flux imaging in a 3D superconductor integrated circuit

We report on imaging magnetic flux distributions in a multilayered superconductor integrated circuit which emerge during magnetization and after field cooling of the circuit in the DC magnetic field. The obtained complicated field maps expose the flux propagation across the patterned superconducting ground planes sandwiching layers with Josephson junction-based logic cells, fine wire grid around the functional units, and multiple superconducting fill structures located in different inner layers. The observed intricate flux distributions are explained by specific patterns of Meissner screening currents and superconducting critical currents in different mutually interacting parts of the integrated circuit. Our results provide important insights into possible ways of improving the protection of superconductor integrated circuits from magnetic fields and their resilience against flux trapping.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Correlative Surface Imaging Reveals Chemical Signatures for Bacterial Hotspots on Plant Roots

The rhizosphere is arguably the most complex microbial habitat on earth, comprising an integrated network of plant roots, soil and a highly diverse microbial community (the rhizosphere microbiome)1. Understanding, predicting and controlling plant-microbe interactions in the rhizosphere will allow us to harness the plant microbiome as a means to increase or restore plant ecosystem productivity, improve plant responses to a wide range of environmental perturbations, and mitigate effects of climate change by designing ecosystems for long-term soil carbon storage1. To this end, it is imperative to develop new molecular approaches with high spatial resolution to capture interactions at the plant-microbe, microbe-microbe, and plant-plant interfaces. In this work, we designed an imaging sample holder that allows integrated surface imaging tools to map the same locations of a plant root-microbe interface with submicron lateral resolutions, providing novel in vivo analysis of root-microbe interactions. Specifically, confocal fluorescence microscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS), X-ray photoelectron spectroscopy (XPS), and scanning electron microscope (SEM) were used for the first time for correlative imaging of the Brachypodium distachyon root and its interaction with Pseudomonas SW25, a typical plant growth-promoting soil bacterium. Imaging data suggest that the root surface is inhomogeneous and that the interaction between Pseudomonas and Brachypodium roots was confined to only few spots along the sampled root segments and that the bacterial attachment spots were enriched in Na- and S-related and high-mass organic species. We conclude that attachment of the Pseudomonas cells to the root surface is outcompeted by strong root-soil mineral interactions but facilitated by formation of extracellular polymeric substances (EPS).

Plant root, Plant growth-promoting bacteria, soil,↗
DOE OSTI2020

Quantum adiabatic machine learning by zooming into a region of the energy surface

Recent work has shown that quantum annealing for machine learning, referred to as QAML, can perform comparably to state-of-the-art machine learning methods with a specific application to Higgs boson classification. Here, we propose QAML-Z, an algorithm that iteratively zooms in on a region of the energy surface by mapping the problem to a continuous space and sequentially applying quantum annealing to an augmented set of weak classifiers. Results on a programmable quantum annealer show that QAML-Z matches classical deep neural network performance at small training set sizes and reduces the performance margin between QAML and classical deep neural networks by almost 50% at large training set sizes, as measured by area under the receiver operating characteristic curve. The significant improvement of quantum annealing algorithms for machine learning and the use of a discrete quantum algorithm on a continuous optimization problem both opens a class of problems that can be solved by quantum annealers and suggests the approach in performance of near-term quantum machine learning towards classical benchmarks.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Implementation of early psychosis services in Latin America: A scoping review

Abstract Aim The evidence of the effectiveness and cost‐effectiveness of early intervention for psychosis (EIP) services has motivated their implementation worldwide. However, complex interventions of such EIP services require local adaptations to successfully match population needs and cultural differences. Latin America is a heterogenous region where EIP services are progressively being adopted. Our aim is to map such initiatives in the region with a focus on implementation outcomes. Methods A scoping review following the Preferred Reporting Items for Systematic review and Meta‐Analysis extension for Scoping Reviews guidelines was conducted. International and regional databases were searched for publications describing EIP programmes in the region. Besides mapping the services, we described implementation outcomes based on the Standards for Reporting Implementation Studies Checklist. Results Ten articles describing seven EIP initiatives from the region were found. Four countries were represented: Argentina, Brazil, Chile and Mexico. The implementation outcomes reporting was heterogenous, although it was possible to ascertain EIP services are feasible and adequate for the region's context. Also, there is some evidence of effectiveness in terms of reducing hospitalizations and improving symptoms. Information about fidelity measures was scarce and there was no information about costs or cost‐effectiveness. Conclusions Only a small proportion of Latin American countries have adopted EIP services. Although these programmes seem to be feasible and effective, data on other implementation outcomes, such as fidelity, cultural appropriateness, cost‐effectiveness and affordability are not available. This might in part explain why this effective approach has not been yet scaled‐up at nationwide levels.

Aceituno, David↗
DOE OSTI2023

Hawai‘i Play Fairway (Final Report)

Most of Hawai'i's geothermal resources are blind—their manifestations, such as hot springs and steam vents, do not appear on the ground surface because the heated water flows far below. With the exception of $K\bar{i}lauea East Rift Zone$, in most areas of Hawai'i, high lateral permeability in the first kilometer below ground surface prevents surface thermal features from developing. As a methodology for discovering these blind resources, Play Fairway Analysis (PFA) involves finding potential locations of blind hydrothermal systems and describing potential geothermal sources in rift-zone settings. Using the PFA to find Hawai'i's geothermal resources, the University of Hawai'i (UH) conducted the Hawai‘i Play Fairway Project, Hawai'i's first statewide geothermal resource assessment since 1985. Sponsored by the U.S. Department of Energy, the Hawai'i Play Fairway Project provided an updated resource assessment, a roadmap for additional exploration activities, and the identification of areas for further exploration. Benefitting from UH's core competency in earth sciences and experienced geothermal researchers, the project comprised three phases. During the first phase, the team identified, compiled, and ranked existing geologic, groundwater, and geophysical datasets relevant to subsurface heat, fluid and permeability. Using a Bayesian statistical approach, the team developed a statistical methodology to integrate these data into a resource probability map. The team evaluated the confidence in the probability value and considered development viability of areas with geothermal resources. With these analyses, the team identified 10 locations in the Hawaiian Islands for exploration activities. For the second phase, the team collected new groundwater data in 10 locations across the state and new geophysical data on $L\bar{a}na‘i, Maui$, and central Hawai'i Island and modeled topographically induced stress to better characterize subsurface permeability. Analyzing the subsurface stresses, the team evaluated the potential for fracture-induced permeability. The team inverted the MT and gravity data to produce 3D models of resistivity and density, respectively, on $L\bar{a}na‘i$, across $Haleakal\bar{a}'s$ SW rift (Maui), and surrounding Mauna Kea (Hawai‘i Island). The team developed and applied a new method for incorporating depth information about resistivity, density, and potential for fracture-induced permeability into the statistical method for computing resource probability in these three focus areas. The team incorporated the new groundwater results with the new geophysical results and the calculations of potential for fracture-induced permeability to produce updated maps of resource probability and confidence. Through combining data from the first and second phases, the team determined locations for further exploration during the third phase. For MT and gravity surveys, the team recommended $Kaua'i's$ $L\bar{i}hu'e$ $Basin$, the east rift of $Maui's$ $Haleakal\bar{a}$ volcano, and the southwest rift of Hawai'i Island's Mauna Loa volcano. The MT and gravity surveys aimed to enable improved confidence in the resource potential in these locations. For drilling deep groundwater well(s), the team recommended Southeast Mauna Kea and $L\bar{a}na's$ $P\bar{a}l\bar{a}wai$ $Basin$. During the third phase, further exploration involved drilling a groundwater well in $L\bar{a}na's$ $P\bar{a}l\bar{a}wai$ $Basin$ and performing more geophysical surveys. We deepened an existing water well proximal to our target area on $L\bar{a}na'i$ due to funding constraints that precluded us from spudding a new well that would exceed 1km depth. Drilling was preceded by a number of substantial elements including: writing an Environmental Assessment and the subsequent legal process, performance of deviation logging, lowering a camera down the well, coordinating site preparation with $P\bar{u}lama$ $L\bar{a}na'i$, shipping the UH-owned rig interisland, procuring supplies, and leading 3 community meetings on $L\bar{a}na'i$. Drilling occurred 24/7 the entire month of June 2019 over which time $L\bar{a}na'i$ $Well$ 10 was deepened from 427 m to 1057 m, with continuous core collected. We measured a roughly linear temperature gradient averaging 42°C/km and a maximum bottom hole temperature of 66°C. This gradient is more than twice the background for Hawai'i and within a range of gradients measured in this depth range for some exploration wells within KERZ. We consider these results encouraging for $L\bar{a}na'i's$ resource potential and recommend following with a slim hole within $L\bar{a}na'i's$ caldera (our target zone) to ~ 2 km. Further, the positive implications such results have for the island of O‘ahu are substantial - the shield stage of O'ahu's volcanoes ended 1-2 My earlier. However, O'ahu uses more electricity than the rest of the islands combined, and the utility recently called for 500-700MW of firm, dispatchable renewable electricity on O'ahu by 2033. In Phase 3, we also collected limited new encouraging groundwater data, and updated our thoughts on the probabilities of fluid and permeability at resource depths (Pr F = 1; Pr P = mostly unconstrained). Ultimately, we advocate for using our final probability of heat, and confidence in this probability, to drive the next phase of exploration. We contend further development of geothermal in Hawai‘i will enable the state to achieve its 100% renewable policy objective and Hawai'i to transition off of fossil fuels through geothermal discovery and development. The project not only produced a large amount of data and expanded the existing knowledge of Hawai'i's geothermal resources, but also produced publications, theses, presentations, core photos, datasets, media reports, television interviews, community events, and a blog. Students and new professionals benefitted from the project's hands-on research experiences and educational opportunities and earned awards and recognition.

15 GEOTHERMAL ENERGY↗
DOE OSTI2025

ChemComp: Compiling and Computing with Chemical Reaction Networks

The exponential growth in computing demands driven by scientific computing, data analytics, and artificial intelligence is pushing conventional CMOS-based high-performance computing systems to their physical and energy efficiency limits. As we approach the era of post-exascale computing, disruptive approaches are necessary to overcome these barriers and achieve substantial gains in energy efficiency. Analog and hybrid digital-analog computing systems have emerged as promising alternatives, offering the potential for orders-of-magnitude improvements in efficiency. Among these, biochemical computing stands out as a novel paradigm capable of leveraging the natural efficiency of chemical reactions, which have shown promise in solving optimization problems by converging to steady states. By scaling up reaction networks or reaction vessel sizes, biochemical systems present an opportunity to meet the high-performance demands of modern computing tasks. Despite their promise, significant theoretical and practical challenges remain, particularly in formulating and mapping computational problems to chemical reaction networks (CRNs) and designing viable biochemical computing devices. This paper addresses these challenges by introducing new ideas to ChemComp, a compilation and emulation framework for chemical computation. This work describes the mechanisms through which solutions to ordinary differential equations (ODEs) that can be represented as CRN systems can be achieved. Furthermore, we explain the design principles of an ODE dialect implemented as a multi-level intermediate representation (MLIR) compiler extension that will be coupled with existing infrastructure. We demonstrate the potential of our framework through a case study emulating a simplified chemical reservoir computing device. This work establishes foundational tools and methodologies necessary to harness the computational power of chemistry, paving the way for the development of energy-efficient, high-performance computing systems tailored to contemporary and future computational needs.

Bohm Agostini, Nicolas↗
DOE OSTI2021

Digital Twin Model for Advanced Manufacture of a Rotating Detonation Engine Injector

A digital twin material model (DTMM) of an additive manufacturing (AM) process was created to advance the state of the art in rotating detonation engine (RDE) injector design. Current RDE injectors are designed with large pressure drops, enabling a stable and repeatable combustion process. However, this comes at the cost of system efficiency. For the technology to transition to commercial fossil-based power generation, it is important to develop injectors with reduced flow losses. Low-loss injectors are difficult to design and manufacture with conventional manufacturing techniques. AM enables new design options, but the AM manufacturing process must be thoroughly understood to result in a robust design. A DTMM provides the necessary insight by defining the cause-effect relationships between process parameters, microstructure features, and properties. Therefore, a DTMM to support the design and manufacturing process was developed and applied to the design of a new additively manufactured low-loss injector. The injector combustion behavior was characterized through hot-fire tests, and mechanical performance was compared to the DTMM predictions. The two project goals were the successful development of the DTMM and the demonstration of an improved RDE injector design. The RDE injector design and DTMM developments occurred on parallel but dependent paths. The injector was designed to reduce pressure drop by increasing the cross-sectional flow area ratio between the injector air passages and the combustor annulus. This resulted in less structural material, raising the concern that thin members would be susceptible to high-cycle fatigue (HCF) under the periodic loading inherent to an RDE. It was most important for the DTMM to predict behavior in these features; therefore, the injector design concept guided the material thicknesses used in fatigue tests. The DTMM development started by manufacturing a series of coupons over the range of possible AM process variations. A design-of-experiment approach was used to select which process variable combinations gave the most efficient coverage relevant to the injector design space. The microstructure in each of these coupons was characterized, and then computational methods were used to create a numerical model of the correlation between process variables and microstructure. Next, a set of HCF samples were tested to calibrate existing models that map microstructure to HCF performance. Together, these two links formed the DTMM that calculates HCF behavior from AM process variables. Two injector prototypes were additively manufactured. The first injector design strategy aggressively pursued low-loss performance by substantially increasing the oxidizer flow area. The combination of manufacturing lead times and the fatigue testing schedule meant that the DTMM was not available when building this first prototype. Therefore, its process parameters were chosen based on a manual review of the available coupon data. This prototype was built successfully and evaluated in 58 combustion tests. Sustained detonation was achieved with remarkably reduced pressure loss, and some tests even displayed pressure loss characteristics similar to conventional gas turbine combustors. This achieved the project goal of improving RDE injector design. The second injector was manufactured according to the optimized parameters predicted by the DTMM. The flow area modifications of this injector were less aggressive than the first injector since demonstrating low pressure loss was not an objective of the second hot-fire test series. Rather, the test objective was to cause high cycle fatigue failure in the part due to periodic loading from the rotating detonation wave. The observed number of cycles to failure was to be compared to the number predicted by the DTMM and thereby assess the utility of the DTMM in component design. However, the required level of vibration was not obtained during combustion. Therefore, high cycle fatigue was not experienced in the hot-fire tests of the second injector. Fatigue data was obtained by further testing the second injector in a conventional HCF test apparatus. The injector demonstrated HCF strength above the DTMM prediction. In fact, it did not fail and testing was only discontinued due to reaching the end of the period of performance. This points to some success in the project’s primary goal of successfully developing and applying the DTMM to a component design. Implementing the DTMM recommendations for optimal processing parameters led to a part with acceptable properties. The DTMM was also shown to be an efficient correlator of data and to provide insight into the relationship between process settings, microstructure, and property performance. However, the failure of the DTMM prediction to match the experimental result of the injector fatigue test also points to the need to include significantly more data in the model development. In this project, coupons made with identical processing parameters exhibited drastically different properties from each other and from the injector part, which clearly influences the accuracy of a model that predicts performance based on parameters. Uncertainties in the build process must be quantified to develop more robust models. A denser and broader matrix of coupon process and geometry variations, several repeated builds of every point, more in-situ build process measurements, and direct observation of tensile and HCF sample microstructure (as opposed to separate microstructure specimens) are recommendations to improve future AM modeling efforts.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2025

Molecular-resolution imaging of ice crystallized from liquid water by cryogenic liquid-cell TEM

Despite the ubiquity of ice, a molecular-resolution image of nanoscopic defects or microstructures in ice crystallized from liquid water has never been obtained. This is mainly due to the difficulties in preparing and preserving crystalline ice samples that can survive under high-resolution imaging conditions. Here, we report the stabilization and Å-resolution electron imaging of ice Ih crystallized from liquid water by developing cryogenic liquid-cell transmission electron microscopy (CRYOLIC-TEM). We combine lattice mapping with molecular dynamics simulations to reveal that ice formation is highly tolerant to nanoscale defects such as misoriented subdomains and trapped gas bubbles, which are stabilized by molecular-scale structural motifs. Importantly, bubble surfaces adopt low-energy nanofacets and create negligible strain fields in the surrounding crystal. These bubbles can dynamically nucleate, grow, migrate, dissolve, and coalesce under electron irradiation and be monitored in situ near a steady state. This work improves our understanding of water crystallization behaviors at a molecular spatial resolution.

Materials science↗
DOE OSTI2020

Microparticle cloud imaging and tracking for data-driven plasma science

Oceans of image and particle track data encountered in plasma interactions with microparticle clouds motivate development and applications of machine-learning (ML) algorithms. A local-constant-velocity tracker, a Kohonen neural network or self-organizing map, the feature tracking kit, and U-Net are described and compared with each other for microparticle cloud datasets generated from exploding wires, dusty plasmas, and atmospheric plasmas. Particle density and the signal-to-noise ratio have been identified as two important factors that affect the tracking accuracy. Fast Fourier transform is used to reveal how U-Net, a deep convolutional neural network developed for non-plasma applications, achieves the improvements for noisy scenes. Viscous effects are revealed in the ballistic motions of the particles from the exploding wires and atmospheric plasmas. Subdiffusion of microparticles satisfying Δr 2 ∝t k (k=0.84±0.02) is obtained from the dusty plasma datasets. Microparticle cloud imaging and tracking, when enhanced with data and ML models, present new possibilities for plasma physics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Model-based Reconstruction for Single Particle Cryo-Electron Microscopy

Single particle cryo-electron microscopy is a vital tool for 3D characterization of protein structures. A typical workflow involves acquiring projection images of a collection of randomly oriented particles, picking and classifying individual particle projections by orientation, and finally using the individual particle projections to reconstruct a 3D map of the electron density profile. The reconstruction is challenging because of the low signal-to-noise ratio of the data, the unknown orientation of the particles, and the sparsity of data especially when dealing with flexible proteins where there may not be sufficient data corresponding to each class to obtain an accurate reconstruction using standard algorithms. In this paper we present a model-based image reconstruction technique that uses a regularized cost function to reconstruct the 3D density map by assuming known orientations for the particles. Our method casts the reconstruction as minimizing a cost function involving a novel forward model term that accounts for the contrast transfer function of the microscope, the orientation of the particles and the center of rotation offsets. We combine the forward model term with a regularizer that enforces desirable properties in the volume to be reconstructed. Using simulated data, we demonstrate how our method can significantly improve upon the typically used approach.

Venkatakrishnan, Singanallur↗
DOE OSTI2022

Spatial Study 2021: Sensor-Based Time Series of Surface Water Temperature, Specific Conductance, Total Dissolved Solids, pH, and Dissolved Oxygen from across Multiple Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of spatial variability in sediment respiration rates in the Yakima River Basin. The dataset provides two-hour time series hydrological and water chemistry sensor data, manual chamber open channel respiration data, handheld sensor water chemistry data, river substrate grain size photos, general environmental context photos, and field metadata (including qualitative information on instream and river corridor characteristics) collected during the same two-week period at 47 sites within multiple rivers throughout the Yakima River Basin in Washington, USA. Grain size photos can be used to improve estimates of channel substrate D50 data. Related sample-based water chemistry data are published separately at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1898914.This dataset is comprised of four main folders, one containing three sensor-specific subfolders and the others containing photographs. The SFA_SpatialStudy_2021_SensorData main data folder includes file-level metadata (FLMD), data dictionary (dd), installation methods, field metadata, Ultrameter water chemistry data, field data collection protocols, international generic sample number (IGSN) mapping file, and a readme file. The “Sensor_Manual_Specifications” subfolder contains pdf files from the manufacturer of each sensor with details on the sensor specifications. Each sensor subfolder (BarotrollAtm, MantaRiver, and MinidotManualChamber) contains a sensor data subfolder for timeseries data and a subfolder for plots and summary statistics. The BarotrollAtm Data subfolder contains In Situ Rugged BaroTROLL pressure and temperature data. The MantaRiver Data subfolder contains Eureka Manta+ 35B multisonde temperature, specific conductance, and pH data. The MinidotManualChamber Data subfolder contains PME MiniDOT Logger dissolved oxygen (mg/L and percent saturation) and temperature data. The folder SFA_SpatialStudy_2021_EnvironmentalContextPhotos contains environmental context photographs and videos. The folders SFA_SpatialStudy_2021_SedimentQuadratPhotos_Part1 and SFA_SpatialStudy_2021_SedimentQuadratPhotos_Part2 contain sediment quadrat photographs. All files are .csv, .pdf, .R, .jpg, .jpeg, .mp4, or .mov. This data package was originally published September 2022. It was updated January 2023 (modified files) and June 2024 (new and modified files). See the change history in data package readme for more details.We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge

Elucidating protein–ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein–ligand interaction is traditionally tackled by molecular docking and simulation, which is based on physical forces and statistical potentials and cannot effectively leverage cryo-EM data and existing protein structural information in the protein–ligand modeling process. In this work, we developed a deep learning bioinformatics pipeline (DeepProLigand) to predict protein–ligand interactions from cryo-EM density maps of proteins and ligands. DeepProLigand first uses a deep learning method to predict the structure of proteins from cryo-EM maps, which is averaged with a reference (template) structure of the proteins to produce a combined structure to add ligands. The ligands are then identified and added into the structure to generate a protein–ligand complex structure, which is further refined. The method based on the deep learning prediction and template-based modeling was blindly tested in the 2021 EMDataResource Ligand Challenge and was ranked first in fitting ligands to cryo-EM density maps. These results demonstrate that the deep learning bioinformatics approach is a promising direction for modeling protein–ligand interactions on cryo-EM data using prior structural information.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Machine Learning Approaches to Predicting Induced Seismicity and Imaging Geothermal Reservoir Properties

This project developed machine learning (ML) methods, lab data sets, and field data to advance geothermal exploration and geothermal energy production. The work had three focus areas. One involved the development of ML methods to use microearthquakes (MEQs) for imaging geothermal reservoir properties and improving subsurface characterization – most importantly the evolution of permeability within the evolving reservoir. This part of the work included development of ML approaches for automated MEQ location, focal mechanism determination and identification of earthquake precursors. The second area focused on using MEQ signals generated by geothermal exploration and production to predict the relationship between fluid injection and seismicity. Here, we extended to reservoir scale our success in using ML to predict laboratory earthquakes and fault zone stress state. The third focus area was on lab experiments. Here, we developed new ML models for lab earthquake prediction and identification of precursors to failure to improve earthquake forecasting and early warning in geothermal settings. Major outcomes of our work include ML models that learn from MEQ signals during geothermal exploration and production to predict induced seismicity. MEQs occur naturally in connection with drilling and energy production. We developed ML methods to use the seismic waves from these events to characterize the elastic, hydraulic and poromechanical properties of reservoirs. Our work illuminated fracture geometry and the evolution of fracture permeability by incorporating seismic coda wave analysis and ML methods to relate fluid injection and seismicity. We significantly expanded laboratory earthquake prediction to include methods that use both passive measurements of microearthquakes within the lab fault zones and also active source acoustic measurements of fault zone elastic properties. These methods can now predict fault zone stress state, time to failure and the magnitude of lab earthquakes. Our work showed that repetitive stick- slip failure events during frictional sliding (the lab equivalent of earthquakes) are preceded by a cascade of micro-failure events that radiate energy in a manner that foretells unstable failure – manifest as laboratory MEQs. We documented a mapping between fracture properties and statistical attributes of elastic radiation. We extended existing works to geothermal reservoir scale and developed ML methods to determine reservoir permeability, fracture properties, and their evolution during geothermal energy production. An attractive feature of ML algorithms is their ability to handle big datasets and reveal patterns and correlations that may remain invisible to conventional analyses. Our work connected data from field, laboratory and intermediate scales to study permeability, stress, strength, fracture stiffness and geometry. At the field scale we used data from the Newberry Volcano field site, UtahFORGE, EGS Collab, and also the Bedretto underground research lab in Switzerland. These data sets are bridging the gap between the lab scale, theory, and reservoir scale. Our work produced plain language summaries to improve public understanding of DOE research. We also developed openly distributed ML and seismicity datasets for use by all researchers and we published connections between induced seismicity in geothermal areas and reservoir properties including permeability, fracture properties, and stress state. Our models are designed for the large data sets of induced seismicity typically associated with geothermal sites. We produced labeled event catalogs and used them on geothermal data to assess how ML can facilitate geothermal production and exploration. All datasets are available on the GDR Productivity: The project produced 32 publications in peer reviewed journals (two are in review). It supported the work of 6 PhD students, 40 conference presentations, 6 keynote talks at national meetings, and mentoring and professional development for 4 postdoctoral fellows.

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