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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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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

X-ray linear dichroic tomography of crystallographic and topological defects

Abstract The functionality of materials is determined by their composition 1–4 and microstructure, that is, the distribution and orientation of crystalline grains, grain boundaries and the defects within them 5,6 . Until now, characterization techniques that map the distribution of grains, their orientation and the presence of defects have been limited to surface investigations, to spatial resolutions of a few hundred nanometres or to systems of thickness around 100 nm, thus requiring destructive sample preparation for measurements and preventing the study of system-representative volumes or the investigation of materials under operational conditions 7–15 . Here we present X-ray linear dichroic orientation tomography (XL-DOT), a quantitative, non-invasive technique that allows for an intragranular and intergranular characterization of extended polycrystalline and non-crystalline 16 materials in three dimensions. We present the detailed characterization of a polycrystalline sample of vanadium pentoxide (V 2 O 5 ), a key catalyst in the production of sulfuric acid 17 . We determine the nanoscale composition, microstructure and crystal orientation throughout the polycrystalline sample with 73 nm spatial resolution. We identify and characterize grains, as well as twist, tilt and twin grain boundaries. We further observe the creation and annihilation of topological defects promoted by the presence of volume crystallographic defects. The non-destructive and spectroscopic nature of our method opens the door to operando combined chemical and microstructural investigations 11,18 of functional materials, including energy, mechanical and quantum materials.

Science & Technology - Other Topics↗
DOE OSTI2020

Improving Elemental Ratio Measurements on Uranyl Fluoride with NanoSIMS

Measurements on samples of calcined uranyl fluoride (UO 2 F 2 ) using Raman spectroscopy, electron microscopy with elemental analysis, and secondary ion mass spectrometry (SIMS) indicate four facts. First, UO 2 F 2 undergoes a previously unreported oxidation reaction beginning around 350 °C in air. The resulting oxidation compound is likely similar to U 3 O 8 /UO 3 , but presently represents a novel chemical species. Second, variations in F/U ratio across samples as measured by electron microscopy with x-ray spectroscopy correlate with variations in F/U ratio as measured with the NanoSIMS 50L instrument. Third, simple mixed powders of LaF 3 +U 3 O 8 are not sufficiently homogeneous to act as a high F+U content standard material. Fourth, additional method development for determining the bulk F/U ratio using an alternative technique is necessary to further develop analytical standards.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Human Performance Analysis Depending on Operator Expertise (Student vs. Operator) and Simulator Complexity (Rancor Microworld vs. Compact Nuclear Simulator)

Human reliability analysis (HRA) evaluates human errors and provides human error probabilities (HEPs) for application in probabilistic safety assessment (PSA), which is a comprehensive safety assessment method for nuclear power plants (NPPs). Generally, HRA methods estimate HEPs based on human reliability data collected from actual historical measurement, simulator experiments, or expert judgement. Most recent HRA data collection studies focus on collecting data via full-scope main control room (MCR) simulators with actual licensed reactor operators. Contrary to this, Idaho National Laboratory (INL) has adopted a different approach, which attempts to collect HRA data based on experiment using simplified simulators and student participants by following the Simplified Human Error Experimental Program (SHEEP). This approach has a couple of advantages compared to full-scope data collection. Representatively, it has relatively low entry point for collecting HRA data, and secures large sample sizes with reasonable cost and labor. In the previous studies, we developed the SHEEP framework, then verified whether the data collected through the framework could support a representative full-scope data collection study, i.e., the Human Reliability Data Extraction (HuREX) study. Also, we analyzed human performance measurements depending on participant type (i.e., student vs. operator). In this paper, we analyze human performance data collected from an experiment comparing operator expertise and simulator complexity when using the more simplified simulator developed by INL, i.e., Rancor Microworld and the less simplified simulator, i.e., Compact Nuclear Simulator (CNS) developed by Korea Atomic Energy Research Institute (KAERI). Analysis of variance (ANOVA) tests and correlation analysis are used for analyzing the experimental data.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Discrete generative diffusion models without stochastic differential equations: A tensor network approach

Diffusion models (DMs) are a class of generative machine learning methods that sample a target distribution by transforming samples of a trivial (often Gaussian) distribution using a learned stochastic differential equation. In standard DMs, this is done by learning a “score function” that reverses the effect of adding diffusive noise to the distribution of interest. Here we consider the generalisation of DMs to lattice systems with discrete degrees of freedom, and where noise is added via Markov chain jump dynamics. We show how to use tensor networks (TNs) to efficiently define and sample such “discrete diffusion models” (DDMs) without explicitly having to solve a stochastic differential equation. We show the following: (i) by parametrising the data and evolution operators as TNs, the denoising dynamics can be represented exactly; (ii) the auto-regressive nature of TNs allows to generate samples efficiently and without bias; (iii) for sampling Boltzmann-like distributions, TNs allow to construct an efficient learning scheme that integrates well with Monte Carlo. We illustrate this approach to study the equilibrium of two models with non-trivial thermodynamics, the d = 1 constrained Fredkin chain and the d = 2 Ising model. Published by the American Physical Society 2025

Causer, Luke (ORCID:0000000194243473)↗
DOE OSTI2025

Viewing is understanding: Graphite microstructure effects on infiltrated molten salt distribution revealed by 3D neutron tomography

Molten salt infiltration in the pore network of nuclear graphite may cause unwanted changes to graphite's local structure and mechanical and thermal properties. A detailed and comprehensive understanding of molten salt intrusion (distribution across sample cross section and penetration depth) is needed to assess its effects. Here, in this work, we report on an improved methodology for the use of neutron imaging (computed tomography) to evaluate salt penetration and distribution of a wide range of graphite grades with diverse microstructures. Neutron tomography data were acquired on the same graphite sample before and after salt intrusion; the 3D reconstructed volumes were digitally co-registered and subtracted. The difference in neutron attenuation coefficient represents direct visualization of FLiNaK (LiF–NaF–KF) salt distribution in the salt-impregnated graphite samples. This improved methodology was applied to investigate the effect of exposure times (12 h and 336 h) and of graphite microstructure when exposed to FLiNaK at 750 °C and 3 bar (gauge) pressure, starting from flowing argon at near atmospheric pressure. The results show that medium-grained and fine-grained graphites evolve to equilibrium at significantly different rates: fast salt uptake in medium-grained graphites produces salt deposits throughout the volume of graphite specimens, whereas salt infiltration in fine-grained graphites is much slower and limited to exposed surfaces.

FLiNaK infiltration↗
DOE OSTI2024

Creating Accurate Methane Emission Inventories through Data-Driven Airborne Survey Strategies: Methods and Results from the Haynesville, Anadarko, and Permian Basins

Significantly reducing methane emissions from the oil and gas sector can decrease the rate of climate change over the next two decades, buying critical time for a global energy transition. However, emissions inventories that can be used by oil and gas operators and environmental regulators to identify optimal methane emission mitigation strategies are either based on conservative emission factor methods, or are inconsistent between studies due to differences in sampling strategies or survey technologies. We developed a new approach for methane emissions survey design that yields representative basinwide methane emissions inventories by surveying a subset of total assets in a given oil and gas basin. We identify several sampling and analysis principles, including large sample sizes, balanced sampling across oil and gas production, careful survey area definition, and a unified protocol for analysis, to be vital to producing an unbiased estimate of basin-scale emissions that can be reconciled with future studies. We further present results from deploying this strategy in two oil and gas producing regions in the United States: the Haynesville Basin in Texas and Louisiana, and the Woodford Shale in the Anadarko Basin in Oklahoma. Aerial surveys were performed in 2023 using the Insight M LeakSurveyor™ technology. Preliminary results from methane emissions detected by Insight M indicate that aerially detected emissions above roughly 30 kg(CH4)/hr by themselves contribute a fractional loss rate of 1.13% of gross gas production across oil and gas operations in the Haynesville Basin, with aerially detected emissions equivalent to 2.67% of gross gas production in the Woodford Shale. We supplement these aerial estimates with modeled emissions that are below the LeakSurveyor’s survey sensitivity using a recently published inventory-based model of methane emissions, which we update for our survey areas. We then combine our aerial detections with modeled emissions to yield methane emission distributions and inventories that incorporate the full range of potential methane emissions from the smallest to the largest. These results can be used to identify the most effective methane mitigation strategies for our study areas, and can be reconciled with future methane emissions surveys that use different technologies.

Sherwin, Evan (ORCID:0000000321804297)↗
DOE OSTI2022

Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily

Abstract Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Characterization and differentiation of aluminum powders used in improvised explosive devices. Part 2: Micromorphometric method refinement and preliminary statistical analysis

Abstract Aluminum (Al) powder is commonly encountered in improvised explosive devices (IEDs) as a metallic fuel due to its availability and low cost. Although available commercially in powder form, amateur bomb‐makers also produce their own Al powder via simple methods found online. In order to provide investigative leads and forensic intelligence, it is important to evaluate not only the composition of homemade devices, but also to distinguish between the various forms of Al powder they contain. To achieve this goal, a method using automated microscopy in combination with statistical techniques has been demonstrated to have the potential to provide source discrimination and investigative leads in source attribution of Al powders in IEDs. The present research refined this method and investigated 59 industrially and amateurly produced Al powder sources with seven subsamples per source using two traditional linear discriminant analyses (LDA), one with a standard data split for training and testing, and another using leave‐one‐out cross‐validation. Averaging the classification accuracies for the two LDA‐based analyses, LDA has the ability to correctly classify 59.26%, 83.35%, and 80.69% of the samples based on their powder source, type, and production method, respectively. This classification accuracy represents a 3407%, 317%, and 61.38% increase in accuracy from random class assignment, respectively. Further, in most instances of incorrect data attribution to a particular source, the subsample has been misidentified with another sample of the same powder type or production method.

Ommen, Danica M.↗
DOE OSTI2020

Microstructure Experiments-Enabled MARMOT Simulations of SiC/SiC-based Accident Tolerant Nuclear Fuel System

We have undertaken an experimental-computational project that addresses a few key technology gaps associated with the use of SiC/SiC composites for light water reactor fuel cladding. Two principal endeavors in this project are to assess the irradiation-induced microstructural changes and swelling in SiC/SiC composites, and to characterize and model the porous oxide surface layer (when exposed to steam) along SiC recession that is detrimental to the clad integrity under accident conditions. The project tasks are: (i) ion irradiation and characterization (University of Tennessee, Knoxville), (ii) mechanical tests and analysis (University of South Carolina), (iii) steam exposure tests (Oak Ridge National Laboratory), (iv) electron microscopy and spectroscopic characterization (NC State University), (v) x-ray microscopy and reconstruction (University of South Carolina and NC State University), (vi) phase field modeling and simulations (NC State University and Idaho National Laboratory). The effects of 10 MeV Au ion irradiation at 350°C on the microstructure evolution in SiC/SiC composites are investigated at doses up to 400 displacements per atom (dpa) at the University of Tennessee, Knoxville. Atomic force microscopy and optical profilometry reveal irradiation induced axial and radial shrinkage of the fibers for doses greater than 10 dpa. Based on detailed electron microscopy characterization, the primary cause of the fiber shrinkage is attributed to irradiation-induced loss of carbon packets. Additionally, the multilayer PyC interface is observed to portray high resistance to irradiation damage. The mechanical response and failure mechanisms of un-irradiated samples is also assessed through loading tests and X-ray imaging at the University of South Carolina. Steam exposure tests are performed at the Oak Ridge National Laboratory in a facility that represents a reactor pressure vessel under a loss-of-coolant-accident scenario. The samples that are analyzed methodically in this report are tested for 32/31 hours at 1200°C with a velocity of 0.25 cm/s for the pressures: 0.1 MPa, 0.45 MPa, 0.92 MPa and 1.38 MPa. Scanning/transmission electron microscopy analysis conducted at the NC State University (NCSU) shows that the oxide layer thickness increases with the steam pressure. While the oxide layer is crystalline (α- cristobalite) for the pressures 0.45 MPa, 0.92 MPa and 1.38 MPa, the layer is amorphous at 0.1 MPa. Results from Raman spectroscopy have also confirmed the formation of α-cristobalite phase of SiO₂. The abrupt increase in the integrated Raman intensity ratio between steam pressures 0.1 and 0.45 MPa suggests the onset of accelerated crystallization. Non-destructive three dimensional X-ray microscopy/tomography (XCT) and computational image processing techniques are employed by the University of South Carolina to probe the porous oxidation features on SiC samples at varying pressures. Interestingly, most pores are observed to be located away from the surface as well as the oxide-SiC interface. The average oxide layer thickness assessed from the XCT analysis is seen to be in excellent agreement with the values determined through scanning electron microscopy analysis for the highest pressures where the oxide layer is relatively more uniform. A phase-field model developed by the NC State University and Idaho National Laboratory for simulating oxidation of SiC by steam captures the paralinear kinetics of SiC oxidation with a high degree of fidelity. Results from quasi-one-dimensional and two dimensional simulations show that the pores with oxidizing species lead to a higher volatilization rate. These simulations indicate that the enhanced apparent volatilization rates at higher pressures observed in experiments can be rationalized by the increased volatilization from the pores. The project team has also successfully developed the capability to import images from experiments for realistic evolution of the oxidizing microstructure.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

A Bayesian Approach for Estimating Uncertainty in Stochastic Economic Dispatch considering Wind Power Penetration

The increasing penetration of renewable energy resources in power systems, represented as random processes, converts the traditional deterministic economic dispatch problem into a stochastic one. To estimate the uncertainty in this stochastic economic dispatch problem for forecasting purposes, the conventional Monte-Carlo method is prohibitively time-consuming for practical applications. To overcome this problem, here we propose a novel Gaussian-process-emulator-based approach to quantify the uncertainty in the stochastic economic dispatch considering wind power penetration. Facing high-dimensional real-world data representing the correlated uncertainties from wind generation, a manifold-learning-based Isomap algorithm is proposed to efficiently represent the low-dimensional hidden probabilistic structure of the data. In this low-dimensional latent space, with Latin hypercube sampling as the computer experimental design, a Gaussian-process emulator is used, for the first time, to serve as a nonparametric, surrogate model for the original complicated stochastic economic dispatch model. This reduced-order representative allows us to evaluate the economic dispatch solver at sampled values with a negligible computational cost while maintaining a desirable accuracy. Simulation results conducted on the IEEE 118-bus test system reveal the impressive performance of the proposed method.

17 WIND ENERGY↗
DOE OSTI2020

Investigating the Chemical Reactivity of Lithium Silicate Model SEI Layers

Silicon anodes suffer from an unstable solid electrolyte interphase (SEI) layer that contributes to undesirable capacity fade with cycling. A key part to addressing this unstable SEI formation is to examine how certain components of the SEI react with the electrolyte over time. One SEI component that has not been thoroughly studied in the context of the chemical reactivity against the electrolyte is lithiated silicate. Four model silicate thin films with increasing lithium content were deposited by radio frequency (RF) magnetron sputtering to study how the lithiation of the native oxide on a silicon anode affects the chemical stability of the anode surface. SiO2, Li2Si2O5, Li2SiO3, and Li3SiOx films were exposed to 1.2 M LiPF6 in the 3:7 wt% ethylene carbonate/ethyl methyl carbonate (EC/EMC) electrolyte for periods of time that are representative of the amount of time it takes to undergo cell formations. Soaked samples were rinsed, dried, and characterized by a combination of attenuated total reflectance-infrared spectroscopy (ATR-IR), focused ion beam-secondary electron microscopy (FIB-SEM), and X-ray photoelectron spectroscopy (XPS) depth profiling. It was found that the rate of the decrease in film thickness of the silicates exposed to the electrolyte over time increases as a function of the lithium content in the thin film. This reaction involves HF etching and LiPF6 salt degradation leading to silicate loss and fluorination throughout the bulk. Understanding this chemical instability is critical to determining the overall mechanism of SEI degradation over time.

ADVANCED PROPULSION SYSTEMS,ENERGY STORAGE↗
DOE OSTI2024

Nondestructive geochemical characterization of fossil hominin taphonomy and burial history

To date, only three Homo habilis specimens have been discovered that have associated craniodental and postcranial elements, providing a limited fossil record of the ontogeny and morphology of early members of the genus Homo. Recently, a nearly complete dentition, likely attributable to H. habilis, was discovered and excavated from early Pleistocene-age fluvial-lacustrine sediments of the upper Burgi Member of the Koobi Fora Formation at site F25787 in Area 13, near Ileret, Kenya. On the surface less than 15 m away, at site F25966, postcranial elements were found, which, if from the same individual as the nearby dentition, would represent the fourth associated craniodental and postcranial assemblage of this species. We developed a geochemical taphonomic history of these ca. 2 Ma hominin fossils using nondestructive X-ray based microanalytical tools (synchrotron and benchtop X-ray fluorescence chemical imaging and micro- and nano-computed tomography volumetric reconstruction), bulk analyses of sediments and paleosols at the excavation sites, and sedimentologic and stratigraphic observations. We integrate the chemical and physical taphonomic histories to test whether teeth (excavated in situ) and postcranial bones (eroded onto the outcrop surface) derive from a single individual. Minor differences in taphonomic history are attributable to the different biomineral properties of the dental and osseous components and to differences in physical damage during early post-mortem scavenging, dispersal, and burial in adjacent depositional settings. Microscale geochemical mapping enabled the temporal ordination of chemical and physical events in the specimens’ chemical taphonomic histories. Specifically, authigenic Fe- and K-bearing clays and Y, U, and Sr uptake occurred in post-burial fractures in bones and were also incorporated pervasively throughout dentin in teeth. Barite mineralization occurred along the latest fractures in both materials, and as a coating on tooth roots. The stratigraphic, taphonomic, and geochemical evidence supports the interpretation that the hominin fossils represent a single individual. Finally, successful application of these nondestructive sample characterization methods demonstrates capabilities for thorough interrogation of the taphonomic histories of other potential hominin fossil associations, enabling more robust and accurate palaeontologic constraints using those relationships.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Membrane-Confined Iron Oxychloride Nanocatalysts for Highly Efficient Heterogeneous Fenton Water Treatment

Heterogeneous advanced oxidation processes (AOPs) allow for the destruction of aqueous organic pollutants via oxidation by hydroxyl radicals ( • OH). However, practical treatment scenarios suffer from the low availability of short-lived • OH in aqueous bulk, due to both mass transfer limitations and quenching by water constituents, such as natural organic matter (NOM). In this work, we overcome these challenges by loading iron oxychloride catalysts within the pores of a ceramic ultrafiltration membrane, resulting in an internal heterogeneous Fenton reaction that can degrade organics in complex water matrices with pH up to 6.2. With • OH confined inside the nanopores (~ 20 nm), this membrane reactor completely removed various organic pollutants with water fluxes of up to 100 L m –2 h –1 (equivalent to a retention time of 10 s). This membrane, with a pore size that excludes NOM (>300 kDa), selectively exposed smaller organics to •OH within the pores under confinement and showed excellent resiliency to representative water matrices (simulated surface water and sand filtration effluent samples). Moreover, the membrane exhibited sustained AOPs (>24 h) and could be regenerated for multiple cycles. Our results suggest the feasibility of exploiting ultrafiltration membrane-based AOP platforms for organic pollutant degradation in complex water scenarios.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Coupling flux balance analysis with reactive transport modeling through machine learning for rapid and stable simulation of microbial metabolic switching

Integrating genome-scale metabolic networks with reactive transport models (RTMs) provides a detailed description of the dynamic changes in microbial growth and metabolism. Despite promising demonstrations in the past, computational inefficiency has been pointed out as a critical issue to overcome because it requires repeated application of linear programming (LP) to obtain flux balance analysis (FBA) solutions in every time step and spatial grid. To address this challenge, we propose a new simulation method where we train and validate artificial neural networks (ANNs) using randomly sampled FBA solutions and incorporate the resulting surrogate FBA model (represented as algebraic equations) into RTMs as source/sink terms. We demonstrate the efficiency of our method via a case study of Shewanella oneidensis MR-1. During aerobic growth on lactate, S. oneidensis produces metabolic byproducts (such as pyruvate and acetate), which are subsequently consumed as alternative carbon sources when the preferred nutrients are depleted. To effectively simulate these complex dynamics, we used a cybernetic approach that models metabolic switches as the outcome of dynamic competition among multiple growth options. In both zero-dimensional batch and one-dimensional column configurations, the ANN-based surrogate models achieved substantial reduction of computational time by several orders of magnitude compared to the original LP-based FBA models. Moreover, the ANN models produced robust solutions without any special measures to prevent numerical instability. These developments significantly promote our ability to utilize genome-scale networks in complex, multi-physics, and multi-dimensional ecosystem modeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Isotope effects on the structural transformation and relaxation of deeply supercooled water

Herein, we have examined the structure of supercooled liquid D 2 O as a function of temperature between 185 and 255 K using pulsed laser heating to rapidly heat and cool the sample on a nanosecond timescale. The liquid structure can be represented as a linear combination of two structural motifs, with a transition between them described by a logistic function centered at 218 K with a width of 10 K. The relaxation to a metastable state, which occurred prior to crystallization, exhibited nonexponential kinetics with a rate that was dependent on the initial structural configuration. When the temperature is scaled by the temperature of maximum density, which is an isostructural point of the isotopologues, the structural transition and the non-equilibrium relaxation kinetics of D 2 O agree remarkably well with those for H 2 O.

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

Spatiotemporal Learning in Power Modules: Wavelet-Enhanced Forecasting of Thermomechanical Degradation

Detecting internal defects in power electronics packages is critical for their performance and reliability, especially under extreme operating conditions, as these defects can lead to catastrophic failure if not properly addressed. Confocal scanning acoustic microscopy (C-SAM) plays a key role in the nondestructive evaluation of bond layer degradation within a power electronics package by detecting defects such as delamination, voids, and cracks. However, accurately quantifying and predicting these defects from C-SAM images remains a significant challenge due to the low noise-to-signal ratio, which typically arises from both imaging process and bond patterns itself. In this paper, we explore machine learning strategies for processing C-SAM images and providing predictive models of defect growth. We use C-SAM images of sintered copper and sintered silver samples, which are obtained under accelerated thermal experiments, as the representative dataset for our study. We investigate the effect of Fourier transforms and wavelet transforms on these datasets to remove high-frequency noise and address noise across multiple scales with histogram equalization to enhance the contrast and improve the visibility of defects. As a result, defect boundaries can be clearly distinguished, enabling more accurate tracking of their growth over time. We then employ different time-series forecasting algorithms on the denoised images to formulate an image-based lifetime prediction model. Statistical models and deep-learning techniques are trained on images obtained in the early stages of thermal shock, and defect growth in the later stages is predicted. Our work serves as a preliminary attempt to improve the accuracy of lifetime prediction models of power electronics packages, which is critical under extreme operating environments.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers

Chronic infection with hepatitis B virus (HBV) is caused by the persistence of closed circular DNA (cccDNA) in the nucleus of infected hepatocytes. Despite available therapeutic anti-HBV agents, eliminating the cccDNA remains challenging. Thus, quantifying and understanding the dynamics of cccDNA are essential for developing effective treatment strategies and new drugs. However, such study requires repeated liver biopsy to measure the intrahepatic cccDNA, which is basically not accepted because liver biopsy is potentially morbid and not common during hepatitis B treatment. We here aimed to develop a noninvasive method for quantifying cccDNA in the liver using surrogate markers in peripheral blood. We constructed a multiscale mathematical model that explicitly incorporates both intracellular and intercellular HBV infection processes. The model, based on age-structured partial differential equations, integrates experimental data from in vitro and in vivo investigations. By applying this model, we roughly predicted the amount and dynamics of intrahepatic cccDNA within a certain range using specific viral markers in serum samples, including HBV DNA, HBsAg, HBeAg, and HBcrAg. Our study represents a significant step towards advancing the understanding of chronic HBV infection. The noninvasive quantification of cccDNA using our proposed method holds promise for improving clinical analyses and treatment strategies. By comprehensively describing the interactions of all components involved in HBV infection, our multiscale mathematical model provides a valuable framework for further research and the development of targeted interventions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics

Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter , particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.

59 BASIC BIOLOGICAL SCIENCES↗