Results for “shear layer” — Page 24

DOE OSTI2023

Triaxial Shear Tests on Simulated Sierra White Fault Gouge & Borehole Simulation in Sierra White Gouge

Laboratory shear tests were conducted on pulverized Sierra White granite (SWG) to investigate slip mechanisms in naturally occurring faults. Synthetic fault geometries were constructed by sandwiching fine grained SWG powder in between steel forcing blocks. For dry experiments, ~3.5 g of SWG powder was poured onto the face of the lower steel forcing block and leveled. For saturated experiments, enough fluid was added to the ~3.5 g of Sierra White granite powder to form a slurry. This slurry was applied to the lower forcing block and leveled. Inclined forcing blocks with 25.4 mm diameter and 35° faces, which were machined from ground steel rods with fine teeth on the faces, help to hold the gouge in place and prevent delamination at the interface. The top forcing block had a 2.03 mm centered hole to allow pore fluid access to the gouge. A fine steel mesh prevented back flow of the gouge into pore fluid lines. Samples were isolated from the confining medium using three layers of heat shrink polyolefin, as shown in Figure 1. The outer layer was shrunk over the o-rings on the end caps to form an impermeable seal, which was reinforced with steel tie wires on both sides of the o-rings. Hardened steel spacers and copper shim stock was placed between the steel forcing blocks and the end caps to preserve the parallelism of the Hastelloy wetted parts. For dry samples, the end caps were plugged, while the end caps for the saturated samples were connected to pore lines.

58 GEOSCIENCES↗

DOE OSTI2023

A reduced-model (nSOLT) simulation of neutral recycling effects on plasma turbulence in the divertor region of MAST-U

The 2D scrape-off-layer turbulence code (nSOLT), which includes 1D kinetic neutral–plasma interactions, is applied to study effects of neutral recycling on plasma turbulence for parameters illustrative of the MAST-U divertor region. Neutral recycling is modeled by injecting a fraction of the parallel plasma flux to the divertor back into the simulation domain as a source of Franck–Condon-distributed neutrals. Stationary sources, concentrated at the magnetic separatrix, model plasma streaming into the divertor region from the upstream scrape-off-layer and sustain plasma turbulence absent neutral recycling. Starting from one such no-neutrals equilibrium, we initiate recycling in a numerical experiment designed to diagnose and identify the effects of various neutral–plasma interactions on the divertor plasma, divertor turbulence, and plasma exhaust. The onset of recycling triggers an initial burst of enhanced cross field plasma transport that is quelled by ionization cooling and charge–exchange (CX) friction, with growing neutral pressure, leading to a quiescent, turbulence-free state. Diagnosis of this transient burst reveals that (1) the sudden increase in plasma density due to ionization dominates the onset of the burst, (2) electron cooling due to ionization increases collisionality and disconnects blob filaments from the sheath, and (3) CX friction drives tripole polarization of a blob that can dominate the curvature-driven dipole polarization, leading to the stagnation of blob propagation and reduced radial turbulent transport. It is shown that CX friction is negligible compared to sheath physics in determining equilibrium mean flow shearing rates, for parameters considered herein (specifically a short connection length to the divertor target), while it can significantly reduce interchange-instability growth rates.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Large-Eddy Simulation of Flow Over Boeing Gaussian Bump Using Multiagent Reinforcement Learning Wall Model: Preprint

We develop a wall model for large-eddy simulation (LES) that takes into account various pressure-gradient effects using multi-agent reinforcement learning. The model is trained using low-Reynolds-number flow over periodic hills with agents distributed on the wall at various computational grid points. It utilizes a wall eddy-viscosity formulation as the boundary condition to apply the modeled wall shear stress. Each agent receives states based on local instantaneous flow quantities at an off-wall location, computes a reward based on the estimated wall-shear stress, and provides an action to update the wall eddy viscosity at each time step. The trained wall model is validated in wall-modeled LES of flow over periodic hills at higher Reynolds numbers, and the results show the effectiveness of the model on flow with pressure gradients. The analysis of the trained model indicates that the model is capable of distinguishing between the various pressure gradient regimes present in the flow. To further assess the robustness of the developed wall model, simulations of flow over the Boeing Gaussian bump are conducted at a Reynolds number of 2 x 10^6, based on the free-stream velocity and the bump width. The results of mean skin friction and pressure on the bump surface, as well as the velocity statistics of the flow field, are compared to those obtained from equilibrium wall model (EQWM) simulations and published experimental data sets. The developed wall model is found to successfully capture the acceleration and deceleration of the turbulent boundary layer on the bump surface, providing better predictions of skin friction near the bump peak and exhibiting comparable performance to the EQWM with respect to the wall pressure and velocity field. We also conclude that the subgrid-scale model is crucial to the accurate prediction of the flow field, in particular the prediction of separation.

boundary layer↗

DOE OSTI2023

Crustal and uppermost mantle structure near the Gloria Fault, North Atlantic, from ocean bottom seismometer surface wave observations

SUMMARY In this work, we present both 1-D and 3-D shear wave velocity (Vs) models of the oceanic crust and uppermost mantle below the Deep OCean Test ARray area, located ∼ 70 km north of the central section of the Gloria Fault, in the eastern North-Atlantic Ocean. The velocity models are inferred from the dispersion of surface waves recorded on ocean bottom seismometers. Dispersion measurements are obtained from the analysis of ambient seismic noise at short periods (< 14 s) and teleseismic surface waves at long periods (> 14 s) using the two-station method. The 1-D Vs model is inferred from the joint inversion of Rayleigh wave phase velocities and Love wave group and phase velocities. The 3-D tomographic model is obtained by inversion of 2-D Love wave group velocity maps as a function of depth, further constrained by the average of Love wave phase velocities obtained from ambient noise (4–9 s) and the average Rayleigh and Love wave phase velocities calculated from teleseismic data (14–44 s). The 1-D Vs model shows a sediment layer with a low velocity of 1.05 km s−1, similar to previous studies in the region. Below the sediments, we find an oceanic crust with velocities ranging from 3.3 to 4.5 km s−1. The model reaches an unusually high velocity of 4.9 km s−1 in a 20 km thick layer at depths between 16 and 36 km. We interpret this fast velocity layer as indicative of the presence of harzburgite, a residue of enhanced melting that might have been formed by the proximity between the Mid-Atlantic Ridge and the Azores mantle plume. At greater depths the velocity decreases, forming a low-velocity zone that reaches a minimum at ∼ 70 km depth, which we interpret as the maximum depth for the lithosphere–asthenosphere boundary. The 3-D model shows a structure that is mostly horizontally layered, with Vs isocontours at 3.5–4.5 km s−1 highlighting oscillations of the crustal structure with wavelengths of ∼25–30 km. These oscillations may be due to changes in the rate of mantle upwelling and magma supply rate.

Pinzón, Juan I. (ORCID:0000000338078068)↗

DOE OSTI2022

Multifunctional fiber-reinforced composites for passive sensing and energy harvesting with enhanced mechanical performance

Fiber-reinforced polymer composites (FRPCs) are valid alternatives to metals, especially in the aerospace industry, for their superior strength-to-weight ratio. FRPCs are generally manufactured by stacking layers of fibers and infusing them with epoxy-based adhesives to result in laminates. Such layer-by-layer structure often ensues a poor interlaminar property of the composites. Additionally, FRPCs can sustain complex damage modes because of their inherent anisotropic characteristics. For example, delamination can occur due to low-velocity impact at a subsurface level, which can result in premature catastrophic failures if undetected. Thus, structural monitoring is crucial to identify such damage. Point-based sensors (e.g., strain gauges, accelerometers, among many) can be embedded in the FRPCs for structural monitoring. However, their electrical power demand often embroils their usage. Therefore, the main objective of this research is to design and implement multifunctional composites that can simultaneously perform passive sensing and energy harvesting while exhibiting better mechanical performance. Previous research efforts have demonstrated that a continuous feed-through deposition of functional materials on fiber surfaces simultaneously enhanced the mechanical and sensing properties of the FRPCs. This study explores a similar approach to encode passive sensing and energy harvesting properties in the FRPCs by integrating ferroelectric microparticles on the fiber surfaces. Upon ensuring their superior interlaminar shear strength, sensing and energy harvesting properties were characterized through experimental studies. The outcome is a multifunctional composite fabricated by coating the fibers with functional microparticles through a high throughput, scalable, and low-cost approach that enables passive sensing, energy harvesting, and improved mechanical performance.

Gupta, Sumit↗

DOE OSTI2025

Influence of simple terrain on the spatial variability of a low-level jet and wind farm performance in the AWAKEN field campaign

In wind energy research, scientific challenges are often associated with complex terrain sites, where orography, vegetation, and buildings disrupt flow uniformity. However, even sites characterized as simple terrain can exhibit significant spatial variability in wind speed, particularly during stable boundary layers (SBLs) and low-level jets (LLJs). This study investigates these terrain interactions using both simulations and observations from the American WAKe ExperimeNt (AWAKEN). We employ a multiscale Weather Research and Forecasting (WRF) model simulation, integrating mesoscale forcing in the coarse domains and representing three rows of turbines from the King Plains wind farm as generalized actuator disks (GAD) in the large-eddy simulation (LES) domains. During a nocturnal LLJ event on 3 April 2023, the downstream, wake-affected turbine rows outperformed the upstream, unwaked row by 25 %–51 %. This counterintuitive result arises from terrain-induced streamwise variations in hub-height wind speed of approximately 4 m s −1 over 5 km – equivalent to ∼50 % of the upstream reference speed. This enhancement outweighs the wake-induced reduction in mean wind speed (∼12 %) and global blockage effects reported in the literature (∼1 %–3.4 %). The multiscale simulations capture the intra-farm spatial variability in power performance observed in SCADA data. Terrain-induced vertical displacement of the LLJ, coupled with large wind shear below the jet maximum, drives the substantial streamwise acceleration within the wind farm. These findings underscore the importance of accounting for spatial variability related to terrain, even in simple landscapes, particularly during LLJ conditions. Incorporating such effects into reduced-order modeling frameworks for wind farm design and control could significantly enhance their effectiveness.

17 WIND ENERGY↗

DOE OSTI2022

Long-Term Aging in Miscible Polymer Nanocomposites

Here we find that the initial, solvent-cast state of nanoparticles (NPs) in a polymer matrix temporally evolves during thermal annealing such that, at steady state, NPs maximize their distance from each other subject to mass balance constraints. The observed timescales for this unexpected structural reorganization, as probed by small-angle X-ray scattering, are temperature-dependent and can be prohibitively large, especially at temperatures around and below 1.2Tg. X-ray photon correlation spectroscopy measurements during reorganization reveal that the collective NP dynamics slow down with annealing at constant temperature; this is accompanied by changes in the low-frequency regime in macroscopic viscoelastic measurements in equilibrated materials. By ruling out other potential sources for these effects (i.e., electrostatic interactions, adsorbed layers), we attribute these results to a long-ranged repulsive force between the NPs caused by fluctuations in the polymer phase, i.e., the "anti-Casimir" effect proposed by Obhukhov and Semenov [Long-range interactions in polymer melts: The anti-Casimir effect. Phys Rev Lett 2005, 95 (3), 038305]. Thus, our results highlight the important role of long-term, slow NP reorganization on the structure and, subsequently, the properties of polymer nanocomposites (PNCs), even in the case of nominally miscible polymer nanoparticle hybrids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Impact of Meteorological Factors on the Mesoscale Morphology of Cloud Streets during a Cold-Air Outbreak over the Western North Atlantic

We report postfrontal clouds (PFC) are ubiquitous in the marine boundary layer, and their morphology is essential to estimating the radiation budget in weather and climate models. Here we examine the roles of sea surface temperature (SST) and meteorological factors in controlling the mesoscale morphology and evolution of shallow clouds associated with a cold-air outbreak that occurred on 1 March 2020 during phase I of the Aerosol Cloud Meteorology Interactions over the Western Atlantic Experiment (ACTIVATE). Our results show that the simulated PFC structure and ambient conditions by the Weather Research and Forecasting (WRF) Model are generally consistent with observations from GOES-16 and dropsonde measurements. We also examine the thermodynamical and dynamical influences in the cloud mesoscale morphology using WRF sensitivity experiments driven by two meteorological forcing datasets with different domain-mean SST and spatial gradients, which lead to dissimilar values of hydrometeor water path and cloud core fraction. The SST from ERA5 leads to weaker stability and higher inversion height than the SST from FNL does. In addition, the use of large-scale meteorological forcings from ERA5 yields a distinctive time evolution of wind direction shear in the inner domain, which favors the formation and persistence of longer cloud rolls. Both factors contribute to a change in the time evolution of domain-mean water path and cloud core fraction of cloud streets. Our study takes advantage of the simulation driven by the differences between two large-scale forcing datasets to illustrate the importance of SST and wind direction shear in the cloud street morphology in a realistic scenario.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Spatial Mapping of Riverbed Grain-Size Distribution Using Machine Learning

Recent alluvial sediments in riverbeds play a significant role in controlling hydrologic exchange flows (HEFs) in river systems. The alluvial layer is usually associated with strong heterogeneity in physical properties (e.g., permeability and hydraulic conductivity), which affects local HEFs and therefore biogeochemical processes. The spatial distribution of these physical properties needs to be determined to inform the numerical models used to reveal the realistic hydro-biogeochemical behaviors. Such information can be obtained based on the intrinsic link between sediment grain-size distribution and hydraulic properties where sediment texture information is available. However, grain-size measurements are usually spatially sparse and do not have adequate coverage and resolution, particularly for a relatively large domain such as the Hanford Reach of the Columbia River. In this paper, we adopted machine learning (ML) approaches for categorizing and mapping the spatial distributions of riverbed substrate grain size and filling in missing areas of substrate data using the ML models along the reach. Such ML models for substrate size mapping were trained at 13,372 locations using measured substrate sizes along with observed and simulated attributes, including bathymetric attributes (e.g., elevation, slope, and aspect ratio) from LIDAR and bathymetric surveys, and hydrodynamic properties (e.g., water depth, velocity, shear stress, and their statistical moments). An ensemble bagging-based ML technique, Random Forest, was adopted to identify the most influential factors as predictors to develop the predictive models with over-fitting issues addressed. The models were evaluated with respect to each individual substrate size class and the lumped group, and then used to generate the final substrate size maps covering all the grid cells in the numerical modeling domain.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Safety First: Stability and Dissipation of Line-tied Force-free Flux Tubes in Magnetized Coronae

Abstract Magnetized plasma columns and extended magnetic structures with both footpoints anchored to a surface layer are an important building block of astrophysical dissipation models. Current loops shining in X-rays during the growth of plasma instabilities are observed in the corona of the Sun and are expected to exist in highly magnetized neutron star magnetospheres and accretion disk coronae. For varying twist and system sizes, we investigate the stability of line-tied force-free flux tubes and the dissipation of twist energy during instabilities using linear analysis and time-dependent force-free electrodynamics simulations. Kink modes ( m = 1) and efficient magnetic energy dissipation develop for plasma safety factors q ≲ 1, where q is the inverse of the number of magnetic field line windings per column length. Higher-order fluting modes ( m > 1) can distort equilibrium flux tubes for q > 1 but induce significantly less dissipation. In our analysis, the characteristic pitch μ ˜ 0 of flux-tube field lines determines the growth rate ( ∝ μ ˜ 0 3 ) and minimum wavelength of the kink instability ( ∝ μ ˜ 0 − 1 ). We use these scalings to determine a minimum flux tube length for the growth of the kink instability for any given μ ˜ 0 . By drawing analogies to idealized magnetar magnetospheres with varying regimes of boundary shearing rates, we discuss the expected impact of the pitch-dependent growth rates for magnetospheric dissipation in magnetar conditions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

Bio-inspired alula-based winglet design for enhanced heat transfer in high temperature fin-and-tube heat exchangers

Fin-and-tube heat exchangers (FTHEs) are widely used for high-temperature flue-gas heat recovery, but their performance is often limited by wake regions and non-uniform fin-surface temperatures. This study proposes and numerically evaluates four bio-inspired longitudinal vortex generator (VG) configurations in a high-temperature FTHE with flue-gas inlet temperature ∼1230 K: double-delta, curved double-delta, alula, and a new curved-alula geometry. The reference fin is not hydraulically plain; it already incorporates leading-edge separation columns and convex protrusions, so the alula-type winglets are assessed as downstream add-ons acting on a strongly disturbed flow. In a second step, perforations (one, two and three circular holes) are introduced into the curved-alula VGs to further tailor the flow field. Three-dimensional simulations with the Shear Stress Transpor (SST) $k - ω$ model, temperature-dependent flue-gas properties and conjugate conduction are carried out for gas-side Reynolds numbers $Re_g ≈ 8.0$ x $10^2 - 3.6$ x $10^3$ (mass flow rates 0.5 – 2.5 g/s), and the designs are compared in terms of surface heat flux, Nusselt number, friction factor and hydrothermal performance factor (HTPF). For this already-promoted fin, the additional downstream winglets provide moderate, incremental hydrothermal gains. At the highest Reynolds number, the best non-perforated design (curved-alula) increases surface heat flux from 1630.9 to 1794.7 kW/m² (∼ 10 % gain) and the Nusselt number from 227.6 to 242.6 (∼ 7 % gain), while the friction factor rises from 0.26 to about 0.30, yielding HTPF values close to unity (∼ 0.9 – 1.0). Introducing circular perforations into the curved-alula winglets acts mainly as a wake-bleeding refinement: the three-hole configuration provides a heat flux of 1824.7 kW/m² and a pressure drop of 127.9 Pa, with HTPF in the range ∼ 1.03 – 1.14 and a small (∼ 1 – 3 %) improvement over the solid curved-alula design. Flow-field analysis shows that the perforated curved-alula VGs shrink tube-wake regions, thin the thermal boundary layer and homogenize the fin-surface temperature (outlet-gas temperature ∼ 510 – 520 K and fin-surface temperature ∼ 420 – 421 K for the three-hole case). An optimal flue-gas mass flow rate of ∼ 1 g/s ($Re_g ≈ 1.5$ x $10^3$) is identified, beyond which additional heat-transfer gains are offset by rapidly increasing pressure losses. Overall, the results highlight that initial fin geometry and VG placement are as important as VG shape: alula-based winglets are expected to yield larger relative gains on simpler flat-fin layouts or when positioned closer to the fin leading edge and tube

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

Convective and Turbulent Motions in Nonprecipitating Cu. Part II: LES Simulated Cloud Represented by a Starting Plume

The dynamic structure of a small trade wind cumulus (Cu) is analyzed using a novel approach. Cu developing in a shear-free environment is simulated by 10-m-resolution LES model with spectral bin microphysics. The aim is to clarify the dynamical nature of cloud updraft zone (CUZ) including entrainment and mixing in growing Cu. The validity of concept stating that a cloud at developing state can be represented by a parcel or a jet is tested. To investigate dynamical entrainment in CUZ performed by motions with scales larger than the turbulence scales, the modeled fields of air velocity were filtered by wavelet filter that separated convective motions from turbulent ones. Two types of objects in developing cloud were investigated: small volume ascending at maximal velocity (point parcel) and CUZ. It was found that the point parcel representing the upper part of cloud core is adiabatic. The motion of the air in this parcel ascending from cloud base determines cloud-top height. The top-hat (i.e., averaged) values of updraft velocity and adiabatic fraction in CUZ are substantially lower than those in the point parcel. Evaluation of the terms in the dynamical equation typically used in 1D cloud parcel models show that this equation can be applied for calculation of vertical velocities at the developing stage of small Cu, at least up to the heights of the inversion layer. Dynamically, the CUZ of developing cloud resembles the starting plume with the tail of nonstationary jet. Both the top-hat vertical velocity and buoyancy acceleration linearly increase with the height, at least up to the inversion layer. An important finding is that lateral entrainment of convective (nonturbulent) nature has a little effect on the top-hat CUZ velocity and cannot explain the vertical changes of conservative variables qt and θl. In contrast, entrained air lifting inside CUZ substantially decreases top-hat liquid water content and its adiabatic fraction. Possible reasons of these effects are discussed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Unveiling the mechanism of surface corrugation formation on a quasi free-standing bi-layer graphene via experimental and modeling investigations

Extensive studies have been conducted to accomplish the controls over the formation of surface corrugations on chemical vapor deposited (CVD) graphene. However, the underlying mechanism of the surface corrugation formation on graphene remains elusive, due to the difficulty delineating the growth-induced surface corrugations from wrinkles formed during graphene transfer with the use of a supporting layer casted on top of the sample. Here, in this study, “quasi free-standing” graphene was realized using the weakly-interacting h-BN layer during a wet transfer process to study the surface corrugation formation on graphene. The weak interaction of graphene with the supporting h-BN layer allows for the growth-induced surface corrugations to be released, enabling the investigation of the primary mechanism for the graphene corrugation behavior during the transfer process. The experimental measurements of surface corrugations were conducted using atomic force microscopy (AFM) to reveal that surface corrugations are formed following the graphene’s crystallographic directions. Density functional theory calculations using the projector augmented-wave (PAW) method and Perdew-Burke-Ernzerhof (PBE) exchange correlation functional were also conducted for two models of “atomic-scale ripples” and “nanoscale wrinkles” and showed that all of them are formed along the crystallographic axis of graphene, which is in good agreement with the experimental observations.

36 MATERIALS SCIENCE↗

DOE OSTI2025

MMMnet: A Neural Network Surrogate for Real-Time Transport Prediction Based on the Updated Multi-Mode Model

The Multi-Mode Model (MMM) is a physics-based anomalous transport model integrated into TRANSP for predicting electron and ion thermal transport, electron and impurity particle transport, and toroidal and poloidal momentum transport. While MMM provides valuable predictive capabilities, its computational cost, although manageable for standard simulations, is too high for real-time control applications. MMMnet, a neural network-based surrogate model, is developed to address this challenge by significantly reducing computation time while maintaining high accuracy. Trained on TRANSP simulations of DIII-D discharges, MMMnet incorporates an updated version of MMM (9.0.10) with enhanced physics, including isotopic effects, plasma shaping via effective magnetic shear, unified correlation lengths for ion-scale modes, and a new physics-based model for the electromagnetic electron temperature gradient mode. A key advancement is MMMnet’s ability to predict all six transport coefficients, providing a comprehensive representation of plasma transport dynamics. MMMnet achieves a two-order-of-magnitude speed improvement while maintaining strong correlation with MMM diffusivities, making it well-suited for real-time tokamak control and scenario optimization.

DIII-D↗

DOE OSTI2022

Modeling the non-Schmid crystallographic slip in MAX phases

We present a crystal plasticity constitutive relation for the description of experimentally observed non-Schmid crystallographic slip in a class of ternary carbides and nitrides commonly referred to as MAX phases. In the constitutive relation, we assume that the evolution of the slip system strength in MAX phases has two components – a classical component that depends on the Taylor cumulative shear strain and a non-Schmid component that depends on the stress normal to the slip plane. The non-Schmid crystal plasticity constitutive relation is then used to carry out finite element simulations of micropillar compression of single crystals of two MAX phases, Ti 2 AlC and Ti 3 AlC 2 . The finite element simulations not only quantitatively predict the stress – strain response of a wide range of crystallographic orientations of the micropillars but also rationalize the non-uniform deformation and the deformed shape of the micropillars observed in the experiments for the two materials. As a result, parametric studies are also carried out to quantify the role of the non-Schmid effect and understand the effects of key experimental parameters on the stress – strain response of the micropillars of the two MAX phases.

36 MATERIALS SCIENCE↗

DOE OSTI2024

KBase Narrative - Porphyromonadaceae sp. W3.11 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗

DOE OSTI2024

KBase Narrative - Lachnospiraceae sp. C1.1 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗

DOE OSTI2020

The Detection of Monoclinic Zirconia and Non-Uniform 3D Crystallographic Strain in a Re-Oxidized Ni-YSZ Solid Oxide Fuel Cell Anode

The solid oxide fuel cell (SOFC) anode is often composed of nickel (Ni) and yttria-stabilized zirconia (YSZ). The yttria is added in small quantities (e.g., 8 mol %) to maintain the crystallographic structure throughout the operating temperatures (e.g., room-temperature to >800 °C). The YSZ skeleton provides a constraining structural support that inhibits degradation mechanisms such as Ni agglomeration and thermal expansion miss-match between the anode and electrolyte layers. Within this structure, the Ni is deposited in the oxide form and then reduced during start-up; however, exposure to oxygen (e.g., during gasket failure) readily re-oxidizes the Ni back to NiO, impeding electrochemical performance and introducing complex structural stresses. In this work, we correlate lab-based X-ray computed tomography using zone plate focusing optics, with X-ray synchrotron diffraction computed tomography to explore the crystal structure of a partially re-oxidized Ni/NiO-YSZ electrode. These state-of-the-art techniques expose several novel findings: non-isotropic YSZ lattice distributions; the presence of monoclinic zirconia around the oxidation boundary; and metallic strain complications in the presence of variable yttria content. This work provides evidence that the reduction–oxidation processes may destabilize the YSZ structure, producing monoclinic zirconia and microscopic YSZ strain, which has implications upon the electrode’s mechanical integrity and thus lifetime of the SOFC.

25 ENERGY STORAGE↗