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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 OSTI2023

Using small building blocks to assemble ultra-complex, multifaceted metal-organic frameworks with zeolitic, mesoporous subnetwork

The assembly of ultra-complex structures from simple building units remains a long-term challenge in chemistry. Using small molecular building blocks (MBBs) in a mixed-ligand approach permitted the assembly of unprecedented metal-organic frameworks (MOFs), M-kum-MOF-1 (M = Y, Tb), exhibiting extra-large mesoporous cavities with small access windows. The ultra-complex cage of M-kum-MOF-1 consists of 240 vertices bridged by 432 edges, leading to a 194 faces-containing tile. This tile exhibits more faces than in any periodic structures (zeolites, MOFs, metal-organic polyhedra [MOPs], etc.) known to date. M-kum-MOF-1 not only possess zeolitic features (anionic framework), but they also contain an underlying wse zeolitic topology, which is observed for the first time.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The Dark Energy Survey Bright Arcs Survey: Candidate Strongly Lensed Galaxy Systems from the Dark Energy Survey 5000 Square Degree Footprint

We report the combined results of eight searches for strong gravitational lens systems in the full 5000 square degrees of Dark Energy Survey (DES) observations. The observations accumulated by the end of the third observing season fully covered the DES footprint in five filters (grizY), with an i-band limiting magnitude (at 10σ) of 23.44. In four searches, a list of potential candidates was identified using a color and magnitude selection from the object catalogs created from the first three observing seasons. Three other searches were conducted at the locations of previously identified galaxy clusters. Cutout images of potential candidates were then visually scanned using an object viewer. An additional set of candidates came from a data-quality check of a subset of the color–coadd tiles created from the full DES six-season data set. A short list of the most promising strong-lens candidates was then numerically ranked according to whether or not we judged them to be bona fide strong gravitational lens systems. These searches discovered a diverse set of 247 strong-lens candidate systems, of which 81 are identified for the first time. We provide the coordinates, magnitudes, and photometric properties of the lens and source objects, and an estimate of the Einstein radius for 81 new systems and 166 previously reported systems. This catalog will be of use for selecting interesting systems for detailed follow up, studies of galaxy cluster and group mass profiles, as well as a training/validation set for automated strong-lens searches.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Aspen ploidy level and cover maps from NEON Airborne Observation Platform, 2018, Crested Butte, Colorado

Maps of aspen ploidy (diploid or triploid) developed using National Ecological Observatory Network (NEON) Airborne Observation Platform visible to shortwave infrared imaging spectroscopy data that were acquired over the Upper East River, Colorado in 2018. Maps of aspen distribution, as well as other land cover types that were used to screen for aspen dominated pixels are also provided. Each image file is provided as a GeoTiff with internal tiling and LZW compression. For use of ploidy maps, it is necessary to mask out non-aspen and shaded pixels. Shaded pixels are provided in an associated data package. For full details, please see associated publication and methods description. This dataset is associated with the publication in Ecological Applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Custom surface reflectance, shade mask, and equivalent water thickness maps for the Colorado Headwaters Ecological Spectroscopy Study (2025)

This dataset contains land surface reflectance estimates and additional derived products generated from NEON Imaging Spectrometer (NIS) data collected in the Upper Gunnison river basin during June and July of 2025. Data was collected over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). These products were derived from radiance and LiDAR data collected by the NEON Airborne Observation Platform (AOP) campaign funded by the Colorado Headwaters Ecological Spectroscopy Study (CHESS) (doi:10.15485/3017965). Products include per-pixel surface reflectance (rfl) and reflectance uncertainty (rfl_unc), observational data (obs), canopy equivalent water thickness (ewt), and shade masks. Atmospheric correction was performed per flightline using the ISOFIT (Imaging Spectrometer Optimal FITting) optimal estimation framework to estimate surface reflectance and the associated per-band reflectance uncertainty. Reflectance retrievals achieved a mean absolute error of 1.5% across diverse validation surfaces (see validation report.pdf). Equivalent water thickness was calculated from surface reflectance using the Beer–Lambert absorption of liquid water. Shade masks were generated based on the geometry between the sun angle, ground surface, and sensor at the time of flight. Data products are provided per-flightline and as mosaics for each domain. Flightline data products are provided as ENVI-formatted binary files (rfl, rfl_unc, ewt) and GeoTIFFs (shade). Reflectance and uncertainty mosaics are provided as tiled NetCDFs, while all other mosaicked products are provided as cloud-optimized GeoTIFFs. These formats are supported by common geospatial software (e.g., QGIS, ArcGIS, ENVI) and programmatic libraries in Python (e.g., rasterio, xarray, spectral, netCDF4) and R (e.g., terra, ncdf4). Processing workflows were designed to be equivalent to those used to generate the 2018 CHESS campaign airborne imaging spectroscopy data products (doi:10.15485/3013527). All outputs were co-registered to a common spatial grid to support time series analyses. CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgment: Data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). Computational research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004) and was funded by EMIT Extended Mission Phase E Science.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2023

Revisiting Temporal Blocking Stencil Optimizations

Iterative stencils are used widely across the spectrum of High Performance Computing (HPC) applications. Many efforts have been put into optimizing stencil GPU kernels, given the prevalence of GPU-accelerated supercomputers. To improve the data locality, temporal blocking is an optimization that combines a batch of time steps to process them together. Under the observation that GPUs are evolving to resemble CPUs in some aspects, we revisit temporal blocking optimizations for GPUs. We explore how temporal blocking schemes can be adapted to the new features in the recent Nvidia GPUs, including large scratchpad memory, hardware prefetching, and device-wide synchronization. We propose a novel temporal blocking method, EBISU, which champions low device occupancy to drive aggressive deep temporal blocking on large tiles that are executed tile-by-tile. We compare EBISU with state-of-the-art temporal blocking libraries: STENCILGEN and AN5D. We also compare with state-of-the-art stencil auto-tuning tools that are equipped with temporal blocking optimizations: ARTEMIS and DRSTENCIL. Over a wide range of stencil benchmarks, EBISU achieves speedups up to 2.53x and a geometric mean speedup of 1.49x over the best state-of-the-art performance in each stencil benchmark.

Zhang, Lingqi↗
DOE OSTI2022

Montage electron tomography of vitrified specimens

Cryo-electron tomography provides detailed views of macromolecules in situ. However, imaging a large field of view to provide more cellular context requires reducing magnification during data collection, which in turn restricts the resolution. To circumvent this trade-off between field of view and resolution, we have developed a montage data collection scheme that uniformly distributes the dose throughout the specimen. In this approach, sets of slightly overlapping circular tiles are collected at high magnification and stitched to form a composite projection image at each tilt angle. These montage tilt-series are then reconstructed into massive tomograms with a small pixel size but a large field of view. For proof-of-principle, we applied this method to the thin edge of HeLa cells. Thon rings to better than 10 Å were detected in the montaged tilt-series, and diverse cellular features were observed in the resulting tomograms. These results indicate that the additional dose required by this technique is not prohibitive to performing structural analysis to intermediate resolution across a large field of view. We anticipate that montage tomography will prove particularly useful for lamellae, increase the likelihood of imaging rare cellular events, and facilitate visual proteomics.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

ORBIT-2 Weather and Climate Downscaling Software Repository

ORBIT-2 is a scalable foundation model for global, hyper-resolution climate and weather downscaling. ORBIT-2 incorporates two key innovations: (1) Residual Slim ViT (Reslim), a lightweight architecture with residual learning and Bayesian regularization for efficient, robust prediction; and (2) TILES, a tile-wise sequence scaling algorithm that reduces self-attention complexity from quadratic to linear, enabling long-sequence processing and massive parallelism. ORBIT-2 scales to 10 billion parameters across 65,536 GPUs, achieving up to 4.1 ExaFLOPS sustained throughput and 74–98% strong scaling efficiency. It supports downscaling to 0.9 km global resolution and processes sequences up to 4.2 billion tokens. On 7 km resolution benchmarks, ORBIT-2 achieves high accuracy with 𝑅2 scores in range of 0.98–0.99 against observation data.

Wang, Xiao [Oak Ridge National Laboratory]↗
DOE OSTI2021

Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein

The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Overview of the COMPASS results *

COMPASS addressed several physical processes that may explain the behaviour of important phenomena. This paper presents results related to the main fields of COMPASS research obtained in the recent two years, including studies of turbulence, L–H transition, plasma material interaction, runaway electron, and disruption physics: Tomographic reconstruction of the edge/SOL turbulence observed by a fast visible camera allowed to visualize turbulent structures without perturbing the plasma. Dependence of the power threshold on the X-point height was studied and related role of radial electric field in the edge/SOL plasma was identified. The effect of high-field-side error fields on the L–H transition was investigated in order to assess the influence of the central solenoid misalignment and the possibility to compensate these error fields by low-field-side coils. Results of fast measurements of electron temperature during ELMs show the ELM peak values at the divertor are around 80% of the initial temperature at the pedestal. Liquid metals were used for the first time as plasma facing material in ELMy H-mode in the tokamak divertor. Good power handling capability was observed for heat fluxes up to 12 MW m –2 and no direct droplet ejection was observed. Partial detachment regime was achieved by impurity seeding in the divertor. The evolution of the heat flux footprint at the outer target was studied. Runaway electrons were studied using new unique systems—impact calorimetry, carbon pellet injection technique, wide variety of magnetic perturbations. Radial feedback control was imposed on the beam. Forces during plasma disruptions were monitored by a number of new diagnostics for vacuum vessel (VV) motion in order to contribute to the scaling laws of sideways disruption forces for ITER. Current flows towards the divertor tiles, incl. possible short-circuiting through PFCs, were investigated during the VDE experiments. The results support ATEC model and improve understanding of disruption loads.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Wall heating by subcritical energetic electrons generated by the runaway electron avalanche source *

Abstract Subcritical energetic electrons (SEEs) produced by the runaway electron (RE) avalanche source at energies below the runaway threshold are found to be the primary contributor to surface heating of plasma-facing components (PFCs) during final loss events. This finding is supported by theoretical analysis, computational modeling with the Kinetic Orbit Runaway electrons Code (KORC), and qualitative agreement with DIII-D experimental observations. The avalanche source generates significantly more secondary electrons below the runaway threshold, which thermalize rapidly when well-confined. However, during a final loss event, the RE beam impacts the first wall, and SEEs are deconfined before they can thermalize. Additionally, because the energy deposition length decreases faster than energy, the deposited energy density, and thus the maximum PFC surface temperature change, is larger for SEEs than REs. KORC simulations employ an analytic first wall to model particle deconfinement onto a non-axisymmetric wall composed of individual tiles. PFC surface heating is calculated using a 1D model extended to include an energy-dependent deposition length scale. Simulations of DIII-D qualitatively agree with infrared (IR) imaging only when SEEs from the avalanche source are included. These results demonstrate that SEEs are the dominant contributor to PFC surface heating and indicate that the avalanche source plays a critical role in the PFC damage caused during final loss events. The prominence of SEEs also has important implications for interpreting IR imaging, one of the primary diagnostics for RE-wall interaction diagnosis, despite REs dominating the energy and current density. This result improves predictions of wall damage due to post-disruption REs to estimate material lifetime and design RE mitigation systems for ITER and future reactors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Motif magnetism and quantum many-body scars

In this work, we generally expect quantum systems to thermalize and satisfy the eigenstate thermalization hypothesis (ETH), which states that finite-energy-density eigenstates are thermal. However, some systems, such as many-body localized systems and systems with quantum many-body scars, violate ETH and have high-energy athermal eigenstates. In systems with scars, most eigenstates thermalize, but a few atypical scar states do not. Scar states can give rise to a periodic revival when time-evolving particular initial product states, which can be detected experimentally. Recently, a family of spin Hamiltonians was found with magnetically ordered three-colored eigenstates that are quantum many-body scars [Lee et al., Phys. Rev. B 101, 241111(R) (2020)]. These models can be realized in any lattice that can be tiled by triangles, such as the triangular or kagome lattices, and have been shown to have close connections to the physics of quantum spin liquids in the Heisenberg kagome antiferromagnet. In this paper, we introduce a generalized family of n-colored Hamiltonians with “spiral colored” eigenstates made from n-spin motifs such as polygons or polyhedra. We show how these models can be realized in many different lattice geometries and provide numerical evidence that they can exhibit quantum many-body scars with periodic revivals that can be observed by time-evolving simple product states. The simple structure of these Hamiltonians makes them promising candidates for future experimental studies of quantum many-body scars.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Entropic formation of a thermodynamically stable colloidal quasicrystal with negligible phason strain

Quasicrystals have been discovered in a variety of materials ranging from metals to polymers. Yet, why and how they form is incompletely understood. In situ transmission electron microscopy of alloy quasicrystal formation in metals suggests an error-and-repair mechanism, whereby quasiperiodic crystals grow imperfectly with phason strain present, and only perfect themselves later into a high-quality quasicrystal with negligible phason strain. The growth mechanism has not been investigated for other types of quasicrystals, such as dendrimeric, polymeric, or colloidal quasicrystals. Soft-matter quasicrystals typically result from entropic, rather than energetic, interactions, and are not usually grown (either in laboratories or in silico) into large-volume quasicrystals. Consequently, it is unknown whether soft-matter quasicrystals form with the high degree of structural quality found in metal alloy quasicrystals. Here, we investigate the entropically driven growth of colloidal dodecagonal quasicrystals (DQCs) via computer simulation of systems of hard tetrahedra, which are simple models for anisotropic colloidal particles that form a quasicrystal. Using a pattern recognition algorithm applied to particle trajectories during DQC growth, we analyze phason strain to follow the evolution of quasiperiodic order. As in alloys, we observe high structural quality; DQCs with low phason strain crystallize directly from the melt and only require minimal further reduction of phason strain. Finally, we also observe transformation from a denser approximant to the DQC via continuous phason strain relaxation. Our results demonstrate that soft-matter quasicrystals dominated by entropy can be thermodynamically stable and grown with high structural quality––just like their alloy quasicrystal counterparts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

National Center for Airborne Laser Mapping (NCALM) LiDAR and DEM data from two NGEE Arctic Sites, Seward Peninsula, Alaska, Winter 2022

From April 3 through April 6 of 2022, airborne remote sensing data was collected by the National Center for Airborne Laser Mapping (NCALM) in collaboration with NGEE Arctic scientists. Snow-on data was collected around two NGEE Arctic study sites on the Seward Peninsula of Alaska: Teller mm 27 and Kougarok mm 64. A Robinson R44 II helicopter with a RIEGL VQ-580 II airborne laser scanner was used to collect the LiDAR point cloud data for each study site. This survey was conducted during expected peak snow cover at the end of the winter on the Seward Peninsula, and can be paired with data collected in 2021 during the snow-off campaign "National Center for Airborne Laser Mapping (NCALM) LiDAR, Imagery, and DEM data from five NGEE Arctic Sites, Seward Peninsula, Alaska, August 2021" (Singhania et al., 2023) (NGA270). This data package contains LiDAR point clouds (.las), Digital Elevation Models (.tif), and shapefiles of the .las tiling system (.shp). A project report detailing data collection details, GNSS stations and GNSS corrections, and processing steps is also included. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Innovative laser-based methods for monitoring fuel retention in ITER

This paper addresses the challenge of tritium inventory management in ITER and future fusion reactors, highlighting the importance of accurate tritium measurement and its spatial distribution within the vacuum vessel. Given ITER’s operational constraints, especially the limit on tritium retention, precise measurement is essential for both safety and regulatory compliance. To tackle these questions, the paper presents the T-monitor diagnostic system developed by Forschungszentrum Jülich, which uses Laser-Induced Desorption (LID) in combination with Diagnostic Residual Gas Analysis (DRGA) to measure hydrogen isotope concentrations on the surface of divertor tiles. The system integrates a high-power laser, advanced optical components, and a Fast Scanning Mirror Unit (FSMU) for accurate laser spot positioning with rapid response. Designed to measure in situ tritium retention, the diagnostic provides high-resolution spatial mapping, vital for evaluating detritiation strategies. The laser heating process increases the divertor surface temperature to 1600 K within the laser spot, promoting hydrogen isotope desorption. Accurate measurements require the precise control of laser parameters, including pulse duration and spot size, with a target relative accuracy of 20%. The optical design includes both in-vessel and ex-vessel components, such as durable high-reflectivity mirrors made of gold and copper, selected not only for their infrared performance but also for their transmission of visible wavelengths for observation purposes. To protect optical components from contamination, a pneumatic shutter is used.

Hydrogen isotopes↗
DOE OSTI2022

High gas throughput SOLPS-ITER simulations extending the ITER database to strong detachment

Abstract SOLPS-ITER simulations performed for Q DT = 10, P SOL = 100 MW burning plasmas on ITER extend the existing database to high values of separatrix averaged neon impurity concentration (⟨ c Ne ⟩ ≈ 6%) and divertor neutral pressure (⟨ p div ⟩ > 25 Pa) in order to determine the heat flux mitigation capability of these scenarios and whether strongly detached states are accessible. In the existing database of ITER simulations, the level of detachment was limited to cases where the integral ion flux to the outer target was greater than 80% of the value at rollover, with the impurity radiation localized near the target. With the possibility of narrow heat flux channels and increased deposited power due to tile shaping, it is important to explore operation at a higher degree of detachment. Two series of simulations were explored to extend the database of SOLPS simulations. By increasing the deuterium and neon puff rates proportionally, the peak divertor energy flux ( q ⊥,max ) is decreased from 5 to 3 MW m −2 while ⟨ p div ⟩ increased from 11 to 27 Pa. By increasing only the neon puff, q ⊥, max can be reduced to <1MW m −2 while ⟨ p div ⟩ is maintained at ∼ 11 Pa. As the neon puff level is increased, the position of the impurity radiation peak is shifted towards the X-point. At the highest neon puff levels with steady-state solutions, the electron temperature is reduced below 1 eV across 50 cm of each divertor target. The new cases extend previously observed tight relationships in power and momentum loss factors to low electron temperature improving their utility for highly detached regimes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Mitigation of ICRF—edge plasma interaction in Alcator C-Mod

The parasitic interaction between ion cyclotron range of frequencies (ICRF) waves and the edge plasma has long limited high-power ICRF utilization in magnetically confined fusion plasmas. In this paper, we report on the successful mitigation of this interaction by power tapering a four-strap field-aligned (FA) antenna in the Alcator C-Mod tokamak. With the antenna operated in dipole phasing ($0\pi0\pi$), the ratio of the power coupled by the central two straps ($P_\mathrm {cent}$) to the power coupled by the outer two straps was varied at fixed total coupled ICRF power ($P_\mathrm {tot}$). With $P_\mathrm {cent}$/$P_\mathrm {tot} \approx 0.8-0.9$, no enhancement of the plasma potential was measured despite 1 MW of coupled ICRF power. When the antenna is powered, energy deposition increases on its four corners and on neighboring limiter tiles magnetically connected to some of those corners. The energy deposited on the antenna and limiter is minimized together with near-field plasma potentials. Additionally, we show that deviation from $P_\mathrm {cent}$/$P_\mathrm {tot} \approx 0.8$ enhances wave-plasma interactions in places not magnetically connected to the antenna. These far-field effects are correlated with changes in the antenna spectrum. Hence, on C-Mod, near-field and far-field interactions were minimized for about the same range of $P_\mathrm {cent}$/$P_\mathrm {tot}$. Optimal power tapering was also found to improve ICRF heating efficiency and facilitate H-mode access. Finally, we show that the heat flux pattern on the toroidally aligned antennas reverses with the direction of the RF-induced E×B flow in front of the antenna, a correlation not observed for the FA antenna. We argue that the RF-induced E×B flow, which carries high-density plasma from the near-SOL, is aligned with the FA antenna and does not intercept its corners, where the plasma potential is large. This could explain the previously reported smaller impurity generation by the FA antenna (Wukitch et al 2013 Phys. Plasmas 20 056117).

Alcator C-Mod↗
DOE OSTI2022

Decoding the Mechanisms of Phase Transitions from In Situ Microscopy Observations

Abstract Analysis of the temperature‐ and stimulus‐dependent imaging data toward elucidation of the physical transformations is an ubiquitous problem in multiple fields. Here, temperature‐induced phase transition in BaTiO 3 is explored using the machine learning analysis of domain morphologies visualized via variable‐temperature scanning transmission electron microscopy (STEM) imaging data. This approach is based on the multivariate statistical analysis of the time or temperature dependence of the statistical descriptors of the system, derived in turn from the categorical classification of observed domain structures or projection on the continuous parameter space of the feature extraction‐dimensionality reduction transform. The proposed workflow offers a powerful tool for the exploration of the dynamic data based on the statistics of image representation as a function of the external control variable to visualize the transformation pathways during phase transitions and chemical reactions. This can include the mesoscopic STEM data as demonstrated here, but also optical, chemical imaging, etc., data. It can further be extended to the higher dimensional spaces, for example, analysis of the combinatorial libraries of materials compositions.

Valleti, Sai Mani Prudhvi↗
DOE OSTI2023

Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures

Bacterial mRNA sequencing is inefficient due to the abundance of ribosomal RNA that is challenging to deplete. While commercial kits target rRNA from common bacterial species, they are frequently inefficient when applied to divergent species, including those from environmental isolates. Similarly, other methods typically employ large probe sets that tile the entire length of rRNAs; however, such approaches are infeasible when applied to many species. Therefore, we present EMBR-seq+, which requires fewer than 10 oligonucleotides per rRNA by combining rRNA blocking primers with RNase H-mediated depletion to achieve rRNA removal efficiencies of up to 99% in diverse bacterial species. Furthermore, in more complex microbial co-cultures between Fibrobacter succinogenes strain UWB7 and anaerobic fungi, EMBR-seq+ depleted both bacterial and fungal rRNA, with a fourfold improvement in bacterial rRNA depletion compared with a commercial kit, thereby demonstrating that the method can be applied to non-model microbial mixtures. Notably, for microbes with unknown rRNA sequences, EMBR-seq+ enables rapid iterations in probe design without requiring to start experiments from total RNA. Finally, efficient depletion of rRNA enabled systematic quantification of the reprogramming of the bacterial transcriptome when cultured in the presence of the anaerobic fungi Anaeromyces robustus or Caecomyces churrovis. We observed that F. succinogenes strain UWB7 downregulated several lignocellulose-degrading carbohydrate-active enzymes in the presence of anaerobic gut fungi, suggesting close interactions between two cellulolytic species that specialize in different aspects of biomass breakdown. Thus, EMBR-seq+ enables efficient, cost-effective, and rapid quantification of the transcriptome to gain insights into non-model microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗