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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

UAS remote sensing (DJI Phantom 4 RTK platform): RGB orthomosaic, digital surface and canopy height models, plant functional type map, Seward Peninsula, Alaska, 2019

Airborne remote sensing data collected using a DJI Phantom 4 RTK unoccupied aerial system (UAS) ? operated by the University of Maine Wheatland Geospatial Lab (https://wheatlandlab.org/). This package includes data from 17 flights flown over the NGEE-Arctic Council, Kougarok, Kougarok Mile80, Teller, and Teller Mile32 sites in July 2019. The Phantom 4 RTK is a drone platform that collects very high spatial resolution optical red/green/blue (RGB) imagery. Derived image products include point cloud, ortho-mosaiced RGB, a digital surface model (DSM) using the structure from motion (SfM) technique, and a canopy height model (CHM). Unprocessed and processed data products (1,000+ files) are included in this package (processing levels 0-3). Data and metadata are provided as text (*.txt, *.json, *hdr,), ENVI image file (*.dat), point cloud (*.laz) and image (*.jpg, *.tif, *png) formats. 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 OSTI2023

UAS remote sensing (3DR SOLO platform): multispectral reflectance, canopy height model, normalized difference vegetation index, Seward Peninsula, Alaska, 2021

Airborne remote sensing data collected using a Parrot Sequoia+ multispectral sensor installed on a 3DR SOLO unoccupied aerial system (UAS) - operated by the Terrestrial Ecosystem Science Technology group at Brookhaven National Laboratory. This package includes data from 10 flights flown over the NGEE-Arctic Council Mile Marker (MM) 71, Kougarok MM64, and Teller MM27 sites on the Seward Peninsula, Alaska, in August 2021. Derived image products include point cloud, ortho-mosaiced multispectral image, ortho-mosaiced RGB image, a digital surface model (DSM) using the structure from motion (SfM) technique, a canopy height model (CHM), and a normalized difference vegetation index (NDVI) map. Unprocessed and processed data products are included in this package (processing levels 0-2). Data and metadata are provided as text (*.txt, *.json, *hdr,), tabular (*.dat, *.csv), point cloud (*.laz), Cloud Optimized GeoTIFF (COG, *.tif), and image (*.jpg, *.tif, *png) formats. 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 OSTI2020

SPRUCE Experimental Plot Top View Aerial Images beginning June 2019

This data set provides a record of the aerial images of the SPRUCE experimental plots obtained periodically using an unmanned aerial vehicle (UAV) with attached camera from 2019-05-05- to 2022-08-25. New images of the plots will be added periodically. The initial RGB images may be used for studies of greenness and snow coverage and compared with ground-based measurements and chamber-based tree and shrub Phenocam images (e.g. Schädel et al., 2022). Also included are NDVI (Normalized Difference Vegetation Index) images showing calculated difference between visible near-infrared (NIR) light reflectance from vegetation, as well as infrared (IR) and multispectral images. Files are presented in JPEG (*.jpg) or PDF (*.pdf) format inside of 28 compressed (*.zip) files. Images were collected for the 10 plots with enclosures, the 7 unchambered plots, and the environmental monitoring instrument cluster area. Images are slightly off-plot center at 12 to 15 meters above ground level or approximately 2 meters above the top of an experimental chamber.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Symmetry breaking during low-temperature domain formation in micron-sized magnetite crystals

We report the results of synchrotron Bragg Coherent x-ray Diffraction Imaging (BCDI) experiments to investigate domain formation in a micron-sized magnetite crystal undergoing the Verwey transition at low temperature. A strong splitting of the measured 311 Bragg reflection was observed in the low-temperature phase, indicating the formation of domains. BCDI revealed pronounced strain distributions, characterized by a clear layered stripe domain structure in real-space. Stripes were seen only along the [001] crystallographic direction, normal to the substrate surface direction, breaking the symmetry of the cubic high-temperature phase. It is argued that other domain directions were suppressed by the sample mounting orientation. More surprisingly, only a single domain orientation was observed, suggesting an additional symmetry-breaking influence originating from the shape of the crystal. Gaining insight into how thermal effects induce the formation of layered or striped phases offers a valuable framework for understanding the development of mesoscopic domains and strain patterns in functional materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

In-situ imaging of nucleation and growth of superlattices from nanoscale colloidal nanoparticles

Nanoparticle-based superlattices have attracted extensive research efforts due to their versatile composition and packing-dependent optical, magnetic, electronic, catalytic, mechanical properties. Yet the experimental understanding of the thermodynamics and pathways of the crystallization processes for these systems, which govern their ultimate morphology, size, and packing structure, has for long remained underexplored. Here, this minireview highlights recent integration of liquid-phase transmission electron microscopy, which allows for real-space, real-time direct imaging of the crystallization processes at the single-particle level, with simulation and the conceptual framework established by pioneers such as Dr. A. A. Chernov. Different aspects of superlattice formation were revealed by direct imaging for the first time, such as the existence of prenucleation precursor in nonclassical crystallization, surface energy-dependent growth, and coalescence, allowing for the charting of phase coordinates and thermodynamic quantities at the nanoscale. We discuss the similarities and differences of crystal growth behaviors in atomic and nanoparticle systems, as well as engineering opportunities to fashion, shape, and achieve quality control in superlattice formation from nanoparticles, for next-generation optical and mechanical metamaterials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Effect of Coaxial Electrode Geometry on the Electric Field Enhancement Factor for a High Voltage Vacuum Gap

We present an experimental analysis of the change in the electric field enhancement factor with varying gap size and penetration depth (P.D) of cathode into anode for a coaxial vacuum gap, diagnosed using Fowler–Nordheim analysis and optical imaging via scanning electron microscope (SEM) and time integrated Digital single lens reflex camera (DSLR). Data were collected on the Coaxial Gap Breakdown Machine (240 A, 25 kV, 150 ns, 0.1 Hz). Experiments using five different gap sizes at nine different P.Ds are compared over runs comprising 50 shots for each case. The results show a strong link between enhancement factor and gap size, with P.D and surface topology. For large gap sizes, 150, 330, and 700 μm, the average enhancement factor value increases with increasing P.D. For smaller gap sizes, 50 and 100 μm, the average enhancement factor decreases with P.D. SEM imaging before and after plasma formation for each gap size allows for quantifying surface finish, microprotrusion growth, average blast diameter, and an estimation of the surface area breakdowns occupy. Time integrated DSLR imaging analysis of the gap at each shot allows for a determination of the distribution of breakdowns about the circumference of the gap for each case tested. Here, the Fowler–Nordheim analysis allows for a quantitative analysis of the surface roughness of all gap sizes tested. Results show that for large gap sizes, the gap geometry and increasing area of breakdown is the main cause for increasing average enhancement factor. For small gap sizes, the dominant driving factor for small average enhancement factors—that subsequently decrease with P.D—is significant changes in surface topology due to an increased number of breakdowns.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

First Images of the Protoplanetary Disk around PDS 201

Scattered light imaging has revealed nearly a dozen circumstellar disks around young Herbig Ae/Be stars—enabling studies of structures in the upper disk layers as potential signs of ongoing planet formation. We present the first images of the disk around the variable Herbig Ae star PDS 201 (V* V351 Ori) and an analysis of the images and spectral energy distribution through 3D Monte Carlo radiative transfer simulations and forward modeling. The disk is detected in three data sets with the Large Binocular Telescope Interferometer/Large Binocular Telescope mid-infrared camera at the Large Binocular Telescope, including direct observations in the Ks and L′ filters, and an L′ observation with the 360° vector apodizing phase plate coronagraph. The scattered light disk extends to a very large radius of ∼250 au, which places it among the largest of such disks. Exterior to the disk, we establish detection limits on substellar companions down to ∼5 M {sub Jup} at ≳1.″5 (≳500 au), assuming the Baraffe et al. models. The images show a radial gap extending to ∼0.″4 (∼140 au at a distance of 340 pc) that is also evident in the spectral energy distribution. The large gap is a possible signpost of multiple high-mass giant planets at orbital distances (∼60–100 au) that are unusually massive and widely separated compared to those of planet populations previously inferred from protoplanetary disk substructures.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Vegetation Warming Experiment: Landscape-scale digital camera imagery for vegetation phenology, Utqiagvik (Barrow), Alaska, 2019

Images captured using a StarDot NetCam SC phenocamera looking east from the top of the Barrow Environmental Observatory (BEO) Sled Shed, Utqiagvik, Alaska. The camera was installed to remotely monitor plant phenology and operation of the Brookhaven National Laboratory (BNL) TEST group's ZPW (Zero Power Warming) chambers during the growing season of 2019. Images were captured from early spring (4 April) through to mid fall (30 October). Snowmelt, vegetation growth and senescence, and snow accumulation were captured. Images were uploaded to the BNL FTP server every hour, then from 2019-06-27 to 2019-10-02 images were recorded every 10 minutes, then at hourly intervals until the end of data collection on 2019-10-30. Files were renamed with the date and time of the image. jpg images have been compressed in *.tar.gz format (5.6 GB). Closer fields of view (northeasterly) were also captured using 4 Wingscapes TimelapseCam cameras mounted on a mast on the sled shed. These cameras were operated from 2019-06-23 to 2019-09-25, with images recorded every 30 minutes from 9:00 to 16:30 Alaska daylight time (AKDT, UTC-8). Individual jpg images have been compressed in zip format for each camera and also presented as mp4 timelapse movies.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 OSTI2025

Local halide heterogeneity drives surface wrinkling in mixed-halide wide-bandgap perovskites

Compositional heterogeneity in wide-bandgap (1.8 - 2.1 eV) mixed-halide perovskites is a key bottleneck in the processing of high-quality solution-processed thin films and prevents their application in efficient multijunction solar cells. Notably, mixed-cation (formamidinium-methylammonium) wide-bandgap perovskite films are prone to form micrometer-scale wrinkles which can interfere with the smooth surfaces ideal for multijunction devices. Here, we study the formation dynamics of wrinkled mixed-halide perovskite films and its impact on the local composition and optoelectronic properties. We use in situ X-ray scattering during perovskite film formation to show that crystallization of bromide-rich perovskites precedes that of mixed-halide phases in wrinkled films cast using an antisolvent-based process. Using nanoscopic X­-ray fluorescence and hyperspectral photoluminescence imaging, we also demonstrate the formation of iodide- and bromide-rich phases in the wrinkled domains. This intrinsic spatial halide segregation results in an increased local bandgap variation and Urbach energy. Morphological disorder and compositional heterogeneity also aggravate the formation of sub-bandgap electronic defects, reducing photostability and accelerating light-induced segregation of iodide and bromide ions in thin films and solar cells.

36 MATERIALS SCIENCE↗
DOE OSTI2022

An image classification deep-learning algorithm for shrapnel detection from ultrasound images

Ultrasound imaging is essential for non-invasively diagnosing injuries where advanced diagnostics may not be possible. However, image interpretation remains a challenge as proper expertise may not be available. In response, artificial intelligence algorithms are being investigated to automate image analysis and diagnosis. Here, we highlight an image classification convolutional neural network for detecting shrapnel in ultrasound images. As an initial application, different shrapnel types and sizes were embedded first in a tissue mimicking phantom and then in swine thigh tissue. The algorithm architecture was optimized stepwise by minimizing validation loss and maximizing F1 score. The final algorithm design trained on tissue phantom image sets had an F1 score of 0.95 and an area under the ROC curve of 0.95. It maintained higher than a 90% accuracy for each of 8 shrapnel types. When trained only on swine image sets, the optimized algorithm format had even higher metrics: F1 and area under the ROC curve of 0.99. Overall, the algorithm developed resulted in strong classification accuracy for both the tissue phantom and animal tissue. This framework can be applied to other trauma relevant imaging applications such as internal bleeding to further simplify trauma medicine when resources and image interpretation are scarce.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Sizes of pure and doped helium droplets from single shot x-ray imaging

Advancements in x-ray free-electron lasers on producing ultrashort, ultrabright, and coherent x-ray pulses enable single-shot imaging of fragile nanostructures, such as superfluid helium droplets. Furthermore, this imaging technique gives unique access to the sizes and shapes of individual droplets. In the past, such droplet characteristics have only been indirectly inferred by ensemble averaging techniques. Here, we report on the size distributions of both pure and doped droplets collected from single-shot x-ray imaging and produced from the free-jet expansion of helium through a 5 μm diameter nozzle at 20 bars and nozzle temperatures ranging from 4.2 to 9 K. This work extends the measurement of large helium nanodroplets containing 10 9 –10 11 atoms, which are shown to follow an exponential size distribution. Additionally, we demonstrate that the size distributions of the doped droplets follow those of the pure droplets at the same stagnation condition but with smaller average sizes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Active Learning Surrogates for Integrating Electron Microscopy and Computational Insights from Simulations in Autonomous Experiments

Artificial Intelligence (AI) combined with simulations and experiments has great potential to accelerate scientific discovery across technology and pharmaceuticals. However, the gap between simulations and experiments is challenging due to disparities in time and scale, making it difficult to estimate properties like energy and electronic states from experiments, and to provide feedback based on theoretical insights.Our research addresses the challenge by developing unique deep kernel based surrogate models that learns from microscopic images, mapping structural features to energy differences from defect formation. We start with full-training using simulated images to determine optimal settings, establishing a baseline for active learning. Using these settings from the baseline, active learning is trained, and predicts structures along simulation trajectories based on uncertainty and energetic stability, thus reducing data requirements, simulation time and computational costs. The results demonstrate that the model achieves a low average error margin of approximately 0.03 meV, indicating good performance. To enhance feature extraction and reconstruction capabilities, we developed an autoencoder-decoder as additional surrogate to create latent space to capture essential features, enabling precise comparisons between simulations and experiments. The results from this model achieved a reconstruction loss of around 0.2 and accurately reconstructed molecular structures.Overall, this work advances the steering of experiments through computational simulations by employing a surrogate models that actively predicts the trajectories of structural evolution, achieving time-to-solution comparable to experimental measurements.

Saranathan, Gayathri [Hewlett-Packard]↗
DOE OSTI2026

Timeseries Photos of a Variably Inundated Stream: Umtanum Creek, Washington, United States

This dataset is associated with a broader study using game camera timeseries photos collected to evaluate stream variable inundation via changes in width (i.e. wet fraction). Four game cameras were deployed along Umtanum Creek (Washington, United States) to track changes in stream inundation over time. Drone imagery was collected at the same location on October 18, 2024 which was used to construct a digital elevation model (DEM) of the streambed topography. The associated paper and data can be found at https://doi.org/10.1016/j.envsoft.2025.106715 (Bao et al., 2025a)) and https://doi.org/10.15485/2589885 (Bao et al., 2025b), respectively. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to this readme, this data package also includes a file-level metadata (FLMD) files that describes each file and a data dictionaries (DD) that describe all column/row headers and variable definitions. This dataset is comprised of (1) file-level metadata; (2) data dictionary; (3) readme; (4) field metadata; (5) field protocol; and (5) folders containing game camera photos. Game camera photos are organized into folders for each camera (CDL, CUL, CDR, CUR; see readme for information on camera naming) by the month photos were collected. All files are .csv, .jpg, or .pdf.

AI image segmentation↗
DOE OSTI2024

Vegetation Warming Experiment: Landscape-scale digital camera imagery for vegetation phenology, Utqiagvik, Alaska, 2021

Images captured using a StarDot NetCam SC phenocamera looking east from the top of the Barrow Environmental Observatory (BEO) Sled Shed, Utqiagvik, Alaska. The camera was installed to remotely monitor plant phenology and operation of the Brookhaven National Laboratory (BNL) TEST group's ZPW (Zero Power Warming) chambers during the growing season of 2021. Images were captured from early spring (1 April) through to mid fall (22 October). Snowmelt, vegetation growth and senescence, and snow accumulation were captured. Images were uploaded to the BNL FTP server every hour, then from 2021-07-09 images were recorded every 10 minutes until the end of data collection on 2021-10-22. Images have been combined in *.zip format (6.1 GB). Closer fields of view (northeasterly) were also captured using 4 Wingscapes TimelapseCam cameras mounted on a mast on the sled shed. These cameras were operated from 2021-06-19 to 2021-09-22, with images recorded every 30 minutes from 9:00 to 16:30 Alaska daylight time (AKDT, UTC-8). Individual jpg images from each camera have been combined in zip format. The data package includes a metadata document with example fields of view from each camera (*.pdf). 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 OSTI2022

Fluid Flow Observations of The Spray Near-Field Using High-Speed X-Ray Imaging

Sprays are important to may industrial processes, but the near-field region where spray formation takes place is difficult to visualize and characterize through visible light imaging because this region is typically optically dense. X-ray imaging is one technique that can penetrate this optically dense region and provide unique observations of the spray formation process. This study uses high-speed white beam X-ray imaging conducted at the Advanced Photon Source to capture spray formation dynamics from a canonical airblast atomizer. In this work, a range of momentum flux ratios are visualized by varying the gas flow rate while the liquid flow rate is held constant. The use of X-rays show overlapping flow structures including bags, ligaments, mushrooms, and webs. Air bubbles are captured within the liquid regions, and a very dynamic crown forms at the liquid needle exit at higher momentum flux ratios. Finally, at the highest momentum flux ratios, air bubbles and liquid droplets are observed migrating upstream in the center of the crown, and this motion is attributed to a toroidal recirculation cell at the nozzle exit.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Landscape-scale Characterization of Arctic Tundra Vegetation Composition, Structure, and Function with a Multi-sensor Unoccupied Aerial System: Supporting Data.

Airborne remote sensing data collected using the Brookhaven National Laboratory's (BNL) heavy-lift unoccupied aerial system (UAS) octocopter platform, the Osprey, operated by the Terrestrial Ecosystem Science and Technology (TEST) group (https://www.bnl.gov/testgroup). This package includes data from three flights flown over the NGEE-Arctic Council, Kougarok and Teller sites in July, 2018. The Osprey is a multi-sensor UAS platform that simultaneously measures very high spatial resolution optical red/green/blue (RGB) and thermal infrared (TIR) surface 'skin' temperature imagery, as well as surface reflectance at 1 nm intervals in the visible to near-infrared spectral range 350 - 1000 nm measured at regular intervals along each flight path. Derived image products include ortho-mosaiced RGB and TIR images, an RGB-based digital surface model (DSM) using the structure from motion (SfM) technique, digital terrain model (DTM), and a canopy height model (CHM). In addition, a VNIR surface reflectance file is provided for the trigger locations collected during each flight campaign. Ancillary aircraft data, flight mission parameters, and general flight conditions provided by the onboard flight and data collection computers are also included. Unprocessed and processed data products are included in this package (processing levels 0-3). Data and metadata are provided as text (*.txt, *.json, *.kml, *hdr, *.enp), tabular (*.dat, *.csv, *.waypoint, ENVI format (no extension)), point cloud (*.laz) and image (*.jpg, *.tif, *png) formats. This metadata document contains flight campaign, instrument and file metadata, along with a description of data processing levels, data products and file naming scheme.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), 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 OSTI2025

Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion

Bacterial biofilms are complex cell communities within a self-produced extracellular matrix, crucial in various fields but challenging to analyze in 3D. We developed a "biofilm-in-capillary" growth method compatible with full-rotation soft X-ray tomography, enabling high-resolution 3D imaging of bacterial cells and their matrix during biofilm formation. This approach offers 50 nm isotropic spatial resolution, rapid imaging, and quantitative native analysis of biofilm structure. Using Bacillus subtilis biofilms, we detected coherent alignment and chaining of wild-type cells towards the oxygen-rich capillary tip. In contrast, the ΔtasA genetic knock-out showed a loss of cellular orientation and changes in the extracellular matrix. Adding TasA protein to the ΔtasA strain restored matrix density and led to cell assembly compaction, but without the chaining observed in wild-type biofilms. This scalable and transferable approach opens new avenues for examining biofilm structure and function across various species, including mixed biofilms, and response to genetic and environmental factors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Data associated with “Different methods of estimating riverbed sediment grain size diverge at the basin scale ” (v2)

This data package is associated with the publication “Different methods of estimating riverbed sediment grain size diverge at the basin scale” published in Frontiers in Earth Science (Regier et al., 2025). The distribution of sediment grain size in streams and rivers is often quantified by the median grain size (d50), a key metric for understanding and predicting hydrologic and biogeochemical function of streams and rivers. Manual methods to measure d50 are time-consuming and ignore larger grains, while model-based methods to estimate d50 often over-generalize basin characteristics, and therefore cannot accurately represent site-scale heterogeneity. Here, we apply a machine learning-enabled photogrammetry methodology (You Only Look Once, or YOLO) for estimating d50 for grains > 2 mm based on images collected from streams and rivers throughout the Yakima River Basin (YRB). To understand how such methods may help bridge the gaps in resolution and accuracy between manual and catchment characteristics model-based d50 estimates, we compared YOLO d50 values to manual and model-based estimates across the YRB. We found distinct differences among methods for d50 averages and variability, and relationships between d50 estimates and basin characteristics. Source images can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1892052. This data package was originally published in May 2023. It was updated August 2025 (v2; new and modified files). File and folder names were not revised to indicate changes. See the change history section in the readme for more details. In addition to the readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) readme; (4) and subfolders containing data, figures, and scripts. The data folder contains datasets used for the analyses in the manuscript in image, text-delimited or geospatially-referenced formats. The figures folder contains the figures from the manuscript in different formats. The scripts folder contains all of the scripts used to complete the analyses in the manuscript. All files are .csv, .rds, .dbf, .prj, .shp, .shx, .jpg, .png, .R, .Rproj, or .pdf. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected some of these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗