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The Fuels Development Team's goal is to try to learn drilling speeds and electrode dimensions to achieve desired diameters on a ZrC disk. We desire to send both the drawing and material to Sodick for drilling.
LLNL National Lab Accelerator Pitch Event, December 2, 2020
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A process for separations and recovery from mixtures via specific adsorption using high-surface area, flexible silica-based nanostructured gel adsorbents and articles of manufacture relating to same.
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Protein structure prediction is an important problem in bioinformatics and has been studied for decades. However, there are still few open-source comprehensive protein structure prediction packages publicly available in the field. In this paper, we present our latest open-source protein tertiary structure prediction system—MULTICOM2, an integration of template-based modeling (TBM) and template-free modeling (FM) methods. The template-based modeling uses sequence alignment tools with deep multiple sequence alignments to search for structural templates, which are much faster and more accurate than MULTICOM1. The template-free (ab initio or de novo) modeling uses the inter-residue distances predicted by DeepDist to reconstruct tertiary structure models without using any known structure as template. In the blind CASP14 experiment, the average TM-score of the models predicted by our server predictor based on the MULTICOM2 system is 0.720 for 58 TBM (regular) domains and 0.514 for 38 FM and FM/TBM (hard) domains, indicating that MULTICOM2 is capable of predicting good tertiary structures across the board. It can predict the correct fold for 76 CASP14 domains (95% regular domains and 55% hard domains) if only one prediction is made for a domain. The success rate is increased to 3% for both regular and hard domains if five predictions are made per domain. Moreover, the prediction accuracy of the pure template-free structure modeling method on both TBM and FM targets is very close to the combination of template-based and template-free modeling methods. This demonstrates that the distance-based template-free modeling method powered by deep learning can largely replace the traditional template-based modeling method even on TBM targets that TBM methods used to dominate and therefore provides a uniform structure modeling approach to any protein. Finally, on the 38 CASP14 FM and FM/TBM hard domains, MULTICOM2 server predictors (MULTICOM-HYBRID, MULTICOM-DEEP, MULTICOM-DIST) were ranked among the top 20 automated server predictors in the CASP14 experiment. After combining multiple predictors from the same research group as one entry, MULTICOM-HYBRID was ranked no. 5. The source code of MULTICOM2 is freely available at https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .
Abstract Substantial progresses in protein structure prediction have been made by utilizing deep‐learning and residue‐residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by incorporating three new components: (a) a new deep learning‐based protein inter‐residue distance predictor to improve template‐free (ab initio) tertiary structure prediction, (b) an enhanced template‐based tertiary structure prediction method, and (c) distance‐based model quality assessment methods empowered by deep learning. In the 2020 CASP14 experiment, MULTICOM predictor was ranked seventh out of 146 predictors in tertiary structure prediction and ranked third out of 136 predictors in inter‐domain structure prediction. The results demonstrate that the template‐free modeling based on deep learning and residue‐residue distance prediction can predict the correct topology for almost all template‐based modeling targets and a majority of hard targets (template‐free targets or targets whose templates cannot be recognized), which is a significant improvement over the CASP13 MULTICOM predictor. Moreover, the template‐free modeling performs better than the template‐based modeling on not only hard targets but also the targets that have homologous templates. The performance of the template‐free modeling largely depends on the accuracy of distance prediction closely related to the quality of multiple sequence alignments. The structural model quality assessment works well on targets for which enough good models can be predicted, but it may perform poorly when only a few good models are predicted for a hard target and the distribution of model quality scores is highly skewed. MULTICOM is available at https://github.com/jianlin-cheng/MULTICOM_Human_CASP14/tree/CASP14_DeepRank3 and https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .
The ESS-DIVE (Environmental Systems Science Data Infrastructure for a Virtual Ecosystem) reporting format for sample-based water and soil chemistry measurements are written guidelines and spreadsheet templates, that facilitate archiving water/soil/sediment chemistry data. The templates and terminology lists provided as part of the reporting format can help organize data and potentially enable data reuse.The reporting format consists of a general instructions file (instructions.md) as well as more detailed instructions files for each template (files beginning “Detailed_Instructions_*.md). The “examples” folder includes an example of each data template with just the limited set of required fields filled out as well as other examples with both required and optional fields complete.The 'templates' folder contains CSV templates for data, methods, and terminology file templates. Similar to the examples folder, the blank templates are provided with versions for required fields only as well as required and optional fields. Lastly, the term list folder provides common terminology used in each of the templates as well as a definition and any constraints for the fields.
Monolithic ultralow-density porous bulk materials have recently attracted much interest due to many emerging applications in the areas of catalysis, energy storage and conversion, and thermal insulation. They are also important components of high energy density (HED) and inertial confinement fusion (ICF) targets. However, despite tremendous progress that has been made in the synthesis of porous materials, deterministic and independent control over microscopic architecture, density and composition remain key issues, and their integration in high precision devices requires cost and time-intensive mechanical machining that not only reduces reproducibility by generating debris but also limits the complexity of the 3D shapes that can be realized. In this project, we overcame these limitations by developing a universal templating capability that provides deterministic and independent control over density, composition, architecture, and macroscopic sample shape. This was achieved by developing the technology to 1) 3D print ultrahigh resolution, ultra-high precision polymeric micro-lattice templates, 2) coat these templates with the desired materials, and 3) removing the template (Fig. 1a). Atomic layer deposition (ALD) provides the atomic scale coating thickness accuracy required for precisely controlling density. While this templating approach had been demonstrated in prior work, limitations in suitable photoresists, 3D print technologies, print design, and template removal techniques did not allow the fabrication of millimeter-sized high-precision parts with sub-micron resolution. To enable this technology, we developed 1) two-photon polymerization (TPP) print designs that enable the fabrication of millimeter-sized, mechanically robust polymeric templates with sub-micron resolution and 2) a continuum level TPP printing simulation capability for additional print design guidance; 3) atomistic models to study photoresist polymerization kinetics and network topography, 4) refractive index matched polymeric and preceramic TPP photoresists, and 5) functional TPP photoresists including porous voxel structures and self-immolative polymer photoresist chemistries; and 6) damage free template removal techniques that enable the fabrication of defect-free high-precision low-density foam components. We also developed a templating approach for pure carbon microlattices with a unique tube-in-tube ligament morphology. As a test platform, we pursued the fabrication of foam liners that promise to further increase the neutron yield in indirect drive ICF experiments by improving implosion symmetry control and coupling between the laser and the deuterium-tritium fuel. This application requires fabrication and integration of a ultra-high precision, millimeter-sized, thin-walled (200-400 micrometer thick), low-density (10-30 mg/cc), high atomic number (high Z) cylindrical foam tube into the gold hohlraum of an indirect drive ICF target (Fig. 1b). While our hohlraum liner test case will mainly find application in HED and ICF experiments, the underlying science will also directly apply to previously developed nanoparticle and additive manufacturing technologies and will advance those techniques as well.
Carbon aerogels (CAs) combine unique properties including ultra-high surface area, high electrical conductivity, corrosion resistance, and robust mechanical properties making them ideal materials for electrochemical applications. Traditional CA synthesis results in isotropic, random nanoporous networks that work well for applications relying on diffusional mass transport. However, many applications would benefit from integration of engineered macroporous network structures that enable directed pressure-gradient-driven mass transport. In this study, we report on using 3D-printed sacrificial polymeric templates to generate templated CAs (t-CAs) with integrated engineered nonrandom macroporous network structures. Specifically, we used projection micro-stereo-lithography (PμSL) and two-photon polymerization direct laser writing (2PP-DLW) to fabricate millimeter-to-centimeter-sized 3D sacrificial polymeric templates with features ranging from tens of microns (PμSL) to 100s of nanometers (2PP-DLW). T-CAs were fabricated by infiltrating the templates with resorcinol-formaldehyde (RF) precursor solution, followed by carbonization at 1050 °C to simultaneously convert the RF gel to a CA and decompose the 3D-printed template, leaving an embedded templated macroporous network structure behind. X-ray computer tomography confirms integration of the macroporous architecture defined by the template. The templated macroporous architecture improves mass transport in t-CAs compared to traditional bulk CA as demonstrated by more uniform activation and their response in electrochemical cyclic voltammetry and galvanostatic charge-discharge tests.
Since the first few reports of its synthesis in 2011 and 20121-3, interest in ZnSnN 2 for diverse applications, including photovoltaics1,3,4, visible light photocatalysis5, and optoelectronics, has been growing. Novel nitride-based LED device designs promise high gains in efficiency at emission wavelengths into the green, amber and even red.6-8 Their realization requires the precise insertion of an ultrathin layer of ZnGeN 2 or ZnSnN 2 into the active region of an InGaAs-GaAs LED structure. While thin films of ZnSnN 2 have been synthesized by RF sputtering1,9 and by MBE 2,10,11, and thin films of ZnGeN 2 , ZnSiN 2 and their alloys by MOCVD, the synthesis of ZnSnN 2 thin films by MOCVD has not yet been reported. It is a challenging goal, given the narrow temperature window between efficient activation of ammonia and the thermal decomposition of ZnSnN 2 at near-atmospheric pressures. We report here the results of studies of ZnSnN 2 films grown on r- and c-plane sapphire substrates, GaN templates on sapphire, and In 0.15 Ga 0.85 N templates on GaN-on-sapphire, at temperatures from 500 °C to 560 °C, using tetramethyltin (TMSn), diethylzinc (DEZn), germane and ammonia. Chamber pressures were varied between 200 and 500 torr. In addition, the ratios of the cation precursors and the total cation-to-anion precursor ratios were varied. Single crystal growth, as evidenced by 2θ-ω x-ray diffraction scans, was achieved on all of these substrates. Wurtzitic (0002) ZnSnN 2 diffraction were observed at 2θ ~ 32.90 for the samples grown on c-sapphire, GaN (0001) and InGaN (0001) templates, and wurtzitic (11-20) peak at 2θ ~ 54.80 for the films grown on r-sapphire. Higher pressures and higher temperatures promoted better crystallinity and more continuous films, as revealed by scanning electron microscopy (SEM) images and 2θ-ω x-ray diffraction peak widths and intensities. Crystal quality was observed to be highly dependent on growth temperature. For example, in one series a 10 °C change in growth temperature resulting in a factor of 15 increase in diffraction peak intensity. SEM images show that films grown on the GaN templates had better uniformity in nucleation than those grown on sapphire. The presence of satellite peaks around the Bragg peak in the XRD 2θ-ω scan for a film grown on a GaN template, and the absence of satellite peaks for the films grown simultaneously on c- and r-sapphire, also indicate superior quality for the film grown on GaN. HAADF-STEM images of films grown on these templates showed smooth interfaces at the film-substrate boundary and show growth rates as high as 167 nm/h, considerably higher than reported previously for MBE growth.9,10 Electron diffraction patterns show single crystallinity. Rocking curves show FWHM as low as 0.100. RMS surfaces roughnesses, measured by atomic force microscopy, are of the order of 3 nm for 1µm x 1µm areas. Current work is focusing on optimizing growth on InGaN templates. These templates are promising for their relatively lower lattice mismatch with ZnSnN 2 . Their use is a next step toward producing LED device structures.
K -corrections – a necessary ingredient for converting between flux in observed bands to flux in rest-frame bands – are critical for comparing galaxies at differing redshifts. These corrections often rely on fits to empirical or theoretical spectral energy distribution (SED) templates of galaxies. However, templates can only produce reliable K-corrections in regimes where SED models are robust. For instance, the templates utilized in some popular software packages are not well-constrained in some bands (e.g. WISE W4 in KCORRECT ), which results in ill-behaved K -corrections. We address this shortcoming by developing an empirically driven approach to K -corrections that limits the dependence on SED templates. We perform a polynomial fit for the K -correction as a function of a galaxy’s rest-frame colour determined in a pair of well-constrained bands (e.g. 0 (g − r)) and redshift, exploiting the fact that galaxy SEDs can be approximated as a one-parameter family at low redshift. For bands well-constrained by SED templates, our empirically driven K -corrections yield results comparable to the SED fitting methods used by KCORRECT and the GSWLC-M2 catalogue (the updated medium-deep GALEX–SDSS–WISE Legacy Catalogue). However, our method dramatically outperforms Kcorrect derived K -corrections for WISE W4 . Our method is also robust to incorrect template assumptions outside of the optical bands and enforces that the K -correction must be zero at z = 0. Our K -corrected photometry and code are publicly available.
This dataset contains identifiers, metadata, and a map of the locations where field measurements have been conducted at the East-Taylor Watershed Community Observatory located in the Upper Colorado River Basin, United States. This is version 3.3 of the dataset and replaces the prior version 3.2 (see below for details on changes between the versions). Dataset description: The East River-Taylor Watershed is the primary field site of the Watershed Function Scientific Focus Area (WFSFA) and the Rocky Mountain Biological Laboratory. Researchers from several institutions generate highly diverse hydrological, biogeochemical, climate, vegetation, geological, remote sensing, and model data at the East-Taylor Watershed in collaboration with the WFSFA. Thus, the purpose of this dataset is to maintain an inventory of the field locations and instrumentation to provide information on the field activities in the East-Taylor Watershed and coordinate data collected across different locations, researchers, and institutions. The dataset contains (1) a README file with information on the various files, (2) three csv files describing the metadata collected for each surface point location, plot and region registered with the WFSFA, (3) csv files with metadata and contact information for each surface point location registered with the WFSFA, (4) a csv file with with metadata and contact information for plots, (5) a csv file with metadata for geographic regions and sub-regions within the watershed, (6) a compiled xlsx file with all the data and metadata which can be opened in Microsoft Excel, (7) a kml map of the locations plotted in the watershed which can be opened in Google Earth, (8) a jpg image of the kml map which can be viewed in any photo viewer, and (9) a zipped file with the registration templates used by the SFA team to collect location metadata. The zipped template file contains two csv files with the blank templates (point and plot), two csv files with instructions for filling out the location templates, and one compiled xlsx file with the instructions and blank templates together. Additionally, the templates in the xlsx include drop down validation for any controlled metadata fields. Persistent location identifiers (Location_ID) are determined by the WFSFA data management team and are used to track data and samples across locations. Dataset uses: This location metadata is used to update the Watershed SFA’s publicly accessible Field Information Portal (an interactive field sampling metadata exploration tool; https://wfsfa-data.lbl.gov/watershed/), the kml map file included in this dataset, and other data management tools internal to the Watershed SFA team. Version Information: The latest version of this dataset publication is version 3.3. This version contains 167 new point locations, 1 new plot, and 2 new geographic regions. Overall, there are a total of 1439 point locations, 75 plots, and 54 geographic regions. Additionally, the kml map of locations and image now includes two boundaries (Upper Ohio Creek (UO) and Carbon Creek (CA)) outside of the East River watershed (USGS HUC-10) and accompanying stream network that represents areas of focus. Refer to methods for further details on the version history. This dataset will be updated on a periodic basis with new measurement location information. Researchers interested in having their East-Taylor Watershed measurement locations added to this list should reach out to the WFSFA data management team at wfsfa-data@googlegroups.com. Acknowledgments: Please cite this dataset if using any of the location metadata in other publications or derived products. If using the location metadata for the 2018 NEON hyperspectral campaign, additionally cite Chadwick et al. (2020). doi:10.15485/1618130. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.
Two balls were dropped approximately 150 m down an open borehole as part of an investigation into the aftershocks from a 51 ton TNT-equivalent chemical explosion. The ball drop sources, a concrete-filled basketball and a bowling ball, were intended to mimic falling debris within an underground explosion borehole and cavity. Falling debris or sloughing of the borehole and cavity walls is thought to be one of the sources of explosion aftershocks. The signals from the ball drop sources were recorded by the same seismic network that monitored the aftershocks of the chemical explosion, so the ball drop recordings were used as templates to search through the continuous stream of aftershocks and detect correlated signals as a proportion of all aftershocks. The search resulted in only four similar event recordings out of the thousands of detected aftershocks. A synthetic test showed that the small, high-frequency ball drop templates were limited to producing highly correlated detections for events occurring in a small region around the impact location at 150 m depth. The high-frequency templates were necessary since the small ball drop signals were only above the noise at frequencies greater than 10 Hz. Unfortunately, the impact location is where the borehole was filled with sand in preparation for the subsequent chemical explosion in the test series, making it 150 m above the explosion created cavity centered at 300 m depth. This puts the ball drop templates 150 m away from the cavity, where many more events from falling debris would be expected. Further synthetic tests confirmed events emanating from the cavity 150 m below the impact site would have correlated with the lower frequency template and been detected had the template been usable below 10 Hz. Therefore, we conclude that the four detected events were most probably falling debris within the open borehole that impacted the floor at 150 m depth just as the ball drop sources had, and that this type of explosion aftershock mechanism comprises less than 1% of all explosion aftershocks.
A continuous or semi-continuous process for fabricating nanowires or microwires makes use of the substantially planar template that may be moved through electrochemical solution to grow nanowires or microwires on exposed conductive edges on the surface of that template. The planar template allows fabrication of the template using standard equipment and techniques. Adhesive transfer may be used to remove the wires from the template and in one embodiment to draw a continuous wire from the template to be wound around the drum.
A method of forming a battery electrode by forming, on a first substrate, a polymer template comprising interconnected polymer fibers, forming, on the polymer template, a carbon coating to form a carbon-coated polymer template, removing the carbon-coated polymer template from the first substrate, subsequent to removing the carbon-coated polymer template from the first substrate, removing the polymer template from the carbon coating, and disposing the carbon coating on a second substrate. A solid electrolyte interphase layer (SEI) comprising the carbon coating produced via the method, a battery electrode comprising such an SEI layer, and a battery comprising such a battery electrode are also provided.
Remdesivir (RDV) prodrug can be metabolized into a triphosphate form nucleotide analogue (RDV-TP) to bind and insert into the active site of viral RNA dependent RNA polymerase (RdRp) to further interfere with viral genome replication. Here in this work, we computationally studied how RDV-TP binds and inserts to the SARS-CoV-2 RdRp active site, in comparison with natural nucleotide substrate adenosine triphosphate (ATP). To do that, we first constructed atomic structural models of an initial binding complex (active site open) and a substrate insertion complex (active site closed), based on high-resolution cryo-EM structures determined recently for SARS-CoV-2 RdRp or non-structural protein (nsp) 12, in complex with accessory protein factors nsp7 and nsp8. By conducting all-atom molecular dynamics simulation with umbrella sampling strategies on the nucleotide insertion between the open and closed state RdRp complexes, our studies show that RDV-TP can initially bind in a comparatively stabilized state to the viral RdRp active site, as it primarily forms base stacking with the template uracil nucleotide (nt +1), which under freely fluctuations supports a low free energy barrier of the RDV-TP insertion (~1.5 kcal mol -1 ). In comparison, the corresponding natural substrate ATP binds initially to the RdRp active site in Watson–Crick base pairing with the template nt, and inserts into the active site with a medium low free energy barrier (~2.6 kcal mol -1 ), when the fluctuations of the template nt are well quenched. The simulations also show that the initial base stacking of RDV-TP with the template can be specifically stabilized by motif C-S759, S682 (near motif B) with the base, and motif G-K500 with the template backbone. Although the RDV-TP insertion can be hindered by motif F-R555/R553 interaction with the triphosphate, the ATP insertion seems to be facilitated by such interactions. The inserted RDV-TP and ATP can be further distinguished by specific sugar interaction with motif B-T687 and motif A-D623, respectively.
The ESS-DIVE reporting format for file-level metadata (FLMD) provides granular information at the data file level to describe the contents, scope, and structure of the data file to enable comparison of data files within a data package. The FLMD are fully consistent with and augment the metadata collected at the data package level. We developed the FLMD template based on a review of a small number of existing FLMD in use at other agencies and repositories with valuable input from the Environmental Systems Science (ESS) Community. Also included is a template for a CSV Data Dictionary where users can provide file-level information about the contents of a CSV data file (e.g., define column names, provide units). Files are in .csv, .xlsx, and .md. Templates are in both .csv and .xlsx (open with e.g. Microsoft Excel, LibreOffice, or Google Sheets). Open the .md files by downloading and using a text editor (e.g. Notepad or TextEdit). Though we provide Excel templates for the file-level metadata reporting format, our instructions encourage users to 'Save the FLMD template as a CSV following the CSV Reporting Format guidance'. In addition, we developed the ESS-DIVE File Level Metadata Extractor which is a lightweight python script that can extract some FLMD fields following the recommended FLMD format and structure.