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Results for “electron microscopy data bank”

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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10 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

EMDB—the Electron Microscopy Data Bank

Abstract The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archive, and the EMDB team is a core member of the consortium. Today, EMDB houses over 30 000 entries with maps containing macromolecules, complexes, viruses, organelles and cells. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Q -score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps

Atomic coordinate models are important for the interpretation of 3D maps produced with cryoEM and cryoET (3D electron microscopy; 3DEM). In addition to visual inspection of such maps and models, quantitative metrics can inform about the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, Q-score, was shown to correlate well with the reported resolution of the map for well fitted models. Here, we present new statistical analyses of Q-score based on its application to ∼10 000 maps and models archived in the EMDB (Electron Microscopy Data Bank) and PDB (Protein Data Bank). Further, we introduce two new metrics based on Q-score to represent each map and model relative to all entries in the EMDB and those with similar resolution. We explore through illustrative examples of proteins, nucleic acids and small molecules how Q-scores can indicate whether the atomic coordinates are well fitted to 3DEM maps and also whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage and/or conformational heterogeneity. These examples and statistical analyses provide a basis for how Q-scores can be interpreted effectively in order to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving.

B factors↗
DOE OSTI2024

Community recommendations on cryoEM data archiving and validation

In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2025

Protein Data Bank (PDB): Fifty-three years young and having a transformative impact on science and society

This review article describes the co-evolution of structural biology as a discipline and the Protein Data Bank (PDB), established in 1971 as the first open-access data resource in biology by like-minded structural scientists. As the PDB archive grew in size and scope to encompass macromolecular crystallography, NMR spectroscopy, and cryo-electron microscopy, new technologies were developed to ingest, validate, curate, store, and distribute the information. Community engagement ensured that the needs of structural biologists (data depositors) and data consumers were met. Today, the archive houses more than 230,000 experimentally determined structures of proteins, nucleic acids, and macromolecular machines and their complexes with one another and small-molecule ligands. Aggregate costs of PDB data preservation are ~1% of the cost of structure determination. The enormous impact of PDB data on basic and applied research and education across the natural and medical sciences is presented and highlighted with illustrative examples. Enablement of de novo protein structure prediction (AlphaFold2, RoseTTAfold, OpenFold, etc.) is the most widely appreciated benefit of having a corpus of rigorously validated, expertly curated 3D biostructure data.

bioinformatics↗
NASA NTRS1988

Arc-textured metal surfaces for high thermal emittance space radiators

Carbon arc electrical discharges struck across the surfaces of metals such as Nb-1 percent Zr, alter the morphology to produce a high thermal emittance surface. Metal from the surface and carbon from the arc electrode vaporize during arcing, and then condense on the metal surface to produce a microscopically rough surface having a high thermal emittance. Quantitative spectral reflectance measurements from 0.33 to 15 microns were made on metal surfaces which were carbon arc treated in an inert gas environment. The resulting spectral reflectance data were then used to calculate thermal emittance as a function of temperature for various methods of arc treatment. The results of arc treatment on various metals are presented for both ac and dc arcs. Surface characterization data, including thermal emittance as a function of temperature, scanning electron microscopy, and atomic oxygen durability, are also presented. The ac arc texturing was found to increase the thermal emittance at 800 K from 0.05 to 0.70.

Banks, Bruce A.↗
NASA NTRS1992

Monte Carlo modeling of atomic oxygen attack of polymers with protective coatings on LDEF

Characterization of the behavior of atomic oxygen interaction with materials on the Long Duration Exposure Facility (LDEF) will assist in understanding the mechanisms involved, and will lead to improved reliability in predicting in-space durability of materials based on ground laboratory testing. A computational simulation of atomic oxygen interaction with protected polymers was developed using Monte Carlo techniques. Through the use of assumed mechanistic behavior of atomic oxygen and results of both ground laboratory and LDEF data, a predictive Monte Carlo model was developed which simulates the oxidation processes that occur on polymers with applied protective coatings that have defects. The use of high atomic oxygen fluence-directed ram LDEF results has enabled mechanistic implications to be made by adjusting Monte Carlo modeling assumptions to match observed results based on scanning electron microscopy. Modeling assumptions, implications, and predictions are presented, along with comparison of observed ground laboratory and LDEF results.

Banks, Bruce A.↗
NASA NTRS1993

Characteristics of hypervelocity impact craters on LDEF experiment S1003 and implications of small particle impacts on reflective surfaces

The Ion Beam textured and coated surfaces EXperiment (IBEX), designated S1003, was flown on LDEF at a location 98 deg in a north facing direction relative to the ram direction. Thirty-six diverse materials were exposed to the micrometeoroid (and some debris) environment for 5.8 years. Optical property measurements indicated no changes for almost all of the materials except S-13G, Kapton, and Kapton-coated surfaces, and these changes can be explained by other environmental effects. From the predicted micrometeoroid flux of NASA SP-8013, no significant changes in optical properties of the surfaces due to micrometeoroids were expected. There were hypervelocity impacts on the various diverse materials flown on IBEX, and the characteristics of these craters were documented using scanning electron microscopy (SEM). The S1003 alumigold-coated aluminum cover tray was sectioned into 2 cm x 2 cm pieces for crater documentation. The flux curve generated from this crater data fits well between the 1969 micrometeoroid model and the Kessler debris model for particles less than 10(exp -9) gm which were corrected for the S1003 positions (98 deg to ram). As the particle mass increases, the S1003 impact data is greater than that predicted by even the debris model. This, however, is consistent with data taken on intercostal F07 by the Micrometeoroid/Debris Special Investigating Group (M/D SIG). The mirrored surface micrometeoroid detector flown on IBEX showed no change in solar reflectance and corroborated the S1003 flux curve, as well as results of this surface flown on SERT 2 and OSO 3 for as long as 21 years.

Mirtich, Michael J.↗
DOE OSTI2026

pyDiSCaMB : enabling the use of multipolar scattering factors in Phenix

Multipolar scattering models, such as the transferable aspherical atom model, account for atomic chemical interactions and provide a more accurate representation of experimental data. However, the simpler independent atom model (IAM), which assumes non-interacting atoms, is the only model available in the most widely used macromolecular refinement programs. This is primarily because IAM offers a hard-to-beat combination of computational efficiency and modelling power at typical macromolecular resolutions. By contrast, more accurate multipolar modelling has historically been limited due to its computational cost and the absence of an interface between software capable of calculating structure factors and gradients based on multipolar models and software designed for macromolecular refinement. This work introduces pyDiSCaMB , a Python software package designed to integrate between the computational crystallography toolbox ( cctbx ) and the quantum crystallography library DiSCaMB ( Densities in Structural Chemistry and Molecular Biology ), thus enabling multipolar scattering models in Phenix 's toolkit. The implementation, features and capabilities of pyDiSCaMB are presented, the runtimes for the calculation of structure factor and target gradients with respect to atomic parameters are explored, and Fourier images of electrostatic potential, electron density and deformation maps are computed as illustrative examples. The pyDiSCaMB library will make multipolar modelling widely available to the structural biology community, potentially transforming refinement and model-building for both crystallography and cryogenic electron microscopy (cryoEM).

MATTS data bank↗
NASA NTRS2018

The Erosion of Diamond and Highly Oriented Pyrolytic Graphite After 1.5 Years of Space Exposure

Polymers and other oxidizable materials on the exterior of spacecraft in the low Earth orbit (LEO) space environment can be eroded due to reaction with atomic oxygen (AO). Therefore, in order to design durable spacecraft, it is important to know the LEO AO erosion yield (Ey, volume loss per incident oxygen atom) of materials susceptible to AO reaction. The Polymers Experiment was developed to determine the AO Ey of various polymers and other materials flown in ram and wake orientations in LEO. The experiment was flown as part of the Materials International Space Station Experiment 7 (MISSE 7) mission for 1.5 years on the exterior of the International Space Station (ISS). As part of the experiment, a sample containing Class 2A diamond (100 plane) and highly oriented pyrolytic graphite (HOPG, basal and edge planes) was exposed to ram AO and characterized for erosion. The materials were salt-sprayed prior to flight to provide isolated sites of AO protection. The Ey of the samples was determined through post-flight electron microscopy recession depth measurements. The experiment also included a Kapton H witness sample for AO fluence determination. This paper provides an overview of the MISSE 7 mission, a description of the flight experiment, the characterization techniques used, the mission AO fluence, and the LEO Ey results for diamond and HOPG (basal and edge planes). The data is compared to the Ey of pyrolytic graphite exposed to four years of space exposure as part of the MISSE 2 mission. The results indicate that diamond erodes, but with a very low Ey of 1.58 +/- 0.04 x 10(exp -26) cm(exp 3)/atom. The different HOPG planes displayed significantly different amounts of erosion from each other. The HOPG basal plane had an Ey of 1.05 +/- 0.08 x 10(exp -24) cm(exp 3)/atom while the edge plane had a lower Ey of only 5.38 +/- 0.90 x 10(exp -25) -cm(exp 3)/atom. The Ey data from this ISS spaceflight experiment provides valuable information for understanding of chemistry and chemical structure dependent modeling of AO erosion.

erosion↗
NASA NTRS2001

Controlling Growth Orientation of Phthalocyanine Films by Electrical Fields

Organic Phthalocyanine films have many applications ranging from data storage to various non-linear optical devices whose quality is affected by the growth orientation of Phthalocyanine films. Due to the structural and electrical properties of Phthalocyanine molecules, the film growth orientation depends strongly on the substrate surface states. In this presentation, an electrical field up to 4000 V/cm is introduced during film growth. The Phthalocyanine films are synthesized on quartz substrates using thermal evaporation. An intermediate layer is deposited on some substrates for introducing the electrical field. Scanning electron microscopy, x-ray diffraction, and Fourier transform infrared spectroscopy are used for measuring surface morphology, film structure, and optical properties, respectively. The comparison of Phthalocyanine films grown with and without the electrical field reveals different morphology, film density, and growth orientation, which eventually change optical properties of these films. These results suggest that the growth method in the electrical field can be used to synthesized Phthalocyanine films with a preferred crystal orientation as well as propose an interaction mechanism between the substrate surface and the depositing molecules. The details of growth conditions and of the growth model of how the Phthalocyanine molecules grow in the electrical field will be discussed.

Zhu, S.↗