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34 results for “atomic resolution”
Imaging surface structure and premelting of ice Ih with atomic resolution
<p>Here lies the tabulated data and the MD trajectories used to create the Figures for the Nature manuscript 2023-08-14175 titled "Imaging surface structure and premelting of ice Ih with atomic resolution".</p>
Dataset 1 for: Multi-eGO: an in-silico lens to look into protein aggregation kinetics at atomic resolution
<p><strong>Dataset</strong></p> <p>Molecular dynamics simulation trajectories of TTR peptide monomers and aggregation kinetics:</p> <ul> <li>Amber99sb_disp: TTR monomer in explicit solvent using amber99disp force field.</li> <li>multi-GO-monomer: TTR monomer simulation using the multi-GO force field.</li> <li>multi-eGO-monomer: TTR monomer simulation using the multi-eGO ensemble force field.</li> <li>multi-eGO-XXmM-Y: aggregation kinetics simulations of TTR using the multi-eGO force field at XXmM concentration replicate Y.</li> <li>.ipynb files: analysis script employed for the aggregation kinetics simulations.</li> <li>TTR aggregation kinetics movies.</li> </ul>
Dataset 3 for: Multi-eGO: an in-silico lens to look into protein aggregation kinetics at atomic resolution
<p><strong>Dataset</strong></p> <p>Multi-GO Molecular dynamics simulation trajectories of TTR peptide and aggregation kinetics; Multi-<em>e</em>GO oligomer structures and trajectories:</p> <ul> <li>multi-GO-XXmM: aggregation kinetics simulations of TTR using the multi-eGO force field at XXmM concentration.</li> <li>TTR structures and trajectories of oligomers from dimers to decamers.</li> </ul>
Atomic resolution high-angle annular dark field scanning transmission electron microscopy imaging of WSe2 encapsulated within hexagonal boron nitride
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Dataset related to the article 'The activation cascade of the broad-spectrum antiviral bemnifosbuvir characterized at atomic resolution'
<p>Raw data related to the scientific article "The activation cascade of the broad-spectrum antiviral bemnifosbuvir characterized at atomic resolution": </p> <ul> <li>Excel file: Numerical data related to the figures 1B, S8AB, S6B as well as Table 1. Raw data related to figure 3A and S4AB are the same than data associated with Table 1.</li> <li>PDF file: Image data of uncropped SDS-PAGE gels. </li> </ul>
Atomic-Resolution Structure of the Protein Encoded by Gene V of fd Bacteriophage in Complex with Viral ssDNA Determined by Magic-Angle Spinning Solid-State NMR
<p>F-specific filamentous phages, elongated particles with circular single-stranded DNA encased in a symmetric protein capsid, undergo an intermediate step, where thousands of homodimers of a non-structural protein, gVp, bind to newly synthesized strands of DNA, preventing further DNA replication and preparing the circular genome in an elongated conformation for assembly of a new virion structure at the membrane. While the structure of the free homodimer is known, the ssDNA-bound conformation has yet to be determined. We report an atomic-resolution structure of the gVp monomer bound to ssDNA of fd phage in the nucleoprotein complex elucidated via Magic-Angle Spinning solid-state NMR. The model presents significant conformational changes with respect to the free form. These modifications facilitate the binding mechanism and possibly promote cooperative binding in the assembly of the gVp-ssDNA complex.</p> <p>The raw NMR data used for structure determination are uploaded as original Bruker directories from topspin version 3.5. Processing details are given in the supporting Information of the manuscript. PDB ID is 8ACZ. BMRB accession number is 51391.</p>
NMR Data: Atomic Resolution Map of the solvent interactions driving SOD1 unfolding in CAPRIN1 condensates
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Data for "Defect detection in atomic-resolution images via unsupervised learning with translational invariance"
<p>This dataset accompanies the paper titled <em>Defect detection in atomic-resolution images via unsupervised learning with translational invariance</em> by Yueming Guo<sup>*</sup>, Sergei V. Kalinin, Hui Cai, Kai Xiao, Sergiy Krylyuk, Albert V Davydov, Qianying Guo, Andrew R. Lupini<sup>* </sup></p>
ATom: L2 Measurements from CU High-Resolution Aerosol Mass Spectrometer (HR-AMS)
This dataset provides the atmospheric concentrations of separated ions from inorganic and organic species measured by the High-Resolution Aerosol Mass Spectrometer (HR-AMS) collected during flights of the NASA ATom Mission. Data are available from all four ATom Campaigns. The HR-AMS detects non-refractory submicron aerosol composition by impaction on a vaporizer at 600 degrees C, followed by electron ionization and time-of-flight mass spectral analysis. The measurements include chemically speciated submicron non-refractory particulate mass at a one second and 60 second resolution, and the size distribution of chemically speciated submicron non-refractory particulate mass at 60 second resolution.
ATom: L2 Particulate Iodine from High-Resolution Aerosol Mass Spectrometer (HR-AMS)
This dataset provides mass concentrations of particulate iodine as measured by the High-Resolution Aerosol Mass Spectrometer (HR-AMS) during the first two deployments of the NASA Atmospheric Tomography airborne missions (ATom-1 and ATom-2) in 2016 and 2017, respectively. The data provided in this dataset result from a reanalysis of the initial HR-AMS data based on post-mission calibrations and are reported at 1-minute resolution. The dataset also includes the fractions of the main ions (I+, HI+, and I2+) that can be used to ascertain the oxidation state of iodine in particles. Each observation includes an air mass classification flag (tropospheric or stratospheric conditions) based on collocated in situ water vapor and ozone measurements and positional data from the HR-AMS data feed.
Protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit
GEO Series GSE157425. Mus musculus. 26 samples. Type: Expression profiling by high throughput sequencing.
RENU2 UltraViolet PhotoMultiplier Tube (UVPMT) Atomic Oxygen Density, High Time Resolution (H0), 42 ms Data
Rocket Experiment for Neutral Upwelling 2, RENU2, UltraViolet PhotoMultiplier Tube, UVPMT, Counts. The UVPMT Instrument is used to observe Atomic Oxygen Signatures in Sunlight, that is, above the Payload.
Multi-eGO: An in silico lens to look into protein aggregation kinetics at atomic resolution
<p>Scalone E, Broggini L, Visentin C, Erba D, Bačić Toplek F, Peqini K, Pellegrino S, Ricagno S, Paissoni C, Camilloni C. Multi-eGO: An in silico lens to look into protein aggregation kinetics at atomic resolution. Proc Natl Acad Sci U S A. 2022 Jun 28;119(26):e2203181119. doi: 10.1073/pnas.2203181119. Epub 2022 Jun 23. PMID: 35737839; PMCID: PMC9245614.</p> <p>Abstract</p> <p>Protein aggregation into amyloid fibrils is the archetype of aberrant biomolecular self-assembly processes, with more than 50 associated diseases that are mostly uncurable. Understanding aggregation mechanisms is thus of fundamental importance and goes in parallel with the structural characterization of the transient oligomers formed during the process. Oligomers have been proven elusive to high-resolution structural techniques, while the large sizes and long time scales, typical of aggregation processes, have limited the use of computational methods to date. To surmount these limitations, we here present multi-<em>e</em>GO, an atomistic, hybrid structure-based model which, leveraging the knowledge of monomers conformational dynamics and of fibril structures, efficiently captures the essential structural and kinetics aspects of protein aggregation. Multi-<em>e</em>GO molecular dynamics simulations can describe the aggregation kinetics of thousands of monomers. The concentration dependence of the simulated kinetics, as well as the structural features of the resulting fibrils, are in qualitative agreement with in vitro experiments carried out on an amyloidogenic peptide from Transthyretin, a protein responsible for one of the most common cardiac amyloidoses. Multi-<em>e</em>GO simulations allow the formation of primary nuclei in a sea of transient lower-order oligomers to be observed over time and at atomic resolution, following their growth and the subsequent secondary nucleation events, until the maturation of multiple fibrils is achieved. Multi-<em>e</em>GO, combined with the many experimental techniques deployed to study protein aggregation, can provide the structural basis needed to advance the design of molecules targeting amyloidogenic diseases.</p>
Data for "Atomic-resolution transmission electron microscopy of electron beam-sensitive crystalline materials"
<p>The dataset contains two files associated with the paper titled "Atomic-resolution transmission electron microscopy of electron beam-sensitive crystalline materials".</p> <p><strong>1. Lowdose HRTEM images.zip</strong></p> <p>A compressed file containing the raw and processed HRTEM images discussed in the paper. </p> <p><strong>2. Plugins.zip</strong></p> <p>A compressed file containing two DigitalMicrograph plugins.</p> <p><em>(i) Zone_Axis_Alignment.gtk</em></p> <p>It is used for the quick alignment of crystal zone axis during TEM imaging. Test environment: Cs-corrected FEI Titan transmission electron microscope operated at 300 kV; Gatan Ultrascan 1000XP CCD camera; Gatan DigitalMicrograph V1.85. </p> <p><em>(ii) Amplitude_Filter.gtk</em></p> <p>It is used for the precise alignment of low-dose HRTEM images, and is referred to as an "Amplitude Filter" in the paper. Test environment: Gatan DigitalMicrograph V3.12. </p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.