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669 results for “ATOM”
Asperity level characterisation of abrasive wear using atomic force microscopy
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A phononic crystal coupled to a transmission line via an artificial atom. Experimental data for the article figures
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Optical and NMR spectra along with atomic coordinates of the title compounds for: Deciphering the Enigma of Unusual Fluorescence in Weakly Coupled Bis-nitro-pyrrolo[3,2-b]pyrroles
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Data for A FinFET with one atomic layer channel
<p>This dataset contains raw optical/SEM images of the nano fabrication, and electrical transport test, etc, which are related to the manuscript of A FinFET with One Atomic Layer Channel.</p>
All Atom Molecular Dynamics Simulations of Ritonavir at the Binding Pocket of SARS-CoV2 Main Protease
<p>Data includes all of the trajectories (2000) of classical all-atom molecular dynamics (MD) simulations of ritonavir at the binding pocket of SARS-CoV2 main protease target. In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein–ligand complexes were obtained by Glide/SP docking program. Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff<br> radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 500 ns production run was performed for the simulation.</p> <p> </p>
All Atom Molecular Dynamics Simulations of inhibitor N3 at the binding pocket of SARS-CoV2 Main Protease (PDB ID: 6LU7)
<p>Data includes all of the trajectories (1000) of classical all-atom molecular dynamics (MD) simulations of inhibitor N3 at the binding pocket of SARS-CoV2 main protease target (PDB ID: 6LU7). In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein–ligand complexes were obtained from RCSB PDB (PDB ID: 6LU7). Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff<br> radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 100 ns production run was performed for the simulations.</p>
Data for 'Complete reversal of the atomic unquenched orbital moment by a single electron'
<p>This folder contains all the raw data needed to generate the figures in the paper '<em>Complete reversal of the atomic unquenched orbital moment by a single electron</em>.'</p> <p><strong>Contents: </strong></p> <p><em>Figure 1 </em></p> <p>(a) STM topography 'Fig1Topography.sxm'<br> (b) and (c) DFT calculations, reproduced with 'public_sis2.pw.in' and the Quantum ESPRESSO package.</p> <p><em>Figure 2 </em></p> <p>(a) Energy levels (in meV) for the spin-orbit Hamiltonian, reproduced using 'Fig2spectra_SM'; multiplet calculations from the point-charge model found in 'Fig2spectra_PCM.' <br> Please note that .out files can be opened with any text editor (e.g. such as TextEdit), and .tar files can be unpacked with any open-source file archiver (e.g. such as 7-zip).<br> (b) dI/dV spectra atop Fe atom and bare Cu2N: 'Fig2Spec_MonomerFullRange' and 'Fig2Spec_CuNFullRange'</p> <p><br> <em>Figure 3</em></p> <p>(a) and (b) field dependence of the spin excitation, with data files 'SJ30_001-036', for 0-4T. Field values indicated in data files.<br> (c) 1T-5T data of orbital excitation, in order of increasing field: 'Fig4Spec_1T', 'Fig4Spec_2T', 'Fig4Spec_3T', 'Fig4Spec_4T', 'Fig4Spec_5T.' PCM transport calculations also provided. <br> (d) Zeeman splitting data in 'ShiftwField'</p> <p><em>Figure 4</em></p> <p>(a) and (b) current sweeps, with data files 'S_J31_016-032'. Current values indicated in data files.<br> (c) Measured data 'Fig4MonomerSpectrum.' Point-charge transport calculations in 'PCMTransport.' Spin-orbit transport calculations in 'SOTransport.'<br> (d) Point-charge calculations in 'Occupations', first column is the Bias (mv), second column is the occupation of the ground state, and third column is occupation of the first excited state.</p>
UKESM1 and ATom data
<p>This dataset was used to produce all plots in the manuscript titled </p> <p>"Constraints on global aerosol number concentration, SO<sub>2</sub> and condensation sink in UKESM1 using ATom measurements"</p>
Data set for "Logic-in-Memory Based on an Atomically Thin Semiconductor"
<p>Curves related to device characteristics from the paper "Logic-in-Memory Based on an Atomically Thin Semiconductor", Nature 2020, doi:10.1038/s41586-020-2861-0</p>
Data from: Adhesion force mapping on wood by atomic force microscopy: influence of surface roughness and tip geometry
This study attempts to address the interpretation of atomic force microscopy (AFM) adhesion force measurements conducted on the heterogeneous rough surface of wood and natural fibre materials. The influences of wood surface roughness, tip geometry and wear on the adhesion force distribution are examined by cyclic measurements conducted on wood surface under dry inert conditions. It was found that both the variation of tip and surface roughness of wood can widen the distribution of adhesion forces, which are essential for data interpretation. When a common Si AFM tip with nanometre size is used, the influence of tip wear can be significant. Therefore, control experiments should take the sequence of measurements into consideration, e.g. repeated experiments with used tip. In comparison, colloidal tips provide highly reproducible results. Similar average values but different distributions are shown for the adhesion measured on two major components of wood surface (cell wall and lumen). Evidence supports the hypothesis that the difference of the adhesion force distribution on these two locations was mainly induced by their surface roughness.
Atomic Force Microscopy data of Poly-3-hydroxybutarate and Poly-3-hydroxyvalerate films
<p>This dataset consists of atomic force microscopy (AFM) scans of <em><strong>Polyhydroxyalkanoate</strong></em> films in text (.txt) format as well as their corresponding previews in (.png) format. </p> <p>The surfaces of <strong><em>Poly-3-hydroxybutarate (P3HB [100%])</em></strong> and <em><strong>Poly-3-hydroxyvalerate (P3HB-co-P3HV) [90% :10%]) </strong></em>of six film thicknesses, three scan sizes (5µm, 10µm and 30µm) and three unique scan areas have been scanned with AFM equipment from NT-MDT spectrum instruments.</p> <p>This dataset has been used in the work <a href="../doi/10.5281/zenodo.10621269" target="_blank" rel="noopener">10.5281/zenodo.10621269</a> within which the scan data has been divided into multiple sub-pools for experimentation. Details on the structure of the dataset are as follows: </p> <ul> <li>The (.txt) format of the scanned images can be opened using Gwyddion (<a href="http://gwyddion.net/">gwyddion.net</a>)</li> </ul> <pre><code>FOLDER INDEX ITMO_PHA-AFM-SCAN-Data/ ├── Set.1_P3HB.(Homopolymer) │ ├── Size_5um │ │ ├── TXT │ │ │ └── 17(.txt)s │ │ └── IMG │ │ │ └── 17(.png)s │ ├── Size_10um │ │ ├── TXT │ │ │ └── 17(.txt)s │ │ └── IMG │ │ │ └── 17(.png)s │ └── Size_30um │ ├── TXT │ │ └── 18(.txt)s │ └── IMG │ └── 18(.png)s ├── Set.2_P3HB-co-P3HV.(Heteropolymer) │ ├── Size_5um │ │ ├── TXT │ │ │ └── 18(.txt)s │ │ └── IMG │ │ │ └── 18(.png)s │ ├── Size_10um │ │ ├── TXT │ │ │ └── 18(.txt)s │ │ └── IMG │ │ │ └── 18(.png)s │ └── Size_30um │ ├── TXT │ │ └── 17(.txt)s │ └── IMG │ └── 17(.png)s │ └── Read_me.txt</code></pre> <p><br>For convenience, we show an example of referencing data pools using the <em><strong>Folder Index</strong></em></p> <p>E.g. </p> <ul> <li>With reference to the article(<a href="https://doi.org/10.1021/acsomega.4c02502">https://doi.org/10.1021/acsomega.4c02502</a>), Case 1(a) is a data pool consisting only of scan data from P3HB polymer with all three sizes of data, in this case the reference is written as: <strong><em>(P1,L2) </em></strong></li> <li>Similarly, in case of Case 2(b), which is a data pool consisting of scan data from P3HB and P3HB-co-P3HV polymers with exclusively 30µm scan sizes, the reference is written as: <strong><em>(P1, L2[30]) + (P2, L2[30])</em></strong></li> </ul> <p>The .txt and .png files have been named using the following nomenculatrue: </p> <h3><strong> P_Thickness.N_Area.A_Size.S.txt</strong></h3> <p> <strong>P </strong>– Polymer (P3HB or P3HBV)<br><strong>Thickness.N</strong> – Film thickness of the scanned sample (1-6)<br><strong> Area.A</strong> – Scanned area within the film (1-3)<br><strong> Size.S</strong> – Size of the scanned area (5µm,10µm,30µm)</p> <p>e.g. (P3HB_Thickness.1_Area.1_Size.5.txt)</p> <p><strong>Please cite this dataset when used in applications as:</strong><br><em>Ireddy, A. T. S., & Ghorabe, F. D. E. (2024). Atomic Force Microscopy data of Poly-3-hydroxybutarate and Poly-3-hydroxyvalerate films [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10649355</em></p> <p><br>For additonal details, please contact: <a href="mailto:ireddy@itmo.ru">ireddy@itmo.ru</a></p>
Source Data for "Atomic-Precision Control of Plasmon-Induced Single-Molecule Switching in a Metal-Semiconductor Nanojunction" and Supplementary Information
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Visualizing sub-atomic orbital and spin moments using a scanning transmission electron microscope: Data and Methodology
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Coherent, atomically thin transition-metal dichalcogenide superlattices with engineered strain
<p>The sample is coherent WS<sub>2</sub>-WSe<sub>2</sub> superlattice (Xie, et al. Science 359, 1131-1136 (2018)). The datasets were collected by electron microscope pixel array detector (EMPAD) under the condition described in this paper (Han, et al. Nano Letters, 18, 3746-3751 (2018)). The rotation angle between the real space and diffraction space in these datasets is 37 degrees. The data have also been analyzed in our recent paper (arXiv:2111.06496) and a conference proceeding (Shi, et al. Microsc. Microanal. 27 Suppl 1, 2021). </p>
Figure 2 from: Dasari S (2016) Studying the effect of Ruthenium on High Temperature Mechanical Properties of Nickel Based Superalloys and Determining the Universal Behavior of Ruthenium at Atomic Scale with respect to alloying elements, Stress and Temperature. Research Ideas and Outcomes 2: e10714. https://doi.org/10.3897/rio.2.e10714
Figure 2 - All features of the microstructures from the six samples taken before and after creep tests
Rational design of stable bimetallic and trimetallic nickel-based single-atom alloys for acetic acid dehydrogenation
<p>Data access for the paper publication.</p>
Machine Learning for Analyzing Atomic Force Microscopy (AFM) Images Generated from Polymer Blends
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All Atom Simulation Trajectories of SSB
<p>The All Atom Simulation of SSB under different NaCl concentration</p>
Multistep screening of transition metal based homonuclear double atom catalysts to unravel the electronic origin of their activity and selectivity challenges for nitrogen reduction.
<p><span>Lack of robust catalyst design strategies for tackling the selectivity and activity challenges poses serious limitations in the development of efficient catalysts for nitrogen reduction to ammonia. The synergistic interactions in double-atom catalysts (DACs) have aroused great interest in developing promising catalytic centers for nitrogen-reduction reaction (NRR). Using a multistep screening strategy based on systematic first-principles simulations, we find that Fe<sub>2</sub>, Co<sub>2,</sub> and W<sub>2</sub> dimer species impregnated in <span>tetracyanoquinodimethane</span> based monolayer achieve suitable adsorption behaviour for the various NRR intermediates leading to excellent activity and selectivity among the 27 DACs considered in this study for NRR. Here we have uploaded input and output files of studied catalysts and reaction intermediates of NRR</span></p>
Kurucz Atomic Database in Exomol Format
<p>This is the Kurucz Atomic Database files re-formatted into Exomol's .states and .trans files.</p>
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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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.