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669 results for “ATOM”
Raman spectroscopic mapping and atomic force microscopy statistical analyses for the determination of WS2 flake thickness
<p><span>This database contains the statistical analyses carried out in order to evaluate the thickness of the WS</span><sub><span>2</span></sub><span> nanoflakes. In order to have a reliable comparison we determine the methodology of comparing Raman spectroscopic mapping and atomic force microscopy (AFM). </span></p> <p><span>In case of Raman spectroscopy, the thickness is evaluated by employing the separation of the two vibrational mode, namely E</span><sub><span>2g</span></sub><span> and A</span><sub><span>1g</span></sub><span>. This method is well-established and the number of layers has been previously tabulated in different articles. </span></p> <p><span>Each spectrum of the Raman analysis, is performed with a 100X objective in a confocal microscope, with a 473 nm laser excitation, a laser power of 0.5 mW and an acquisition time of 1 s.</span></p> <p><span>The AFM analysis are carried out in tapping mode with a 512-pixel x 512-pixel resolution and and a scan rate of 1Hz per line.</span></p>
Dataset for Hydrogen Atom Abstraction from Methane by Hydroxyl Radical
<p>Data for the reaction OH + CH4 −−→ CH3 + H2O. Contains 167196 geometries and corresponding {omega}B97X/6-31G(D) energies, 12416 geometries and corresponding CCSD(T)/aug-cc-pvtz energies.</p>
Data for Sampling Real‐Time Atomic Dynamics in Metal Nanoparticles by Combining Experiments, Simulations, and Machine Learning
<div> <p>Even at low temperatures, metal nanoparticles (NPs) possess atomic dynamics that are key for their properties but challenging to elucidate. Recent experimental advances allow obtaining atomic‐resolution snapshots of the NPs in realistic regimes, but data acquisition limitations hinder the experimental reconstruction of the atomic dynamics present within them. Molecular simulations have the advantage that these allow directly tracking the motion of atoms over time. However, these typically start from ideal/perfect NP structures and, suffering from sampling limits, provide results that are often dependent on the initial/putative structure and remain purely indicative. Here, by combining state‐of‐the‐art experimental and computational approaches, how it is possible to tackle the limitations of both approaches and resolve the atomistic dynamics present in metal NPs in realistic conditions is demonstrated. Annular dark‐field scanning transmission electron microscopy enables the acquisition of ten high‐resolution images of an Au NP at intervals of 0.6 s. These are used to reconstruct atomistic 3D models of the real NP used to run ten independent molecular dynamics simulations. Machine learning analyses of the simulation trajectories allows resolving the real‐time atomic dynamics present within the NP. This provides a robust combined experimental/computational approach to characterize the structural dynamics of metal NPs in realistic conditions.</p> </div> <div></div>
Magic running and standing wave optical traps for Rydberg atoms - Data and code for analysis
<p>Data, theory calculation and plotting scripts for the publication titled "Magic running and standing wave optical traps for Rydberg atoms" (<a href="https://arxiv.org/abs/2410.20901" target="_blank" rel="noopener">arXiv:2410.20901</a>).</p> <p> </p> <p><strong>File legend</strong></p> <ul> <li> <code>data_FIGx_yyy.mat</code> contains the calculated or measured data used in Figure x</li> <li> <code>calc_FIGx_yyy.py</code> is the script to calculate the theoretical data used in Figure x</li> <li> <code>plot_FIGx_yy.py</code> is the script to create the Figure x of the paper</li> <li> <code>simulation_class.py</code> is a class with theory functions</li> <li> <code>paperstyle.mplstyle</code> is a matplotlib style file</li> <li> <code>requirements.txt</code> lists all the required python packages</li> </ul> <p> </p> <p><strong>Abstract</strong></p> <p>Magic trapping of ground and Rydberg states, which equalizes the AC Stark shifts of these two levels, enables increased ground-to-Rydberg state coherence times. We measure via photon storage and retrieval how the ground-to-Rydberg state coherence depends on trap wavelength for two different traps and find different optimal wavelengths for a 1D optical lattice trap and a running wave optical dipole trap. Comparison to theory reveals that this is caused by the Rydberg electron sampling different potential landscapes. The observed difference increases for higher principal quantum numbers, where the extent of the Rydberg electron wave function becomes larger than the optical lattice period. Our analysis shows that optimal magic trapping conditions depend on the trap geometry, in particular for optical lattices and tweezers.</p> <p> </p> <p><strong>Theory calculation</strong></p> <p>We implemented the potential arising from the Hamiltonians described in the paper. The functions are shared here in the python class <code>simulation_class.py</code>. This class is used in the calculation scripts named <code>calc_FIGx_yyy.py</code> and saves the data as <code>data_FIGx_yyy.mat</code> for the respective Figure x.</p> <p>In case of questions to the code or calculations, please contact Chris Nill or Lukas Ahlheit.</p> <p> </p> <p><strong>Experimental data</strong></p> <p>The experimental data published here are photon storage and retrieval traces of 780 nm probe photons as function of storage duration. We recorded photon traces for different trap laser detunings and Rydberg states.</p> <p>In case of questions to the data, please contact Lukas Ahlheit or Sebastian Hofferberth.</p> <p> </p> <p><strong>Inkscape modification to specific figures</strong></p> <ul> <li>Figure 1: The plotted data is joined in Inkscape with schematic drawings</li> <li>Figure 2: The plot created by the python file is edited in Inkscape for readability</li> <li>Figure 5: We add two schematics into the figure created by the python file</li> </ul>
Theoretical analysis of reliability of the "Hypothesis of the atomic (quantum) motion"
<p>This article is based on the "Hypothesis of the atomic (quantum) motion", <br>registered on the site of intellectual protection: <br>http://www.a-priority.ru/Priority/1estestv/1estestv_catalog.html?SHOWALL_1=1 <br>registration number: A1B031 (project of the European Academy of Natural <br>Sciences). <br>The content of the article is the theoretical test of the reliability of the hypothesis, <br>that based on - the famous discovery of the wave properties of the material bodies by Louis de <br>Broglie; - centripetal acceleration of the planets of the solar system. <br>The theoretical test of the reliability of the hypothesis is indicate the need for <br>further research to confirm the hypothesis, which is the goal of this article. </p>
Atomic coordinates for "Optimizing Surface Active Sites via Burying Single Atom in Subsurface Lattice for Boosted Alkaline Methanol Oxidation"
<p>Atomic coordinates of the optimized computational models in the manuscript of "Optimizing Surface Active Sites via Burying Single Atom in Subsurface Lattice for Boosted Alkaline Methanol Oxidation"</p>
Constant - quantum of speed or continuation of theoretical analysis of the reliability of the "Hypothesis of atomic (quantum) motion"
<p><span><span> В основу статьи легла моя «Гипотеза атомного (квантового) движения», зарегистрированная на </span></span><br><span><span>сайте по защите интеллектуальной собственности: </span></span><br><span><span>http://www.a-priority.ru/Priority/1estestv/1estestv_catalog.html?SHOWALL_1=1 </span></span><br><span><span>регистрационный номер: A1B031 (проект Европейской академии естественных наук). </span></span><br><span><span> Содержание статьи является продолжением теоретического анализа достоверности гипотезы </span></span><br><span><span>, основанной на: -центростремительных ускорениях Луны относительно Земли, спутников планет </span></span><br><span><span>Солнечной системы, Солнца относительно центра Млечного Пути, планет </span></span><br><span><span>Проксимы Центавра, галактики Большое Магелланово Облако относительно </span></span><br><span><span>галактики Млечный Путь, -графической программе Graph.</span></span></p>
Atom Probe Tomoghraphy Pure Aluminium Dataset
<p>This dataset presents Atom Probe Tomography (APT) data for pure aluminum, acquired using the Oxcart instrument—a titanium APT system. The experiment was conducted and recorded by the PyCCAPT control module.</p> <p>The primary data file, "2382_Jan-10-2025_15-12_NiC9_Al.h5," collects raw data captured by the PyCCAPT control module.</p> <p>The dataset includes a calibrated files: "1748_Al.h5" and a range file "1748_Al_range.h5." The former contains calibrated APT data, while the latter provides information on the range data.</p> <p> </p>
All-atom simulations elucidate the molecular mechanism underlying RNA-membrane interactions
<p>Topology files and frames extracted from the minimum of the free energy profile F(d_z) (or F(d_min) for single-stranded RNAs), within 2.5kBT. These files can be used to reproduce the hydrogen bond analyses in the manuscript.</p> <p>Scripts which were used to extract hydrogen bond information are available on <a href="https://github.com/salvatoredimarco/rna-membrane">https://github.com/salvatoredimarco/rna-membrane</a></p> <p><strong>Systems:</strong></p> <p>4xN: nucleosides</p> <p>4xN2: dinucleotides</p> <p>4xN3: trinucleotides</p> <p>4xN_OPC: nucleosides simulated with OPC water model. Energy threshold is here 1.0*kBT, because of weaker binding.</p> <p>1xGA, 1xGU, 1xGC, 1xCU</p> <p>1xGGC, 1xGCG</p> <p>1xquadruplex: G-quadruplex</p> <p>1xstrand: 19-mer RNA strand</p> <p>1xhairpin: 16-mer folded hairpin</p> <p>1x16mer_elong: 16-mer unfolded, restrained</p> <p>2x16mer_loose1/2: 16-mer unfolded, unrestrained</p>
Evaluating quantum alchemy of atoms with thermodynamic cycles: Beyond ground electronic states
<p>Data at the time of submission.</p>
Laser-equipped gas reaction chamber for probing environmentally sensitive materials at near atomic scale
<p>Five atom probe datasets as featured in the PLOSone journal concerning the methodology of laser-assisted thermochemical gas treatments of atom probe needles, two comparing the deuterium charged and uncharged states of a steel and comparing various early states of direct hydrogen reduction of FeO.</p>
United-atom P3HT workspace
<p><a href="https://docs.signac.io/en/latest/index.html">Signac</a> workspace of united-atom P3HT <a href="https://hoomd-blue.readthedocs.io/en/latest/">HOOMD</a> molecular dynamics simulation data created using <a href="https://github.com/cmelab/planckton-flow">PlanckTon-flow</a> and <a href="https://github.com/cmelab/planckton/releases/tag/v0.6.1">PlanckTon v0.6.1</a>.</p>
Visualizing local fast ionic conduction pathways in nanocrystalline lanthanum manganite by isotope exchange-atom probe tomography - dataset
<p>Raw data for atom probe tomography 2D elemental reconstructions of 18O-exchanged La0.8Sr0.2MnO3 thin films. LSM thin films were deposited by large-area PLD (PVD Systems – PLD 5000) using a 248 nm KrF excimer laser (Lambda Physics – COMPex PRO 205). The layers were deposited on Al<sub>2</sub>O<sub>3</sub> (0001) single crystal substrate (Crystec GmbH). A thin barrier layer of Ce<sub>0.8</sub>Sm<sub>0.2</sub>O<sub>1.9</sub> (SDC) was deposited before the LSM film in order to avoid cationic intermixing at the interface. Both layers were deposited at 700 °C, under an oxygen pressure of 2.6 × 10<sup>−2</sup> mbar, target–substrate distance of 95 mm, laser fluency ≈1.2 J cm<sup>−2</sup> and 5 Hz of laser frequency. The thickness of LSM and SDC layers deposited was ≈45 nm and ≈35 nm, respectively, as measured by spectroscopy ellipsometry (UVISEL, Horiba scientific).The nominal oxygen exchange temperature and time were 550 °C and 1 h and 40 min, respectively. Instrument Cameca LEAP 4000X Si. APT performed at 45.5 K using a 30 pJ laser energy and 500 kHz pulse rate. The flight path length was 90 mm and the ion detection rate was set to 5 ions per 1000 pulses, resulting in a bias range of 5000–7400 V during the data collection. Reconstructions were generated in Cameca's IVAS 3.6.18 software. A systematic energy deficit correction was employed to improve the mass spectral resolution.</p>
Nanotubes from the Misfit Layered Compound (SmS)1.19TaS2: Atomic Structure, Charge Transfer, and Electrical Properties_experimental dataset
<p>This dataset contains the raw experimental data for the Sreedhara et al., Nanotubes from the Misfit Layered Compound (SmS)1.19TaS2: Atomic Structure, Charge Transfer, and Electrical Properties, <em>Chem. Mater.</em> 2022, 34, 4, 1838–1853</p>
Data publication for "First-principles derivation and properties of density-functional average-atom models"
<p>Data for the pre-print "First-principles derivation and properties of density-functional average-atom models", https://arxiv.org/abs/2103.09928.</p> <p>Each data folder is named according to the corresponding figure in the paper. For any questions, please contact the authors.</p>
ANI-1 dataset with added atomic volume ratios restricted to CHNO atoms for DNN-MBD
<p>ANI-1 dataset with added atomic volume ratios restricted to CHNO atoms for DNN-MBD</p>
Dataset for the paper "High Loading of Single Atomic Iron Sites in Pyrolysed Fe-NC Oxygen Reduction Catalysts for Proton Exchange Membrane Fuel Cells", DOI:10.1038/s41929-022-00772-9
<p>The data in this spreadsheet was used to produce the figures in the paper </p> <p>Authors: Asad Mehmood, Mengjun Gong, Frédéric Jaouen, Aaron Roy, Andrea Zitolo, Anastassiya Khan, Moulay-Tahar Sougrati, Mathias Primbs, Alex Martinez Bonastre, Dash Fongalland, Goran Drazic, Peter Strasser, Anthony Kucernak</p> <p>Title: High Loading of Single Atomic Iron Sites in Pyrolysed Fe-NC Oxygen Reduction Catalysts for Proton Exchange Membrane Fuel Cells</p> <p>Journal: Nature Materials</p> <p>DOI: 10.1038/s41929-022-00772-9</p> <p>Please cite the above reference if you wish to use this data </p> <p> </p> <p>DOI of data: 10.5281/zenodo.6411262</p>
Dissipation-enhanced collapse singularity of a nonlocal fluid of light in a hot atomic vapor
<p>This repository contains the data presented in the manuscript titled " Dissipation-enhanced collapse singularity of a nonlocal fluid of light in a hot atomic vapor " by P.Azam et al., Phys. Rev. A <strong>104</strong>, 013515 – Published 15 July 2021</p> <p>The .zip file contains a folder for each figure, a folder ("mesures") with the full dataset and analyzed measured and a code .mat to plot fig 1,2,3,6.</p> <p>Codes to plot fig 4 and 5 are in respective folders.</p>
Pseudo-atomic model of a complete gas vesicle
<p>This pseudo-atomic model is shown in our preprint:</p> <p>Huber, S. T., Terwiel, D., Evers, W. H., Maresca, D. & Jakobi, A. J. Cryo-EM structure of gas vesicles for buoyancy-controlled motility.<em> BioRxiv (2022)</em></p> <p>(Update 26.04.2023), Now in:</p> <p>Huber, S. T., Terwiel, D., Evers, W. H., Maresca, D. & Jakobi, A. J. Cryo-EM structure of gas vesicles for buoyancy-controlled motility. <em>Cell </em>186, 975–986 (2023)</p> <p> </p> <p>We use the atomic model from our determined 3.2 Å cryo-EM structure of the <em>B.megaterium</em> gas vesicle (GV) wall and copy+place it on a helical path that narrows at the tips of the GVs. Placement at the seam in the GV center is informed by high-resolution 2D class averages. The helical arrangement is informed by the determined helical symmetry of this particular helical polymorph (92.93 units per helical turn) and the tip by measurement of the cone semi-angle.</p> <p>The pseudo-atomic model consists only of copies of the wall protein GvpA2. This is likely a simplification, and the homologous proteins GvpJ and GvpS might be involved in small parts of the assembly, such as the ends of the cones. The arrangement at the contact point of the two GV halves is informed only by high-resolution 2D data, therefore the 3D arrangement of these features is hypothetical.</p> <p>For display in ChimeraX I recommend this style:</p> <blockquote> <p>car style protein modeh default arrows f xsect oval width 3 thick 3 divisions 2 barSides 4</p> </blockquote> <p>The rainbow color scheme highlighting the main chain can be displayed:</p> <blockquote> <p>select :2-13; color sel #2c2a70; select :14-23; color sel #45639a; select :24-34; color sel #98b45a; select :35-39; color sel #abb24e; select :40-50; color sel #dddb20; select :51-61; color sel #e15a3d; select :62-66; color sel #ec1e24; ~sel;</p> </blockquote> <p>The color scheme for physico-chemical properties:</p> <blockquote> <p>select :Met,Ile,Leu,Ala,Val; color sel #e1b13e; select :Ser,Thr,Gln,Asn; color sel #49c2c6; select :Glu,Asp; color sel #cb2026; select :Lys,Arg,His; color sel #3e58a8; select :Phe,Trp,Tyr; color sel #715321; select :Gly,Pro; color sel #7b7b7b; ~sel;</p> </blockquote> <p>Python dictionary with color scheme:</p> <blockquote> <p>colorscheme = {'#e1b13e':'MILAV', '#49c2c6':'STNQ', '#cb2026':'DE', '#3e58a8':'KRH', '#715321':'FYW', '#7b7b7b':'GPC'}</p> </blockquote> <p>To highlight both halves in different colors in the full model:</p> <blockquote> <p>color #1.1-865 gray; color #1.866-1730 steel blue</p> </blockquote> <p>ChimeraX command to impose helical symmetry on a single GvpA monomer:</p> <blockquote> <p>sym #1 h,0.5257,-3.87399,500,-250 coordinateSystem #1 copies True</p> </blockquote> <p> </p>
Data for 'Confined vacuum resonances as artificial atoms with tunable lifetime'
<p>This folder contains all the raw data needed to generate the figures in the paper '<em>Confined vacuum resonances as artificial<br> atoms with tunable lifetime</em><em>.</em>' The data are seperated by the figures in which they appear, with a text folder in each folder that contains any relevant additional information. </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.
Annotated Behaviour and Observability Dataset (ABODe)
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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.