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669 results for “ATOM”
Cooperative O-atom binding produces the active configuration for OH formation in high-temperature catalytic hydrogen oxidation
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Atomic force microscopy of transfer film development
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The dataset of interatomic distances between the atoms, not linked with a covalent bond
<p><strong>non-bonded_b3lyp.txt non-bonded_B97-3c.txt non-bonded_PBEh-3c.txt </strong>- the datasets of the atomic pairs, not linked with a covalent bond. Each line in each file has the following format:</p> <p><em>Element Element </em>0<em> MoleculeId AtomId1 AtomId2</em></p> <p>Here <em>MoleculeId </em>is the same as identifiers used in the dataset of covalent bond lengths resulting from the first-principle calculations, available at <a href="https://doi.org/10.5281/zenodo.2631844">https://doi.org/10.5281/zenodo.2631844</a> (the underlying optimized molecular geometries are available via this link as well).</p>
On Strong Scaling and Open Source Tools for Analyzing Atom Probe Tomography Data
<p>This repository contains supplemental results to the paper "On Strong Scaling and Open Source Tools<br> for Analyzing Atom Probe Tomography Data".</p> <p>Specifically, the input parameter and result files from all synthetic benchmark studies.<br> The results file for all synthetic specimen benchmark studies are available from the<br> authors upon serious request.</p> <p><strong>The repository content is as follows:</strong></p> <p><strong>Real world data:<br> Three triplets of *.tar.gz archive files document the settings and analysis files for the real world case studies</strong><br> 3013902 is the incipient specimen,<br> 2763207 the intermediate specimen, and<br> 3345501 the mature specimen.</p> <p><strong>Scripts.zip</strong><br> Contains all batch scripts we used for performing the analyses as a queue</p> <p><strong>Synthetic data:</strong></p> <p><strong>APTCrystallography.zip</strong><br> Contains all results from the benchmarking of the reimplemented Vicente Araullo-Peters et al. method</p> <p><strong>FullVolumeTessellation.zip</strong><br> Contains all results from the benchmarking of the Voro++ Voronoi volume tessellation method except for the HDF5/XDMF volume tessellation files of the 200 and 2000 million ion datasets</p> <p><strong>TwoPointStatistics.zip</strong><br> Contains all results from benchmarking the computing of 2-point spatial statistics</p> <p><strong>TipSurfaceDescrSpatialStatistics.zip</strong><br> Contains all results from benchmarking the alpha shape computation, descriptive spatial statistics, and clustering analyses</p> <p><strong>PARAPROBE.Results.2Mio.tar.gz<br> PARAPROBE.Results.20Mio.tar.gz</strong><br> <strong>PARAPROBE.Results.200Mio.tar.gz</strong><br> Contains all settings files and some results from benchmarking the hybrid implementation.</p> <p><strong>Unpack the individual repositories using tar through Linux console as follows:</strong><br> tar -xvf <archivename> <br> where <archivename> is a placeholder for the respective tar gz compressed archives within the ZIP file.<br> Alternatively WinRAR can be used on a Windows system.</p> <p><strong>We would kindly like to ask you to use the following repository<br> to access source code of PARAPROBE in the future:</strong></p> <p><strong>https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe<br> https://paraprobe-toolbox.readthedocs.io/en/latest/</strong><br> <br> <strong>Only above repository will be updated in the future! </strong><br> <strong>Only there new code additions and bugfixes are posted!<br> The examples folder of this repository contains a folder examples/tasks/paper14 which shows how<br> to run a workflow of paraprobe tools from this above repository to run analyses akin as reported in this paper.</strong></p> <p>Recommendations and bug reports to M. Kühbach are appreciated! Happy APT analyzing!</p> <p>------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br> <strong>The PARAPROBE source code version we used for analyzing the synthetic and real world APT<br> specimens in the paper used an earlier development version of the PARAPROBE tool, the source code</strong><br> <strong>is here:</strong></p> <p>PARAPROBE_20190117_VersionUsedForPaper.zip</p> <p>https://github.com/mkuehbach/PARAPROBE<br> https://paraprobe.readthedocs.io/en/latest/</p> <p> </p>
The Atomic-Level Structure of Cementitious Calcium Aluminate Silicate Hydrate
<p>Experimental NMR data for: The Atomic-Level Structure of Cementitious Calcium Aluminate Silicate Hydrate</p> <p><a href="https://doi.org/10.1021/jacs.0c02988">https://doi.org/10.1021/jacs.0c02988</a></p> <p> </p>
Data for "Hot-Carrier Generation in Plasmonic Nanoparticles: The Importance of Atomic Structure"
<p>This upload includes the data presented and analyzed in the article "Hot-Carrier Generation in Plasmonic Nanoparticles: The Importance of Atomic Structure" by Tuomas P. Rossi, Paul Erhart, and Mikael Kuisma.</p> <p>The codes for reproducing the data are provided at <a href="http://doi.org/10.5281/zenodo.3964229">doi:10.5281/zenodo.3964229</a>.</p> <p>See <em>README.md</em> in <em>data.zip</em> for a detailed description.</p>
A phononic crystal coupled to a transmission line via an artificial atom. Experimental data for the article figures
<p>We study a phononic crystal interacting with an articial atom - a superconducting quantum system - in the quantum regime. The phononic crystal is made of a long lattice of narrow metallic stripes on a quatz surface. The articial atom in turn interacts with a transmission line. Therefore, two degrees of freedom of different nature, acoustic and electromagnetic, are coupled with a single quantum object. A scattering spectrum of propagating electromagnetic waves on the articial atom visualizes acoustic modes of the phononic crystal. We simulate the system and found quasinormal modes of our phononic crystal and their properties. The calculations are consistent with the experimentally found modes, which are tted to the dispersion branches of the phononic crystal near the rst Brillouin zone edge. Our geometry allows to realize effects of quantum acoustics on a simple and compact phononic crystal.</p>
Raw Data to "Can Small Polyaromatics Describe Their Larger Counterparts for Local Reactions? A Computational Study on the H-Abstraction Reaction by an H-Atom from Polyaromatics"
<p>This data includes the Turbomole input files (without molecular orbitals) and output files (under <strong> DFT_and_CC_*tar</strong>) as well as the output of the xTB calculations (under <strong>xtb*tar</strong>) for different reactive sites of the polyaromatics (PAHs) studied in the related publication, for the reaction:<br> C<sub>X</sub>H<sub>Y</sub> + H -> C<sub>X</sub>H<sub>Y-1</sub> + H<sub>2</sub><br> <br> <strong>File structure:</strong></p> <ul> <li>The xtb*tar contains the xTB (xTB version 6.3.1) optimized structures for the parameterizations <strong>GFN0</strong>, <strong>GFN1</strong> and <strong>GFN2</strong>. The parameter set is indicated by the folder name "<strong>BACK_XTB_NATIVE_GFN0</strong>", "<strong>BACK_XTB_NATIVE_GFN1</strong>" and "<strong>BACK_XTB_NATIVE_GFN2</strong>"<br> </li> <li>The DFT calculations are carried out at the <strong>TPSSh-D3/TZVP </strong>level and they are directly under the subdirectories of dft*tar folders (C*H*) and are used to calculate the data under <strong>Figure 3</strong> and <strong>4</strong> of the related publication, as well as to calculate partition functions which are listed under <strong>freeh.out</strong>,<strong> </strong>the output of the freeh program of Turbomole.<br> </li> <li>The coupled cluster calculations are always located under the subdirectories of the DFT calculations.<br> </li> <li>The subdirectories <strong>PNO-CC.tz</strong> are <strong>PNO-CCSD/cc-pVTZ</strong> calculations and the output files are named as 'pnoccsd.out.tpno.7' or 'pnoccsd.out.tpno.8', where 7 and 8 stands for the PNO selection thresholds of 10<sup>-7 </sup>and 10<sup>-8</sup>, which are used to produce the data under <strong>Table 11</strong> of the related publication.<br> </li> <li>The subdirectories <strong>CC.atz.f12</strong>, <strong>CC.dz</strong>, and <strong>CC.tz</strong> under<strong> </strong>C6H6* and C10H8* correspond to <strong>R(O)HF-CCSD(F12*)(T)/aug-cc-pVTZ</strong>, <strong>R(O)HF-CCSD(T)/cc-pvDZ </strong>and <strong>R(O)HF-CCSD(T)/cc-pvTZ </strong>calculations respectively, which is used for the calculation of the data under <strong>Table</strong> <strong>10</strong> of the related publication.<br> </li> <li>The subdirectories <strong>UHF-CC.atz.f12</strong> under C6H6-* and C10H8-* include <strong>UHF-CCSD(F12*)(T)/aug-cc-pVTZ </strong>calculations for the transition states and the products. The subdirectories <strong>CC.atz.f12 </strong>under C6H6 and C10H8 include <strong>RHF-CCSD(F12*)(T)/aug-cc-pVTZ</strong> calculations for the reactants benzene and naphthalene.<strong> </strong>These are used to calculate the data under <strong>Table 9</strong> in the related publication<br> </li> <li>The subdirectories <strong>rij.grid_m3.scfconv_7</strong> under C14H10* includes the DFT calculations with m3 integration grid and RI-J approximation. Under these, the subfolders <strong>(UHF-)PNO-CC.atz.f12</strong> include the <strong>PNO-(UHF-)CCSD(F12*)(T)/aug-cc-pVTZ</strong> calculations which are used to produce the data under <strong>Table 9</strong> in the related publication.<br> </li> <li>The subdirectories <strong>(UHF-)PNO-CC.atz.f12</strong> under C6H6* and C10H8* include<strong> PNO-(UHF-)CCSD(F12*)(T)/aug-cc-pVTZ</strong> calculations which are used for<strong> PNO threshold selection</strong> for the UHF-CCSD(F12*)(T) calculations (<strong>Table S2 </strong>of the Supporting Information of the related publication).</li> </ul>
Unravelling CO adsorption on model single-atom catalysts (SAC)
<p>This dataset contains atomic position files (VASP POSCAR format) of structures relevant for our study regarding CO adsorption on SAC.</p> <p>The computational details are given in the supplement material.</p> <p>The dataset contains files for the following elements: Me=[Cu,Ag,Au,Ni,Pd,Pt,Rh,Ir].</p> <p>1) for 2- or 5- fold coordinated SAC sites on the Fe3O4(001) surface,</p> <p>POSCAR_Me_Fe3O4_001_2fold and POSCAR_Me_Fe3O4_001_5fold,</p> <p> </p> <p>2) for atop sites on Me(111) and Me(001) surfaces,</p> <p>(with larger reconstructions to avoid coverage effects, see discussion and details in SI),</p> <p>POSCAR_Me_111 and POSCAR_Me_001</p> <p> </p> <p>3) for sites on stable oxide surfaces,</p> <p>POSCAR_Me_ox</p> <p>The exact list of which oxides and surfaces are investigated can be found again in the SI.</p> <p> </p> <p>Additionally, the same above mention structure files can be found in their CO-adsorbed version (Me+CO).</p> <p> </p> <p> </p>
Carbene‐Catalyzed Activation of Remote Nitrogen Atoms of (benz)imidazole‐derived aldimines for Enantioselective Synthesis of Heterocycles
<p>This folder /xyz_structures/ contains the geometries (in .xyz format together with the gas-phase energy, E) accompanying the paper</p> <p>"Carbene‐Catalyzed Activation of Remote Nitrogen Atoms of (benz)imidazole‐derived aldimines for Enantioselective Synthesis of Heterocycles"</p> <p>citation: X. Yang, Y. Xie, J. Xu, S. Ren, B. Mondal, L. Zhou, W. Tian, X. Zhang, L. Hao, Z. Jin, Y. R. Chi, Angew. Chem. Int. Ed. 2021, 60, 7906.</p> <p>Where conformers occur, they are always named from the lowest Gibbs energy to the highest in ascending order from c1 (sometimes omitted), c2, c3, ...</p> <p>This folder has the following structure and they correspond to the raw data in the SI:</p> <p>/DFT_optimized_structures/ </p> <p> --> contains DFT-optimized structures for the computational study of the mechanism for the reaction between intermediates IV-3b/IV-3ac and isatin substrate 2b.</p> <p>/DI-AS_analysis/ </p> <p> --> structures along the IRC pathways for Si-ts1 (in subfolder /Si-ts1/) and Re-ts1 (in subfolder /Re-ts1/) taken for distortion interaction-activation strain (DI-AS) model analysis.</p> <p> --> structures along the IRC points are named p<num>.xyz where <num> denotes number of points along the IRC from the TS; fragments results from each point are denoted p<num>_f1.xyz and p<num>_f2.xyz. For example, the first point along the IRC is named p1.xyz and its component fragments are denoted p1_f1.xyz and p2_f2.xyz.</p>
Highly Conductive Collagen by Low-Temperature Atomic Layer Deposition of Platinum
<p>In modern biomaterial-based electronics, conductive and flexible biomaterials are gaining increasing attention for their wide range of applications in biomedical and wearable electronics industries. The ecofriendly, biodegradable, and self-resorbable nature of these materials makes them an excellent choice in fabricating green and transient electronics. Surface functionalization of these biomaterials is required to cater to the need of designing electronics based on these substrate materials. In this work, a low-temperature atomic layer deposition (ALD) process of platinum (Pt) is presented to deposit a conductive thin film on collagen biomaterials, for the first time. Surface characterization revealed that a very thin ALD-deposited seed layer of TiO2 on the collagen surface prior to Pt deposition is an alternative for achieving a better nucleation and 100% surface coverage of ultrathin Pt on collagen surfaces. The presence of a pure metallic Pt thin film was confirmed from surface chemical characterization. Electrical characterization proved the existence of a continuous and conductive Pt thin film (∼27.8 ± 1.4 nm) on collagen with a resistivity of 295 ± 30 μΩ cm, which occurred because of the virtue of TiO2. Analysis of its electronic structures showed that the presence of metastable state due to the presence of TiO2enables electrons to easily flow from valence into conductive bands. As a result, this turned collagen into a flexible conductive biomaterial.</p>
Optical pumping and readout of bismuth hyperfine states in silicon for atomic clock applications
<p>Published in</p> <p>Sci. Rep. 5, 10493 (2015)</p> <p>DOI: 10.1038/srep10493</p>
Atomically Precise Incorporation of BN-Doped Rubicene into Graphene Nanoribbons
<p>Raw file of publication entitled "Atomically Precise Incorporation of BN-Doped Rubicene into Graphene Nanoribbons"</p><p>https://doi.org/10.1021/acs.jpcc.2c05866</p>
AFM data of ice clusters on Cu(111) and Au(111) in paper "Structure discovery in Atomic Force Microscopy imaging of ice"
<p>Frequency shift CO-tip atomic force microscopy data of small ice clusters on Cu(111) and Au(111) surfaces as they appear in the paper "Structure discovery in Atomic Force Microscopy imaging of ice".</p><p>The data are saved in a compressed .tar.gz archive. The unpacked archive contains each experiment as a Numpy .npz file. Each file contains the measurement data as a 3D array in the key 'data' and the physical extent of the scan region in the x and y directions in Ånströms in the keys 'lengthX' and 'lengthY'.</p>
The dynamics of protein-RNA interfaces using all-atom molecular dynamics simulations
<p>We investigated to characterize the dynamics of protein-RNA complexes and their interfaces at molecular level by performing a more systematic analysis. To get insights on the dynamics of protein-RNA complexes, all-atom MD simulations were generated for the manuscript "The dynamics of protein-RNA interfaces using all-atom molecular dynamics simulations". Nine protein-RNA complexes are studied in this work: 1ASY (an aspartyl-tRNA synthase/tRNA), 1JBS (a ribotoxin restrictocin/SRD RNA), 1MMS (a ribosomal protein L11/23S), 1OOA (a nuclear factor NF-kappaB p105 subunit/RNA aptamer), 1RKJ (a nucleolin/pre-rRNA), 2R8S (a FAB/P4-P6 RNA ribozyme domain), 2VPL (a 50S ribosomal protein/mRNA), 2ZM5 (a tRNA delta(2)-isopentenylpyrophosphate transferase/tRNA), 3IEV (a GTP-binding protein era/3' end of 16S rRNA). </p><p>Each folder for a complex is organised as followed:</p><ul><li>in <strong>complex</strong> there are the dry MD simulations for the complex protein-RNA with the starting structure</li><li>in <strong>protein</strong> there are the dry MD simulations for the unbound protein with the starting structure</li><li>in <strong>rna</strong> there are the dry MD simulations for the unbound RNA with the starting structure</li></ul><p>In each folder, all the trajectory files are named : <strong>md_(times of simulations).xtc</strong> and the starting structure called : <strong>start.gro</strong>.</p>
Tracking conformational transitions of the gonadotropin hormone receptors in a bilayer of (SDPC) poly-unsaturated lipids from all-atom molecular dynamics simulations.
<p>In the present study, we describe the results from a computational microscopy perspective (also known as molecular dynamics simulation) at the atomistic resolution for the two gonadotropin hormone receptors, the follicle-stimulant hormone receptor and the luteinizing/chorionic gonadotropin hormone receptor, which are essential for reproduction in humans.</p>
Atom-by-atom Imaging of Moiré Transformations in 2D Transition Metal Dichalcogenides
<p>This dataset contains the images used in the manuscript "Atom-by-atom Imaging of Moiré Transformations in 2D Transition Metal Dichalcogenides".</p>
United Atom Parameters for United Atom Multiscale Modelling Of Bio-Nano Interactions Of PEG Coated Nanoparticles
<p>Short-range surface adsorption potentials of carbohydrates, lipid fragments, and amino acid side chains in tabulated form.</p><p>Recovered from radial distribution functions</p><p>Force Fields: adapted CHARMM36.</p><p>Material: PEG</p><p>Status: updated on November 6, 2023</p>
Hartree potentials and geometries of relaxed on-surface ice clusters in "Structure discovery in Atomic Force Microscopy imaging of ice"
<p>Hartree potentials and geometries of on-surface DFT-relaxed ice clusters used in the paper "Structure discovery in Atomic Force Microscopy imaging of ice".</p><p>The data are saved in a compressed .tar.gz archive. The unpacked archive contains the data for each ice cluster in the .xsf format. The density functional theory (DFT) calculations were done using the Vienna Ab-initio Simulation Package with the optB86b-vdW density functional.</p>
All-atom simulations of DOPE/DOPC lipid bilayers (0%, 50% and 100% DOPC).
<p>All-atom (CHARMM C36) simulations of DOPE/DOPC bilayers (0, 50 and 100 % DOPE). Size sufficient to get the bending modulus and spontaneous curvature difference using our "Spatial Extent" paper methodology.</p><p>DCD format trajectories have frames saved every 0.5 nanoseconds (500 picoseconds).</p><p>Amber dynamics input file included.</p>
ScienceDex guides
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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)
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.