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669 results for “ATOM”
Opacities for atoms and molecules relevant to the spectra of hot rocky planets
<p>This dataset contains opacities for atoms and molecules that are relevant to the sector of hot rocky planets, such as magma ocean planets, post-giant impact atmospheres, or planets in ultra-short period orbits. These species can arise above a magma ocean with a composition specific to the continental crust or bulk silicate earth. We do not include opacities for major species that are not specific to hot rocky planet atmospheres, such as water, methane, carbon dioxide, ammonia, etc., as these can be found elsewhere, for example in datasets related to brown dwarf and hot Jupiter atmospheres. </p> <p>Most of the species included in this dataset can be seen in the attached plot, hot_spectra.pdf, which shows a secondary eclipse model of a lava planet and the contributions of individual species to this spectrum. The references for the line lists used to generate these opacities can be found in the file reference_table.pdf.</p> <p>Each *.zip file contains a set of 1060 opacity layers in ASCII format, each identified with the temperature and pressure it corresponds to. Each layer file contains a header showing the layer number, the temperature (in K), and pressure (in mbar). The data consists of to columns: wavelength in microns and opacity in cm<sup>2</sup>/molecule. The wavelength grid goes from 0.4 to 50 microns. A list of all the layers calculated for each molecule is given in the file layer_list.</p> <p><em>Resources supporting this work were provided by the NASA High-End Computing (HEC) Program through the NASA Advanced Supercomputing (NAS) Division at Ames Research Center.</em></p>
All-atom molecular dynamics simulations of synaptic vesicle fusion I: a glimpse at the primed Synaptotagmin-SNARE-complexin complex
<p>Synaptic vesicles are primed into a state that is ready for fast neurotransmitter release upon Ca<sup>2+</sup>-binding to Syt1. This state likely includes trans-SNARE complexes between the vesicle and plasma membranes that are bound to Syt1 and complexins. However, the nature of this state and the steps leading to membrane fusion are unclear, in part because of the difficulty of studying this dynamic process experimentally. To shed light into these questions, we performed all-atom molecular dynamics simulations of systems containing trans-SNARE complexes between two flat bilayers or a vesicle and a flat bilayer with or without fragments of Syt1 and/or complexin-1. Our results need to be interpreted with caution because of the limited simulation times and the absence of key components, but suggest mechanistic features that may control release and help visualize potential states of the primed Syt1-SNARE-complexin-1 complex. In particular, the simulations suggest that SNAREs alone induce formation of extended membrane-membrane contact interfaces that may fuse slowly, and that the primed state contains macromolecular assemblies of trans-SNARE complexes bound to the Syt1 C<sub>2</sub>B domain and complexin-1 in a spring-loaded configuration that prevents premature membrane merger and formation of extended interfaces but keeps the system ready for fast fusion upon Ca<sup>2+</sup> influx.</p>
Original data for publication: The Atomically Precise Gold/Captopril Nanocluster Au25(Capt)18 Gains Anticancer Activity by Inhibiting Mitochondrial Oxidative Phosphorylation
<p> Original data for publication: The Atomically Precise Gold/Captopril Nanocluster Au<sub>25</sub>(Capt)<sub>18</sub> Gains Anticancer Activity by Inhibiting Mitochondrial Oxidative Phosphorylation, ACS Applied Materials & Interfaces</p>
Recordings of Electron Beam Effects on Individual Dopant Atoms in Graphene
<p>This data are scanning transmission electron microscopy (STEM) images whose contrast comes from high angle annular dark field (HAADF) scattering as well as medium angle annular dark field (MAADF). The specimen is single layer graphene (courtesy Ondrej Dyck), placed on a Protochips TEM grid which allows to rapidly heat the material upwards of 1200 C, which is primarily to reduce contamination from the electron beam. There are also various single dopant atoms scattered throughout - silicon naturally is present, but there may also be chromium atoms that were very lightly evaporated.</p> <p>The electron beam in the STEM, which is generally used to image the specimen, can also be used to modify the structure - i.e., move dopant atoms around the surface and into vacancy sites, or even knock out individual carbon atoms, which can depend on accelerating voltage of the beam. This data then consists of sets of the following: The purpose of this data is to utilize reinforcement learning (RL) to explore and ultimately learn the rules of the dynamics of single dopant atom movement due to various characteristics of the electron beam (position relative to dopant atom, dwell time of beam, current in the beam, etc.), and therefore consists of the following:</p> <ol> <li>Image 1 (before)</li> <li>Beam positions in time</li> <li>Image 2 (after)</li> </ol>
Replication data for: "Ultrafast energy exchange between two single Rydberg atoms on the nanosecond timescale"
<p>Replication data for Figure 3 and 4 of "Ultrafast energy exchange between two single Rydberg atoms on the nanosecond timescale"</p> <p>Preprint at: https://arxiv.org/abs/2111.12314</p> <p> </p>
Energy differences between multielectron atoms (H to Ne) with non-integer nuclear charges using SCF methods and AIT
<p>Energy difference predictions for multi-electron atoms: for the basis set def2-TZVP and the basis functions of the reference atom xenon, self-consistent field (SCF) energy differences between an atom's initial charge and an atom of final charge have been calculated using the unrestricted Hartree-Fock method of <a href="https://pyscf.org/">PySCF</a>. Each energy difference is complemented by the prediction of the same difference using the <a href="https://arxiv.org/abs/2203.13794">Alchemical Integral Transform</a> (AIT), given in separate perturbative orders 1,2,3,4,5.</p>
Tardis He Atomic Dataset, 2016 paper (2022 version)
<p>The updated atomic dataset associated with Boyle et al., 2016 ("Helium in Double-Detonation Models of Type Ia Supernovae", https://doi.org/10.1051/0004-6361/201629712, https://arxiv.org/abs/1611.05938). This version is compatible with Tardis in 2022. </p>
Tardis He Atomic Dataset, 2016 paper (original version)
<p>The original atomic dataset associated with Boyle et al., 2016 ("Helium in Double-Detonation Models of Type Ia Supernovae", https://doi.org/10.1051/0004-6361/201629712, https://arxiv.org/abs/1611.05938). This version of the dataset is no longer compatible with Tardis but is stored here for reference. </p>
Heterogeneous cavitation from atomically smooth liquid-liquid interfaces
<p>Original research data on "Heterogeneous cavitation from atomically smooth liquid-liquid interfaces"</p> <p> </p> <p>Magnetic beads: diameter 4.5 µm<br> Framerate 5x10^6 fps<br> scale: 1px = 1.45 µm</p> <p>PFOB: 1-Bromoheptadecafluorooctane<br> Framerate 5x10^6 fps<br> scale: 1px = 1.60 µm</p> <p>4H-PFOB: 1H,1H,2H,2H-Perfluorooctyl bromide<br> Framerate 5x10^6 fps<br> scale: 1px = 1.23 µm</p> <p>"Luminity": Perfluteren 150 µl/ml<br> Framerate 5x10^6 fps<br> scale: 1px = 1.60 µm</p> <p>single_Interface: 4H-PFOB (left;laser impact) and water (right)<br> Framerate 5x10^6 fps<br> scale: 1px = 1.33 µm</p> <p>multi_cav: PFOB droplets<br> Framerate 5x10^6 fps<br> scale: 1px = 1.34 µm</p>
Overcoming contrast reversals in focused probe ptychography of thick materials: an optimal pipeline for efficiently determining local atomic structure in materials science
<p>Files concerning the publication "Overcoming contrast reversals in focused probe ptychography of thick materials: an optimal pipeline for efficiently determining local atomic structure in materials science"(arxiv:2205.13308 )</p>
Data for publication: Nanomechanical and Structural Study of Au38 Nanocluster Langmuir-Blodgett Films Using Bimodal Atomic Force Microscopy and X-Ray Reflectivity
<p>Original data of Figures published in:</p> <p><strong>Nanomechanical and Structural Study of Au<sub>38</sub> Nanocluster Langmuir-Blodgett Films Using Bimodal Atomic Force Microscopy and X-Ray Reflectivity</strong></p> <p>Journal of Colloid and Interface Science, 2022, Michal Swierczewski<sup>,</sup> Alexis Chenneviere, Lay-Theng Lee, Plinio Maroni and Thomas Bürgi*<sup>[</sup></p> <p> </p>
The design of optimal mixtures from atom groups using Generalized Disjunctive Programming
<p>The files contain all the mixture design problems implemented in GAMS for this publication.</p> <p>All problems are solved in GAMS version 24.8.3 and are run on a single core of a dual 6 core Intel Xeon E5-1660 machine at<br> 3.30 GHz.</p> <p> </p>
Simultaneous Control of Aluminum Atoms and Defects in MOR Zeolite Framework by Post-Synthetic Treatments
<p><span>Input and output files used to calculate 27Al NMR chemical shifts in Quantum Espresso 6.5 for modernities with various defects and Al substitutions.</span></p>
Dataset for "Formal Single Atom Editing of the Glycosylated Natural Product Fidaxomicin Improves Acid Stability and Retains Antibiotic Activity"
<p>ZIP File:</p> <p>Characterisation data (such as e.g. NMR, IR, MS spectra)</p> <p>NMR raw data, .mnova files</p> <p>DP4+ data (final conformer coordinate files, result tables)</p> <p>DFT simulation data (coordinate files, results table)</p> <p>PDF file:</p> <p>Supporting information for</p> <p>Formal Single Atom Editing of the Glycosylated Natural Product Fidaxomicin Improves Acid Stability and Retains Antibiotic Activity</p>
All-atom molecular dynamics simulations of iRFP713/C15S/V254C/N136R
<p>The trajectories of all-atom MD simulations of monomeric and dimeric iRFP713/C15S/V254C/N136R with PCB (phycocyanobilin) and BV (biliverdin).</p> <p> </p> <p>Simulations have been performed using the CHARMM36 force field, running with the GROMACS 2022 package.</p>
Molecular dynamics trajectories of pYEEI:SH2 recognition, unbiased, at all-atom resolution.
<div> </div> <p>Set of 772 all-atom trajectories simulated from an unbound (apo) configuration of the human p56 -lck tyrosine kinase SH2 domain with its high-specificity phosphopeptide recognition substrate pYEEI (initial structure based on PDB:<a href="https://www.rcsb.org/structure/1LKK">1LKK</a> ). Approximately 24 trajectories spontaneously reach a bound state with ligand RMSD < 2 Â from the crystal. System building and run details are described in [1].</p> <p>A preliminary version of this dataset have been analyzed and discussed in [1] (approx 200 ns per trajectory were available and used in [1]). </p> <p>The trajectories provided here are extended to ~800 ns each, for a total of ~640 μs sampled time. The full dataset is analyzed in [2] with a SOM-based technique.</p> <div> <h2>Notes</h2> </div> <div> <ul> <li>These are all-atom simulations (with TIP3P water). Water molecules have been stripped off from these files (filtered).</li> <li>Not all trajectories have the same length. Some are cut short due to the distributed computing setup.</li> <li>Frame-to-frame interval is 1 ns.</li> </ul> </div> <h2>Acknowledgments</h2> <p>We thank the volunteers of the GPUGRID.net project for donating computing time.</p> <p> </p> <h2>References</h2> <p>[1] T. Giorgino, I. Buch, and G. De Fabritiis. <a href="https://pubs.acs.org/doi/10.1021/ct300003f">Visualizing the Induced Binding of SH2-Phosphopeptide</a>, J. Chem. Theory Comput. 2012, 8, 4, 1171-1175. doi:10.1021/ct300003f</p> <p>[2] Lara Callea, Camilla Caprai, Laura Bonati, Toni Giorgino, Stefano Motta. Self-Organizing Maps of Unbiased Ligand-Target Binding Pathways and Kinetics. J. Chem. Phys, 2024. https://doi.org/10.1063/5.0225183 </p> <p> </p> <div> </div> <div> <p> </p> </div>
Unraveling the interaction between singlet state atomic oxygen and water: toward the formation of oxywater and hydrogen peroxide
<p>We provide example input files to perform simulations of our article "Unraveling the interaction between singlet state atomic oxygen O(1D) and water: toward the formation of oxywater and hydrogen peroxide". In addition, we provide the output files together with a python script to caclulate the reaction rate of oxywater transition to hydrogenperoxide. You can find the paper via this link: <a title="Link to landing page via DOI" href="https://doi.org/10.1039/D4CP00969J">https://doi.org/10.1039/D4CP00969J</a></p>
Magneto-Seebeck Tunneling on the Atomic Scale
<p>Data files for the figures in the publication "Magneto-Seebeck Tunneling on the Atomic Scale".</p>
Aligning of water molecules into proton-conducing transmembrane water wires by oxygen atoms of phospholipid ester linkers
<p>A media AVI file that shows how oxygen atoms of ester linkers of the two converging phospholipid molecules form an "oxygen passage" along which water molecules align in a proton-conducting wire. Further details could be found in our article</p>
Atomic-resolution imaging of surface and core melting in individual size-selected Au nanoclusters on carbon
<p>Experimental and theoretical data sets for the Nature Communications paper "Atomic-resolution imaging of surface and core melting in individual size-selected Au nanoclusters on carbon". Data structure and formats are described in the README.docx file.</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.