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669 results for “ATOM”
i-Tasser 3D Strucutres of Milk Proteins for United Atom Multiscale Modelling Of Bio-Nano Interactions
<p>The list of milk proteins was obtained from this work:</p> <blockquote> <p>Tacoma R, Fields J, Ebenstein DB, Lam YW, Greenwood SL. Characterization of the bovine milk proteome in early-lactation Holstein and Jersey breeds of dairy cows. Journal of Proteomics, 2016 (130), 200-210.</p> </blockquote> <p>Files were prepared with I-TASSER utility:</p> <blockquote> <p>J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8 (2015).</p> </blockquote>
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>
United Atom Parameters for United Atom Multiscale Modelling Of Bio-Nano Interactions Of Citrate Trianion Stabilized Nanoparticles
<p>Short-range surface adsorption potentials of carbohydrates, lipid fragments, and amino acid side chains onto Cit(3-) stabilized surfaces (in tabulated form).</p> <p>Recovered from radial distribution functions</p> <p>Force Fields: adapted CHARMM36.</p> <p>Material: CIT(3-)</p>
United Atom Parameters for United Atom Multiscale Modelling Of Bio-Nano Interactions Of Zero-Valent Gold Nanoparticles
<p>Short-range surface adsorption potentials of carbohydrates, lipid fragments, and amino acid side chains in tabulated form.</p> <p>Calculated via AWT-MetaD (Gromacs/Plumed).</p> <p>Force Fields: INTERFACE/CHARMM36.</p> <p>Material: zero-valent gold</p>
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>
Source data and codes for the paper "Inviting atomic mechanics to macro-continua: A study on monocrystalline Si using a spatial multilevel coarsening model"
<p>Source data and codes for the paper "Inviting atomic mechanics to macro-continua: A study on monocrystalline Si using a spatial multilevel coarsening model"</p> <p>This file includes </p> <p>- Source data for Figs 1-5 and Supplementary Materials</p> <p>- LAMMPS codes and raw log files used to produce the results of this study</p> <p> </p>
Supporting materials for the article "Neutral atomic hydrogen as an efficient catalyst for interstellar formation of adenine and guanine"
<p>The data files contain the computed atomic coordinate data of all optimized molecular structures in the standard XYZ chemical file format. </p> <p>The PDF file contains 1) the potential diagrams of reaction paths for producing adenine and guanine from H-catalyzed reactions between h-pyrimidine-2-one and (cyanamide or carbodiimide), and 2) the IR and electronic adsorption spectra of intermediates, as well as 3) a detailed description to the aformentioned data files.</p>
Supporting materials for the article "Neutral atomic hydrogen as an efficient catalyst for interstellar formation of adenine and guanine"
<p>The data files contain the computed atomic coordinate data of all optimized molecular structures in the standard XYZ chemical file format. </p> <p>The PDF file contains 1) the potential diagrams of reaction paths for producing adenine and guanine from H-catalyzed reactions between h-pyrimidine-2-one and (cyanamide or carbodiimide), and 2) the IR and electronic adsorption spectra of intermediates, as well as 3) a detailed description to the aformentioned data files.</p>
All-atom accelerated molecular dynamics (aMD) simulations of Filamin-A (FLNa) actin-binding Domain, immunoglobulin-like Domains 3, 4, 5, 21 and 24 to investagate the impact of known missense mutations associated with periventricular nodular heterotopia in the liveborn males
<p>Data includes all of the wild-type and mutant trajectories of accelerated all-atom molecular dynamics (aMD) simulations of Filamin-A (FLNa, the product of <em>FLNA</em> gene located on chromosome X). Wild-type proteins are from the PDB structures with IDs: 4M9P, 3HOP, 3CNK. The mutations, including R484Q that we discovered in a Turkish family, were formerly found in the liveborn males with <em>FLNA</em>-associated periventricular nodular heterotopia (PNH), who survived with the only copy of mutated <em>FLNA</em>. To understand how these mutations lead to the PNH and simultaneously allow their survival, we performed these MD simulations for the wild-type and mutant systems.</p> <p>Systems were prepared in Visual Molecular Dynamics (VMD 1.9.3) by placing them in a TIP3P water box with approximately 20 Å thickness from the protein surface and neutralizing the system by adding counter ions in the form of NaCl. Of note, only protein parts were kept for the submission to reduce the size of files. Nanoscale Molecular Dynamics (NAMD 2.13-CUDA) was used to perform MD simulations with CHARMM36m force field. For pressure and temperature controls, Nosé-Hoover Langevin barostat and Langevin thermostat were used. ShakeH algorithm of NAMD was applied for water molecule constraints. 12 Å cut-off distance was used for van der Waals interactions. Switching function starts at 10 Å and reaches zero at 14 Å. Integration time-step was 2 fs. To compute the long-range Coulomb interactions, the particle-mash Ewald method was used. After a 10000-step minimization with conjugate gradient algorithm and an equilibration for 1 ns at 298 K under NVT ensemble, production simulations were run along 100 ns. Only the production simulations were supplied in this dataset. Further details are available in the regarding configuration files.</p> <p>Resulting analysis files and scripts are included with the carbon alpha-containing dcd files of the simulations.</p> <p>This dataset is not used directly for any study, but they are preliminary results for the usage of aMD to understand rare disease mechanisms.</p> <p>Related publications:</p> <pre>Zenodo repo of classical MD for these variants: https://doi.org/10.5281/zenodo.4483108</pre> <p>Journal article based on classical MD:</p> <p>Gerlevik U, Saygı C, Cangül H, Kutlu A, Çaralan EF, Topçu Y, et al. (2022) Computational analysis of missense filamin-A variants, including the novel p.Arg484Gln variant of two brothers with periventricular nodular heterotopia. PLoS ONE 17(5): e0265400. https://doi.org/10.1371/journal.pone.0265400</p>
Data for 'Experimental Determination of a Single Atom Ground State Orbital through Hyperfine Anisotropy'
<p>This folder contains the raw data and scripts used for the paper <em>'Experimental Determination of a Single Atom Ground State Orbital through Hyperfine Anisotropy'</em>.</p>
Atomic partial wave meter by attosecond coincidence metrology
<p>all the raw data for the main figures of our literature "Atomic partial wave meter by attosecond coincidence metrology"</p>
Size spectrum, time series and atom number distribution of macroalgal emission vapors and oxidation products
<p>We conducted oxidation and NPF experiments with vapor emissions from real-world coastal macroalgae in a bag reactor. The dataset showed the measurement results of volatile precursors and their oxidation products. The dataset was organized by the order of figures in our submitted manuscript.</p>
Atomic structures derived from high-temperature and -pressure transformations from C60 fullerenes
<p>These are XYZ files containing the atomic structures depicted in the high-temperature and high-pressure C<sub>60</sub> phase diagram (figure 7) of this publication:</p> <blockquote> <p>Machine learning force fields based on local parametrization of dispersion interactions: Application to the phase diagram of C<sub>60</sub><br> Heikki Muhli, Xi Chen, Albert P. Bartók, Patricia Hernández-León, Gábor Csányi, Tapio Ala-Nissila, and Miguel A. Caro<br> Phys. Rev. B 104, 054106 (2021)</p> <p><a href="https://doi.org/10.1103/PhysRevB.104.054106">https://doi.org/10.1103/PhysRevB.104.054106</a></p> </blockquote> <p>The structures were generated with a general-purpose Gaussian approximation potential (GAP) for carbon whose training database included a large number of C<sub>60</sub> structures. Refer to the publication listed above for the details of the simulation and an analysis of the structures.</p>
Simulation Input Data for "Atomic Origins of Biomass Recalcitrance in Organic Solvents"
<p>This is the reduced data behind an upcoming manuscript investigating lignocellulosic interactions in plant secondary wall, when exposed to different organic solvent pretreatment. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was:</p> <pre><code class="language-bash">tar -zcvf lignincelluloseindustrialsolvent.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*xtc" --exclude="*gro" --exclude="*log" --exclude="*[0-9].out" --exclude="*npz" --exclude="*pkl" --exclude="*npy" --exclude="*png" --exclude="*bmim*" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*xst" --exclude="*edr" --exclude="*txt" --exclude="*state_prev.cpt" --exclude="*ppm" --exclude="Simulations" FaceDifferences</code></pre> <p>Within the FaceDifferences directory, there are 2 primary subdirectories:</p> <ul> <li><strong>Build </strong>contains the scripts and files to build the individual lignin cellulose in organic solvent molecular systems.</li> <li><strong>NewSolventSimulations</strong> contains the all-atom MD simulation inputs and the analysis scripts (subdirectory <strong>Analysis</strong>)</li> </ul>
Atoms of Confusion Dataset in Java Programs
<p>Double-checked gold standard dataset of Atoms of Confusion in Java. Data extracted from the main source code package of four open-source projects, excluding the test files. This dataset also includes a sample created from two other open-source projects. </p> <table> <thead> <tr> <th scope="col">Project</th> <th scope="col">Version</th> <th scope="col">Repository</th> </tr> </thead> <tbody> <tr> <td>FastUtil</td> <td>8.5.6</td> <td>https://github.com/vigna/fastutil </td> </tr> <tr> <td>Moshi</td> <td>1.12.0</td> <td>https://github.com/square/moshi</td> </tr> <tr> <td>Jimfs</td> <td>1.2</td> <td>https://github.com/google/jimfs</td> </tr> <tr> <td>uCrop</td> <td>2.2.7</td> <td>https://github.com/Yalantis/uCrop</td> </tr> </tbody> </table> <p> </p> <p>The sample was created by extracting Java files from the following projects:</p> <table> <thead> <tr> <th scope="col">Project</th> <th scope="col">Version</th> <th scope="col">Repository</th> </tr> </thead> <tbody> <tr> <td>Guava</td> <td>31.0.1</td> <td>https://github.com/google/guava</td> </tr> <tr> <td>Redisson</td> <td>3.6.16</td> <td>https://github.com/redisson/redisson</td> </tr> </tbody> </table> <p> </p>
Results of a Study on the Prevalence of Atoms of Confusion in Java Programs
<p>CSV reports and XLSX files of study on the prevalence of Atoms of Confusion in Java programs, generated from the BOHR tool (<a href="https://github.com/wendellmfm/bohr">https://github.com/wendellmfm/bohr</a>). </p>
Engineering random spin models with atoms in a high-finesse cavity
<p>Data corresponding to the article "Engineering random spin models with atoms in a high-finesse cavity".</p>
Small atom doping: A synergistic strategy to reduce SnZn recombination center concentration in Cu2ZnSnSe4?
<p>Dataset for the publication 10.1002/solr.202200580. Details can be found at the manuscript.</p>
Chemistry in Astrophysics : Atoms and Molecules
<p>The presentation corresponds to a IUPAC WorldFair Chemistry Webinar. The presentation aims at presenting in 5mn the type of chemistry data that are used in astrophysics, how we annotate those data, how we manipulate those data, what are the challenges and the issues linked to FAIR implementation, and what could be the collaboration with IUPAC. The PDF are uploaded at DOI 10.5281/zenodo.7101252</p> <p>IUPAC : https://iupac.org/worldfair-global-cooperation-on-fair-data-policy-and-practice/ and https://iupac.org/project/2022-012-1-024/</p> <p>VAMDC: https://vamdc.org</p>
Non-destructive imaging of atomically-thin nanostructures buried in silicon
<p>Original data in support of our publication, "Non-destructive imaging of atomically-thin nanostructures buried in silicon".</p>
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Allen Brain Atlas
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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.