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78 results for “atomistic”
Atomistic Structures discussed in "Segregation-enhanced grain boundary embrittlement of recrystallised tungsten evidenced by site-specific microcantilever fracture"
<p>The tar file Sigma7_GB.tar contains all data to reproduce the results shown and discussed in the Publication "Segregation-enhanced grain boundary embrittlement of recrystallised tungsten evidenced by site-specific microcantilever fracture", DOI: <a href="https://doi.org/10.1016/j.actamat.2023.119256">10.1016/j.actamat.2023.119256</a></p><p>It contains three folders for the grain boundary creation, decoration with P atoms, and fracture simulations.<br>The naming conventions and additional information are provided in README.txt files in the directories.</p>
Atomistic trajectories from ab-initio molecular dynamics simulations of wetted TiO2 nanoparticle
<p>This repository contains atomistic trajectories from ab-initio molecular dynamics simulations of water and TiO2 nanoparticle described in the paper:</p> <p>E. G. Brandt, L. Agosta and A.P.Lyubartsev, " Reactive wetting properties of TiO2 nanoparticles predicted by ab initio molecular dynamics simulations", Nanoscale, 8, 13385-13398 (2016) DOI: 10.1039/c6nr02791a</p> <p>The trajectories are saved in the .xtc format, and initial structures with specification of atom types are given in the .pdb format.</p> <p>The name of each file contains brief information about the simulated system:</p> <p>TiO2 : composition of the nanoparticle<br> n24 : number of TiO2 units in the nanoparticle<br> anatase/brookite/rutile : type of crystall structure<br> - a number 0 - 30 : number of water molecules in the simulation<br> 2fs - the time step</p> <p>For more details, see the referred paper</p>
Unveiling the atomistic and electronic structure of NiII–NO adduct in a MOF-based catalyst by EPR spectroscopy and quantum chemical modelling
<p><strong>Description of the dataset: </strong></p> <ul> <li><strong>Data type</strong>: Experimental spectroscopic measurements, computer simulation and analysis</li> <li>Files are with filename extensions: <strong>DSC</strong>, <strong>DAT</strong>, <strong>m</strong>, <strong>txt</strong></li> <li>Information on <strong>origin of the data</strong>:</li> </ul> <ul> <li>EPR spectroscopic measurements with filename extensions <strong>DSC</strong>, <strong>DTA.</strong></li> <li>EPR spectroscopic simulation and analyses with filename extension <strong>m</strong>.</li> <li>EPR spectra are exported as <strong>txt</strong> files in ASCII format.</li> </ul> <ul> <li>X-band CW-EPR spectroscopic measurements were generated by EMX spectrometer equipped with SHQ cavity produced by Bruker.</li> <li><strong>If the dataset includes multiple files that relate to each other:</strong> <ul> <li>Files in <strong>PARACAT_WP4_20230706_01_CW_Xband </strong>folder includes X-band CW-EPR spectroscopic measurements; original data are in DTA/DSC and txt formats.</li> <li>Files in <strong>PARACAT_WP4_20230706_02_HYSCORE </strong>and <strong>PARACAT_WP4_20230706_03_ENDOR </strong>folders include X-band HYSCORE and ENDOR data; original data are in DTA/DSC and txt formats.</li> <li>Files in <strong>PARACAT_WP4_20230706_ 04_MATLAB</strong> and<strong> PARACAT_WP4_20230706_ 05_Modelling</strong> folders include matlab and computer simulations/analyses of the EPR measurements; data are in m and txt formats.</li> <li>File <strong>PARACAT_WP4_20230706_ 06_Origin</strong> include origin plotted data</li> </ul> </li> </ul> <p> </p> <ul> <li><strong>Information on</strong>: <ul> <li>specialized abbreviations: <strong>MFU– </strong>MFU-4l:NO<sub>2</sub> MOF material</li> <li>NiNO – NO adsorbed MFU-4l:NO<sub>2</sub> MOF</li> <li>@10K – measured at 10 K</li> <li>definitions of variables: <strong>Magnetic field, Temperature.</strong></li> <li>units of measurement: <strong>Gauss (G), K, degree (°), milliTesla (mT)</strong>.</li> </ul> </li> </ul>
The Unfolding Journey of Superoxide Dismutase 1 Barrels Under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions With Crowders
<p>This data accompanies the article entitled <em>The Unfolding Journey of Superoxide Dismutase 1 Barrels Under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions With Crowders</em>, published in J. Phys. Chem. Lett. (<a href="https://doi.org/10.1021/acs.jpclett.0c00699">https://doi.org/10.1021/acs.jpclett.0c00699</a>).</p> <p><strong>01_SOD1bar_unfolding_REST2.zip: </strong>The zip archive includes REST2 trajectories for the three systems investigated in the paper: 1:1 packing, 2:1 packing, and the dilute case. The trajectories are saved in the GROMACS XTC file format, separately for each temperature (i=0,...,23). Given the large trajectory sizes, only protein coordinates (SOD1bar + crowders) are reported, and the output frequency is reduced to 100 ps. A starting geometry (in the Gromos87 GRO format) after equilibration of the initial packing is provided for each REST2 simulation (conf_prot.gro). Moreover, for each REST2 simulation, an xarray (http://xarray.pydata.org) dataset, saved in the netCDF file format, is included with computed fraction of native contacts, secondary structure content, and the Calpha RMSD of the barrel core (beta sheets beta1 - beta8) with respect to the crystal structure.</p> <p><strong>02_SOD1bar_geometries_representative_unfolding.zip:</strong> Representative SOD1bar geometries along the unfolding pathway (presented in Figure 3 of the paper).</p> <p><strong>03_SOD1bar_geometries_loopVII.zip: </strong>SOD1bar geometries with varying loop VII conformation which were isolated from dilute REST2 and which are presented in Figure S9 of the paper.</p>
Fracture Toughness of Off-Stoichiometric B2 NiAl as determined by micromechanical tests and atomistic simulations
<p>KQJ-Alconcentration-NiAl_experiment.csv : semicolon-separated ASCII file containing the fracture toughness (2nd column) and the contribution of the plastic deformation to the fracture toughness (3rd column) as function of Al concentration (1st column) for off-stoichiometric B2 NiAl as determined by micro mechanical tests on notched cantilever beams.</p> <p>KIc-Alconcentration-NiAl_static-simulations.dat : space-separated ASCII file containing the fracture toughness (K_Ic) of B2 NiAl (2nd column) for different Al concentrations (first column) as as determined by static atomistic calculations with the<br> # Potential by G. P. P. Pun, Y. Mishin, (Phil. Mag. 89 (34-36) (2009) 3245– 3267).</p> <p>NiAl_Pun_conc_0.40-0.65Ni_Esurf110_Cij.dat : space-separated ASCII file containing the energy of {110} surfaces (2nd column) and elastic constants (columns 3-5) of B2 NiAl for different Ni concentrations (f1st column) as determined by atomistic simulations using the the potential by G. P. P. Pun, Y. Mishin, (Phil. Mag. 89 (34-36) (2009) 3245– 3267)</p> <p>KIc-Alconcentration-NiAl_theory.dat : space-separated ASCII file containing the fracture toughness (K_Ic) of B2 NiAl (2nd column) for different Al concentrations (1st column) as calculated by the Griffith equation.</p> <p> </p>
Dataset for article - Dislocation dynamics in Ni: Parameterising dislocation trajectories from atomistic simulations
<p>Data supporting findings in "Dislocation dynamics in Ni: Parameterising dislocation trajectories from atomistic simulations". In this work, 8 identical Molecular Dynamics (MD) simulations of edge dislocations in pure Nickel were run and analysed, where dislocation positions were extracted and each dislocation is tracked for further analysis. Each simulation only differs in the random seed used for setting the initial atom velocities. Files needed to reproduce a specific simulation can be found in the directories provided in <em>data.zip</em>:</p> <ul> <li>fr_18430</li> <li>fr_27743</li> <li>fr_44345</li> <li>fr_46165</li> <li>fr_54382</li> <li>fr_54992</li> <li>fr_97181</li> <li>fr_98232</li> </ul> <p>The random seed needed to set the initial velocities of the atoms are set in the LAMMPS script. The log files generated by LAMMPS are provided for the different stages of a given simulation in the <em>LAMMPS_logs</em> sub-directories. The corresponding output files from the OVITO DXA are also included in the sub-directory <em>Ni_disloc_const</em>. The files <em>disloc_data_*.ca</em> contain the raw output from the OVITO DXA and can be opened directly in OVITO. The <em>disloc_data_*.txt </em>files contain information extracted from the OVITO DXA in a format that can be read in and processed by the dislocation tracking code (<a href="https://github.com/geraldineanis/DislocCode/tree/v1.0.0">https://github.com/geraldineanis/DislocCode/tree/v1.0.0</a>). The wildcard character "*" is replaced with the simulation timestep. In each directory, the dislocation position vs. time data is included as a text file<em> </em>named<em> </em><em>perfect_pos_<seed>.txt</em>. The Mishin 2004 EAM interatomic potential file <em>NiAl_Mishin_2004.eam.alloy</em> used to generate the data is also provided.</p> <p>Additional simulations were carried out at a range of applied shear stresses (20 MPa - 50 MPa). Files needed to reproduce theses simulations are provided in <em>data_stress.zip </em>and follow the same format described above.</p> <p>The data provided here was generated with the <code>LAMMPS/29Sep2021-kokkos</code><em> </em>module on the SULIS Tier 2 HPC platform, which has been built with the OpenMP backend of the <code>kokkos</code> package and uses the <code>foss-2021b</code> toolchain (<a href="https://docs.easybuild.io/common-toolchains/">https://docs.easybuild.io/common-toolchains/</a>). For further information, please refer to <a href="https://sulis-hpc.github.io/appnotes/lammps.html">https://sulis-hpc.github.io/appnotes/lammps.html</a>.</p> <p>For more details on the calculations, please refer to the publication (in preparation). Please refer to the GitHub repository at <a href="https://github.com/geraldineanis/DislocCode/tree/v1.0.0">https://github.com/geraldineanis/DislocCode/tree/v1.0.0</a> for the analysis tools developed and for detailed instructuctions for their use.</p>
Dataset for the publication: First-principles studies on the atomistic properties of metallic magnesium as anode material in magnesium-ion batteries
<p>This dataset contains the input and output files from the calculation of the atomistic properties of metallic magnesium, such as bulk, surface, adsorption, and diffusion properties.</p> <p>The discussion of the results were published in the ChemSusChem article: 'First-principles studies on the atomistic properties of metallic magnesium as anode material in magnesium-ion batteries' (<a href="https://doi.org/10.1002/cssc.202200414">https://doi.org/10.1002/cssc.202200414</a>). A preprint of the publication is further available under: <a href="http://doi.org/10.26434/chemrxiv-2022-qz055">https://doi.org/10.26434/chemrxiv-2022-qz055</a>.</p> <p>All calculations were performed using the density function theory code Vienna <em>ab initio</em> simulation package (VASP).</p> <p>The dataset contains all raw data for the performed convergence studies and calculated bulk-, surface-, adsorption-, and diffusion properties. An overview of the folder structure of the Zip archive, more precisely in which folders the data for the respective figures or tables of the underlying publication (<a href="https://doi.org/10.1002/cssc.202200414">https://doi.org/10.1002/cssc.202200414</a>) are stored, is provided in the following table:</p> <table> <tbody> <tr> <td>Convergence_study</td> <td>Figure S1</td> </tr> <tr> <td>Bulk_properties</td> <td>Table S3</td> </tr> <tr> <td>Surface_properties</td> <td>Table 1, Table 2, Figure 1, Table S5</td> </tr> <tr> <td>Adsorption_properties</td> <td>Monomer: Table S6; Dimer: Table 4, Table 5, Table 6; Islands: Figure S5, Table S9</td> </tr> <tr> <td>Diffusion_properties</td> <td>Table 3, Table 7, Table 8, Table 9, Table 10, Table 11, Table 12, Figure 13, Figure 14, Table S7, Table S8, Table S10 Table S11, Figure S4, Figure S7, Figure S9</td> </tr> </tbody> </table> <p> </p>
Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling: Datasets.
<p>Datasets related to the publication [1].<br> Including:</p> <ul> <li>KRAS G12X mutations derived from COSMIC v.79 [http://cancer.sanger.ac.uk/cosmic/] (KRAS_G12X_mut_COSMICv79..xlsx)</li> <li>RMSFs (300-2000ns) of GDP-systems (300_2000rmsf_GDP_systems_RAW_AVG_SE.xlsx)</li> <li>RMSFs (300-2000ns) of GTP-systems (300_2000RMSF_GTP_systems_RAW_AVG_SE.xlsx)</li> <li>PyInteraph analysis data for salt-bridges and hydrophobic clusters (.dat files for each system in the PyInteraph_data.zip-file)</li> <li>Backbone trajectories for each system (residues 4-164; frames for every 1ns). Last number (e.g. _1) refers to the replica of the simulated system.</li> <li>backbone_4-164.gro/.pdb/.tpr -files (resid 4-164) </li> </ul> <p><br> [1] Pantsar T et al. Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling. <em>PLoS Comput Biol Submitted</em> (2018)</p>
Data for 'Grain boundary segregation and phase separation in ceria-zirconia from atomistic simulation'
<p>Data for the article 'Grain boundary segregation and phase separation in ceria-zirconia from atomistic simulation', including input and output files for simulations, and scripts to perform data analysis and generate figures.</p>
Topology and structure of Au144(SRNH3+)60 from "Atomistic Simulations of Functional Au144(SR)60 Gold Nanoparticles in Aqueous Environment"
<p>Positively charged monolayer-protected gold nanoparticles (AuNPs) structure and topology files for GROMACS used in DOI: 10.1021/jp301094m. The final structure of the simulation reported in DOI: 10.1021/jp301094m for the neutral case is provided.</p> <p>The gold nanoparticle contain a core of 144 Au atoms and 60 functionalized alkanethiol side groups (undecanyl chain, R = C11H22), each possessing a positively charged amonium terminal group.</p> <p>When using this structure do not forget to cite DOI: 10.1021/jp301094m. </p> <p>NOTE1: Different versions for the topology files are provided of both AuNPs. All versions were used for the publication. The changes only affect the core surface and therefore had no influence in the reported properties. Still we recommentd using the latest version: AU144SRNH360_v3.itp.</p> <p>NOTE2: The original simulations used GROMACS 4.0.5. The files should work, however, as well up to GROMACS 4.6.7.</p>
Topology and structure of Au144(SRCOO-)60 from "Atomistic Simulations of Functional Au144(SR)60 Gold Nanoparticles in Aqueous Environment"
<p>Negatively charged monolayer-protected gold nanoparticles (AuNPs) structure and topology files for GROMACS used in DOI: 10.1021/jp301094m. The final structure of the simulation reported in DOI: 10.1021/jp301094m for the neutral case is provided.</p> <p>The gold nanoparticle contain a core of 144 Au atoms and 60 functionalized alkanethiol side groups (undecanyl chain, R = C11H22), each possessing a negatively charged carboxylic terminal group.</p> <p>When using this structure do not forget to cite DOI: 10.1021/jp301094m. </p> <p>NOTE1: Different versions for the topology files are provided of both AuNPs. All versions were used for the publication. The changes only affect the core surface and therefore had no influence in the reported properties. Still we recommentd using the latest version: AU144SRCOO60_v2.itp.</p> <p>NOTE2: The original simulations used GROMACS 4.0.5. The files should work, however, as well up to GROMACS 4.6.7.</p>
Atomistic spin dynamics simulations of iron and cobalt
<p>Atomistic spin dynamics (ASD) simulations of ultrafast demagnetization in ferromagnetic iron and cobalt. The ASD simulations here are energy-conserving, which means that energy flow into and out of the spin system is considered.</p> <p>The dataset contains simulations at four different pump laser fluences for iron and six different fluences for cobalt. The excitation was assumed to be homogeneous throughout the simulated volume.</p> <p>The heat capacities and electron-phonon coupling parameters which were used in the ASD simulations are provided in the folder "heat capacities and G_ep".</p> <p>More information is available here:<br> - https://arxiv.org/abs/2110.00525<br> - Zahn et al. Phys. Rev. Research 3, 023032 (2021)<br> https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.3.023032</p> <p> </p>
Supplementary data for Atomistic Mechanism of the Nucleation of Methylammonium Lead Iodide Perovskite from Solution
<p>Supplementary data for "Atomistic Mechanism of the Nucleation of Methylammonium Lead Iodide Perovskite from Solution"</p>
Raw data to: Molecular Interplay of ADAMTS13-MDTCS and von Willebrand Factor-A2: Deepened Insights from Extensive Atomistic Simulations
<p>Structural ensembles of ADAMTS13-MDTCS in isolation and in interaction with the von Willebrand factor A2 domain, as obtained from extensive TIGER2h replica exchange simulations. Scripts to filter for certain binding states by given contacts, extract conformational clusters, a movie illustrating the binding transition between recruitment (Model2) and proteolytic (Model1) states, PDB files of both models for further investigation along with upcoming experimental verification.</p>
Data Supplement for "Impact of Charged Surfaces on the Structure and Dynamics of Polymer Electrolytes: Insights from Atomistic Simulations"
<p>Data set containing the molecular dynamics simulation data used for the journal article "Impact of Charged Surfaces on the Structure and Dynamics of Polymer Electrolytes: Insights from Atomistic Simulations" (<span>Andreas Thum, </span><span>Diddo Diddens, </span><span>Andreas Heuer, </span><em>J. Phys. Chem. C</em> <strong>2021</strong>, <em>125</em>, 25392−25403, <a href="https://doi.org/10.1021/acs.jpcc.1c07751">https://doi.org/10.1021/acs.jpcc.1c07751</a>).</p>
Dataset for: Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins
<p>This dataset provides input/output files and scripts for the publication: Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins.</p>
Extended ensemble molecular dynamics study of ammonia–cellulose I complex crystal models: free-energy landscape and atomistic pictures of ammonia diffusion in the crystalline phase.
<p>The data deposited here accompany the manuscript "Extended ensemble molecular dynamics study of ammonia–cellulose I complex crystal models: free-energy landscape and atomistic pictures of ammonia diffusion in the crystalline phase" and include the molecular dynamics trajectories and the AMBER topology (parm) files. Detailed file contents are summarized in the README file.</p>
Dataset 3 of 5 from: Atomistic mechanisms of the regulation of small conductance Ca 2+ -activated K + channel (SK2) by PIP2
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Dataset 5 of 5 from: Atomistic mechanisms of the regulation of small conductance Ca 2+ -activated K + channel (SK2) by PIP2
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Parent dataset and code from: Atomistic Mechanisms of the regulation of small conductance Ca 2+ -activated K + channel (SK2) by PIP2
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