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Dataset results
3 results for “nanoscale system”
Molecular simulations of nanoscale two-phase Couette flow of a water-hexane system on a hydrophobic substrate
<p>This dataset contains the output of Molecular Dynamics simulations (MD) of two-phase Couette flow of water/hexane biphasic systems, in terms of density, velocity and temperature fields. Instructions on how to read and analyze the output files in the <code>.tar.gz</code> archives can be found in these previously-published datasets: <a href="https://doi.org/10.5281/zenodo.8077915">https://doi.org/10.5281/zenodo.8077915</a>, <a href="https://doi.org/10.5281/zenodo.6541983">https://doi.org/10.5281/zenodo.6541983</a></p> <p>The run output files are labeled using the following pattern: <code>hex-ca<capillary-number>-q<partial-charge>.tar.gz</code>. It is possible to obtain the wall speed/contact line speed from the capillary number using the following formula: <code>u_w = U_0*<capillary-number></code>, with <code>U_0 = 37.246 m/s</code>.</p> <p>To reproduce the runs it is necessary to use a specific version of Gromacs that allows for a special algorithm of pressure scaling with position restraints. The code can be obtained by cloning <a href="https://github.com/MicPellegrino/gromacs-flow-field.git">https://github.com/MicPellegrino/gromacs-flow-field.git</a>, and switching to the <code>flow-field-grid-visco-coms-deform</code> branch.</p> <p>The folder <code>conf-wat-hex.zip</code> contains the configuration files to reproduce MD simulations. To prepare the equilibration runs at constant pressure, run after having installed Gromacs:</p> <p><code>gmx grompp -f npt.mdp -p topology.top -c before-npt.gro -r before-npt.gro -o system-npt.tpr</code></p> <p>while to prepare the shear runs:</p> <p><code>gmx grompp -f shear.mdp -p topology.top -c after-npt.gro -r lambda0.gro -rb lambda1.gro -o system-shear.tpr</code></p> <p>Simulations are launched by running:</p> <p><code>gmx mdrun -v -s <tpr-file-name>.tpr <possibly-other-mdrun-flags></code></p> <p>Have fun simulating!</p>
Molecular simulations of nanoscale two-phase Couette flow of a water-hexane system on a hydrophilic substrate
<p>This dataset contains the output of Molecular Dynamics simulations (MD) of two-phase Couette flow of water/hexane biphasic systems, in terms of density, velocity and temperature fields. Instructions on how to read and analyze the output files in the <code>.tar.gz</code> archives can be found in these previously-published datasets: <a href="https://doi.org/10.5281/zenodo.8077915">https://doi.org/10.5281/zenodo.8077915</a>, <a href="https://doi.org/10.5281/zenodo.6541983">https://doi.org/10.5281/zenodo.6541983</a></p> <p>The run output files are labeled using the following pattern: <code>hex-ca<capillary-number>-q<partial-charge>.tar.gz</code>. It is possible to obtain the wall speed/contact line speed from the capillary number using the following formula: <code>u_w = U_0*<capillary-number></code>, with <code>U_0 = 37.246 m/s</code>.</p> <p>To reproduce the runs it is necessary to use a specific version of Gromacs that allows for a special algorithm of pressure scaling with position restraints. The code can be obtained by cloning <a href="https://github.com/MicPellegrino/gromacs-flow-field.git">https://github.com/MicPellegrino/gromacs-flow-field.git</a>, and switching to the <code>flow-field-grid-visco-coms-deform</code> branch.</p> <p>The folder <code>conf-wat-hex.zip</code> contains the configuration files to reproduce MD simulations. To prepare the equilibration runs at constant pressure, run after having installed Gromacs:</p> <p><code>gmx grompp -f npt.mdp -p topology.top -c before-npt.gro -r before-npt.gro -o system-npt.tpr</code></p> <p>while to prepare the shear runs:</p> <p><code>gmx grompp -f shear.mdp -p topology.top -c after-npt.gro -r lambda0.gro -rb lambda1.gro -o system-shear.tpr</code></p> <p>Simulations are launched by running:</p> <p><code>gmx mdrun -v -s <tpr-file-name>.tpr <possibly-other-mdrun-flags></code></p> <p>Have fun simulating!</p>
Dissolved iron released from nanoscale zero-valent iron (nZVI) activates the defense system in bacterium Pseudomonas putida, leading to high tolerance to oxidative stress
GEO Series GSE197899. Pseudomonas putida. 18 samples. Type: Expression profiling by high throughput sequencing.
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International Brain Laboratory public data
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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.