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68 results for “electrostatics”
Input files for publication: Binding of DEP Domain to Phospholipid Membranes: More Than Just Electrostatics
<p>Input files for publication: Francesco L. Falginella, Marek Kravec, Martina Drabinová, Petra Paclíková, Vítězslav Bryja, and Robert Vácha: Binding of DEP Domain to Phospholipid Membranes: More Than Just Electrostatics</p>
Input files for "Predicting the orientation of adsorbed proteins steered with electric fields using a simple electrostatic model"
<p>In files to run PyGBe (https://github.com/pygbe/pygbe), and reproduce the results from the J. Phys. Chem. B article "Predicting the orientation of adsorbed proteins steered with electric fields using a simple electrostatic model". </p>
2D honeycomb transformation into dodecagonal quasicrystals driven by electrostatic forces
<p>This repository contains the SXRD data measured for the 48-18-6 approximant in Sr-Ti-O on Pt(111). The data has been acquired at the SixS beamline of the Synchrotron SOLEIL in France on 19.09.2019.</p> <p>Monochromatic x-rays with photon energy of 11 keV were used to avoid Pt fluorescence (at 11.1 and 13 keV) and consequently reduced the background signal. The diffraction experiment was performed under grazing incidence at an angle of 0.2 °. The orientation matrix was defined relative to the Pt substrate lattice with its lattice constants of a = 392 pm.</p> <p>Additionally, the 3D voxel map generated from the raw data for further use in the binoculars software is provided as well as the input and output of SHELXL, which has been used for structure relaxation.</p>
2D honeycomb transformation into dodecagonal quasicrystals driven by electrostatic forces
<p>This repository contains the key input and output files used for the density fucntional theory calculations of the paper "Mechanism of 2D Oxide Quasicrystal formation from honeycomb structures" by Sebastian Schenk, Oliver Krahn, Eric Cockayne, Holger L. Meyerheim, Marc deBoissieu, Stefan F"orster, and Wolf Widdra (2022).</p> <p>The calculations were performed using the DFT code VASP, version 5.4.4 [Commercial software is mentioned in this README file to adquately described the procedure. This does not imply an endorsement or recommendation by the National Institute of Standards and Technology, nor that the software used is necessarily the best for the given<br> purpose.]</p> <p>The subfolder large_approximant contains the files for the large Sr<sub>48</sub>Ti<sub>132</sub>O<sub>204</sub> approximant on a Pt monolayer. Subfolders honeycomb/Pt<sub>N</sub> and sigma/Pt<sub>N</sub> contain the files for honeycomb and sigma Ba<sub>8</sub>Ti<sub>24</sub>O<sub>36</sub> structures on Pt trilayers with N Pt per layer per periodic cell. Subfolders honeycomb/Pt<sub>N</sub>/substrate contain the corresponding files<br> for the Pt substrate alone. The honeycomb and sigma structures are at the equilibrium strain as determined by matching interpolated stress results, as described in the Supplementary Information associated with the main Article.</p> <p>The input files are the standard VASP input files: POSCAR (structure information), POTCAR_TITEL (pseudopotential information. Because the VASP pseudopotential files are proprietary, only the titles of the pseudopotentials used are given), KPOINTS (k-point generation) and INCAR (most calculation details). To accelerate the DFT van der Waals calculation, the file vdw_kernel.bindat from the VASP package (not included here) should also be used. The output files are OSZICAR (summarizes energy at each iteration) and OUTCAR (full ouput).</p>
Supporting Information for the Journal Article "The electrostatic potential as a descriptor for the protonation propensity in automated exploration of reaction mechanisms"
<p>This dataset contains the supporting information published together with the article "The electrostatic potential as a descriptor for the protonation propensity in automated exploration of reaction mechanisms" (<a href="https://doi.org/10.1039/C9FD00061E"><em>Faraday Discuss.</em>, <strong>2019</strong>, <em>220</em>, 443</a>).</p>
Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations to Accurately Model Glycosaminoglycan Electrostatic Interactions
<p>To cite and for more details: Riopedre-Fernandez et al. <em>J. Chem. Inf. Model.</em> <strong>2024</strong>, 64 (18), 7122–7134. DOI: <a href="https://doi.org/10.1021/acs.jcim.4c00981">https://doi.org/10.1021/acs.jcim.4c00981</a></p> <p>The dataset includes molecular dynamics simulations of sulfated saccharides and their sulfated analogs in the presence of calcium cations in aqueous solution. Several force field parameter sets were compared (CHARMM36, GLYCAM06, AMOEBA, Drude) and new have been developed (prosECCo75 and GLYCAM-ECC75).</p> <p>The uploaded files contain the following simulation input files or/and simulation trajectories:</p> <p>1) Sulfated_Molecules_Umbrella_Sampling_AIMD: Umbrella sampling ab initio molecular dynamics simulations of calcium-methylsufate and calcium N-methylsulfamate ion pairs in water.</p> <p>2) Sulfated_Molecules_Umbrella_Sampling_FFMD: Umbrella sampling force field molecular dynamics simulations of calcium-methylsufate and calcium N-methylsulfamate ion pairs in water.</p> <p>3) Sulfated_Molecules_AWH_FFMD: Accelerated weight histogram force field molecular dynamics simulations of calcium interacting with both methylsufate and N-methylsulfamate in water.</p> <p>4) Disaccharides_FFMD: Unbiased force field molecular dynamics simulations of calcium-sulfated disaccharide aqueous solutions.</p> <p>UPD. Version 2.0 has updated one of the disaccharide-containing simulations (GLYCAM06, N-sulfation) due to incorrect calcium LJ parameters in the original upload.</p>
Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape
<p>Raw images and datasets regarding the manuscript "Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape" by De la Concepcion et al. 2024</p>
Literature Survey of Electrostatic Incidents- Fire Protection Research Foundation report data
<p>The attached spreadsheet includes 89 incidents gathered as part of a FPRF report (report number FPRF-2021-07) "Static Electricity Incident Review" produced in August 2021. The report is available at: <a href="https://www.nfpa.org/News-and-Research/Data-research-and-tools/Electrical/Static-Electricity-Incident-Review ">https://www.nfpa.org/News-and-Research/Data-research-and-tools/Electrical/Static-Electricity-Incident-Review </a></p> <p>The incidents gathered are on electrostatic incidents found in the literature or public domain, and categorized in the following 10 columns:</p> <ol> <li>Incident Date</li> <li>Incident Location</li> <li>Incident Type</li> <li>Summary of Incident</li> <li>Potential NFPA 77 technical item that was breached</li> <li>Link/references to incident (if available)</li> <li>Number of Casualties</li> <li>Date last accessed</li> <li>Conclusions</li> <li>Why the incident happened.<br> </li> </ol>
Simulation data of electrostatic wave dispersion relation measurement by MMS
<p>We simulate electrostatic wave packets with an ion-acoustic like dispersion relation traveling at different directions in the probe coordinate system. We then set up a model spacecraft and measure the dispersion relation of the simulated wave packets using a method based on spin-plane interferometry. </p>
Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery
<p>Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery (<a href="https://zenodo.org/record/7423328">https://zenodo.org/record/7423328</a>)</p>
Input files for binding energy calculations in "Coupling finite and boundary element methods to solve the Poisson--Boltzmann equation for electrostatics in molecular solvation"
<p>Input files (meshes, pqr, cavities) for binding energy calculations in the manuscript "Coupling finite and boundary element methods to solve the Poisson--Boltzmann equation for electrostatics in molecular solvation" (preprint at https://arxiv.org/abs/2305.11886). This data set of molecular structures was originally proposed by Harris, R.C., Boschtisch, A.H., and Fenley, M.O., JCTC 9 (8) (2013) (<a href="https://doi.org/10.1021/ct300765w">https://doi.org/10.1021/ct300765w</a>). Scripts to generate results are available in https://github.com/MichalBosy/FEM_BEM_coupling/.</p>
Data supporting the paper "Simulating the electrostatic patch force in sphere-plate and plate-plate geometries"
<p>This dataset accompanies the paper titled "Simulating the electrostatic patch force in sphere-plate and plate-plate geometries" by M.H.J. de Jong and L. Mercier de Lepinay. It is a zip file that contains the figures of the publication, the raw data supporting those figures, the analysis and plotting scripts, and the toolbox to simulate the electrostatic patch force in various geometries. The structure, relation and contents of the files are detailed exhaustively in the "README.txt" file in the top level folder.</p> <p>The contents of the .zip file are common image formats (.png and .pdf), readable text and data files (.txt, .csv), data files that can be opened with the python library pandas (.h5), matlab scripts (.m), python scripts (.py), and COMSOL models (.mph).</p>
Data from: Electrostatic compatibilization of amorphous and semi-crystalline immiscible polymer blends
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Data from: Plasma refilling of the lunar wake: Plasma-vacuum interactions, electrostatic shocks, and electromagnetic instabilities
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Data from: Intrinsic doping and electrostatic complexation of sulfonated poly(3,4-ethylenedioxythiophenes) (PEDOTs)
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Data from: Electrostatic complexation of conjugated and bottlebrush polyelectrolytes forms printable conductive inks
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Simulation of Ion recirculation during -1 kV operation inside Inertial Electrostatic Confinement Fusion (IECF) device
<p>Ion phase space structure recorded during -1 kV cathode voltage indicating the re-circulation of ions across the cathode grid openings in a cylindrical Inertial Electrostatic Confinement Fusion (IECF) device.</p>
Numerical Electrostatic Simulations Output
<p>A .zip file containing the following:</p> <p>Simulation outputs saved as Matlab .mat files.</p> <p>Matlab .m scripts to make figures from each of the .mat files.</p>
Electrostatic interactions contribute to the control of intramolecular thiol–disulfide isomerization in a protein
<p>The role of structural factors and of electrostatic interactions with the environment on the outcome of thiol–disulfide exchange reactions were investigated in a mutated immunoglobulin domain (I27*) under mechanical stress. An extensive ensemble of molecular dynamics trajectories was generated by means of QM/MM simulations for a total sampling of 5.7 μs. A significant number of thiol–disulfide exchanges were observed, and the Cys32 thiolate preferred to attack Cys55 over Cys24, in agreement with previous experimental and computational studies. The structural features as well as electronic structures of the thiol–disulfide system along the reaction were analyzed, as were the electrostatic interactions with the environment. The previous findings of better accessibility of Cys55 were confirmed. Additionally, the reaction is found to be directed by the electrostatic interactions of the involved sulfur atoms with the molecular environment. The relationships of atomic charges, which stem from the electrostatic interactions, lead to the kinetic preference of the attack on Cys55. Further, QM/MM metadynamics simulations of thiol–disulfide exchange in a small model system with varied artificial external electric potentials revealed changes in reaction kinetics of the same magnitude as in I27*. Therefore, the electrostatic interactions are confirmed to play a role in the regioselectivity of the thiol–disulfide exchange reactions in the protein.</p>
Structural Dynamics Support Electrostatic Interactions in the Active Site of Adenylate Kinase - V142G mutant
<p>Tinker MD trajectories of AdK WT and mutants as described in the paper published in ChemBioChem, e202200097.</p>
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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.