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7 results for “electrostatic force”
Quantitative electrostatic force tomography for virus capsids in interaction with an approaching nanoscale probe
<p>This repository contains the simulated data of a simple electrostatic model, based on the Poisson-Boltzmann equation, that quantifies the subnanometric electrostatic interactions between an AFM tip and a proteinaceous capsid (Zika Virus) from molecular snapshots. This allows us to describe the contributions of specific amino acids and atoms to the interaction force.</p> <p>The contains of this repository can be easily visualized through Jupyter Notebooks contained here:</p> <p>https://github.com/pyF4all/eTipVirusForce</p>
Underlying data for "The role of electrostatics in enzymes: do biomolecular force fields reflect protein electric fields?"
<p>This dataset contains code, data, trajectories, and figures used in the article "The role of electrostatics in enzymes: do biomolecular force fields reflect protein electric fields?".</p> <p> </p> <p>Contents:</p> <p>code/* - Code used to calculate electric fields from simulation trajectories with either polarizable or additive force fields</p> <p>data/* - Electric fields calculated for the CypA WT cis, WT trans, R55A cis, and R55A trans systems, with AMOEBA, Amber, or Charmm force fields. Each subfolder also includes a set of structural coordinates extracted at 2.5 ns intervals from the first simulation trajectory and used to calculate ONETEP DFT electric fields.</p> <p>figures/* - Underlying data and scripts used to create all figures and movies used in the article.</p> <p>trajectories/* - Simulation trajectories of the CypA WT cis, WT trans, R55A cis, and R55A trans systems</p> <p> </p> <p>Where appropriate, README files include instructions for regenerating data used in the article, and details of the Python packages and other software used to generate data are available in Dependencies.txt</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>
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>
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>
Experimental Estimation of Gap Thickness and Electrostatic Forces Between Contacting Surfaces Under Electroadhesion
<p>Electroadhesion (EA) is a promising technology with potential applications in robotics, automation, space missions, textiles, tactile displays, and some other fields where efficient and versatile adhesion is required. However, a comprehensive understanding of the physics behind it is lacking due to the limited development of theoretical models and insufficient experimental data to validate them. This article proposes a new and systematic approach based on electrical impedance measurements to infer the electrostatic forces between two dielectric materials under EA. The proposed approach is applied to tactile displays, where skin and voltage-induced touchscreen impedances are measured and subtracted from the total impedance to obtain the remaining impedance to estimate the electrostatic forces between the finger and the touchscreen. This approach also marks the first instance of experimental estimation of the average air gap thickness between a human finger and a voltage-induced capacitive touchscreen. Moreover, the effect of electrode polarization impedance on EA is investigated. Precise measurements of electrical impedances confirm that electrode polarization impedance exists in parallel with the impedance of the air gap, particularly at low frequencies, giving rise to the commonly observed charge leakage phenomenon in EA.</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.