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23 results for “Simulation of polymers”
Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging
<p><strong>Dataset description</strong></p> <p>This dataset contains coordinates of the two anchors of a 150 kb simulated loop (static imaging) and anchor-anchor distances of a 150 kb loop in simulations where the extruder was allowed to unbind from the polymer (dynamic imaging).</p> <p><strong>Dataset description - Static imaging</strong></p> <p>This dataset contains coordinates of the two anchors of a 150 kb simulated loop.</p> <p>The subfolder 'Free' contains coordinates from a polymer not submitted to loop extrusion (1,000 independent simulations). The subfolder 'Loop' contains loop anchor coordinates in a polymer submitted to loop extrusion (4,000 independent simulations). In simulations with extrusion, the polymer chain was simulated such as it went through 3 different states : i) Open state (absence of loops) ii) Extruding state where the loop size increases with time (anchor-anchor distance decreases) and iii) Closed state corresponding to a stable loop with the two anchors in contact.</p> <p> </p> <p><strong>Structure of data - Static imaging</strong></p> <p>In each .txt file, the first three columns correspond to the XYZ coordinates of the anchor (in µm), the fourth column indicates the state label (0=Open, 1=Extruding, 2=Closed). Each row corresponds to a simulation timepoint (2991 timepoints in polymers submitted to loop extrusion).</p> <p>The simulation ID is indicated at the end of each .txt file.</p> <p>The two anchors of the loop are bead #275 and bead #324.</p> <p> </p> <p><strong>Structure of data - Dynamic imaging</strong></p> <p>Each .txt file contains the anchor-anchor distance (in µm) as function of time for approximately 10,000 independent simulations. Each column is an independent simulation. Each row is a simulation timepoint (0.3 s / simulation unit). The different .txt files correspond to different localization errors, indicated in µm in XY and Z.</p> <p>'list_deb_closed_10000.p' is a dictionary whose keys are the simulation ID (corresponding to the columns of the .txt files), and the values are the frame at which extrusion begins.</p> <p>'list_end_closed_10000.p' is a dictionary whose keys are the simulation ID (corresponding to the columns of the .txt files), and the values are the frame at which extrusion ends.</p>
Fine-Tuning of Colloidal Polymer Crystals by Molecular Simulation
<p>Data archive corresponding to the manuscript "Fine-Tuning of Colloidal Polymer Crystals by Molecular Simulation" by M. Herranz et al., Phys. Rev. E 107, 064605 (2023); DOI: 10.1103/PhysRevE.107.064605</p> <p>Please see README.txt for instructions on how to access and read the files from the crystallographic analysis based on the CCE norm descriptor.</p> <p>All snapshots have been generated and successively analyzed by the Simu-D software.</p>
Molecular dynamics simulation based analysis of celecoxib-polymer interactions
<p>This dataset contains scripts and coordinate files for running and analysing molecular dynamics simulations to investigate celecoxib-polymer interactions in aqueous solution. Trajectory files (stripped of water and ions) are included.</p> <p>The associated study is described in:</p> <p>" Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance", Sumit Mukesh, Goutam Mukherjee, Ridhima Singh, Nathan Steenbuck, Carolina Demidova, Prachi Joshi, Abhay T. Sangamwar, Rebecca C. Wade, submitted.</p>
FORECASTING MOLECULAR DYNAMICS SIMULATIONS OF POLYMER-LIPIDS IN SOLUTION WITH RNNs
<p>Files and scripts pertaining to our work: </p> <ul> <li>GROMACS files for the topology (DSPE+PEG.top) and the initial structure of the aggregate (DSPE+PEG_EA_NPT.gro)</li> <li>GROMACS topology file for the ethyl acetate molecule: EA_SI.top</li> <li>Scripts to submit the <em>GROMACS</em> utilities for calculation of the interaction energies are described in README.txt (Subset_energy.sh , Interaction_energies.sh)</li> <li>Scripts pertaining to <em>PyTorch</em> use and access of methods are described in README.txt (Multiple-run.sh. Job.sh, Pytorch_train-model.py)</li> <li>Scripts pertaining to <em>scikit learn </em>access for the Expectation Maximization clustering are described in the README.txt (Job_EM.sh, EM_Clustering.py)</li> <li>Files with the time series of the potential energy (PE) and interaction energy (IE) of the DSPE-PEG aggregate with the ethyl acetate solvent. Series contain 500,000 snapshots taken every 10 fs along the NVT Molecular Dynamics trajectory at 300 K and 906.3 kg/m<sup>3</sup> density. The molecular solution is in a cubic box of edge length 13.76 nm, containing 16,000 ethyl acetate molecules and one aggregate of 4 DSPE-PEG-amide macromolecules (224,000 atoms): Data_Andrews_etal_DSPE-PEG_2022.zip</li> <li>ArXiv preprint: https://doi.org/10.48550/arXiv.2203.00151 (JAndrews_etal_arXiv-doi.pdf)</li> </ul>
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>
Collection: Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes Confined Between Electrodes
<p>Metadata record collecting related data sets that contain molecular dynamics simulations of PEO-LiTFSI polymer electrolytes confined between model electrodes.</p> <p>Related data sets:</p> <ul> <li>Uncharged electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13164944">https://doi.org/10.5281/zenodo.13164944</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13165450">https://doi.org/10.5281/zenodo.13165450</a>:<br>Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13165725">https://doi.org/10.5281/zenodo.13165725</a>:<br>Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13166024">https://doi.org/10.5281/zenodo.13166024</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> </ul> </li> <li>Charged electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13166152">https://doi.org/10.5281/zenodo.13166152</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167128">https://doi.org/10.5281/zenodo.13167128</a>:<br>Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167338">https://doi.org/10.5281/zenodo.13167338</a>:<br>Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167551">https://doi.org/10.5281/zenodo.13167551</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167614">https://doi.org/10.5281/zenodo.13167614</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes With Various Surface Charges</li> </ul> </li> <li>Plots: <ul> <li><a href="https://doi.org/10.5281/zenodo.13168242">https://doi.org/10.5281/zenodo.13168242</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths and Salt Concentrations Confined Between Charged Electrodes With Various Surface Charges: Plots</li> </ul> </li> </ul>
Collection: Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes in the Bulk and Confined Between Electrodes
<p>Metadata record collecting related data sets that contain molecular dynamics simulations of PEO-LiTFSI polymer electrolytes in the bulk and confined between model electrodes.</p> <p>Related data sets:</p> <ul> <li>In the Bulk: <ul> <li><a href="https://doi.org/10.5281/zenodo.13144737">https://doi.org/10.5281/zenodo.13144737</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths and Salt Concentrations in the Bulk</li> </ul> </li> <li>Confined Between Electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13169120">https://doi.org/10.5281/zenodo.13169120</a>:<br>Collection: Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes Confined Between Electrodes</li> </ul> </li> </ul>
Input files for the MD simulations and free energy calculations for the article "Water Dissolved in a Variety of Polymers Studied by Molecular Dynamics Simulation and a Theory of Solutions"
<p>Article:<em> </em><a href="https://pubs.acs.org/doi/10.1021/acs.jpcb.1c04818">J. Phys. Chem. B. 125, 9357–9371 (2021) [DOI: 10.1021/acs.jpcb.1c04818]</a></p> <p>The structures of the homopolymers and copolymers simulated are shown in Figures 1 and S1 and Tables 2 and 3. All-atom MD simulation was carried out using GROMACS, and this repository provides the input files with the GAFF/RESP force and initial coordinate files. The free energy of water dissolution was obtained with <a href="https://sourceforge.net/projects/ermod/">ERmod</a>, and the input files for the free-energy calculations are also contained. See the README files for details.</p>
Files for MD simulation of the interaction between LCC-ICCG cutinase and PET polymer
<p>500 ns MD simulation of Cutinase adsorption onto the PET surface and cutinase in water.</p> <p>MD simulations were done using Gromacs package</p> <p>Force field:Charmm36</p>
Data and Code For: Closing the Loop Between Microstructure and Charge Transport in Conjugated Polymers by Combining Microscopy and Simulation.
<p>This repository contains the datasets and scripts used in the article "Closing the Loop Between Microstructure and Charge Transport in Conjugated Polymers by Combining Microscopy and Simulation." </p> <p>Contents:</p> <p>4D-STEM data of the polymer PBTTT, annealed at 180C for 2h, vapor doped with the molecule F4TCNQ</p> <ul> <li>3_80x80_ss=10nm_spot9_alpha=p48_cl=480_RT_300kV_33ms_bin=4.zip ("Scan 3", Main case study)</li> <li>05 CL480 alpha p48 300kV spot11 50ms 80x80 s10.zip</li> </ul> <p>4D-STEM data of the polymer PBTTT, annealed at 180C for 2h, undoped</p> <ul> <li>10 A1 CL480 alpha p48 300kV spot11 50ms 80x80 s10.zip</li> <li>15 A1 CL480 alpha p48 300kV spot11 50ms 80x80 s10.zip</li> </ul> <p>Preprocessed data from "Scan 3." Images are centered, artifacts are removed, and images are binned and converted to radial coordinates.</p> <ul> <li>4D-STEM Preprocessed.zip <ul> <li>sample_preprocessed_data_80x80_ss=10_cl=480__q 1.00 3.00 0.05 a 5.00.npy (medium resolution, wide range, used in paper)</li> <li>sample_data_cube_q_1.0_2.0_0.1_angle_5.npy (low resolution, narrow range)</li> </ul> </li> </ul> <p>Grazing-Incidence Wide-Angle X-ray scattering (GIWAXs) scan of annealed PBTTT, supporting our interpretation of the 4D-STEM data.</p> <ul> <li>3 raw images</li> <li>Calibration files</li> <li>Combined processed image</li> </ul> <p>Spatially resolved diffraction intensity mapped onto a spherical harmonic basis set, for use as an input to structural simulations. One for each of the four 4D-STEM datasets.</p> <ul> <li>spherical_harmonics.zip</li> </ul> <p>Simulated structures of polymer chains based on the processed 4D-STEM data, created using code at https://github.com/SpakowitzLab/wlcsim. Each simulation produced 15 structures using different levels of chain alignment.</p> <ul> <li>chain_geometries.zip <ul> <li>main_dataset_03 (main case study)</li> <li>hi_align_03 (3.3x higher alignment factors than main dataset)</li> <li>undoped_10</li> <li>undoped_15</li> </ul> </li> </ul> <p>Simulations of charge transport through the structures</p> <ul> <li>transport_simulations.zip <ul> <li>ct_16_n100 (explores structural modifications and their effects on mobility)</li> <li>ct_18_n1000 (explores transport in all 4 directions and is used for making GIFs of simulations)</li> <li>ct_20_n1000 (explores the effect of degree of chain alignment)</li> <li>ct_28_n1000 (explores the effect of electric field strength)</li> <li>ct_29_n100 (tracks distances of individual on-chain moves)</li> <li>ct_30_n10000 (uses a high sample size and varied start positions to sample both short-time and long-time mobility)</li> </ul> </li> </ul> <p>Code for 4D-STEM analysis and simulations of charge transport. (Code for structural simulations can be found at https://github.com/SpakowitzLab/wlcsim).</p> <ul> <li>code.zip <ul> <li>preprocess_4dstem.py: package for preprocessing 4D-STEM files</li> <li>flow_fields.py: package for visualizing 4D-STEM data using director maps</li> <li>autocorrelation.py: package for measuring correlation lengths in 4D-STEM data via multiple methods</li> <li>spherical_harmonics.py: package for mapping diffraction intensity onto a spherical harmonic basis set. The results can be used as an input for structural simulations. </li> <li>charge_transfer_assets.py: package for performing charge transfer simulation on simulated chain coordinates</li> </ul> </li> <li>examples.zip <ul> <li>preprocess_demo: sample usage for preprocess_4dstem.py</li> <li>visualization_demo: sample usage for flow_fields.py, autocorrelation.py, and spherical_harmonics.py</li> <li>charge_tranpsort_demo: sample usage for charge_transfer_assets.py</li> <li>paper_figures: shows the code for producing several figures from the paper, using the included simulation datasets. </li> </ul> </li> </ul>
On equilibrating non-periodic molecular dynamics samples for coupled particle-continuum simulations of amorphous polymers: dataset
<p><strong>Abstract:</strong><br> (from [1])<br> In the context of fracture simulations of polymers, the molecular mechanisms in the vicinity of the<br> crack tip are of particular interest. Nevertheless, to keep the computational cost to a minimum, a<br> coarser resolution must be used in the remaining regions of the numerical sample. For the specific<br> case of amorphous polymers, the Capriccio method bridges the gap between the length and time scales<br> involved at the different levels of resolution by concurrently coupling molecular dynamics (MD) with<br> the finite element method (FEM). Within the scope of the Capriccio approach, the coupling to the<br> molecular MD region introduces non-periodic, so-called stochastic boundary conditions (SBC). In<br> similarity to typical simulations under periodic boundary conditions (PBC), the SBC MD simulations<br> must reach an equilibrium state before mechanical loads are exerted on the coupled systems. In this<br> contribution, we hence extensively study the equilibration properties of non-periodic MD samples<br> using the Capriccio method. We demonstrate that the relaxation behavior of an MD-FE coupled<br> MD domain utilizing non-periodic boundary conditions is rather insensitive to the specific coupling<br> parameters of the method chosen to implement the boundary conditions. The behavior of an exemplary<br> system equilibrated with the parameter set considered as optimal is further studied under uniaxial<br> tension and we observe some peculiarities in view of creep and relaxation phenomena. This raises<br> important questions to be addressed in the further development of the Capriccio method.<br> <br> <strong>Contact:</strong><br> Felix Weber<br> Institute of Applied Mechanics<br> Friedrich-Alexander-Universität Erlangen-Nürnberg<br> Egerlandstr. 5<br> 91058 Erlangen<br> Germany<br> <br> <strong>Context:</strong><br> This dataset contains the results presented in [1] and related data.</p> <p><strong>Content:</strong><br> Throughout this data set, Lammps [2] real units are used. The following folders contain the results obtained under periodic boundary conditions:<br> - biax_PBC: biaxial loading <br> - equil_PBC: equilibration<br> - ut_PBC: uniaxial tension<br> Each simulation directory contains:<br> - input.prm: input parameters of the specific simulation (read by the input file)<br> - job.out: simulation log file<br> - meta.info: meta data of the specific simulation run<br> - Lammps input file (*.in) of the specific simulation<br> - Lammps data file (*.data, molecular style) of the investigated sample<br> - LAMMPS_out: resulting Lammps data and restart (*.rst) files and simulation results (Lammps thermo_out) in <br> tabulated form, an overview of the columns is given in the respective folders</p> <p>The following folders contain the results obtained under stochastic boundary conditions using the Capriccio method [3]:<br> - best: equilibration with the parameter set considered to be most suitable for the MD-FE coupled equilibration<br> - biax: biaxial loading<br> - bridging: equilibration with different adaptivity levels of the bridging domain<br> - descr_obs: equilibration with a Lagrangian frame for the description of the observation region<br> - dpd: equilibration with different thicknesses of the dissipative particle dynamics (DPD) region<br> - friccoeff: equilibration with different friction coefficients applied in the dissipative particle dynamics region<br> - fur: equilibration with different numbers of fur beads <br> - gausspoints: equilibration with different numbers of quadrature points per direction <br> - min: equilibration applying an initial, static energy minimization<br> - nodes: equilibration with a higher number of finite element nodes<br> - shifted: equilibration with particle systems obtained at different positions and points in time within the periodic master system<br> - smdcub: equilibration with different remaining stiffness ratios for the cubic modified weighting factor<br> - smdlin: equilibration with different remaining stiffness ratios for the linear modified weighting factor<br> - timestepsize: equilibration with different molecular dynamics time step sizes<br> - ut: uniaxial tension<br> - ut_friccoeff: uniaxial tension with different friction coefficients applied in the dissipative particle dynamics region<br> - weighting: equilibration with different energy weighting functions<br> - youngsmod: equilibration with different Young's moduli<br> Each simulation directory contains:<br> - input_files: Abaqus [4] input file (*.inp) and Lammps data file (*.data, molecular style) of the investigated sample<br> - MD_data: Results evaluated in the molecular dynamics region. MD_data contains the following subfolders: <br> anchorforces (dumped force components on the anchor points (AP) in kcal/mol, files anchorforce_[load step]_[MD-FE iteration].AF), <br> data (resulting Lammps data files *.[load step].[MD-FE iteration].data), Density (dumped mass density in the observation region in kg/m^3), <br> Energy (dumped total (kinetic + potential), angle, bond, and pair energies in kcal/(mol*Angstrom)), Strain (integral strains in the<br> observation region in x-, y-, and z-direction calculated by means of the Matlab [5] script calc_OBSstrain.m),<br> Stress (stresses in the observation region in MPa), and Temperature (temperature in the observation region in K)<br> - job.out: simulation log file<br> - meta.info: meta data of the specific Lammps simulation<br> Information on the subfolders is given in the respective folders.</p> <p><strong>References:</strong><br> [1] F. Weber, M. Ries, C. Bauer, C. R. Wick, S. Pfaller, "On equilibrating non-periodic molecular dynamics samples for coupled<br> particle-continuum simulations of amorphous polymers", Forces in Mechanics, 2023, 10, 100159.<br> [2] A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in 't Veld, A. Kohlmeyer, <br> S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott, S. J. Plimpton, "LAMMPS - a flexible simulation tool <br> for particle-based materials modeling at the atomic, meso, and continuum scales", Computer Physics Communications, 2022, 271, 108171.<br> [3] S. Pfaller, M. Rahimi, G. Possart, P. Steinmann, F. Müller-Plathe, M. C. Böhm, "An Arlequin-based method to couple molecular dynamics <br> and finite element simulations of amorphous polymers and nanocomposites", Computer Methods in Applied Mechanics and Engineering, <br> 2013, 260, 109-129. <br> [4] Dassault Systèmes, "Abaqus documentation", URL: https://abaqus-docs.mit.edu/2017/English/SIMACAEEXCRefMap/simaexc-c-docproc.htm.<br> [5] The MathWorks, Inc, "MATLAB. The Language of Technical Computing", URL: https://de.mathworks.com/help/matlab/.</p> <p><strong>Funding:</strong><br> This research was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) -<br> 377472739/GRK 2423/1-2019. The authors are very grateful for this support. Sebastian Pfaller is furthermore<br> funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 396414850 (Individual<br> Research Grant ’Identifikation von Interphaseneigenschaften in Nanokompositen’).</p>
Data from: Slip-spring simulations of different constraint release environments for linear polymer chains
The constraint release(CR) mechanism has important effects on polymer relaxation and the chains will show different relaxation behavior in conditions of monodisperse, bidisperse and other topological environments. By comparing relaxation data of linear PI chains dissolved in very long matrix and monodisperse melts, Matsumiya et al. showed that CR mechanism accelerates both dielectric and viscoelastic relaxation[Matsumiya et al., 2013,46, 6067]. In this work, the experimental data reported by Matsumiya et al. are reproduced using the single slip-spring model(SSp) and the CR accelerating effects are validated by simulations. A variant of SSp with each entanglement assigning a characteristic lifetime is also proposed to simulate various CR environment flexibly. Using this lifetime version SSp model, the correct relaxation function can be obtained with equal numbers of entanglements destructions by CR and reptation/Contour length fluctuation(CLF) for monodisperse melts. Good agreement with published experiment data is also obtained for bidisperse melts, which validates the ability to correctly describe the CR environment of the lifetime version model.
Investigating fracture mechanisms in glassy polymers using coupled particle-continuum simulations
<p>This repository contains public data for the publication "Investigating fracture mechanisms in glassy polymers using coupled atomistic-continuum simulations" [1].</p> <p>These scripts, force fields, topologies and other files may be used to reproduce the simulations and calculations that led to the above publication.</p> <p>The folder "md simulations" contains data files for pure MD simulations that were used as a reference for understanding molecular fracture mechanisms in our model.</p> <p>The folder "coupled simulations" contains data files for coupled MD-FE simulations which are the highlight of our publication.</p> <p> </p> <p>Reference:</p> <p>[1] W. Zhao, Y. Jain, F. Müller-Plathe, P. Steinmann, S. Pfaller, "Investigating fracture mechanisms in glassy polymers using coupled particle-continuum simulations", Journal of the Mechanics and Physics of Solids, 2024, 105884. DOI: <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.jmps.2024.105884" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.jmps.2024.105884</span></span></a></p>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths and Salt Concentrations in the Bulk
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of polymer chain length and salt concentration on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the bulk.</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> <li>Various plots of the data</li> </ul> <p>The zip archives contain:</p> <ul> <li><code>coiling.zip</code>: MD simulations of single PEO chains in vacuum that were performed to produce coiled PEO chains, which were used to generate the starting structures for the bulk simulations.</li> <li><code>bulk.zip</code>: MD simulations of PEO-LiTFSI polymer electrolytes in the bulk.</li> <li><code>plots.zip</code>: Plots of various structural and dynamic quantities as function of the PEO chain length and the salt concentration.</li> </ul>
Data set for graphene/GO polymer molecular dynamics simulation
<p>Lammps input files and log files for molecular dynamics simulations of graphene and graphene-oxide nano ribbons for paper "Molecular dynamics reveals the origin of the enhancement of polymer properties by graphene". Log files include stress-strain behaviour during uniaxial strain. </p> <p> </p>
Data from: Slip-spring simulations of different constraint release environments for linear polymer chains
Open the record for dataset details and reuse information.
Simulation data for "Tuning Adhesion and Energy Dissipation in Polymer Films between Solid Surfaces via Grafting and Cross-Linking"
<p>LAMMPS input and data files, Jupyter notebooks used for the analysis of the MD simulations.</p>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of salt concentration on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the vicinity of uncharged, graphite-like model electrodes.</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Uncharged Electrodes
<p>Data set containing molecular dynamics (MD) simulations performed with <a href="https://www.gromacs.org/">Gromacs</a> to investigate the effect of polymer chain length on the atomistic structure and dynamics of PEO-LiTFSI polymer electrolytes in the vicinity of uncharged, graphite-like model electrodes.</p> <p>PEO = Methoxy-terminated poly(ethylene oxide), sometimes also abbreviated as PEGDME for polyethylene glycol dimethyl ether<br>LiTFSI = Lithium bis(trifluoromethanesulfonyl)imide, sometimes also abbreviated as Li[NTf2].</p> <p>The data set contains:</p> <ul> <li>Gromacs input and output files (except trajectories due to their huge filesize)</li> <li>Processed data</li> </ul>
Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths and Salt Concentrations Confined Between Charged Electrodes With Various Surface Charges: Plots
<p>Plots of the data contained in the data sets</p> <ul> <li>Uncharged electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13164944">https://doi.org/10.5281/zenodo.13164944</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13165450">https://doi.org/10.5281/zenodo.13165450</a>:<br>Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13165725">https://doi.org/10.5281/zenodo.13165725</a>:<br>Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13166024">https://doi.org/10.5281/zenodo.13166024</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> </ul> </li> <li>Charged electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13166152">https://doi.org/10.5281/zenodo.13166152</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167128">https://doi.org/10.5281/zenodo.13167128</a>:<br>Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167338">https://doi.org/10.5281/zenodo.13167338</a>:<br>Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167551">https://doi.org/10.5281/zenodo.13167551</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167614">https://doi.org/10.5281/zenodo.13167614</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes With Various Surface Charges</li> </ul> </li> </ul>
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