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This is the simulation data set for the manuscript: Arvelo DM, Comer J, Schmit J, Garcia R (2024) Interfacial water is separated from a hydrophobic silica surface by a gap of 1.2 nm. ACS Nano 18:18683–18692. https://doi.org/10.1021/acsnano.4c05689 This data set includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. LAMMPS input files for the ReaxFF simulations are also included. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or LAMMPS data), force field parameter files (in CHARMM format or ReaxFF format), initial atomic coordinates (pdb format), NAMD or LAMMPS configuration files, Colvars configuration files, NAMD or LAMMPS log files, and output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled with a stride of 100 to 20 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included. Version: 1.0. Figure5AC: Simulation of pentadecane on a 5 chains/nm^2 OTS layer. Figure5B_FigureS7: Calculation of force profile for an SiO2 tip asperity model using adaptive biasing force. Systems: octane with 5 chains/nm^2 OTS, octane with 4 chains/nm^2 OTS, decane with 5 chains/nm^2 OTS, water with 5 chains/nm^2 OTS. FigureS6: Simulations showing the effect of octadecane on the structure of the OTS layer for 3 and 5 chains/nm^2 densities. FigureS8: Calculation of the adsorption free energy of tetracosane (C24) at the OTS–water interface using ABF. FigureS9: Python script for estimating the critical concentration to form an alkane layer at the OTS–water interface using the mean-field Ising model. FigureS10: ReaxFF simulation and modeling to create the silanol-terminated amorphous silica model of an AFM tip asperity. FigureS11: Molecular dynamics simulations showing spontaneous assembly of twelve or twenty-four tetracosane (C24) molecules at the interface between water and the alkyl groups of an OTS-conjugated silica surface.
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Monte Carlo (MC) and molecular dynamics (MD) simulation data for PDE identification
Included in this dataset are: 1. Monte Carlo (MC) simulation data used for PDE identification 2. Molecular dynamics (MD) simulation data used for PDE identification 3. LAMMPS input file for PDE validation, Case 1: linear initial C profile 4. LAMMPS input file for PDE validation, Case 2: exponential initial C profile They are used in our manuscript, Learning the Governing PDE of Solid Diffusion from Atomistic Simulations, by Wongelemengist Nadew and Haoran Wang
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- Award ID(s):
- 2138431
- PAR ID:
- 10594355
- Publisher / Repository:
- Researchgate/Digital Commons/Github
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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{"Abstract":["This data set provides files needed to run the simulations described in the manuscript entitled "Organic contaminants and atmospheric nitrogen at the graphene\u2013water interface: A simulation study" using the molecular dynamics software NAMD and LAMMPS. The output of the simulations, as well as scripts used to analyze this output, are also included. The files are organized into directories corresponding to the figures of the main text and supplementary information. They include molecular model structure files (NAMD psf), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD or LAMMPS configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and some trajectories in dcd format (downsampled). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts. A modified LAMMPS C++ source file is also included.<\/p>"],"Other":["This material is based upon work supported by the National Science Foundation under Grant No. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE) and Stampede2 at the Texas Advanced Computing Center through allocation BIO200030, which is supported by National Science Foundation grant number ACI-1548562."]}more » « less
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This archive contains COAWST model input, grids and initial conditions, and output used to produce the results in a submitted manuscript. The files are:</p> model_input.zip: input files for simulations presented in this paper ocean_rip_current.in: ROMS ocean model input file swan_rip_current.in: SWAN wave model input file (example with Hs=1m) coupling_rip_current.in: model coupling file rip_current.h: model header file model_grids_forcing.zip: bathymetry and initial condition files hbeach_grid_isbathy_2m.nc: ROMS bathymetry input file hbeach_grid_isbathy_2m.bot: SWAN bathymetry input file hbeach_grid_isbathy_2m.grd: SWAN grid input file hbeach_init_isbathy_14_18_17.nc: Initial temperature, cool surf zone dT=-1C case hbeach_init_isbathy_14_18_19.nc: Initial temperature, warm surf zone dT=+1C case hbeach_init_isbathy_14_18_16.nc: Initial temperature, cool surf zone dT=-2C case hbeach_init_isbathy_14_18_20.nc: Initial temperature, warm surf zone dT=+2C case hbeach_init_isbathy_14_18_17p5.nc: Initial temperature, cool surf zone dT=-0.5C case hbeach_init_isbathy_14_18_18p5.nc: Initial temperature, warm surf zone dT=+0.5C case</p> model_output files: model output used to produce the figures netcdf files, zipped variables included: x_rho (cross-shore coordinate, m) y_rho (alongshore coordinate, m) z_rho (vertical coordinate, m) ocean_time (time since initialization, s, output every 5 mins) h (bathymetry, m) temp (temperature, Celsius) dye_02 (surfzone-released dye) Hwave (wave height, m) Dissip_break (wave dissipation W/m2) ubar (cross-shore depth-average velocity, m/s, interpolated to rho-points) Case_141817.nc: cool surf zone dT=-1C Hs=1m Case_141819.nc: warm surf zone dT=+1C Hs=1m Case_141816.nc: cool surf zone dT=-2C Hs=1m Case_141820.nc: warm surf zone dT=-2C Hs=1m Case_141817p5.nc: cool surf zone dT=-0.5C Hs=1m Case_141818p5.nc: warm surf zone dT=+0.5C Hs=1m Case_141817_Hp5.nc: cool surf zone dT=-1C Hs=0.5m Case_141819_Hp5.nc: warm surf zone dT=+1C Hs=0.5m Case_141817_Hp75.nc: cool surf zone dT=-1C Hs=0.75m Case_141819_Hp75.nc: warm surf zone dT=+1C Hs=0.75m</p> COAWST is an open source code and can be download at https://coawstmodel-trac.sourcerepo.com/coawstmodel_COAWST/. Descriptions of the input and output files can be found in the manual distributed with the model code and in the glossary at the end of the ocean.in file.</p> Corresponding author: Melissa Moulton, mmoulton@uw.edu</p>more » « less
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Raw data of optical microscopy, scanning electron microscopy (SEM), atomic force microscopy (AFM), and diameter measurements of the exfoliated and self-assembled nanofibrils for our manuscript. File Formats AFM raw data is provided in Gwyddion format, which can be viewed using the Gwyddion AFM viewer, which has been released under the GNU public software licence GPLv3 and can be downloaded free of charge at http://gwyddion.net/ Optical microscopy data is provided in JPEG format SEM raw data is provided in TIFF format Data analysis codes were written in MATLAB (https://www.mathworks.com/products/matlab) and stored as *.m files Data analysis results were stored as MATLAB multidimensional arrays (MATLAB “struct” data format, *.mat files) Data (Folder Structure) The data in the dataverse is best viewed in Tree mode. ReadMe.md This description in Markdown format. Figure 2 - Microscopy Raw Data Figure 2 - panel a.jpg (7.2 MB) Optical micrograph (JPEG format) Figure 2 - panel b.jpg (6.1 MB) Optical micrograph (JPEG format) Figure 2 - panel c f.tif (1.2 MB) SEM raw data (TIFF format) Figure 2 - panel d.tif (1.2 MB) SEM raw data (TIFF format) Figure 2 - panel e - Exfoliated Fibrils.gwy (32.0 MB) AFM raw data (Gwyddion format) Figure 3 - AFM Raw Data Figure 3 - Panel a - Exfoliated fibrils.gwy (81.5 MB) AFM raw data (Gwyddion format) Figure 3 - Panel c - Self-assembled fibrils.gwy (24.0 MB) AFM raw data (Gwyddion format) Figure 3 - Diameter Measurements Figure 3a and Figure 3c show the AFM images of exfoliated and self-assembled nanofibrils, respectively. However, due to the AFM tip-induced broadening of lateral dimensions of small features (such as nanofibrils), the diameters of nanofibrils are generally overestimated in AFM images. Hence, the diameters of the nanofibrils were estimated as the full width at half maximum (FWHM) value of line scans taken over nanofibrils perpendicular to their axial direction. Line profiles were taken at multiple locations using Gwyddion, and the raw data were stored in MATLAB struct files (lineProfileData_Exfoliated.mat and lineProfileData_Self-Assembled.mat). These data files can be directly imported into MATLAB and will appear as “DataExf” and “DataSA” in MATLAB workspace. For instance, “DataExf.x{i}” contains the x-axis data of i-th line profile, and “DataExf.y{i}” contains the y-axis data of i-th line profile. The MATLAB codes MainCode_Exf.m and MainCode_SA.m are used to fit Gaussian curves for each line profile and calculate the FWHM. The *.m files for functions gaussian.m and createFit.m must be in the same folder as the file for the main code. The main code generates figures for each line profile containing raw line profile, related Gaussian fit, and FWHM. These FWHM values are considered as the diameters of the fibrils and stored in variables called “Exf_Dia” and “SA_Dia”. Finally, these values are plotted in a histogram and calculate the statistics such as the mean and the standard deviation. Exfoliated createFit.m (1.1 KB) MATLAB code file (see above) gaussian.m (134 B) MATLAB code file (see above) lineProfileData_Exfoliated.mat (11.7 KB) Line profiles for exfoliated nanofibrils (MATLAB struct format) MainCode_Exf.m (1.8 KB) MATLAB code file (see above) Line profile raw data - Exfoliated Folder with all corresponding cross section raw data in ASCII format Self Assembled createFit.m (1.1 KB) MATLAB code file (see above) gaussian.m (134 B) MATLAB code file (see above) lineProfileData_Self-Assembled.mat (9.9 KB) Line profiles for self-assembled nanofibrils (MATLAB struct format) MainCode_SA.m (1.8 KB) MATLAB code file (see above) Line profile raw data - SelfAssembled Folder with all corresponding cross section raw data in ASCII format Figure 4 - AFM Raw Data Figure 4 - Panal a.gwy (73.4 MB) AFM raw data (Gwyddion format) Figure 4 - Panel e.gwy (42.0 MB) AFM raw data (Gwyddion format)more » « less
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New functionality is added to the LAMMPS molecular simulation package, which increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the “type label” framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools, such as VMD and OVITO. An introductory primer on the forms and use of bonded force fields is provided to motivate this new functionality and serve as an entry point for LAMMPS and OpenKIM users unfamiliar with bonded force fields. The type label framework has the potential to streamline modeling workflows that use LAMMPS by increasing the portability of software, files, and scripts for preprocessing, running, and postprocessing a molecular simulation.more » « less
