Data for article "Non-Stokesian dynamics of magnetic helical nanoswimmers under confinement
DOI10.5281/zenodo.11091027Zenodo11091027MaRDI QIDQ6697856FDOQ6697856
Dataset published at Zenodo repository.
Mikko Karttunen, Alireza Fazeli, Tapio Ala-Nissila, Vaibhav Thakore
Publication date: 30 April 2024
Copyright license: Creative Commons Attribution 4.0 International
Data for article "Non-Stokesian dynamics of magnetic helical nanoswimmers under confinement", A. Fazeli, V. Thakore, T. Ala-Nissila, M. Karttunen ●Published version: https://doi.org/10.1093/pnasnexus/pgae182 ●Preprint version: https://doi.org/10.48550/arXiv.2311.00839 The article studied the effect of the degree of confinement on the propulsion of electromagnetically propelled helical nanoswimmers. The helices were subjected to different degrees of confinement between two infinite parallel plates and driven using a rotating magnetic field at different frequencies. The degree of confinement (Gamma) is defined as the ratio of a helixs outer diameter over the distance between the two boundary plates. At the highest level in the directory hierarchy, there are two folders, i.e., Simulation_Production_Files, and Simulations_by_Nanoswimmers. The first one consists of the source code of the Lattice-Boltzmann Method package implemented in LAMMPS used for running the simulations. It also includes a Matlab script used for calculating the required simulation variables to put in the LAMMPS input script for a given simulation. The other folder, i.e., Simulations_by_Nanoswimmers, has subfolders first broken down by the swimmers name (i.e., H0-8), then by Gamma, and finally by field driving frequency. Each simulation folder, i.e., at Simulations_by_Nanoswimmers/H0*/Gamma_0.*/Field_Frequency_*/, consists of seven types of file as described in the table below. File Description script.in LAMMPS input script. LAMMPS executes calculations by reading commands from this file. H*.data Swimmers geometry data file. This lists the xyz coordinates of the constituent atoms of the helixs surface area. bodies-*.lammpstrj A simulation output file. This lists the xyz coordinates of all helixs atoms per timestep. H1cm-*.lammpstrj A simulation output file. This lists the xyz coordinates and linear velocities of the helixs center of mass per timestep. H1omega-*.lammpstrj A simulation output file. This lists the xyz coordinates and linear velocities of an outer atom (i.e., an atom with a distance of minor radius plus major radius from the helixs centerline). The tangential velocities of this atom are used to calculate the helixs angular velocity. H1plane-*.lammpstrj A simulation output file. This lists the xyz coordinates of the three atoms used to construct a hypothetical plane fixed with respect to the helix body. This plane is used to keep track of orientation when calculating the helixs angular velocity. torques-*.txt A simulation output file. These list the viscous drag torque experienced by the helix around the x-, y-, and z- axes. The asterisks refer to the Shell (bash) wildcard character.
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