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Published April 30, 2024 | Version v1
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Data for article "Non-Stokesian dynamics of magnetic helical nanoswimmers under confinement

Creators

  • 1. ROR icon Western University
  • 2. ROR icon Aalto University

Description

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 helix’s 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 swimmer’s 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

Swimmer’s geometry data file. This lists the xyz coordinates of the constituent atoms of the helix’s surface area.  

bodies-*.lammpstrj

A simulation output file. This lists the xyz coordinates of all helix’s atoms per timestep.

H1cm-*.lammpstrj

A simulation output file. This lists the xyz coordinates and linear velocities of the helix’s 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 helix’s centerline). The tangential velocities of this atom are used to calculate the helix’s 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 helix’s 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.

 

Files

Paper_Support_Files.zip

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