Published September 12, 2022 | Version v1
Software Open

Simulation code for the distribution of gyrotactic microorganisms near a wall

Authors/Creators

  • 1. State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
  • 2. Department of Hydraulic Engineering, Tsinghua University, Beijing 100084, China
  • 3. Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom

Description

This is the simulation code used in the manuscript:

Zeng, L., Jiang, W., Pedley, T.J., 2022. Sharp turns and gyrotaxis modulate surface accumulation of microorganisms. Proceedings of the National Academy of Sciences (PNAS), in press.

The file numerical_simulation.ipynb is the main file, and the called functions are located in the file folder "Functions_needed". The computational results are located in the file folder "Results". The measured velocity, angular velocity, rotational diffusivity and cell concentration for the horizontal and vertical planes are located in the file folders "Horizontal_Ha " and "Vertical_Ha", respectively. The corresponding files are:

  • ang_vel_dimensionless.csv: file for the measured angular velocity (dimensionless)
  • vel_z_dimensionless.csv: file for the measured swimming velocity (dimensionless)
  • Dr_dimensionless.csv: file for the measured rotational diffusivity (dimensionless)
  • con_z_exp.csv: file for the measured concentration distribution

Some descriptions of this code can be found in the associated article. 

Files

Data.zip

Files (512.5 kB)

Name Size Download all
md5:9525af9a13a7c32c13191d476571eeab
512.5 kB Preview Download