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.