Abstract:

This dataset contains results of numerical simulations of the motion of a chemotactic microorganism (modeled as a force dipole) around a rigid, spherical nutrient. In the simulations, a model microorganism is 'released' at a fixed distance from the nutrient source and at an arbitrary orientation, and its trajectory evolves according to the hydrodynamic and chemotactic interactions underpinning its motion. The simulations are run until a steady-state is reached, and the final separation of the microorganism from the nutrient source is the main quantity of interest. The data files contain distributions of this final separation as a function of a number of relevant biophysical parameters that govern this process. A 'read_me.txt' file has been included with the data for details. This dataset supports the publication: Desai, N. & Ardekani, A.M. (2018). Combined influence of hydrodynamics and chemotaxis in the distribution of microorganisms around spherical nutrient sources. Phys. Rev. E, 98. doi: 10.1103/PhysRevE.98.012419

Suggested Citation:

Nikhil Desai, Arezoo Ardekani. 2018. Dataset for: Combined influence of hydrodynamics and chemotaxis in the distribution of microorganisms around spherical nutrient sources. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7GQ6W92

Publications:

Desai, N., & Ardekani, A. M. (2018). Combined influence of hydrodynamics and chemotaxis in the distribution of microorganisms around spherical nutrient sources. Physical Review E, 98(1). doi:10.1103/physreve.98.012419

Purpose:

The study was performed to investigate the combined effects of hydrodynamic interactions and chemotaxis in the distribution of microorganisms around spherical nutrient sources.

Data Parameters and Units:

The data (distribution of separation of bacteria from the center of a nutrient source) is provided in the form of dimensionless numbers. The distance is normalized by the length of the bacterium 'b', which is typically 1-10 microns. The (dimensionless) radius of the nutrient source is 20, and so the separations that range from 20 to 21.5 are actually for the bacteria that get trapped onto the surface of the nutrient source. Separations that are larger than 21.5 correspond to the bacteria that do not get trapped at the end of their simulations. C0_by_KD refers to the quantity C_0/K_D, where C_0 is the concentration (molarity) of the chemoattractant at the nutrient surface. A typical value of K_D is 10^(-4) molar. The dipole strength (alpha_D) is scaled by the quantity F/(8*\pi*\mu_e*b^2*V_s), where 'F' is the bacterium's dimensional dipole strength (SI units of 'F' -> Newton-meter), '\mu_e' is the viscosity of the fluid in which the bacterium is swimming, 'b' is the size of the bacterium, and 'V_s' is its swimming speed. The rotary diffusivity (D_h) is scaled by the quantity b*V_s. Each .dat file contains 10000 numerical entries (of the final separation) corresponding to the parametric regime listed on the first line of the file. There are four major parameters: C0_by_KD (the dimensionless chemoattractant concentration on the surface of the nutrient source), (ii) tau_st (the dimensionless mean run-time of the chemotactic bacterium), (iii) D_h (the dimensionless rotary diffusivity of the bacterium), (iv) alpha_D (the dimensionless dipole strength of the bacterium). The contents of each folder are as follows: effect_C0_by_KD: A typical .dat file is named C0_by_KD=_.dat. Here is the value of the dimensionless surface concentration of the chemoattractant. corresponds to the value of alpha_D, and corresponds to the value of D_h. , refer to the letters 'H' (meaning 'high') and 'L' (meaning 'low'). If is 'H', then alpha_D = 0.8, and if it is 'L', then alpha_D = 1e-3 (alpha_D = 1e-3 corresponds to the case of \alpha_D ~ 0 in the manuscript). Similarly, if is 'H', then D_h = 7.5e-4, and if is 'L', then D_h = 3.75e-10. effect_tau_st: A typical .dat file is named tau_st=_.dat. Here is the value of the dimensionless mean run-time of the chemotactic bacterium. The rest of the entries of the file name follow the same description as in point 1 above. effect_Dh: Folder “D_h=3.75e-10” contains the value of the rotary diffusivity of the bacterium D_h = 3.75e-10. The data in this folder is for the D ~ 0. Folder “D_h=7.5e-4” contains the value of the rotary diffusivity of the bacterium D_h = 7.5e-4. Here, is the value of the dipole strength.

Individual Files: