Abstract:
This dataset contains results of numerical simulations of the motion of chemotactic bacteria (modeled as a force dipole) around a rigid, spherical nutrient source. The source is moving under the influence of gravity, and hydrodynamic interactions with the microorganism. The data has been obtained as a result of numerical simulations of bacteria motion near a sinking, spherical nutrient source of radius 'a'. In the simulation, a given number (1000 or 5000) of non-interacting bacteria are initially 'placed' uniformly within a disk of radius '2a' at a vertical separation '5a' below the source (e.g., a marine snow particle). The bacteria are assigned random initial orientations. The simulations run until either the bacteria are at separations greater than '50a' away from the center of the source, or a maximum simulation time is reached. The bacterial trajectories evolve according to the hydrodynamic and chemotactic interactions underpinning their motion. The data contains the time-averaged nutrient concentrations experienced by the bacteria in the simulations. This nutrient-exposure, in general, depend on a number of biophysical parameters, e.g., the size and speed of the nutrient source, the diffusivity of the nutrient emanating from the source, and the morphology of the bacteria involved. The dependency on each of these parameters is reflected in this dataset. This dataset supports the publication: Desai, N., Shaik, V. A., & Ardekani, A. M. (2019). Hydrodynamic Interaction Enhances Colonization of Sinking Nutrient Sources by Motile Microorganisms. Frontiers in Microbiology, 10. doi:10.3389/fmicb.2019.00289
Suggested Citation:
Nikhil Desai, Vaseem A. Shaik, Dr. Arezoo M. Ardekani. 2019. Dataset for: Hydrodynamic interaction enhances colonization of sinking nutrient sources by motile microorganisms. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-1wdy-1e57
Purpose:
The study was performed, and the corresponding data generated, to investigate whether and/or how hydrodynamic interactions affect the average nutrient exposure of microorganisms in marine environments.
Data Parameters and Units:
The data files for 'Sc=z_noChemo_dip=2.mat' (z = [500, 2500, [5000:25000:5000] ]) can be found in the folder for figure 6b. The data/figure for non-chemotactic bacteria with dipole=2 is the same in figure 9a and 6b. Similarly, the data corresponding to 'R=z_noChemo_dip=2.mat' (z = [20:65:5]) can be found in the folder for figure 8. Readme files are included within all the directories of the dataset to better explain the data.
All lengths in the datasets are made dimensionless by the size of the bacterium, 'b'. All speeds in the datasets are made dimensionless by the swimming speed of the bacterium, 'V_s'. All times in the datasets are made dimensionless by the bacterium size divided by its swimming speed, i.e., 'b/V_s'.
The data parameters, their units and the dimensional scales used to normalize the data are as follows:
1. The values of the time-averaged nutrient concentration 'C_t_avg' are normalized by a reference concentration 'C_0', which is the concentration of the nutrient at the surface of the sinking nutrient source. Typical units of 'C_0' are expressed in 'moles/liter'.
2. The dimensionless dipole strength '\alpha_D' (called 'dipole' in the datasets) is normalized as \alpha_D = F_D/(8*\pi*\mu*b^2*V_s), where 'F_D' is the dimensional dipole strength, '\mu' is the density of the suspending fluid, 'b' is the size of a bacterium, 'V_s' is the swimming speed of the bacterium. The units of the dimensional dipole strength are 'Newton-meter'.
3. The dimensionless rotary diffusivity of the bacterium, 'D_r' (called 'Dr' in the datasets) is normalized as D_r = D/(V_s/b), where 'D' is the dimensional rotary diffusivity, 'b' is the size of a bacterium, 'V_s' is the swimming speed of the bacterium. The units of the dimensional rotary diffusivity are '1/second'.
4. The dimensionless time step of the simulations, 'dt' (called 'dt' in the datasets) is normalized as dt = \delta_T/(b/V_s), where '\delta_T' is the dimensional time step, 'b' is the size of a bacterium, 'V_s' is the swimming speed of the bacterium. The units of the dimensional time step are 'seconds'.
5. The dimensionless final time until which the simulations were run, 'T_end' (called 'end_time' in the datasets) is normalized as T_end = t_end/(b/V_s), where 't_end' ('small t' as opposed to 'large T' for the dimensionless 'end_time') is the dimensional final time until which simulations are run, 'b' is the size of a bacterium, 'V_s' is the swimming speed of the bacterium. The units of the final time until which the simulations were run are 'seconds'.
6. The dimensionless excess density of the settling nutrient source, 'K_del_rho' (called 'K_del_rho' in the datasets) is normalized as K_del_rho = (2*delta_rho*g*b^2)/(9*\mu*V_s), where 'delta_rho' is the dimensional excess density, 'g' is the acceleration due to gravity, 'b' is the size of a bacterium, '\mu' is the density of the suspending fluid, 'V_s' is the swimming speed of the bacterium. The units of the dimensional excess density are 'g/cm^3'.
7. The dimensionless radius of the settling nutrient source, 'R' (called 'R' in the datasets) is normalized as R = a/b, where 'a' is the dimensional radius of the spherical nutrient source, 'b' is the size of a bacterium. Similarly, the dimensionless coordinates of bacterial trajectories are also normalized by 'b'. The units of the dimensional radius and bacteria coordinates are 'cm'.
8. The dimensional mean run-time of bacteria, '\tau_0' is given in seconds.
9. The dimensionless trapping times for bacteria, 'T_h' (called 'Th' in the datasets) are normalized as T_h = t_h/(b/V_s), where 't_h' ('small t' as opposed to 'large T' for the dimensionless 'Th' values) is the dimensional trapping time, 'b' is the size of a bacterium, 'V_s' is the swimming speed of the bacterium. The units of the dimensional trapping time are 'seconds'.
View Metadata