Abstract:

The data being shared contains the results of direct numerical simulations (DNS) of multi-phase fluid flow (buoyant rise of oil drops in water) coupled with the transport of three scalars/species: (i) a dissolved nutrient/chemoeffector, (ii) motile, chemotactic bacteria, and (iii) non-motile bacteria. The nutrient is transported (advection-diffusion) due to the fluid flow and its own diffusivity. The chemotactic bacteria can swim with respect to the fluid and are attracted to the dissolved nutrient and are also transported by the fluid-flow. The non-motile bacteria only act as passive tracers in the flow. Two types of data are being shared: (1) raw result of the DNS for the case of a baseline simulation and (2) time evolution of the dimensionless values of the rates of nutrient consumption by motile and non-motile bacteria, for various bio-physical parameters involved in the study.

Suggested Citation:

Nikhil Desai, Sadegh Dabiri, Arezoo Ardekani. 2018. Dataset for: Nutrient uptake by chemotactic microorganisms in presence of rising oil drops. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N71G0JWT

Publications:

Desai, N., Dabiri, S., & Ardekani, A. M. (2018). Nutrient uptake by chemotactic microorganisms in presence of rising oil drops. International Journal of Multiphase Flow. doi:10.1016/j.ijmultiphaseflow.2018.06.016

Purpose:

The aim of this study was to quantify the differences in the rate of nutrient consumption–under external multi-phase fluid flow–by motile and non-motile bacteria. These differences stem from the chemotactic ability of the former, and its variation with the bio-physical parameters involved. This study is representative of the consumption of dissolved hydrocarbons, e.g. methane, in hydrocarbon plumes in the ocean.

Data Parameters and Units:

We provide 'plot' files for a baseline simulation (for visualization purposes), that can be plotted via TecPlot and contain following information about the fluid flow and species transport: Position (x,y,z): the spatial coordinates of a point in the computational domain at which the values of the following variables are given; (units: cm) Flow-field (u,v,w): the fluid velocity along the x, y and z directions, respectively, generated due to rising motion of oil drops in water; (units: cm/s) Pressure (p): the fluid pressure; (units: dyne/cm^2) Bacterial number density (B,B_nm for motile and non-motile bacteria respectively): the number density of the bacteria; (units: number/cm^3) Chemoattractant concentration (C_m): the molar concentration of the dissolved nutrient/chemoattractant; (units: M) The ‘phase-indicator’ function (color): a function that takes values between 0 and 1, 0 in the oil (dispersed) phase and 1 in the water (matrix) phase; (units: dimensionless number) In addition, we provide .dat files having three columns: (1) t - the time of the simulations; (2) C_M - volume-averaged consumption rate by motile bacteria; and, (3) C_NM - volume-averaged consumption rate by non-motile bacteria. The evaluation of volume-averaged consumption rates is defined in eqn. 8 in the manuscript titled "Nutrient uptake by chemotactic microorganisms in presence of rising oil drops", by Desai, N., Dabiri, S. and Ardekani, A.M. To be published in the International Journal of Multi-phase Flow (2018). doi: 10.1016/j.ijmultiphaseflow.2018.06.016. The difference (C_M - C_NM) is called the 'motility benefit' and the ratio (C_M + C_NM)/(2*C_NM) is called the 'chemotactic amplification'. The evolution of these quantities with time has been plotted in the manuscript, for different values of various bio-physical parameters like bacterial swimming speed (Vs), sensitivity to nutrient gradients (1/beta_C), nutrient uptake rate constant (alpha_C); and diameter (d) and volume fraction (phi) of the oil drops. The data for each of these plots has been shared. A 'read_me.txt' file has been added with the dataset for details about the meaning of various directories, sub-directories and their contents.

Individual Files: