Dynamic fluid layer around immotile yeast colonies mediates the spread of bacteria

Brief intro: The dataset and model were created to study the coexistence of yeast and bacteria on a plate-based assay. The files include CSV tables, MATLAB dataset along with MATLAB script, and MATLAB script of the model. These were submitted along with the paper titled "Dynamic fluid layer around immotile yeast colonies mediates the spread of bacteria", written by Divakar Badal(1), Aloke Kumar(2), Varsha Singh(1,3), and Danny Raj M(4);(1) Department of Bioengineering, Indian Institute of Science, Bengaluru, India; (current) Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, NY, USA (2)Department of Mechanical Engineering, Indian Institute of Science, Bengaluru, India; (3)Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India; (current) School of Life Sciences, University of Dundee, UK (4)Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India; (current) Department of Applied mechanics and biomedical engineering, Indian Institute of Technology Madras, Chennai, India.

Model Fig 4 zip file includes the model custom written on MATLAB 2022b. It includes following files:
1) parMacrosimulation.m (main file)
2) macro_function.m (MATLAB function)
3) imageOut.m (MATLAB function)

We created a grid of 100 x 100, representing 10 x 10 cm area. We randomly seeded yeast agents (area of each agent = 6.3617e-07 cm2) on the grid and placed bacteria agents (area of each agent = 5.8905e-09 cm2) on the central pixel. We inoculated yeast agents 9.4 times more than the number of bacteria agents. The carrying capacity of a pixel on the grid is a 0.01 cm^2 area. Therefore, each pixel can hold certain number of yeast and/or bacteria agents. We allowed the agents to grow at the certain growth rate and consume nutrient. Thus, in a pixel, number of agents can easily cross carrying capacity which lead to overflow in immediate neighbour such that the nutrient rich neighbour will have higher probability of getting these cells.

Parameters:
Yeast division time = 4500 sec
Bacteria division time = 2100 sec
Fluid effect constant = 0.9e-5
dt = 1/3600 hours
Fluid pumping rate = 0.3e-9 cm3/sec/cell
Diffusivity of nutrient = 1.24e-5 cm2/sec
Diffusivity of fluid = 2.3e-5 cm2/sec
Bacteria nutrient consumption rate = 1.94e-12 m/cell/sec
Yeast nutrient consumption rate = 4.4e-12 m/cell/sec
area of bacteria agent = 5.8905e-09 cm^2
area of yeast agent = 6.3617e-07 cm^2
Simulation time = 6 hours

Input parameters:
Number of realizations (1-1000)
Fluid Pumping Rate Factor (0.5-1.5)
Agent count Multiplier (0.5-1.5)
Growth rate Multiplier (0.5-1.5)
imFlag (1 or 0)

Exporting each frame
if ‘imFlag’ is 1, then script will create folder named 'Frames' at current directory. Inside 'Frames' folder, there will be three folders namely 'FluidLayer', 'CoExit', and 'YeastLayer'. Further, inside each of these folders there will be three folders representing without yeast, with yeast with fluid pool, and with yeast and without fluid pool named as '0', '1', and '2' folder names respectively.