A set of MATLAB codes that simulate a model for the motion of phototactic cyanobacterial cells, described in the manuscript:
Varuni P, Menon SN and Menon GI (2017) Phototaxis as a Collective Phenomenon in Cyanobacterial Colonies. Sci Rep 7: 17799. https://doi.org/10.1038/s41598-017-18160-w
This model uses an active matter framework to describe the forces experienced by individual cyanobacterial cells upon being subjected to a light source. It captures experimentally observed changes in colony morphology, namely dense finger-like projections that extend outwards from the colony towards the direction of the light source.
The repository contains the following files:
-
cyano_main.m: main file (start here) -
set_parameters.m: sets parameters -
setup_colony.m: initializes a cyanobacterial colony, specifying the cell positions and slime content -
cyano_motion.m: simulates the motion of cyanobacterial cells -
determine_force.m: determines the force on each cell at each time point -
covered_area.m: finds the grid indices lying under a circle of specified radius -
pack_balls_circle.m: pack balls of a given radius within a circular region
The following table provides a description of the parameters specified in set_parameters.m, and supplied to the function cyano_motion.m:
| Variable | Description |
|---|---|
| N | the number of cells in the colony |
| RHO | the initial colony density |
| DTUG | max. tugging distance between cell edges |
| NTUG | the avg. no of cells that a cell can tug on |
| P_PHOT | the probility that cells move in direction of light |
| SPD0 | the initial speed of each cell (# body length/sec) |
| S0 | the initial slime content |
| RS | the rate at which slime is deposited |
| AMP | amplitude of force function |
| W | steepness of force function |
| CH_FRC | fraction of cheaters |
| LC | length of domain along columns |
| LR | length of domain along rows |
| CTYPE | colony type |
| NT | the total number of time steps |
| TRL | the trial number |