varuni85/cyanobacterialphototaxis

A set of MATLAB codes that simulate a model for the motion of phototactic cyanobacterial cells

Phototaxis as a Collective Phenomenon in Cyanobacterial Colonies

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