mesoCells repository

By Jack Treado, Yale University

Downloading code

You can download this whole repository to get access to the code.

The code is all located in the src directory. You can only run the code while the src directory is your working directory in MATLAB.

Getting started

The main file that runs the simulation is the function runMesoCellExtension.m. This is a MATLAB function that you can run from the command line in the MATLAB editor screen.

There is another function, vertexFIREPinnedVerts.m, included in the src directory. This is needed during the simulation, so make sure it always stays in the same working directory as runMesoCellExtension.m.

The main function is defined as follows:

function [hList, xList, yList, shapeList, calAList] = runMesoCellExtension(NV,NPINS,calA0Init,Kl,KbInit,cL,cB,cKb,plotIt,movieFileStr)

Inputs:

• NV: integer number of vertices that make up the deformable particle (DP)
• NPINS: integer number of pins to force the DP to change shape during extension
  • NOTE: MUST be at least less than NV
• calA0Init: initial preferred shape parameter, will change if you make cL greater than 0.
  • Note that calA0Init should be greater than or equal to 1 always.
• Kl: mechanical constant for perimeter
• KbInit: mechanical constant for curvature
  • NOTE: KbInit will change if parameter cKb > 0.
• cL: rate constant for growth/decay of the preferred shape parameter calA0 based on the instantaneous shape parameter calA
• cB: rate constant for growth of preferred angles th0 during stretching simulation
• cKb: rate constant for change in bending energy, currently updates based on magnitude of angle
• plotIt: Binary var. to either draw (1) or not draw (0) cells during simulation

Optional Input:

• movieFileStr: If included, save animation to movie file.
  • NOTE: File string must end with the .mp4 extension, currently does not support other formats.

Outputs:

• hList: List of pin stretch steps parametrized by variable .
  • NOTE: h is unitless, defined as the distance travelled outside of the original perimeter divided by the vertex radius.
• xList: x-coordinates of all cell vertices at each stretch step
• yList: y-coordinates of all cell vertices at each stretch step
  • NOTE: Coordinates are stored as MATLAB cell variables. To access at step ii, use syntax x{ii} or y{ii}.
• shapeList: List of relevant shape information during simulation. Column 1 is calA0 (double), column 2 is Kb (array), column 3 is preferred angles th0 (array)
• calAList: Instantaneous shape parameter during stretching simulation.

Running the code

To run the code on the command line, simply use

>> [hList, xList, yList, shapeList, calAList] = runMesoCellExtension(NV,NPINS,calA0Init,Kl,KbInit,cL,cB,cKb,plotIt,movieFileStr);

You can use values instead of variable names for the inputs. If you want to use variables, make sure they are defined in the MATLAB workspace. Remember that you do not need to include movieFileStr.

End of README.md