Configuration

Configuration file

You need to create a config.txt file in the root dir of the project. This file will contain :

// RENDER -------------------
WINDOW_SIZE=800
// SIMULATION CONSTANTS -----
LENGTH_BOX=200
SAFETY_DISTANCE=50
NUMBER_OF_MCS=5000
NB_OF_SAVINGS=100
KT=50
HAMILTONIAN=1,1,1,1,1
// CELLS VALUES -------------
NB_CELLS=0,300,0
TARGET_SURFACE_CELL=0,50,50
TARGET_LENGTH_CELL=0,20,20
J=0,0,0;10,20,0;0,0,0
LAMBDA_SURFACE=25,25,25
LAMBDA_LENGTH=10,10,10
LAMBDA_CHEMOTAXIS=10,10000,10
// DIFFUSION PROCESS --------
DT = 0.01
DX = 1
D = 1
BOUNDARY_CONDITION = 0
ETA0 = 1e-2
GAMMA0 = 0.5

Definitions of parameters

You can see here the parameters and what they means.

Render

• WINDOW_SIZE : the size of the window for the visualization.

Simulation Constants

• LENGTH_BOX : the length of the box $L$.
• SAFETY_DISTANCE : the safety distance between the spawn of the cells and the border of the box.
• NUMBER_OF_MCS : the number of Monte Carlo steps to run in total in simulation without render.
• NB_OF_SAVINGS : the number of Monte Carlo steps between each saving of the lattice.
• KT : the temperature of the simulation $kT$.
• HAMILTONIAN : the Hamiltonian terms to use in the simulation, respectively : H_interaction, H_surface, H_length, H_chemotaxis, H_connectivity$

Cells Values

• NB_CELLS : the number of cells in the simulation $N$ for each cell type. The first number is the background (ECM) (set to 0).
• TARGET_SURFACE_CELL : the target surface of cells $A$ for each cell type.
• TARGET_LENGTH_CELL : the target length of cells $L$ for each cell type.
• J : the parameters of the Hamiltonian J, which is a matrix representing the interactions between the cells types.
• LAMBDA_SURFACE : the parameters of the Hamiltonian for the surface for each cell type.
• LAMBDA_LENGTH : the parameters of the Hamiltonian for the length for each cell type.
• LAMBDA_CHEMOTAXIS : the parameters of the Hamiltonian for the chemotaxis for each cell type.

Diffusion process

• dt : the time step of the PDE, careful, this needs to be small enough to have a stable solution (Delta_t < Delta_x^2/(2D)).
• dx : the step of the PDE in x direction.
• D : the diffusion coefficient of the PDE.
• BOUNDARY_CONDITION : the boundary value of the PDE.
• ETA_0 : the secretion rate of the chemoattractant molecule.
• GAMMA_0 : the degradation rate of the chemoattractant molecule.