Few examples

Few examples

Sorting cells

The goal here is to simulate a sorting of cell. The interaction matrix $J$ has lower values on the diagonal and higher values on the off-diagonal. This means that cells tends to be together if they are the same type and tend to be separated if they are different.

Render

Configuration file

// RENDER -------------------
WINDOW_SIZE=800
// SIMULATION CONSTANTS -----
LENGTH_BOX=200
SAFETY_DISTANCE=50
NUMBER_OF_MCS=500
NB_OF_SAVINGS=500
KT=50
HAMILTONIAN=1,1,0,0,0
// CELLS VALUES -------------
NB_CELLS=0,2000,2000
TARGET_SURFACE_CELL=0,16,16
TARGET_LENGTH_CELL=0,40,20
J=0,0,0;50,5,20;50,20,5
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

Networking cells

The goal here is to simulate a network of cells. The chemotaxis, length, and connectivity are activated. The cells balance between the chemotaxis that attracts them to one another, and the interaction that tends to separate them at low distances. This results in a beautiful network of cells.

Render

Configuration file

// 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

Chemotaxis