Here are the codes to study cell organization based on the implementation of Ising Model.
The Contact Process Ising Model (CPIM) is a stochastic model for surface colony growth and cell-state differentiation based on cell-cell and cell-external field interactions.
This is and hybrid model mixing the Contact Process (CP), which is a general stochastic model of discrete surface spreading, and the Ising Model (IM), which is a statistical mechanics model originally developed to describe the ferromagnetic materials bechaviour.
Contact Process source code:
https://github.com/jekeymer/Contact-Process
Random Number Generator (RNG) source code:
https://github.com/shivakar/rng-reference/blob/master/MT19937/mt64.h
which implement the Mersenne Twister algorithm:
They are written in C++
Currently there are 4 versions which works independently:
Ising_Model_V0.c --> Starting working version
Ising_Model_V1.c --> Current version but JUST INCLUDE COUPLING term (J)
ising_Model_V1_woGTK.c --> V1 without the simulation window. It just store an end point image of the simulation
Ising_Model_V2.c --> Current version which includes the INTERNAL COUPLING term (J) together the EXTERNAL FIELD term (F)
Simpson, K., Keymer, J., & Federici, F. (2023). Spatial biology of Ising-like synthetic genetic networks (p. 2023.05.10.540292). bioRxiv. https://doi.org/10.1101/2023.05.10.540292