Code for carrying out the Gillespie simulations, polymer simulations and pseudo-likelihood maximasation introduced in A. Sood, G. Schuette and B. Zhang, Dynamical phase transition in models that couple chromatin folding with histone modifications, Phys. Rev. E (in review)
The folders polymer_simulation and pseudolikelihood_maximization contain codes to carry out homopolymer simulations and perform pseudo-likelihood maximization to learn
and ising-like hamiltonian to capture the entropic effects of the homopolymer.
The folder ising_gssa contains the codes used to perform the Gillespie stochastic simulations using an ising-like hamiltonian for chromatin contacts.
The folder mft_gssa contains the codes used to perform the Gillespie stochastic simulations using a simplified mean field freen energy functional for chromatin contacts.