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About

Repository contains code for running simulations published in Hnisz et al., 2017.

Running the code

MATLAB is required to run the program. The main simulation file is submit_cycle_job.m.

Broadly, the mean field simulations model systems of chains, which upon reversible modifications, can form weak cross-linking bonds. (De)modification reactions are catalyzed by (de)modifier enzymes, whose concentrations are parameters of the model.

Key parameters

  • params.Nc : Number of chains
  • params.f : Number of modifiable sites per chain
  • params.kcr_on : Cross-link on-rate
  • params.kcr_off : Cross-link off-rate
  • params.Mod : Concentration of modifiers
  • params.Demod : Concentration of demodifiers
  • params.k_mod : On-rate for modifications
  • params.k_demod : On-rate for modifications
  • params.t_end : Time for simulations

Running modifier/demodifier flips

  • params.change_flag : Binary parameter which toggles whether you want flip or not (0 for no flip, 1 for flip)
  • params.Mod_change : If flag is on, this is the new value of Modifier after t_change
  • params.t_change : Time at which flip in modifier levels happen

Functions/Modules

[t,cluster_max_size,no_of_clusters,Str,Val] = cyclic_clusters(params,Ntraj)

This function is called from submit_job() and it takes in the simulation parameters, and returns the following variables:

  • t: Cell vector of time trajectory for each replicate
  • cluster_max_size: Cell vector of largest cluster for each trajectory
  • no_of_clusters: Cell vector of number of clusters for each trajectory
  • Str: Adjacency matrix of cluster connections from the last trajectory
  • Val: Valency status of cluster connections at last trajectory

Gillespie code for reaction events

[Str,Val,deltaT] = cyclic_reaction_cluster(Str,Val,params)

Takes in:

  • Str: adjacency matrix showing how chains are connected,
  • Val: modification status of every chain
  • params: reaction parameters

and returns:

  • Str: Adjacency matrix updated after a reaction event
  • Val: Updated modification status for all chains after a reaction event
  • deltaT: Time takes before the subsequent reaction event occurs

Visualization

The visualisation file is visualisation_data.m

This takes in the filename of the matlab file where the standard output data is stored and plots the mean cluster size (+-2 sigma) over multiple trajectories.

* if N is the sweeping variable, then the output has to be rescaled by Nc, rather than params.Nc.