Molecular Population Dynamics as a Markov Process
Stochastic simulation of transcriptional bursting
We are going to simulate the gene regulation Markov process that we described in class. The process includes 6 reactions.
Implement the Gillespie algorithm to generate 5 time trajectories for (a) gene activity, (b) RNA population, and (c) protein populations.
Plot the trajectories of those stochastic processes, and compare to their steady-state solutions.
Design one set of rate values that would produce transcriptional bursting, and another set of values that would not. Reason your findings.
I have also added hints about how to sample from a exponential distributions easily, and about implementing the Gillespie algorithm.