Simulating the Folding Kinetics

The program treekin is used to simulate the evolution over time of the population densities of local minima starting from an initial population density distribution $p0$ (given on the command-line) and the transition rate matrix in the file rates.out.

  $ treekin -m I --p0 5=1 < barseq.bar | xmgrace -log x -nxy -

The simulation starts with all the population density in the open chain (local minimum 5, see barseq.bar). Over time the population density of this state decays (yellow curve) and other local minima get populated. The simulation ends with the population densities of the thermodynamic equilibrium in which the MFE (black curve) and local minimum 2 (red curve) are the only ones populated. (Look at the dot plot of the sequence created with RNAsubopt and RNAfold!)