The model as such do not reproduced any of the plots in the paper. However, the steady state 

concentrations of the model has been checked and is consistent with that of the paper. 

The direct solution of dCME in the paper is obtained 

using the author's previous method FBS-dCME based on finite buffer state space enumeration. The software package can be downloaded from https://code.google.com/p/fibose-dcme/downloads/list. Or, the dCME can also be directly solved using the online tool on nanoHub: 

https://nanohub.org/tools/fbsdcme. This needs registration. The nanoHub tool is still under developing, so far only steady state distribution can be obtained.