Fig 2(a) and 2(c) are reproduced and shown here.

To reproduce Fig 2(A), I used COPASI and any file attached would work, but I need to change gamma_S=2 1/day, delta_S=0.2 1/day, as the author described in the paper. Set the duration to 5 days.
To reproduce Fig 2(C), I used COPASI and any file attached would work, there is no need to change any parameters. Set the duration to 50 or 800 to reproduce middle left, or bottom pictures.