# File lac_operon.ode
# model of lac operon in E. coli
# from Santillan et al. (2007) Biophys. J. 92, pp. 3830-3842
# Figure 7.7

#parameters
par delta_M=0.48
par delta_Y=0.03
par delta_L=0.02
par a1=0.29
par K2=2920000
par RToverK1=213.2
par c1=18.8
par kL=60000
par KML=680
par kg=3600
par KMg=700000

#input profile
Le=50*heav(t-500.001)+50*heav(t-1000.001)+50*heav(t-1500.001)-150*heav(t-2000.001)

#dynamics

%dynamics
M'= a1*1/(1+RToverK1*(K2/(K2+L))^4) - delta_M*M
Y'=c1*M - delta_Y*Y
L'=kL*Y*Le/(KML+Le) - 2*kg*(Y/4)*L/(KMg+L) - delta_L*L


# initial condition
init M=0.01, Y=0.1, L=0

# final time
@ total=2500
@ maxstor=100000
@ dt=0.05
@ bound=100000000000
# set the plotting window size:
@ xlo=0, xhi=120, ylo=0, yhi=2.5

# run the simulation in the GUI by selecting (I)nitialconds|(G)o
# plot other species by selecting (G)raphic stuff|(A)dd curve and 
# assigning the y-axis

done