#friedland1



#reactions
r0:
 {1.0}ara = $pool
  cell * piecewise(cAra, and(eq(pulse_flag, 1), gt(ara, 0)), dAra * ara)
r10a:
 $pool = {1.0}mT3cr
  cell * (s0_mT3cr + k_pT7 * pow(pT7, n7) / (pow(km7, n7) + pow(pT7, n7)))
r10b:
 {1.0}mT3cr = $pool
  cell * d_mT3 * mT3cr
r11:
 $pool = {1.0}pT3
  cell * (s0_pT3 * mT3cr + s_pT3k * taRNA * mT3cr)
r12:
 {1.0}pT3 = $pool
  cell * d_pT3 * pT3
r1a:
 $pool = {1.0}taRNA
  cell * (sT * ara / (ara + k_ara) + s0_taRNA)
r1b:
 {1.0}taRNA = $pool
  cell * d_taRNA * taRNA
r2a:
 $pool = {1.0}mT7cr
  cell * s0_mT7cr
r2b:
 {1.0}mT7cr = $pool
  cell * d_mT7 * mT7cr
r3a:
 $pool = {1.0}mGFPcr
  cell * (s0_mGFPcr + k_pT3 * pow(pT3, n3) / (pow(km3, n3) + pow(pT3, n3)))
r3b:
 {1.0}mGFPcr = $pool
  cell * d_mGFP * mGFPcr
r6:
 $pool = {1.0}pT7
  cell * (s0_pT7 * mT7cr + s_pT7k * mT7cr * taRNA)
r7:
 $pool = {1.0}pGFP
  cell * (s0_pGFP * mGFPcr + s_pGFPk * mGFPcr * taRNA)
r8:
 {1.0}pT7 = $pool
  cell * d_pT7 * pT7
r9:
 {1.0}pGFP = $pool
  cell * d_pGFP * pGFP


#parameters
cAra = 0.0003
dAra = 0.1201
d_mGFP = 0.07
d_mT3 = 0.0701
d_mT7 = 0.0706
d_pGFP = 0.003
d_pT3 = 0.0069
d_pT7 = 0.0056
d_taRNA = 0.1177
k_ara = 0.0571
k_pT3 = 3.006
k_pT7 = 3.8009
km3 = 7.9075
km7 = 3.0455
n3 = 0.8892
n7 = 2.602
pulse1_length = 11.0
pulse1_start = 0.01
pulse2_length = 11.0
pulse3_length = 22.0
pulse_conc = 0.01
pulse_flag = 0.0
pulse_interval = 20.0
s0_mGFPcr = 0.0123
s0_mT3cr = 0.0003
s0_mT7cr = 0.0252
s0_pGFP = 0.1007
s0_pT3 = 0.0
s0_pT7 = 0.0003
s0_taRNA = 0.0008
sT = 0.8467
s_pGFPk = 0.9923
s_pT3k = 0.0115
s_pT7k = 0.0766
cell = 1.0


#initial values
ara = 0.0
mGFPcr = 0.176991329
mT3cr = 0.00566438
mT7cr = 0.3569405099
pGFP = 6.338921181
pT3 = 6.41674e-05
pT7 = 0.05230744612
taRNA = 0.006796941377


#assignment rules
!F pulse3_start = pulse2_start + pulse2_length + pulse_interval
!F pulse2_start = pulse1_start + pulse1_length + pulse_interval