#leloup6



#reactions
CN_decay:
 {1.0}CN = $pool
  kd_CN * CN * nucleus
C_decay:
 {1.0}C = $pool
  kd_C * C * cytoplasm
C_form:
 {1.0}P2 + {1.0}T2 = {1.0}C
  (k3 * T2 * P2 - k4 * C) * cytoplasm
C_transp:
 {1.0}C = {1.0}CN
  k1 * C * cytoplasm - k2 * CN * nucleus
M_P_decay:
 {1.0}M_P = $pool
  (v_mP / (K_mP + M_P) + kd) * M_P * cytoplasm
M_T_decay:
 {1.0}M_T = $pool
  (v_mT / (K_mT + M_T) + kd) * M_T * cytoplasm
P1_decay:
 {1.0}P1 = $pool
  kd * P1 * cytoplasm
P1_depho:
 {1.0}P1 = {1.0}P0
  V_2P * P1 / (K_2P + P1) * cytoplasm
P1_pho:
 {1.0}P1 = {1.0}P2
  V_3P * P1 / (K_3P + P1) * cytoplasm
P2_decay:
 {1.0}P2 = $pool
  kd * P2 * cytoplasm
P2_depho:
 {1.0}P2 = {1.0}P1
  V_4P * P2 / (K_4P + P2) * cytoplasm
P2_light_deact:
 {1.0}P2 = $pool
  v_dP * P2 / (K_dP + P2) * cytoplasm
PER_transl:
 $pool = {1.0}P0
  k_sP * M_P * cytoplasm
PO_decay:
 {1.0}P0 = $pool
  kd * P0 * cytoplasm
P_pho:
 {1.0}P0 = {1.0}P1
  V_1P * P0 / (K_1P + P0) * cytoplasm
T0_decay:
 {1.0}T0 = $pool
  kd * T0 * cytoplasm
T1_decay:
 {1.0}T1 = $pool
  kd * T1 * cytoplasm
T1_depho:
 {1.0}T1 = {1.0}T0
  V_2T * T1 / (K_2T + T1) * cytoplasm
T1_pho:
 {1.0}T1 = {1.0}T2
  V_3T * T1 / (K_3T + T1) * cytoplasm
T2_decay:
 {1.0}T2 = $pool
  kd * T2 * cytoplasm
T2_depho:
 {1.0}T2 = {1.0}T1
  V_4T * T2 / (K_4T + T2) * cytoplasm
T2_light_deact:
 {1.0}T2 = $pool
  v_dT * T2 / (K_dT + T2) * cytoplasm
TIM_transl:
 $pool = {1.0}T0
  k_sT * M_T * cytoplasm
T_pho:
 {1.0}T0 = {1.0}T1
  V_1T * T0 / (K_1T + T0) * cytoplasm
per_trans:
 $pool = {1.0}M_P
  v_sP * pow(Ki_P, n) / (pow(Ki_P, n) + pow(CN, n))
tim_trans:
 $pool = {1.0}M_T
  v_sT * pow(Ki_T, n) / (pow(Ki_T, n) + pow(CN, n))


#parameters
kd = 0.01
l_d = 12.0
n = 4.0
v_dT_dark = 2.0
v_dT_fac = 2.0
per_trans_v_sP = 0.8
per_trans_Ki_P = 1.0
tim_trans_v_sT = 1.0
tim_trans_Ki_T = 1.0
M_T_decay_v_mT = 0.7
M_T_decay_K_mT = 0.2
M_P_decay_v_mP = 0.8
M_P_decay_K_mP = 0.2
PER_transl_k_sP = 0.9
TIM_transl_k_sT = 0.9
C_form_k3 = 1.2
C_form_k4 = 0.6
C_decay_kd_C = 0.01
CN_decay_kd_CN = 0.01
C_transp_k1 = 1.2
C_transp_k2 = 0.2
P_pho_V_1P = 8.0
P_pho_K_1P = 2.0
P1_pho_V_3P = 8.0
P1_pho_K_3P = 2.0
P1_depho_K_2P = 2.0
P1_depho_V_2P = 1.0
P2_depho_V_4P = 1.0
P2_depho_K_4P = 2.0
T_pho_V_1T = 8.0
T_pho_K_1T = 2.0
T1_pho_V_3T = 8.0
T1_pho_K_3T = 2.0
T1_depho_K_2T = 2.0
T1_depho_V_2T = 1.0
T2_depho_V_4T = 1.0
T2_depho_K_4T = 2.0
T2_light_deact_K_dT = 0.2
P2_light_deact_v_dP = 2.0
P2_light_deact_K_dP = 0.2
cytoplasm = 1.0
nucleus = 1.0


#initial values
C = 0.18
CN = 1.2
M_P = 0.09
M_T = 1.41
P0 = 0.02
P1 = 0.02
P2 = 0.01
T0 = 0.54
T1 = 0.79
T2 = 4.65


#assignment rules
!F v_dT = (1.0 + (v_dT_fac - 1.0) * ceil(sin(time / l_d * pi) * 0.9)) * v_dT_dark
!F Pt = P0 + P1 + P2 + C + CN * nucleus / cytoplasm
!F Tt = T0 + T1 + T2 + C + CN * nucleus / cytoplasm