begin name
leloup6
end name

begin reactions
CNdecay {1.0}CN = {1.0}$EXTERNAL
Cdecay {1.0}C = {1.0}$EXTERNAL
Cform {1.0}P2 + {1.0}T2 = {1.0}C
Ctransp {1.0}C = {1.0}CN
MPdecay {1.0}MP = {1.0}$EXTERNAL
MTdecay {1.0}MT = {1.0}$EXTERNAL
P1decay {1.0}P1 = {1.0}$EXTERNAL
P1depho {1.0}P1 = {1.0}P0
P1pho {1.0}P1 = {1.0}P2
P2decay {1.0}P2 = {1.0}$EXTERNAL
P2depho {1.0}P2 = {1.0}P1
P2lightdeact {1.0}P2 = {1.0}$EXTERNAL
PERtransl {1.0}$EXTERNAL = {1.0}P0
POdecay {1.0}P0 = {1.0}$EXTERNAL
Ppho {1.0}P0 = {1.0}P1
T0decay {1.0}T0 = {1.0}$EXTERNAL
T1decay {1.0}T1 = {1.0}$EXTERNAL
T1depho {1.0}T1 = {1.0}T0
T1pho {1.0}T1 = {1.0}T2
T2decay {1.0}T2 = {1.0}$EXTERNAL
T2depho {1.0}T2 = {1.0}T1
T2lightdeact {1.0}T2 = {1.0}$EXTERNAL
TIMtransl {1.0}$EXTERNAL = {1.0}T0
Tpho {1.0}T0 = {1.0}T1
pertrans {1.0}$EXTERNAL = {1.0}MP
timtrans {1.0}$EXTERNAL = {1.0}MT
end reactions

begin rate equations
CNdecay = CNdecaykdCN*nucleus*CN[t]
Cdecay = cytoplasm*CdecaykdC*C[t]
Cform = cytoplasm*(-(Cformk4*C[t]) + Cformk3*P2[t]*T2[t])
Ctransp = cytoplasm*Ctranspk1*C[t] - Ctranspk2*nucleus*CN[t]
MPdecay = cytoplasm*MP[t]*(kd + MPdecayvmP/(MPdecayKmP + MP[t]))
MTdecay = cytoplasm*MT[t]*(kd + MTdecayvmT/(MTdecayKmT + MT[t]))
P1decay = cytoplasm*kd*P1[t]
P1depho = (cytoplasm*P1dephoV2P*P1[t])/(P1dephoK2P + P1[t])
P1pho = (cytoplasm*P1phoV3P*P1[t])/(P1phoK3P + P1[t])
P2decay = cytoplasm*kd*P2[t]
P2depho = (cytoplasm*P2dephoV4P*P2[t])/(P2dephoK4P + P2[t])
P2lightdeact = (cytoplasm*P2lightdeactvdP*P2[t])/(P2lightdeactKdP + P2[t])
PERtransl = cytoplasm*PERtranslksP*MP[t]
POdecay = cytoplasm*kd*P0[t]
Ppho = (cytoplasm*PphoV1P*P0[t])/(PphoK1P + P0[t])
T0decay = cytoplasm*kd*T0[t]
T1decay = cytoplasm*kd*T1[t]
T1depho = (cytoplasm*T1dephoV2T*T1[t])/(T1dephoK2T + T1[t])
T1pho = (cytoplasm*T1phoV3T*T1[t])/(T1phoK3T + T1[t])
T2decay = cytoplasm*kd*T2[t]
T2depho = (cytoplasm*T2dephoV4T*T2[t])/(T2dephoK4T + T2[t])
T2lightdeact = (cytoplasm*vdT*T2[t])/(T2lightdeactKdT + T2[t])
TIMtransl = cytoplasm*TIMtranslksT*MT[t]
Tpho = (cytoplasm*TphoV1T*T0[t])/(TphoK1T + T0[t])
pertrans = (pertransKiP^n*pertransvsP)/(pertransKiP^n + CN[t]^n)
timtrans = (timtransKiT^n*timtransvsT)/(timtransKiT^n + CN[t]^n)
end rate equations

begin parameters
kd = 0.01
ld = 12.0
n = 4.0
vdTdark = 2.0
vdTfac = 2.0
pertransvsP = 0.8
pertransKiP = 1.0
timtransvsT = 1.0
timtransKiT = 1.0
MTdecayvmT = 0.7
MTdecayKmT = 0.2
MPdecayvmP = 0.8
MPdecayKmP = 0.2
PERtranslksP = 0.9
TIMtranslksT = 0.9
Cformk3 = 1.2
Cformk4 = 0.6
CdecaykdC = 0.01
CNdecaykdCN = 0.01
Ctranspk1 = 1.2
Ctranspk2 = 0.2
PphoV1P = 8.0
PphoK1P = 2.0
P1phoV3P = 8.0
P1phoK3P = 2.0
P1dephoK2P = 2.0
P1dephoV2P = 1.0
P2dephoV4P = 1.0
P2dephoK4P = 2.0
TphoV1T = 8.0
TphoK1T = 2.0
T1phoV3T = 8.0
T1phoK3T = 2.0
T1dephoK2T = 2.0
T1dephoV2T = 1.0
T2dephoV4T = 1.0
T2dephoK4T = 2.0
T2lightdeactKdT = 0.2
P2lightdeactvdP = 2.0
P2lightdeactKdP = 0.2
cytoplasm = 1.0
nucleus = 1.0
end parameters

begin initial conditions
C[0] = Ci
CN[0] = CNi
MP[0] = MPi
MT[0] = MTi
P0[0] = P0i
P1[0] = P1i
P2[0] = P2i
T0[0] = T0i
T1[0] = T1i
T2[0] = T2i
end initial conditions

begin initial values
Ci = 0.18
CNi = 1.2
MPi = 0.09
MTi = 1.41
P0i = 0.02
P1i = 0.02
P2i = 0.01
T0i = 0.54
T1i = 0.79
T2i = 4.65
end initial values

begin assignment rules
vdT := vdTdark*(1 + (-1 + vdTfac)*Ceiling[0.9*Sin[(Pi*t)/ld]])
Pt := C[t] + (nucleus*CN[t])/cytoplasm + P0[t] + P1[t] + P2[t]
Tt := C[t] + (nucleus*CN[t])/cytoplasm + T0[t] + T1[t] + T2[t]
end assignment rules

begin function definitions
end function definitions

begin events
end events

begin process annotations
tim_trans http://identifiers.org/go/GO:0009299
end process annotations

begin species annotations
end species annotations

begin units
end units