begin name
veening1
end name

begin reactions
AprEdeg {1.0}AprE = {1.0}$EXTERNAL
AprEsyn {1.0}$EXTERNAL = {1.0}AprE
DimerAss {2.0}DegUP = {1.0}Dim
DimerDis {1.0}Dim = {2.0}DegUP
degradation1 {1.0}DegU = {1.0}$EXTERNAL
degradation2 {1.0}DegUP = {1.0}$EXTERNAL
degradation3 {1.0}Dim = {1.0}$EXTERNAL
degradationmRNA {1.0}mDegU = {1.0}$EXTERNAL
dephosphorylation {1.0}DegUP = {1.0}DegU
mRNAAprEdeg {1.0}mAprE = {1.0}$EXTERNAL
mRNAAprEsyn {1.0}$EXTERNAL = {1.0}mAprE
phosphorylation {1.0}DegU = {1.0}DegUP
synthesisDegU {1.0}$EXTERNAL = {1.0}DegU
synthesismRNA {1.0}$EXTERNAL = {1.0}mDegU
end reactions

begin rate equations
AprEdeg = kdeg*AprE[t]
AprEsyn = ksyn*univ*mAprE[t]
DimerAss = ka*DegUP[t]^2
DimerDis = kd*Dim[t]
degradation1 = kdeg*univ*DegU[t]
degradation2 = kdeg*univ*DegUP[t]
degradation3 = kdeg*univ*Dim[t]
degradationmRNA = kdegm*mDegU[t]
dephosphorylation = kdephos*DegUP[t]
mRNAAprEdeg = kdegm*mAprE[t]
mRNAAprEsyn = (Kr1*((Irmax*univ^2*Dim[t]^2)/(Kdim^2*(1 + R/Kr + (univ*Dim[t])/Kdim + (univ^2*Dim[t]^2)/Kdim^2)) + (Iro*(1 + (univ*Dim[t])/Kdim))/(1 + R/Kr + (univ*Dim[t])/Kdim + (univ^2*Dim[t]^2)/Kdim^2)))/(Kr1 + R)
phosphorylation = kphos*DegU[t]
synthesisDegU = ksyn1*univ*mDegU[t]
synthesismRNA = (Io*K)/(K + univ*Dim[t]) + (Imax*univ*Dim[t])/(K + univ*Dim[t])
end rate equations

begin parameters
Imax = 0.048
Io = 0.004
Irmax = 0.4
Iro = 0.02
K = 7.0
Kdim = 12.0
Kr = 7.0
Kr1 = 7.0
R = 7.0
V = 1.0
ka = 0.025
kd = 0.1
kdeg = 0.0004
kdegA = 0.0001
kdegm = 0.01
ksyn = 0.04
ksyn1 = 0.04
p = 0.15
q = 0.004
ratio = 0.026666667
univ = 1.0
end parameters

begin initial conditions
AprE[0] = AprEi
DegU[0] = DegUi
DegUP[0] = DegUPi
Dim[0] = Dimi
mAprE[0] = mAprEi
mDegU[0] = mDegUi
end initial conditions

begin initial values
AprEi = 0.0
DegUi = 0.0
DegUPi = 0.0
Dimi = 0.0
mAprEi = 0.0
mDegUi = 0.0
end initial values

begin assignment rules
DegUTotal := DegU[t] + DegUP[t] + 2*Dim[t]
kdephos := q/ratio
kphos := p*ratio
end assignment rules

begin function definitions
end function definitions

begin events
end events

begin process annotations
end process annotations

begin species annotations
end species annotations

begin units
end units