source: palm/trunk/UTIL/chemistry/gasphase_preproc/kpp/models/cell_cycle.def

{Model of hysteresis and irreversible transition in eukaryotic cell}

#DEFVAR
A  = ignore; {protein that activates Cdh1 at finish}
AYp= ignore; {complex}
Yp = ignore; {inactive (phosphorylated) Cdh1-P/APC}
XY = ignore; {complex}
Y  = ignore; {active Cdh1/APC complex}
X  = ignore; {cyclin/Cdk dimer}
YX = ignore; {complex}
XYX= ignore; {complex}
G  = ignore; {complex}
TF = ignore; {complex}
TFp= ignore; {complex}
C1 = ignore; {complex}
C2 = ignore; {complex}
mas= ignore; {mass of the cell} 


#EQUATIONS
mas    = 2mas    : (0.01);
2mas    = mas    : (0.001);
PROD    = X      : (0.02);   {k1}
X      =  PROD   : (0.05);   {k2 prime}
Y + X  =  YX     : (1000);   {k2f double prime}
YX     =  Y + X  : (3);      {k2r double prime}
YX     =  Y      : (1);      {k2  double prime}
X + Y  =  XY     : (1200);   {k4f}
XY     =  X + Y  : (35);     {k4r}
XY     =  X + Yp : (80);     {k4}
A + Yp =  AYp    : (4000);   {k3f}
AYp    =  A + Yp : (75);     {k3r}
AYp    =  A + Y  : (60);     {k3}
X + YX =  XYX    : (360);    {k5f}
XYX    =  X + YX : (18);     {k5r}
XYX    =  2X + Yp: (16);     {k6}
A      = PROD    : (0.4);    {k6 prime}
AYp      = Yp    : (0.4);    {k6 prime}
G       = G + A  : (0.00075);{k5 prime}
TF + X  = X + TFp: (2.6);    {k7f}
TFp     = TF     : (4.0);    {k7r}
TFp + G = C1     : (1.2);    {k8f}
C1      = TFp + G   : (320); {k8r}
C1      =  C1 + A   : (0.15);{k9}
TFp + C1= C2        : (65);  {k10f}
C2      =  C1 + TFp : (0.2); {k10r}
C2      = C2 + A    : (3);   {k11}

#LOOKAT X;
#MONITOR X;

#INITVALUES
CFACTOR = 1;
mas=0.1046E+01; 
TF=0.8979E+01; 
XY=0.5458E-02; 
XYX=0.8918E-02; 
YX=0.2989E-02; 
X=0.1275E+00; 
Y=0.1714E-02; 
Yp=0.9605E+00; 
AYp=0.2046E-01; 
A=0.8577E-03; 
C2=0.1692E-02; 
C1=0.1769E-04; 
TFp=0.1731E-01; 
G=0.9983E+00;

#INLINE F77_INIT
      TSTART = 0.d0
      TEND   = 1000.d0
      DT     = 5.d0
      Volume = 1000.d0
#ENDINLINE

#INLINE F77_UTIL
      DOUBLE PRECISION FUNCTION CellMass(t)
       ! Cell mass evolution in time
       DOUBLE PRECISION t
       DOUBLE PRECISION m0, mstar, mu, one
       PARAMETER (m0    = 1.0d0)
       PARAMETER (mstar = 10.0d0)
       PARAMETER (mu    = 0.01d0)
       PARAMETER (one   = 1.0d0)
       CellMass = mstar/(one-(one-mstar/m0)*EXP(-mu*t))
      END
#ENDINLINE

#INLINE F90_INIT
   TSTART = 0.d0
   TEND   = 1000.d0
   DT     = 5.d0
   !Volume = 1000.d0
#ENDINLINE

#INLINE F90_UTIL
   DOUBLE PRECISION FUNCTION CellMass(t)
     ! Cell mass evolution in time
     DOUBLE PRECISION, INTENT(IN) :: t
     DOUBLE PRECISION, PARAMETER:: m0    = 1.0d0
     DOUBLE PRECISION, PARAMETER:: mstar = 10.0d0
     DOUBLE PRECISION, PARAMETER:: mu    = 0.01d0
     DOUBLE PRECISION, PARAMETER:: one   = 1.0d0
     CellMass = mstar/(one-(one-mstar/m0)*EXP(-mu*t))
   END FUNCTION CellMass
#ENDINLINE

#INLINE MATLAB_INIT
   global TSTART TEND DT TEMP
   TSTART = 0;
   TEND   = 1000;
   DT     = 5.0;
   Volume = 1000.0;
#ENDINLINE

#INLINE MATLAB_UTIL
   function m = CellMass(t)
     % Cell mass evolution in time
     m = 10/(1+9*exp(-0.01*t));
   return
#ENDINLINE

#INLINE C_INIT
   TSTART = 0.0;
   TEND   = 1000.0;
   DT     = 5.0;
   Volume = 1000.0;
#ENDINLINE

#INLINE C_UTIL
   double CellMass(double t)
   {/* Cell mass evolution in time */
     const double m0    = 1.0;
     const double mstar = 10.0;
     const double mu    = 0.01;
     const double one   = 1.0;
     return mstar/(one-(one-mstar/m0)*exp(-mu*t));
   }
#ENDINLINE