source: palm/trunk/UTIL/chemistry/gasphase_preproc/kpp/models/cell_cycle.def @ 3872

Last change on this file since 3872 was 2696, checked in by kanani, 7 years ago

Merge of branch palm4u into trunk

File size: 3.4 KB
Line 
1{Model of hysteresis and irreversible transition in eukaryotic cell}
2
3#DEFVAR
4A  = ignore; {protein that activates Cdh1 at finish}
5AYp= ignore; {complex}
6Yp = ignore; {inactive (phosphorylated) Cdh1-P/APC}
7XY = ignore; {complex}
8Y  = ignore; {active Cdh1/APC complex}
9X  = ignore; {cyclin/Cdk dimer}
10YX = ignore; {complex}
11XYX= ignore; {complex}
12G  = ignore; {complex}
13TF = ignore; {complex}
14TFp= ignore; {complex}
15C1 = ignore; {complex}
16C2 = ignore; {complex}
17mas= ignore; {mass of the cell}
18
19
20#EQUATIONS
21mas    = 2mas    : (0.01);
222mas    = mas    : (0.001);
23PROD    = X      : (0.02);   {k1}
24X      =  PROD   : (0.05);   {k2 prime}
25Y + X  =  YX     : (1000);   {k2f double prime}
26YX     =  Y + X  : (3);      {k2r double prime}
27YX     =  Y      : (1);      {k2  double prime}
28X + Y  =  XY     : (1200);   {k4f}
29XY     =  X + Y  : (35);     {k4r}
30XY     =  X + Yp : (80);     {k4}
31A + Yp =  AYp    : (4000);   {k3f}
32AYp    =  A + Yp : (75);     {k3r}
33AYp    =  A + Y  : (60);     {k3}
34X + YX =  XYX    : (360);    {k5f}
35XYX    =  X + YX : (18);     {k5r}
36XYX    =  2X + Yp: (16);     {k6}
37A      = PROD    : (0.4);    {k6 prime}
38AYp      = Yp    : (0.4);    {k6 prime}
39G       = G + A  : (0.00075);{k5 prime}
40TF + X  = X + TFp: (2.6);    {k7f}
41TFp     = TF     : (4.0);    {k7r}
42TFp + G = C1     : (1.2);    {k8f}
43C1      = TFp + G   : (320); {k8r}
44C1      =  C1 + A   : (0.15);{k9}
45TFp + C1= C2        : (65);  {k10f}
46C2      =  C1 + TFp : (0.2); {k10r}
47C2      = C2 + A    : (3);   {k11}
48
49#LOOKAT X;
50#MONITOR X;
51
52#INITVALUES
53CFACTOR = 1;
54mas=0.1046E+01;
55TF=0.8979E+01;
56XY=0.5458E-02;
57XYX=0.8918E-02;
58YX=0.2989E-02;
59X=0.1275E+00;
60Y=0.1714E-02;
61Yp=0.9605E+00;
62AYp=0.2046E-01;
63A=0.8577E-03;
64C2=0.1692E-02;
65C1=0.1769E-04;
66TFp=0.1731E-01;
67G=0.9983E+00;
68
69#INLINE F77_INIT
70      TSTART = 0.d0
71      TEND   = 1000.d0
72      DT     = 5.d0
73      Volume = 1000.d0
74#ENDINLINE
75
76#INLINE F77_UTIL
77      DOUBLE PRECISION FUNCTION CellMass(t)
78       ! Cell mass evolution in time
79       DOUBLE PRECISION t
80       DOUBLE PRECISION m0, mstar, mu, one
81       PARAMETER (m0    = 1.0d0)
82       PARAMETER (mstar = 10.0d0)
83       PARAMETER (mu    = 0.01d0)
84       PARAMETER (one   = 1.0d0)
85       CellMass = mstar/(one-(one-mstar/m0)*EXP(-mu*t))
86      END
87#ENDINLINE
88
89#INLINE F90_INIT
90   TSTART = 0.d0
91   TEND   = 1000.d0
92   DT     = 5.d0
93   !Volume = 1000.d0
94#ENDINLINE
95
96#INLINE F90_UTIL
97   DOUBLE PRECISION FUNCTION CellMass(t)
98     ! Cell mass evolution in time
99     DOUBLE PRECISION, INTENT(IN) :: t
100     DOUBLE PRECISION, PARAMETER:: m0    = 1.0d0
101     DOUBLE PRECISION, PARAMETER:: mstar = 10.0d0
102     DOUBLE PRECISION, PARAMETER:: mu    = 0.01d0
103     DOUBLE PRECISION, PARAMETER:: one   = 1.0d0
104     CellMass = mstar/(one-(one-mstar/m0)*EXP(-mu*t))
105   END FUNCTION CellMass
106#ENDINLINE
107
108#INLINE MATLAB_INIT
109   global TSTART TEND DT TEMP
110   TSTART = 0;
111   TEND   = 1000;
112   DT     = 5.0;
113   Volume = 1000.0;
114#ENDINLINE
115
116#INLINE MATLAB_UTIL
117   function m = CellMass(t)
118     % Cell mass evolution in time
119     m = 10/(1+9*exp(-0.01*t));
120   return
121#ENDINLINE
122
123#INLINE C_INIT
124   TSTART = 0.0;
125   TEND   = 1000.0;
126   DT     = 5.0;
127   Volume = 1000.0;
128#ENDINLINE
129
130#INLINE C_UTIL
131   double CellMass(double t)
132   {/* Cell mass evolution in time */
133     const double m0    = 1.0;
134     const double mstar = 10.0;
135     const double mu    = 0.01;
136     const double one   = 1.0;
137     return mstar/(one-(one-mstar/m0)*exp(-mu*t));
138   }
139#ENDINLINE
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