[2696] | 1 | {Model of hysteresis and irreversible transition in eukaryotic cell |
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| 2 | WITH mRNA! } |
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| 3 | |
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| 4 | #DEFVAR |
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| 5 | A = ignore; {protein that activates Cdh1 at finish} |
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| 6 | AYp= ignore; {complex} |
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| 7 | Yp = ignore; {inactive (phosphorylated) Cdh1-P/APC} |
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| 8 | XY = ignore; {complex} |
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| 9 | Y = ignore; {active Cdh1/APC complex} |
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| 10 | X = ignore; {cyclin/Cdk dimer} |
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| 11 | YX = ignore; {complex} |
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| 12 | XYX= ignore; {complex} |
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| 13 | G = ignore; {complex} |
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| 14 | TF = ignore; {complex} |
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| 15 | TFp= ignore; {complex} |
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| 16 | C1 = ignore; {complex} |
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| 17 | C2 = ignore; {complex} |
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| 18 | R = ignore; {mRNA} |
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| 19 | mas= ignore; {mass of the cell} |
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| 20 | |
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| 21 | |
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| 22 | #EQUATIONS |
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| 23 | mas = 2mas : (0.01); |
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| 24 | 2mas = mas : (0.001); |
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| 25 | PROD = X : (0.02); {k1} |
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| 26 | X = PROD : (0.05); {k2 prime} |
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| 27 | Y + X = YX : (1000); {k2f double prime} |
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| 28 | YX = Y + X : (3); {k2r double prime} |
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| 29 | YX = Y : (1); {k2 double prime} |
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| 30 | X + Y = XY : (1200); {k4f} |
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| 31 | XY = X + Y : (35); {k4r} |
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| 32 | XY = X + Yp : (80); {k4} |
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| 33 | A + Yp = AYp : (4000); {k3f} |
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| 34 | AYp = A + Yp : (75); {k3r} |
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| 35 | AYp = A + Y : (60); {k3} |
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| 36 | X + YX = XYX : (360); {k5f} |
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| 37 | XYX = X + YX : (18); {k5r} |
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| 38 | G = G + R : (0.00075);{k5 prime} |
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| 39 | XYX = 2X + Yp : (16); {k6} |
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| 40 | A = PROD : (0.4); {k6 prime} |
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| 41 | AYp = Yp : (0.4); {k6 prime} |
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| 42 | TF + X = X + TFp : (2.5); {k7f} |
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| 43 | TFp = TF : (4.0); {k7r} |
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| 44 | TFp + G = C1 : (1.2); {k8f} |
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| 45 | C1 = TFp + G : (320); {k8r} |
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| 46 | C1 = C1 + R : (0.15); {k9} |
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| 47 | TFp + C1= C2 : (65); {k10f} |
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| 48 | C2 = C1 + TFp : (0.2); {k10r} |
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| 49 | C2 = C2 + R : (3); {k11} |
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| 50 | R = PROD : (1); {krd} |
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| 51 | R = R + A : (1); {krs} |
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| 52 | |
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| 53 | #LOOKAT X; |
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| 54 | #MONITOR X; |
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| 55 | |
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| 56 | #INITVALUES |
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| 57 | CFACTOR = 1; |
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| 58 | mas = 0.1046E+01; |
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| 59 | TF = 0.8979E+01; |
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| 60 | XY = 0.5458E-02; |
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| 61 | XYX = 0.8918E-02; |
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| 62 | YX = 0.2989E-02; |
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| 63 | X = 0.1275E+00; |
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| 64 | Y = 0.1714E-02; |
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| 65 | Yp = 0.9605E+00; |
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| 66 | AYp = 0.2046E-01; |
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| 67 | A = 0.8577E-03; |
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| 68 | C2 = 0.1692E-02; |
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| 69 | C1 = 0.1769E-04; |
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| 70 | TFp = 0.1731E-01; |
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| 71 | G = 0.9983E+00; |
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| 72 | R = 0; |
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| 73 | |
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| 74 | #INLINE F77_INIT |
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| 75 | TSTART = 0.d0 |
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| 76 | TEND = 1000.d0 |
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| 77 | DT = 5.d0 |
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| 78 | Volume = 1000.d0 |
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| 79 | #ENDINLINE |
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| 80 | |
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| 81 | #INLINE F77_UTIL |
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| 82 | DOUBLE PRECISION FUNCTION CellMass(t) |
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| 83 | ! Cell mass evolution in time |
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| 84 | DOUBLE PRECISION t |
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| 85 | DOUBLE PRECISION m0, mstar, mu, one |
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| 86 | PARAMETER (m0 = 1.0d0) |
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| 87 | PARAMETER (mstar = 10.0d0) |
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| 88 | PARAMETER (mu = 0.01d0) |
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| 89 | PARAMETER (one = 1.0d0) |
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| 90 | CellMass = mstar/(one-(one-mstar/m0)*EXP(-mu*t)) |
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| 91 | END |
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| 92 | #ENDINLINE |
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| 93 | |
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| 94 | #INLINE F90_INIT |
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| 95 | TSTART = 0.d0 |
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| 96 | TEND = 1000.d0 |
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| 97 | DT = 5.d0 |
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| 98 | !Volume = 1000.d0 |
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| 99 | #ENDINLINE |
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| 100 | |
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| 101 | #INLINE F90_UTIL |
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| 102 | DOUBLE PRECISION FUNCTION CellMass(t) |
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| 103 | ! Cell mass evolution in time |
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| 104 | DOUBLE PRECISION, INTENT(IN) :: t |
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| 105 | DOUBLE PRECISION, PARAMETER:: m0 = 1.0d0 |
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| 106 | DOUBLE PRECISION, PARAMETER:: mstar = 10.0d0 |
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| 107 | DOUBLE PRECISION, PARAMETER:: mu = 0.01d0 |
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| 108 | DOUBLE PRECISION, PARAMETER:: one = 1.0d0 |
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| 109 | CellMass = mstar/(one-(one-mstar/m0)*EXP(-mu*t)) |
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| 110 | END FUNCTION CellMass |
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| 111 | #ENDINLINE |
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| 112 | |
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| 113 | #INLINE MATLAB_INIT |
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| 114 | global TSTART TEND DT TEMP |
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| 115 | TSTART = 0; |
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| 116 | TEND = 1000; |
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| 117 | DT = 5.0; |
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| 118 | Volume = 1000.0; |
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| 119 | #ENDINLINE |
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| 120 | |
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| 121 | #INLINE MATLAB_UTIL |
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| 122 | function m = CellMass(t) |
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| 123 | % Cell mass evolution in time |
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| 124 | m = 10/(1+9*exp(-0.01*t)); |
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| 125 | return |
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| 126 | #ENDINLINE |
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| 127 | |
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| 128 | #INLINE C_INIT |
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| 129 | TSTART = 0.0; |
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| 130 | TEND = 1000.0; |
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| 131 | DT = 5.0; |
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| 132 | Volume = 1000.0; |
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| 133 | #ENDINLINE |
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| 134 | |
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| 135 | #INLINE C_UTIL |
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| 136 | double CellMass(double t) |
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| 137 | {/* Cell mass evolution in time */ |
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| 138 | const double m0 = 1.0; |
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| 139 | const double mstar = 10.0; |
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| 140 | const double mu = 0.01; |
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| 141 | const double one = 1.0; |
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| 142 | return mstar/(one-(one-mstar/m0)*exp(-mu*t)); |
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| 143 | } |
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| 144 | #ENDINLINE |
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