// This model generated automatically from SBML

// unit definitions
import nsrunit;
unit conversion off;
unit item=scalar;
unit substance = 1E-9 mole;
unit time = 3600 second;
unit volume = litre;
unit area = metre^2;
unit length = metre;

// SBML property definitions
property sbmlRole=string;
property sbmlName=string;
property sbmlCompartment=string;

// SBML reactions
// P0_to_P1: P0 <=> P1 
// T0_to_T1: T0 <=> T1 
// P1_to_P0: P1 <=> P0 
// T1_to_T0: T1 <=> T0 
// P1_to_P2: P1 <=> P2 
// T1_to_T2: T1 <=> T2 
// P2_to_P1: P2 <=> P1 
// T2_to_T1: T2 <=> T1 
// P0_degradation: P0 
// T0_degradation: T0 
// P1_degradation: P1 
// T1_degradation: T1 
// P2_degradation: P2 
// T2_degradation: T2 
// PT_complex_formation: P2 T2 => CC 
// PT_complex_nucleation: CC => Cn 
// PT_complex_degradation: CC 
// PTnucl_complex_degradation: Cn 
// Mp_production: <=> Mp 
// Mt_production: <=> Mt 
// P0_production: <=> P0 
// T0_production: <=> T0 
// Mp_degradation: Mp 
// Mt_degradation: Mt 

math main {
  realDomain time second;
  time.min=0;
  extern time.max;
  extern time.delta;

  // variable definitions
  real Cell = 1 volume;
  real compartment_0000002 = 1 volume;
  real Pt(time);
  real Tt(time);
  real V_mT = .7;
  real V_dT = 2;
  private real P0.amt(time) substance;
  real P0(time) substance/volume;
  real P0.init substance/volume;
  private real T0.amt(time) substance;
  real T0(time) substance/volume;
  real T0.init substance/volume;
  private real P1.amt(time) substance;
  real P1(time) substance/volume;
  real P1.init substance/volume;
  private real T1.amt(time) substance;
  real T1(time) substance/volume;
  real T1.init substance/volume;
  private real P2.amt(time) substance;
  real P2(time) substance/volume;
  real P2.init substance/volume;
  private real T2.amt(time) substance;
  real T2(time) substance/volume;
  real T2.init substance/volume;
  private real CC.amt(time) substance;
  real CC(time) substance/volume;
  real CC.init substance/volume;
  private real Cn.amt(time) substance;
  real Cn(time) substance/volume;
  real Cn.init substance/volume;
  private real Mp.amt(time) substance;
  real Mp(time) substance/volume;
  real Mp.init substance/volume;
  private real Mt.amt(time) substance;
  real Mt(time) substance/volume;
  real Mt.init substance/volume;
  real P0_to_P1.rate(time) substance/time;
  real K1_P = 2;
  real V_1P = 8;
  real T0_to_T1.rate(time) substance/time;
  real K_1T = 2;
  real V_1T = 8;
  real P1_to_P0.rate(time) substance/time;
  real K_2P = 2;
  real V_2P = 1;
  real T1_to_T0.rate(time) substance/time;
  real K_2T = 2;
  real V_2T = 1;
  real P1_to_P2.rate(time) substance/time;
  real K_3P = 2;
  real V_3P = 8;
  real T1_to_T2.rate(time) substance/time;
  real K_3T = 2;
  real V_3T = 8;
  real P2_to_P1.rate(time) substance/time;
  real K_4P = 2;
  real V_4P = 1;
  real T2_to_T1.rate(time) substance/time;
  real K_4T = 2;
  real V_4T = 1;
  real P0_degradation.rate(time) substance/time;
  real k_d = .01;
  real T0_degradation.rate(time) substance/time;
  real P1_degradation.rate(time) substance/time;
  real T1_degradation.rate(time) substance/time;
  real P2_degradation.rate(time) substance/time;
  real V_dP = 2;
  real K_dP = .2;
  real T2_degradation.rate(time) substance/time;
  real K_dT = .2;
  real PT_complex_formation.rate(time) substance/time;
  real k3 = 1.2;
  real k4 = .6;
  real PT_complex_nucleation.rate(time) substance/time;
  real k1 = .6;
  real k2 = .2;
  real PT_complex_degradation.rate(time) substance/time;
  real k_dC = .01;
  real PTnucl_complex_degradation.rate(time) substance/time;
  real k_dN = .01;
  real Mp_production.rate(time) substance/time;
  real v_sP = 1;
  real K_IP = 1;
  real n = 4;
  real Mt_production.rate(time) substance/time;
  real V_sT = 1;
  real K_IT = 1;
  real P0_production.rate(time) substance/time;
  real k_sP = .9;
  real T0_production.rate(time) substance/time;
  real k_sT = .9;
  real Mp_degradation.rate(time) substance/time;
  real V_mP = .7;
  real K_mP = .2;
  real Mt_degradation.rate(time) substance/time;
  real K_mT = .2;

  // equations
  Pt = CC+Cn+P0+P1+P2;
  Tt = CC+Cn+T0+T1+T2;
  when (time=time.min) P0.amt = P0.init*Cell;
  P0.amt:time = -1*P0_to_P1.rate + P1_to_P0.rate + -1*P0_degradation.rate + P0_production.rate;
  P0 = P0.amt/Cell;
  P0.init = 0;
  when (time=time.min) T0.amt = T0.init*Cell;
  T0.amt:time = -1*T0_to_T1.rate + T1_to_T0.rate + -1*T0_degradation.rate + T0_production.rate;
  T0 = T0.amt/Cell;
  T0.init = 0;
  when (time=time.min) P1.amt = P1.init*Cell;
  P1.amt:time = P0_to_P1.rate + -1*P1_to_P0.rate + -1*P1_to_P2.rate + P2_to_P1.rate + -1*P1_degradation.rate;
  P1 = P1.amt/Cell;
  P1.init = 0;
  when (time=time.min) T1.amt = T1.init*Cell;
  T1.amt:time = T0_to_T1.rate + -1*T1_to_T0.rate + -1*T1_to_T2.rate + T2_to_T1.rate + -1*T1_degradation.rate;
  T1 = T1.amt/Cell;
  T1.init = 0;
  when (time=time.min) P2.amt = P2.init*Cell;
  P2.amt:time = P1_to_P2.rate + -1*P2_to_P1.rate + -1*P2_degradation.rate + -1*PT_complex_formation.rate;
  P2 = P2.amt/Cell;
  P2.init = 0;
  when (time=time.min) T2.amt = T2.init*Cell;
  T2.amt:time = T1_to_T2.rate + -1*T2_to_T1.rate + -1*T2_degradation.rate + -1*PT_complex_formation.rate;
  T2 = T2.amt/Cell;
  T2.init = 0;
  when (time=time.min) CC.amt = CC.init*Cell;
  CC.amt:time = PT_complex_formation.rate + -1*PT_complex_nucleation.rate + -1*PT_complex_degradation.rate;
  CC = CC.amt/Cell;
  CC.init = 0;
  when (time=time.min) Cn.amt = Cn.init*compartment_0000002;
  Cn.amt:time = PT_complex_nucleation.rate + -1*PTnucl_complex_degradation.rate;
  Cn = Cn.amt/compartment_0000002;
  Cn.init = 0;
  when (time=time.min) Mp.amt = Mp.init*Cell;
  Mp.amt:time = Mp_production.rate + -1*Mp_degradation.rate;
  Mp = Mp.amt/Cell;
  Mp.init = 0;
  when (time=time.min) Mt.amt = Mt.init*Cell;
  Mt.amt:time = Mt_production.rate + -1*Mt_degradation.rate;
  Mt = Mt.amt/Cell;
  Mt.init = 0;
  P0_to_P1.rate = Cell*V_1P*P0/(K1_P+P0);
  T0_to_T1.rate = Cell*V_1T*T0/(K_1T+T0);
  P1_to_P0.rate = Cell*V_2P*P1/(K_2P+P1);
  T1_to_T0.rate = Cell*V_2T*T1/(K_2T+T1);
  P1_to_P2.rate = Cell*V_3P*P1/(K_3P+P1);
  T1_to_T2.rate = Cell*V_3T*T1/(K_3T+T1);
  P2_to_P1.rate = Cell*V_4P*P2/(K_4P+P2);
  T2_to_T1.rate = Cell*V_4T*T2/(K_4T+T2);
  P0_degradation.rate = Cell*k_d*P0;
  T0_degradation.rate = Cell*k_d*T0;
  P1_degradation.rate = Cell*k_d*P1;
  T1_degradation.rate = Cell*k_d*T1;
  P2_degradation.rate = Cell*k_d*P2+Cell*V_dP*P2/(K_dP+P2);
  T2_degradation.rate = Cell*k_d*T2+Cell*V_dT*T2/(K_dT+T2);
  PT_complex_formation.rate = Cell*k3*P2*T2-Cell*k4*CC;
  PT_complex_nucleation.rate = Cell*k1*CC-compartment_0000002*k2*Cn;
  PT_complex_degradation.rate = Cell*k_dC*CC;
  PTnucl_complex_degradation.rate = compartment_0000002*k_dN*Cn;
  Mp_production.rate = Cell*v_sP*K_IP^n/(K_IP^n+Cn^n);
  Mt_production.rate = Cell*V_sT*K_IT^n/(K_IT^n+Cn^n);
  P0_production.rate = Cell*k_sP*Mp;
  T0_production.rate = Cell*k_sT*Mt;
  Mp_degradation.rate = Cell*k_d*Mp+Cell*V_mP*Mp/(K_mP+Mp);
  Mt_degradation.rate = Cell*k_d*Mt+Cell*V_mT*Mt/(K_mT+Mt);

  // variable properties
  Cell.sbmlRole="compartment";
  Cell.sbmlName="cytoplasm";
  compartment_0000002.sbmlRole="compartment";
  compartment_0000002.sbmlName="nucleus";
  Pt.sbmlRole="parameter";
  Pt.sbmlName="Total Per";
  Tt.sbmlRole="parameter";
  Tt.sbmlName="Total Tim";
  V_mT.sbmlRole="parameter";
  V_dT.sbmlRole="parameter";
  P0.amt.sbmlRole="speciesAmount";
  P0.sbmlRole="speciesConcentration";
  P0.sbmlName="PER Protein (unphosphorylated)";
  P0.sbmlCompartment="Cell";
  P0.init.sbmlRole="speciesInitialConcentration";
  T0.amt.sbmlRole="speciesAmount";
  T0.sbmlRole="speciesConcentration";
  T0.sbmlName="TIM Protein (unphosphorylated)";
  T0.sbmlCompartment="Cell";
  T0.init.sbmlRole="speciesInitialConcentration";
  P1.amt.sbmlRole="speciesAmount";
  P1.sbmlRole="speciesConcentration";
  P1.sbmlName="PER Protein (mono-phosphorylated)";
  P1.sbmlCompartment="Cell";
  P1.init.sbmlRole="speciesInitialConcentration";
  T1.amt.sbmlRole="speciesAmount";
  T1.sbmlRole="speciesConcentration";
  T1.sbmlName="TIM Protein (mono-phosphorylated)";
  T1.sbmlCompartment="Cell";
  T1.init.sbmlRole="speciesInitialConcentration";
  P2.amt.sbmlRole="speciesAmount";
  P2.sbmlRole="speciesConcentration";
  P2.sbmlName="PER Protein (bi-phosphorylated)";
  P2.sbmlCompartment="Cell";
  P2.init.sbmlRole="speciesInitialConcentration";
  T2.amt.sbmlRole="speciesAmount";
  T2.sbmlRole="speciesConcentration";
  T2.sbmlName="TIM Protein (bi-phosphorylated) ";
  T2.sbmlCompartment="Cell";
  T2.init.sbmlRole="speciesInitialConcentration";
  CC.amt.sbmlRole="speciesAmount";
  CC.sbmlRole="speciesConcentration";
  CC.sbmlName="Cytosolic PER-TIM Complex";
  CC.sbmlCompartment="Cell";
  CC.init.sbmlRole="speciesInitialConcentration";
  Cn.amt.sbmlRole="speciesAmount";
  Cn.sbmlRole="speciesConcentration";
  Cn.sbmlName="Nuclear PER-TIM Complex";
  Cn.sbmlCompartment="compartment_0000002";
  Cn.init.sbmlRole="speciesInitialConcentration";
  Mp.amt.sbmlRole="speciesAmount";
  Mp.sbmlRole="speciesConcentration";
  Mp.sbmlName="PER mRNA";
  Mp.sbmlCompartment="Cell";
  Mp.init.sbmlRole="speciesInitialConcentration";
  Mt.amt.sbmlRole="speciesAmount";
  Mt.sbmlRole="speciesConcentration";
  Mt.sbmlName="TIM mRNA";
  Mt.sbmlCompartment="Cell";
  Mt.init.sbmlRole="speciesInitialConcentration";
  P0_to_P1.rate.sbmlRole="rate";
  K1_P.sbmlRole="parameter";
  V_1P.sbmlRole="parameter";
  T0_to_T1.rate.sbmlRole="rate";
  K_1T.sbmlRole="parameter";
  V_1T.sbmlRole="parameter";
  P1_to_P0.rate.sbmlRole="rate";
  K_2P.sbmlRole="parameter";
  V_2P.sbmlRole="parameter";
  T1_to_T0.rate.sbmlRole="rate";
  K_2T.sbmlRole="parameter";
  V_2T.sbmlRole="parameter";
  P1_to_P2.rate.sbmlRole="rate";
  K_3P.sbmlRole="parameter";
  V_3P.sbmlRole="parameter";
  T1_to_T2.rate.sbmlRole="rate";
  K_3T.sbmlRole="parameter";
  V_3T.sbmlRole="parameter";
  P2_to_P1.rate.sbmlRole="rate";
  K_4P.sbmlRole="parameter";
  V_4P.sbmlRole="parameter";
  T2_to_T1.rate.sbmlRole="rate";
  K_4T.sbmlRole="parameter";
  V_4T.sbmlRole="parameter";
  P0_degradation.rate.sbmlRole="rate";
  k_d.sbmlRole="parameter";
  T0_degradation.rate.sbmlRole="rate";
  P1_degradation.rate.sbmlRole="rate";
  T1_degradation.rate.sbmlRole="rate";
  P2_degradation.rate.sbmlRole="rate";
  V_dP.sbmlRole="parameter";
  K_dP.sbmlRole="parameter";
  T2_degradation.rate.sbmlRole="rate";
  K_dT.sbmlRole="parameter";
  PT_complex_formation.rate.sbmlRole="rate";
  k3.sbmlRole="parameter";
  k4.sbmlRole="parameter";
  PT_complex_nucleation.rate.sbmlRole="rate";
  k1.sbmlRole="parameter";
  k2.sbmlRole="parameter";
  PT_complex_degradation.rate.sbmlRole="rate";
  k_dC.sbmlRole="parameter";
  PTnucl_complex_degradation.rate.sbmlRole="rate";
  k_dN.sbmlRole="parameter";
  Mp_production.rate.sbmlRole="rate";
  v_sP.sbmlRole="parameter";
  K_IP.sbmlRole="parameter";
  n.sbmlRole="parameter";
  Mt_production.rate.sbmlRole="rate";
  V_sT.sbmlRole="parameter";
  K_IT.sbmlRole="parameter";
  P0_production.rate.sbmlRole="rate";
  k_sP.sbmlRole="parameter";
  T0_production.rate.sbmlRole="rate";
  k_sT.sbmlRole="parameter";
  Mp_degradation.rate.sbmlRole="rate";
  V_mP.sbmlRole="parameter";
  K_mP.sbmlRole="parameter";
  Mt_degradation.rate.sbmlRole="rate";
  K_mT.sbmlRole="parameter";
}