// Created by libAntimony v2.8.0
model *Passos2010_DNAdamage_CellularSenescence()

  // Compartments and Species:
  compartment cell;
  substanceOnly species Mdm2 in cell, p53 in cell, Mdm2_p53 in cell, Mdm2_mRNA in cell;
  substanceOnly species p53_mRNA in cell, ATMA in cell, ATMI in cell, p21 in cell;
  substanceOnly species p21_mRNA in cell, p21step1 in cell, p21step2 in cell;
  substanceOnly species p53_P in cell, Mdm2_P in cell, p21_basal in cell;
  substanceOnly species p38 in cell, p38_P in cell, GADD45 in cell, IR in cell;
  substanceOnly species damDNA in cell, ROS in cell, basalROS in cell, $Sink in cell;
  substanceOnly species $Source in cell;

  // Reactions:
  p53mRNASynthesis: $Source => p53_mRNA; ksynp53mRNA*Source;
  p53mRNADegradation: p53_mRNA => $Sink; kdegp53mRNA*p53_mRNA;
  Mdm2Synthesis: Mdm2_mRNA => Mdm2_mRNA + Mdm2; ksynMdm2*Mdm2_mRNA;
  Mdm2mRNASynthesis1: p53 => p53 + Mdm2_mRNA; ksynMdm2mRNA*p53;
  Mdm2mRNASynthesis2: p53_P => p53_P + Mdm2_mRNA; ksynMdm2mRNA*p53_P;
  Mdm2mRNADegradation: Mdm2_mRNA => $Sink; kdegMdm2mRNA*Mdm2_mRNA;
  Mdm2Degradation: Mdm2 => $Sink; kdegMdm2*Mdm2;
  p53Synthesis: p53_mRNA => p53 + p53_mRNA; ksynp53*p53_mRNA;
  p53Degradation: Mdm2_p53 => Mdm2; kdegp53*Mdm2_p53;
  p53Mdm2IndepDegradation1: p53_P => $Sink; kdegp53mdm2ind*p53_P;
  p53Mdm2IndepDegradation2: p53 => $Sink; kdegp53mdm2ind*p53;
  P53_Mdm2Binding: p53 + Mdm2 => Mdm2_p53; kbinMdm2p53*p53*Mdm2;
  P53_Mdm2Release: Mdm2_p53 => p53 + Mdm2; krelMdm2p53*Mdm2_p53;
  DNAdamage: IR => IR + damDNA; kdam*IR;
  DNArepair: damDNA => $Sink; krepair*damDNA;
  ATMactivation: damDNA + ATMI => damDNA + ATMA; kactATM*damDNA*ATMI;
  p53phoshorylation: p53 + ATMA => p53_P + ATMA; kphosp53*p53*ATMA;
  p53dephosorylation: p53_P => p53; kdephosp53*p53_P;
  Mdm2phoshorylation: Mdm2 + ATMA => Mdm2_P + ATMA; kphosMdm2*Mdm2*ATMA;
  Mdm2dephosorylation: Mdm2_P => Mdm2; kdephosMdm2*Mdm2_P;
  Mdm2Pdegradation: Mdm2_P => $Sink; kdegATMMdm2*Mdm2_P;
  ATMInactivation: ATMA => ATMI; kinactATM*ATMA;
  p21mRNASynthesis1: p53 => p53 + p21_mRNA; ksynp21mRNAp53*p53;
  p21mRNASynthesis2: p53_P => p53_P + p21_mRNA; ksynp21mRNAp53P*p53_P;
  p21mRNADegradation: p21_mRNA => $Sink; kdegp21mRNA*p21_mRNA;
  p21Synthesis1: p21_mRNA => p21_mRNA + p21step1; ksynp21step1*p21_mRNA;
  p21Synthesis2: p21step1 => p21step2; ksynp21step2*p21step1;
  p21Synthesis3: p21step2 => p21; ksynp21step3*p21step2;
  p21degradation: p21 => $Sink; kdegp21*p21;
  GADD45activation2: p21 => p21 + GADD45; kGADD45*p21;
  GADD45degradation: GADD45 => $Sink; kdegGADD45*GADD45;
  p38activation: p38 + GADD45 => p38_P + GADD45; kphosp38*p38*GADD45;
  p38inactivation: p38_P => p38; kdephosp38*p38_P;
  ROSgenerationP38: p38_P => p38_P + ROS; kgenROSp38*p38_P*kp38ROS;
  ROSremoval: ROS => $Sink; kremROS*ROS;
  ROSDNAdamage: ROS => ROS + damDNA; kdamROS*ROS;
  basalROSDNAdamage: basalROS => basalROS + damDNA; kdamBasalROS*basalROS;

  // Events:
  stressCell: at time >= 172800: IR = 200;
  stopStress: at time >= 172860: IR = 0;
  stopp38ROS: at time >= 691200: kp38ROS = 0.6;

  // Species initializations:
  Mdm2 = 5/cell;
  p53 = 5/cell;
  Mdm2_p53 = 95/cell;
  Mdm2_mRNA = 10/cell;
  p53_mRNA = 10/cell;
  ATMA = 0;
  ATMI = 200/cell;
  p21 = 0;
  p21_mRNA = 1/cell;
  p21step1 = 0;
  p21step2 = 0;
  p53_P = 0;
  Mdm2_P = 0;
  p21_basal = 7/cell;
  p38 = 100/cell;
  p38_P = 0;
  GADD45 = 0;
  IR = 0;
  damDNA = 0;
  ROS = 0;
  basalROS = 10/cell;
  Sink = 1/cell;
  Source = 1/cell;

  // Compartment initializations:
  cell = 1;

  // Variable initializations:
  kp38ROS = 1;
  ksynMdm2 = 0.000495;
  kdegMdm2 = 0.000433;
  ksynp53 = 0.006;
  kdegp53 = 0.000825;
  kdegp53mdm2ind = 8.25e-007;
  kbinMdm2p53 = 0.001155;
  krelMdm2p53 = 1.155e-006;
  ksynMdm2mRNA = 0.0001;
  kdegMdm2mRNA = 0.0001;
  kactATM = 2e-005;
  kdegATMMdm2 = 0.0004;
  kinactATM = 0.0005;
  kphosp53 = 0.006;
  kdephosp53 = 0.5;
  kphosMdm2 = 2;
  kdephosMdm2 = 0.5;
  kphosp38 = 0.008;
  kdephosp38 = 0.1;
  kdam = 0.007;
  krepair = 6e-005;
  kGADD45 = 4e-006;
  kdegGADD45 = 1e-005;
  ksynp53mRNA = 0.001;
  kdegp53mRNA = 0.0001;
  ksynp21mRNAp53P = 6e-006;
  ksynp21mRNAp53 = 6e-008;
  kdegp21mRNA = 2.4e-005;
  ksynp21step1 = 0.0004;
  ksynp21step2 = 4e-005;
  ksynp21step3 = 4e-005;
  kdegp21 = 0.00019;
  kremROS = 0.000383;
  kgenROSp38 = 0.00045;
  kdamROS = 1e-005;
  kdamBasalROS = 1e-009;

  // Other declarations:
  var kp38ROS;
  const cell, ksynMdm2, kdegMdm2, ksynp53, kdegp53, kdegp53mdm2ind, kbinMdm2p53;
  const krelMdm2p53, ksynMdm2mRNA, kdegMdm2mRNA, kactATM, kdegATMMdm2, kinactATM;
  const kphosp53, kdephosp53, kphosMdm2, kdephosMdm2, kphosp38, kdephosp38;
  const kdam, krepair, kGADD45, kdegGADD45, ksynp53mRNA, kdegp53mRNA, ksynp21mRNAp53P;
  const ksynp21mRNAp53, kdegp21mRNA, ksynp21step1, ksynp21step2, ksynp21step3;
  const kdegp21, kremROS, kgenROSp38, kdamROS, kdamBasalROS;

  // Unit definitions:
  unit substance = item;
end