// Created by libAntimony v2.8.0
model *Tang2010_PolyGlutamate()

  // Compartments and Species:
  compartment cytosol;
  substanceOnly species PolyQ in cytosol, Proteasome in cytosol, NatP in cytosol;
  substanceOnly species MisP in cytosol, MisP_Proteasome in cytosol, AggP1 in cytosol;
  substanceOnly species AggP2 in cytosol, AggP3 in cytosol, AggP4 in cytosol;
  substanceOnly species AggP5 in cytosol, AggPolyQ1 in cytosol, AggPolyQ2 in cytosol;
  substanceOnly species AggPolyQ3 in cytosol, AggPolyQ4 in cytosol, AggPolyQ5 in cytosol;
  substanceOnly species SeqAggP in cytosol, AggP_Proteasome in cytosol, mRFPu in cytosol;
  substanceOnly species mRFPu_Proteasome in cytosol, PolyQ_Proteasome in cytosol;
  substanceOnly species ROS in cytosol, p38_P in cytosol, p38 in cytosol;
  substanceOnly species $Source in cytosol, $Sink in cytosol, p38death in cytosol;
  substanceOnly species PIdeath in cytosol;

  // Assignment Rules:
  oligomers := AggPolyQ1 + AggPolyQ2 + AggPolyQ3 + AggPolyQ4 + AggPolyQ5;

  // Reactions:
  polyQSynthesis: $Source => PolyQ; ksynPolyQ*Source*kalive;
  polyqProteasomeBinding: PolyQ + Proteasome => PolyQ_Proteasome; kbinPolyQ*PolyQ*Proteasome*kalive;
  polyqProteasomeRelease: PolyQ_Proteasome => PolyQ + Proteasome; krelPolyQ*PolyQ_Proteasome*kalive;
  PolyQDegradation: PolyQ_Proteasome => Proteasome; kdegPolyQ*PolyQ_Proteasome*kalive*kproteff;
  mRFPuSynthesis: $Source => mRFPu; ksynmRFPu*Source*kalive;
  mRFPuProteasomeBinding: mRFPu + Proteasome => mRFPu_Proteasome; kbinmRFPu*mRFPu*Proteasome*kalive;
  mRFPuProteasomeRelease: mRFPu_Proteasome => mRFPu + Proteasome; krelmRFPu*mRFPu_Proteasome*kalive;
  mRFPuDegradation: mRFPu_Proteasome => Proteasome; kdegmRFPu*mRFPu_Proteasome*kalive*kproteff;
  PolyQAggregation1: 2PolyQ + ROS => AggPolyQ1 + ROS; kaggPolyQ*PolyQ*(PolyQ - 1)*0.5*(ROS^2/(10^2 + ROS^2))*kalive;
  PolyQAggregation2: PolyQ + AggPolyQ1 + ROS => AggPolyQ2 + ROS; kaggPolyQ*PolyQ*AggPolyQ1*(ROS^2/(10^2 + ROS^2))*kalive;
  PolyQAggregation3: PolyQ + AggPolyQ2 + ROS => AggPolyQ3 + ROS; kaggPolyQ*PolyQ*AggPolyQ2*(ROS^2/(10^2 + ROS^2))*kalive;
  PolyQAggregation4: PolyQ + AggPolyQ3 + ROS => AggPolyQ4 + ROS; kaggPolyQ*PolyQ*AggPolyQ3*(ROS^2/(10^2 + ROS^2))*kalive;
  PolyQAggregation5: PolyQ + AggPolyQ4 + ROS => AggPolyQ5 + ROS; kaggPolyQ*PolyQ*AggPolyQ4*(ROS^2/(10^2 + ROS^2))*kalive;
  PolyQDisaggregation5: AggPolyQ5 => PolyQ + AggPolyQ4; kdisaggPolyQ5*AggPolyQ5*kalive;
  PolyQDisaggregation4: AggPolyQ4 => PolyQ + AggPolyQ3; kdisaggPolyQ4*AggPolyQ4*kalive;
  PolyQDisaggregation3: AggPolyQ3 => PolyQ + AggPolyQ2; kdisaggPolyQ3*AggPolyQ3*kalive;
  PolyQDisaggregation2: AggPolyQ2 => PolyQ + AggPolyQ1; kdisaggPolyQ2*AggPolyQ2*kalive;
  PolyQDisaggregation1: AggPolyQ1 => 2PolyQ; kdisaggPolyQ1*AggPolyQ1*kalive;
  PolyQInclusionFormation: PolyQ + AggPolyQ5 => 7SeqAggP; kaggPolyQ*PolyQ*AggPolyQ5*kalive;
  PolyQInclusionGrowth: PolyQ + SeqAggP => 2SeqAggP; kseqPolyQ*PolyQ*SeqAggP*kalive;
  ProteasomeInhibition1: AggPolyQ1 + Proteasome => AggP_Proteasome; kinhprot*AggPolyQ1*Proteasome*kalive;
  ProteasomeInhibition2: AggPolyQ2 + Proteasome => AggP_Proteasome; kinhprot*AggPolyQ2*Proteasome*kalive;
  ProteasomeInhibition3: AggPolyQ3 + Proteasome => AggP_Proteasome; kinhprot*AggPolyQ3*Proteasome*kalive;
  ProteasomeInhibition4: AggPolyQ4 + Proteasome => AggP_Proteasome; kinhprot*AggPolyQ4*Proteasome*kalive;
  ProteasomeInhibition5: AggPolyQ5 + Proteasome => AggP_Proteasome; kinhprot*AggPolyQ5*Proteasome*kalive;
  mRFPuProteasomeSequestering: mRFPu_Proteasome + SeqAggP => 2SeqAggP; kseqmRFPuProt*mRFPu_Proteasome*SeqAggP*kalive;
  mRFPuSequestering: mRFPu + SeqAggP => 2SeqAggP; kseqmRFPu*mRFPu*SeqAggP*kalive;
  ROSgenerationBasal: $Source => ROS; kgenROS*Source*kalive;
  ROSgenerationSmallAggPolyQ1: AggPolyQ1 => AggPolyQ1 + ROS; kgenROSAggP*AggPolyQ1*kalive;
  ROSgenerationSmallAggPolyQ2: AggPolyQ2 => AggPolyQ2 + ROS; kgenROSAggP*AggPolyQ2*kalive;
  ROSgenerationSmallAggPolyQ3: AggPolyQ3 => AggPolyQ3 + ROS; kgenROSAggP*AggPolyQ3*kalive;
  ROSgenerationSmallAggPolyQ4: AggPolyQ4 => AggPolyQ4 + ROS; kgenROSAggP*AggPolyQ4*kalive;
  ROSgenerationSmallAggPolyQ5: AggPolyQ5 => AggPolyQ5 + ROS; kgenROSAggP*AggPolyQ5*kalive;
  ROSgenerationAggPProteasome: AggP_Proteasome => AggP_Proteasome + ROS; kgenROSAggP*AggP_Proteasome*kalive;
  ROSremoval: ROS => $Sink; kremROS*ROS*kalive;
  p38activation: ROS + p38 => ROS + p38_P; kactp38*ROS*p38*kalive;
  p38inactivation: p38_P => p38; kinactp38*p38_P*kalive;
  AggP_ProteasomeSequestering: AggP_Proteasome + SeqAggP => 2SeqAggP; kseqAggPProt*AggP_Proteasome*SeqAggP*kalive;
  PolyQ_ProteasomeSequestering: PolyQ_Proteasome + SeqAggP => 2SeqAggP; kseqPolyQProt*PolyQ_Proteasome*SeqAggP*kalive;
  MisP_ProteasomeSequestering: MisP_Proteasome + SeqAggP => 2SeqAggP; kseqMisPProt*MisP_Proteasome*SeqAggP*kalive;
  ProteinSynthesis: $Source => NatP; ksynNatP*Source*kalive;
  Misfolding: NatP + ROS => MisP + ROS; kmisfold*NatP*ROS*kalive;
  Refolding: MisP => NatP; krefold*MisP*kalive;
  MisP_ProteasomeBinding: MisP + Proteasome => MisP_Proteasome; kbinMisPProt*MisP*Proteasome*kalive;
  MisP_ProteasomeRelease: MisP_Proteasome => MisP + Proteasome; krelMisPProt*MisP_Proteasome*kalive;
  MisP_Degradation: MisP_Proteasome => Proteasome; kdegMisP*MisP_Proteasome*kalive*kproteff;
  MisP_Aggregation1: 2MisP => AggP1; kaggMisP*MisP*(MisP - 1)*0.5*kalive;
  MisP_Aggregation2: MisP + AggP1 => AggP2; kagg2MisP*MisP*AggP1*kalive;
  MisP_Aggregation3: MisP + AggP2 => AggP3; kagg2MisP*MisP*AggP2*kalive;
  MisP_Aggregation4: MisP + AggP3 => AggP4; kagg2MisP*MisP*AggP3*kalive;
  MisP_Aggregation5: MisP + AggP4 => AggP5; kagg2MisP*MisP*AggP4*kalive;
  MisP_Disaggregation1: AggP1 => 2MisP; kdisaggMisP1*AggP1*kalive;
  MisP_Disaggregation2: AggP2 => MisP + AggP1; kdisaggMisP2*AggP2*kalive;
  MisP_Disaggregation3: AggP3 => MisP + AggP2; kdisaggMisP3*AggP3*kalive;
  MisP_Disaggregation4: AggP4 => MisP + AggP3; kdisaggMisP4*AggP4*kalive;
  MisP_Disaggregation5: AggP5 => MisP + AggP4; kdisaggMisP5*AggP5*kalive;
  MisP_InclusionFormation: MisP + AggP5 => 7SeqAggP; kagg2MisP*MisP*AggP5*kalive;
  MisPInclusionGrowth: MisP + SeqAggP => 2SeqAggP; kseqMisP*MisP*SeqAggP*kalive;
  ProteasomeInhibitionAggP1: AggP1 + Proteasome => AggP_Proteasome; kinhprot*AggP1*Proteasome*kalive;
  ProteasomeInhibitionAggP2: AggP2 + Proteasome => AggP_Proteasome; kinhprot*AggP2*Proteasome*kalive;
  ProteasomeInhibitionAggP3: AggP3 + Proteasome => AggP_Proteasome; kinhprot*AggP3*Proteasome*kalive;
  ProteasomeInhibitionAggP4: AggP4 + Proteasome => AggP_Proteasome; kinhprot*AggP4*Proteasome*kalive;
  ProteasomeInhibitionAggP5: AggP5 + Proteasome => AggP_Proteasome; kinhprot*AggP5*Proteasome*kalive;
  ROSgenerationSmallAggP1: AggP1 => AggP1 + ROS; kgenROSAggP*AggP1*kalive;
  ROSgenerationSmallAggP2: AggP2 => AggP2 + ROS; kgenROSAggP*AggP2*kalive;
  ROSgenerationSmallAggP3: AggP3 => AggP3 + ROS; kgenROSAggP*AggP3*kalive;
  ROSgenerationSmallAggP4: AggP4 => AggP4 + ROS; kgenROSAggP*AggP4*kalive;
  ROSgenerationSmallAggP5: AggP5 => AggP5 + ROS; kgenROSAggP*AggP5*kalive;
  p38_P_ROS_Generation: p38_P => p38_P + ROS; kgenROSp38*p38_P*kp38act*kalive;
  ROSgenerationSeqAggP: SeqAggP => SeqAggP + ROS; kgenROSSeqAggP*SeqAggP*kalive;
  P38DeathPathway: p38_P => p38_P + p38death; kp38death*p38_P*kalive*kp38act;
  PIDeathPathway: AggP_Proteasome => AggP_Proteasome + PIdeath; kPIdeath*AggP_Proteasome*kalive;

  // Events:
  PIcellDeath: at PIdeath > 0: kalive = 0;
  p38cellDeath: at p38death > 0: kalive = 0;

  // Species initializations:
  PolyQ = 1000/cytosol;
  Proteasome = 1000/cytosol;
  NatP = 19500/cytosol;
  MisP = 0;
  MisP_Proteasome = 0;
  AggP1 = 0;
  AggP2 = 0;
  AggP3 = 0;
  AggP4 = 0;
  AggP5 = 0;
  AggPolyQ1 = 0;
  AggPolyQ2 = 0;
  AggPolyQ3 = 0;
  AggPolyQ4 = 0;
  AggPolyQ5 = 0;
  SeqAggP = 0;
  AggP_Proteasome = 0;
  mRFPu = 300/cytosol;
  mRFPu_Proteasome = 0;
  PolyQ_Proteasome = 0;
  ROS = 10/cytosol;
  p38_P = 0;
  p38 = 100/cytosol;
  Source = 1/cytosol;
  Sink = 1/cytosol;
  p38death = 0;
  PIdeath = 0;

  // Compartment initializations:
  cytosol = 1;

  // Variable initializations:
  kalive = 1;
  kaggPolyQ = 5e-008;
  kdisaggPolyQ1 = 5e-007;
  kdisaggPolyQ2 = 4e-007;
  kdisaggPolyQ3 = 3e-007;
  kdisaggPolyQ4 = 2e-007;
  kdisaggPolyQ5 = 1e-007;
  kseqPolyQ = 8e-007;
  kinhprot = 5e-009;
  kaggMisP = 1e-011;
  kagg2MisP = 1e-010;
  kdisaggMisP1 = 5e-007;
  kdisaggMisP2 = 4e-007;
  kdisaggMisP3 = 3e-007;
  kdisaggMisP4 = 2e-007;
  kdisaggMisP5 = 1e-007;
  ksynmRFPu = 0.138;
  kbinmRFPu = 5e-007;
  krelmRFPu = 1e-008;
  kdegmRFPu = 0.005;
  ksynPolyQ = 0.007;
  kbinPolyQ = 5e-008;
  krelPolyQ = 1e-009;
  kdegPolyQ = 0.0025;
  kgenROS = 0.0017;
  kremROS = 0.0002;
  kgenROSAggP = 5e-006;
  kgenROSSeqAggP = 1e-007;
  kactp38 = 5e-006;
  kinactp38 = 0.002;
  kseqMisP = 1e-009;
  kseqAggPProt = 5e-007;
  kseqPolyQProt = 5e-007;
  kseqMisPProt = 5e-007;
  kseqmRFPuProt = 5e-007;
  kseqmRFPu = 1e-010;
  ksynNatP = 2.4;
  kmisfold = 2e-006;
  krefold = 8e-005;
  kbinMisPProt = 5e-008;
  krelMisPProt = 1e-008;
  kdegMisP = 0.01;
  kgenROSp38 = 0.0007;
  kp38act = 1;
  kp38death = 9e-008;
  kPIdeath = 2.5e-008;
  kproteff = 1;

  // Other declarations:
  var kalive, kp38act, kproteff, oligomers;
  const cytosol, kaggPolyQ, kdisaggPolyQ1, kdisaggPolyQ2, kdisaggPolyQ3, kdisaggPolyQ4;
  const kdisaggPolyQ5, kseqPolyQ, kinhprot, kaggMisP, kagg2MisP, kdisaggMisP1;
  const kdisaggMisP2, kdisaggMisP3, kdisaggMisP4, kdisaggMisP5, ksynmRFPu;
  const kbinmRFPu, krelmRFPu, kdegmRFPu, ksynPolyQ, kbinPolyQ, krelPolyQ;
  const kdegPolyQ, kgenROS, kremROS, kgenROSAggP, kgenROSSeqAggP, kactp38;
  const kinactp38, kseqMisP, kseqAggPProt, kseqPolyQProt, kseqMisPProt, kseqmRFPuProt;
  const kseqmRFPu, ksynNatP, kmisfold, krefold, kbinMisPProt, krelMisPProt;
  const kdegMisP, kgenROSp38, kp38death, kPIdeath;

  // Unit definitions:
  unit substance = item;
end