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

  // Compartments and Species:
  compartment cell, mitochondrion;
  species L in cell, R in cell, flip in cell, pC8 in cell, C8 in cell, C6 in cell;
  species BAR in cell, pC3 in cell, C3 in cell, Bid in cell, tBid in cell;
  species pC6 in cell, XIAP in cell, C3_Ub in cell, PARP in cell, CPARP in cell;
  species Smac in cell, Bcl2c in cell, Bax in cell, Bax_hash in cell, Bcl2 in mitochondrion;
  species L_R in cell, R_hash in cell, flip_R_hash in cell, R_hash_pC8 in cell;
  species C6_pC8 in cell, BAR_C8 in cell, C8_pC3 in cell, pC3_Apop in cell;
  species Apop in cell, C8_Bid in cell, C3_pC6 in cell, XIAP_C3 in cell, PARP_C3 in cell;
  species Apop_XIAP in cell, Smac_XIAP in cell, Bcl2c_tBid in cell, Bax_tBid in cell;
  species Baxm_Bcl2 in mitochondrion, Bax4 in mitochondrion, Bax2_Bcl2 in mitochondrion;
  species Bax4_Bcl2 in mitochondrion, M in mitochondrion, Bax4_M in mitochondrion;
  species M_hash in mitochondrion, Smacm in mitochondrion, M_hash_Smacm in mitochondrion;
  species Smacr in mitochondrion, CytoCm in mitochondrion, M_hash_CytoCm in mitochondrion;
  species CytoCr in mitochondrion, CytoC in cell, Apaf in cell, CytoC_Apaf in cell;
  species Apaf_hash in cell, pC9 in cell, Baxm in mitochondrion, Bax2 in mitochondrion;

  // Assignment Rules:
  pC3_frac := (pC3 + C8_pC3 + pC3_Apop)/C3_tot;
  C3_tot := pC3 + C8_pC3 + pC3_Apop + C3 + C3_pC6 + XIAP_C3 + PARP_C3 + C3_Ub;
  C3_frac := (C3 + C3_pC6 + XIAP_C3 + PARP_C3)/C3_tot;
  C3_UB_frac := C3_Ub/C3_tot;
  cPARP_frac := CPARP/(CPARP + PARP + PARP_C3);
  fC3_fract := C3/C3_tot;

  // Reactions:
  re1: L + R -> L_R; cell*(L*R*k1 - L_R*k_1);
  re2: L_R => R_hash; cell*L_R*kc1;
  re3: R_hash + flip -> flip_R_hash; cell*(R_hash*flip*k2 - flip_R_hash*k_2);
  re4: R_hash + pC8 -> R_hash_pC8; cell*(R_hash*pC8*k3 - R_hash_pC8*k_3);
  re5: R_hash_pC8 => C8 + R_hash; cell*R_hash_pC8*kc3;
  re6: C6 + pC8 -> C6_pC8; cell*(C6*pC8*k7 - C6_pC8*k_7);
  re7: C6_pC8 => C8 + C6; cell*C6_pC8*kc7;
  re8: C8 + BAR -> BAR_C8; cell*(C8*BAR*k4 - BAR_C8*k_4);
  re9: pC3 + C8 -> C8_pC3; cell*(pC3*C8*k5 - C8_pC3*k_5);
  re10: C8_pC3 => C8 + C3; cell*C8_pC3*kc5;
  re11: C8 + Bid -> C8_Bid; cell*(C8*Bid*k10 - C8_Bid*k_10);
  re12: C8_Bid => tBid + C8; cell*C8_Bid*kc10;
  re13: pC3 + Apop -> pC3_Apop; cell*(pC3*Apop*k25 - pC3_Apop*k_25);
  re14: pC3_Apop => C3 + Apop; cell*pC3_Apop*kc25;
  re15: C3 + pC6 -> C3_pC6; cell*(C3*pC6*k6 - C3_pC6*k_6);
  re16: C3_pC6 => C3 + C6; cell*C3_pC6*kc6;
  re17: C3 + XIAP -> XIAP_C3; cell*(C3*XIAP*k8 - XIAP_C3*k_8);
  re18: XIAP_C3 => C3_Ub + XIAP; cell*XIAP_C3*kc8;
  re19: PARP + C3 -> PARP_C3; cell*(PARP*C3*k9 - PARP_C3*k_9);
  re20: PARP_C3 => CPARP + C3; cell*PARP_C3*kc9;
  re21: XIAP + Apop -> Apop_XIAP; cell*(XIAP*Apop*k27 - Apop_XIAP*k_27);
  re22: XIAP + Smac -> Smac_XIAP; cell*(XIAP*Smac*k28 - Smac_XIAP*k_28);
  re23: tBid + Bcl2c -> Bcl2c_tBid; cell*(tBid*Bcl2c*k11 - Bcl2c_tBid*k_11);
  re24: tBid + Bax -> Bax_tBid; cell*(tBid*Bax*k12 - Bax_tBid*k_12);
  re25: Bax_tBid => tBid + Bax_hash; cell*Bax_tBid*kc12;
  re26: Bax_hash -> Baxm; cell*(Bax_hash*k13 - Baxm*k_13);
  re27: Baxm + Bcl2 -> Baxm_Bcl2; mitochondrion*((Baxm*Bcl2*k14)/v - Baxm_Bcl2*k_14);
  re29: Baxm + Baxm -> Bax2; mitochondrion*((Baxm*Baxm*k15)/v - Bax2*k_15);
  re30: Bax2 + Bax2 -> Bax4; mitochondrion*((Bax2*Bax2*k17)/v - Bax4*k_17);
  re31: Bcl2 + Bax2 -> Bax2_Bcl2; mitochondrion*((Bcl2*Bax2*k16)/v - Bax2_Bcl2*k_16);
  re32: Bcl2 + Bax4 -> Bax4_Bcl2; mitochondrion*((Bcl2*Bax4*k18)/v - Bax4_Bcl2*k_18);
  re33: Bax4 + M -> Bax4_M; mitochondrion*((Bax4*M*k19)/v - Bax4_M*k_19);
  re34: Bax4_M => M_hash; mitochondrion*Bax4_M*kc19;
  re35: M_hash + Smacm -> M_hash_Smacm; mitochondrion*((M_hash*Smacm*k21)/v - M_hash_Smacm*k_21);
  re36: M_hash_Smacm => M_hash + Smacr; mitochondrion*M_hash_Smacm*kc21;
  re37: Smacr -> Smac; cell*(Smacr*k26 - Smac*k_26);
  re38: M_hash + CytoCm -> M_hash_CytoCm; mitochondrion*((M_hash*CytoCm*k20)/v - M_hash_CytoCm*k_20);
  re39: M_hash_CytoCm => CytoCr + M_hash; mitochondrion*M_hash_CytoCm*kc20;
  re40: CytoCr -> CytoC; cell*(CytoCr*k22 - CytoC*k_22);
  re41: CytoC + Apaf -> CytoC_Apaf; cell*(CytoC*Apaf*k23 - CytoC_Apaf*k_23);
  re42: CytoC_Apaf => CytoC + Apaf_hash; cell*CytoC_Apaf*kc23;
  re43: Apaf_hash + pC9 -> Apop; cell*(Apaf_hash*pC9*k24 - Apop*k_24);

  // Species initializations:
  L = 3000/cell;
  R = 200/cell;
  flip = 100/cell;
  pC8 = 20000/cell;
  C8 = 0;
  C6 = 0;
  BAR = 1000/cell;
  pC3 = 10000/cell;
  C3 = 0;
  Bid = 40000/cell;
  tBid = 0;
  pC6 = 10000/cell;
  XIAP = 100000/cell;
  C3_Ub = 0;
  PARP = 1000000/cell;
  CPARP = 0;
  Smac = 0;
  Bcl2c = 20000/cell;
  Bax = 100000/cell;
  Bax_hash = 0;
  Bcl2 = 20000/mitochondrion;
  L_R = 0;
  R_hash = 0;
  flip_R_hash = 0;
  R_hash_pC8 = 0;
  C6_pC8 = 0;
  BAR_C8 = 0;
  C8_pC3 = 0;
  pC3_Apop = 0;
  Apop = 0;
  C8_Bid = 0;
  C3_pC6 = 0;
  XIAP_C3 = 0;
  PARP_C3 = 0;
  Apop_XIAP = 0;
  Smac_XIAP = 0;
  Bcl2c_tBid = 0;
  Bax_tBid = 0;
  Baxm_Bcl2 = 0;
  Bax4 = 0;
  Bax2_Bcl2 = 0;
  Bax4_Bcl2 = 0;
  M = 500000/mitochondrion;
  Bax4_M = 0;
  M_hash = 0;
  Smacm = 100000/mitochondrion;
  M_hash_Smacm = 0;
  Smacr = 0;
  CytoCm = 500000/mitochondrion;
  M_hash_CytoCm = 0;
  CytoCr = 0;
  CytoC = 0;
  Apaf = 100000/cell;
  CytoC_Apaf = 0;
  Apaf_hash = 0;
  pC9 = 100000/cell;
  Baxm = 0;
  Bax2 = 0;

  // Compartment initializations:
  cell = 1;
  mitochondrion = 1;

  // Variable initializations:
  k1 = 4e-007;
  k_1 = 0.001;
  kc1 = 1e-005;
  k2 = 1e-006;
  k_2 = 0.001;
  k3 = 1e-006;
  k_3 = 0.001;
  kc3 = 1;
  k4 = 1e-006;
  k_4 = 0.001;
  k5 = 1e-007;
  k_5 = 0.001;
  kc5 = 1;
  k6 = 1e-006;
  k_6 = 0.001;
  kc6 = 1;
  k7 = 3e-008;
  k_7 = 0.001;
  k8 = 2e-006;
  k_8 = 0.001;
  kc8 = 0.1;
  k9 = 1e-006;
  k_9 = 0.01;
  kc9 = 1;
  k10 = 1e-007;
  k_10 = 0.001;
  kc10 = 1;
  k11 = 1e-006;
  k_11 = 0.001;
  k12 = 1e-007;
  k_12 = 0.001;
  kc12 = 1;
  k13 = 0.01;
  k_13 = 0.01;
  k14 = 1e-006;
  k_14 = 0.001;
  k15 = 1e-006;
  k_15 = 0.001;
  k16 = 1e-006;
  k_16 = 0.001;
  k17 = 1e-006;
  k_17 = 0.001;
  k18 = 1e-006;
  k_18 = 0.001;
  k19 = 1e-006;
  k_19 = 0.001;
  kc19 = 1;
  k20 = 2e-006;
  k_20 = 0.001;
  kc20 = 10;
  k21 = 2e-006;
  k_21 = 0.001;
  kc21 = 10;
  k22 = 0.01;
  k_22 = 0.01;
  k23 = 5e-007;
  k_23 = 0.001;
  kc23 = 1;
  k24 = 5e-008;
  k_24 = 0.001;
  k25 = 5e-009;
  k_25 = 0.001;
  kc25 = 1;
  k26 = 0.01;
  k_26 = 0.01;
  k27 = 2e-006;
  k_27 = 0.001;
  k28 = 7e-006;
  k_28 = 0.001;
  kc7 = 1;
  v = 0.07;

  // Other declarations:
  var pC3_frac, C3_tot, C3_frac, C3_UB_frac, cPARP_frac, fC3_fract;
  const cell, mitochondrion, k1, k_1, kc1, k2, k_2, k3, k_3, kc3, k4, k_4;
  const k5, k_5, kc5, k6, k_6, kc6, k7, k_7, k8, k_8, kc8, k9, k_9, kc9, k10;
  const k_10, kc10, k11, k_11, k12, k_12, kc12, k13, k_13, k14, k_14, k15;
  const k_15, k16, k_16, k17, k_17, k18, k_18, k19, k_19, kc19, k20, k_20;
  const kc20, k21, k_21, kc21, k22, k_22, k23, k_23, kc23, k24, k_24, k25;
  const k_25, kc25, k26, k_26, k27, k_27, k28, k_28, kc7, v;

  // Display Names:
  pC8 is "proC8";
  C8 is "casp8";
  C6 is "casp6";
  pC3 is "proC3";
  C3 is "casp3";
  pC6 is "proC6";
  C3_Ub is "Ub C3";
  CPARP is "cPARP";
  Bcl2c is "cytosolic Bcl-2";
  Bax_hash is "Bax#";
  Bcl2 is "Bcl-2";
  L_R is "L:R";
  R_hash is "R#";
  flip_R_hash is "flip:R#";
  R_hash_pC8 is "R#:pC8";
  C6_pC8 is "C6:pC8";
  BAR_C8 is "BAR:C8";
  C8_pC3 is "C8:pC3";
  pC3_Apop is "pC3:Apop";
  C8_Bid is "C8:Bid";
  C3_pC6 is "C3:pC6";
  XIAP_C3 is "XIAP:C3";
  PARP_C3 is "PARP:C3";
  Apop_XIAP is "Apop:XIAP";
  Smac_XIAP is "Smac:XIAP";
  Bcl2c_tBid is "Bcl2c:tBid";
  Bax_tBid is "Bax:tBid";
  Baxm_Bcl2 is "Baxm:Bcl2";
  Bax2_Bcl2 is "Bax2:Bcl2";
  Bax4_Bcl2 is "Bax4:Bcl2";
  Bax4_M is "Bax4:M";
  M_hash is "M#";
  Smacm is "Smac_m";
  M_hash_Smacm is "M#:Smac_m";
  Smacr is "Smac released";
  CytoCm is "CytoC_m";
  M_hash_CytoCm is "M#:CytoC_m";
  CytoCr is "CytoC released";
  CytoC_Apaf is "CytoC:Apaf";
  Apaf_hash is "Apaf#";
  pC9 is "proC9";
  pC3_frac is "pC3 fraction";
  C3_tot is "total Caspase 3";
  C3_frac is "C3 fraction";
  C3_UB_frac is "degraded C3 fraction";
  cPARP_frac is "cPARP fraction";
  fC3_fract is "free C3 fraction";
end