// Created by libAntimony v2.13.0
function function_4_motor_r1(M, MYp, Yp, cell, ka, kappa)
  ka*(M*Yp - (kappa/4)*MYp)/cell;
end

function_4_motor_r1 is "function_4_motor_r1"

function function_4_motor_r2(MYp, MYpYp, Yp, alpha, cell, ka, kappa)
  ka*(MYp*Yp - (2*alpha*kappa/3)*MYpYp)/cell;
end

function_4_motor_r2 is "function_4_motor_r2"

function function_4_motor_r3(MYpYp, MYpYpYp, Yp, alpha, cell, ka, kappa)
  ka*(MYpYp*Yp - (3*alpha*alpha*kappa/2)*MYpYpYp)/cell;
end

function_4_motor_r3 is "function_4_motor_r3"

function function_4_motor_r4(MYpYpYp, MYpYpYpYp, Yp, alpha, cell, ka, kappa)
  ka*(MYpYpYp*Yp - 4*alpha*alpha*alpha*kappa*MYpYpYpYp)/cell;
end

function_4_motor_r4 is "function_4_motor_r4"

function Autophosphorylation(kcat, correction, E)
  kcat*correction*E;
end

Autophosphorylation is "Autophosphorylation"

function ModAutophosphorylation(M, S, kcat, correction)
  M*S*kcat*correction;
end

ModAutophosphorylation is "ModAutophosphorylation"


model *Bray1993_chemotaxis()

  // Compartments and Species:
  compartment cell;
  species $asp in cell, $ni in cell, T in cell, Tasp in cell, Tni in cell;
  species W in cell, TW in cell, Tasp_W in cell, Tni_W in cell, TA in cell;
  species Tasp_A in cell, Tni_A in cell, WA in cell, TWA in cell, Tasp_WA in cell;
  species Tni_WA in cell, A in cell, Ap in cell, B in cell, Bp in cell, Z in cell;
  species Y in cell, Yp in cell, M in cell, MYp in cell, MYpYp in cell, MYpYpYp in cell;
  species MYpYpYpYp in cell, $species_1 in cell;

  // Assignment Rules:
  Bias := (M + MYp)/(M + MYp + MYpYp + MYpYpYp + MYpYpYpYp);
  parameter_2 := species_1/(species_1 + parameter_3);

  // Reactions:
  phosphorylation_r1: A => Ap; cell*Autophosphorylation(phosphorylation_r1_kcat, parameter_2, A);
  phosphorylation_r2: A => Ap; cell*ModAutophosphorylation(TWA, A, phosphorylation_r2_kcat, parameter_2);
  phosphorylation_r3: A => Ap; cell*ModAutophosphorylation(Tni_WA, A, phosphorylation_r3_kcat, parameter_2);
  phosphorylation_r4: Tasp_WA + Yp => Tasp_WA + Y; cell*phosphorylation_r4_k1*Tasp_WA*Yp;
  phosphorylation_r5: Ap + Y => A + Yp; cell*phosphorylation_r5_k1*Ap*Y;
  phosphorylation_r6: Y => Yp; cell*Autophosphorylation(phosphorylation_r6_kcat, parameter_2, Y);
  phosphorylation_r7: Yp => Y; cell*phosphorylation_r7_k1*Yp;
  phosphorylation_r8: Yp + Z => Y + Z; cell*phosphorylation_r8_k1*Yp*Z;
  phosphorylation_r9: Ap + B => A + Bp; cell*phosphorylation_r9_k1*Ap*B;
  phosphorylation_r10: Bp => B; cell*phosphorylation_r10_k1*Bp;
  regulatory_r1: T + $asp -> Tasp; cell*(regulatory_r1_k1*T*asp - regulatory_r1_k2*Tasp);
  regulatory_r2: T + $ni -> Tni; cell*(regulatory_r2_k1*T*ni - regulatory_r2_k2*Tni);
  regulatory_r3: T + W -> TW; cell*(regulatory_r3_k1*T*W - regulatory_r3_k2*TW);
  regulatory_r4: T + A -> TA; cell*(regulatory_r4_k1*T*A - regulatory_r4_k2*TA);
  regulatory_r5: W + A -> WA; cell*(regulatory_r5_k1*W*A - regulatory_r5_k2*WA);
  regulatory_r6: TW + A -> TWA; cell*(regulatory_r6_k1*TW*A - regulatory_r6_k2*TWA);
  regulatory_r7: TA + W -> TWA; cell*(regulatory_r7_k1*TA*W - regulatory_r7_k2*TWA);
  regulatory_r8: T + WA -> TWA; cell*(regulatory_r8_k1*T*WA - regulatory_r8_k2*TWA);
  regulatory_r9: Tasp + W -> Tasp_W; cell*(regulatory_r9_k1*Tasp*W - regulatory_r9_k2*Tasp_W);
  regulatory_r10: Tasp + A -> Tasp_A; cell*(regulatory_r10_k1*Tasp*A - regulatory_r10_k2*Tasp_A);
  regulatory_r11: Tasp_W + A -> Tasp_WA; cell*(regulatory_r11_k1*Tasp_W*A - regulatory_r11_k2*Tasp_WA);
  regulatory_r12: Tasp_A + W -> Tasp_WA; cell*(regulatory_r12_k1*Tasp_A*W - regulatory_r12_k2*Tasp_WA);
  regulatory_r13: Tasp + WA -> Tasp_WA; cell*(regulatory_r13_k1*Tasp*WA - regulatory_r13_k2*Tasp_WA);
  regulatory_r14: Tni + W -> Tni_W; cell*(regulatory_r14_k1*Tni*W - regulatory_r14_k2*Tni_W);
  regulatory_r15: Tni + A -> Tni_A; cell*(regulatory_r15_k1*Tni*A - regulatory_r15_k2*Tni_A);
  regulatory_r16: Tni_W + A -> Tni_WA; cell*(regulatory_r16_k1*Tni_W*A - regulatory_r16_k2*Tni_WA);
  regulatory_r17: Tni_A + W -> Tni_WA; cell*(regulatory_r17_k1*Tni_A*W - regulatory_r17_k2*Tni_WA);
  regulatory_r18: Tni + WA -> Tni_WA; cell*(regulatory_r18_k1*Tni*WA - regulatory_r18_k2*Tni_WA);
  motor_r1: M + Yp -> MYp; cell*function_4_motor_r1(M, MYp, Yp, cell, ka, kappa);
  motor_r2: MYp + Yp -> MYpYp; cell*function_4_motor_r2(MYp, MYpYp, Yp, alpha, cell, ka, kappa);
  motor_r3: MYpYp + Yp -> MYpYpYp; cell*function_4_motor_r3(MYpYp, MYpYpYp, Yp, alpha, cell, ka, kappa);
  motor_r4: MYpYpYp + Yp -> MYpYpYpYp; cell*function_4_motor_r4(MYpYpYp, MYpYpYpYp, Yp, alpha, cell, ka, kappa);
  reaction_1: TA + $asp -> Tasp_A; cell*(reaction_1_k1*TA*asp - reaction_1_k2*Tasp_A);
  reaction_2: TW + $asp -> Tasp_W; cell*(reaction_2_k1*TW*asp - reaction_2_k2*Tasp_W);
  reaction_3: TWA + $asp -> Tasp_WA; cell*(reaction_3_k1*TWA*asp - reaction_3_k2*Tasp_WA);

  // Events:
  event_1: at time >= 5: asp = parameter_1;
  event_2: at time >= 10: asp = 0;

  // Species initializations:
  asp = 0;
  ni = 0;
  T = 3.12e-06;
  Tasp = 0;
  Tni = 0;
  W = 2.89e-06;
  TW = 5.91e-07;
  Tasp_W = 0;
  Tni_W = 0;
  TA = 4.44e-07;
  Tasp_A = 0;
  Tni_A = 0;
  WA = 6.78e-07;
  TWA = 8.47e-07;
  Tasp_WA = 0;
  Tni_WA = 0;
  A = 3e-06;
  Ap = 3.48e-08;
  B = 1.93e-06;
  Bp = 6.87e-08;
  Z = 2e-05;
  Y = 9.9e-06;
  Yp = 7e-09;
  M = 6.24e-09;
  MYp = 7.77e-10;
  MYpYp = 2.99e-10;
  MYpYpYp = 3.78e-10;
  MYpYpYpYp = 2.31e-09;
  species_1 = 0.1;

  // Compartment initializations:
  cell = 1.41e-15;

  // Variable initializations:
  parameter_1 = 1e-07;
  alpha = 0.14;
  kappa = 2.25e-07;
  ka = 0.1;
  parameter_3 = 0.0003;
  phosphorylation_r1_kcat = 0.001;
  phosphorylation_r2_kcat = 75000;
  phosphorylation_r3_kcat = 200000;
  phosphorylation_r4_k1 = 100000000;
  phosphorylation_r5_k1 = 200000;
  phosphorylation_r6_kcat = 0;
  phosphorylation_r7_k1 = 0.037;
  phosphorylation_r8_k1 = 500000;
  phosphorylation_r9_k1 = 1000000;
  phosphorylation_r10_k1 = 1;
  regulatory_r1_k1 = 1000000;
  regulatory_r1_k2 = 1;
  regulatory_r2_k1 = 1000;
  regulatory_r2_k2 = 1;
  regulatory_r3_k1 = 100000;
  regulatory_r3_k2 = 1;
  regulatory_r4_k1 = 10000;
  regulatory_r4_k2 = 1;
  regulatory_r5_k1 = 100000;
  regulatory_r5_k2 = 1;
  regulatory_r6_k1 = 400000;
  regulatory_r6_k2 = 1;
  regulatory_r7_k1 = 400000;
  regulatory_r7_k2 = 1;
  regulatory_r8_k1 = 400000;
  regulatory_r8_k2 = 1;
  regulatory_r9_k1 = 100000;
  regulatory_r9_k2 = 1;
  regulatory_r10_k1 = 10000;
  regulatory_r10_k2 = 1;
  regulatory_r11_k1 = 400000;
  regulatory_r11_k2 = 1;
  regulatory_r12_k1 = 400000;
  regulatory_r12_k2 = 1;
  regulatory_r13_k1 = 400000;
  regulatory_r13_k2 = 1;
  regulatory_r14_k1 = 0.1;
  regulatory_r14_k2 = 1;
  regulatory_r15_k1 = 0.01;
  regulatory_r15_k2 = 1;
  regulatory_r16_k1 = 0.4;
  regulatory_r16_k2 = 1;
  regulatory_r17_k1 = 0.4;
  regulatory_r17_k2 = 1;
  regulatory_r18_k1 = 0.4;
  regulatory_r18_k2 = 1;
  reaction_1_k1 = 1000000;
  reaction_1_k2 = 1;
  reaction_2_k1 = 1000000;
  reaction_2_k2 = 1;
  reaction_3_k1 = 1000000;
  reaction_3_k2 = 1;

  // Other declarations:
  var Bias, parameter_2;
  const cell, parameter_1, alpha, kappa, ka, parameter_3;

  // Display Names:
  species_1 is "ATP";
  event_1 is "Add ASP";
  parameter_1 is "asp_pulse";
  event_2 is "Remove ASP";
  parameter_2 is "autoPhospho";
  parameter_3 is "KmATP";
  phosphorylation_r1 is "A->Ap";
  phosphorylation_r2 is "TWA+A->TWA+Ap";
  phosphorylation_r3 is "Tni_WA+A->Tni_WA+Ap";
  phosphorylation_r4 is "Tasp_WA+Yp->Tasp_WA+Y";
  phosphorylation_r5 is "Ap+Y->A+Yp";
  phosphorylation_r6 is "Y ->Yp";
  phosphorylation_r7 is "Yp->Y";
  phosphorylation_r8 is "Yp+Z->Y+Z";
  phosphorylation_r9 is "Ap+B->A+Bp";
  phosphorylation_r10 is "Bp->B";
  regulatory_r1 is "T+asp<->Tasp";
  regulatory_r2 is "T+ni<->Tni";
  regulatory_r3 is "T+W<->TW";
  regulatory_r4 is "T+A<->TA";
  regulatory_r5 is "W+A<->WA";
  regulatory_r6 is "TW+A<->TWA";
  regulatory_r7 is "TA+W<->TWA";
  regulatory_r8 is "T+WA<->TWA";
  regulatory_r9 is "Tasp+W<->Tasp_W";
  regulatory_r10 is "Tasp+A<->Tasp_A";
  regulatory_r11 is "Tasp_W+A<->Tasp_WA";
  regulatory_r12 is "Tasp_A+W<->Tasp_WA";
  regulatory_r13 is "Tasp+WA<->Tasp_WA";
  regulatory_r14 is "Tni+W<->Tni_W";
  regulatory_r15 is "Tni+A<->Tni_A";
  regulatory_r16 is "Tni_W+A<->Tni_WA";
  regulatory_r17 is "Tni_A+W<->Tni_WA";
  regulatory_r18 is "Tni+WA<->Tni_WA";
  motor_r1 is "M+Yp<->MYp";
  motor_r2 is "MYp+Yp<->MYpYp";
  motor_r3 is "MYpYp+Yp<->MYpYpYp";
  motor_r4 is "MYpYpYp+Yp<->MYpYpYpYp";
  reaction_1 is "TA + asp <-> Tasp_A";
  reaction_2 is "TW+asp <-> Tasp_W";
  reaction_3 is "TWA+asp <-> Tasp_WA";

  // SBO terms:
  cell.sboTerm = 290
  asp.sboTerm = 247
  ni.sboTerm = 247
  T.sboTerm = 245
  Tasp.sboTerm = 253
  Tni.sboTerm = 253
  W.sboTerm = 245
  TW.sboTerm = 253
  Tasp_W.sboTerm = 253
  Tni_W.sboTerm = 253
  TA.sboTerm = 253
  Tasp_A.sboTerm = 253
  Tni_A.sboTerm = 253
  WA.sboTerm = 253
  TWA.sboTerm = 253
  Tasp_WA.sboTerm = 253
  Tni_WA.sboTerm = 253
  A.sboTerm = 245
  Ap.sboTerm = 245
  B.sboTerm = 245
  Z.sboTerm = 245
  Y.sboTerm = 245
  M.sboTerm = 245
  MYp.sboTerm = 253
  MYpYp.sboTerm = 253
  MYpYpYp.sboTerm = 253
  MYpYpYpYp.sboTerm = 253
  species_1.sboTerm = 247
  phosphorylation_r1.sboTerm = 216
  phosphorylation_r2.sboTerm = 216
  phosphorylation_r3.sboTerm = 216
  phosphorylation_r4.sboTerm = 330
  phosphorylation_r5.sboTerm = 216
  phosphorylation_r6.sboTerm = 216
  phosphorylation_r7.sboTerm = 330
  phosphorylation_r8.sboTerm = 330
  phosphorylation_r9.sboTerm = 402
  phosphorylation_r10.sboTerm = 330
  regulatory_r1.sboTerm = 177
  regulatory_r2.sboTerm = 177
  regulatory_r3.sboTerm = 177
  regulatory_r4.sboTerm = 177
  regulatory_r5.sboTerm = 177
  regulatory_r6.sboTerm = 177
  regulatory_r7.sboTerm = 177
  regulatory_r8.sboTerm = 177
  regulatory_r9.sboTerm = 177
  regulatory_r10.sboTerm = 177
  regulatory_r11.sboTerm = 177
  regulatory_r12.sboTerm = 177
  regulatory_r13.sboTerm = 177
  regulatory_r14.sboTerm = 177
  regulatory_r15.sboTerm = 177
  regulatory_r16.sboTerm = 177
  regulatory_r17.sboTerm = 177
  regulatory_r18.sboTerm = 177
  motor_r1.sboTerm = 177
  motor_r2.sboTerm = 177
  motor_r3.sboTerm = 177
  motor_r4.sboTerm = 177
  reaction_1.sboTerm = 177
  reaction_2.sboTerm = 177
  reaction_3.sboTerm = 177

  // CV terms:
  cell hypernym "http://identifiers.org/obo.go/GO:0005623"
  asp identity "http://identifiers.org/obo.chebi/CHEBI:35391"
  ni identity "http://identifiers.org/obo.chebi/CHEBI:49786"
  T identity "http://identifiers.org/uniprot/P07017"
  Tasp part "http://identifiers.org/obo.chebi/CHEBI:35391",
            "http://identifiers.org/uniprot/P07017"
  Tni part "http://identifiers.org/obo.chebi/CHEBI:49786",
           "http://identifiers.org/uniprot/P07017"
  W identity "http://identifiers.org/uniprot/P0A964"
  TW part "http://identifiers.org/uniprot/P0A964",
          "http://identifiers.org/uniprot/P07017"
  Tasp_W part "http://identifiers.org/obo.chebi/CHEBI:35391",
              "http://identifiers.org/uniprot/P07017",
              "http://identifiers.org/uniprot/P0A964"
  Tni_W part "http://identifiers.org/obo.chebi/CHEBI:49786",
             "http://identifiers.org/uniprot/P07017",
             "http://identifiers.org/uniprot/P0A964"
  TA part "http://identifiers.org/uniprot/P07017",
          "http://identifiers.org/uniprot/P07363"
  Tasp_A part "http://identifiers.org/obo.chebi/CHEBI:35391",
              "http://identifiers.org/uniprot/P07017",
              "http://identifiers.org/uniprot/P07363"
  Tni_A part "http://identifiers.org/obo.chebi/CHEBI:49786",
             "http://identifiers.org/uniprot/P07017",
             "http://identifiers.org/uniprot/P07363"
  WA part "http://identifiers.org/uniprot/P07363",
          "http://identifiers.org/uniprot/P0A964"
  TWA part "http://identifiers.org/uniprot/P07017",
           "http://identifiers.org/uniprot/P07363",
           "http://identifiers.org/uniprot/P0A964"
  Tasp_WA part "http://identifiers.org/obo.chebi/CHEBI:35391",
               "http://identifiers.org/uniprot/P07017",
               "http://identifiers.org/uniprot/P07363",
               "http://identifiers.org/uniprot/P0A964"
  Tni_WA part "http://identifiers.org/obo.chebi/CHEBI:49786",
              "http://identifiers.org/uniprot/P07017",
              "http://identifiers.org/uniprot/P07363",
              "http://identifiers.org/uniprot/P0A964"
  A hypernym "http://identifiers.org/uniprot/P07363"
  Ap property "http://identifiers.org/obo.psi-mod/MOD:00696"
  Ap hypernym "http://identifiers.org/uniprot/P07363"
  B hypernym "http://identifiers.org/uniprot/P07330"
  Bp property "http://identifiers.org/obo.psi-mod/MOD:00696"
  Bp hypernym "http://identifiers.org/uniprot/P07330"
  Z identity "http://identifiers.org/uniprot/P0A9H9"
  Y hypernym "http://identifiers.org/uniprot/P0AE67"
  Yp property "http://identifiers.org/obo.psi-mod/MOD:00696"
  Yp hypernym "http://identifiers.org/uniprot/P0AE67"
  M identity "http://identifiers.org/uniprot/P06974"
  MYp part "http://identifiers.org/uniprot/P06974",
           "http://identifiers.org/uniprot/P0AE67"
  MYpYp part "http://identifiers.org/uniprot/P0AE67",
             "http://identifiers.org/uniprot/P06974"
  MYpYpYp part "http://identifiers.org/uniprot/P0AE67",
               "http://identifiers.org/uniprot/P06974"
  MYpYpYpYp part "http://identifiers.org/uniprot/P06974",
                 "http://identifiers.org/uniprot/P0AE67"
  species_1 identity "http://identifiers.org/obo.chebi/CHEBI:15422"
  phosphorylation_r1 hypernym "http://identifiers.org/ec-code/2.7.11.1",
                              "http://identifiers.org/obo.go/GO:0006468"
  phosphorylation_r2 hypernym "http://identifiers.org/ec-code/2.7.11.1",
                              "http://identifiers.org/obo.go/GO:0006468"
  phosphorylation_r3 hypernym "http://identifiers.org/ec-code/2.7.11.1",
                              "http://identifiers.org/obo.go/GO:0006468"
  phosphorylation_r4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
                              "http://identifiers.org/obo.go/GO:0006470"
  phosphorylation_r5 hypernym "http://identifiers.org/ec-code/2.7.11.1",
                              "http://identifiers.org/obo.go/GO:0006468"
  phosphorylation_r6 hypernym "http://identifiers.org/ec-code/2.7.11.1",
                              "http://identifiers.org/obo.go/GO:0006468"
  phosphorylation_r7 hypernym "http://identifiers.org/ec-code/3.1.3.16",
                              "http://identifiers.org/obo.go/GO:0006470"
  phosphorylation_r8 hypernym "http://identifiers.org/ec-code/3.1.3.16",
                              "http://identifiers.org/obo.go/GO:0006470"
  phosphorylation_r9 part "http://identifiers.org/obo.go/GO:0006470",
                          "http://identifiers.org/obo.go/GO:0006468"
  phosphorylation_r9 part "http://identifiers.org/ec-code/3.1.3.16",
                          "http://identifiers.org/ec-code/2.7.11.1"
  phosphorylation_r10 hypernym "http://identifiers.org/ec-code/3.1.3.16",
                               "http://identifiers.org/obo.go/GO:0006470"
  regulatory_r1 hypernym "http://identifiers.org/obo.go/GO:0070335"
  regulatory_r2 hypernym "http://identifiers.org/obo.go/GO:0016151"
  regulatory_r3 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r4 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r5 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r6 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r7 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r8 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r9 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r10 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r11 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r12 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r13 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r14 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r15 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r16 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r17 hypernym "http://identifiers.org/obo.go/GO:0006461"
  regulatory_r18 hypernym "http://identifiers.org/obo.go/GO:0006461"
  motor_r1 hypernym "http://identifiers.org/obo.go/GO:0006461"
  motor_r2 hypernym "http://identifiers.org/obo.go/GO:0006461"
  motor_r3 hypernym "http://identifiers.org/obo.go/GO:0006461"
  motor_r4 hypernym "http://identifiers.org/obo.go/GO:0006461"
  reaction_1 hypernym "http://identifiers.org/obo.go/GO:0070335"
  reaction_2 hypernym "http://identifiers.org/obo.go/GO:0070335"
  reaction_3 hypernym "http://identifiers.org/obo.go/GO:0070335"
end

Bray1993_chemotaxis is "Bray1993_chemotaxis"

Bray1993_chemotaxis model_entity_is "http://identifiers.org/biomodels.db/MODEL6929313478"
Bray1993_chemotaxis model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000404"
Bray1993_chemotaxis description "http://identifiers.org/pubmed/8334303"
Bray1993_chemotaxis taxon "http://identifiers.org/taxonomy/562"
Bray1993_chemotaxis hypernym "http://identifiers.org/kegg.pathway/map02030",
                             "http://identifiers.org/obo.go/GO:0006935"
