QuorumSensingNetwork.cpp Source File

00001 // QuorumSensingNetwork.cpp: implementation of the CQuorumSensingNetwork class.
00002 //
00004 
00005 #include "QuorumSensingNetwork.h"
00006 #include <iostream>
00007 
00009 // Construction/Destruction
00011 
00012 CQuorumSensingNetwork::CQuorumSensingNetwork()
00013 {
00014         // chemicals
00015         Chemical *octopine = new Chemical(chemicals.size(),0.0,"octopine");
00016         chemicals.push_back(octopine);
00017 
00018         Chemical *OOHL = new Chemical(chemicals.size(),200.0,"OOHL");
00019         chemicals.push_back(OOHL);
00020 
00021         Chemical *mannopine = new Chemical(chemicals.size(),0.0,"mannopine");
00022         chemicals.push_back(mannopine);
00023 
00024         Chemical *traAFreePromoter = new Chemical(chemicals.size(),1.0,"traAFreePromoter");
00025         chemicals.push_back(traAFreePromoter);
00026         
00027         Chemical *traABoundPromoter = new Chemical(chemicals.size(),0.0,"traABoundPromoter");
00028         chemicals.push_back(traABoundPromoter);
00029 
00030         Chemical *traABasalPromoter = new Chemical(chemicals.size(),0.0,"traABasalPromoter");
00031         chemicals.push_back(traABasalPromoter);
00032 
00033         Chemical *traAmRNA = new Chemical(chemicals.size(),10.0,"traAmRNA");
00034         chemicals.push_back(traAmRNA);
00035 
00036         Chemical *TraA = new Chemical(chemicals.size(),10.0,"TraA");
00037         chemicals.push_back(TraA);
00038 
00039         Chemical *traRFreePromoter = new Chemical(chemicals.size(),1.0,"traRFreePromoter");
00040         chemicals.push_back(traRFreePromoter);
00041 
00042         Chemical *traRBoundPromoter = new Chemical(chemicals.size(),0.0,"traRBoundPromoter");
00043         chemicals.push_back(traRBoundPromoter);
00044 
00045         Chemical *traRBasalPromoter = new Chemical(chemicals.size(),1.0,"traRBasalPromoter");
00046         chemicals.push_back(traRBasalPromoter);
00047 
00048         Chemical *traRmRNA = new Chemical(chemicals.size(),10.0,"traRmRNA");
00049         chemicals.push_back(traRmRNA);
00050 
00051         Chemical *FreeTraR = new Chemical(chemicals.size(),1.0,"FreeTraR");
00052         chemicals.push_back(FreeTraR);
00053 
00054         Chemical *BoundTraR = new Chemical(chemicals.size(),0.0,"BoundTraR");
00055         chemicals.push_back(BoundTraR);
00056 
00057         Chemical *TraRDimer = new Chemical(chemicals.size(),0.0,"TraRDimer");
00058         chemicals.push_back(TraRDimer);
00059 
00060         Chemical *traMFreePromoter = new Chemical(chemicals.size(),1.0,"traMFreePromoter");
00061         chemicals.push_back(traMFreePromoter);
00062 
00063         Chemical *traMBoundPromoter = new Chemical(chemicals.size(),0.0,"traMBoundPromoter");
00064         chemicals.push_back(traMBoundPromoter);
00065 
00066         Chemical *traMBasalPromoter = new Chemical(chemicals.size(),1.0,"traMBasalPromoter");
00067         chemicals.push_back(traMBasalPromoter);
00068 
00069         Chemical *traMmRNA = new Chemical(chemicals.size(),10.0,"traMmRNA");
00070         chemicals.push_back(traMmRNA);
00071 
00072         Chemical *TraM = new Chemical(chemicals.size(),10.0,"TraM");
00073         chemicals.push_back(TraM);
00074 
00075         Chemical *TraRTraMDimer = new Chemical(chemicals.size(),0.0,"TraRTraMDimer");
00076         chemicals.push_back(TraRTraMDimer);
00077 
00078         Chemical *trlRFreePromoter = new Chemical(chemicals.size(),1.0,"trlRFreePromoter");
00079         chemicals.push_back(trlRFreePromoter);
00080 
00081         Chemical *trlRBoundPromoter = new Chemical(chemicals.size(),0.0,"trlRBoundPromoter");
00082         chemicals.push_back(trlRBoundPromoter);
00083 
00084         Chemical *trlRBasalPromoter = new Chemical(chemicals.size(),1.0,"trlRBasalPromoter");
00085         chemicals.push_back(trlRBasalPromoter);
00086 
00087         Chemical *trlRmRNA = new Chemical(chemicals.size(),10.0,"trlRmRNA");
00088         chemicals.push_back(trlRmRNA);
00089         
00090         Chemical *FreeTrlR = new Chemical(chemicals.size(),0.0,"FreeTrlR");
00091         chemicals.push_back(FreeTrlR);
00092 
00093         Chemical *BoundTrlR = new Chemical(chemicals.size(),0.0,"BoundTrlR");
00094         chemicals.push_back(BoundTrlR);
00095 
00096         Chemical *TrlRTraRDimer = new Chemical(chemicals.size(),0.0,"TrlRTraRDimer");
00097         chemicals.push_back(TrlRTraRDimer);
00098 
00099         Chemical *traIFreePromoter = new Chemical(chemicals.size(),1.0,"traIFreePromoter");
00100         chemicals.push_back(traIFreePromoter);
00101 
00102         Chemical *traIBoundPromoter = new Chemical(chemicals.size(),0.0,"traIBoundPromoter");
00103         chemicals.push_back(traIBoundPromoter);
00104 
00105         Chemical *traIBasalPromoter = new Chemical(chemicals.size(),1.0,"traIBasalPromoter");
00106         chemicals.push_back(traIBasalPromoter);
00107 
00108         Chemical *traImRNA = new Chemical(chemicals.size(),10.0,"traImRNA");
00109         chemicals.push_back(traImRNA);
00110 
00111         Chemical *TraI = new Chemical(chemicals.size(),10.0,"TraI");
00112         chemicals.push_back(TraI);
00113 
00114 //      Chemical *FreeoccR = new Chemical(chemicals.size(),10.0,"FreeoccR");
00115 //      chemicals.push_back(FreeoccR);
00116 
00117 //      Chemical *BoundoccR = new Chemical(chemicals.size(),0.0,"BoundoccR");
00118 //      chemicals.push_back(BoundoccR);
00119 
00120         Chemical *FreeMocR = new Chemical(chemicals.size(),10.0,"FreeMocR");
00121         chemicals.push_back(FreeMocR);
00122 
00123         Chemical *BoundMocR = new Chemical(chemicals.size(),0.0,"BoundMocR");
00124         chemicals.push_back(BoundMocR);
00125 
00126         Chemical *radiolabel = new Chemical(chemicals.size(),0.0,"radiolabel");
00127         chemicals.push_back(radiolabel);
00128 
00129         Chemical *unradiolabel = new Chemical(chemicals.size(),1.0,"unradiolabel");
00130         chemicals.push_back(unradiolabel);
00131 
00132         Chemical *hotFreeTraR = new Chemical(chemicals.size(),0.0,"hotFreeTraR");
00133         chemicals.push_back(hotFreeTraR);
00134 
00135         Chemical *hotBoundTraR = new Chemical(chemicals.size(),0.0,"hotBoundTraR");
00136         chemicals.push_back(hotBoundTraR);
00137 
00138         Chemical *hotTraRDimer = new Chemical(chemicals.size(),0.0,"hotTraRDimer");
00139         chemicals.push_back(hotTraRDimer);
00140 
00141         Chemical *hotTrlRTraRDimer = new Chemical(chemicals.size(),0.0,"hotTrlRTraRDimer");
00142         chemicals.push_back(hotTrlRTraRDimer);
00143 
00144         Chemical *hotTraRTraMDimer = new Chemical(chemicals.size(),0.0,"hotTraRTraMDimer");
00145         chemicals.push_back(hotTraRTraMDimer);
00146 
00147         Chemical *hottraABoundPromoter = new Chemical(chemicals.size(),0.0,"hottraABoundPromoter");
00148         chemicals.push_back(hottraABoundPromoter);
00149 
00150         Chemical *hottraMBoundPromoter = new Chemical(chemicals.size(),0.0,"hottraMBoundPromoter");
00151         chemicals.push_back(hottraMBoundPromoter);
00152 
00153         Chemical *hottraIBoundPromoter = new Chemical(chemicals.size(),0.0,"hottraIBoundPromoter");
00154         chemicals.push_back(hottraIBoundPromoter);
00155 
00156         std::vector<Chemical *> tIplasmid;
00157         tIplasmid.push_back(traAFreePromoter);
00158         tIplasmid.push_back(traRFreePromoter);
00159         tIplasmid.push_back(traMFreePromoter);
00160         tIplasmid.push_back(traIFreePromoter);
00161         tIplasmid.push_back(trlRFreePromoter);
00162 
00163         std::vector<Chemical *> vec1;
00164         vec1.push_back(FreeTraR);
00165         vec1.push_back(BoundTraR);
00166         vec1.push_back(TraRDimer);
00167         vec1.push_back(TraRDimer);
00168         vec1.push_back(TraRTraMDimer);
00169         vec1.push_back(TraRTraMDimer);
00170         vec1.push_back(TrlRTraRDimer);
00171         vec1.push_back(traABoundPromoter);
00172         vec1.push_back(traABoundPromoter);
00173         vec1.push_back(traMBoundPromoter);
00174         vec1.push_back(traMBoundPromoter);
00175         vec1.push_back(traIBoundPromoter);
00176         vec1.push_back(traIBoundPromoter);
00177         CAlgebraicChemical *TotalTraR = new CSumChemical(chemicals.size(),"TotalTraR",vec1);
00178         TotalTraR->SetAll();
00179         chemicals.push_back(TotalTraR);
00180         this->AddAlgebraicIndex(TotalTraR);
00181 
00182         std::vector<Chemical *> vec2;
00183         vec2.push_back(TotalTraR);
00184         CAlgebraicChemical *LogTotalTraR = new CLogChemical(chemicals.size(),"LogTotalTraR",vec2);
00185         LogTotalTraR->SetAll();
00186         chemicals.push_back(LogTotalTraR);
00187         this->AddAlgebraicIndex(LogTotalTraR);
00188 
00189         std::vector<Chemical *> vec1b;
00190         vec1b.push_back(hotFreeTraR);
00191         vec1b.push_back(hotBoundTraR);
00192         vec1b.push_back(hotTraRDimer);
00193         vec1b.push_back(hotTraRDimer);
00194         vec1b.push_back(hotTraRTraMDimer);
00195         vec1b.push_back(hotTraRTraMDimer);
00196         vec1b.push_back(hotTrlRTraRDimer);
00197         vec1b.push_back(hottraABoundPromoter);
00198         vec1b.push_back(hottraABoundPromoter);
00199         vec1b.push_back(hottraMBoundPromoter);
00200         vec1b.push_back(hottraMBoundPromoter);
00201         vec1b.push_back(hottraIBoundPromoter);
00202         vec1b.push_back(hottraIBoundPromoter);
00203         CAlgebraicChemical *hotTotalTraR = new CSumChemical(chemicals.size(),"hotTotalTraR",vec1b);
00204         hotTotalTraR->SetAll();
00205         chemicals.push_back(hotTotalTraR);
00206         this->AddAlgebraicIndex(hotTotalTraR);
00207 
00208         std::vector<Chemical *> vec2b;
00209         vec2b.push_back(hotTotalTraR);
00210         CAlgebraicChemical *hotLogTotalTraR = new CLogChemical(chemicals.size(),"hotLogTotalTraR",vec2b);
00211         hotLogTotalTraR->SetAll();
00212         chemicals.push_back(hotLogTotalTraR);
00213         this->AddAlgebraicIndex(hotLogTotalTraR);
00214 
00215 /*      std::vector<Chemical *> vec3;
00216         vec3.push_back(TotalTraR);
00217 //      vec3.push_back(traRBasalPromoter);
00218         vec3.push_back(traRFreePromoter);
00219         CAlgebraicChemical *TraRLacZ = new CFractionChemical(chemicals.size(), "TraRLacZ", vec3, 1);
00220         TraRLacZ->SetAll();
00221         chemicals.push_back(TraRLacZ);
00222         this->AddAlgebraicIndex(TraRLacZ);
00223 */
00224         std::vector<Chemical *> vec4;
00225         vec4.push_back(traABoundPromoter);
00226         vec4.push_back(traAFreePromoter);
00227         CAlgebraicChemical *TotaltraAPromoter = new CSumChemical(chemicals.size(), "TotaltraAPromoter", vec4);
00228         TotaltraAPromoter->SetAll();
00229         chemicals.push_back(TotaltraAPromoter);
00230         this->AddAlgebraicIndex(TotaltraAPromoter);
00231 
00232         std::vector<Chemical *> vec5;
00233         vec5.push_back(TotaltraAPromoter);
00234         vec5.push_back(TotaltraAPromoter);
00235         CAlgebraicChemical *PlasmidRatio = new CCurrentToInitialRatioChemical(chemicals.size(), "PlasmidRatio", vec5);
00236         PlasmidRatio->SetAll();
00237         chemicals.push_back(PlasmidRatio);
00238         this->AddAlgebraicIndex(PlasmidRatio);
00239 
00240         // rate constants
00241 
00242 //      RateConstant *kO = new RateConstant(1.0e-07,"kO");
00243 //      rateConstants.push_back(kO);
00244 
00245 //      RateConstant *kuO = new RateConstant(0.02,"kuO");
00246 //      rateConstants.push_back(kuO);
00247 
00248         RateConstant *kocct = new RateConstant(7.7e-11,"kocct");
00249         rateConstants.push_back(kocct);
00250 
00251         RateConstant *kuocct = new RateConstant(9.9e-12,"kuocct");
00252         rateConstants.push_back(kuocct);
00253 
00254         RateConstant *ktmR = new RateConstant(0.062,"ktmR");
00255         rateConstants.push_back(ktmR);
00256 
00257         RateConstant *kdmR = new RateConstant(0.023,"kdmR");
00258         rateConstants.push_back(kdmR);
00259 
00260         RateConstant *ktpR = new RateConstant(0.036,"ktpR");
00261         rateConstants.push_back(ktpR);
00262 
00263         RateConstant *kdpR = new RateConstant(0.0012,"kdpR");
00264         rateConstants.push_back(kdpR);
00265 
00266         RateConstant *kROOHL = new RateConstant(5.8e-10,"kROOHL");
00267         rateConstants.push_back(kROOHL);
00268 
00269         RateConstant *kuROOHL = new RateConstant(1.0e-12,"kuROOHL");
00270         rateConstants.push_back(kuROOHL);
00271 
00272         RateConstant *kdimR = new RateConstant(0.086,"kdimR");
00273         rateConstants.push_back(kdimR);
00274 
00275         RateConstant *kRM = new RateConstant(0.01, "kRM");
00276         rateConstants.push_back(kRM);
00277 
00278         RateConstant *kuRM = new RateConstant(0.1, "kuRM");
00279         rateConstants.push_back(kuRM);
00280 
00281         RateConstant *kRlR = new RateConstant(0.011, "kRlR");
00282         rateConstants.push_back(kRlR);
00283 
00284         RateConstant *kuRlR = new RateConstant(0.1, "kuRlR");
00285         rateConstants.push_back(kuRlR);
00286 
00287         RateConstant *kI = new RateConstant(0.01, "kI");
00288         rateConstants.push_back(kI);
00289 
00290         RateConstant *kuI = new RateConstant(0.001, "kuI");
00291         rateConstants.push_back(kuI);
00292 
00293         RateConstant *ktmI = new RateConstant(0.1, "ktmI");
00294         rateConstants.push_back(ktmI);
00295 
00296         RateConstant *kdmI = new RateConstant(0.014, "kdmI");
00297         rateConstants.push_back(kdmI);
00298 
00299         RateConstant *ktpI = new RateConstant(0.059, "ktpI");
00300         rateConstants.push_back(ktpI);
00301 
00302         RateConstant *kdpI = new RateConstant(0.0011, "kdpI");
00303         rateConstants.push_back(kdpI);
00304         
00305         RateConstant *kOOHL = new RateConstant(61.0, "kOOHL");
00306         rateConstants.push_back(kOOHL);
00307 
00308         RateConstant *kM = new RateConstant(0.011, "kM");
00309         rateConstants.push_back(kM);
00310 
00311         RateConstant *kuM = new RateConstant(0.001, "kuM");
00312         rateConstants.push_back(kuM);
00313 
00314         RateConstant *ktmM = new RateConstant(0.12, "ktmM");
00315         rateConstants.push_back(ktmM);
00316 
00317         RateConstant *kdmM = new RateConstant(0.008, "kdmM");
00318         rateConstants.push_back(kdmM);
00319 
00320         RateConstant *ktpM = new RateConstant(0.12, "ktpM");
00321         rateConstants.push_back(ktpM);
00322 
00323         RateConstant *kdpM = new RateConstant(0.00099, "kdpM");
00324         rateConstants.push_back(kdpM);
00325 
00326         RateConstant *klR = new RateConstant(0.01, "klR");
00327         rateConstants.push_back(klR);
00328 
00329         RateConstant *kulR = new RateConstant(0.001, "kulR");
00330         rateConstants.push_back(kulR);
00331 
00332         RateConstant *ktmlR = new RateConstant(0.1, "ktmlR");
00333         rateConstants.push_back(ktmlR);
00334 
00335         RateConstant *kdmlR = new RateConstant(0.0078, "kdmlR");
00336         rateConstants.push_back(kdmlR);
00337 
00338         RateConstant *ktplR = new RateConstant(0.14, "ktplR");
00339         rateConstants.push_back(ktplR);
00340 
00341         RateConstant *kdplR = new RateConstant(0.0009, "kdplR");
00342         rateConstants.push_back(kdplR);
00343 
00344         RateConstant *kA = new RateConstant(0.0046, "kA");
00345         rateConstants.push_back(kA);
00346 
00347         RateConstant *kuA = new RateConstant(0.0011, "kuA");
00348         rateConstants.push_back(kuA);
00349 
00350         RateConstant *ktmA = new RateConstant(0.038, "ktmA");
00351         rateConstants.push_back(ktmA);
00352 
00353         RateConstant *kdmA = new RateConstant(0.057, "kdmA");
00354         rateConstants.push_back(kdmA);
00355 
00356         RateConstant *ktpA = new RateConstant(0.012, "ktpA");
00357         rateConstants.push_back(ktpA);
00358 
00359         RateConstant *kdpA = new RateConstant(0.001, "kdpA");
00360         rateConstants.push_back(kdpA);
00361 
00362         RateConstant *kMa = new RateConstant(0.01,"kMa");
00363         rateConstants.push_back(kMa);
00364 
00365         RateConstant *kuMa = new RateConstant(0.001,"kuMa");
00366         rateConstants.push_back(kuMa);
00367 
00368         RateConstant *kPlasmid = new RateConstant(1.0e-05, "KPlasmid");
00369         rateConstants.push_back(kPlasmid);
00370 
00371         RateConstant *ktraAbasal = new RateConstant(9.9e-05, "ktraAbasal");
00372         rateConstants.push_back(ktraAbasal);
00373 
00374         RateConstant *ktraRbasal = new RateConstant(1.0e-04, "ktraRbasal");
00375         rateConstants.push_back(ktraRbasal);
00376 
00377         RateConstant *ktraMbasal = new RateConstant(9.8e-05, "ktraMbasal");
00378         rateConstants.push_back(ktraMbasal);
00379 
00380         RateConstant *ktrlRbasal = new RateConstant(9.7e-05, "ktrlRbasal");
00381         rateConstants.push_back(ktrlRbasal);
00382 
00383         RateConstant *ktraIbasal = new RateConstant(1.0e-04, "ktraIbasal");
00384         rateConstants.push_back(ktraIbasal);
00385 
00386         RateConstant *kdOOHL = new RateConstant(6.10, "kdOOHL");
00387         rateConstants.push_back(kdOOHL);
00388 
00389         // reactions
00390 //      HeterodimerizationReaction *OctopineBinding = new HeterodimerizationReaction(octopine,FreeoccR,BoundoccR,kO,"OctopineBinding");
00391 //      reactions.push_back(OctopineBinding);
00392 
00393 //      HeterodimerDissociationReaction *OctopineUnbinding = new HeterodimerDissociationReaction(BoundoccR,FreeoccR,octopine,kuO,"OctopineUnbinding");
00394 //      reactions.push_back(OctopineUnbinding);
00395 
00396         TranscriptionReaction *TraRBasalTranscription = new TranscriptionReaction(traRFreePromoter, traRmRNA, ktraRbasal, "TraRBasalTranscription");
00397         reactions.push_back(TraRBasalTranscription);
00398 
00399         HeterodimerizationReaction *TraRPromoterBinding = new HeterodimerizationReaction(octopine,traRFreePromoter,traRBoundPromoter,kocct,"TraRPromoterBinding");
00400         reactions.push_back(TraRPromoterBinding);
00401 
00402         HeterodimerDissociationReaction *TraRPromoterUnbinding = new HeterodimerDissociationReaction(traRBoundPromoter,traRFreePromoter,octopine, kuocct, "TraRPromoterUnbinding");
00403         reactions.push_back(TraRPromoterUnbinding);
00404 
00405         TranscriptionInducedByBindingReaction *TraRTranscription = new TranscriptionInducedByBindingReaction(traRBoundPromoter,traRmRNA,ktmR,"TraRTranscription");
00406         reactions.push_back(TraRTranscription);
00407 
00408         UnstableProteinDegradationReaction *TraRmRNADegradation = new UnstableProteinDegradationReaction(traRmRNA,kdmR,"TraRmRNADegradation");
00409         reactions.push_back(TraRmRNADegradation);
00410 
00411         CatalyzedTranslationReaction *TraRTranslation = new CatalyzedTranslationReaction(traRmRNA,unradiolabel,FreeTraR,ktpR,"TraRTranslation");
00412         reactions.push_back(TraRTranslation);
00413 
00414         UnstableProteinDegradationReaction *TraRDegradation = new UnstableProteinDegradationReaction(FreeTraR,kdpR,"TraRDegradation");
00415         reactions.push_back(TraRDegradation);
00416 
00417         HeterodimerizationReaction *TraROOHLBinding = new HeterodimerizationReaction(FreeTraR,OOHL,BoundTraR,kROOHL,"TraROOHLBinding");
00418         reactions.push_back(TraROOHLBinding);
00419 
00420         HeterodimerDissociationReaction *TraROOHLUnbinding = new HeterodimerDissociationReaction(BoundTraR, FreeTraR, OOHL, kuROOHL, "TraROOHLUnbinding");
00421         reactions.push_back(TraROOHLUnbinding);
00422 
00423         HomodimerizationReaction *TraRDimerization = new HomodimerizationReaction(BoundTraR, TraRDimer, kdimR, "TraRDimerization");
00424         reactions.push_back(TraRDimerization);
00425 
00426 //      HeterodimerizationReaction *TraRDimerization = new HomodimerizationStochasticReaction(BoundTraR, TraRDimer, kdimR, "TraRDimerization");
00427 //      reactions.push_back(TraRDimerization);
00428 
00429         HeterodimerizationReaction *TraRTraMTrimerization = new HeterodimerizationReaction(TraRDimer,TraM,TraRTraMDimer,kRM,"TraRTraMTrimerization");
00430         reactions.push_back(TraRTraMTrimerization);
00431 
00432 //      HeterodimerDissociationReaction *TraRTraMUntrimerization = new HeterodimerDissociationReaction(TraRTraMDimer,TraRDimer,TraM, kuRM, "TraRTraMUntrimerization");
00433 //      reactions.push_back(TraRTraMUntrimerization);
00434 
00435         HeterodimerizationReaction *TraRTrlRDimerization = new HeterodimerizationReaction(BoundTraR,BoundTrlR,TrlRTraRDimer,kRlR,"TraRTrlRDimerization");
00436         reactions.push_back(TraRTrlRDimerization);
00437 
00438 //      HeterodimerDissociationReaction *TraRTrlRUndimerization = new HeterodimerDissociationReaction(TrlRTraRDimer,BoundTraR,BoundTrlR, kuRlR, "TraRTrlRUndimerization");
00439 //      reactions.push_back(TraRTrlRUndimerization);
00440 
00441         TranscriptionReaction *TraIBasalTranscription = new TranscriptionReaction(traIFreePromoter, traImRNA, ktraIbasal, "TraIBasalTranscription");
00442         reactions.push_back(TraIBasalTranscription);
00443 
00444         HeterodimerizationReaction *TraIPromoterBinding = new HeterodimerizationReaction(TraRDimer,traIFreePromoter,traIBoundPromoter,kI,"TraIPromoterBinding");
00445         reactions.push_back(TraIPromoterBinding);
00446 
00447         HeterodimerDissociationReaction *TraIPromoterUnbinding = new HeterodimerDissociationReaction(traIBoundPromoter,traIFreePromoter,TraRDimer, kuI, "TraIPromoterUnbinding");
00448         reactions.push_back(TraIPromoterUnbinding);
00449 
00450         TranscriptionInducedByBindingReaction *TraITranscription = new TranscriptionInducedByBindingReaction(traIBoundPromoter,traImRNA,ktmI,"TraITranscription");
00451         reactions.push_back(TraITranscription);
00452 
00453         UnstableProteinDegradationReaction *TraImRNADegradation = new UnstableProteinDegradationReaction(traImRNA,kdmI,"TraImRNADegradation");
00454         reactions.push_back(TraImRNADegradation);
00455 
00456         TranscriptionInducedByBindingReaction *TraITranslation = new TranscriptionInducedByBindingReaction(traImRNA,TraI,ktpI,"TraITranslation");
00457         reactions.push_back(TraITranslation);
00458 
00459         UnstableProteinDegradationReaction *TraIDegradation = new UnstableProteinDegradationReaction(TraI,kdpI,"TraIDegradation");
00460         reactions.push_back(TraIDegradation);
00461 
00462         GenerationReaction *OOHLSynthesis = new GenerationReaction(TraI, OOHL, kOOHL, "OOHLSynthesis");
00463         reactions.push_back(OOHLSynthesis);
00464 
00465         TranscriptionReaction *TraMBasalTranscription = new TranscriptionReaction(traMFreePromoter, traMmRNA, ktraMbasal, "TraMBasalTranscription");
00466         reactions.push_back(TraMBasalTranscription);
00467 
00468         HeterodimerizationReaction *TraMPromoterBinding = new HeterodimerizationReaction(TraRDimer,traMFreePromoter,traMBoundPromoter,kM,"TraMPromoterBinding");
00469         reactions.push_back(TraMPromoterBinding);
00470 
00471         HeterodimerDissociationReaction *TraMPromoterUnbinding = new HeterodimerDissociationReaction(traMBoundPromoter,traMFreePromoter,TraRDimer, kuM, "TraMPromoterUnbinding");
00472         reactions.push_back(TraMPromoterUnbinding);
00473 
00474         TranscriptionInducedByBindingReaction *TraMTranscription = new TranscriptionInducedByBindingReaction(traMBoundPromoter,traMmRNA,ktmM,"TraMTranscription");
00475         reactions.push_back(TraMTranscription);
00476 
00477         UnstableProteinDegradationReaction *TraMmRNADegradation = new UnstableProteinDegradationReaction(traMmRNA,kdmM,"TraMmRNADegradation");
00478         reactions.push_back(TraMmRNADegradation);
00479 
00480         TranscriptionInducedByBindingReaction *TraMTranslation = new TranscriptionInducedByBindingReaction(traMmRNA,TraM,ktpM,"TraMTranslation");
00481         reactions.push_back(TraMTranslation);
00482 
00483         UnstableProteinDegradationReaction *TraMDegradation = new UnstableProteinDegradationReaction(TraM,kdpM,"TraMDegradation");
00484         reactions.push_back(TraMDegradation);
00485 
00486         TranscriptionReaction *TrlRBasalTranscription = new TranscriptionReaction(trlRFreePromoter, trlRmRNA, ktrlRbasal, "TrlRBasalTranscription");
00487         reactions.push_back(TrlRBasalTranscription);
00488 
00489         HeterodimerizationReaction *TrlRPromoterBinding = new HeterodimerizationReaction(BoundMocR,trlRFreePromoter,trlRBoundPromoter,klR,"TrlRPromoterBinding");
00490         reactions.push_back(TrlRPromoterBinding);
00491 
00492         HeterodimerDissociationReaction *TrlRPromoterUnbinding = new HeterodimerDissociationReaction(trlRBoundPromoter,trlRFreePromoter,BoundMocR, kulR, "TrlRPromoterUnbinding");
00493         reactions.push_back(TrlRPromoterUnbinding);
00494 
00495         TranscriptionInducedByBindingReaction *TrlRTranscription = new TranscriptionInducedByBindingReaction(trlRBoundPromoter,trlRmRNA,ktmlR,"TrlRTranscription");
00496         reactions.push_back(TrlRTranscription);
00497 
00498         UnstableProteinDegradationReaction *TrlRmRNADegradation = new UnstableProteinDegradationReaction(trlRmRNA,kdmlR,"TrlRmRNADegradation");
00499         reactions.push_back(TrlRmRNADegradation);
00500 
00501         TranscriptionInducedByBindingReaction *TrlRTranslation = new TranscriptionInducedByBindingReaction(trlRmRNA,FreeTrlR,ktplR,"TrlRTranslation");
00502         reactions.push_back(TrlRTranslation);
00503 
00504         UnstableProteinDegradationReaction *TrlRDegradation = new UnstableProteinDegradationReaction(FreeTrlR,kdplR,"TrlRDegradation");
00505         reactions.push_back(TrlRDegradation);
00506 
00507         HeterodimerizationReaction *TrlROOHLBinding = new HeterodimerizationReaction(FreeTrlR,OOHL,BoundTrlR,kROOHL,"TrlROOHLBinding");
00508         reactions.push_back(TrlROOHLBinding);
00509 
00510 //      HeterodimerDissociationReaction *TrlROOHLUnbinding = new HeterodimerDissociationReaction(BoundTrlR,FreeTrlR, OOHL, kuROOHL, "TrlROOHLUnbinding");
00511 //      reactions.push_back(TrlROOHLUnbinding);
00512 
00513         TranscriptionReaction *TraABasalTranscription = new TranscriptionReaction(traAFreePromoter, traAmRNA, ktraAbasal, "TraABasalTranscription");
00514         reactions.push_back(TraABasalTranscription);
00515 
00516         HeterodimerizationReaction *TraAPromoterBinding = new HeterodimerizationReaction(TraRDimer,traAFreePromoter,traABoundPromoter,kA,"TraAPromoterBinding");
00517         reactions.push_back(TraAPromoterBinding);
00518 
00519         HeterodimerDissociationReaction *TraAPromoterUnbinding = new HeterodimerDissociationReaction(traABoundPromoter,traAFreePromoter,TraRDimer, kuA, "TraAPromoterUnbinding");
00520         reactions.push_back(TraAPromoterUnbinding);
00521 
00522         TranscriptionInducedByBindingReaction *TraATranscription = new TranscriptionInducedByBindingReaction(traABoundPromoter,traAmRNA,ktmA,"TraATranscription");
00523         reactions.push_back(TraATranscription);
00524 
00525         UnstableProteinDegradationReaction *TraAmRNADegradation = new UnstableProteinDegradationReaction(traAmRNA,kdmA,"TraAmRNADegradation");
00526         reactions.push_back(TraAmRNADegradation);
00527 
00528         TranscriptionInducedByBindingReaction *TraATranslation = new TranscriptionInducedByBindingReaction(traAmRNA,TraA,ktpA,"TraATranslation");
00529         reactions.push_back(TraATranslation);
00530 
00531         UnstableProteinDegradationReaction *TraADegradation = new UnstableProteinDegradationReaction(TraA,kdpA,"TraADegradation");
00532         reactions.push_back(TraADegradation);
00533 
00534         HeterodimerizationReaction *MannopineBinding = new HeterodimerizationReaction(mannopine,FreeMocR,BoundMocR,kMa,"MannopineBinding");
00535         reactions.push_back(MannopineBinding);
00536 
00537         HeterodimerDissociationReaction *MannopineUnbinding = new HeterodimerDissociationReaction(BoundMocR,FreeMocR,mannopine,kuMa,"MannopineUnbinding");
00538         reactions.push_back(MannopineUnbinding);
00539 
00540         CatalyzedTranslationReaction *hotTraRTranslation = new CatalyzedTranslationReaction(traRmRNA,radiolabel,hotFreeTraR,ktpR,"hotTraRTranslation");
00541         reactions.push_back(hotTraRTranslation);
00542 
00543         UnstableProteinDegradationReaction *hotTraRDegradation = new UnstableProteinDegradationReaction(hotFreeTraR,kdpR,"hotTraRDegradation");
00544         reactions.push_back(hotTraRDegradation);
00545 
00546         HeterodimerizationReaction *hotTraROOHLBinding = new HeterodimerizationReaction(hotFreeTraR,OOHL,hotBoundTraR,kROOHL,"hotTraROOHLBinding");
00547         reactions.push_back(hotTraROOHLBinding);
00548 
00549         HeterodimerDissociationReaction *hotTraROOHLUnbinding = new HeterodimerDissociationReaction(hotBoundTraR, hotFreeTraR, OOHL, kuROOHL, "hotTraROOHLUnbinding");
00550         reactions.push_back(hotTraROOHLUnbinding);
00551 
00552         HomodimerizationReaction *hotTraRDimerization = new HomodimerizationReaction(hotBoundTraR, hotTraRDimer, kdimR, "hotTraRDimerization");
00553         reactions.push_back(hotTraRDimerization);
00554 
00555         HeterodimerizationReaction *hotTraRTraMTrimerization = new HeterodimerizationReaction(hotTraRDimer,TraM,hotTraRTraMDimer,kRM,"hotTraRTraMTrimerization");
00556         reactions.push_back(hotTraRTraMTrimerization);
00557 
00558         HeterodimerizationReaction *hotTraRTrlRDimerization = new HeterodimerizationReaction(hotBoundTraR,BoundTrlR,hotTrlRTraRDimer,kRlR,"hotTraRTrlRDimerization");
00559         reactions.push_back(hotTraRTrlRDimerization);
00560 
00561         HeterodimerizationReaction *hotTraIPromoterBinding = new HeterodimerizationReaction(hotTraRDimer,traIFreePromoter,hottraIBoundPromoter,kI,"hotTraIPromoterBinding");
00562         reactions.push_back(hotTraIPromoterBinding);
00563 
00564         HeterodimerDissociationReaction *hotTraIPromoterUnbinding = new HeterodimerDissociationReaction(hottraIBoundPromoter,traIFreePromoter,hotTraRDimer, kuI, "hotTraIPromoterUnbinding");
00565         reactions.push_back(hotTraIPromoterUnbinding);
00566 
00567         TranscriptionInducedByBindingReaction *hotTraITranscription = new TranscriptionInducedByBindingReaction(hottraIBoundPromoter,traImRNA,ktmI,"hotTraITranscription");
00568         reactions.push_back(hotTraITranscription);
00569 
00570         HeterodimerizationReaction *hotTraMPromoterBinding = new HeterodimerizationReaction(hotTraRDimer,traMFreePromoter,hottraMBoundPromoter,kM,"hotTraMPromoterBinding");
00571         reactions.push_back(hotTraMPromoterBinding);
00572 
00573         HeterodimerDissociationReaction *hotTraMPromoterUnbinding = new HeterodimerDissociationReaction(hottraMBoundPromoter,traMFreePromoter,hotTraRDimer, kuM, "hotTraMPromoterUnbinding");
00574         reactions.push_back(hotTraMPromoterUnbinding);
00575 
00576         TranscriptionInducedByBindingReaction *hotTraMTranscription = new TranscriptionInducedByBindingReaction(hottraMBoundPromoter,traMmRNA,ktmM,"hotTraMTranscription");
00577         reactions.push_back(hotTraMTranscription);
00578 
00579         HeterodimerizationReaction *hotTraAPromoterBinding = new HeterodimerizationReaction(hotTraRDimer,traAFreePromoter,hottraABoundPromoter,kA,"hotTraAPromoterBinding");
00580         reactions.push_back(hotTraAPromoterBinding);
00581 
00582         HeterodimerDissociationReaction *hotTraAPromoterUnbinding = new HeterodimerDissociationReaction(hottraABoundPromoter,traAFreePromoter,hotTraRDimer, kuA, "hotTraAPromoterUnbinding");
00583         reactions.push_back(hotTraAPromoterUnbinding);
00584 
00585         TranscriptionInducedByBindingReaction *hotTraATranscription = new TranscriptionInducedByBindingReaction(hottraABoundPromoter,traAmRNA,ktmA,"hotTraATranscription");
00586         reactions.push_back(hotTraATranscription);
00587 
00588 //      PlasmidReplicationReaction *TiPlasmidReplication = new PlasmidReplicationReaction(TraRDimer, tIplasmid, kPlasmid, "tIPlasmidReplication");
00589 //      reactions.push_back(TiPlasmidReplication);
00590 
00591         UnstableProteinDegradationReaction *OOHLLoss = new UnstableProteinDegradationReaction(OOHL,kdOOHL,"OOHLLoss");
00592         reactions.push_back(OOHLLoss);
00593 
00594 /*
00595         TranscriptionReaction *TraABasalTranscription = new TranscriptionReaction(traABasalPromoter, traAmRNA, ktraAbasal, "TraABasalTranscription");
00596         reactions.push_back(TraABasalTranscription);
00597 
00598         TranscriptionReaction *TraRBasalTranscription = new TranscriptionReaction(traRBasalPromoter, traRmRNA, ktraRbasal, "TraRBasalTranscription");
00599         reactions.push_back(TraRBasalTranscription);
00600 
00601         TranscriptionReaction *TraMBasalTranscription = new TranscriptionReaction(traMBasalPromoter, traMmRNA, ktraMbasal, "TraMBasalTranscription");
00602         reactions.push_back(TraMBasalTranscription);
00603 
00604         TranscriptionReaction *TrlRBasalTranscription = new TranscriptionReaction(trlRBasalPromoter, trlRmRNA, ktrlRbasal, "TrlRBasalTranscription");
00605         reactions.push_back(TrlRBasalTranscription);
00606 
00607         TranscriptionReaction *TraIBasalTranscription = new TranscriptionReaction(traIBasalPromoter, traImRNA, ktraIbasal, "TraIBasalTranscription");
00608         reactions.push_back(TraIBasalTranscription);
00609 */
00610 }
00611 
00612 CQuorumSensingNetwork::~CQuorumSensingNetwork()
00613 {
00614 
00615 }