dnadamage2/src/G4EmDNAChemistryForPlasmids.cc

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0025 //
0026 //
0027 // G4EmDNAChemistryForPlasmids.cc
0028 //
0029 //  Created on: Feb 10, 2021
0030 //      Authors: J. Naoki D. Kondo
0031 //               W. G. Shin, J. Ramos-Mendez and B. Faddegon
0032 //
0033 /// \file G4EmDNAChemistryForPlasmids.cc
0034 /// \brief Implementation of the Chemistry parameters with DNA reactions
0035
0036 #include "G4EmDNAChemistryForPlasmids.hh"
0037
0038 #include "G4DNAChemistryManager.hh"
0039 #include "G4DNAGenericIonsManager.hh"
0040 #include "G4DNAWaterDissociationDisplacer.hh"
0041 #include "G4DNAWaterExcitationStructure.hh"
0042 #include "G4PhysicalConstants.hh"
0043 #include "G4ProcessManager.hh"
0044 #include "G4SystemOfUnits.hh"
0045
0046 // *** Processes and models for Geant4-DNA
0047
0048 #include "G4DNABrownianTransportation.hh"
0049 #include "G4DNAElectronHoleRecombination.hh"
0050 #include "G4DNAElectronSolvation.hh"
0051 #include "G4DNAIRT.hh"
0052 #include "G4DNAMolecularDissociation.hh"
0053 #include "G4DNAMolecularIRTModel.hh"
0054 #include "G4DNAMolecularReactionTable.hh"
0055 #include "G4DNASancheExcitationModel.hh"
0056 #include "G4DNAVibExcitation.hh"
0057 #include "G4VDNAReactionModel.hh"
0058
0059 // particles
0060
0061 #include "PlasmidMolecules.hh"
0062 #include "ScavengerMolecules.hh"
0063
0064 #include "G4BuilderType.hh"
0065 #include "G4Electron.hh"
0066 #include "G4Electron_aq.hh"
0067 #include "G4FakeMolecule.hh"
0068 #include "G4GenericIon.hh"
0069 #include "G4H2.hh"
0070 #include "G4H2O.hh"
0071 #include "G4H2O2.hh"
0072 #include "G4H3O.hh"
0073 #include "G4HO2.hh"
0074 #include "G4Hydrogen.hh"
0075 #include "G4MoleculeTable.hh"
0076 #include "G4O2.hh"
0077 #include "G4O3.hh"
0078 #include "G4OH.hh"
0079 #include "G4Oxygen.hh"
0080 #include "G4PhysicsListHelper.hh"
0081 #include "G4Proton.hh"
0082
0083 /****/
0084 #include "G4DNAMoleculeEncounterStepper.hh"
0085 #include "G4MolecularConfiguration.hh"
0086 #include "G4ProcessTable.hh"
0087 /****/
0088 // factory
0089 #include "G4PhysicsConstructorFactory.hh"
0090 #include "G4ChemDissociationChannels_option1.hh"
0091 G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistryForPlasmids);
0092
0093 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0094
0095 G4EmDNAChemistryForPlasmids::G4EmDNAChemistryForPlasmids() : G4VUserChemistryList(true)
0096 {
0097   G4DNAChemistryManager::Instance()->SetChemistryList(this);
0098
0099   fDMSO = 0;
0100   fOxygen = 0;
0101 }
0102
0103 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0104
0105 G4EmDNAChemistryForPlasmids::G4EmDNAChemistryForPlasmids(G4double dmso, G4double oxygen)
0106   : G4VUserChemistryList(true)
0107 {
0108   G4DNAChemistryManager::Instance()->SetChemistryList(this);
0109
0110   fDMSO = dmso;
0111   fOxygen = oxygen;
0112 }
0113
0114 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0115
0116 void G4EmDNAChemistryForPlasmids::ConstructMolecule()
0117 {
0118   G4ChemDissociationChannels_option1::ConstructMolecule();
0119   auto molTab = G4MoleculeTable::Instance();
0120
0121   molTab->CreateConfiguration("DMSO", G4DMSO::Definition(), 0, 0 * (m2 / s));
0122
0123   molTab->CreateConfiguration("O2", G4O2::Definition());
0124   molTab->GetConfiguration("O2")->SetVanDerVaalsRadius(0.17 * nm);
0125   molTab->CreateConfiguration("Oxygen", G4OxygenB::Definition(), 0,
0126                                                    0 * (m2 / s));
0127   molTab->CreateConfiguration("Deoxyribose", G4DNA_Deoxyribose::Definition(),
0128                                                    0, 1E-150 * (m2 / s));
0129   molTab->CreateConfiguration(
0130     "Damaged_DeoxyriboseOH", G4DNA_DamagedDeoxyriboseOH::Definition(), 0, 1E-150 * (m2 / s));
0131   molTab->CreateConfiguration(
0132     "Damaged_DeoxyriboseH", G4DNA_DamagedDeoxyriboseH::Definition(), 0, 1E-150 * (m2 / s));
0133   molTab->CreateConfiguration(
0134     "Damaged_DeoxyriboseEAQ", G4DNA_DamagedDeoxyriboseEAQ::Definition(), 0, 1E-150 * (m2 / s));
0135 }
0136
0137 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0138
0139 void G4EmDNAChemistryForPlasmids::ConstructDissociationChannels()
0140 {
0141   G4ChemDissociationChannels_option1::ConstructDissociationChannels();
0142 }
0143
0144 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0145
0146 void G4EmDNAChemistryForPlasmids::ConstructReactionTable(
0147   G4DNAMolecularReactionTable* theReactionTable)
0148 {
0149   // fReactionTable = theReactionTable;
0150
0151   //-----------------------------------
0152   // Get the molecular configuration
0153   auto molTab = G4MoleculeTable::Instance();
0154
0155   auto OH = molTab->GetConfiguration("°OH");
0156   auto OHm = molTab->GetConfiguration("OHm");
0157   auto e_aq = molTab->GetConfiguration("e_aq");
0158   auto H2 = molTab->GetConfiguration("H2");
0159   auto H3Op = molTab->GetConfiguration("H3Op");
0160   auto H = molTab->GetConfiguration("H");
0161   auto H2O2 = molTab->GetConfiguration("H2O2");
0162
0163   //----------------------------------------------------------------//
0164   // Type II                                                        //
0165   //----------------------------------------------------------------//
0166   // e_aq + *OH -> OH-    prob: 0.49
0167   auto reactionData =
0168     new G4DNAMolecularReactionData(2.95e10 * (1e-3 * m3 / (mole * s)), e_aq, OH);
0169   reactionData->AddProduct(OHm);
0170   reactionData->SetReactionType(1);
0171   theReactionTable->SetReaction(reactionData);
0172   //----------------------------------------------------------------//
0173   // e_aq + H2O2 -> OH- + *OH        prob: 0.11
0174   reactionData = new G4DNAMolecularReactionData(1.10e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
0175   reactionData->AddProduct(OHm);
0176   reactionData->AddProduct(OH);
0177   reactionData->SetReactionType(1);
0178   theReactionTable->SetReaction(reactionData);
0179   //----------------------------------------------------------------//
0180   // *OH + *H -> H2O        prob: 0.33
0181   reactionData = new G4DNAMolecularReactionData(1.55e10 * (1e-3 * m3 / (mole * s)), OH, H);
0182   reactionData->SetReactionType(1);
0183   theReactionTable->SetReaction(reactionData);
0184   //----------------------------------------------------------------//
0185   // H + H2O2 -> OH                prob: 0.00
0186   reactionData = new G4DNAMolecularReactionData(0.009e10 * (1e-3 * m3 / (mole * s)), H, H2O2);
0187   reactionData->AddProduct(OH);
0188   reactionData->SetReactionType(1);
0189   theReactionTable->SetReaction(reactionData);
0190   //----------------------------------------------------------------//
0191   // *OH + *OH -> H2O2                prob: 0.55
0192   reactionData = new G4DNAMolecularReactionData(0.55e10 * (1e-3 * m3 / (mole * s)), OH, OH);
0193   reactionData->AddProduct(H2O2);
0194   reactionData->SetReactionType(1);
0195   theReactionTable->SetReaction(reactionData);
0196   //----------------------------------------------------------------//
0197
0198   //----------------------------------------------------------------//
0199   // Type III                                                       //
0200   //----------------------------------------------------------------//
0201   // e_aq + e_aq + 2H2O -> H2 + 2OH-
0202   reactionData = new G4DNAMolecularReactionData(0.636e10 * (1e-3 * m3 / (mole * s)), e_aq, e_aq);
0203   reactionData->AddProduct(OHm);
0204   reactionData->AddProduct(OHm);
0205   reactionData->AddProduct(H2);
0206   reactionData->SetReactionType(0);
0207   theReactionTable->SetReaction(reactionData);
0208   //------------------------------------------------------------------
0209   // H3O+ + OH- -> 2H2O
0210   reactionData = new G4DNAMolecularReactionData(11.3e10 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
0211   reactionData->SetReactionType(0);
0212   theReactionTable->SetReaction(reactionData);
0213   //------------------------------------------------------------------
0214
0215   //----------------------------------------------------------------//
0216   // Type IV                                                        //
0217   //----------------------------------------------------------------//
0218   // e_aq + H3O+ -> H* + H2O        prob: 0.04
0219   reactionData = new G4DNAMolecularReactionData(2.11e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
0220   reactionData->AddProduct(H);
0221   reactionData->SetReactionType(1);
0222   theReactionTable->SetReaction(reactionData);
0223   //----------------------------------------------------------------//
0224
0225   //----------------------------------------------------------------//
0226   // Type V                                                         //
0227   // First order reaction                                           //
0228   //----------------------------------------------------------------//
0229   // e_aq + *H -> OH- + H2
0230   reactionData = new G4DNAMolecularReactionData(2.5e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
0231   reactionData->AddProduct(OHm);
0232   reactionData->AddProduct(H2);
0233   reactionData->SetReactionType(0);
0234   theReactionTable->SetReaction(reactionData);
0235   //----------------------------------------------------------------//
0236   // *H + *H -> H2
0237   reactionData = new G4DNAMolecularReactionData(0.503e10 * (1e-3 * m3 / (mole * s)), H, H);
0238   reactionData->AddProduct(H2);
0239   reactionData->SetReactionType(0);
0240   theReactionTable->SetReaction(reactionData);
0241
0242   if (fDMSO > 0) DeclareDMSOAndDNAReactions(theReactionTable);
0243
0244   if (fOxygen > 0) DeclareOxygenReactions(theReactionTable);
0245 }
0246
0247 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0248
0249 void G4EmDNAChemistryForPlasmids::ConstructProcess()
0250 {
0251   G4PhysicsListHelper* ph = G4PhysicsListHelper::GetPhysicsListHelper();
0252
0253   //===============================================================
0254   // Extend vibrational to low energy
0255   // Anyway, solvation of electrons is taken into account from 7.4 eV
0256   // So below this threshold, for now, no accurate modeling is done
0257   //
0258   G4VProcess* process =
0259     G4ProcessTable::GetProcessTable()->FindProcess("e-_G4DNAVibExcitation", "e-");
0260
0261   if (process) {
0262     G4DNAVibExcitation* vibExcitation = (G4DNAVibExcitation*)process;
0263     G4VEmModel* model = vibExcitation->EmModel();
0264     G4DNASancheExcitationModel* sancheExcitationMod =
0265       dynamic_cast<G4DNASancheExcitationModel*>(model);
0266     if (sancheExcitationMod) {
0267       sancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
0268     }
0269   }
0270
0271   //===============================================================
0272   // *** Electron Solvatation ***
0273   //
0274   process = G4ProcessTable::GetProcessTable()->FindProcess("e-_G4DNAElectronSolvation", "e-");
0275
0276   if (process == 0) {
0277     ph->RegisterProcess(new G4DNAElectronSolvation("e-_G4DNAElectronSolvation"),
0278                         G4Electron::Definition());
0279   }
0280
0281   //===============================================================
0282   // Define processes for molecules
0283   //
0284   G4MoleculeTable* theMoleculeTable = G4MoleculeTable::Instance();
0285   G4MoleculeDefinitionIterator iterator = theMoleculeTable->GetDefintionIterator();
0286   iterator.reset();
0287   while (iterator()) {
0288     G4MoleculeDefinition* moleculeDef = iterator.value();
0289
0290     if (moleculeDef != G4H2O::Definition()) {
0291       // G4cout << "Brownian motion added for: "<< moleculeDef->GetName() << G4endl;
0292       //      G4DNABrownianTransportation* brown = new G4DNABrownianTransportation();
0293       //      ph->RegisterProcess(brown, moleculeDef);
0294     }
0295     else {
0296       moleculeDef->GetProcessManager()->AddRestProcess(new G4DNAElectronHoleRecombination(), 2);
0297       G4DNAMolecularDissociation* dissociationProcess =
0298         new G4DNAMolecularDissociation("H2O_DNAMolecularDecay");
0299       dissociationProcess->SetDisplacer(moleculeDef, new G4DNAWaterDissociationDisplacer);
0300       dissociationProcess->SetVerboseLevel(3);
0301
0302       moleculeDef->GetProcessManager()->AddRestProcess(dissociationProcess, 1);
0303     }
0304     /*
0305      * Warning : end of particles and processes are needed by
0306      * EM Physics builders
0307      */
0308   }
0309
0310   G4DNAChemistryManager::Instance()->Initialize();
0311 }
0312
0313 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0314
0315 void G4EmDNAChemistryForPlasmids::ConstructTimeStepModel(G4DNAMolecularReactionTable*
0316                                                          /*reactionTable*/)
0317 {
0318   RegisterTimeStepModel(new G4DNAMolecularIRTModel(), 0);
0319 }
0320
0321 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0322
0323 void G4EmDNAChemistryForPlasmids::DeclareDMSOAndDNAReactions(
0324   G4DNAMolecularReactionTable* theReactionTable)
0325 {
0326   auto molTab = G4MoleculeTable::Instance();
0327   auto DMSO = molTab->GetConfiguration("DMSO");
0328   auto OH = molTab->GetConfiguration("°OH");
0329   auto H = molTab->GetConfiguration("H");
0330   auto e_aq = molTab->GetConfiguration("e_aq");
0331   auto deoxyribose =
0332       molTab->GetConfiguration("Deoxyribose");
0333   auto damage_deoxyribose_OH =
0334       molTab->GetConfiguration("Damaged_DeoxyriboseOH");
0335   auto damage_deoxyribose_H =
0336       molTab->GetConfiguration("Damaged_DeoxyriboseH");
0337   auto damage_deoxyribose_eaq =
0338       molTab->GetConfiguration("Damaged_DeoxyriboseEAQ");
0339
0340   G4double DNA_OH_Rate = 1.32E7 * std::pow(fDMSO * 7.1E9, 0.29);
0341
0342   // DMSO Reactions
0343   // OH + DMSO
0344   auto reactionData = new G4DNAMolecularReactionData(fDMSO * 7.1E9 / s, OH, DMSO);
0345   theReactionTable->SetReaction(reactionData);
0346   //----------------------------------------------------------------//
0347   // H + DMSO
0348   reactionData = new G4DNAMolecularReactionData(fDMSO * 2.7E7 / s, H, DMSO);
0349   theReactionTable->SetReaction(reactionData);
0350   //----------------------------------------------------------------//
0351   // e-_aq + DMSO
0352   reactionData = new G4DNAMolecularReactionData(fDMSO * 3.8E6 / s, e_aq, DMSO);
0353   theReactionTable->SetReaction(reactionData);
0354   //----------------------------------------------------------------//
0355
0356   //----------------------------------------------------------------//
0357   // DNA Type                                                       //
0358   //----------------------------------------------------------------//
0359   // DNA + OH -> Damage
0360   reactionData =
0361     new G4DNAMolecularReactionData(DNA_OH_Rate * (1e-3 * m3 / (mole * s)), deoxyribose, OH);
0362   reactionData->AddProduct(damage_deoxyribose_OH);
0363   theReactionTable->SetReaction(reactionData);
0364   //----------------------------------------------------------------//
0365   // DNA + H
0366   reactionData = new G4DNAMolecularReactionData(0.03e9 * (1e-3 * m3 / (mole * s)), deoxyribose, H);
0367   reactionData->AddProduct(damage_deoxyribose_H);
0368   theReactionTable->SetReaction(reactionData);
0369   //----------------------------------------------------------------//
0370   // DNA + e-_aq
0371   reactionData =
0372     new G4DNAMolecularReactionData(0.01e9 * (1e-3 * m3 / (mole * s)), deoxyribose, e_aq);
0373   reactionData->AddProduct(damage_deoxyribose_eaq);
0374   theReactionTable->SetReaction(reactionData);
0375   //----------------------------------------------------------------//
0376 }
0377
0378 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0379
0380 void G4EmDNAChemistryForPlasmids::DeclareOxygenReactions(
0381   G4DNAMolecularReactionTable* theReactionTable)
0382 {
0383   auto molTab = G4MoleculeTable::Instance();
0384   auto Oxygen = molTab->GetConfiguration("Oxygen");
0385   auto H = molTab->GetConfiguration("H");
0386   auto e_aq = molTab->GetConfiguration("e_aq");
0387   auto O2m = molTab->GetConfiguration("O2m");
0388   auto HO2 = molTab->GetConfiguration("HO2°");
0389   auto O2 = molTab->GetConfiguration("O2");
0390   auto OH = molTab->GetConfiguration("°OH");
0391
0392   // Oxygen Reactions
0393   // e_aq + O2B
0394   auto reactionData =
0395     new G4DNAMolecularReactionData((fOxygen * 1.9E10) / s, e_aq, Oxygen);
0396   reactionData->AddProduct(O2m);
0397   theReactionTable->SetReaction(reactionData);
0398   //------------------------------------------------------------------
0399   // H + O2B
0400   reactionData = new G4DNAMolecularReactionData((fOxygen * 2.1E10) / s, H, Oxygen);
0401   reactionData->AddProduct(HO2);
0402   theReactionTable->SetReaction(reactionData);
0403   //------------------------------------------------------------------
0404   // e_aq + O2
0405   reactionData = new G4DNAMolecularReactionData(1.9E10 * (1e-3 * m3 / (mole * s)), e_aq, O2);
0406   reactionData->AddProduct(O2m);
0407   reactionData->SetReactionType(1);
0408   theReactionTable->SetReaction(reactionData);
0409   //------------------------------------------------------------------
0410   // H + O2
0411   reactionData = new G4DNAMolecularReactionData(2.1E10 * (1e-3 * m3 / (mole * s)), H, O2);
0412   reactionData->AddProduct(HO2);
0413   reactionData->SetReactionType(1);
0414   theReactionTable->SetReaction(reactionData);
0415   //------------------------------------------------------------------
0416   // OH + HO2
0417   reactionData = new G4DNAMolecularReactionData(7.9E9 * (1e-3 * m3 / (mole * s)), OH, HO2);
0418   reactionData->AddProduct(O2);
0419   reactionData->SetReactionType(1);
0420   theReactionTable->SetReaction(reactionData);
0421   //------------------------------------------------------------------
0422 }
0423
0424 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......