dnadamage2/src/G4EmDNAChemistryForPlasmids.cc

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0025 //
0026 /// \file G4EmDNAChemistryForPlasmids.cc
0027 /// \brief Implementation of the G4EmDNAChemistryForPlasmids class
0028 ///
0029 /// Implementation of the Chemistry parameters with DNA reactions
0030
0031 // G4EmDNAChemistryForPlasmids.cc
0032 //
0033 //  Created on: Feb 10, 2021
0034 //      Authors: J. Naoki D. Kondo
0035 //               W. G. Shin, J. Ramos-Mendez and B. Faddegon
0036 //
0037
0038 #include "G4EmDNAChemistryForPlasmids.hh"
0039
0040 #include "G4DNAChemistryManager.hh"
0041 #include "G4DNAGenericIonsManager.hh"
0042 #include "G4DNAWaterDissociationDisplacer.hh"
0043 #include "G4DNAWaterExcitationStructure.hh"
0044 #include "G4PhysicalConstants.hh"
0045 #include "G4ProcessManager.hh"
0046 #include "G4SystemOfUnits.hh"
0047
0048 // *** Processes and models for Geant4-DNA
0049
0050 #include "G4DNABrownianTransportation.hh"
0051 #include "G4DNAElectronHoleRecombination.hh"
0052 #include "G4DNAElectronSolvation.hh"
0053 #include "G4DNAIRT.hh"
0054 #include "G4DNAMolecularDissociation.hh"
0055 #include "G4DNAMolecularIRTModel.hh"
0056 #include "G4DNAMolecularReactionTable.hh"
0057 #include "G4DNASancheExcitationModel.hh"
0058 #include "G4DNAVibExcitation.hh"
0059 #include "G4VDNAReactionModel.hh"
0060
0061 // particles
0062
0063 #include "PlasmidMolecules.hh"
0064 #include "ScavengerMolecules.hh"
0065
0066 #include "G4BuilderType.hh"
0067 #include "G4Electron.hh"
0068 #include "G4Electron_aq.hh"
0069 #include "G4FakeMolecule.hh"
0070 #include "G4GenericIon.hh"
0071 #include "G4H2.hh"
0072 #include "G4H2O.hh"
0073 #include "G4H2O2.hh"
0074 #include "G4H3O.hh"
0075 #include "G4HO2.hh"
0076 #include "G4Hydrogen.hh"
0077 #include "G4MoleculeTable.hh"
0078 #include "G4O2.hh"
0079 #include "G4O3.hh"
0080 #include "G4OH.hh"
0081 #include "G4Oxygen.hh"
0082 #include "G4PhysicsListHelper.hh"
0083 #include "G4Proton.hh"
0084
0085 /****/
0086 #include "G4DNAMoleculeEncounterStepper.hh"
0087 #include "G4MolecularConfiguration.hh"
0088 #include "G4ProcessTable.hh"
0089 /****/
0090 // factory
0091 #include "G4PhysicsConstructorFactory.hh"
0092 #include "G4ChemDissociationChannels_option1.hh"
0093 G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistryForPlasmids);
0094
0095 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0096
0097 G4EmDNAChemistryForPlasmids::G4EmDNAChemistryForPlasmids() : G4VUserChemistryList(true)
0098 {
0099   G4DNAChemistryManager::Instance()->SetChemistryList(this);
0100
0101   fDMSO = 0;
0102   fOxygen = 0;
0103 }
0104
0105 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0106
0107 G4EmDNAChemistryForPlasmids::G4EmDNAChemistryForPlasmids(G4double dmso, G4double oxygen)
0108   : G4VUserChemistryList(true)
0109 {
0110   G4DNAChemistryManager::Instance()->SetChemistryList(this);
0111
0112   fDMSO = dmso;
0113   fOxygen = oxygen;
0114 }
0115
0116 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0117
0118 void G4EmDNAChemistryForPlasmids::ConstructMolecule()
0119 {
0120   G4ChemDissociationChannels_option1::ConstructMolecule();
0121   auto molTab = G4MoleculeTable::Instance();
0122
0123   molTab->CreateConfiguration("DMSO", G4DMSO::Definition(), 0, 0 * (m2 / s));
0124
0125   molTab->CreateConfiguration("O2", G4O2::Definition());
0126   molTab->GetConfiguration("O2")->SetVanDerVaalsRadius(0.17 * nm);
0127   molTab->CreateConfiguration("Oxygen", G4OxygenB::Definition(), 0,
0128                                                    0 * (m2 / s));
0129   molTab->CreateConfiguration("Deoxyribose", G4DNA_Deoxyribose::Definition(),
0130                                                    0, 1E-150 * (m2 / s));
0131   molTab->CreateConfiguration(
0132     "Damaged_DeoxyriboseOH", G4DNA_DamagedDeoxyriboseOH::Definition(), 0, 1E-150 * (m2 / s));
0133   molTab->CreateConfiguration(
0134     "Damaged_DeoxyriboseH", G4DNA_DamagedDeoxyriboseH::Definition(), 0, 1E-150 * (m2 / s));
0135   molTab->CreateConfiguration(
0136     "Damaged_DeoxyriboseEAQ", G4DNA_DamagedDeoxyriboseEAQ::Definition(), 0, 1E-150 * (m2 / s));
0137 }
0138
0139 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0140
0141 void G4EmDNAChemistryForPlasmids::ConstructDissociationChannels()
0142 {
0143   G4ChemDissociationChannels_option1::ConstructDissociationChannels();
0144 }
0145
0146 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0147
0148 void G4EmDNAChemistryForPlasmids::ConstructReactionTable(
0149   G4DNAMolecularReactionTable* theReactionTable)
0150 {
0151   // fReactionTable = theReactionTable;
0152
0153   //-----------------------------------
0154   // Get the molecular configuration
0155   auto molTab = G4MoleculeTable::Instance();
0156
0157   auto OH = molTab->GetConfiguration("°OH");
0158   auto OHm = molTab->GetConfiguration("OHm");
0159   auto e_aq = molTab->GetConfiguration("e_aq");
0160   auto H2 = molTab->GetConfiguration("H2");
0161   auto H3Op = molTab->GetConfiguration("H3Op");
0162   auto H = molTab->GetConfiguration("H");
0163   auto H2O2 = molTab->GetConfiguration("H2O2");
0164
0165   //----------------------------------------------------------------//
0166   // Type II                                                        //
0167   //----------------------------------------------------------------//
0168   // e_aq + *OH -> OH-    prob: 0.49
0169   auto reactionData =
0170     new G4DNAMolecularReactionData(2.95e10 * (1e-3 * m3 / (mole * s)), e_aq, OH);
0171   reactionData->AddProduct(OHm);
0172   reactionData->SetReactionType(1);
0173   theReactionTable->SetReaction(reactionData);
0174   //----------------------------------------------------------------//
0175   // e_aq + H2O2 -> OH- + *OH        prob: 0.11
0176   reactionData = new G4DNAMolecularReactionData(1.10e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
0177   reactionData->AddProduct(OHm);
0178   reactionData->AddProduct(OH);
0179   reactionData->SetReactionType(1);
0180   theReactionTable->SetReaction(reactionData);
0181   //----------------------------------------------------------------//
0182   // *OH + *H -> H2O        prob: 0.33
0183   reactionData = new G4DNAMolecularReactionData(1.55e10 * (1e-3 * m3 / (mole * s)), OH, H);
0184   reactionData->SetReactionType(1);
0185   theReactionTable->SetReaction(reactionData);
0186   //----------------------------------------------------------------//
0187   // H + H2O2 -> OH                prob: 0.00
0188   reactionData = new G4DNAMolecularReactionData(0.009e10 * (1e-3 * m3 / (mole * s)), H, H2O2);
0189   reactionData->AddProduct(OH);
0190   reactionData->SetReactionType(1);
0191   theReactionTable->SetReaction(reactionData);
0192   //----------------------------------------------------------------//
0193   // *OH + *OH -> H2O2                prob: 0.55
0194   reactionData = new G4DNAMolecularReactionData(0.55e10 * (1e-3 * m3 / (mole * s)), OH, OH);
0195   reactionData->AddProduct(H2O2);
0196   reactionData->SetReactionType(1);
0197   theReactionTable->SetReaction(reactionData);
0198   //----------------------------------------------------------------//
0199
0200   //----------------------------------------------------------------//
0201   // Type III                                                       //
0202   //----------------------------------------------------------------//
0203   // e_aq + e_aq + 2H2O -> H2 + 2OH-
0204   reactionData = new G4DNAMolecularReactionData(0.636e10 * (1e-3 * m3 / (mole * s)), e_aq, e_aq);
0205   reactionData->AddProduct(OHm);
0206   reactionData->AddProduct(OHm);
0207   reactionData->AddProduct(H2);
0208   reactionData->SetReactionType(0);
0209   theReactionTable->SetReaction(reactionData);
0210   //------------------------------------------------------------------
0211   // H3O+ + OH- -> 2H2O
0212   reactionData = new G4DNAMolecularReactionData(11.3e10 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
0213   reactionData->SetReactionType(0);
0214   theReactionTable->SetReaction(reactionData);
0215   //------------------------------------------------------------------
0216
0217   //----------------------------------------------------------------//
0218   // Type IV                                                        //
0219   //----------------------------------------------------------------//
0220   // e_aq + H3O+ -> H* + H2O        prob: 0.04
0221   reactionData = new G4DNAMolecularReactionData(2.11e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
0222   reactionData->AddProduct(H);
0223   reactionData->SetReactionType(1);
0224   theReactionTable->SetReaction(reactionData);
0225   //----------------------------------------------------------------//
0226
0227   //----------------------------------------------------------------//
0228   // Type V                                                         //
0229   // First order reaction                                           //
0230   //----------------------------------------------------------------//
0231   // e_aq + *H -> OH- + H2
0232   reactionData = new G4DNAMolecularReactionData(2.5e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
0233   reactionData->AddProduct(OHm);
0234   reactionData->AddProduct(H2);
0235   reactionData->SetReactionType(0);
0236   theReactionTable->SetReaction(reactionData);
0237   //----------------------------------------------------------------//
0238   // *H + *H -> H2
0239   reactionData = new G4DNAMolecularReactionData(0.503e10 * (1e-3 * m3 / (mole * s)), H, H);
0240   reactionData->AddProduct(H2);
0241   reactionData->SetReactionType(0);
0242   theReactionTable->SetReaction(reactionData);
0243
0244   if (fDMSO > 0) DeclareDMSOAndDNAReactions(theReactionTable);
0245
0246   if (fOxygen > 0) DeclareOxygenReactions(theReactionTable);
0247 }
0248
0249 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0250
0251 void G4EmDNAChemistryForPlasmids::ConstructProcess()
0252 {
0253   G4PhysicsListHelper* ph = G4PhysicsListHelper::GetPhysicsListHelper();
0254
0255   //===============================================================
0256   // Extend vibrational to low energy
0257   // Anyway, solvation of electrons is taken into account from 7.4 eV
0258   // So below this threshold, for now, no accurate modeling is done
0259   //
0260   G4VProcess* process =
0261     G4ProcessTable::GetProcessTable()->FindProcess("e-_G4DNAVibExcitation", "e-");
0262
0263   if (process) {
0264     G4DNAVibExcitation* vibExcitation = (G4DNAVibExcitation*)process;
0265     G4VEmModel* model = vibExcitation->EmModel();
0266     G4DNASancheExcitationModel* sancheExcitationMod =
0267       dynamic_cast<G4DNASancheExcitationModel*>(model);
0268     if (sancheExcitationMod) {
0269       sancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
0270     }
0271   }
0272
0273   //===============================================================
0274   // *** Electron Solvatation ***
0275   //
0276   process = G4ProcessTable::GetProcessTable()->FindProcess("e-_G4DNAElectronSolvation", "e-");
0277
0278   if (process == 0) {
0279     ph->RegisterProcess(new G4DNAElectronSolvation("e-_G4DNAElectronSolvation"),
0280                         G4Electron::Definition());
0281   }
0282
0283   //===============================================================
0284   // Define processes for molecules
0285   //
0286   G4MoleculeTable* theMoleculeTable = G4MoleculeTable::Instance();
0287   G4MoleculeDefinitionIterator iterator = theMoleculeTable->GetDefintionIterator();
0288   iterator.reset();
0289   while (iterator()) {
0290     G4MoleculeDefinition* moleculeDef = iterator.value();
0291
0292     if (moleculeDef != G4H2O::Definition()) {
0293       // G4cout << "Brownian motion added for: "<< moleculeDef->GetName() << G4endl;
0294       //      G4DNABrownianTransportation* brown = new G4DNABrownianTransportation();
0295       //      ph->RegisterProcess(brown, moleculeDef);
0296     }
0297     else {
0298       moleculeDef->GetProcessManager()->AddRestProcess(new G4DNAElectronHoleRecombination(), 2);
0299       G4DNAMolecularDissociation* dissociationProcess =
0300         new G4DNAMolecularDissociation("H2O_DNAMolecularDecay");
0301       dissociationProcess->SetDisplacer(moleculeDef, new G4DNAWaterDissociationDisplacer);
0302       dissociationProcess->SetVerboseLevel(3);
0303
0304       moleculeDef->GetProcessManager()->AddRestProcess(dissociationProcess, 1);
0305     }
0306     /*
0307      * Warning : end of particles and processes are needed by
0308      * EM Physics builders
0309      */
0310   }
0311
0312   G4DNAChemistryManager::Instance()->Initialize();
0313 }
0314
0315 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0316
0317 void G4EmDNAChemistryForPlasmids::ConstructTimeStepModel(G4DNAMolecularReactionTable*
0318                                                          /*reactionTable*/)
0319 {
0320   RegisterTimeStepModel(new G4DNAMolecularIRTModel(), 0);
0321 }
0322
0323 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0324
0325 void G4EmDNAChemistryForPlasmids::DeclareDMSOAndDNAReactions(
0326   G4DNAMolecularReactionTable* theReactionTable)
0327 {
0328   auto molTab = G4MoleculeTable::Instance();
0329   auto DMSO = molTab->GetConfiguration("DMSO");
0330   auto OH = molTab->GetConfiguration("°OH");
0331   auto H = molTab->GetConfiguration("H");
0332   auto e_aq = molTab->GetConfiguration("e_aq");
0333   auto deoxyribose =
0334       molTab->GetConfiguration("Deoxyribose");
0335   auto damage_deoxyribose_OH =
0336       molTab->GetConfiguration("Damaged_DeoxyriboseOH");
0337   auto damage_deoxyribose_H =
0338       molTab->GetConfiguration("Damaged_DeoxyriboseH");
0339   auto damage_deoxyribose_eaq =
0340       molTab->GetConfiguration("Damaged_DeoxyriboseEAQ");
0341
0342   G4double DNA_OH_Rate = 1.32E7 * std::pow(fDMSO * 7.1E9, 0.29);
0343
0344   // DMSO Reactions
0345   // OH + DMSO
0346   auto reactionData = new G4DNAMolecularReactionData(fDMSO * 7.1E9 / s, OH, DMSO);
0347   theReactionTable->SetReaction(reactionData);
0348   //----------------------------------------------------------------//
0349   // H + DMSO
0350   reactionData = new G4DNAMolecularReactionData(fDMSO * 2.7E7 / s, H, DMSO);
0351   theReactionTable->SetReaction(reactionData);
0352   //----------------------------------------------------------------//
0353   // e-_aq + DMSO
0354   reactionData = new G4DNAMolecularReactionData(fDMSO * 3.8E6 / s, e_aq, DMSO);
0355   theReactionTable->SetReaction(reactionData);
0356   //----------------------------------------------------------------//
0357
0358   //----------------------------------------------------------------//
0359   // DNA Type                                                       //
0360   //----------------------------------------------------------------//
0361   // DNA + OH -> Damage
0362   reactionData =
0363     new G4DNAMolecularReactionData(DNA_OH_Rate * (1e-3 * m3 / (mole * s)), deoxyribose, OH);
0364   reactionData->AddProduct(damage_deoxyribose_OH);
0365   theReactionTable->SetReaction(reactionData);
0366   //----------------------------------------------------------------//
0367   // DNA + H
0368   reactionData = new G4DNAMolecularReactionData(0.03e9 * (1e-3 * m3 / (mole * s)), deoxyribose, H);
0369   reactionData->AddProduct(damage_deoxyribose_H);
0370   theReactionTable->SetReaction(reactionData);
0371   //----------------------------------------------------------------//
0372   // DNA + e-_aq
0373   reactionData =
0374     new G4DNAMolecularReactionData(0.01e9 * (1e-3 * m3 / (mole * s)), deoxyribose, e_aq);
0375   reactionData->AddProduct(damage_deoxyribose_eaq);
0376   theReactionTable->SetReaction(reactionData);
0377   //----------------------------------------------------------------//
0378 }
0379
0380 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0381
0382 void G4EmDNAChemistryForPlasmids::DeclareOxygenReactions(
0383   G4DNAMolecularReactionTable* theReactionTable)
0384 {
0385   auto molTab = G4MoleculeTable::Instance();
0386   auto Oxygen = molTab->GetConfiguration("Oxygen");
0387   auto H = molTab->GetConfiguration("H");
0388   auto e_aq = molTab->GetConfiguration("e_aq");
0389   auto O2m = molTab->GetConfiguration("O2m");
0390   auto HO2 = molTab->GetConfiguration("HO2°");
0391   auto O2 = molTab->GetConfiguration("O2");
0392   auto OH = molTab->GetConfiguration("°OH");
0393
0394   // Oxygen Reactions
0395   // e_aq + O2B
0396   auto reactionData =
0397     new G4DNAMolecularReactionData((fOxygen * 1.9E10) / s, e_aq, Oxygen);
0398   reactionData->AddProduct(O2m);
0399   theReactionTable->SetReaction(reactionData);
0400   //------------------------------------------------------------------
0401   // H + O2B
0402   reactionData = new G4DNAMolecularReactionData((fOxygen * 2.1E10) / s, H, Oxygen);
0403   reactionData->AddProduct(HO2);
0404   theReactionTable->SetReaction(reactionData);
0405   //------------------------------------------------------------------
0406   // e_aq + O2
0407   reactionData = new G4DNAMolecularReactionData(1.9E10 * (1e-3 * m3 / (mole * s)), e_aq, O2);
0408   reactionData->AddProduct(O2m);
0409   reactionData->SetReactionType(1);
0410   theReactionTable->SetReaction(reactionData);
0411   //------------------------------------------------------------------
0412   // H + O2
0413   reactionData = new G4DNAMolecularReactionData(2.1E10 * (1e-3 * m3 / (mole * s)), H, O2);
0414   reactionData->AddProduct(HO2);
0415   reactionData->SetReactionType(1);
0416   theReactionTable->SetReaction(reactionData);
0417   //------------------------------------------------------------------
0418   // OH + HO2
0419   reactionData = new G4DNAMolecularReactionData(7.9E9 * (1e-3 * m3 / (mole * s)), OH, HO2);
0420   reactionData->AddProduct(O2);
0421   reactionData->SetReactionType(1);
0422   theReactionTable->SetReaction(reactionData);
0423   //------------------------------------------------------------------
0424 }
0425
0426 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......