G4EmDNAChemistry_option2.cc

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#include "G4EmDNAChemistry_option2.hh"
#include "G4DNAMolecule.hh"
#include "G4DNAChemistryManager.hh"
#include "G4DNASmoluchowskiReactionModel.hh"
#include "G4PhysicalConstants.hh"
#include "G4SystemOfUnits.hh"
#include "G4DNAWaterDissociationDisplacer.hh"
#include "G4DNAWaterExcitationStructure.hh"
#include "G4ProcessManager.hh"
#include "G4DNAElectronSolvation.hh"
#include "G4DNAVibExcitation.hh"
#include "G4DNAMolecularDissociation.hh"
#include "G4DNABrownianTransportation.hh"
#include "G4DNAMolecularReactionTable.hh"
#include "G4DNAMolecularStepByStepModel.hh"
#include "G4DNAElectronHoleRecombination.hh"
#include "G4Electron.hh"
#include "G4MoleculeTable.hh"
#include "G4H2O.hh"
#include "G4H2.hh"
#include "G4Hydrogen.hh"
#include "G4OH.hh"
#include "G4H3O.hh"
#include "G4Electron_aq.hh"
#include "G4H2O2.hh"
#include "G4PhysicsListHelper.hh"
#include "G4ProcessTable.hh"
#include "G4MolecularConfiguration.hh"
#include "G4PhysicsConstructorFactory.hh"
#include "G4VDNAReactionModel.hh"
 
G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistry_option2);
 
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
 
G4EmDNAChemistry_option2::G4EmDNAChemistry_option2() 
    : G4VUserChemistryList(true)
{
    G4DNAChemistryManager::Instance()->SetChemistryList(this);
}
 
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
 
G4EmDNAChemistry_option2::~G4EmDNAChemistry_option2()
{}
 
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
 
void G4EmDNAChemistry_option2::ConstructMolecule()
{
  //-----------------------------------
    G4Electron::Definition(); // safety
  //-----------------------------------
    G4H2O::Definition();
    G4Hydrogen::Definition();
    G4H3O::Definition();
    G4OH::Definition();
    G4Electron_aq::Definition();
    G4H2O2::Definition();
    G4H2::Definition();
    G4Deoxyribose::Definition();
    G4Phosphate::Definition();
    G4Adenine::Definition();
    G4Guanine::Definition();
    G4Thymine::Definition();
    G4Cytosine::Definition();
    G4Histone::Definition();
//damaged molecules
    G4DamagedDeoxyribose::Definition();
    G4DamagedAdenine::Definition();
    G4DamagedGuanine::Definition();
    G4DamagedThymine::Definition();
    G4DamagedCytosine::Definition();
    G4ModifiedHistone::Definition();
 
//_________________species___________________________________________________________
 
    G4MoleculeTable::Instance()->
    CreateConfiguration("H3Op", G4H3O::Definition());
    G4MolecularConfiguration* OHm = G4MoleculeTable::Instance()->
    CreateConfiguration("OHm",
                        G4OH::Definition(),
                        -1, // charge
                        5.0e-9 * (m2 / s));
    OHm->SetMass(17.0079 * g / Avogadro * c_squared);
    G4MoleculeTable::Instance()->
    CreateConfiguration("OH", G4OH::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("e_aq",G4Electron_aq::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("H",G4Hydrogen::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("H2", G4H2::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("H2O2", G4H2O2::Definition());
 
//________________DNA_______________________________________________
 
    G4MoleculeTable::Instance()->
    CreateConfiguration("Deoxyribose",G4Deoxyribose::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("Phosphate",G4Phosphate::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("Adenine",G4Adenine::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("Thymine",G4Thymine::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("Guanine",G4Guanine::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("Cytosine",G4Cytosine::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("Histone",G4Histone::Definition());
  
//damaged DNAElement Configuration
 
    G4MoleculeTable::Instance()->
    CreateConfiguration("Damaged_Deoxyribose",
    G4DamagedDeoxyribose::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("Damaged_Adenine",
    G4DamagedAdenine::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("Damaged_Thymine",
    G4DamagedThymine::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("Damaged_Guanine",
    G4DamagedGuanine::Definition());
    G4MoleculeTable::Instance()->
    CreateConfiguration("Damaged_Cytosine",
    G4DamagedCytosine::Definition());
}
 
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
 
void G4EmDNAChemistry_option2::ConstructDissociationChannels()
{
//-----------------------------------
//Get the molecular configuration
    G4MolecularConfiguration* OH =
    G4MoleculeTable::Instance()->GetConfiguration("OH");
    G4MolecularConfiguration* OHm =
    G4MoleculeTable::Instance()->GetConfiguration("OHm");
    G4MolecularConfiguration* e_aq =
    G4MoleculeTable::Instance()->GetConfiguration("e_aq");
    G4MolecularConfiguration* H2 =
    G4MoleculeTable::Instance()->GetConfiguration("H2");
    G4MolecularConfiguration* H3O =
    G4MoleculeTable::Instance()->GetConfiguration("H3Op");
    G4MolecularConfiguration* H =
    G4MoleculeTable::Instance()->GetConfiguration("H");
 
//-------------------------------------
//Define the decay channels
    G4MoleculeDefinition* water = G4H2O::Definition();
    G4MolecularDissociationChannel* decCh1;
    G4MolecularDissociationChannel* decCh2;
 
    G4ElectronOccupancy* occ = new G4ElectronOccupancy(
    *(water->GetGroundStateElectronOccupancy()));
 
//////////////////////////////////////////////////////////
//            EXCITATIONS                               //
//////////////////////////////////////////////////////////
    G4DNAWaterExcitationStructure waterExcitation;
//--------------------------------------------------------
//---------------Excitation on the fifth layer------------
 
    decCh1 = new G4MolecularDissociationChannel(
    "A^1B_1_Relaxation");
    decCh2 = new G4MolecularDissociationChannel(
    "A^1B_1_DissociativeDecay");
  
//Decay 1 : OH + H
    decCh1->SetEnergy(waterExcitation.ExcitationEnergy(0));
    decCh1->SetProbability(0.35);
    decCh1->SetDisplacementType(
    G4DNAWaterDissociationDisplacer::NoDisplacement);
 
    decCh2->AddProduct(OH);
    decCh2->AddProduct(H);
    decCh2->SetProbability(0.65);
    decCh2->SetDisplacementType(
    G4DNAWaterDissociationDisplacer::A1B1_DissociationDecay);
 
//  water->AddExcitedState("A^1B_1");
// this is the transition form ground state to
    occ->RemoveElectron(4, 1); 
// the first unoccupied orbital: A^1B_1
    occ->AddElectron(5, 1); 
 
    water->NewConfigurationWithElectronOccupancy("A^1B_1", *occ);
    water->AddDecayChannel("A^1B_1", decCh1);
    water->AddDecayChannel("A^1B_1", decCh2);
 
//--------------------------------------------------------
//---------------Excitation on the fourth layer-----------
    decCh1 = new G4MolecularDissociationChannel(
    "B^1A_1_Relaxation_Channel");
    decCh2 = new G4MolecularDissociationChannel(
    "B^1A_1_DissociativeDecay");
    G4MolecularDissociationChannel* decCh3 = 
    new G4MolecularDissociationChannel("B^1A_1_AutoIonisation_Channel");
 
//Decay 1 : energy
    decCh1->SetEnergy(waterExcitation.ExcitationEnergy(1));
    decCh1->SetProbability(0.3);
 
//Decay 2 : 2OH + H_2
    decCh2->AddProduct(H2);
    decCh2->AddProduct(OH);
    decCh2->AddProduct(OH);
    decCh2->SetProbability(0.15);
    decCh2->SetDisplacementType(
    G4DNAWaterDissociationDisplacer::B1A1_DissociationDecay);
 
//Decay 3 : OH + H_3Op + e_aq
    decCh3->AddProduct(OH);
    decCh3->AddProduct(H3O);
    decCh3->AddProduct(e_aq);
    decCh3->SetProbability(0.55);
    decCh3->SetDisplacementType(
    G4DNAWaterDissociationDisplacer::AutoIonisation);
 
    *occ = *(water->GetGroundStateElectronOccupancy());
    occ->RemoveElectron(3); // this is the transition form ground state to
    occ->AddElectron(5, 1); // the first unoccupied orbital: B^1A_1
 
    water->NewConfigurationWithElectronOccupancy("B^1A_1", *occ);
    water->AddDecayChannel("B^1A_1", decCh1);
    water->AddDecayChannel("B^1A_1", decCh2);
    water->AddDecayChannel("B^1A_1", decCh3);
 
//-------------------------------------------------------
//-------------------Excitation of 3rd layer-----------------
    decCh1 = new G4MolecularDissociationChannel(
    "Excitation3rdLayer_AutoIonisation_Channel");
    decCh2 = new G4MolecularDissociationChannel(
    "Excitation3rdLayer_Relaxation_Channel");
 
//Decay channel 1 : : OH + H_3Op + e_aq
    decCh1->AddProduct(OH);
    decCh1->AddProduct(H3O);
    decCh1->AddProduct(e_aq);
 
    decCh1->SetProbability(0.5);
    decCh1->SetDisplacementType(
    G4DNAWaterDissociationDisplacer::AutoIonisation);
 
//Decay channel 2 : energy
    decCh2->SetEnergy(waterExcitation.ExcitationEnergy(2));
    decCh2->SetProbability(0.5);
 
//Electronic configuration of this decay
    *occ = *(water->GetGroundStateElectronOccupancy());
    occ->RemoveElectron(2, 1);
    occ->AddElectron(5, 1);
 
//Configure the water molecule
    water->NewConfigurationWithElectronOccupancy(
    "Excitation3rdLayer", *occ);
    water->AddDecayChannel("Excitation3rdLayer", decCh1);
    water->AddDecayChannel("Excitation3rdLayer", decCh2);
 
//-------------------------------------------------------
//-------------------Excitation of 2nd layer-----------------
    decCh1 = new G4MolecularDissociationChannel(
    "Excitation2ndLayer_AutoIonisation_Channel");
    decCh2 = new G4MolecularDissociationChannel(
    "Excitation2ndLayer_Relaxation_Channel");
 
//Decay Channel 1 : : OH + H_3Op + e_aq
    decCh1->AddProduct(OH);
    decCh1->AddProduct(H3O);
    decCh1->AddProduct(e_aq);
 
    decCh1->SetProbability(0.5);
    decCh1->SetDisplacementType(
    G4DNAWaterDissociationDisplacer::AutoIonisation);
 
//Decay channel 2 : energy
    decCh2->SetEnergy(waterExcitation.ExcitationEnergy(3));
    decCh2->SetProbability(0.5);
 
    *occ = *(water->GetGroundStateElectronOccupancy());
    occ->RemoveElectron(1, 1);
    occ->AddElectron(5, 1);
 
    water->NewConfigurationWithElectronOccupancy(
    "Excitation2ndLayer", *occ);
    water->AddDecayChannel("Excitation2ndLayer", decCh1);
    water->AddDecayChannel("Excitation2ndLayer", decCh2);
 
//-------------------------------------------------------
//-------------------Excitation of 1st layer-----------------
    decCh1 = new G4MolecularDissociationChannel(
    "Excitation1stLayer_AutoIonisation_Channel");
    decCh2 = new G4MolecularDissociationChannel(
    "Excitation1stLayer_Relaxation_Channel");
 
    *occ = *(water->GetGroundStateElectronOccupancy());
    occ->RemoveElectron(0, 1);
    occ->AddElectron(5, 1);
 
//Decay Channel 1 : : OH + H_3Op + e_aq
    decCh1->AddProduct(OH);
    decCh1->AddProduct(H3O);
    decCh1->AddProduct(e_aq);
    decCh1->SetProbability(0.5);
    decCh1->SetDisplacementType(
    G4DNAWaterDissociationDisplacer::AutoIonisation);
 
//Decay channel 2 : energy
    decCh2->SetEnergy(waterExcitation.ExcitationEnergy(4));
    decCh2->SetProbability(0.5);
 
    water->NewConfigurationWithElectronOccupancy(
    "Excitation1stLayer", *occ);
    water->AddDecayChannel("Excitation1stLayer", decCh1);
    water->AddDecayChannel("Excitation1stLayer", decCh2);
 
/////////////////////////////////////////////////////////
//                  IONISATION                         //
/////////////////////////////////////////////////////////
//--------------------------------------------------------
//------------------- Ionisation -------------------------
 
    decCh1 = new G4MolecularDissociationChannel("Ionisation_Channel");
 
//Decay Channel 1 : : OH + H_3Op
    decCh1->AddProduct(H3O);
    decCh1->AddProduct(OH);
    decCh1->SetProbability(1);
    decCh1->SetDisplacementType(
    G4DNAWaterDissociationDisplacer::Ionisation_DissociationDecay);
 
    *occ = *(water->GetGroundStateElectronOccupancy());
    occ->RemoveElectron(4, 1);
// this is a ionized h2O with a hole in its last orbital
    water->NewConfigurationWithElectronOccupancy("Ionisation5", *occ);
    water->AddDecayChannel("Ionisation5", decCh1);
 
    *occ = *(water->GetGroundStateElectronOccupancy());
    occ->RemoveElectron(3, 1);
    water->NewConfigurationWithElectronOccupancy("Ionisation4", *occ);
    water->AddDecayChannel("Ionisation4",
                         new G4MolecularDissociationChannel(*decCh1));
 
    *occ = *(water->GetGroundStateElectronOccupancy());
    occ->RemoveElectron(2, 1);
    water->NewConfigurationWithElectronOccupancy("Ionisation3", *occ);
    water->AddDecayChannel("Ionisation3",
                         new G4MolecularDissociationChannel(*decCh1));
 
    *occ = *(water->GetGroundStateElectronOccupancy());
    occ->RemoveElectron(1, 1);
    water->NewConfigurationWithElectronOccupancy("Ionisation2", *occ);
    water->AddDecayChannel("Ionisation2",
                         new G4MolecularDissociationChannel(*decCh1));
 
    *occ = *(water->GetGroundStateElectronOccupancy());
    occ->RemoveElectron(0, 1);
    water->NewConfigurationWithElectronOccupancy("Ionisation1", *occ);
    water->AddDecayChannel("Ionisation1",
                         new G4MolecularDissociationChannel(*decCh1));
 
//////////////////////////////////////////////////////////
//            Dissociative Attachment                   //
//////////////////////////////////////////////////////////
    decCh1 = new G4MolecularDissociationChannel(
    "DissociativeAttachment");
 
//Decay 1 : 2OH + H_2
    decCh1->AddProduct(H2);
    decCh1->AddProduct(OHm);
    decCh1->AddProduct(OH);
    decCh1->SetProbability(1);
    decCh1->SetDisplacementType(
    G4DNAWaterDissociationDisplacer::DissociativeAttachment);
 
    *occ = *(water->GetGroundStateElectronOccupancy());
    occ->AddElectron(5, 1); // H_2O^-
    water->NewConfigurationWithElectronOccupancy(
    "DissociativeAttachment", *occ);
    water->AddDecayChannel(
    "DissociativeAttachment", decCh1);
 
    delete occ;
}
 
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
 
void G4EmDNAChemistry_option2::ConstructReactionTable(
                          G4DNAMolecularReactionTable* theReactionTable)
{
//-----------------------------------
//Get the molecular configuration
    G4MolecularConfiguration* OH =
    G4MoleculeTable::Instance()->GetConfiguration("OH");
    G4MolecularConfiguration* OHm =
    G4MoleculeTable::Instance()->GetConfiguration("OHm");
    G4MolecularConfiguration* e_aq =
    G4MoleculeTable::Instance()->GetConfiguration("e_aq");
    G4MolecularConfiguration* H2 =
    G4MoleculeTable::Instance()->GetConfiguration("H2");
    G4MolecularConfiguration* H3Op =
    G4MoleculeTable::Instance()->GetConfiguration("H3Op");
    G4MolecularConfiguration* H =
    G4MoleculeTable::Instance()->GetConfiguration("H");
    G4MolecularConfiguration* H2O2 =
    G4MoleculeTable::Instance()->GetConfiguration("H2O2");
 
    G4MolecularConfiguration* deoxyribose = 
    G4MoleculeTable::Instance()->GetConfiguration("Deoxyribose");
    G4MolecularConfiguration* adenine = 
    G4MoleculeTable::Instance()->GetConfiguration("Adenine");
    G4MolecularConfiguration* guanine = 
    G4MoleculeTable::Instance()->GetConfiguration("Guanine");
    G4MolecularConfiguration* thymine = 
    G4MoleculeTable::Instance()->GetConfiguration("Thymine");
    G4MolecularConfiguration* cytosine = 
    G4MoleculeTable::Instance()->GetConfiguration("Cytosine");
    G4MolecularConfiguration* histone = 
    G4MoleculeTable::Instance()->GetConfiguration("Histone");
 
    G4MolecularConfiguration* damage_deoxyribose = 
    G4MoleculeTable::Instance()->GetConfiguration("Damaged_Deoxyribose");
    G4MolecularConfiguration* damage_adenine = 
    G4MoleculeTable::Instance()->GetConfiguration("Damaged_Adenine");
    G4MolecularConfiguration* damage_guanine = 
    G4MoleculeTable::Instance()->GetConfiguration("Damaged_Guanine");
    G4MolecularConfiguration* damage_thymine = 
    G4MoleculeTable::Instance()->GetConfiguration("Damaged_Thymine");
    G4MolecularConfiguration* damage_cytosine = 
    G4MoleculeTable::Instance()->GetConfiguration("Damaged_Cytosine");
 
//------------------------------------------------------------------
// e_aq + e_aq + 2H2O -> H2 + 2OH-
    G4DNAMolecularReactionData* reactionData =
    new G4DNAMolecularReactionData(
    0.5e10 * (1e-3 * m3 / (mole * s)), e_aq, e_aq);
    reactionData->AddProduct(OHm);
    reactionData->AddProduct(OHm);
    reactionData->AddProduct(H2);
    theReactionTable->SetReaction(reactionData);
//------------------------------------------------------------------
// e_aq + *OH -> OH-
    reactionData = new G4DNAMolecularReactionData(
    2.95e10 * (1e-3 * m3 / (mole * s)), e_aq, OH);
    reactionData->AddProduct(OHm);
    theReactionTable->SetReaction(reactionData);
//------------------------------------------------------------------
// e_aq + H* + H2O -> H2 + OH-
    reactionData = new G4DNAMolecularReactionData(
    2.65e10 * (1e-3 * m3 / (mole * s)), e_aq, H);
    reactionData->AddProduct(OHm);
    reactionData->AddProduct(H2);
    theReactionTable->SetReaction(reactionData);
//------------------------------------------------------------------
// e_aq + H3O+ -> H* + H2O
    reactionData = new G4DNAMolecularReactionData(
    2.11e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
    reactionData->AddProduct(H);
    theReactionTable->SetReaction(reactionData);
 
//------------------------------------------------------------------
// e_aq + H2O2 -> OH- + *OH
    reactionData = new G4DNAMolecularReactionData(
    1.41e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
    reactionData->AddProduct(OHm);
    reactionData->AddProduct(OH);
    theReactionTable->SetReaction(reactionData);
//------------------------------------------------------------------
// *OH + *OH -> H2O2
    reactionData = new G4DNAMolecularReactionData(
    0.44e10 * (1e-3 * m3 / (mole * s)), OH, OH);
    reactionData->AddProduct(H2O2);
    theReactionTable->SetReaction(reactionData);
//------------------------------------------------------------------
// *OH + *H -> H2O
    theReactionTable->SetReaction(
    1.44e10 * (1e-3 * m3 / (mole * s)), OH, H);
//------------------------------------------------------------------
// *H + *H -> H2
    reactionData = new G4DNAMolecularReactionData(
    1.20e10 * (1e-3 * m3 / (mole * s)), H, H);
    reactionData->AddProduct(H2);
    theReactionTable->SetReaction(reactionData);
//------------------------------------------------------------------
// H3O+ + OH- -> 2H2O
    theReactionTable->SetReaction(
    1.43e11 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
//------------------------------------------------------------------
 
// DNA additions
 
// OH and DNA
 
// 2-Deoxyribose + OH -> damagedDeoxyribose
    reactionData = new G4DNAMolecularReactionData(
    1.80e9*(1e-3*m3/(mole*s)), deoxyribose, OH);
    reactionData->AddProduct(damage_deoxyribose);
    theReactionTable->SetReaction(reactionData);
 
    // adenine + OH -> ...
    reactionData = new G4DNAMolecularReactionData(
    6.10e9*(1e-3*m3/(mole*s)), adenine, OH);
    reactionData->AddProduct(damage_adenine);
    theReactionTable->SetReaction(reactionData);
 
    // guanine + OH -> ...
    reactionData = new G4DNAMolecularReactionData(
    9.20e9*(1e-3*m3/(mole*s)), guanine, OH);
    reactionData->AddProduct(damage_guanine);
    theReactionTable->SetReaction(reactionData);
 
    // thymine + OH -> ...
    reactionData = new G4DNAMolecularReactionData(
    6.40e9*(1e-3*m3/(mole*s)), thymine, OH);
    reactionData->AddProduct(damage_thymine);
    theReactionTable->SetReaction(reactionData);
 
    // cytosine + OH -> ...
    reactionData = new G4DNAMolecularReactionData(
    6.10e9*(1e-3*m3/(mole*s)), cytosine, OH);
    reactionData->AddProduct(damage_cytosine);
    theReactionTable->SetReaction(reactionData);
 
    // Hydrated e- and DNA
 
    // Deoxyribose + Hydrated e-  -> ...
    reactionData = new G4DNAMolecularReactionData(
    0.01e9*(1e-3*m3/(mole*s)), deoxyribose, e_aq);
    reactionData->AddProduct(damage_deoxyribose);
    theReactionTable->SetReaction(reactionData);
 
    // adenine + Hydrated e- -> ...
    reactionData = new G4DNAMolecularReactionData(
    9e9*(1e-3*m3/(mole*s)), adenine, e_aq);
    reactionData->AddProduct(damage_adenine);
    theReactionTable->SetReaction(reactionData);
 
    // guanine + Hydrated e- -> ...
    reactionData = new G4DNAMolecularReactionData(
    14e9*(1e-3*m3/(mole*s)), guanine, e_aq);
    reactionData->AddProduct(damage_guanine);
    theReactionTable->SetReaction(reactionData);
 
    // thymine + Hydrated e- -> ...
    reactionData = new G4DNAMolecularReactionData(
    18e9*(1e-3*m3/(mole*s)), thymine, e_aq);
    reactionData->AddProduct(damage_thymine);
    theReactionTable->SetReaction(reactionData);
 
    // cytosine + Hydrated e- -> ...
    reactionData = new G4DNAMolecularReactionData(
    13e9*(1e-3*m3/(mole*s)), cytosine, e_aq);
    reactionData->AddProduct(damage_cytosine);
    theReactionTable->SetReaction(reactionData);
 
    // Radical H and DNA
 
    // Deoxyribose + Radical H -> ...
    reactionData = new G4DNAMolecularReactionData(
    0.029e9*(1e-3*m3/(mole*s)), deoxyribose, H);
    reactionData->AddProduct(damage_deoxyribose);
    //eactionData->SetEffectiveReactionRadius(0);
 
    theReactionTable->SetReaction(reactionData);
 
    // adenine + Radical H -> ...
    reactionData = new G4DNAMolecularReactionData(
    0.10e9*(1e-3*m3/(mole*s)), adenine, H);
    reactionData->AddProduct(damage_adenine);
    theReactionTable->SetReaction(reactionData);
 
    // thymine + Radical H -> ...
    reactionData = new G4DNAMolecularReactionData(
    0.57e9*(1e-3*m3/(mole*s)), thymine, H);
    reactionData->AddProduct(damage_thymine);
    theReactionTable->SetReaction(reactionData);
 
    // cytosine + Radical H -> ...
    reactionData = new G4DNAMolecularReactionData(
    0.092e9*(1e-3*m3/(mole*s)), cytosine, H);
    reactionData->AddProduct(damage_cytosine);
    theReactionTable->SetReaction(reactionData);
 
    //histone + all molecules -> modification(or "damage")
 
    reactionData = new G4DNAMolecularReactionData(
    0.0*(1e-3*m3/(mole*s)), histone, OH);
    reactionData->AddProduct(histone);
    reactionData->SetEffectiveReactionRadius(
    2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
    theReactionTable->SetReaction(reactionData);
 
    reactionData = new G4DNAMolecularReactionData(
    0.0*(1e-3*m3/(mole*s)), histone, OHm);
    reactionData->AddProduct(histone);
    reactionData->SetEffectiveReactionRadius(
    2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
    theReactionTable->SetReaction(reactionData);
 
    reactionData = new G4DNAMolecularReactionData(
    0.0*(1e-3*m3/(mole*s)), histone, e_aq);
    reactionData->AddProduct(histone);
    reactionData->SetEffectiveReactionRadius(
    2.4*nm + G4Electron_aq::Definition()->GetVanDerVaalsRadius());
    theReactionTable->SetReaction(reactionData);
 
    reactionData = new G4DNAMolecularReactionData(
    0.0*(1e-3*m3/(mole*s)), histone, H2);
    reactionData->AddProduct(histone);
    reactionData->SetEffectiveReactionRadius(
    2.4*nm + G4H2::Definition()->GetVanDerVaalsRadius());
    theReactionTable->SetReaction(reactionData);
 
    reactionData = new G4DNAMolecularReactionData(
    0.0*(1e-3*m3/(mole*s)), histone, H3Op);
    reactionData->AddProduct(histone);
    reactionData->SetEffectiveReactionRadius(
    2.4*nm + G4H3O::Definition()->GetVanDerVaalsRadius());
    theReactionTable->SetReaction(reactionData);
 
    reactionData = new G4DNAMolecularReactionData(
    0.0*(1e-3*m3/(mole*s)), histone, H);
    reactionData->AddProduct(histone);
    reactionData->SetEffectiveReactionRadius(
    2.4*nm + G4Hydrogen::Definition()->GetVanDerVaalsRadius());
    theReactionTable->SetReaction(reactionData);
 
    reactionData = new G4DNAMolecularReactionData(
    0.0*(1e-3*m3/(mole*s)), histone, H2O2);
    reactionData->AddProduct(histone);
    reactionData->SetEffectiveReactionRadius(
    2.4*nm + G4H2O2::Definition()->GetVanDerVaalsRadius());
    theReactionTable->SetReaction(reactionData);
}
 
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
 
void G4EmDNAChemistry_option2::ConstructProcess()
{
    auto pPhysicsListHelper = 
    G4PhysicsListHelper::GetPhysicsListHelper();
    G4VProcess* pProcess = 
    G4ProcessTable::GetProcessTable()->
    FindProcess("e-_G4DNAVibExcitation", "e-");
 
    if (pProcess != nullptr)
    {
        G4DNAVibExcitation* pVibExcitation = 
        (G4DNAVibExcitation*) pProcess;
        G4VEmModel* pModel = pVibExcitation->EmModel();
        G4DNASancheExcitationModel* pSancheExcitationMod =
        dynamic_cast<G4DNASancheExcitationModel*>(pModel);
        if(pSancheExcitationMod != nullptr)
        {
            pSancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
        }
    }
 
//===============================================================
// Electron Solvatation
//
    pProcess = G4ProcessTable::GetProcessTable()->
    FindProcess("e-_G4DNAElectronSolvation", "e-");
  
    if (pProcess == nullptr)
    {
        pPhysicsListHelper->
        RegisterProcess(new G4DNAElectronSolvation(
        "e-_G4DNAElectronSolvation"), G4Electron::Definition());
    }
 
//===============================================================
// Define processes for molecules
//
    G4MoleculeTable* pMoleculeTable = 
    G4MoleculeTable::Instance();
    G4MoleculeDefinitionIterator iterator = 
    pMoleculeTable->GetDefintionIterator();
    iterator.reset();
    while (iterator())
    {
        G4MoleculeDefinition* pMoleculeDef = iterator.value();
 
        if(pMoleculeDef != G4H2O::Definition())
        {
            G4DNABrownianTransportation* pBrownianTransport = 
            new G4DNABrownianTransportation();
            pPhysicsListHelper->
            RegisterProcess(pBrownianTransport, pMoleculeDef);
        }
        else
        {
            pMoleculeDef->GetProcessManager()->
            AddRestProcess(new G4DNAElectronHoleRecombination(), 2);
            G4DNAMolecularDissociation* pDissociationProcess = 
            new G4DNAMolecularDissociation("H2O_DNAMolecularDecay");
            pDissociationProcess->SetDisplacer(pMoleculeDef, 
            new G4DNAWaterDissociationDisplacer);
            pDissociationProcess->SetVerboseLevel(1);
 
            pMoleculeDef->GetProcessManager()->
            AddRestProcess(pDissociationProcess, 1);
        }
    }
    G4DNAChemistryManager::Instance()->Initialize();
}
 
 
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
 
void G4EmDNAChemistry_option2::ConstructTimeStepModel(
G4DNAMolecularReactionTable* reactionTable)
{
    G4VDNAReactionModel* reactionRadiusComputer = 
    new G4DNASmoluchowskiReactionModel();
    reactionTable->PrintTable(reactionRadiusComputer);
 
    G4DNAMolecularStepByStepModel* stepByStep = 
    new G4DNAMolecularStepByStepModel();
    stepByStep->SetReactionModel(reactionRadiusComputer);
    
    RegisterTimeStepModel(stepByStep, 0);
}