G4DNAPartiallyDiffusionControlled Class Reference

#include <G4DNAPartiallyDiffusionControlled.hh>

Inheritance diagram for G4DNAPartiallyDiffusionControlled:

Public Member Functions
	G4DNAPartiallyDiffusionControlled ()
	G4DNAPartiallyDiffusionControlled (const G4DNAPartiallyDiffusionControlled &other)=delete
G4bool	GeminateRecombinationProbability (const G4MolecularConfiguration *, const G4MolecularConfiguration *) override
G4double	GetTimeToEncounter (const G4Track &trackA, const G4Track &trackB) override
G4DNAPartiallyDiffusionControlled &	operator= (const G4DNAPartiallyDiffusionControlled &other)=delete
	~G4DNAPartiallyDiffusionControlled () override

Private Member Functions
G4double	GetDiffusionCoefficient (const G4MolecularConfiguration *, const G4MolecularConfiguration *)

Detailed Description

Definition at line 36 of file G4DNAPartiallyDiffusionControlled.hh.

Constructor & Destructor Documentation

G4DNAPartiallyDiffusionControlled() [1/2]

G4DNAPartiallyDiffusionControlled::G4DNAPartiallyDiffusionControlled

(

)

Definition at line 40 of file G4DNAPartiallyDiffusionControlled.cc.

    : G4VReactionType()
{}

~G4DNAPartiallyDiffusionControlled()

G4DNAPartiallyDiffusionControlled::~G4DNAPartiallyDiffusionControlled ( )

overridedefault

G4DNAPartiallyDiffusionControlled() [2/2]

G4DNAPartiallyDiffusionControlled::G4DNAPartiallyDiffusionControlled ( const G4DNAPartiallyDiffusionControlled &  other )

delete

Member Function Documentation

GeminateRecombinationProbability()

G4bool G4DNAPartiallyDiffusionControlled::GeminateRecombinationProbability ( const G4MolecularConfiguration *  mA, const G4MolecularConfiguration *  mB  )

overridevirtual

Implements G4VReactionType.

Definition at line 47 of file G4DNAPartiallyDiffusionControlled.cc.

{
    auto reactionData = G4DNAMolecularReactionTable::Instance()
        ->GetReactionData(mA, mB);
 
    G4double D = GetDiffusionCoefficient(mA, mB);
    G4double R = mA->GetVanDerVaalsRadius() + mB->GetVanDerVaalsRadius();
    
    const G4double Rs = 0.3 * nm;
    G4double kobs = reactionData->GetObservedReactionRateConstant() / Avogadro;
    if(mA->GetCharge() * mB->GetCharge() == 0)
    {
        G4double kdif = 4 * CLHEP::pi * D * R * Avogadro;
        G4double kact = G4IRTUtils::GetKact(kobs, kdif);
        return G4UniformRand() < Rs / ( Rs + ( kdif / kact ) * ( R + Rs ));
    }
    else
    {
        G4double rc = 0.71 * nm * mA->GetCharge() *
                                  mB->GetCharge();
        G4double sigmaEff = G4IRTUtils::EffectiveDistance(rc, R);
        G4double kdif = 4 * CLHEP::pi * D * sigmaEff;
        G4double kact = G4IRTUtils::GetKact(kobs, kdif);
        G4double a = std::exp( -rc / R );
        G4double b = std::exp( -rc / ( R + Rs ) );
        G4double Preact = ( a - b ) / ( a - b - ( kdif / kact ) * ( 1 - a ) );
        
        return G4UniformRand() < Preact;
    }
}

References source.hepunit::Avogadro, D(), G4IRTUtils::EffectiveDistance(), G4UniformRand, G4MolecularConfiguration::GetCharge(), GetDiffusionCoefficient(), G4IRTUtils::GetKact(), G4DNAMolecularReactionTable::GetReactionData(), G4MolecularConfiguration::GetVanDerVaalsRadius(), G4DNAMolecularReactionTable::Instance(), nm, and CLHEP::pi.

GetDiffusionCoefficient()

G4double G4DNAPartiallyDiffusionControlled::GetDiffusionCoefficient ( const G4MolecularConfiguration *  mA, const G4MolecularConfiguration *  mB  )

private

Definition at line 80 of file G4DNAPartiallyDiffusionControlled.cc.

{
    G4double D;
 
    if(mA == mB)
    {    
        D = (mA->GetDiffusionCoefficient());
    }
    else
    {
        D = (mA->GetDiffusionCoefficient() +
             mB->GetDiffusionCoefficient());
    }
    return D;
}

References D(), and G4MolecularConfiguration::GetDiffusionCoefficient().

Referenced by GeminateRecombinationProbability(), and GetTimeToEncounter().

GetTimeToEncounter()

G4double G4DNAPartiallyDiffusionControlled::GetTimeToEncounter ( const G4Track &  trackA, const G4Track &  trackB  )

overridevirtual

Implements G4VReactionType.

Definition at line 97 of file G4DNAPartiallyDiffusionControlled.cc.

{
    auto pMolConfA = GetMolecule(trackA)->GetMolecularConfiguration();
    auto pMolConfB = GetMolecule(trackB)->GetMolecularConfiguration();
 
    G4double D = GetDiffusionCoefficient(pMolConfA, pMolConfB);
    auto reactionData = G4DNAMolecularReactionTable::Instance()
    ->GetReactionData(pMolConfA, pMolConfB);
    G4double Reff;
    G4double kobs = reactionData->GetObservedReactionRateConstant();
    G4double distance = (trackA.GetPosition() - trackB.GetPosition()).mag();
    G4double SmoluchowskiRadius;
    G4double RVal = pMolConfA->GetVanDerVaalsRadius() + pMolConfB->GetVanDerVaalsRadius();
    
    if((pMolConfA->GetCharge() != 0) &&
       (pMolConfB->GetCharge() != 0))
    {
        G4double rc = 0.71 * nm * pMolConfA->GetCharge() *
        pMolConfB->GetCharge();
        distance = G4IRTUtils::EffectiveDistance( rc, distance );
        Reff = G4IRTUtils::EffectiveDistance( rc, RVal );
        SmoluchowskiRadius = Reff;
    }
    else
    {
        SmoluchowskiRadius = RVal;
    }
    
    G4double Winf = SmoluchowskiRadius / distance;
    G4double U1 = G4UniformRand();
    G4double U2 = G4UniformRand();
    G4double U = G4UniformRand();
    G4double X = 0;
    G4double irt_1 = -1.0 * ps;
    G4double irt_2;
 
    G4double kdif = 4 * CLHEP::pi * D * SmoluchowskiRadius * Avogadro;
    G4double kact = G4IRTUtils::GetKact(kobs, kdif);
    
    if ( U < Winf )
    {
        G4double d = ( distance - SmoluchowskiRadius ) /
                     G4ErrorFunction::erfcInv( U / Winf );
        irt_1 = ( 1.0 / ( 4 * D ) ) * d * d;
    }
    
    if( irt_1 < 0)
    {
        return irt_1;
    }
    else
    {
        G4double rateFactor = kact / ( kact + kdif );
        if( U1 > rateFactor )
        {
            return -1.0 * ps;
        }
        G4double Y = std::abs(G4RandGauss::shoot(0.0,std::sqrt(2)));
 
        if( Y > 0)
        {
            X = - ( G4Log( U2 ) ) / Y;
        }
 
        G4double f = X * SmoluchowskiRadius * kdif / ( kact + kdif );
        irt_2 = ( f * f ) / D ;
    }
    
    return irt_1 + irt_2;
}

References source.hepunit::Avogadro, D(), G4IRTUtils::EffectiveDistance(), G4ErrorFunction::erfcInv(), G4Log(), G4UniformRand, GetDiffusionCoefficient(), G4IRTUtils::GetKact(), G4Molecule::GetMolecularConfiguration(), GetMolecule(), G4DNAMolecularReactionData::GetObservedReactionRateConstant(), G4Track::GetPosition(), G4DNAMolecularReactionTable::GetReactionData(), G4DNAMolecularReactionTable::Instance(), nm, CLHEP::pi, ps, G4INCL::DeJongSpin::shoot(), and Y().

operator=()

G4DNAPartiallyDiffusionControlled & G4DNAPartiallyDiffusionControlled::operator= ( const G4DNAPartiallyDiffusionControlled &  other )

delete

---

The documentation for this class was generated from the following files:

• source/processes/electromagnetic/dna/models/include/G4DNAPartiallyDiffusionControlled.hh
• source/processes/electromagnetic/dna/models/src/G4DNAPartiallyDiffusionControlled.cc