ContactInhibitionCellCycleModel.cpp

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*/

#include "ContactInhibitionCellCycleModel.hpp"
#include "CellLabel.hpp"
#include "DifferentiatedCellProliferativeType.hpp"

ContactInhibitionCellCycleModel::ContactInhibitionCellCycleModel()
    : AbstractSimpleCellCycleModel(),
      mQuiescentVolumeFraction(DOUBLE_UNSET),
      mEquilibriumVolume(DOUBLE_UNSET),
      mCurrentQuiescentOnsetTime(SimulationTime::Instance()->GetTime()),
      mCurrentQuiescentDuration(0.0)
{
}

void ContactInhibitionCellCycleModel::UpdateCellCyclePhase()
{
    if ((mQuiescentVolumeFraction == DOUBLE_UNSET) || (mEquilibriumVolume == DOUBLE_UNSET))
    {
        EXCEPTION("The member variables mQuiescentVolumeFraction and mEquilibriumVolume have not yet been set.");
    }

    // Get cell volume
    double cell_volume = mpCell->GetCellData()->GetItem("volume");

    // Removes the cell label
    mpCell->RemoveCellProperty<CellLabel>();

    if (mCurrentCellCyclePhase == G_ONE_PHASE)
    {
        // Update G1 duration based on cell volume
        double dt = SimulationTime::Instance()->GetTimeStep();
        double quiescent_volume = mEquilibriumVolume * mQuiescentVolumeFraction;

        if (cell_volume < quiescent_volume)
        {
            // Update the duration of the current period of contact inhibition.
            mCurrentQuiescentDuration = SimulationTime::Instance()->GetTime() - mCurrentQuiescentOnsetTime;
            mG1Duration += dt;

            /*
             * This method is usually called within a CellBasedSimulation, after the CellPopulation
             * has called CellPropertyRegistry::TakeOwnership(). This means that were we to call
             * CellPropertyRegistry::Instance() here when adding the CellLabel, we would be creating
             * a new CellPropertyRegistry. In this case the CellLabel's cell count would be incorrect.
             * We must therefore access the CellLabel via the cell's CellPropertyCollection.
             */
            boost::shared_ptr<AbstractCellProperty> p_label =
                mpCell->rGetCellPropertyCollection().GetCellPropertyRegistry()->Get<CellLabel>();
            mpCell->AddCellProperty(p_label);
        }
        else
        {
            // Reset the cell's quiescent duration and update the time at which the onset of quiescent occurs
            mCurrentQuiescentDuration = 0.0;
            mCurrentQuiescentOnsetTime = SimulationTime::Instance()->GetTime();
        }
    }

    double time_since_birth = GetAge();
    assert(time_since_birth >= 0);

    if (mpCell->GetCellProliferativeType()->IsType<DifferentiatedCellProliferativeType>())
    {
        mCurrentCellCyclePhase = G_ZERO_PHASE;
    }
    else if ( time_since_birth < GetMDuration() )
    {
        mCurrentCellCyclePhase = M_PHASE;
    }
    else if ( time_since_birth < GetMDuration() + mG1Duration)
    {
        mCurrentCellCyclePhase = G_ONE_PHASE;
    }
    else if ( time_since_birth < GetMDuration() + mG1Duration + GetSDuration())
    {
        mCurrentCellCyclePhase = S_PHASE;
    }
    else if ( time_since_birth < GetMDuration() + mG1Duration + GetSDuration() + GetG2Duration())
    {
        mCurrentCellCyclePhase = G_TWO_PHASE;
    }
}

AbstractCellCycleModel* ContactInhibitionCellCycleModel::CreateCellCycleModel()
{
    // Create a new cell-cycle model
    ContactInhibitionCellCycleModel* p_model = new ContactInhibitionCellCycleModel();

    /*
     * Set each member variable of the new cell-cycle model that inherits
     * its value from the parent.
     *
     * Note 1: some of the new cell-cycle model's member variables (namely
     * mBirthTime, mCurrentCellCyclePhase, mReadyToDivide, mTimeSpentInG1Phase,
     * mCurrentHypoxicDuration, mCurrentHypoxiaOnsetTime) will already have been
     * correctly initialized in its constructor.
     *
     * Note 2: one or more of the new cell-cycle model's member variables
     * may be set/overwritten as soon as InitialiseDaughterCell() is called on
     * the new cell-cycle model.
     */
    p_model->SetBirthTime(mBirthTime);
    p_model->SetDimension(mDimension);
    p_model->SetMinimumGapDuration(mMinimumGapDuration);
    p_model->SetStemCellG1Duration(mStemCellG1Duration);
    p_model->SetTransitCellG1Duration(mTransitCellG1Duration);
    p_model->SetSDuration(mSDuration);
    p_model->SetG2Duration(mG2Duration);
    p_model->SetMDuration(mMDuration);
    p_model->SetQuiescentVolumeFraction(mQuiescentVolumeFraction);
    p_model->SetEquilibriumVolume(mEquilibriumVolume);
    p_model->SetCurrentQuiescentOnsetTime(mCurrentQuiescentOnsetTime);
    p_model->SetCurrentQuiescentDuration(mCurrentQuiescentDuration);

    return p_model;
}

void ContactInhibitionCellCycleModel::SetQuiescentVolumeFraction(double quiescentVolumeFraction)
{
    mQuiescentVolumeFraction = quiescentVolumeFraction;
}

double ContactInhibitionCellCycleModel::GetQuiescentVolumeFraction()
{
    return mQuiescentVolumeFraction;
}

void ContactInhibitionCellCycleModel::SetEquilibriumVolume(double equilibriumVolume)
{
    mEquilibriumVolume = equilibriumVolume;
}

double ContactInhibitionCellCycleModel::GetEquilibriumVolume()
{
    return mEquilibriumVolume;
}

void ContactInhibitionCellCycleModel::SetCurrentQuiescentDuration(double currentQuiescentDuration)
{
    mCurrentQuiescentDuration = currentQuiescentDuration;
}

double ContactInhibitionCellCycleModel::GetCurrentQuiescentDuration()
{
    return mCurrentQuiescentDuration;
}

void ContactInhibitionCellCycleModel::SetCurrentQuiescentOnsetTime(double currentQuiescentOnsetTime)
{
    mCurrentQuiescentOnsetTime = currentQuiescentOnsetTime;
}

double ContactInhibitionCellCycleModel::GetCurrentQuiescentOnsetTime()
{
    return mCurrentQuiescentOnsetTime;
}

void ContactInhibitionCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<QuiescentVolumeFraction>" << mQuiescentVolumeFraction << "</QuiescentVolumeFraction>\n";
    *rParamsFile << "\t\t\t<EquilibriumVolume>" << mEquilibriumVolume << "</EquilibriumVolume>\n";

    // Call method on direct parent class
    AbstractSimpleCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(ContactInhibitionCellCycleModel)