DeltaNotchEdgeSrnModel.cpp

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*/
 
#include "DeltaNotchEdgeSrnModel.hpp"
 
DeltaNotchEdgeSrnModel::DeltaNotchEdgeSrnModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
    : AbstractOdeSrnModel(2, pOdeSolver)
{
    if (mpOdeSolver == boost::shared_ptr<AbstractCellCycleModelOdeSolver>())
    {
#ifdef CHASTE_CVODE
        mpOdeSolver = CellCycleModelOdeSolver<DeltaNotchEdgeSrnModel, CvodeAdaptor>::Instance();
        mpOdeSolver->Initialise();
        mpOdeSolver->SetMaxSteps(10000);
#else
        mpOdeSolver = CellCycleModelOdeSolver<DeltaNotchEdgeSrnModel, RungeKutta4IvpOdeSolver>::Instance();
        mpOdeSolver->Initialise();
        SetDt(0.001);
#endif //CHASTE_CVODE
    }
    assert(mpOdeSolver->IsSetUp());
}
 
DeltaNotchEdgeSrnModel::DeltaNotchEdgeSrnModel(const DeltaNotchEdgeSrnModel& rModel)
    : AbstractOdeSrnModel(rModel)
{
    /*
     * Set each member variable of the new SRN model that inherits
     * its value from the parent.
     *
     * Note 1: some of the new SRN model's member variables
     * will already have been correctly initialized in its constructor.
     *
     * Note 2: one or more of the new SRN model's member variables
     * may be set/overwritten as soon as InitialiseDaughterCell() is called on
     * the new SRN model.
     *
     * Note 3: Only set the variables defined in this class. Variables defined
     * in parent classes will be defined there.
     */
    assert(rModel.GetOdeSystem());
    AbstractOdeSystem* p_parent_system(rModel.GetOdeSystem());
    SetOdeSystem(new DeltaNotchEdgeOdeSystem(p_parent_system->rGetStateVariables()));
    for (unsigned i=0; i < p_parent_system->GetNumberOfParameters(); ++i)
    {
        mpOdeSystem->SetParameter(i, p_parent_system->GetParameter(i));
    }
}
 
AbstractSrnModel* DeltaNotchEdgeSrnModel::CreateSrnModel()
{
    return new DeltaNotchEdgeSrnModel(*this);
}
 
void DeltaNotchEdgeSrnModel::SimulateToCurrentTime()
{
    // Update information before running simulation
    UpdateDeltaNotch();
 
    // Run the ODE simulation as needed
    AbstractOdeSrnModel::SimulateToCurrentTime();
}
 
void DeltaNotchEdgeSrnModel::Initialise()
{
    AbstractOdeSrnModel::Initialise(new DeltaNotchEdgeOdeSystem);
}
 
void DeltaNotchEdgeSrnModel::InitialiseDaughterCell()
{
    assert(mpOdeSystem != nullptr);
    assert(mpCell != nullptr);
 
    // A new edge is initialised with zero concentrations
    mpOdeSystem->SetStateVariable("Notch", 0.0);
    mpOdeSystem->SetStateVariable("Delta", 0.0);
    mpOdeSystem->SetParameter("neighbour delta", 0.0);
    mpOdeSystem->SetParameter("interior delta", 0.0);
    mpOdeSystem->SetParameter("interior notch", 0.0);
}
 
void DeltaNotchEdgeSrnModel::UpdateDeltaNotch()
{
    assert(mpOdeSystem != nullptr);
    assert(mpCell != nullptr);
 
    double neigh_delta = mpCell->GetCellEdgeData()->GetItem("neighbour delta")[this->GetEdgeLocalIndex()];
    mpOdeSystem->SetParameter("neighbour delta", neigh_delta);
 
    double interior_delta = mpCell->GetCellData()->GetItem("interior delta");
    mpOdeSystem->SetParameter("interior delta", interior_delta);
 
    double interior_notch = mpCell->GetCellData()->GetItem("interior notch");
    mpOdeSystem->SetParameter("interior notch", interior_notch);
}
 
double DeltaNotchEdgeSrnModel::GetNotch()
{
    assert(mpOdeSystem != nullptr);
    double notch = mpOdeSystem->rGetStateVariables()[0];
    return notch;
}
 
void DeltaNotchEdgeSrnModel::SetNotch(double value)
{
    assert(mpOdeSystem != nullptr);
    mpOdeSystem->rGetStateVariables()[0] = value;
}
 
double DeltaNotchEdgeSrnModel::GetDelta()
{
    assert(mpOdeSystem != nullptr);
    double delta = mpOdeSystem->rGetStateVariables()[1];
    return delta;
}
 
void DeltaNotchEdgeSrnModel::SetDelta(double value)
{
    assert(mpOdeSystem != nullptr);
    mpOdeSystem->rGetStateVariables()[1] = value;
}
 
double DeltaNotchEdgeSrnModel::GetNeighbouringDelta() const
{
    assert(mpOdeSystem != nullptr);
    return mpOdeSystem->GetParameter("neighbour delta");
}
 
double DeltaNotchEdgeSrnModel::GetInteriorDelta() const
{
    assert(mpOdeSystem != nullptr);
    return mpOdeSystem->GetParameter("interior delta");
}
 
double DeltaNotchEdgeSrnModel::GetInteriorNotch() const
{
    assert(mpOdeSystem != nullptr);
    return mpOdeSystem->GetParameter("interior notch");
}
 
void DeltaNotchEdgeSrnModel::OutputSrnModelParameters(out_stream& rParamsFile)
{
    // No new parameters to output, so just call method on direct parent class
    AbstractOdeSrnModel::OutputSrnModelParameters(rParamsFile);
}
 
void DeltaNotchEdgeSrnModel::AddSrnQuantities(AbstractSrnModel* pOtherSrn,
                                              const double scale)
{
    auto p_other_srn = static_cast<DeltaNotchEdgeSrnModel*>(pOtherSrn);
    const double other_delta = p_other_srn->GetDelta();
    const double other_notch = p_other_srn->GetNotch();
    const double this_delta = GetDelta();
    const double this_notch = GetNotch();
    SetDelta(this_delta + scale*other_delta);
    SetNotch(this_notch + scale*other_notch);
}
 
void DeltaNotchEdgeSrnModel::AddShrunkEdgeSrn(AbstractSrnModel* pShrunkEdgeSrn)
{
    /*
     * Here we assume that one half of SRN quantities are endocytosed and the remaining
     * half are split between neighbouring junctions, hence we add 1/4 of SRN variables.
    */
    AddSrnQuantities(pShrunkEdgeSrn, 0.25);
}
 
void DeltaNotchEdgeSrnModel::AddMergedEdgeSrn(AbstractSrnModel* pMergedEdgeSrn)
{
    // Add all SRN variables to this edge SRN
    AddSrnQuantities(pMergedEdgeSrn);
}
 
void DeltaNotchEdgeSrnModel::SplitEdgeSrn(const double relativePosition)
{
    // Edges with longer relative lengths after split have higher concentration
    ScaleSrnVariables(relativePosition);
}
 
// Declare identifier for the serializer
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(DeltaNotchEdgeSrnModel)
#include "CellCycleModelOdeSolverExportWrapper.hpp"
EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(DeltaNotchEdgeSrnModel)