Mirams2010WntOdeSystem.cpp

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*/
#include "Mirams2010WntOdeSystem.hpp"
#include "CellwiseOdeSystemInformation.hpp"

// These #includes are needed for the constructor and EvaluateYDerivatives()
#include "ApcOneHitCellMutationState.hpp"
#include "ApcTwoHitCellMutationState.hpp"
#include "BetaCateninOneHitCellMutationState.hpp"
#include "CellLabel.hpp"
#include "WildTypeCellMutationState.hpp"

Mirams2010WntOdeSystem::Mirams2010WntOdeSystem(double wntLevel,
                                               boost::shared_ptr<AbstractCellMutationState> pMutationState,
                                               std::vector<double> stateVariables)
    : AbstractOdeSystem(3),
      mpMutationState(pMutationState),
      mWntLevel(wntLevel)
{
    mpSystemInfo.reset(new CellwiseOdeSystemInformation<Mirams2010WntOdeSystem>);

    Init(); // set up parameter values

    // Set up rough guesses for the initial steady states in this Wnt conc.
    double b1 = 0;
    double b2 = 0;
    b1 = (mA/2.0) / (((wntLevel + mB)/(mC*wntLevel + mD)) + mF);
    if (!mpMutationState)
    {
        // No mutations specified
    }
    else if (mpMutationState->IsType<BetaCateninOneHitCellMutationState>())
    {
        b2 = (mA/2.0)/mF;
    }
    else
    {
        b2 = (mA/2.0) / (((wntLevel + mB)/(mC*wntLevel + mD)) + mF);
    }

    SetDefaultInitialCondition(0, b1);
    SetDefaultInitialCondition(1, b2);
    SetDefaultInitialCondition(2, wntLevel);

    if (stateVariables != std::vector<double>())
    {
        SetStateVariables(stateVariables);
    }
}

void Mirams2010WntOdeSystem::SetMutationState(boost::shared_ptr<AbstractCellMutationState> pMutationState)
{
    mpMutationState = pMutationState;
}

Mirams2010WntOdeSystem::~Mirams2010WntOdeSystem()
{
    // Do nothing
}

void Mirams2010WntOdeSystem::Init()
{
    // Initialise model parameter values
    mA = 25.38;     // nM hr^{-1}
    mB = 0.1;       // dimensionless
    mC = 6.386;     // hr
    mD = 9.818e-2;  // hr
    mE = 1.2e3;     // nM
    mF = 1.54e-2;   // hr^{-1}
}

void Mirams2010WntOdeSystem::EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY)
{
    double x1 = rY[0];
    double x2 = rY[1];
    double wnt_level = rY[2];

    double dx1 = 0.0;
    double dx2 = 0.0;
    /*
     * The variables are
     * 1. b = Beta-Catenin1
     * 2. b = Beta-Catenin2
    */

    double c = mC;
    double d = mD;
    // Mutations take effect by altering the parameters
    if (mpMutationState->IsType<ApcOneHitCellMutationState>()) // APC +/-
    {
        c = 31.87;
        d = 0.490;
    }
    else if (mpMutationState->IsType<ApcTwoHitCellMutationState>()) // APC -/-
    {
        c = 71.21;
        d = 1.095;
    }

    // da
    dx1 = mA/2.0 - (((wnt_level + mB)/(c*wnt_level + d))*(mE/(mE+x1)) + mF)*x1;
    // db
    if (mpMutationState->IsType<BetaCateninOneHitCellMutationState>())
    {
        dx2 = mA/2.0 - mF*x2;
    }
    else
    {
        dx2 = mA/2.0 - (((wnt_level + mB)/(c*wnt_level + d))*(mE/(mE+x2)) + mF)*x2;
    }

    rDY[0] = dx1;
    rDY[1] = dx2;
    rDY[2] = 0.0; // do not change the Wnt level
}

const boost::shared_ptr<AbstractCellMutationState> Mirams2010WntOdeSystem::GetMutationState() const
{
    return mpMutationState;
}

template<>
void CellwiseOdeSystemInformation<Mirams2010WntOdeSystem>::Initialise()
{
    this->mVariableNames.push_back("Beta_Cat_Allele1");
    this->mVariableUnits.push_back("nM");
    this->mInitialConditions.push_back(50.0); // will be filled in later

    this->mVariableNames.push_back("Beta_Cat_Allele2");
    this->mVariableUnits.push_back("nM");
    this->mInitialConditions.push_back(50.0); // will be filled in later

    this->mVariableNames.push_back("Wnt Level");
    this->mVariableUnits.push_back("non-dim");
    this->mInitialConditions.push_back(0.5); // will be filled in later

    this->mInitialised = true;
}

double Mirams2010WntOdeSystem::GetWntLevel() const
{
    return mWntLevel;
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(Mirams2010WntOdeSystem)