TysonNovak2001OdeSystem.cpp

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#include "TysonNovak2001OdeSystem.hpp"
#include "OdeSystemInformation.hpp"
#include "MathsCustomFunctions.hpp"

TysonNovak2001OdeSystem::TysonNovak2001OdeSystem(std::vector<double> stateVariables)
    : AbstractOdeSystemWithAnalyticJacobian(6)
{
    mpSystemInfo = OdeSystemInformation<TysonNovak2001OdeSystem>::Instance();

    Init();

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

TysonNovak2001OdeSystem::~TysonNovak2001OdeSystem()
{
    // Do nothing
}

void TysonNovak2001OdeSystem::Init()
{
    // Initialise model parameter values
    mK1 = 0.04;
    mK2d = 0.04;
    mK2dd = 1.0;
    mK2ddd = 1.0;
    mCycB_threshold = 0.1;
    mK3d = 1.0;
    mK3dd = 10.0;
    mK4d = 2.0;
    mK4 = 35;
    mJ3 = 0.04;
    mJ4 = 0.04;
    mK5d = 0.005;
    mK5dd = 0.2;
    mK6 = 0.1;
    mJ5 = 0.3;
    mN = 4u;
    mK7 = 1.0;
    mK8 = 0.5;
    mJ7 = 1e-3;
    mJ8 = 1e-3;
    mMad = 1.0;
    mK9 = 0.1;
    mK10 = 0.02;
    mK11 = 1.0;
    mK12d = 0.2;
    mK12dd = 50.0;
    mK12ddd = 100.0;
    mKeq = 1e3;
    mK13 = 1.0;
    mK14 = 1.0;
    mK15d = 1.5;
    mK15dd = 0.05;
    mK16d = 1.0;
    mK16dd = 3.0;
    mJ15 = 0.01;
    mJ16 = 0.01;
    mMu = 0.01;
    mMstar = 10.0;
}

void TysonNovak2001OdeSystem::EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY)
{
    double x1 = rY[0];
    double x2 = rY[1];
    double x3 = rY[2];
    double x4 = rY[3];
    double x5 = rY[4];
    double x6 = rY[5];

    double dx1 = 0.0;
    double dx2 = 0.0;
    double dx3 = 0.0;
    double dx4 = 0.0;
    double dx5 = 0.0;
    double dx6 = 0.0;

    double temp1 = 0.0;
    double temp2 = 0.0;
    double temp3 = 0.0;

    dx1 = mK1-(mK2d+mK2dd*x2)*x1;

    // The commented line below models the start transition, no cycling, without Cdc20A
//    temp1 = ((mK3d)*(1.0-x2))/(mJ3+1.0-x2);

    temp1 = ((mK3d+mK3dd*x4)*(1.0-x2))/(mJ3+1.0-x2);
    temp2 = (mK4*x6*x1*x2)/(mJ4+x2);
    dx2 = temp1-temp2;

    temp1 = mK5dd*(SmallPow(x1*x6/mJ5,mN)/(1+SmallPow(x1*x6/mJ5,mN)));
    temp2 = mK6*x3;
    dx3 = mK5d + temp1 - temp2;

    temp1 = (mK7*x5*(x3-x4))/(mJ7+x3-x4);
    temp2 = (mK8*mMad*x4)/(mJ8+x4);
    temp3 = mK6*x4;
    dx4 = temp1 - temp2 - temp3;

    dx5 = mK9*x6*x1*(1.0-x5) - mK10*x5;

    dx6 = mMu*x6*(1.0-x6/mMstar);

    // Multiply by 60 beacuase the Tyson and Noval 2001 paper has time in minutes, not hours
    rDY[0] = dx1*60.0;
    rDY[1] = dx2*60.0;
    rDY[2] = dx3*60.0;
    rDY[3] = dx4*60.0;
    rDY[4] = dx5*60.0;
    rDY[5] = dx6*60.0;
}

void TysonNovak2001OdeSystem::AnalyticJacobian(const std::vector<double>& rSolutionGuess, double** jacobian, double time, double timeStep)
{
    timeStep *= 60.0; // to scale Jacobian so in hours not minutes
    double x1 = rSolutionGuess[0];
    double x2 = rSolutionGuess[1];
    double x3 = rSolutionGuess[2];
    double x4 = rSolutionGuess[3];
    double x5 = rSolutionGuess[4];
    double x6 = rSolutionGuess[5];

    // f1
    double df1_dx1 = -mK2d - mK2dd*x2;
    double df1_dx2 = -mK2dd*x1;

    jacobian[0][0] =  1-timeStep*df1_dx1;
    jacobian[0][1] = -timeStep*df1_dx2;

    // f2
    double df2_dx1 = -mK4*x6*x2/(mJ4+x2);
    double df2_dx2 = -mJ3*(mK3d + mK3dd*x4)/(SmallPow((mJ3 + 1 - x2),2))
                     -mJ4*mK4*x6*x1/(SmallPow((mJ4+x2),2));
    double df2_dx4 =  mK3dd*(1-x2)/(mJ3+1-x2);
    double df2_dx6 = -mK4*x1*x2/(mJ4+x2);

    jacobian[1][0] = -timeStep*df2_dx1;
    jacobian[1][1] =  1-timeStep*df2_dx2;
    jacobian[1][3] = -timeStep*df2_dx4;
    jacobian[1][5] = -timeStep*df2_dx6;

    //f3
    double z = x1*x6/mJ5;
    double df3_dx1 = (mK5dd*x6/mJ5)*mN*SmallPow(z,mN-1)/(SmallPow((1-SmallPow(z,mN)),2));
    double df3_dx3 = -mK6;
    double df3_dx6 = (mK5dd*x1/mJ5)*mN*SmallPow(z,mN-1)/(SmallPow((1-SmallPow(z,mN)),2));

    jacobian[2][0] = -timeStep*df3_dx1;
    jacobian[2][2] = 1-timeStep*df3_dx3;
    jacobian[2][5] = -timeStep*df3_dx6;

    // f4
    double df4_dx3 =  mJ7*mK7*x5/(SmallPow(mJ7+x3-x4,2));
    double df4_dx4 = -mJ7*mK7*x5/(SmallPow(mJ7+x3-x4,2)) - mK6 - mJ8*mK8*mMad/(SmallPow(mJ8+x4,2));
    double df4_dx5 =  mK7*(x3-x4)/(mJ7+x3-x4);

    jacobian[3][2] = -timeStep*df4_dx3;
    jacobian[3][3] = 1-timeStep*df4_dx4;
    jacobian[3][4] = -timeStep*df4_dx5;

    // f5
    double df5_dx1 =  mK9*x6*(1-x5);
    double df5_dx5 = -mK10 - mK9*x6*x1;
    double df5_dx6 =  mK9*x1*(1-x5);

    jacobian[4][0] = -timeStep*df5_dx1;
    jacobian[4][4] = 1-timeStep*df5_dx5;
    jacobian[4][5] = -timeStep*df5_dx6;

    // f6
    double df6_dx6 = mMu - 2*mMu*x6/mMstar;

    jacobian[5][5] = 1-timeStep*df6_dx6;
}

bool TysonNovak2001OdeSystem::CalculateStoppingEvent(double time, const std::vector<double>& rY)
{
    std::vector<double> dy(rY.size());
    EvaluateYDerivatives(time, rY, dy);

    // Only call this a stopping condition if the mass of the cell is over 0.6
    // (normally cycles from 0.5-1.0 ish!)
    return ( (rY[5] > 0.6 ) && (rY[0] < mCycB_threshold) && dy[0] < 0.0 );
}

double TysonNovak2001OdeSystem::CalculateRootFunction(double time, const std::vector<double>& rY)
{
    std::vector<double> dy(rY.size());
    EvaluateYDerivatives(time, rY, dy);

    // Only call this a stopping condition if the mass of the cell is over 0.6
    // (normally cycles from 0.5-1.0 ish!)
    if (rY[5]<0.6)
    {
        return 1.0;
    }

    if (dy[0] >= 0.0)
    {
        return 1.0;
    }
    return rY[0]-mCycB_threshold;
}

template<>
void OdeSystemInformation<TysonNovak2001OdeSystem>::Initialise()
{
    /*
     * Initialise state variables.
     *
     * These initial conditions are the approximate steady state
     * solution values while the commented out conditions are taken
     * from the Tyson and Novak 2001 paper.
     */
    this->mVariableNames.push_back("CycB");
    this->mVariableUnits.push_back("nM");
//    this->mInitialConditions.push_back(0.1);
    this->mInitialConditions.push_back(0.099999999999977);

    this->mVariableNames.push_back("Cdh1");
    this->mVariableUnits.push_back("nM");
//    this->mInitialConditions.push_back(9.8770e-01);
    this->mInitialConditions.push_back(0.989026454281841);

    this->mVariableNames.push_back("Cdc20T");
    this->mVariableUnits.push_back("nM");
//    this->mInitialConditions.push_back(1.5011e+00);
    this->mInitialConditions.push_back(1.547942029285891);

    this->mVariableNames.push_back("Cdc20A");
    this->mVariableUnits.push_back("nM");
//    this->mInitialConditions.push_back(1.2924e+00);
    this->mInitialConditions.push_back(1.421110920135839);

    this->mVariableNames.push_back("IEP");
    this->mVariableUnits.push_back("nM");
//    this->mInitialConditions.push_back(6.5405e-01);
    this->mInitialConditions.push_back(0.672838844290094);

    this->mVariableNames.push_back("mass");
    this->mVariableUnits.push_back("");
//    this->mInitialConditions.push_back(4.7039e-01);
    this->mInitialConditions.push_back(0.970831277863956 / 2);

    this->mInitialised = true;
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(TysonNovak2001OdeSystem)