CorriasBuistSMCModified.hpp

/*
 
Copyright (c) 2005-2024, University of Oxford.
All rights reserved.
 
University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.
 
This file is part of Chaste.
 
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.
 
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
*/
 
#ifndef CorriasBuistSMCModified_HPP_
#define CorriasBuistSMCModified_HPP_
 
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include "AbstractCardiacCell.hpp"
#include "AbstractStimulusFunction.hpp"
class CorriasBuistSMCModified : public AbstractCardiacCell
{
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCardiacCell >(*this);
    }
 
private:
 
    double mScaleFactorCarbonMonoxide;
 
    bool mFakeIccStimulusPresent;
 
    double Cm;
    double Asurf_in_cm_square;
    double Asurf;
    double VolCell;
    double hCa;
    double sCa;
    /* concentrations */
    double Ki;       
    double Nai;        
    double ACh;       
    double CaiRest;     
    /* maximum conductances*/
    double gLVA_max;                  // (0.18 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gCaL_max;                  // (65.0 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gBK_max;                  // (45.7 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gKb_max;                   // (0.0144 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gKA_max;                   // (9.0  nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gKr_max;                   // (35.0 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gNa_max;                    // (3.0  nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gnsCC_max;                 // (50.0 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gcouple;           // 1.3 nS * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double JCaExt_max;     
    /* Temperature corrections */
    double Q10Ca;         
    double Q10K;          //1.365
    double Q10Na;        
    double Texp;       
    double T_correct_Ca ;
    double T_correct_K ;  
    double T_correct_Na;
    double T_correct_gBK;   // (nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
 
    /* Nernst potentials */
    double EK;                  
    double ENa ;               
    double EnsCC;                          
    double Ca_o;         
    double K_o;          
    double Na_o;         
    /* Nernst parameters */
    double R;    
    double T;       
    double F;     
    double FoRT;     
    double RToF;    
public:
 
    CorriasBuistSMCModified(boost::shared_ptr<AbstractIvpOdeSolver> pSolver, boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);
 
    ~CorriasBuistSMCModified();
 
    void VerifyStateVariables();
 
    double GetIIonic(const std::vector<double>* pStateVariables=NULL);
 
    void EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY);
 
 
    void SetFakeIccStimulusPresent(bool present);
 
    bool GetFakeIccStimulusPresent();
 
    double SetCarbonMonoxideScaleFactor();
 
    void SetCarbonMonoxideScaleFactor(double scaleFactor);
 
    double GetCarbonMonoxideScaleFactor();
};
 
// Needs to be included last
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(CorriasBuistSMCModified)
 
namespace boost
{
    namespace serialization
    {
        template<class Archive>
        inline void save_construct_data(
            Archive & ar, const CorriasBuistSMCModified * t, const unsigned int fileVersion)
        {
            const boost::shared_ptr<AbstractIvpOdeSolver> p_solver = t->GetSolver();
            const boost::shared_ptr<AbstractStimulusFunction> p_stimulus = t->GetStimulusFunction();
            ar << p_solver;
            ar << p_stimulus;
        }
 
        template<class Archive>
        inline void load_construct_data(
            Archive & ar, CorriasBuistSMCModified * t, const unsigned int fileVersion)
        {
            boost::shared_ptr<AbstractIvpOdeSolver> p_solver;
            boost::shared_ptr<AbstractStimulusFunction> p_stimulus;
            ar >> p_solver;
            ar >> p_stimulus;
            ::new(t)CorriasBuistSMCModified(p_solver, p_stimulus);
        }
    }
}
 
#endif // CorriasBuistSMCModified_HPP_