HodgkinHuxleySquidAxon1952OriginalOdeSystem.cpp

/*

Copyright (C) University of Oxford, 2005-2009

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.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/
#include "HodgkinHuxleySquidAxon1952OriginalOdeSystem.hpp"
#include "AbstractOdeSystem.hpp"
#include "OdeSystemInformation.hpp"
#include <cmath>


HodgkinHuxleySquidAxon1952OriginalOdeSystem::HodgkinHuxleySquidAxon1952OriginalOdeSystem(
    AbstractIvpOdeSolver *pOdeSolver,
    AbstractStimulusFunction *pIntracellularStimulus)
        : AbstractCardiacCell(pOdeSolver, 4, 0, pIntracellularStimulus)
{
    mpSystemInfo = OdeSystemInformation<HodgkinHuxleySquidAxon1952OriginalOdeSystem>::Instance();
    
    AbstractCardiacCell::Init();
}

HodgkinHuxleySquidAxon1952OriginalOdeSystem::~HodgkinHuxleySquidAxon1952OriginalOdeSystem(void)
{
}

void HodgkinHuxleySquidAxon1952OriginalOdeSystem::EvaluateYDerivatives(double time, const std::vector<double> &rY, std::vector<double>& rDY)
{
    /*
     * Typical initial conditions for the HodgkinHuxleySquidAxon1952OriginalOdeSystem model
     *
     * membrane_V = 0.0
     * potassium_channel_n_gate_n = 0.325
     * sodium_channel_h_gate_h = 0.6
     * sodium_channel_m_gate_m = 0.05
     */
    
    double membrane_V = rY[0];
    double potassium_channel_n_gate_n = rY[1];
    double sodium_channel_h_gate_h = rY[2];
    double sodium_channel_m_gate_m = rY[3];
    
    /*
     * Compute the HodgkinHuxleySquidAxon1952OriginalOdeSystem model
     */
    
    double leakage_current_E_L = membrane_E_R+10.613;
    double leakage_current_i_L = leakage_current_g_L*(membrane_V-leakage_current_E_L);
    
    double membrane_i_Stim = GetStimulus(time);
    
    double sodium_channel_E_Na = membrane_E_R+115.0;
    double sodium_channel_i_Na = sodium_channel_g_Na*sodium_channel_m_gate_m*sodium_channel_m_gate_m*sodium_channel_m_gate_m*sodium_channel_h_gate_h*(membrane_V-sodium_channel_E_Na);
    double potassium_channel_E_K = membrane_E_R-12.0;
    double potassium_channel_i_K = potassium_channel_g_K*potassium_channel_n_gate_n*potassium_channel_n_gate_n*potassium_channel_n_gate_n*potassium_channel_n_gate_n*(membrane_V-potassium_channel_E_K);
    
    double membrane_V_prime = -(-membrane_i_Stim+sodium_channel_i_Na+potassium_channel_i_K+leakage_current_i_L)/membrane_Cm;
    // do not update voltage if the mSetVoltageDerivativeToZero flag has been set
    if (mSetVoltageDerivativeToZero)
    {
        membrane_V_prime = 0;
    }
    
    double potassium_channel_n_gate_alpha_n;
    if (-65.0001<membrane_V && membrane_V<-64.9999)
    {
        potassium_channel_n_gate_alpha_n = 0.1;
    }
    else
    {
        potassium_channel_n_gate_alpha_n = -0.01*(membrane_V+65.0)/(exp(-(membrane_V+65.0)/10.0)-1.0);
    }
    
    double potassium_channel_n_gate_beta_n = 0.125*exp((membrane_V+75.0)/80.0);
    double potassium_channel_n_gate_n_prime = potassium_channel_n_gate_alpha_n*(1.0-potassium_channel_n_gate_n)-potassium_channel_n_gate_beta_n*potassium_channel_n_gate_n;
    double sodium_channel_h_gate_alpha_h = 0.07*exp(-(membrane_V+75.0)/20.0);
    double sodium_channel_h_gate_beta_h = 1.0/(exp(-(membrane_V+45.0)/10.0)+1.0);
    double sodium_channel_h_gate_h_prime = sodium_channel_h_gate_alpha_h*(1.0-sodium_channel_h_gate_h)-sodium_channel_h_gate_beta_h*sodium_channel_h_gate_h;
    
    double sodium_channel_m_gate_alpha_m;
    if (-50.0001<membrane_V && membrane_V<-49.9999)
    {
        sodium_channel_m_gate_alpha_m = 1;
    }
    else
    {
        sodium_channel_m_gate_alpha_m = -0.1*(membrane_V+50.0)/(exp(-(membrane_V+50.0)/10.0)-1.0);
    }
    double sodium_channel_m_gate_beta_m = 4.0*exp(-(membrane_V+75.0)/18.0);
    double sodium_channel_m_gate_m_prime = sodium_channel_m_gate_alpha_m*(1.0-sodium_channel_m_gate_m)-sodium_channel_m_gate_beta_m*sodium_channel_m_gate_m;
    
    rDY[0] = membrane_V_prime;
    rDY[1] = potassium_channel_n_gate_n_prime;
    rDY[2] = sodium_channel_h_gate_h_prime;
    rDY[3] = sodium_channel_m_gate_m_prime;
}


double HodgkinHuxleySquidAxon1952OriginalOdeSystem::GetIIonic()
{
    double membrane_V = mStateVariables[mVoltageIndex];
    double potassium_channel_n_gate_n = mStateVariables[1];
    double sodium_channel_h_gate_h = mStateVariables[2];
    double sodium_channel_m_gate_m = mStateVariables[3];
    
    /*
     * Compute the HodgkinHuxleySquidAxon1952OriginalOdeSystem model
     */
    
    double leakage_current_E_L = membrane_E_R+10.613;
    double leakage_current_i_L = leakage_current_g_L*(membrane_V-leakage_current_E_L);
    
    double sodium_channel_E_Na = membrane_E_R+115.0;
    double sodium_channel_i_Na = sodium_channel_g_Na*sodium_channel_m_gate_m*sodium_channel_m_gate_m*sodium_channel_m_gate_m*sodium_channel_h_gate_h*(membrane_V-sodium_channel_E_Na);
    double potassium_channel_E_K = membrane_E_R-12.0;
    double potassium_channel_i_K = potassium_channel_g_K*potassium_channel_n_gate_n*potassium_channel_n_gate_n*potassium_channel_n_gate_n*potassium_channel_n_gate_n*(membrane_V-potassium_channel_E_K);
    double i_ionic = sodium_channel_i_Na+potassium_channel_i_K+leakage_current_i_L;
    return i_ionic;
}


template<>
void OdeSystemInformation<HodgkinHuxleySquidAxon1952OriginalOdeSystem>::Initialise(void)
{
    /*
     * State variables
     */
    this->mVariableNames.push_back("V");
    this->mVariableUnits.push_back("mV");
    this->mInitialConditions.push_back(-75.0);
    
    this->mVariableNames.push_back("n");
    this->mVariableUnits.push_back("");
    this->mInitialConditions.push_back(0.325);
    
    this->mVariableNames.push_back("h");
    this->mVariableUnits.push_back("");
    this->mInitialConditions.push_back(0.6);
    
    this->mVariableNames.push_back("m");
    this->mVariableUnits.push_back("");
    this->mInitialConditions.push_back(0.05);
    
    this->mInitialised = true;
}

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