BackwardEulerLuoRudyIModel1991.cpp
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00028 #include "BackwardEulerLuoRudyIModel1991.hpp"
00029 #include "Exception.hpp"
00030 #include "CardiacNewtonSolver.hpp"
00031 #include "OdeSystemInformation.hpp"
00032
00033 #include <cmath>
00034 #include <cassert>
00035
00036
00037
00038
00039
00040
00041 const double BackwardEulerLuoRudyIModel1991::membrane_C = 1.0;
00042 const double BackwardEulerLuoRudyIModel1991::membrane_F = 96484.6;
00043 const double BackwardEulerLuoRudyIModel1991::membrane_R = 8314;
00044 const double BackwardEulerLuoRudyIModel1991::membrane_T = 310.0;
00045 const double BackwardEulerLuoRudyIModel1991::background_current_E_b = -59.87;
00046 const double BackwardEulerLuoRudyIModel1991::background_current_g_b = 0.03921;
00047 const double BackwardEulerLuoRudyIModel1991::fast_sodium_current_g_Na = 23.0;
00048 const double BackwardEulerLuoRudyIModel1991::ionic_concentrations_Ki = 145.0;
00049 const double BackwardEulerLuoRudyIModel1991::ionic_concentrations_Ko = 5.4;
00050 const double BackwardEulerLuoRudyIModel1991::ionic_concentrations_Nai = 18.0;
00051 const double BackwardEulerLuoRudyIModel1991::ionic_concentrations_Nao = 140.0;
00052 const double BackwardEulerLuoRudyIModel1991::plateau_potassium_current_g_Kp = 0.0183;
00053 const double BackwardEulerLuoRudyIModel1991::time_dependent_potassium_current_PR_NaK = 0.01833;
00054
00055
00056 BackwardEulerLuoRudyIModel1991::BackwardEulerLuoRudyIModel1991(
00057 boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
00058 : AbstractBackwardEulerCardiacCell<1>(8, 4, pIntracellularStimulus)
00059 {
00060 Init();
00061 }
00062
00063 BackwardEulerLuoRudyIModel1991::BackwardEulerLuoRudyIModel1991(
00064 boost::shared_ptr<AbstractIvpOdeSolver> ,
00065 boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
00066 : AbstractBackwardEulerCardiacCell<1>(8, 4, pIntracellularStimulus)
00067 {
00068 Init();
00069 }
00070
00071 BackwardEulerLuoRudyIModel1991::~BackwardEulerLuoRudyIModel1991(void)
00072 {
00073 }
00074
00075
00076 void BackwardEulerLuoRudyIModel1991::Init()
00077 {
00078 mpSystemInfo = OdeSystemInformation<BackwardEulerLuoRudyIModel1991>::Instance();
00079
00080
00081 fast_sodium_current_E_Na = ((membrane_R * membrane_T) / membrane_F) *
00082 log(ionic_concentrations_Nao / ionic_concentrations_Nai);
00083
00084 AbstractCardiacCell::Init();
00085 }
00086
00087 template<>
00088 void OdeSystemInformation<BackwardEulerLuoRudyIModel1991>::Initialise(void)
00089 {
00090 this->mVariableNames.push_back("h");
00091 this->mVariableUnits.push_back("");
00092 this->mInitialConditions.push_back(0.9804713);
00093
00094 this->mVariableNames.push_back("j");
00095 this->mVariableUnits.push_back("");
00096 this->mInitialConditions.push_back(0.98767124);
00097
00098 this->mVariableNames.push_back("m");
00099 this->mVariableUnits.push_back("");
00100 this->mInitialConditions.push_back(0.00187018);
00101
00102 this->mVariableNames.push_back("CaI");
00103 this->mVariableUnits.push_back("mMol");
00104 this->mInitialConditions.push_back(0.0002);
00105
00106 this->mVariableNames.push_back("V");
00107 this->mVariableUnits.push_back("mV");
00108 this->mInitialConditions.push_back(-83.853);
00109
00110 this->mVariableNames.push_back("d");
00111 this->mVariableUnits.push_back("");
00112 this->mInitialConditions.push_back(0.00316354);
00113
00114 this->mVariableNames.push_back("f");
00115 this->mVariableUnits.push_back("");
00116 this->mInitialConditions.push_back(0.99427859);
00117
00118 this->mVariableNames.push_back("x");
00119 this->mVariableUnits.push_back("");
00120 this->mInitialConditions.push_back(0.16647703);
00121
00122 this->mInitialised = true;
00123 }
00124
00125 double BackwardEulerLuoRudyIModel1991::GetIntracellularCalciumConcentration()
00126 {
00127 return mStateVariables[3];
00128 }
00129
00130
00131 void BackwardEulerLuoRudyIModel1991::UpdateTransmembranePotential(double time)
00132 {
00133
00134 std::vector<double> &rY = rGetStateVariables();
00135
00136 double fast_sodium_current_h_gate_h = rY[0];
00137 double fast_sodium_current_j_gate_j = rY[1];
00138 double fast_sodium_current_m_gate_m = rY[2];
00139 double intracellular_calcium_concentration_Cai = rY[3];
00140 double membrane_V = rY[4];
00141 double slow_inward_current_d_gate_d = rY[5];
00142 double slow_inward_current_f_gate_f = rY[6];
00143 double time_dependent_potassium_current_X_gate_X = rY[7];
00144
00145 double background_current_i_b = background_current_g_b*(membrane_V-background_current_E_b);
00146 double fast_sodium_current_i_Na = fast_sodium_current_g_Na*pow(fast_sodium_current_m_gate_m, 3.0)*fast_sodium_current_h_gate_h*fast_sodium_current_j_gate_j*(membrane_V-fast_sodium_current_E_Na);
00147 double slow_inward_current_E_si = 7.7-13.0287*log(intracellular_calcium_concentration_Cai);
00148 double slow_inward_current_i_si = 0.09*slow_inward_current_d_gate_d*slow_inward_current_f_gate_f*(membrane_V-slow_inward_current_E_si);
00149
00150 double time_dependent_potassium_current_g_K = 0.282*sqrt(ionic_concentrations_Ko/5.4);
00151 double time_dependent_potassium_current_Xi_gate_Xi;
00152
00153 if (membrane_V > -100.0)
00154 {
00155 time_dependent_potassium_current_Xi_gate_Xi = 2.837*(exp(0.04*(membrane_V+77.0))-1.0)/((membrane_V+77.0)*exp(0.04*(membrane_V+35.0)));
00156 }
00157 else
00158 {
00159 #define COVERAGE_IGNORE
00160 time_dependent_potassium_current_Xi_gate_Xi = 1.0;
00161 #undef COVERAGE_IGNORE
00162 }
00163
00164 double time_dependent_potassium_current_E_K = ((membrane_R*membrane_T)/membrane_F)*log((ionic_concentrations_Ko+time_dependent_potassium_current_PR_NaK*ionic_concentrations_Nao)/(ionic_concentrations_Ki+time_dependent_potassium_current_PR_NaK*ionic_concentrations_Nai));
00165 double time_dependent_potassium_current_i_K = time_dependent_potassium_current_g_K*time_dependent_potassium_current_X_gate_X*time_dependent_potassium_current_Xi_gate_Xi*(membrane_V-time_dependent_potassium_current_E_K);
00166 double time_independent_potassium_current_g_K1 = 0.6047*sqrt(ionic_concentrations_Ko/5.4);
00167 double time_independent_potassium_current_E_K1 =((membrane_R*membrane_T)/membrane_F)*log(ionic_concentrations_Ko/ionic_concentrations_Ki);
00168 double time_independent_potassium_current_K1_gate_alpha_K1 = 1.02/(1.0+exp(0.2385*(membrane_V-time_independent_potassium_current_E_K1-59.215)));
00169 double time_independent_potassium_current_K1_gate_beta_K1 = (0.49124*exp(0.08032*(membrane_V+5.476-time_independent_potassium_current_E_K1))+exp(0.06175*(membrane_V-(time_independent_potassium_current_E_K1+594.31))))/(1.0+exp(-0.5143*(membrane_V-time_independent_potassium_current_E_K1+4.753)));
00170 double time_independent_potassium_current_K1_gate_K1_infinity = time_independent_potassium_current_K1_gate_alpha_K1/(time_independent_potassium_current_K1_gate_alpha_K1+time_independent_potassium_current_K1_gate_beta_K1);
00171 double time_independent_potassium_current_i_K1 = time_independent_potassium_current_g_K1*time_independent_potassium_current_K1_gate_K1_infinity*(membrane_V-time_independent_potassium_current_E_K1);
00172 double plateau_potassium_current_Kp = 1.0/(1.0+exp((7.488-membrane_V)/5.98));
00173 double plateau_potassium_current_E_Kp = time_independent_potassium_current_E_K1;
00174 double plateau_potassium_current_i_Kp = plateau_potassium_current_g_Kp*plateau_potassium_current_Kp*(membrane_V-plateau_potassium_current_E_Kp);
00175 double i_stim = GetStimulus(time);
00176
00177
00178 double membrane_V_prime = (-1.0/membrane_C)*(fast_sodium_current_i_Na+slow_inward_current_i_si+time_dependent_potassium_current_i_K+time_independent_potassium_current_i_K1+plateau_potassium_current_i_Kp+background_current_i_b + i_stim);
00179
00180 rY[4] += mDt * membrane_V_prime;
00181 }
00182
00183 void BackwardEulerLuoRudyIModel1991::ComputeOneStepExceptVoltage(double tStart)
00184 {
00185
00186
00187 std::vector<double>& rY = rGetStateVariables();
00188 double fast_sodium_current_h_gate_h = rY[0];
00189 double fast_sodium_current_j_gate_j = rY[1];
00190 double fast_sodium_current_m_gate_m = rY[2];
00191
00192 double membrane_V = rY[4];
00193 double slow_inward_current_d_gate_d = rY[5];
00194 double slow_inward_current_f_gate_f = rY[6];
00195 double time_dependent_potassium_current_X_gate_X = rY[7];
00196
00197 double fast_sodium_current_h_gate_alpha_h;
00198
00199 if (membrane_V < -40.0)
00200 {
00201 fast_sodium_current_h_gate_alpha_h = 0.135*exp((80.0+membrane_V)/-6.8);
00202 }
00203 else
00204 {
00205 fast_sodium_current_h_gate_alpha_h = 0.0;
00206 }
00207
00208 double fast_sodium_current_h_gate_beta_h;
00209
00210 if (membrane_V < -40.0)
00211 {
00212 fast_sodium_current_h_gate_beta_h = 3.56*exp(0.079*membrane_V)+3.1e5*exp(0.35*membrane_V);
00213 }
00214 else
00215 {
00216 fast_sodium_current_h_gate_beta_h = 1.0/(0.13*(1.0+exp((membrane_V+10.66)/-11.1)));
00217 }
00218
00219 double fast_sodium_current_j_gate_alpha_j;
00220
00221 if (membrane_V < -40.0)
00222 {
00223 fast_sodium_current_j_gate_alpha_j = (-1.2714e5*exp(0.2444*membrane_V)-3.474e-5*exp(-0.04391*membrane_V))*(membrane_V+37.78)/(1.0+exp(0.311*(membrane_V+79.23)));
00224 }
00225 else
00226 {
00227 fast_sodium_current_j_gate_alpha_j = 0.0;
00228 }
00229
00230 double fast_sodium_current_j_gate_beta_j;
00231
00232 if (membrane_V < -40.0)
00233 {
00234 fast_sodium_current_j_gate_beta_j = 0.1212*exp(-0.01052*membrane_V)/(1.0+exp(-0.1378*(membrane_V+40.14)));
00235 }
00236 else
00237 {
00238 fast_sodium_current_j_gate_beta_j = 0.3*exp(-2.535e-7*membrane_V)/(1.0+exp(-0.1*(membrane_V+32.0)));
00239 }
00240
00241 double fast_sodium_current_m_gate_alpha_m = 0.32*(membrane_V+47.13)/(1.0-exp(-0.1*(membrane_V+47.13)));
00242 double fast_sodium_current_m_gate_beta_m = 0.08*exp(-membrane_V/11.0);
00243
00244 double slow_inward_current_d_gate_alpha_d = 0.095*exp(-0.01*(membrane_V-5.0))/(1.0+exp(-0.072*(membrane_V-5.0)));
00245 double slow_inward_current_d_gate_beta_d = 0.07*exp(-0.017*(membrane_V+44.0))/(1.0+exp(0.05*(membrane_V+44.0)));
00246
00247 double slow_inward_current_f_gate_alpha_f = 0.012*exp(-0.008*(membrane_V+28.0))/(1.0+exp(0.15*(membrane_V+28.0)));
00248 double slow_inward_current_f_gate_beta_f = 0.0065*exp(-0.02*(membrane_V+30.0))/(1.0+exp(-0.2*(membrane_V+30.0)));
00249
00250 double time_dependent_potassium_current_X_gate_alpha_X = 0.0005*exp(0.083*(membrane_V+50.0))/(1.0+exp(0.057*(membrane_V+50.0)));
00251 double time_dependent_potassium_current_X_gate_beta_X = 0.0013*exp(-0.06*(membrane_V+20.0))/(1.0+exp(-0.04*(membrane_V+20.0)));
00252
00253
00254 fast_sodium_current_h_gate_h = (fast_sodium_current_h_gate_h + fast_sodium_current_h_gate_alpha_h*mDt)
00255 / (1 + (fast_sodium_current_h_gate_alpha_h + fast_sodium_current_h_gate_beta_h)*mDt);
00256
00257
00258 fast_sodium_current_m_gate_m = (fast_sodium_current_m_gate_m + fast_sodium_current_m_gate_alpha_m*mDt)
00259 / (1 + (fast_sodium_current_m_gate_alpha_m + fast_sodium_current_m_gate_beta_m)*mDt);
00260
00261
00262 fast_sodium_current_j_gate_j = (fast_sodium_current_j_gate_j + fast_sodium_current_j_gate_alpha_j*mDt)
00263 / (1 + (fast_sodium_current_j_gate_alpha_j + fast_sodium_current_j_gate_beta_j)*mDt);
00264
00265
00266 slow_inward_current_d_gate_d = (slow_inward_current_d_gate_d + slow_inward_current_d_gate_alpha_d*mDt)
00267 / (1 + (slow_inward_current_d_gate_alpha_d + slow_inward_current_d_gate_beta_d)*mDt);
00268
00269
00270 slow_inward_current_f_gate_f = (slow_inward_current_f_gate_f + slow_inward_current_f_gate_alpha_f*mDt)
00271 / (1 + (slow_inward_current_f_gate_alpha_f + slow_inward_current_f_gate_beta_f)*mDt);
00272
00273
00274 time_dependent_potassium_current_X_gate_X = ( time_dependent_potassium_current_X_gate_X + time_dependent_potassium_current_X_gate_alpha_X*mDt)
00275 / ( 1 + (time_dependent_potassium_current_X_gate_alpha_X+time_dependent_potassium_current_X_gate_beta_X)*mDt);
00276
00277 rY[0] = fast_sodium_current_h_gate_h;
00278 rY[1] = fast_sodium_current_j_gate_j;
00279 rY[2] = fast_sodium_current_m_gate_m;
00280
00281 rY[5] = slow_inward_current_d_gate_d;
00282 rY[6] = slow_inward_current_f_gate_f;
00283 rY[7] = time_dependent_potassium_current_X_gate_X;
00284
00285
00286 double guess[1] = {rY[3]};
00287
00288 CardiacNewtonSolver<1> *solver = CardiacNewtonSolver<1>::Instance();
00289 solver->Solve(*this, tStart, guess);
00290
00291 rY[3] = guess[0];
00292
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00315
00316 }
00317
00318 void BackwardEulerLuoRudyIModel1991::ComputeResidual(double var_environment__time, const double rCurrentGuess[1], double rResidual[1])
00319 {
00320 std::vector<double>& rY = rGetStateVariables();
00321 double membrane_V = rY[4];
00322 double slow_inward_current_d_gate_d = rY[5];
00323 double slow_inward_current_f_gate_f = rY[6];
00324
00325 double slow_inward_current_E_si = 7.7-13.0287*log(rCurrentGuess[0]);
00326 double slow_inward_current_i_si = 0.09*slow_inward_current_d_gate_d*slow_inward_current_f_gate_f*(membrane_V-slow_inward_current_E_si);
00327
00328 double dCdt_using_current_guess = -1e-4*slow_inward_current_i_si+0.07*(1e-4-rCurrentGuess[0]);
00329
00330 rResidual[0] = rCurrentGuess[0] - rY[3] - mDt*dCdt_using_current_guess;
00331 }
00332
00333 void BackwardEulerLuoRudyIModel1991::ComputeJacobian(double var_environment__time, const double rCurrentGuess[1], double rJacobian[1][1])
00334 {
00335 std::vector<double>& rY = rGetStateVariables();
00336 double slow_inward_current_d_gate_d = rY[5];
00337 double slow_inward_current_f_gate_f = rY[6];
00338
00339 rJacobian[0][0] = 1 - mDt*(-0.1172583e-3*slow_inward_current_d_gate_d*slow_inward_current_f_gate_f/rCurrentGuess[0]
00340 - 0.07);
00341 }
00342
00343 double BackwardEulerLuoRudyIModel1991::GetIIonic()
00344 {
00345 double fast_sodium_current_h_gate_h = mStateVariables[0];
00346 double fast_sodium_current_j_gate_j = mStateVariables[1];
00347 double fast_sodium_current_m_gate_m = mStateVariables[2];
00348 double intracellular_calcium_concentration_Cai = mStateVariables[3];
00349 double membrane_V = mStateVariables[4];
00350 double slow_inward_current_d_gate_d = mStateVariables[5];
00351 double slow_inward_current_f_gate_f = mStateVariables[6];
00352 double time_dependent_potassium_current_X_gate_X = mStateVariables[7];
00353
00354
00355
00356
00357 double background_current_i_b = background_current_g_b*(membrane_V-background_current_E_b);
00358
00359 double fast_sodium_current_i_Na = fast_sodium_current_g_Na*pow(fast_sodium_current_m_gate_m, 3.0)*fast_sodium_current_h_gate_h*fast_sodium_current_j_gate_j*(membrane_V-fast_sodium_current_E_Na);
00360 double slow_inward_current_E_si = 7.7-13.0287*log(intracellular_calcium_concentration_Cai);
00361
00362 double slow_inward_current_i_si = 0.09*slow_inward_current_d_gate_d*slow_inward_current_f_gate_f*(membrane_V-slow_inward_current_E_si);
00363
00364 double time_dependent_potassium_current_g_K = 0.282*sqrt(ionic_concentrations_Ko/5.4);
00365 double time_dependent_potassium_current_Xi_gate_Xi;
00366
00367
00368
00369 if (membrane_V > -100.0)
00370 {
00371 time_dependent_potassium_current_Xi_gate_Xi = 2.837*(exp(0.04*(membrane_V+77.0))-1.0)/((membrane_V+77.0)*exp(0.04*(membrane_V+35.0)));
00372 }
00373 else
00374 {
00375 #define COVERAGE_IGNORE
00376 time_dependent_potassium_current_Xi_gate_Xi = 1.0;
00377 #undef COVERAGE_IGNORE
00378 }
00379
00380 double time_dependent_potassium_current_E_K = ((membrane_R*membrane_T)/membrane_F)*log((ionic_concentrations_Ko+time_dependent_potassium_current_PR_NaK*ionic_concentrations_Nao)/(ionic_concentrations_Ki+time_dependent_potassium_current_PR_NaK*ionic_concentrations_Nai));
00381 double time_dependent_potassium_current_i_K = time_dependent_potassium_current_g_K*time_dependent_potassium_current_X_gate_X*time_dependent_potassium_current_Xi_gate_Xi*(membrane_V-time_dependent_potassium_current_E_K);
00382
00383 double time_independent_potassium_current_g_K1 = 0.6047*sqrt(ionic_concentrations_Ko/5.4);
00384 double time_independent_potassium_current_E_K1 =((membrane_R*membrane_T)/membrane_F)*log(ionic_concentrations_Ko/ionic_concentrations_Ki);
00385 double time_independent_potassium_current_K1_gate_alpha_K1 = 1.02/(1.0+exp(0.2385*(membrane_V-time_independent_potassium_current_E_K1-59.215)));
00386 double time_independent_potassium_current_K1_gate_beta_K1 = (0.49124*exp(0.08032*(membrane_V+5.476-time_independent_potassium_current_E_K1))+exp(0.06175*(membrane_V-(time_independent_potassium_current_E_K1+594.31))))/(1.0+exp(-0.5143*(membrane_V-time_independent_potassium_current_E_K1+4.753)));
00387 double time_independent_potassium_current_K1_gate_K1_infinity = time_independent_potassium_current_K1_gate_alpha_K1/(time_independent_potassium_current_K1_gate_alpha_K1+time_independent_potassium_current_K1_gate_beta_K1);
00388 double time_independent_potassium_current_i_K1 = time_independent_potassium_current_g_K1*time_independent_potassium_current_K1_gate_K1_infinity*(membrane_V-time_independent_potassium_current_E_K1);
00389
00390 double plateau_potassium_current_Kp = 1.0/(1.0+exp((7.488-membrane_V)/5.98));
00391 double plateau_potassium_current_E_Kp = time_independent_potassium_current_E_K1;
00392 double plateau_potassium_current_i_Kp = plateau_potassium_current_g_Kp*plateau_potassium_current_Kp*(membrane_V-plateau_potassium_current_E_Kp);
00393
00394 double i_ionic = fast_sodium_current_i_Na+slow_inward_current_i_si+time_dependent_potassium_current_i_K+time_independent_potassium_current_i_K1+plateau_potassium_current_i_Kp+background_current_i_b;
00395
00396 assert( !std::isnan(i_ionic));
00397 return i_ionic;
00398 }
00399
00400
00401 void BackwardEulerLuoRudyIModel1991::VerifyStateVariables()
00402 {
00403 const std::vector<double>& rY = rGetStateVariables();
00404
00405 const double fast_sodium_current_h_gate_h = rY[0];
00406 const double fast_sodium_current_j_gate_j = rY[1];
00407 const double fast_sodium_current_m_gate_m = rY[2];
00408 const double intracellular_calcium_concentration_Cai = rY[3];
00409 const double slow_inward_current_d_gate_d = rY[5];
00410 const double slow_inward_current_f_gate_f = rY[6];
00411 const double time_dependent_potassium_current_X_gate_X = rY[7];
00412
00413 #define COVERAGE_IGNORE
00414 if (!(0.0<=fast_sodium_current_h_gate_h && fast_sodium_current_h_gate_h<=1.0))
00415 {
00416 EXCEPTION("h gate for fast sodium current has gone out of range. Check model parameters, for example spatial stepsize");
00417 }
00418
00419 if (!(0.0<=fast_sodium_current_j_gate_j && fast_sodium_current_j_gate_j<=1.0))
00420 {
00421 EXCEPTION("j gate for fast sodium current has gone out of range. Check model parameters, for example spatial stepsize");
00422 }
00423
00424 if (!(0.0<=fast_sodium_current_m_gate_m && fast_sodium_current_m_gate_m<=1.0))
00425 {
00426 EXCEPTION("m gate for fast sodium current has gone out of range. Check model parameters, for example spatial stepsize");
00427 }
00428
00429 if (!(0.0<intracellular_calcium_concentration_Cai))
00430 {
00431 EXCEPTION("intracellular_calcium_concentration_Cai has become non-positive, ie gone out of range. Check model parameters, for example spatial stepsize");
00432 }
00433
00434 if (!(0.0<=slow_inward_current_d_gate_d && slow_inward_current_d_gate_d<=1.0))
00435 {
00436 EXCEPTION("d gate for slow inward current has gone out of range. Check model parameters, for example spatial stepsize");
00437 }
00438
00439 if (!(0.0<=slow_inward_current_f_gate_f && slow_inward_current_f_gate_f<=1.0))
00440 {
00441 EXCEPTION("f gate for slow inward current has gone out of range. Check model parameters, for example spatial stepsize");
00442 }
00443
00444 if (!(0.0<=time_dependent_potassium_current_X_gate_X && time_dependent_potassium_current_X_gate_X<=1.0))
00445 {
00446 EXCEPTION("X gate for time dependent potassium current has gone out of range. Check model parameters, for example spatial stepsize");
00447 }
00448 #undef COVERAGE_IGNORE
00449 }
00450
00451
00452
00453
00454 #include "SerializationExportWrapperForCpp.hpp"
00455 CHASTE_CLASS_EXPORT(BackwardEulerLuoRudyIModel1991)