Generated Code
The following is matlab code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = mainFunction()
% This is the "main function". In Matlab, things work best if you rename this function to match the filename.
[VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel();
end
function [algebraicVariableCount] = getAlgebraicVariableCount()
% Used later when setting a global variable with the number of algebraic variables.
% Note: This is not the "main method".
algebraicVariableCount =21;
end
% There are a total of 20 entries in each of the rate and state variable arrays.
% There are a total of 50 entries in the constant variable array.
%
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()
% Create ALGEBRAIC of correct size
global algebraicVariableCount; algebraicVariableCount = getAlgebraicVariableCount();
% Initialise constants and state variables
[INIT_STATES, CONSTANTS] = initConsts;
% Set timespan to solve over
tspan = [0, 10];
% Set numerical accuracy options for ODE solver
options = odeset('RelTol', 1e-06, 'AbsTol', 1e-06, 'MaxStep', 1);
% Solve model with ODE solver
[VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI, STATES, CONSTANTS), tspan, INIT_STATES, options);
% Compute algebraic variables
[RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS);
ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI);
% Plot state variables against variable of integration
[LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends();
figure();
plot(VOI, STATES);
xlabel(LEGEND_VOI);
l = legend(LEGEND_STATES);
set(l,'Interpreter','none');
end
function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends()
LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = ''; LEGEND_CONSTANTS = '';
LEGEND_VOI = strpad('time in component environment (second)');
LEGEND_ALGEBRAIC(:,6) = strpad('LRG in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_ALGEBRAIC(:,8) = strpad('RG in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_ALGEBRAIC(:,1) = strpad('LR in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_STATES(:,1) = strpad('beta1_AR in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_STATES(:,2) = strpad('Gs in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_STATES(:,3) = strpad('beta1_ARact in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_STATES(:,4) = strpad('beta1_AR_S464 in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_STATES(:,5) = strpad('beta1_AR_S301 in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_STATES(:,6) = strpad('L in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_CONSTANTS(:,1) = strpad('Ltotmax in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_CONSTANTS(:,2) = strpad('KL in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_CONSTANTS(:,3) = strpad('KR in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_CONSTANTS(:,4) = strpad('KC in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_CONSTANTS(:,5) = strpad('Gstot in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_CONSTANTS(:,6) = strpad('k_betaARK_plus in component beta_adrenergic_receptor_module (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('k_betaARK_minus in component beta_adrenergic_receptor_module (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('k_PKA_plus in component beta_adrenergic_receptor_module (second_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('k_PKA_minus in component beta_adrenergic_receptor_module (first_order_rate_constant)');
LEGEND_STATES(:,7) = strpad('Gs_beta_gamma in component Gs_activation_module (micromolar)');
LEGEND_ALGEBRAIC(:,10) = strpad('PKACI in component PKA_activation_module (micromolar)');
LEGEND_STATES(:,8) = strpad('Gs_alpha_GTPtot in component Gs_activation_module (micromolar)');
LEGEND_STATES(:,9) = strpad('Gs_alpha_GDP in component Gs_activation_module (micromolar)');
LEGEND_CONSTANTS(:,10) = strpad('k_gact in component Gs_activation_module (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('k_hyd in component Gs_activation_module (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('k_reassoc in component Gs_activation_module (second_order_rate_constant)');
LEGEND_STATES(:,10) = strpad('cAMPtot in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_STATES(:,11) = strpad('AC in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_STATES(:,12) = strpad('Gs_alpha_GTP in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_ALGEBRAIC(:,3) = strpad('Gs_alpha_GTP_AC in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_STATES(:,13) = strpad('PDE in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,13) = strpad('ACtot in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,14) = strpad('ATP in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,15) = strpad('PDEtot in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_ALGEBRAIC(:,2) = strpad('PDEinhib in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,16) = strpad('IBMXtot in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_STATES(:,14) = strpad('IBMX in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,17) = strpad('fsktot in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_STATES(:,15) = strpad('fsk in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_ALGEBRAIC(:,7) = strpad('fsk_AC in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,18) = strpad('kAC_basal in component cyclic_AMP_metabolism_module (first_order_rate_constant)');
LEGEND_CONSTANTS(:,19) = strpad('kAC_fsk in component cyclic_AMP_metabolism_module (first_order_rate_constant)');
LEGEND_CONSTANTS(:,20) = strpad('k_PDE in component cyclic_AMP_metabolism_module (first_order_rate_constant)');
LEGEND_CONSTANTS(:,21) = strpad('kAC_Gs_alpha in component cyclic_AMP_metabolism_module (first_order_rate_constant)');
LEGEND_CONSTANTS(:,22) = strpad('Km_basal in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,23) = strpad('Km_PDE in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,24) = strpad('Km_fsk in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,25) = strpad('K_fsk in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,26) = strpad('Km_Gs_alpha_GTP in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,27) = strpad('K_Gs_alpha in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_CONSTANTS(:,28) = strpad('K_IBMX in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_ALGEBRAIC(:,11) = strpad('cAMP in component PKA_activation_module (micromolar)');
LEGEND_ALGEBRAIC(:,12) = strpad('PKACII in component PKA_activation_module (micromolar)');
LEGEND_ALGEBRAIC(:,13) = strpad('PKAtemp in component PKA_activation_module (micromolar)');
LEGEND_ALGEBRAIC(:,14) = strpad('ARCI in component PKA_activation_module (micromolar)');
LEGEND_ALGEBRAIC(:,15) = strpad('A2RCI in component PKA_activation_module (micromolar)');
LEGEND_ALGEBRAIC(:,16) = strpad('A2RI in component PKA_activation_module (micromolar)');
LEGEND_ALGEBRAIC(:,17) = strpad('A2RCII in component PKA_activation_module (micromolar)');
LEGEND_ALGEBRAIC(:,18) = strpad('A2RII in component PKA_activation_module (micromolar)');
LEGEND_ALGEBRAIC(:,19) = strpad('ARCII in component PKA_activation_module (micromolar)');
LEGEND_CONSTANTS(:,29) = strpad('Ki_pki in component PKA_activation_module (micromolar)');
LEGEND_CONSTANTS(:,30) = strpad('PKAItot in component PKA_activation_module (micromolar)');
LEGEND_CONSTANTS(:,31) = strpad('PKAIItot in component PKA_activation_module (micromolar)');
LEGEND_CONSTANTS(:,32) = strpad('PKItot in component PKA_activation_module (micromolar)');
LEGEND_CONSTANTS(:,33) = strpad('KA in component PKA_activation_module (micromolar)');
LEGEND_CONSTANTS(:,34) = strpad('KB in component PKA_activation_module (micromolar)');
LEGEND_CONSTANTS(:,35) = strpad('KD in component PKA_activation_module (micromolar)');
LEGEND_CONSTANTS(:,36) = strpad('KPKI in component PKA_activation_module (micromolar)');
LEGEND_ALGEBRAIC(:,20) = strpad('PKI in component PKA_activation_module (micromolar)');
LEGEND_ALGEBRAIC(:,4) = strpad('fracPLBp in component phospholamban_regulation_module (dimensionless)');
LEGEND_ALGEBRAIC(:,21) = strpad('fracPLB in component phospholamban_regulation_module (dimensionless)');
LEGEND_CONSTANTS(:,37) = strpad('fracPLBo in component phospholamban_regulation_module (dimensionless)');
LEGEND_STATES(:,16) = strpad('PLBp in component phospholamban_regulation_module (micromolar)');
LEGEND_ALGEBRAIC(:,9) = strpad('PLB in component phospholamban_regulation_module (micromolar)');
LEGEND_STATES(:,17) = strpad('Inhib1ptot in component phospholamban_regulation_module (micromolar)');
LEGEND_STATES(:,18) = strpad('Inhib1 in component phospholamban_regulation_module (micromolar)');
LEGEND_STATES(:,19) = strpad('Inhib1p in component phospholamban_regulation_module (micromolar)');
LEGEND_ALGEBRAIC(:,5) = strpad('PP1_Inhib1p in component phospholamban_regulation_module (micromolar)');
LEGEND_STATES(:,20) = strpad('PP1 in component phospholamban_regulation_module (micromolar)');
LEGEND_CONSTANTS(:,38) = strpad('PP1tot in component phospholamban_regulation_module (micromolar)');
LEGEND_CONSTANTS(:,39) = strpad('PLBtot in component phospholamban_regulation_module (micromolar)');
LEGEND_CONSTANTS(:,40) = strpad('Inhib1tot in component phospholamban_regulation_module (micromolar)');
LEGEND_CONSTANTS(:,41) = strpad('epsilon in component phospholamban_regulation_module (dimensionless)');
LEGEND_CONSTANTS(:,42) = strpad('kPKA_PLB in component phospholamban_regulation_module (first_order_rate_constant)');
LEGEND_CONSTANTS(:,43) = strpad('KmPKA_PLB in component phospholamban_regulation_module (micromolar)');
LEGEND_CONSTANTS(:,44) = strpad('kPKA_Inhib1 in component phospholamban_regulation_module (first_order_rate_constant)');
LEGEND_CONSTANTS(:,45) = strpad('kPP1_PLB in component phospholamban_regulation_module (first_order_rate_constant)');
LEGEND_CONSTANTS(:,46) = strpad('KmPP1_PLB in component phospholamban_regulation_module (micromolar)');
LEGEND_CONSTANTS(:,47) = strpad('KmPKA_Inhib1 in component phospholamban_regulation_module (micromolar)');
LEGEND_CONSTANTS(:,48) = strpad('VmaxPP2A_Inhib1 in component phospholamban_regulation_module (flux)');
LEGEND_CONSTANTS(:,49) = strpad('KmPP2A_Inhib1 in component phospholamban_regulation_module (micromolar)');
LEGEND_CONSTANTS(:,50) = strpad('KInhib1 in component phospholamban_regulation_module (micromolar)');
LEGEND_RATES(:,6) = strpad('d/dt L in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt Gs in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_RATES(:,1) = strpad('d/dt beta1_AR in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_RATES(:,3) = strpad('d/dt beta1_ARact in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_RATES(:,4) = strpad('d/dt beta1_AR_S464 in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_RATES(:,5) = strpad('d/dt beta1_AR_S301 in component beta_adrenergic_receptor_module (micromolar)');
LEGEND_RATES(:,8) = strpad('d/dt Gs_alpha_GTPtot in component Gs_activation_module (micromolar)');
LEGEND_RATES(:,7) = strpad('d/dt Gs_beta_gamma in component Gs_activation_module (micromolar)');
LEGEND_RATES(:,9) = strpad('d/dt Gs_alpha_GDP in component Gs_activation_module (micromolar)');
LEGEND_RATES(:,12) = strpad('d/dt Gs_alpha_GTP in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_RATES(:,15) = strpad('d/dt fsk in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_RATES(:,11) = strpad('d/dt AC in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_RATES(:,13) = strpad('d/dt PDE in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_RATES(:,14) = strpad('d/dt IBMX in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_RATES(:,10) = strpad('d/dt cAMPtot in component cyclic_AMP_metabolism_module (micromolar)');
LEGEND_RATES(:,20) = strpad('d/dt PP1 in component phospholamban_regulation_module (micromolar)');
LEGEND_RATES(:,19) = strpad('d/dt Inhib1p in component phospholamban_regulation_module (micromolar)');
LEGEND_RATES(:,16) = strpad('d/dt PLBp in component phospholamban_regulation_module (micromolar)');
LEGEND_RATES(:,17) = strpad('d/dt Inhib1ptot in component phospholamban_regulation_module (micromolar)');
LEGEND_RATES(:,18) = strpad('d/dt Inhib1 in component phospholamban_regulation_module (micromolar)');
LEGEND_STATES = LEGEND_STATES';
LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';
LEGEND_RATES = LEGEND_RATES';
LEGEND_CONSTANTS = LEGEND_CONSTANTS';
end
function [STATES, CONSTANTS] = initConsts()
VOI = 0; CONSTANTS = []; STATES = []; ALGEBRAIC = [];
STATES(:,1) = 0.0001;
STATES(:,2) = 3.182;
STATES(:,3) = 0.01205;
STATES(:,4) = 0;
STATES(:,5) = 1.154e-3;
STATES(:,6) = 0.988;
CONSTANTS(:,1) = 1;
CONSTANTS(:,2) = 0.285;
CONSTANTS(:,3) = 0.062;
CONSTANTS(:,4) = 33;
CONSTANTS(:,5) = 3.83;
CONSTANTS(:,6) = 1.1e-3;
CONSTANTS(:,7) = 2.2e-3;
CONSTANTS(:,8) = 3.6e-3;
CONSTANTS(:,9) = 2.2e-3;
STATES(:,7) = 0.02569;
STATES(:,8) = 0.02505;
STATES(:,9) = 6.44e-4;
CONSTANTS(:,10) = 16;
CONSTANTS(:,11) = 0.8;
CONSTANTS(:,12) = 1.21e3;
STATES(:,10) = 0.8453;
STATES(:,11) = 0.04706295;
STATES(:,12) = 0.02241295;
STATES(:,13) = 0.0389;
CONSTANTS(:,13) = 49.7e-3;
CONSTANTS(:,14) = 5e3;
CONSTANTS(:,15) = 38.9e-3;
CONSTANTS(:,16) = 0;
STATES(:,14) = 0;
CONSTANTS(:,17) = 0;
STATES(:,15) = 0;
CONSTANTS(:,18) = 0.2;
CONSTANTS(:,19) = 7.3;
CONSTANTS(:,20) = 5;
CONSTANTS(:,21) = 8.5;
CONSTANTS(:,22) = 1.03e3;
CONSTANTS(:,23) = 1.3;
CONSTANTS(:,24) = 860;
CONSTANTS(:,25) = 44;
CONSTANTS(:,26) = 0.4;
CONSTANTS(:,27) = 0.4;
CONSTANTS(:,28) = 30;
CONSTANTS(:,29) = 0.2e-3;
CONSTANTS(:,30) = 0.59;
CONSTANTS(:,31) = 0.025;
CONSTANTS(:,32) = 0.18;
CONSTANTS(:,33) = 9.14e-3;
CONSTANTS(:,34) = 1.64e-3;
CONSTANTS(:,35) = 4.375e-3;
CONSTANTS(:,36) = 2e-4;
CONSTANTS(:,37) = 0.9613;
STATES(:,16) = 4.105;
STATES(:,17) = 0.0526;
STATES(:,18) = 0.2474;
STATES(:,19) = 6.27339e-5;
STATES(:,20) = 0.8374627;
CONSTANTS(:,38) = 0.89;
CONSTANTS(:,39) = 106;
CONSTANTS(:,40) = 0.3;
CONSTANTS(:,41) = 10;
CONSTANTS(:,42) = 54;
CONSTANTS(:,43) = 21;
CONSTANTS(:,44) = 60;
CONSTANTS(:,45) = 8.5;
CONSTANTS(:,46) = 7;
CONSTANTS(:,47) = 1;
CONSTANTS(:,48) = 14;
CONSTANTS(:,49) = 1;
CONSTANTS(:,50) = 1e-3;
if (isempty(STATES)), warning('Initial values for states not set');, end
end
function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
global algebraicVariableCount;
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
ALGEBRAIC = zeros(1, algebraicVariableCount);
utilOnes = 1;
else
statesRowCount = statesSize(1);
ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
RATES = zeros(statesRowCount, statesColumnCount);
utilOnes = ones(statesRowCount, 1);
end
RATES(:,9) = CONSTANTS(:,11).*STATES(:,8) - CONSTANTS(:,12).*STATES(:,9).*STATES(:,7);
ALGEBRAIC(:,3) = ( STATES(:,12).*STATES(:,11))./CONSTANTS(:,27);
RATES(:,12) = STATES(:,8) - (ALGEBRAIC(:,3)+STATES(:,12));
RATES(:,11) = CONSTANTS(:,13) - (ALGEBRAIC(:,3)+STATES(:,11));
ALGEBRAIC(:,2) = ( STATES(:,13).*STATES(:,14))./CONSTANTS(:,28);
RATES(:,13) = CONSTANTS(:,15) - (ALGEBRAIC(:,2)+STATES(:,13));
RATES(:,14) = CONSTANTS(:,16) - (ALGEBRAIC(:,2)+STATES(:,14));
ALGEBRAIC(:,5) = ( STATES(:,20).*STATES(:,19))./CONSTANTS(:,50);
RATES(:,20) = CONSTANTS(:,38) - (ALGEBRAIC(:,5)+STATES(:,20));
RATES(:,19) = STATES(:,17) - (ALGEBRAIC(:,5)+STATES(:,19));
ALGEBRAIC(:,6) = ( STATES(:,6).*STATES(:,1).*STATES(:,2))./( CONSTANTS(:,2).*CONSTANTS(:,3));
ALGEBRAIC(:,1) = ( STATES(:,6).*STATES(:,1))./CONSTANTS(:,2);
RATES(:,6) = CONSTANTS(:,1) - (ALGEBRAIC(:,1)+ALGEBRAIC(:,6)+STATES(:,6));
RATES(:,4) = CONSTANTS(:,6).*(ALGEBRAIC(:,1)+ALGEBRAIC(:,6)) - CONSTANTS(:,7).*STATES(:,4);
ALGEBRAIC(:,7) = ( STATES(:,15).*STATES(:,11))./CONSTANTS(:,25);
RATES(:,15) = CONSTANTS(:,17) - (ALGEBRAIC(:,7)+STATES(:,15));
RATES(:,10) = (( CONSTANTS(:,18).*STATES(:,11).*CONSTANTS(:,14))./(CONSTANTS(:,22)+CONSTANTS(:,14))+( CONSTANTS(:,21).*ALGEBRAIC(:,3).*CONSTANTS(:,14))./(CONSTANTS(:,26)+CONSTANTS(:,14))+( CONSTANTS(:,19).*ALGEBRAIC(:,7).*CONSTANTS(:,14))./(CONSTANTS(:,24)+CONSTANTS(:,14))) - ( CONSTANTS(:,20).*STATES(:,13).*STATES(:,10))./(CONSTANTS(:,23)+STATES(:,10));
ALGEBRAIC(:,8) = ( STATES(:,1).*STATES(:,2))./CONSTANTS(:,4);
RATES(:,2) = CONSTANTS(:,5) - (ALGEBRAIC(:,8)+ALGEBRAIC(:,6)+STATES(:,2));
RATES(:,1) = STATES(:,3) - (ALGEBRAIC(:,1)+ALGEBRAIC(:,6)+ALGEBRAIC(:,8)+STATES(:,1));
RATES(:,8) = CONSTANTS(:,10).*(ALGEBRAIC(:,8)+ALGEBRAIC(:,6)) - CONSTANTS(:,11).*STATES(:,8);
RATES(:,7) = CONSTANTS(:,10).*(ALGEBRAIC(:,8)+ALGEBRAIC(:,6)) - CONSTANTS(:,12).*STATES(:,9).*STATES(:,7);
[CONSTANTS, STATES, ALGEBRAIC] = rootfind_0(VOI, CONSTANTS, STATES, ALGEBRAIC);
RATES(:,3) = ( CONSTANTS(:,7).*STATES(:,4) - CONSTANTS(:,6).*(ALGEBRAIC(:,1)+ALGEBRAIC(:,6)))+( CONSTANTS(:,9).*STATES(:,5) - CONSTANTS(:,8).*ALGEBRAIC(:,10).*STATES(:,3));
RATES(:,5) = CONSTANTS(:,8).*ALGEBRAIC(:,10).*STATES(:,3) - CONSTANTS(:,9).*STATES(:,5);
ALGEBRAIC(:,9) = CONSTANTS(:,39) - STATES(:,16);
RATES(:,16) = ( CONSTANTS(:,42).*ALGEBRAIC(:,10).*ALGEBRAIC(:,9))./(CONSTANTS(:,43)+ALGEBRAIC(:,9)) - ( CONSTANTS(:,45).*STATES(:,20).*STATES(:,16))./(CONSTANTS(:,46)+STATES(:,16));
RATES(:,17) = ( CONSTANTS(:,44).*ALGEBRAIC(:,10).*STATES(:,17))./(CONSTANTS(:,47)+STATES(:,17)) - ( CONSTANTS(:,48).*STATES(:,18))./(CONSTANTS(:,49)+STATES(:,18));
RATES(:,18) = ( CONSTANTS(:,48).*STATES(:,18))./(CONSTANTS(:,49)+STATES(:,18)) - ( CONSTANTS(:,44).*ALGEBRAIC(:,10).*STATES(:,17))./(CONSTANTS(:,47)+STATES(:,17));
RATES = RATES';
end
% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
utilOnes = 1;
else
statesRowCount = statesSize(1);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,3) = ( STATES(:,12).*STATES(:,11))./CONSTANTS(:,27);
ALGEBRAIC(:,2) = ( STATES(:,13).*STATES(:,14))./CONSTANTS(:,28);
ALGEBRAIC(:,5) = ( STATES(:,20).*STATES(:,19))./CONSTANTS(:,50);
ALGEBRAIC(:,6) = ( STATES(:,6).*STATES(:,1).*STATES(:,2))./( CONSTANTS(:,2).*CONSTANTS(:,3));
ALGEBRAIC(:,1) = ( STATES(:,6).*STATES(:,1))./CONSTANTS(:,2);
ALGEBRAIC(:,7) = ( STATES(:,15).*STATES(:,11))./CONSTANTS(:,25);
ALGEBRAIC(:,8) = ( STATES(:,1).*STATES(:,2))./CONSTANTS(:,4);
ALGEBRAIC(:,9) = CONSTANTS(:,39) - STATES(:,16);
ALGEBRAIC(:,4) = STATES(:,16)./CONSTANTS(:,39);
ALGEBRAIC(:,21) = ALGEBRAIC(:,9)./CONSTANTS(:,39);
end
% Functions required for solving differential algebraic equation
function [CONSTANTS, STATES, ALGEBRAIC] = rootfind_0(VOI, CONSTANTS_IN, STATES_IN, ALGEBRAIC_IN)
ALGEBRAIC = ALGEBRAIC_IN;
CONSTANTS = CONSTANTS_IN;
STATES = STATES_IN;
global initialGuess_0;
if (length(initialGuess_0) ~= 11), initialGuess_0 = [0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1];, end
options = optimset('Display', 'off', 'TolX', 1E-6);
if length(VOI) == 1
residualfn = @(algebraicCandidate)residualSN_0(algebraicCandidate, ALGEBRAIC, VOI, CONSTANTS, STATES);
soln = fsolve(residualfn, initialGuess_0, options);
initialGuess_0 = soln;
ALGEBRAIC(:,10) = soln(1);
ALGEBRAIC(:,11) = soln(2);
ALGEBRAIC(:,12) = soln(3);
ALGEBRAIC(:,13) = soln(4);
ALGEBRAIC(:,14) = soln(5);
ALGEBRAIC(:,15) = soln(6);
ALGEBRAIC(:,16) = soln(7);
ALGEBRAIC(:,17) = soln(8);
ALGEBRAIC(:,18) = soln(9);
ALGEBRAIC(:,19) = soln(10);
ALGEBRAIC(:,20) = soln(11);
else
SET_ALGEBRAIC(:,10) = logical(1);
SET_ALGEBRAIC(:,11) = logical(1);
SET_ALGEBRAIC(:,12) = logical(1);
SET_ALGEBRAIC(:,13) = logical(1);
SET_ALGEBRAIC(:,14) = logical(1);
SET_ALGEBRAIC(:,15) = logical(1);
SET_ALGEBRAIC(:,16) = logical(1);
SET_ALGEBRAIC(:,17) = logical(1);
SET_ALGEBRAIC(:,18) = logical(1);
SET_ALGEBRAIC(:,19) = logical(1);
SET_ALGEBRAIC(:,20) = logical(1);
for i=1:length(VOI)
residualfn = @(algebraicCandidate)residualSN_0(algebraicCandidate, ALGEBRAIC(i,:), VOI(i), CONSTANTS, STATES(i,:));
soln = fsolve(residualfn, initialGuess_0, options);
initialGuess_0 = soln;
TEMP_ALGEBRAIC(:,10) = soln(1);
TEMP_ALGEBRAIC(:,11) = soln(2);
TEMP_ALGEBRAIC(:,12) = soln(3);
TEMP_ALGEBRAIC(:,13) = soln(4);
TEMP_ALGEBRAIC(:,14) = soln(5);
TEMP_ALGEBRAIC(:,15) = soln(6);
TEMP_ALGEBRAIC(:,16) = soln(7);
TEMP_ALGEBRAIC(:,17) = soln(8);
TEMP_ALGEBRAIC(:,18) = soln(9);
TEMP_ALGEBRAIC(:,19) = soln(10);
TEMP_ALGEBRAIC(:,20) = soln(11);
ALGEBRAIC(i,SET_ALGEBRAIC) = TEMP_ALGEBRAIC(SET_ALGEBRAIC);
end
end
end
function resid = residualSN_0(algebraicCandidate, ALGEBRAIC, VOI, CONSTANTS, STATES)
ALGEBRAIC(:,10) = algebraicCandidate(1);
ALGEBRAIC(:,11) = algebraicCandidate(2);
ALGEBRAIC(:,12) = algebraicCandidate(3);
ALGEBRAIC(:,13) = algebraicCandidate(4);
ALGEBRAIC(:,14) = algebraicCandidate(5);
ALGEBRAIC(:,15) = algebraicCandidate(6);
ALGEBRAIC(:,16) = algebraicCandidate(7);
ALGEBRAIC(:,17) = algebraicCandidate(8);
ALGEBRAIC(:,18) = algebraicCandidate(9);
ALGEBRAIC(:,19) = algebraicCandidate(10);
ALGEBRAIC(:,20) = algebraicCandidate(11);
resid(1) = ALGEBRAIC(:,20) - ( CONSTANTS(:,32).*CONSTANTS(:,29))./(CONSTANTS(:,29)+ALGEBRAIC(:,10)+ALGEBRAIC(:,12));
resid(2) = ALGEBRAIC(:,15) - (ALGEBRAIC(:,10)./CONSTANTS(:,35)).*ALGEBRAIC(:,10).*(1.00000+ALGEBRAIC(:,20)./CONSTANTS(:,29));
resid(3) = ALGEBRAIC(:,16) - ALGEBRAIC(:,10).*(1.00000+ALGEBRAIC(:,20)./CONSTANTS(:,29));
resid(4) = ALGEBRAIC(:,17) - (ALGEBRAIC(:,12)./CONSTANTS(:,35)).*ALGEBRAIC(:,12).*(1.00000+ALGEBRAIC(:,20)./CONSTANTS(:,29));
resid(5) = ALGEBRAIC(:,18) - ALGEBRAIC(:,12).*(1.00000+ALGEBRAIC(:,20)./CONSTANTS(:,29));
resid(6) = ALGEBRAIC(:,14) - (CONSTANTS(:,33)./ALGEBRAIC(:,11)).*ALGEBRAIC(:,15);
resid(7) = ALGEBRAIC(:,19) - (CONSTANTS(:,33)./ALGEBRAIC(:,11)).*ALGEBRAIC(:,17);
resid(8) = ALGEBRAIC(:,11) - ((STATES(:,10) - (ALGEBRAIC(:,14)+ 2.00000.*ALGEBRAIC(:,15)+ 2.00000.*ALGEBRAIC(:,16))) - (ALGEBRAIC(:,19)+ 2.00000.*ALGEBRAIC(:,17)+ 2.00000.*ALGEBRAIC(:,18)));
resid(9) = ALGEBRAIC(:,13) - (( CONSTANTS(:,33).*CONSTANTS(:,34))./CONSTANTS(:,35)+( CONSTANTS(:,33).*ALGEBRAIC(:,11))./CONSTANTS(:,35)+( ALGEBRAIC(:,11).*ALGEBRAIC(:,11))./CONSTANTS(:,35));
resid(10) = ALGEBRAIC(:,10) - ( 2.00000.*CONSTANTS(:,30).*ALGEBRAIC(:,11).*ALGEBRAIC(:,11) - ALGEBRAIC(:,10).*(1.00000+ALGEBRAIC(:,20)./CONSTANTS(:,29)).*( ALGEBRAIC(:,13).*ALGEBRAIC(:,10)+ ALGEBRAIC(:,11).*ALGEBRAIC(:,11)));
resid(11) = ALGEBRAIC(:,12) - ( 2.00000.*CONSTANTS(:,31).*ALGEBRAIC(:,11).*ALGEBRAIC(:,11) - ALGEBRAIC(:,12).*(1.00000+ALGEBRAIC(:,20)./CONSTANTS(:,29)).*( ALGEBRAIC(:,13).*ALGEBRAIC(:,12)+ ALGEBRAIC(:,11).*ALGEBRAIC(:,11)));
end
% Pad out or shorten strings to a set length
function strout = strpad(strin)
req_length = 160;
insize = size(strin,2);
if insize > req_length
strout = strin(1:req_length);
else
strout = [strin, blanks(req_length - insize)];
end
end