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 =55; end % There are a total of 19 entries in each of the rate and state variable arrays. % There are a total of 59 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_CONSTANTS(:,1) = strpad('q_RB1_inactive_init in component environment (fmol)'); LEGEND_CONSTANTS(:,2) = strpad('q_L_RB1_inactive_init in component environment (fmol)'); LEGEND_ALGEBRAIC(:,1) = strpad('q_LB1_init in component environment (fmol)'); LEGEND_CONSTANTS(:,3) = strpad('q_RB1_init in component environment (fmol)'); LEGEND_CONSTANTS(:,4) = strpad('q_Gs_init in component environment (fmol)'); LEGEND_CONSTANTS(:,5) = strpad('q_RB1_Gs_init in component environment (fmol)'); LEGEND_CONSTANTS(:,6) = strpad('q_L_RB1_init in component environment (fmol)'); LEGEND_CONSTANTS(:,7) = strpad('q_L_RB1_Gs_init in component environment (fmol)'); LEGEND_CONSTANTS(:,8) = strpad('q_Gsa_GTP_init in component environment (fmol)'); LEGEND_CONSTANTS(:,9) = strpad('q_Gsbetagamma_init in component environment (fmol)'); LEGEND_CONSTANTS(:,10) = strpad('q_Gsa_GDP_init in component environment (fmol)'); LEGEND_CONSTANTS(:,11) = strpad('q_GTP_init in component environment (fmol)'); LEGEND_CONSTANTS(:,12) = strpad('q_GDP_init in component environment (fmol)'); LEGEND_CONSTANTS(:,13) = strpad('q_Pi_init in component environment (fmol)'); LEGEND_CONSTANTS(:,14) = strpad('q_RB1_tag_init in component environment (fmol)'); LEGEND_CONSTANTS(:,15) = strpad('q_L_RB1_tag_init in component environment (fmol)'); LEGEND_CONSTANTS(:,16) = strpad('q_RB1_GRKArr_init in component environment (fmol)'); LEGEND_CONSTANTS(:,17) = strpad('q_L_RB1_GRKArr_init in component environment (fmol)'); LEGEND_CONSTANTS(:,18) = strpad('q_GRKArr_init in component environment (fmol)'); LEGEND_CONSTANTS(:,19) = strpad('stimSt in component environment (second)'); LEGEND_CONSTANTS(:,20) = strpad('stimDur in component environment (second)'); LEGEND_CONSTANTS(:,21) = strpad('tR in component environment (second)'); LEGEND_CONSTANTS(:,22) = strpad('stimMag in component environment (fmol)'); LEGEND_CONSTANTS(:,23) = strpad('stimHolding in component environment (fmol)'); LEGEND_CONSTANTS(:,58) = strpad('m in component environment (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,2) = strpad('q_RB1_inactive in component environment (fmol)'); LEGEND_ALGEBRAIC(:,3) = strpad('q_L_RB1_inactive in component environment (fmol)'); LEGEND_ALGEBRAIC(:,4) = strpad('q_LB1 in component environment (fmol)'); LEGEND_ALGEBRAIC(:,5) = strpad('q_RB1 in component environment (fmol)'); LEGEND_ALGEBRAIC(:,6) = strpad('q_Gs in component environment (fmol)'); LEGEND_ALGEBRAIC(:,7) = strpad('q_RB1_Gs in component environment (fmol)'); LEGEND_ALGEBRAIC(:,8) = strpad('q_L_RB1 in component environment (fmol)'); LEGEND_ALGEBRAIC(:,9) = strpad('q_L_RB1_Gs in component environment (fmol)'); LEGEND_ALGEBRAIC(:,10) = strpad('q_Gsa_GTP in component environment (fmol)'); LEGEND_ALGEBRAIC(:,11) = strpad('q_Gsbetagamma in component environment (fmol)'); LEGEND_ALGEBRAIC(:,12) = strpad('q_Gsa_GDP in component environment (fmol)'); LEGEND_ALGEBRAIC(:,14) = strpad('q_GTP in component environment (fmol)'); LEGEND_ALGEBRAIC(:,15) = strpad('q_GDP in component environment (fmol)'); LEGEND_ALGEBRAIC(:,16) = strpad('q_Pi in component environment (fmol)'); LEGEND_ALGEBRAIC(:,17) = strpad('q_RB1_tag in component environment (fmol)'); LEGEND_ALGEBRAIC(:,18) = strpad('q_L_RB1_tag in component environment (fmol)'); LEGEND_ALGEBRAIC(:,19) = strpad('q_RB1_GRKArr in component environment (fmol)'); LEGEND_ALGEBRAIC(:,20) = strpad('q_L_RB1_GRKArr in component environment (fmol)'); LEGEND_ALGEBRAIC(:,23) = strpad('q_GRKArr in component environment (fmol)'); LEGEND_STATES(:,1) = strpad('q_RB1_inactive in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,2) = strpad('q_L_RB1_inactive in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,3) = strpad('q_LB1 in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,4) = strpad('q_RB1 in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,5) = strpad('q_Gs in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,6) = strpad('q_RB1_Gs in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,7) = strpad('q_L_RB1 in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,8) = strpad('q_L_RB1_Gs in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,9) = strpad('q_Gsa_GTP in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,10) = strpad('q_Gsbetagamma in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,11) = strpad('q_Gsa_GDP in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,12) = strpad('q_GTP in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,13) = strpad('q_GDP in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,14) = strpad('q_Pi in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,15) = strpad('q_RB1_tag in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,16) = strpad('q_L_RB1_tag in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,17) = strpad('q_RB1_GRKArr in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,18) = strpad('q_L_RB1_GRKArr in component GPCR_B1AR_reduced (fmol)'); LEGEND_STATES(:,19) = strpad('q_GRKArr in component GPCR_B1AR_reduced (fmol)'); LEGEND_ALGEBRAIC(:,21) = strpad('conserv_R_T in component environment (fmol)'); LEGEND_ALGEBRAIC(:,22) = strpad('conserv_L_T in component environment (fmol)'); LEGEND_ALGEBRAIC(:,13) = strpad('conserv_G_T in component environment (fmol)'); LEGEND_CONSTANTS(:,59) = strpad('total_R_init in component environment (fmol)'); LEGEND_CONSTANTS(:,24) = strpad('kappa_Rswitch_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,25) = strpad('kappa_LRswitch_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,26) = strpad('kappa_C_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,27) = strpad('kappa_R_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,28) = strpad('kappa_L_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,29) = strpad('kappa_L_actR in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,30) = strpad('kappa_Act1_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,31) = strpad('kappa_Act2_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,32) = strpad('kappa_Hyd_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,33) = strpad('kappa_Reassoc_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,34) = strpad('kappa_InternR_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,35) = strpad('kappa_InternLR_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)'); LEGEND_CONSTANTS(:,36) = strpad('K_RB1_inactive in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,37) = strpad('K_L_RB1_inactive in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,38) = strpad('K_LB1 in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,39) = strpad('K_RB1 in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,40) = strpad('K_Gs in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,41) = strpad('K_RB1_Gs in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,42) = strpad('K_L_RB1 in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,43) = strpad('K_L_RB1_Gs in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,44) = strpad('K_Gsa_GTP in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,45) = strpad('K_Gsbetagamma in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,46) = strpad('K_Gsa_GDP in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,47) = strpad('K_GTP in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,48) = strpad('K_GDP in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,49) = strpad('K_Pi in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,50) = strpad('K_RB1_tag in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,51) = strpad('K_L_RB1_tag in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,52) = strpad('K_RB1_GRKArr in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,53) = strpad('K_L_RB1_GRKArr in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,54) = strpad('K_GRKArr in component GPCR_B1AR_reduced_parameters (per_fmol)'); LEGEND_CONSTANTS(:,55) = strpad('R in component constants (J_per_K_per_mol)'); LEGEND_CONSTANTS(:,56) = strpad('T in component constants (kelvin)'); LEGEND_ALGEBRAIC(:,24) = strpad('mu_RB1_inactive in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,25) = strpad('mu_L_RB1_inactive in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,26) = strpad('mu_LB1 in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,27) = strpad('mu_RB1 in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,28) = strpad('mu_Gs in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,29) = strpad('mu_RB1_Gs in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,30) = strpad('mu_L_RB1 in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,31) = strpad('mu_L_RB1_Gs in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,32) = strpad('mu_Gsa_GTP in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,33) = strpad('mu_Gsbetagamma in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,34) = strpad('mu_Gsa_GDP in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,35) = strpad('mu_GTP in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,36) = strpad('mu_GDP in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,37) = strpad('mu_Pi in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,38) = strpad('mu_RB1_tag in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,39) = strpad('mu_L_RB1_tag in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,40) = strpad('mu_RB1_GRKArr in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,41) = strpad('mu_L_RB1_GRKArr in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,42) = strpad('mu_GRKArr in component GPCR_B1AR_reduced (J_per_mol)'); LEGEND_ALGEBRAIC(:,43) = strpad('v_Rswitch_B1 in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,44) = strpad('v_LRswitch_B1 in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,45) = strpad('v_C_B1 in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,46) = strpad('v_R_B1 in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,47) = strpad('v_L_B1 in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,49) = strpad('v_L_actR in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,48) = strpad('v_Act1_Gs in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,50) = strpad('v_Act2_Gs in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,51) = strpad('v_Hyd_Gs in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,54) = strpad('v_Reassoc_Gs in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,52) = strpad('v_InternR_B1 in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,55) = strpad('v_InternLR_B1 in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_ALGEBRAIC(:,53) = strpad('v_Rsynthesis in component GPCR_B1AR_reduced (fmol_per_sec)'); LEGEND_CONSTANTS(:,57) = strpad('F in component constants (C_per_mol)'); LEGEND_RATES(:,1) = strpad('d/dt q_RB1_inactive in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,2) = strpad('d/dt q_L_RB1_inactive in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,3) = strpad('d/dt q_LB1 in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,4) = strpad('d/dt q_RB1 in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,5) = strpad('d/dt q_Gs in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,6) = strpad('d/dt q_RB1_Gs in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,7) = strpad('d/dt q_L_RB1 in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,8) = strpad('d/dt q_L_RB1_Gs in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,9) = strpad('d/dt q_Gsa_GTP in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,10) = strpad('d/dt q_Gsbetagamma in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,11) = strpad('d/dt q_Gsa_GDP in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,12) = strpad('d/dt q_GTP in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,13) = strpad('d/dt q_GDP in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,14) = strpad('d/dt q_Pi in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,15) = strpad('d/dt q_RB1_tag in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,16) = strpad('d/dt q_L_RB1_tag in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,17) = strpad('d/dt q_RB1_GRKArr in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,18) = strpad('d/dt q_L_RB1_GRKArr in component GPCR_B1AR_reduced (fmol)'); LEGEND_RATES(:,19) = strpad('d/dt q_GRKArr in component GPCR_B1AR_reduced (fmol)'); 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 = []; CONSTANTS(:,1) = 0.0004579000e0; CONSTANTS(:,2) = 1e-18; CONSTANTS(:,3) = 1e-18; CONSTANTS(:,4) = 0.1455400000; CONSTANTS(:,5) = 1e-18; CONSTANTS(:,6) = 1e-18; CONSTANTS(:,7) = 1e-18; CONSTANTS(:,8) = 0.01; CONSTANTS(:,9) = 0.02; CONSTANTS(:,10) = 0.01; CONSTANTS(:,11) = 2.2; CONSTANTS(:,12) = 1.1; CONSTANTS(:,13) = 570; CONSTANTS(:,14) = 1e-18; CONSTANTS(:,15) = 1e-18; CONSTANTS(:,16) = 1e-18; CONSTANTS(:,17) = 1e-18; CONSTANTS(:,18) = 1e-3; CONSTANTS(:,19) = 2.5; CONSTANTS(:,20) = 5e-1; CONSTANTS(:,21) = 5e0; CONSTANTS(:,22) = 1e1; CONSTANTS(:,23) = 1e-8; STATES(:,1) = 1e-16; STATES(:,2) = 1e-16; STATES(:,3) = 1e-16; STATES(:,4) = 1e-16; STATES(:,5) = 1e-16; STATES(:,6) = 1e-16; STATES(:,7) = 1e-16; STATES(:,8) = 1e-16; STATES(:,9) = 1e-16; STATES(:,10) = 1e-16; STATES(:,11) = 1e-16; STATES(:,12) = 1e-16; STATES(:,13) = 1e-16; STATES(:,14) = 1e-16; STATES(:,15) = 1e-16; STATES(:,16) = 1e-16; STATES(:,17) = 1e-16; STATES(:,18) = 1e-16; STATES(:,19) = 1e-16; CONSTANTS(:,24) = 1036.38; CONSTANTS(:,25) = 1.83921e-07; CONSTANTS(:,26) = 891573; CONSTANTS(:,27) = 1.58222e+06; CONSTANTS(:,28) = 0; CONSTANTS(:,29) = 52417.5; CONSTANTS(:,30) = 0.000610519; CONSTANTS(:,31) = 0.576677; CONSTANTS(:,32) = 0.0661821; CONSTANTS(:,33) = 8.60273e-06; CONSTANTS(:,34) = 0.00230556; CONSTANTS(:,35) = 2.17775; CONSTANTS(:,36) = 28.0492; CONSTANTS(:,37) = 1.58056e+11; CONSTANTS(:,38) = 0.0574759; CONSTANTS(:,39) = 0.280492; CONSTANTS(:,40) = 0.00337913; CONSTANTS(:,41) = 1.07597; CONSTANTS(:,42) = 0.158056; CONSTANTS(:,43) = 0.00113911; CONSTANTS(:,44) = 0.00878478; CONSTANTS(:,45) = 736.699; CONSTANTS(:,46) = 161.34; CONSTANTS(:,47) = 823.314; CONSTANTS(:,48) = 3.61368e-10; CONSTANTS(:,49) = 7.91408e-11; CONSTANTS(:,50) = 0.500146; CONSTANTS(:,51) = 0.000529497; CONSTANTS(:,52) = 1.26086e-05; CONSTANTS(:,53) = 1.33485e-08; CONSTANTS(:,54) = 732843; CONSTANTS(:,55) = 8.31; CONSTANTS(:,56) = 310; CONSTANTS(:,57) = 96485; CONSTANTS(:,58) = CONSTANTS(:,22)./CONSTANTS(:,21); CONSTANTS(:,59) = CONSTANTS(:,1)+CONSTANTS(:,2)+CONSTANTS(:,3)+CONSTANTS(:,5)+CONSTANTS(:,6)+CONSTANTS(:,7); 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 ALGEBRAIC(:,3) = STATES(:,2)+CONSTANTS(:,2); ALGEBRAIC(:,25) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,37).*ALGEBRAIC(:,3)); ALGEBRAIC(:,8) = STATES(:,7)+CONSTANTS(:,6); ALGEBRAIC(:,30) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,42).*ALGEBRAIC(:,8)); ALGEBRAIC(:,44) = CONSTANTS(:,25).*(exp(ALGEBRAIC(:,25)./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,30)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,2) = STATES(:,1)+CONSTANTS(:,1); ALGEBRAIC(:,24) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,36).*ALGEBRAIC(:,2)); ALGEBRAIC(:,1) = piecewise({VOICONSTANTS(:,19) - CONSTANTS(:,21), CONSTANTS(:,23)+ CONSTANTS(:,58).*((VOI - CONSTANTS(:,19))+CONSTANTS(:,21)) , VOI>=CONSTANTS(:,19)&VOI=CONSTANTS(:,19)+CONSTANTS(:,20), CONSTANTS(:,23)+ - CONSTANTS(:,58).*(((VOI - CONSTANTS(:,19)) - CONSTANTS(:,21)) - CONSTANTS(:,20)) }, CONSTANTS(:,23)); ALGEBRAIC(:,4) = STATES(:,3)+ALGEBRAIC(:,1); ALGEBRAIC(:,26) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,38).*ALGEBRAIC(:,4)); ALGEBRAIC(:,47) = CONSTANTS(:,28).*(exp((ALGEBRAIC(:,24)+ALGEBRAIC(:,26))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,25)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); RATES(:,2) = - ALGEBRAIC(:,44)+ALGEBRAIC(:,47); ALGEBRAIC(:,5) = STATES(:,4)+CONSTANTS(:,3); ALGEBRAIC(:,27) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,39).*ALGEBRAIC(:,5)); ALGEBRAIC(:,6) = STATES(:,5)+CONSTANTS(:,4); ALGEBRAIC(:,28) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,40).*ALGEBRAIC(:,6)); ALGEBRAIC(:,7) = STATES(:,6)+CONSTANTS(:,5); ALGEBRAIC(:,29) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,41).*ALGEBRAIC(:,7)); ALGEBRAIC(:,45) = CONSTANTS(:,26).*(exp((ALGEBRAIC(:,27)+ALGEBRAIC(:,28))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,29)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,10) = STATES(:,9)+CONSTANTS(:,8); ALGEBRAIC(:,32) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,44).*ALGEBRAIC(:,10)); ALGEBRAIC(:,11) = STATES(:,10)+CONSTANTS(:,9); ALGEBRAIC(:,33) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,45).*ALGEBRAIC(:,11)); ALGEBRAIC(:,14) = STATES(:,12)+CONSTANTS(:,11); ALGEBRAIC(:,35) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,47).*ALGEBRAIC(:,14)); ALGEBRAIC(:,15) = STATES(:,13)+CONSTANTS(:,12); ALGEBRAIC(:,36) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,48).*ALGEBRAIC(:,15)); ALGEBRAIC(:,17) = STATES(:,15)+CONSTANTS(:,14); ALGEBRAIC(:,38) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,50).*ALGEBRAIC(:,17)); ALGEBRAIC(:,48) = CONSTANTS(:,30).*(exp((ALGEBRAIC(:,29)+ALGEBRAIC(:,35))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp((ALGEBRAIC(:,32)+ALGEBRAIC(:,33)+ALGEBRAIC(:,38)+ALGEBRAIC(:,36))./( CONSTANTS(:,55).*CONSTANTS(:,56)))); RATES(:,6) = ALGEBRAIC(:,45) - ALGEBRAIC(:,48); ALGEBRAIC(:,49) = CONSTANTS(:,29).*(exp((ALGEBRAIC(:,27)+ALGEBRAIC(:,26))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,30)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); RATES(:,3) = - ALGEBRAIC(:,47) - ALGEBRAIC(:,49); ALGEBRAIC(:,43) = CONSTANTS(:,24).*(exp(ALGEBRAIC(:,24)./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,27)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); RATES(:,4) = (ALGEBRAIC(:,43) - ALGEBRAIC(:,45)) - ALGEBRAIC(:,49); ALGEBRAIC(:,9) = STATES(:,8)+CONSTANTS(:,7); ALGEBRAIC(:,31) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,43).*ALGEBRAIC(:,9)); ALGEBRAIC(:,46) = CONSTANTS(:,27).*(exp((ALGEBRAIC(:,30)+ALGEBRAIC(:,28))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,31)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); RATES(:,7) = (ALGEBRAIC(:,44) - ALGEBRAIC(:,46))+ALGEBRAIC(:,49); ALGEBRAIC(:,18) = STATES(:,16)+CONSTANTS(:,15); ALGEBRAIC(:,39) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,51).*ALGEBRAIC(:,18)); ALGEBRAIC(:,50) = CONSTANTS(:,31).*(exp((ALGEBRAIC(:,31)+ALGEBRAIC(:,35))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp((ALGEBRAIC(:,32)+ALGEBRAIC(:,33)+ALGEBRAIC(:,39)+ALGEBRAIC(:,36))./( CONSTANTS(:,55).*CONSTANTS(:,56)))); RATES(:,8) = ALGEBRAIC(:,46) - ALGEBRAIC(:,50); RATES(:,12) = - ALGEBRAIC(:,48) - ALGEBRAIC(:,50); RATES(:,13) = ALGEBRAIC(:,48)+ALGEBRAIC(:,50); ALGEBRAIC(:,53) = ALGEBRAIC(:,43)+ALGEBRAIC(:,49); RATES(:,1) = ( - ALGEBRAIC(:,43) - ALGEBRAIC(:,47))+ 0.00000.*ALGEBRAIC(:,53); ALGEBRAIC(:,12) = STATES(:,11)+CONSTANTS(:,10); ALGEBRAIC(:,34) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,46).*ALGEBRAIC(:,12)); ALGEBRAIC(:,16) = STATES(:,14)+CONSTANTS(:,13); ALGEBRAIC(:,37) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,49).*ALGEBRAIC(:,16)); ALGEBRAIC(:,51) = CONSTANTS(:,32).*(exp(ALGEBRAIC(:,32)./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp((ALGEBRAIC(:,34)+ALGEBRAIC(:,37))./( CONSTANTS(:,55).*CONSTANTS(:,56)))); RATES(:,9) = (ALGEBRAIC(:,48)+ALGEBRAIC(:,50)) - ALGEBRAIC(:,51); RATES(:,14) = ALGEBRAIC(:,51); ALGEBRAIC(:,19) = STATES(:,17)+CONSTANTS(:,16); ALGEBRAIC(:,40) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,52).*ALGEBRAIC(:,19)); ALGEBRAIC(:,23) = STATES(:,19)+CONSTANTS(:,18); ALGEBRAIC(:,42) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,54).*ALGEBRAIC(:,23)); ALGEBRAIC(:,52) = CONSTANTS(:,34).*(exp((ALGEBRAIC(:,38)+ALGEBRAIC(:,42))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,40)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); RATES(:,15) = ALGEBRAIC(:,48) - ALGEBRAIC(:,52); RATES(:,17) = ALGEBRAIC(:,52); ALGEBRAIC(:,54) = CONSTANTS(:,33).*(exp((ALGEBRAIC(:,34)+ALGEBRAIC(:,33))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,28)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); RATES(:,5) = ( - ALGEBRAIC(:,45) - ALGEBRAIC(:,46))+ALGEBRAIC(:,54); RATES(:,10) = (ALGEBRAIC(:,48)+ALGEBRAIC(:,50)) - ALGEBRAIC(:,54); RATES(:,11) = ALGEBRAIC(:,51) - ALGEBRAIC(:,54); ALGEBRAIC(:,20) = STATES(:,18)+CONSTANTS(:,17); ALGEBRAIC(:,41) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,53).*ALGEBRAIC(:,20)); ALGEBRAIC(:,55) = CONSTANTS(:,35).*(exp((ALGEBRAIC(:,39)+ALGEBRAIC(:,42))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,41)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); RATES(:,16) = ALGEBRAIC(:,50) - ALGEBRAIC(:,55); RATES(:,18) = ALGEBRAIC(:,55); RATES(:,19) = - ALGEBRAIC(:,52) - ALGEBRAIC(:,55); 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(:,2)+CONSTANTS(:,2); ALGEBRAIC(:,25) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,37).*ALGEBRAIC(:,3)); ALGEBRAIC(:,8) = STATES(:,7)+CONSTANTS(:,6); ALGEBRAIC(:,30) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,42).*ALGEBRAIC(:,8)); ALGEBRAIC(:,44) = CONSTANTS(:,25).*(exp(ALGEBRAIC(:,25)./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,30)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,2) = STATES(:,1)+CONSTANTS(:,1); ALGEBRAIC(:,24) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,36).*ALGEBRAIC(:,2)); ALGEBRAIC(:,1) = piecewise({VOICONSTANTS(:,19) - CONSTANTS(:,21), CONSTANTS(:,23)+ CONSTANTS(:,58).*((VOI - CONSTANTS(:,19))+CONSTANTS(:,21)) , VOI>=CONSTANTS(:,19)&VOI=CONSTANTS(:,19)+CONSTANTS(:,20), CONSTANTS(:,23)+ - CONSTANTS(:,58).*(((VOI - CONSTANTS(:,19)) - CONSTANTS(:,21)) - CONSTANTS(:,20)) }, CONSTANTS(:,23)); ALGEBRAIC(:,4) = STATES(:,3)+ALGEBRAIC(:,1); ALGEBRAIC(:,26) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,38).*ALGEBRAIC(:,4)); ALGEBRAIC(:,47) = CONSTANTS(:,28).*(exp((ALGEBRAIC(:,24)+ALGEBRAIC(:,26))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,25)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,5) = STATES(:,4)+CONSTANTS(:,3); ALGEBRAIC(:,27) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,39).*ALGEBRAIC(:,5)); ALGEBRAIC(:,6) = STATES(:,5)+CONSTANTS(:,4); ALGEBRAIC(:,28) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,40).*ALGEBRAIC(:,6)); ALGEBRAIC(:,7) = STATES(:,6)+CONSTANTS(:,5); ALGEBRAIC(:,29) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,41).*ALGEBRAIC(:,7)); ALGEBRAIC(:,45) = CONSTANTS(:,26).*(exp((ALGEBRAIC(:,27)+ALGEBRAIC(:,28))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,29)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,10) = STATES(:,9)+CONSTANTS(:,8); ALGEBRAIC(:,32) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,44).*ALGEBRAIC(:,10)); ALGEBRAIC(:,11) = STATES(:,10)+CONSTANTS(:,9); ALGEBRAIC(:,33) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,45).*ALGEBRAIC(:,11)); ALGEBRAIC(:,14) = STATES(:,12)+CONSTANTS(:,11); ALGEBRAIC(:,35) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,47).*ALGEBRAIC(:,14)); ALGEBRAIC(:,15) = STATES(:,13)+CONSTANTS(:,12); ALGEBRAIC(:,36) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,48).*ALGEBRAIC(:,15)); ALGEBRAIC(:,17) = STATES(:,15)+CONSTANTS(:,14); ALGEBRAIC(:,38) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,50).*ALGEBRAIC(:,17)); ALGEBRAIC(:,48) = CONSTANTS(:,30).*(exp((ALGEBRAIC(:,29)+ALGEBRAIC(:,35))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp((ALGEBRAIC(:,32)+ALGEBRAIC(:,33)+ALGEBRAIC(:,38)+ALGEBRAIC(:,36))./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,49) = CONSTANTS(:,29).*(exp((ALGEBRAIC(:,27)+ALGEBRAIC(:,26))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,30)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,43) = CONSTANTS(:,24).*(exp(ALGEBRAIC(:,24)./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,27)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,9) = STATES(:,8)+CONSTANTS(:,7); ALGEBRAIC(:,31) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,43).*ALGEBRAIC(:,9)); ALGEBRAIC(:,46) = CONSTANTS(:,27).*(exp((ALGEBRAIC(:,30)+ALGEBRAIC(:,28))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,31)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,18) = STATES(:,16)+CONSTANTS(:,15); ALGEBRAIC(:,39) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,51).*ALGEBRAIC(:,18)); ALGEBRAIC(:,50) = CONSTANTS(:,31).*(exp((ALGEBRAIC(:,31)+ALGEBRAIC(:,35))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp((ALGEBRAIC(:,32)+ALGEBRAIC(:,33)+ALGEBRAIC(:,39)+ALGEBRAIC(:,36))./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,53) = ALGEBRAIC(:,43)+ALGEBRAIC(:,49); ALGEBRAIC(:,12) = STATES(:,11)+CONSTANTS(:,10); ALGEBRAIC(:,34) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,46).*ALGEBRAIC(:,12)); ALGEBRAIC(:,16) = STATES(:,14)+CONSTANTS(:,13); ALGEBRAIC(:,37) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,49).*ALGEBRAIC(:,16)); ALGEBRAIC(:,51) = CONSTANTS(:,32).*(exp(ALGEBRAIC(:,32)./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp((ALGEBRAIC(:,34)+ALGEBRAIC(:,37))./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,19) = STATES(:,17)+CONSTANTS(:,16); ALGEBRAIC(:,40) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,52).*ALGEBRAIC(:,19)); ALGEBRAIC(:,23) = STATES(:,19)+CONSTANTS(:,18); ALGEBRAIC(:,42) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,54).*ALGEBRAIC(:,23)); ALGEBRAIC(:,52) = CONSTANTS(:,34).*(exp((ALGEBRAIC(:,38)+ALGEBRAIC(:,42))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,40)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,54) = CONSTANTS(:,33).*(exp((ALGEBRAIC(:,34)+ALGEBRAIC(:,33))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,28)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,20) = STATES(:,18)+CONSTANTS(:,17); ALGEBRAIC(:,41) = CONSTANTS(:,55).*CONSTANTS(:,56).*log( CONSTANTS(:,53).*ALGEBRAIC(:,20)); ALGEBRAIC(:,55) = CONSTANTS(:,35).*(exp((ALGEBRAIC(:,39)+ALGEBRAIC(:,42))./( CONSTANTS(:,55).*CONSTANTS(:,56))) - exp(ALGEBRAIC(:,41)./( CONSTANTS(:,55).*CONSTANTS(:,56)))); ALGEBRAIC(:,13) = ALGEBRAIC(:,6)+ALGEBRAIC(:,7)+ALGEBRAIC(:,9)+ALGEBRAIC(:,10)+ALGEBRAIC(:,12); ALGEBRAIC(:,21) = ALGEBRAIC(:,2)+ALGEBRAIC(:,3)+ALGEBRAIC(:,5)+ALGEBRAIC(:,7)+ALGEBRAIC(:,8)+ALGEBRAIC(:,9)+ALGEBRAIC(:,17)+ALGEBRAIC(:,18)+ALGEBRAIC(:,19)+ALGEBRAIC(:,20); ALGEBRAIC(:,22) = ALGEBRAIC(:,3)+ALGEBRAIC(:,4)+ALGEBRAIC(:,8)+ALGEBRAIC(:,9)+ALGEBRAIC(:,18)+ALGEBRAIC(:,20); end % Compute result of a piecewise function function x = piecewise(cases, default) set = [0]; for i = 1:2:length(cases) if (length(cases{i+1}) == 1) x(cases{i} & ~set,:) = cases{i+1}; else x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set); end set = set | cases{i}; if(set), break, end end if (length(default) == 1) x(~set,:) = default; else x(~set,:) = default(~set); end 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