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 =28; end % There are a total of 8 entries in each of the rate and state variable arrays. % There are a total of 31 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_STATES(:,1) = strpad('wi in component wi (micrometre)'); LEGEND_CONSTANTS(:,1) = strpad('Lp in component model_parameters (cm_per_millimolar_second)'); LEGEND_CONSTANTS(:,2) = strpad('Xi in component model_parameters (millimolar_micrometre)'); LEGEND_ALGEBRAIC(:,11) = strpad('Nao in component model_parameters (millimolar)'); LEGEND_ALGEBRAIC(:,7) = strpad('Ko in component model_parameters (millimolar)'); LEGEND_ALGEBRAIC(:,14) = strpad('Clo in component model_parameters (millimolar)'); LEGEND_ALGEBRAIC(:,19) = strpad('HCO3o in component model_parameters (millimolar)'); LEGEND_ALGEBRAIC(:,9) = strpad('Nai in component model_parameters (millimolar)'); LEGEND_ALGEBRAIC(:,6) = strpad('Ki in component model_parameters (millimolar)'); LEGEND_ALGEBRAIC(:,13) = strpad('Cli in component model_parameters (millimolar)'); LEGEND_ALGEBRAIC(:,18) = strpad('HCO3i in component model_parameters (millimolar)'); LEGEND_ALGEBRAIC(:,1) = strpad('wo in component wo (micrometre)'); LEGEND_CONSTANTS(:,3) = strpad('w_tot in component wo (micrometre)'); LEGEND_STATES(:,2) = strpad('N_Nai in component N_Nai (millimolar_micrometre)'); LEGEND_ALGEBRAIC(:,26) = strpad('dN_Nai_dt in component N_Nai (millimolar_micrometre_per_second)'); LEGEND_CONSTANTS(:,4) = strpad('gNa in component model_parameters (per_ohm_cm2)'); LEGEND_ALGEBRAIC(:,12) = strpad('ENa in component Nernst_potentials (volt)'); LEGEND_ALGEBRAIC(:,21) = strpad('Vm in component membrane (volt)'); LEGEND_ALGEBRAIC(:,10) = strpad('J_NaKATPase in component J_NaKATPase (mole_per_cm2_second)'); LEGEND_CONSTANTS(:,5) = strpad('F in component model_parameters (C_per_mol)'); LEGEND_CONSTANTS(:,6) = strpad('theta_NKCC1 in component model_parameters (dimensionless)'); LEGEND_ALGEBRAIC(:,17) = strpad('J_NKCC1 in component J_NKCC1 (millimolar_micrometre_per_second)'); LEGEND_CONSTANTS(:,7) = strpad('theta_NBC in component model_parameters (dimensionless)'); LEGEND_ALGEBRAIC(:,25) = strpad('J_NBC in component J_NBC (millimolar_micrometre_per_second)'); LEGEND_STATES(:,3) = strpad('N_Ki in component N_Ki (millimolar_micrometre)'); LEGEND_ALGEBRAIC(:,22) = strpad('dN_Ki_dt in component N_Ki (millimolar_micrometre_per_second)'); LEGEND_CONSTANTS(:,8) = strpad('gK in component model_parameters (per_ohm_cm2)'); LEGEND_ALGEBRAIC(:,8) = strpad('EK in component Nernst_potentials (volt)'); LEGEND_CONSTANTS(:,9) = strpad('theta_KCC1 in component model_parameters (dimensionless)'); LEGEND_ALGEBRAIC(:,16) = strpad('J_KCC1 in component J_KCC1 (millimolar_micrometre_per_second)'); LEGEND_STATES(:,4) = strpad('N_HCO3i in component N_HCO3i (millimolar_micrometre)'); LEGEND_ALGEBRAIC(:,28) = strpad('dN_HCO3i_dt in component N_HCO3i (millimolar_micrometre_per_second)'); LEGEND_STATES(:,5) = strpad('N_Cli in component N_Cli (millimolar_micrometre)'); LEGEND_STATES(:,6) = strpad('N_Nao in component N_Nao (millimolar_micrometre)'); LEGEND_ALGEBRAIC(:,5) = strpad('y in component model_parameters (dimensionless)'); LEGEND_CONSTANTS(:,10) = strpad('kc in component model_parameters (micrometre_millimolar_per_second)'); LEGEND_STATES(:,7) = strpad('N_Ko in component N_Ko (millimolar_micrometre)'); LEGEND_STATES(:,8) = strpad('N_HCO3o in component N_HCO3o (millimolar_micrometre)'); LEGEND_ALGEBRAIC(:,2) = strpad('N_Clo in component N_Clo (millimolar_micrometre)'); LEGEND_ALGEBRAIC(:,15) = strpad('ECl in component Nernst_potentials (volt)'); LEGEND_CONSTANTS(:,11) = strpad('T in component model_parameters (kelvin)'); LEGEND_CONSTANTS(:,12) = strpad('R in component model_parameters (J_per_mol_K)'); LEGEND_CONSTANTS(:,13) = strpad('gKCC1 in component J_KCC1 (per_ohm_cm2)'); LEGEND_ALGEBRAIC(:,3) = strpad('ft in component J_KCC1 (dimensionless)'); LEGEND_CONSTANTS(:,14) = strpad('gNBC in component J_NBC (per_ohm_cm2)'); LEGEND_ALGEBRAIC(:,20) = strpad('ENBC in component ENBC (volt)'); LEGEND_CONSTANTS(:,15) = strpad('gNKCC1 in component J_NKCC1 (per_ohm_cm2)'); LEGEND_ALGEBRAIC(:,4) = strpad('ft in component J_NKCC1 (dimensionless)'); LEGEND_CONSTANTS(:,16) = strpad('zNBC in component ENBC (dimensionless)'); LEGEND_CONSTANTS(:,17) = strpad('gCl in component model_parameters (per_ohm_cm2)'); LEGEND_CONSTANTS(:,18) = strpad('Pmax in component J_NaKATPase (mole_per_cm2_second)'); LEGEND_CONSTANTS(:,19) = strpad('K_Nai in component J_NaKATPase (millimolar)'); LEGEND_CONSTANTS(:,20) = strpad('K_Ko in component J_NaKATPase (millimolar)'); LEGEND_ALGEBRAIC(:,23) = strpad('I_K in component I_K (millimolar_micrometre_per_second)'); LEGEND_CONSTANTS(:,21) = strpad('nA in component model_parameters (per_mole)'); LEGEND_CONSTANTS(:,22) = strpad('elementary_charge in component model_parameters (C)'); LEGEND_ALGEBRAIC(:,24) = strpad('I_Cl in component I_Cl (millimolar_micrometre_per_second)'); LEGEND_ALGEBRAIC(:,27) = strpad('I_Na in component I_Na (millimolar_micrometre_per_second)'); LEGEND_CONSTANTS(:,23) = strpad('t0 in component model_parameters (second)'); LEGEND_CONSTANTS(:,24) = strpad('t1 in component model_parameters (second)'); LEGEND_CONSTANTS(:,25) = strpad('t2 in component model_parameters (second)'); LEGEND_CONSTANTS(:,26) = strpad('alpha in component model_parameters (dimensionless)'); LEGEND_CONSTANTS(:,27) = strpad('beta in component model_parameters (dimensionless)'); LEGEND_CONSTANTS(:,28) = strpad('deltaT in component model_parameters (second)'); LEGEND_CONSTANTS(:,29) = strpad('gamma_alpha_beta in component model_parameters (dimensionless)'); LEGEND_CONSTANTS(:,30) = strpad('gamma_alpha in component model_parameters (dimensionless)'); LEGEND_CONSTANTS(:,31) = strpad('gamma_beta in component model_parameters (dimensionless)'); LEGEND_RATES(:,1) = strpad('d/dt wi in component wi (micrometre)'); LEGEND_RATES(:,2) = strpad('d/dt N_Nai in component N_Nai (millimolar_micrometre)'); LEGEND_RATES(:,3) = strpad('d/dt N_Ki in component N_Ki (millimolar_micrometre)'); LEGEND_RATES(:,4) = strpad('d/dt N_HCO3i in component N_HCO3i (millimolar_micrometre)'); LEGEND_RATES(:,5) = strpad('d/dt N_Cli in component N_Cli (millimolar_micrometre)'); LEGEND_RATES(:,6) = strpad('d/dt N_Nao in component N_Nao (millimolar_micrometre)'); LEGEND_RATES(:,7) = strpad('d/dt N_Ko in component N_Ko (millimolar_micrometre)'); LEGEND_RATES(:,8) = strpad('d/dt N_HCO3o in component N_HCO3o (millimolar_micrometre)'); 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) = 0.061; CONSTANTS(:,1) = 2.1e-4; CONSTANTS(:,2) = 12.41; CONSTANTS(:,3) = 0.0879; STATES(:,2) = 0.99796; CONSTANTS(:,4) = 1.314e-4; CONSTANTS(:,5) = 9.649e4; CONSTANTS(:,6) = 1; CONSTANTS(:,7) = 1; STATES(:,3) = 5.52782; CONSTANTS(:,8) = 0.004; CONSTANTS(:,9) = 1; STATES(:,4) = 0.58804; STATES(:,5) = 0.32879; STATES(:,6) = 4.301041; CONSTANTS(:,10) = 7.35e-2; STATES(:,7) = 0.0807; STATES(:,8) = 0.432552; CONSTANTS(:,11) = 300; CONSTANTS(:,12) = 8.315; CONSTANTS(:,13) = 1e-6; CONSTANTS(:,14) = 9.03e-5; CONSTANTS(:,15) = 5.54e-6; CONSTANTS(:,16) = -1; CONSTANTS(:,17) = 8.797e-5; CONSTANTS(:,18) = 1.4207e-10; CONSTANTS(:,19) = 10; CONSTANTS(:,20) = 1.5; CONSTANTS(:,21) = 6.0221415e23; CONSTANTS(:,22) = 1.6e-19; CONSTANTS(:,23) = 10; CONSTANTS(:,24) = 20; CONSTANTS(:,25) = 30; CONSTANTS(:,26) = 2; CONSTANTS(:,27) = 14; CONSTANTS(:,28) = CONSTANTS(:,24) - CONSTANTS(:,23); CONSTANTS(:,29) = factorial((CONSTANTS(:,26)+CONSTANTS(:,27)) - 1.00000); CONSTANTS(:,30) = factorial(CONSTANTS(:,26) - 1.00000); CONSTANTS(:,31) = factorial(CONSTANTS(:,27) - 1.00000); 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(:,1) = CONSTANTS(:,3) - STATES(:,1); ALGEBRAIC(:,11) = piecewise({STATES(:,6)./ALGEBRAIC(:,1)>0.00000, STATES(:,6)./ALGEBRAIC(:,1) }, 1.00000e-180); ALGEBRAIC(:,7) = piecewise({STATES(:,7)./ALGEBRAIC(:,1)>0.00000, STATES(:,7)./ALGEBRAIC(:,1) }, 1.00000e-180); ALGEBRAIC(:,2) = (STATES(:,6)+STATES(:,7)) - STATES(:,8); ALGEBRAIC(:,14) = piecewise({ALGEBRAIC(:,2)./ALGEBRAIC(:,1)>0.00000, ALGEBRAIC(:,2)./ALGEBRAIC(:,1) }, 1.00000e-180); ALGEBRAIC(:,19) = piecewise({STATES(:,8)./ALGEBRAIC(:,1)>0.00000, STATES(:,8)./ALGEBRAIC(:,1) }, 1.00000e-180); ALGEBRAIC(:,9) = piecewise({STATES(:,2)./STATES(:,1)>0.00000, STATES(:,2)./STATES(:,1) }, 1.00000e-180); ALGEBRAIC(:,6) = piecewise({STATES(:,3)./STATES(:,1)>0.00000, STATES(:,3)./STATES(:,1) }, 1.00000e-180); ALGEBRAIC(:,13) = piecewise({STATES(:,5)./STATES(:,1)>0.00000, STATES(:,5)./STATES(:,1) }, 1.00000e-180); ALGEBRAIC(:,18) = piecewise({STATES(:,4)./STATES(:,1)>0.00000, STATES(:,4)./STATES(:,1) }, 1.00000e-180); RATES(:,1) = 1.00000.*CONSTANTS(:,1).*((ALGEBRAIC(:,9)+ALGEBRAIC(:,6)+ALGEBRAIC(:,13)+ALGEBRAIC(:,18)+CONSTANTS(:,2)./STATES(:,1)) - (ALGEBRAIC(:,11)+ALGEBRAIC(:,7)+ALGEBRAIC(:,14)+ALGEBRAIC(:,19))); ALGEBRAIC(:,12) = (( CONSTANTS(:,12).*CONSTANTS(:,11))./( 1.00000.*CONSTANTS(:,5))).*log(ALGEBRAIC(:,11)./ALGEBRAIC(:,9)); ALGEBRAIC(:,10) = ( (( CONSTANTS(:,18).*power(ALGEBRAIC(:,9), 1.50000))./(power(ALGEBRAIC(:,9), 1.50000)+power(CONSTANTS(:,19), 1.50000))).*ALGEBRAIC(:,7))./(ALGEBRAIC(:,7)+CONSTANTS(:,20)); ALGEBRAIC(:,8) = (( CONSTANTS(:,12).*CONSTANTS(:,11))./( 1.00000.*CONSTANTS(:,5))).*log(ALGEBRAIC(:,7)./ALGEBRAIC(:,6)); ALGEBRAIC(:,15) = (( CONSTANTS(:,12).*CONSTANTS(:,11))./( - 1.00000.*CONSTANTS(:,5))).*log(ALGEBRAIC(:,14)./ALGEBRAIC(:,13)); ALGEBRAIC(:,20) = (( CONSTANTS(:,12).*CONSTANTS(:,11))./( CONSTANTS(:,16).*CONSTANTS(:,5))).*log(( (ALGEBRAIC(:,11)./ALGEBRAIC(:,9)).*power(ALGEBRAIC(:,19), 2.00000))./power(ALGEBRAIC(:,18), 2.00000)); ALGEBRAIC(:,21) = (( CONSTANTS(:,4).*ALGEBRAIC(:,12)+ CONSTANTS(:,8).*ALGEBRAIC(:,8)+ CONSTANTS(:,17).*ALGEBRAIC(:,15)+ CONSTANTS(:,7).*CONSTANTS(:,14).*ALGEBRAIC(:,20)) - ALGEBRAIC(:,10).*CONSTANTS(:,5))./(CONSTANTS(:,4)+CONSTANTS(:,8)+CONSTANTS(:,17)+ CONSTANTS(:,7).*CONSTANTS(:,14)); ALGEBRAIC(:,4) = piecewise({VOI>=10.0000&VOI<20.0000, 1.00000 }, 0.00000); ALGEBRAIC(:,17) = (( (( 1.00000e+10.*CONSTANTS(:,15).*ALGEBRAIC(:,4))./CONSTANTS(:,5)).*CONSTANTS(:,12).*CONSTANTS(:,11))./CONSTANTS(:,5)).*log( (( (ALGEBRAIC(:,11)./ALGEBRAIC(:,9)).*ALGEBRAIC(:,7))./ALGEBRAIC(:,6)).*power(ALGEBRAIC(:,14)./ALGEBRAIC(:,13), 2.00000)); ALGEBRAIC(:,3) = piecewise({VOI>=10.0000&VOI<20.0000, 1.00000 }, 0.00000); ALGEBRAIC(:,16) = (( (( 1.00000e+10.*CONSTANTS(:,13).*ALGEBRAIC(:,3))./CONSTANTS(:,5)).*CONSTANTS(:,12).*CONSTANTS(:,11))./CONSTANTS(:,5)).*log(( ALGEBRAIC(:,7).*ALGEBRAIC(:,14))./( ALGEBRAIC(:,6).*ALGEBRAIC(:,13))); ALGEBRAIC(:,5) = piecewise({VOI>=CONSTANTS(:,23)&VOI<=CONSTANTS(:,24), (CONSTANTS(:,29)./( CONSTANTS(:,30).*CONSTANTS(:,31))).*power(1.00000 - (VOI - CONSTANTS(:,23))./CONSTANTS(:,28), CONSTANTS(:,27) - 1.00000).*power((VOI - CONSTANTS(:,23))./CONSTANTS(:,28), CONSTANTS(:,26) - 1.00000) , VOI>CONSTANTS(:,24)&VOI0.00000, STATES(:,6)./ALGEBRAIC(:,1) }, 1.00000e-180); ALGEBRAIC(:,7) = piecewise({STATES(:,7)./ALGEBRAIC(:,1)>0.00000, STATES(:,7)./ALGEBRAIC(:,1) }, 1.00000e-180); ALGEBRAIC(:,2) = (STATES(:,6)+STATES(:,7)) - STATES(:,8); ALGEBRAIC(:,14) = piecewise({ALGEBRAIC(:,2)./ALGEBRAIC(:,1)>0.00000, ALGEBRAIC(:,2)./ALGEBRAIC(:,1) }, 1.00000e-180); ALGEBRAIC(:,19) = piecewise({STATES(:,8)./ALGEBRAIC(:,1)>0.00000, STATES(:,8)./ALGEBRAIC(:,1) }, 1.00000e-180); ALGEBRAIC(:,9) = piecewise({STATES(:,2)./STATES(:,1)>0.00000, STATES(:,2)./STATES(:,1) }, 1.00000e-180); ALGEBRAIC(:,6) = piecewise({STATES(:,3)./STATES(:,1)>0.00000, STATES(:,3)./STATES(:,1) }, 1.00000e-180); ALGEBRAIC(:,13) = piecewise({STATES(:,5)./STATES(:,1)>0.00000, STATES(:,5)./STATES(:,1) }, 1.00000e-180); ALGEBRAIC(:,18) = piecewise({STATES(:,4)./STATES(:,1)>0.00000, STATES(:,4)./STATES(:,1) }, 1.00000e-180); ALGEBRAIC(:,12) = (( CONSTANTS(:,12).*CONSTANTS(:,11))./( 1.00000.*CONSTANTS(:,5))).*log(ALGEBRAIC(:,11)./ALGEBRAIC(:,9)); ALGEBRAIC(:,10) = ( (( CONSTANTS(:,18).*power(ALGEBRAIC(:,9), 1.50000))./(power(ALGEBRAIC(:,9), 1.50000)+power(CONSTANTS(:,19), 1.50000))).*ALGEBRAIC(:,7))./(ALGEBRAIC(:,7)+CONSTANTS(:,20)); ALGEBRAIC(:,8) = (( CONSTANTS(:,12).*CONSTANTS(:,11))./( 1.00000.*CONSTANTS(:,5))).*log(ALGEBRAIC(:,7)./ALGEBRAIC(:,6)); ALGEBRAIC(:,15) = (( CONSTANTS(:,12).*CONSTANTS(:,11))./( - 1.00000.*CONSTANTS(:,5))).*log(ALGEBRAIC(:,14)./ALGEBRAIC(:,13)); ALGEBRAIC(:,20) = (( CONSTANTS(:,12).*CONSTANTS(:,11))./( CONSTANTS(:,16).*CONSTANTS(:,5))).*log(( (ALGEBRAIC(:,11)./ALGEBRAIC(:,9)).*power(ALGEBRAIC(:,19), 2.00000))./power(ALGEBRAIC(:,18), 2.00000)); ALGEBRAIC(:,21) = (( CONSTANTS(:,4).*ALGEBRAIC(:,12)+ CONSTANTS(:,8).*ALGEBRAIC(:,8)+ CONSTANTS(:,17).*ALGEBRAIC(:,15)+ CONSTANTS(:,7).*CONSTANTS(:,14).*ALGEBRAIC(:,20)) - ALGEBRAIC(:,10).*CONSTANTS(:,5))./(CONSTANTS(:,4)+CONSTANTS(:,8)+CONSTANTS(:,17)+ CONSTANTS(:,7).*CONSTANTS(:,14)); ALGEBRAIC(:,4) = piecewise({VOI>=10.0000&VOI<20.0000, 1.00000 }, 0.00000); ALGEBRAIC(:,17) = (( (( 1.00000e+10.*CONSTANTS(:,15).*ALGEBRAIC(:,4))./CONSTANTS(:,5)).*CONSTANTS(:,12).*CONSTANTS(:,11))./CONSTANTS(:,5)).*log( (( (ALGEBRAIC(:,11)./ALGEBRAIC(:,9)).*ALGEBRAIC(:,7))./ALGEBRAIC(:,6)).*power(ALGEBRAIC(:,14)./ALGEBRAIC(:,13), 2.00000)); ALGEBRAIC(:,3) = piecewise({VOI>=10.0000&VOI<20.0000, 1.00000 }, 0.00000); ALGEBRAIC(:,16) = (( (( 1.00000e+10.*CONSTANTS(:,13).*ALGEBRAIC(:,3))./CONSTANTS(:,5)).*CONSTANTS(:,12).*CONSTANTS(:,11))./CONSTANTS(:,5)).*log(( ALGEBRAIC(:,7).*ALGEBRAIC(:,14))./( ALGEBRAIC(:,6).*ALGEBRAIC(:,13))); ALGEBRAIC(:,5) = piecewise({VOI>=CONSTANTS(:,23)&VOI<=CONSTANTS(:,24), (CONSTANTS(:,29)./( CONSTANTS(:,30).*CONSTANTS(:,31))).*power(1.00000 - (VOI - CONSTANTS(:,23))./CONSTANTS(:,28), CONSTANTS(:,27) - 1.00000).*power((VOI - CONSTANTS(:,23))./CONSTANTS(:,28), CONSTANTS(:,26) - 1.00000) , VOI>CONSTANTS(:,24)&VOI req_length strout = strin(1:req_length); else strout = [strin, blanks(req_length - insize)]; end end