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 =50;
end
% There are a total of 13 entries in each of the rate and state variable arrays.
% There are a total of 53 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('R_cm in component cell (dimensionless)');
    LEGEND_CONSTANTS(:,2) = strpad('R in component cell (kilojoule_per_mole_kelvin)');
    LEGEND_CONSTANTS(:,3) = strpad('T in component cell (kelvin)');
    LEGEND_CONSTANTS(:,4) = strpad('F in component cell (kilojoule_per_mole_millivolt)');
    LEGEND_CONSTANTS(:,51) = strpad('S in component cell (kilojoule_per_mole)');
    LEGEND_CONSTANTS(:,52) = strpad('Z in component cell (millivolt)');
    LEGEND_ALGEBRAIC(:,9) = strpad('electric_potential in component cell (millivolt)');
    LEGEND_CONSTANTS(:,5) = strpad('protonmotive_force in component cell (millivolt)');
    LEGEND_ALGEBRAIC(:,10) = strpad('ex_membrane_potential in component cell (millivolt)');
    LEGEND_ALGEBRAIC(:,11) = strpad('in_membrane_potential in component cell (millivolt)');
    LEGEND_CONSTANTS(:,6) = strpad('c_buffi in component cell (molar_proton_per_pH_unit)');
    LEGEND_CONSTANTS(:,7) = strpad('c_buffe in component cell (molar_proton_per_pH_unit)');
    LEGEND_ALGEBRAIC(:,1) = strpad('pH_e in component cell (dimensionless)');
    LEGEND_ALGEBRAIC(:,5) = strpad('pH_i in component cell (dimensionless)');
    LEGEND_CONSTANTS(:,8) = strpad('pKa in component cell (dimensionless)');
    LEGEND_STATES(:,1) = strpad('He in component He (micromolar)');
    LEGEND_STATES(:,2) = strpad('Hi in component Hi (micromolar)');
    LEGEND_ALGEBRAIC(:,8) = strpad('delta_pH in component cell (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('dpH in component cell (dimensionless)');
    LEGEND_ALGEBRAIC(:,6) = strpad('C0_i in component cell (molar_proton_per_pH_unit)');
    LEGEND_ALGEBRAIC(:,3) = strpad('C0_e in component cell (molar_proton_per_pH_unit)');
    LEGEND_ALGEBRAIC(:,7) = strpad('r_buffi in component cell (dimensionless)');
    LEGEND_ALGEBRAIC(:,4) = strpad('r_buffe in component cell (dimensionless)');
    LEGEND_CONSTANTS(:,10) = strpad('BN in component cell (dimensionless)');
    LEGEND_ALGEBRAIC(:,12) = strpad('u in component cell (dimensionless)');
    LEGEND_ALGEBRAIC(:,14) = strpad('EmN in component redox_potentials (millivolt)');
    LEGEND_ALGEBRAIC(:,33) = strpad('EmU in component redox_potentials (millivolt)');
    LEGEND_ALGEBRAIC(:,30) = strpad('Emc in component redox_potentials (millivolt)');
    LEGEND_ALGEBRAIC(:,32) = strpad('Ema in component redox_potentials (millivolt)');
    LEGEND_CONSTANTS(:,11) = strpad('EmN0 in component redox_potentials (millivolt)');
    LEGEND_CONSTANTS(:,12) = strpad('EmU0 in component redox_potentials (millivolt)');
    LEGEND_CONSTANTS(:,13) = strpad('Emc0 in component redox_potentials (millivolt)');
    LEGEND_ALGEBRAIC(:,13) = strpad('NAD in component NAD (micromolar)');
    LEGEND_STATES(:,3) = strpad('NADH in component NADH (micromolar)');
    LEGEND_ALGEBRAIC(:,31) = strpad('UQ in component UQ (micromolar)');
    LEGEND_STATES(:,4) = strpad('UQH2 in component UQH2 (micromolar)');
    LEGEND_STATES(:,5) = strpad('c_2 in component c_2 (micromolar)');
    LEGEND_ALGEBRAIC(:,29) = strpad('c_3 in component c_3 (micromolar)');
    LEGEND_CONSTANTS(:,14) = strpad('Nt in component NAD (micromolar)');
    LEGEND_ALGEBRAIC(:,35) = strpad('vDH in component vDH (flux)');
    LEGEND_ALGEBRAIC(:,37) = strpad('vC1 in component vC1 (flux)');
    LEGEND_STATES(:,6) = strpad('O2 in component O2 (micromolar)');
    LEGEND_ALGEBRAIC(:,40) = strpad('vC4 in component vC4 (flux)');
    LEGEND_CONSTANTS(:,15) = strpad('nA in component vSN (dimensionless)');
    LEGEND_ALGEBRAIC(:,39) = strpad('vC3 in component vC3 (flux)');
    LEGEND_ALGEBRAIC(:,44) = strpad('vSN in component vSN (flux)');
    LEGEND_ALGEBRAIC(:,45) = strpad('vEX in component vEX (flux)');
    LEGEND_ALGEBRAIC(:,48) = strpad('vPI in component vPI (flux)');
    LEGEND_CONSTANTS(:,53) = strpad('vLK in component vLK (flux)');
    LEGEND_ALGEBRAIC(:,49) = strpad('vCK in component vCK (flux)');
    LEGEND_ALGEBRAIC(:,50) = strpad('vEFF in component vEFF (flux)');
    LEGEND_ALGEBRAIC(:,18) = strpad('ADP_mi in component ADP_mi (micromolar)');
    LEGEND_ALGEBRAIC(:,15) = strpad('ADP_ti in component ADP_ti (micromolar)');
    LEGEND_ALGEBRAIC(:,16) = strpad('ADP_fi in component ADP_fi (micromolar)');
    LEGEND_CONSTANTS(:,16) = strpad('kDDi in component ADP_fi (micromolar)');
    LEGEND_CONSTANTS(:,17) = strpad('Mg_fi in component Mg_fi (micromolar)');
    LEGEND_CONSTANTS(:,18) = strpad('Ai_SUM in component ADP_ti (micromolar)');
    LEGEND_STATES(:,7) = strpad('ATP_ti in component ATP_ti (micromolar)');
    LEGEND_ALGEBRAIC(:,20) = strpad('ATP_mi in component ATP_mi (micromolar)');
    LEGEND_ALGEBRAIC(:,17) = strpad('ATP_fi in component ATP_fi (micromolar)');
    LEGEND_CONSTANTS(:,19) = strpad('kDTi in component ATP_fi (micromolar)');
    LEGEND_ALGEBRAIC(:,21) = strpad('ADP_me in component ADP_me (micromolar)');
    LEGEND_STATES(:,8) = strpad('ADP_te in component ADP_te (micromolar)');
    LEGEND_ALGEBRAIC(:,19) = strpad('ADP_fe in component ADP_fe (micromolar)');
    LEGEND_CONSTANTS(:,20) = strpad('kDDe in component ADP_fe (micromolar)');
    LEGEND_CONSTANTS(:,21) = strpad('Mg_fe in component Mg_fe (micromolar)');
    LEGEND_ALGEBRAIC(:,46) = strpad('vUT in component vUT (flux)');
    LEGEND_ALGEBRAIC(:,47) = strpad('vAK in component vAK (flux)');
    LEGEND_ALGEBRAIC(:,23) = strpad('ATP_me in component ATP_me (micromolar)');
    LEGEND_STATES(:,9) = strpad('ATP_te in component ATP_te (micromolar)');
    LEGEND_ALGEBRAIC(:,22) = strpad('ATP_fe in component ATP_fe (micromolar)');
    LEGEND_CONSTANTS(:,22) = strpad('kDTe in component ATP_fe (micromolar)');
    LEGEND_ALGEBRAIC(:,24) = strpad('AMP_e in component AMP_e (micromolar)');
    LEGEND_CONSTANTS(:,23) = strpad('Ae_SUM in component AMP_e (micromolar)');
    LEGEND_ALGEBRAIC(:,25) = strpad('Cr in component Cr (micromolar)');
    LEGEND_CONSTANTS(:,24) = strpad('C_SUM in component Cr (micromolar)');
    LEGEND_STATES(:,10) = strpad('PCr in component PCr (micromolar)');
    LEGEND_ALGEBRAIC(:,27) = strpad('Pi_ji in component Pi_ji (micromolar)');
    LEGEND_STATES(:,11) = strpad('Pi_ti in component Pi_ti (micromolar)');
    LEGEND_ALGEBRAIC(:,28) = strpad('Pi_je in component Pi_je (micromolar)');
    LEGEND_STATES(:,12) = strpad('Pi_te in component Pi_te (micromolar)');
    LEGEND_ALGEBRAIC(:,26) = strpad('P_SUM in component P_SUM (micromolar)');
    LEGEND_CONSTANTS(:,25) = strpad('ct in component c_3 (micromolar)');
    LEGEND_CONSTANTS(:,26) = strpad('Ut in component UQ (micromolar)');
    LEGEND_STATES(:,13) = strpad('a_2 in component a_2 (micromolar)');
    LEGEND_ALGEBRAIC(:,34) = strpad('A3_2 in component a_2 (dimensionless)');
    LEGEND_CONSTANTS(:,27) = strpad('Ema0 in component a_2 (millivolt)');
    LEGEND_CONSTANTS(:,28) = strpad('at in component a_2 (micromolar)');
    LEGEND_ALGEBRAIC(:,2) = strpad('a_3 in component a_3 (micromolar)');
    LEGEND_CONSTANTS(:,29) = strpad('kDH in component vDH (flux)');
    LEGEND_CONSTANTS(:,30) = strpad('KmN in component vDH (micromolar)');
    LEGEND_CONSTANTS(:,31) = strpad('pD in component vDH (dimensionless)');
    LEGEND_CONSTANTS(:,32) = strpad('kC1 in component vC1 (flux)');
    LEGEND_ALGEBRAIC(:,36) = strpad('delta_GC1 in component vC1 (millivolt)');
    LEGEND_CONSTANTS(:,33) = strpad('kC3 in component vC3 (flux)');
    LEGEND_ALGEBRAIC(:,38) = strpad('delta_GC3 in component vC3 (millivolt)');
    LEGEND_CONSTANTS(:,34) = strpad('kC4 in component vC4 (flux)');
    LEGEND_CONSTANTS(:,35) = strpad('KmO in component vC4 (micromolar)');
    LEGEND_CONSTANTS(:,36) = strpad('kSN in component vSN (flux)');
    LEGEND_ALGEBRAIC(:,42) = strpad('delta_GSN in component vSN (millivolt)');
    LEGEND_ALGEBRAIC(:,41) = strpad('delta_Gp in component vSN (kilojoule_per_mole)');
    LEGEND_CONSTANTS(:,37) = strpad('delta_Gp0 in component vSN (kilojoule_per_mole)');
    LEGEND_ALGEBRAIC(:,43) = strpad('gamma in component vSN (dimensionless)');
    LEGEND_CONSTANTS(:,38) = strpad('kEX in component vEX (flux)');
    LEGEND_CONSTANTS(:,39) = strpad('km_ADP in component vEX (micromolar)');
    LEGEND_CONSTANTS(:,40) = strpad('km_A in component vUT (micromolar)');
    LEGEND_CONSTANTS(:,41) = strpad('kUT in component vUT (flux)');
    LEGEND_CONSTANTS(:,42) = strpad('kf_AK in component vAK (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,43) = strpad('kb_AK in component vAK (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,44) = strpad('kL1 in component vLK (flux)');
    LEGEND_CONSTANTS(:,45) = strpad('kL2 in component vLK (per_millivolt)');
    LEGEND_CONSTANTS(:,46) = strpad('kPI in component vPI (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,47) = strpad('kf_CK in component vCK (third_order_rate_constant)');
    LEGEND_CONSTANTS(:,48) = strpad('kb_CK in component vCK (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,49) = strpad('pH_o in component vEFF (dimensionless)');
    LEGEND_CONSTANTS(:,50) = strpad('k_EFF in component vEFF (flux)');
    LEGEND_RATES(:,3) = strpad('d/dt NADH in component NADH (micromolar)');
    LEGEND_RATES(:,6) = strpad('d/dt O2 in component O2 (micromolar)');
    LEGEND_RATES(:,2) = strpad('d/dt Hi in component Hi (micromolar)');
    LEGEND_RATES(:,1) = strpad('d/dt He in component He (micromolar)');
    LEGEND_RATES(:,7) = strpad('d/dt ATP_ti in component ATP_ti (micromolar)');
    LEGEND_RATES(:,8) = strpad('d/dt ADP_te in component ADP_te (micromolar)');
    LEGEND_RATES(:,9) = strpad('d/dt ATP_te in component ATP_te (micromolar)');
    LEGEND_RATES(:,10) = strpad('d/dt PCr in component PCr (micromolar)');
    LEGEND_RATES(:,11) = strpad('d/dt Pi_ti in component Pi_ti (micromolar)');
    LEGEND_RATES(:,12) = strpad('d/dt Pi_te in component Pi_te (micromolar)');
    LEGEND_RATES(:,5) = strpad('d/dt c_2 in component c_2 (micromolar)');
    LEGEND_RATES(:,4) = strpad('d/dt UQH2 in component UQH2 (micromolar)');
    LEGEND_RATES(:,13) = strpad('d/dt a_2 in component a_2 (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 = [];
    CONSTANTS(:,1) = 15.0;
    CONSTANTS(:,2) = 0.0083;
    CONSTANTS(:,3) = 289.0;
    CONSTANTS(:,4) = 0.0965;
    CONSTANTS(:,5) = 190.0;
    CONSTANTS(:,6) = 0.022;
    CONSTANTS(:,7) = 0.025;
    CONSTANTS(:,8) = 6.8;
    STATES(:,1) = 1.00;
    STATES(:,2) = 1.00;
    CONSTANTS(:,9) = 0.001;
    CONSTANTS(:,10) = 5.0;
    CONSTANTS(:,11) = -320.0;
    CONSTANTS(:,12) = 85.0;
    CONSTANTS(:,13) = 250.0;
    STATES(:,3) = 500.0;
    STATES(:,4) = 1.00;
    STATES(:,5) = 1.00;
    CONSTANTS(:,14) = 2970.0;
    STATES(:,6) = 1.00;
    CONSTANTS(:,15) = 2.5;
    CONSTANTS(:,16) = 282;
    CONSTANTS(:,17) = 380.0;
    CONSTANTS(:,18) = 16260.0;
    STATES(:,7) = 1.00;
    CONSTANTS(:,19) = 17;
    STATES(:,8) = 1.00;
    CONSTANTS(:,20) = 347;
    CONSTANTS(:,21) = 4000.0;
    STATES(:,9) = 1.00;
    CONSTANTS(:,22) = 24;
    CONSTANTS(:,23) = 1600.2;
    CONSTANTS(:,24) = 35000.0;
    STATES(:,10) = 1.00;
    STATES(:,11) = 1.00;
    STATES(:,12) = 1.00;
    CONSTANTS(:,25) = 270.0;
    CONSTANTS(:,26) = 1350.0;
    STATES(:,13) = 1.00;
    CONSTANTS(:,27) = 540.0;
    CONSTANTS(:,28) = 135.0;
    CONSTANTS(:,29) = 28074;
    CONSTANTS(:,30) = 100.0;
    CONSTANTS(:,31) = 0.8;
    CONSTANTS(:,32) = 238.95;
    CONSTANTS(:,33) = 136.41;
    CONSTANTS(:,34) = 136.41;
    CONSTANTS(:,35) = 120.0;
    CONSTANTS(:,36) = 34316.0;
    CONSTANTS(:,37) = 31.9;
    CONSTANTS(:,38) = 54572;
    CONSTANTS(:,39) = 3.5;
    CONSTANTS(:,40) = 150.0;
    CONSTANTS(:,41) = 686.5;
    CONSTANTS(:,42) = 862.10;
    CONSTANTS(:,43) = 22.747;
    CONSTANTS(:,44) = 2.5;
    CONSTANTS(:,45) = 0.038;
    CONSTANTS(:,46) = 69.421;
    CONSTANTS(:,47) = 1.9258;
    CONSTANTS(:,48) = 0.00087538;
    CONSTANTS(:,49) = 7.0;
    CONSTANTS(:,50) = 1.9258;
    CONSTANTS(:,51) =  2.30300.*CONSTANTS(:,2).*CONSTANTS(:,3);
    CONSTANTS(:,52) =  2.30300.*CONSTANTS(:,2).*(CONSTANTS(:,3)./CONSTANTS(:,4));
    CONSTANTS(:,53) =  CONSTANTS(:,44).*(exp( CONSTANTS(:,45).*CONSTANTS(:,5)) - 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) =  - arbitrary_log(STATES(:,1)./1.00000e+06, 10);
    ALGEBRAIC(:,5) =  - arbitrary_log(STATES(:,2)./1.00000e+06, 10);
    ALGEBRAIC(:,8) =  CONSTANTS(:,52).*(ALGEBRAIC(:,5) - ALGEBRAIC(:,1));
    ALGEBRAIC(:,9) =  - (CONSTANTS(:,5) - ALGEBRAIC(:,8));
    ALGEBRAIC(:,12) = ALGEBRAIC(:,9)./CONSTANTS(:,5);
    ALGEBRAIC(:,29) = CONSTANTS(:,25) - STATES(:,5);
    ALGEBRAIC(:,30) = CONSTANTS(:,13)+ CONSTANTS(:,52).*arbitrary_log(ALGEBRAIC(:,29)./STATES(:,5), 10);
    ALGEBRAIC(:,32) = ALGEBRAIC(:,30)+ CONSTANTS(:,5).*((2.00000+ 2.00000.*ALGEBRAIC(:,12))./2.00000);
    ALGEBRAIC(:,34) = power(10.0000, (ALGEBRAIC(:,32) - CONSTANTS(:,27))./CONSTANTS(:,52));
    RATES(:,13) = CONSTANTS(:,28)./(1.00000+ALGEBRAIC(:,34));
    ALGEBRAIC(:,13) = CONSTANTS(:,14) - STATES(:,3);
    ALGEBRAIC(:,35) =  CONSTANTS(:,29).*(1.00000./power(1.00000+CONSTANTS(:,30)./(ALGEBRAIC(:,13)./STATES(:,3)), CONSTANTS(:,31)));
    ALGEBRAIC(:,14) = CONSTANTS(:,11)+ (CONSTANTS(:,52)./2.00000).*arbitrary_log(ALGEBRAIC(:,13)./STATES(:,3), 10);
    ALGEBRAIC(:,31) = CONSTANTS(:,26) - STATES(:,4);
    ALGEBRAIC(:,33) = CONSTANTS(:,12)+ (CONSTANTS(:,52)./2.00000).*arbitrary_log(ALGEBRAIC(:,31)./STATES(:,4), 10);
    ALGEBRAIC(:,36) = ALGEBRAIC(:,33) - (ALGEBRAIC(:,14)+ CONSTANTS(:,5).*(4.00000./2.00000));
    ALGEBRAIC(:,37) =  CONSTANTS(:,32).*ALGEBRAIC(:,36);
    RATES(:,3) =  (ALGEBRAIC(:,35) - ALGEBRAIC(:,37)).*(CONSTANTS(:,1)./CONSTANTS(:,10));
    ALGEBRAIC(:,38) = ALGEBRAIC(:,30) - (ALGEBRAIC(:,33)+ CONSTANTS(:,5).*((4.00000 -  2.00000.*ALGEBRAIC(:,12))./2.00000));
    ALGEBRAIC(:,39) =  CONSTANTS(:,33).*ALGEBRAIC(:,38);
    RATES(:,4) =  CONSTANTS(:,1).*(ALGEBRAIC(:,37) - ALGEBRAIC(:,39));
    ALGEBRAIC(:,40) =  CONSTANTS(:,34).*STATES(:,13).*STATES(:,5).*(1.00000./(1.00000+CONSTANTS(:,35)./STATES(:,6)));
    RATES(:,6) =  - ALGEBRAIC(:,40);
    RATES(:,5) =  (ALGEBRAIC(:,39)+ ALGEBRAIC(:,40).*2.00000).*CONSTANTS(:,1).*2.00000;
    ALGEBRAIC(:,15) = CONSTANTS(:,18) - STATES(:,7);
    ALGEBRAIC(:,41) = CONSTANTS(:,37)./(CONSTANTS(:,4)+ CONSTANTS(:,52).*arbitrary_log( 1.00000e+06.*(STATES(:,7)./( ALGEBRAIC(:,15).*STATES(:,11))), 10));
    ALGEBRAIC(:,42) =  CONSTANTS(:,15).*CONSTANTS(:,5) - ALGEBRAIC(:,41);
    ALGEBRAIC(:,43) = power(10.0000, ALGEBRAIC(:,42)./CONSTANTS(:,52));
    ALGEBRAIC(:,44) =  CONSTANTS(:,36).*((ALGEBRAIC(:,43) - 1.00000)./(ALGEBRAIC(:,43)+1.00000));
    ALGEBRAIC(:,11) =  0.650000.*ALGEBRAIC(:,9);
    ALGEBRAIC(:,16) = ALGEBRAIC(:,15)./(1.00000+CONSTANTS(:,17)./CONSTANTS(:,16));
    ALGEBRAIC(:,17) = STATES(:,7)./(1.00000+CONSTANTS(:,17)./CONSTANTS(:,19));
    ALGEBRAIC(:,19) = STATES(:,8)./(1.00000+CONSTANTS(:,21)./CONSTANTS(:,20));
    ALGEBRAIC(:,22) = STATES(:,9)./(1.00000+CONSTANTS(:,21)./CONSTANTS(:,22));
    ALGEBRAIC(:,45) =  CONSTANTS(:,38).*(ALGEBRAIC(:,19)./(ALGEBRAIC(:,19)+ ALGEBRAIC(:,22).*power(10.0000,  - ALGEBRAIC(:,11)./CONSTANTS(:,52))) - ALGEBRAIC(:,16)./(ALGEBRAIC(:,16)+ ALGEBRAIC(:,17).*power(10.0000,  - ALGEBRAIC(:,11)./CONSTANTS(:,52)))).*(1.00000./(1.00000+CONSTANTS(:,39)./ALGEBRAIC(:,19)));
    RATES(:,7) =  (ALGEBRAIC(:,44) - ALGEBRAIC(:,45)).*CONSTANTS(:,1);
    ALGEBRAIC(:,6) = (power(10.0000,  - ALGEBRAIC(:,5)) - power(10.0000,  - ALGEBRAIC(:,5) - CONSTANTS(:,9)))./CONSTANTS(:,9);
    ALGEBRAIC(:,7) = CONSTANTS(:,6)./ALGEBRAIC(:,6);
    ALGEBRAIC(:,27) = STATES(:,11)./(1.00000+power(10.0000, ALGEBRAIC(:,5) - CONSTANTS(:,8)));
    ALGEBRAIC(:,28) = STATES(:,12)./(1.00000+power(10.0000, ALGEBRAIC(:,1) - CONSTANTS(:,8)));
    ALGEBRAIC(:,48) =  CONSTANTS(:,46).*( STATES(:,1).*ALGEBRAIC(:,28) -  STATES(:,2).*ALGEBRAIC(:,27));
    RATES(:,2) = ( (( (4.00000 -  2.00000.*ALGEBRAIC(:,12)).*ALGEBRAIC(:,39)+ 4.00000.*ALGEBRAIC(:,37)) - ( 2.00000.*(2.00000+ 2.00000.*ALGEBRAIC(:,12)).*ALGEBRAIC(:,40)+ CONSTANTS(:,15).*ALGEBRAIC(:,44)+ ALGEBRAIC(:,12).*ALGEBRAIC(:,45)+ (1.00000 - ALGEBRAIC(:,12)).*ALGEBRAIC(:,48)+CONSTANTS(:,53))).*CONSTANTS(:,1))./ALGEBRAIC(:,7);
    RATES(:,11) =  (ALGEBRAIC(:,48) - ALGEBRAIC(:,44)).*CONSTANTS(:,1);
    ALGEBRAIC(:,46) =  CONSTANTS(:,41).*(1.00000./(1.00000+CONSTANTS(:,40)./STATES(:,9)));
    RATES(:,12) = ALGEBRAIC(:,46) - ALGEBRAIC(:,48);
    ALGEBRAIC(:,25) = CONSTANTS(:,24) - STATES(:,10);
    ALGEBRAIC(:,49) =  CONSTANTS(:,47).*STATES(:,8).*STATES(:,10).*STATES(:,1) -  CONSTANTS(:,48).*STATES(:,9).*ALGEBRAIC(:,25);
    ALGEBRAIC(:,21) = STATES(:,8) - ALGEBRAIC(:,19);
    ALGEBRAIC(:,23) = STATES(:,9) - ALGEBRAIC(:,22);
    ALGEBRAIC(:,24) = CONSTANTS(:,23) - (STATES(:,9)+STATES(:,8));
    ALGEBRAIC(:,47) =  CONSTANTS(:,42).*ALGEBRAIC(:,21).*ALGEBRAIC(:,19) -  CONSTANTS(:,43).*ALGEBRAIC(:,23).*ALGEBRAIC(:,24);
    RATES(:,8) = ALGEBRAIC(:,46) - (ALGEBRAIC(:,45)+ 2.00000.*ALGEBRAIC(:,47)+ALGEBRAIC(:,49));
    RATES(:,9) = (ALGEBRAIC(:,45)+ALGEBRAIC(:,47)+ALGEBRAIC(:,49)) - ALGEBRAIC(:,46);
    RATES(:,10) =  - ALGEBRAIC(:,49);
    ALGEBRAIC(:,3) = (power(10.0000,  - ALGEBRAIC(:,1)) - power(10.0000,  - ALGEBRAIC(:,1) - CONSTANTS(:,9)))./CONSTANTS(:,9);
    ALGEBRAIC(:,4) = CONSTANTS(:,7)./ALGEBRAIC(:,3);
    ALGEBRAIC(:,50) =  CONSTANTS(:,50).*(CONSTANTS(:,49) - ALGEBRAIC(:,1));
    RATES(:,1) = (( 2.00000.*(2.00000+ 2.00000.*ALGEBRAIC(:,12)).*ALGEBRAIC(:,40)+ (4.00000 -  2.00000.*ALGEBRAIC(:,12)).*ALGEBRAIC(:,39)+ 4.00000.*ALGEBRAIC(:,37)) - ( CONSTANTS(:,15).*ALGEBRAIC(:,44)+ ALGEBRAIC(:,12).*ALGEBRAIC(:,45)+ (1.00000 - ALGEBRAIC(:,12)).*ALGEBRAIC(:,48)+CONSTANTS(:,53)+ALGEBRAIC(:,49)+ALGEBRAIC(:,50)))./ALGEBRAIC(:,4);
   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(:,1) =  - arbitrary_log(STATES(:,1)./1.00000e+06, 10);
    ALGEBRAIC(:,5) =  - arbitrary_log(STATES(:,2)./1.00000e+06, 10);
    ALGEBRAIC(:,8) =  CONSTANTS(:,52).*(ALGEBRAIC(:,5) - ALGEBRAIC(:,1));
    ALGEBRAIC(:,9) =  - (CONSTANTS(:,5) - ALGEBRAIC(:,8));
    ALGEBRAIC(:,12) = ALGEBRAIC(:,9)./CONSTANTS(:,5);
    ALGEBRAIC(:,29) = CONSTANTS(:,25) - STATES(:,5);
    ALGEBRAIC(:,30) = CONSTANTS(:,13)+ CONSTANTS(:,52).*arbitrary_log(ALGEBRAIC(:,29)./STATES(:,5), 10);
    ALGEBRAIC(:,32) = ALGEBRAIC(:,30)+ CONSTANTS(:,5).*((2.00000+ 2.00000.*ALGEBRAIC(:,12))./2.00000);
    ALGEBRAIC(:,34) = power(10.0000, (ALGEBRAIC(:,32) - CONSTANTS(:,27))./CONSTANTS(:,52));
    ALGEBRAIC(:,13) = CONSTANTS(:,14) - STATES(:,3);
    ALGEBRAIC(:,35) =  CONSTANTS(:,29).*(1.00000./power(1.00000+CONSTANTS(:,30)./(ALGEBRAIC(:,13)./STATES(:,3)), CONSTANTS(:,31)));
    ALGEBRAIC(:,14) = CONSTANTS(:,11)+ (CONSTANTS(:,52)./2.00000).*arbitrary_log(ALGEBRAIC(:,13)./STATES(:,3), 10);
    ALGEBRAIC(:,31) = CONSTANTS(:,26) - STATES(:,4);
    ALGEBRAIC(:,33) = CONSTANTS(:,12)+ (CONSTANTS(:,52)./2.00000).*arbitrary_log(ALGEBRAIC(:,31)./STATES(:,4), 10);
    ALGEBRAIC(:,36) = ALGEBRAIC(:,33) - (ALGEBRAIC(:,14)+ CONSTANTS(:,5).*(4.00000./2.00000));
    ALGEBRAIC(:,37) =  CONSTANTS(:,32).*ALGEBRAIC(:,36);
    ALGEBRAIC(:,38) = ALGEBRAIC(:,30) - (ALGEBRAIC(:,33)+ CONSTANTS(:,5).*((4.00000 -  2.00000.*ALGEBRAIC(:,12))./2.00000));
    ALGEBRAIC(:,39) =  CONSTANTS(:,33).*ALGEBRAIC(:,38);
    ALGEBRAIC(:,40) =  CONSTANTS(:,34).*STATES(:,13).*STATES(:,5).*(1.00000./(1.00000+CONSTANTS(:,35)./STATES(:,6)));
    ALGEBRAIC(:,15) = CONSTANTS(:,18) - STATES(:,7);
    ALGEBRAIC(:,41) = CONSTANTS(:,37)./(CONSTANTS(:,4)+ CONSTANTS(:,52).*arbitrary_log( 1.00000e+06.*(STATES(:,7)./( ALGEBRAIC(:,15).*STATES(:,11))), 10));
    ALGEBRAIC(:,42) =  CONSTANTS(:,15).*CONSTANTS(:,5) - ALGEBRAIC(:,41);
    ALGEBRAIC(:,43) = power(10.0000, ALGEBRAIC(:,42)./CONSTANTS(:,52));
    ALGEBRAIC(:,44) =  CONSTANTS(:,36).*((ALGEBRAIC(:,43) - 1.00000)./(ALGEBRAIC(:,43)+1.00000));
    ALGEBRAIC(:,11) =  0.650000.*ALGEBRAIC(:,9);
    ALGEBRAIC(:,16) = ALGEBRAIC(:,15)./(1.00000+CONSTANTS(:,17)./CONSTANTS(:,16));
    ALGEBRAIC(:,17) = STATES(:,7)./(1.00000+CONSTANTS(:,17)./CONSTANTS(:,19));
    ALGEBRAIC(:,19) = STATES(:,8)./(1.00000+CONSTANTS(:,21)./CONSTANTS(:,20));
    ALGEBRAIC(:,22) = STATES(:,9)./(1.00000+CONSTANTS(:,21)./CONSTANTS(:,22));
    ALGEBRAIC(:,45) =  CONSTANTS(:,38).*(ALGEBRAIC(:,19)./(ALGEBRAIC(:,19)+ ALGEBRAIC(:,22).*power(10.0000,  - ALGEBRAIC(:,11)./CONSTANTS(:,52))) - ALGEBRAIC(:,16)./(ALGEBRAIC(:,16)+ ALGEBRAIC(:,17).*power(10.0000,  - ALGEBRAIC(:,11)./CONSTANTS(:,52)))).*(1.00000./(1.00000+CONSTANTS(:,39)./ALGEBRAIC(:,19)));
    ALGEBRAIC(:,6) = (power(10.0000,  - ALGEBRAIC(:,5)) - power(10.0000,  - ALGEBRAIC(:,5) - CONSTANTS(:,9)))./CONSTANTS(:,9);
    ALGEBRAIC(:,7) = CONSTANTS(:,6)./ALGEBRAIC(:,6);
    ALGEBRAIC(:,27) = STATES(:,11)./(1.00000+power(10.0000, ALGEBRAIC(:,5) - CONSTANTS(:,8)));
    ALGEBRAIC(:,28) = STATES(:,12)./(1.00000+power(10.0000, ALGEBRAIC(:,1) - CONSTANTS(:,8)));
    ALGEBRAIC(:,48) =  CONSTANTS(:,46).*( STATES(:,1).*ALGEBRAIC(:,28) -  STATES(:,2).*ALGEBRAIC(:,27));
    ALGEBRAIC(:,46) =  CONSTANTS(:,41).*(1.00000./(1.00000+CONSTANTS(:,40)./STATES(:,9)));
    ALGEBRAIC(:,25) = CONSTANTS(:,24) - STATES(:,10);
    ALGEBRAIC(:,49) =  CONSTANTS(:,47).*STATES(:,8).*STATES(:,10).*STATES(:,1) -  CONSTANTS(:,48).*STATES(:,9).*ALGEBRAIC(:,25);
    ALGEBRAIC(:,21) = STATES(:,8) - ALGEBRAIC(:,19);
    ALGEBRAIC(:,23) = STATES(:,9) - ALGEBRAIC(:,22);
    ALGEBRAIC(:,24) = CONSTANTS(:,23) - (STATES(:,9)+STATES(:,8));
    ALGEBRAIC(:,47) =  CONSTANTS(:,42).*ALGEBRAIC(:,21).*ALGEBRAIC(:,19) -  CONSTANTS(:,43).*ALGEBRAIC(:,23).*ALGEBRAIC(:,24);
    ALGEBRAIC(:,3) = (power(10.0000,  - ALGEBRAIC(:,1)) - power(10.0000,  - ALGEBRAIC(:,1) - CONSTANTS(:,9)))./CONSTANTS(:,9);
    ALGEBRAIC(:,4) = CONSTANTS(:,7)./ALGEBRAIC(:,3);
    ALGEBRAIC(:,50) =  CONSTANTS(:,50).*(CONSTANTS(:,49) - ALGEBRAIC(:,1));
    ALGEBRAIC(:,2) = CONSTANTS(:,28) - STATES(:,13);
    ALGEBRAIC(:,10) =  -0.350000.*ALGEBRAIC(:,9);
    ALGEBRAIC(:,18) = ALGEBRAIC(:,15) - ALGEBRAIC(:,16);
    ALGEBRAIC(:,20) = STATES(:,7) - ALGEBRAIC(:,17);
    ALGEBRAIC(:,26) = STATES(:,10)+ STATES(:,9).*3.00000+ STATES(:,8).*2.00000+ALGEBRAIC(:,24)+STATES(:,12)+( STATES(:,7).*3.00000+ ALGEBRAIC(:,15).*2.00000+STATES(:,11))./CONSTANTS(:,1);
end

% Compute a logarithm to any base" +
function x = arbitrary_log(a, base)
    x = log(a) ./ log(base);
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