function dydt = model_ode( t, y, params, times )

% Parameter name assignments, of form 'name = params( x, y )'
B0 = params( 1, 1 );
C0 = params( 1, 2 );
Dn3 = params( 1, 3 );
Jn3 = params( 1, 4 );
ksn2_c = params( 2, 1 );
ksn2_r = params( 2, 2 );
kdn2 = params( 2, 3 );
kasbf = params( 3, 1 );
kisbf_c = params( 3, 2 );
kisbf_r = params( 3, 3 );
Jasbf = params( 3, 4 );
Jisbf = params( 3, 5 );
esbfn2 = params( 3, 6 );
esbfn3 = params( 3, 7 );
esbfb5 = params( 3, 8 );
ksb2_c = params( 4, 1 );
ksb2_r = params( 4, 2 );
kdb2_c = params( 4, 3 );
kdb2_r = params( 4, 4 );
kdb2p = params( 4, 5 );
kamcm = params( 5, 1 );
kimcm = params( 5, 2 );
Jamcm = params( 5, 3 );
Jimcm = params( 5, 4 );
ksb5_c = params( 6, 1 );
ksb5_r = params( 6, 2 );
kdb5_c = params( 6, 3 );
kdb5_r = params( 6, 4 );
ksc1_c = params( 7, 1 );
ksc1_r = params( 7, 2 );
kd1c1 = params( 7, 3 );
kd2c1 = params( 7, 4 );
Jd2c1 = params( 7, 5 );
ec1k2 = params( 7, 6 );
ec1n2 = params( 7, 7 );
ec1b5 = params( 7, 8 );
ec1b2 = params( 7, 9 );
ec1n3 = params( 7, 10 );
kasb2 = params( 7, 11 );
kdib2 = params( 7, 12 );
kasb5 = params( 7, 13 );
kdib5 = params( 7, 14 );
kd3c1 = params( 7, 15 );
kppc1 = params( 7, 16 );
ksf6_c = params( 8, 1 );
ksf6_r = params( 8, 2 );
ksf6_r2 = params( 8, 3 );
kd1f6 = params( 8, 4 );
kd2f6 = params( 8, 5 );
Jd2f6 = params( 8, 6 );
ef6k2 = params( 8, 7 );
ef6n2 = params( 8, 8 );
ef6b5 = params( 8, 9 );
ef6b2 = params( 8, 10 );
ef6n3 = params( 8, 11 );
kasf2 = params( 8, 12 );
kdif2 = params( 8, 13 );
kasf5 = params( 8, 14 );
kdif5 = params( 8, 15 );
kd3f6 = params( 8, 16 );
kppf6 = params( 8, 17 );
ksswi_c = params( 9, 1 );
ksswi_r = params( 9, 2 );
kdswi = params( 9, 3 );
kaswi = params( 9, 4 );
kiswi = params( 9, 5 );
kaiep = params( 10, 1 );
kiiep = params( 10, 2 );
Jaiep = params( 10, 3 );
Jiiep = params( 10, 4 );
ks20_c = params( 11, 1 );
ks20_r = params( 11, 2 );
kd20 = params( 11, 3 );
ka20_c = params( 11, 4 );
ka20_r = params( 11, 5 );
%% ki20_c = params( 11, 6 );
%% ki20_r = params( 11, 7 );
kscdh = params( 12, 1 );
kdcdh = params( 12, 2 );
kacdh_c = params( 12, 3 );
kacdh_r = params( 12, 4 );
Jicdh = params( 12, 5 );
Jacdh = params( 12, 6 );
kicdh_c = params( 12, 7 );
kicdh_r = params( 12, 8 );
eicdhn2 = params( 12, 9 );
eicdhn3 = params( 12, 10 );
eicdhb5 = params( 12, 11 );
eicdhb2 = params( 12, 12 );
ks14 = params( 13, 1 );
kd14 = params( 13, 2 );
ksnet = params( 14, 1 );
kdnet = params( 14, 2 );
kasrent = params( 15, 1 );
kasrentp = params( 15, 2 );
kdirent = params( 15, 3 );
% kdirentp = params( 15, 4 );
kdirentp = params( 15, 4 ); % kdirentp = 20;
kppnet_c = params( 16, 1 );
kppnet_r = params( 16, 2 );
kkpnet_c = params( 16, 3 );
kkpnet_r = params( 16, 4 );
kspds_c = params( 17, 1 );
ks1pds_r = params( 17, 2 );
ks2pds_r = params( 17, 3 );
kd1pds_c = params( 17, 4 );
kd2pds_r = params( 17, 5 );
kd3pds_r = params( 17, 6 );
kkp1pds = params( 17, 7 );
kkp2pds = params( 17, 8 );
Jpds = params( 17, 7 );
kasesp = params( 18, 1 );
kdiesp = params( 18, 2 );
ESP1T = params( 18, 3 );
ksppx = params( 19, 1 );
kdppx_c = params( 19, 2 );
kdppx_r = params( 19, 3 );
J20ppx = params( 19, 4 );
ksori = params( 20, 1 );
kdori = params( 20, 2 );
eorib5 = params( 20, 3 );
eorib2 = params( 20, 4 );
ksbud = params( 21, 1 );
kdbud = params( 21, 2 );
ebudn2 = params( 21, 3 );
ebudn3 = params( 21, 4 );
ebudb5 = params( 21, 5 );
ksspn = params( 22, 1 );
kdspn = params( 22, 2 );
Jspn = params( 22, 3 );
%% Lte1l = params( 23, 1 );
%% Lte1h = params( 23, 2 );
%% Bub2l = params( 23, 3 );
%% Bub2h = params( 23, 4 );
Tem1T = params( 24, 1 );
JaTem = params( 24, 2 );
JiTem = params( 24, 3 );
Cdc15T = params( 25, 1 );
ka15_c = params( 25, 2 );
ka15_r = params( 25, 3 );
ka15p = params( 25, 4 );
ki15 = params( 25, 5 );
%% KEZ = params( 26, 1 );
mdt = params( 26, 2 );
%% MorD = params( 26, 3 );
%% kez2 = params( 26, 4 );
MCM1T = params( 27, 1 );
SBFT = params( 27, 2 );
MBFT = params( 27, 3 );

% Variable name assignments, of form v_name = y( x )
MASS = y( 1 );
CLN2 = y( 2 );
Clb2 = y( 3 );
Clb5 = y( 4 );
Sic1 = y( 5 );
CDC6 = y( 6 );
C2 = y( 7 );
C5 = y( 8 );
F2 = y( 9 );
F5 = y( 10 );
Sic1P = y( 11 );
C2P = y( 12 );
C5P = y( 13 );
CDC6P = y( 14 );
F2P = y( 15 );
F5P = y( 16 );
Swi5T = y( 17 );
Swi5 = y( 18 );
IEP = y( 19 );
Cdc20T = y( 20 );
Cdc20 = y( 21 );
CDH1T = y( 22 );
CDH1 = y( 23 );
Cdc14T = y( 24 );
Cdc14 = y( 25 );
NET1T = y( 26 );
NET1 = y( 27 );
RENT = y( 28 );
Tem1 = y( 29 );
Cdc15 = y( 30 );
PPX = y( 31 );
PDS1 = y( 32 );
ESP1 = y( 33 );
ORI = y( 34 );
BUD = y( 35 );
SPN = y( 36 );
Vi20 = y( 37 );
Lte1 = y( 38 );
Bub2 = y( 39 );

% Intermediate calculations
BCK2 = B0 * MASS;
CLN3 = C0 * Dn3 * MASS / ( Jn3 + Dn3 * MASS );
Sic1T = Sic1 + C2 + C5 + Sic1P + C2P + C5P ;
CDC6T = CDC6 + F2 + F5 + CDC6P + F2P + F5P;
RENTP = Cdc14T - RENT - Cdc14;
NET1P = NET1T - NET1 - Cdc14T + Cdc14;
PE = ESP1T - ESP1;

Vasbf = kasbf * ( esbfn2 * CLN2 + esbfn3 * ( CLN3 + BCK2 ) + ...
                  esbfb5 * Clb5 );
Vdb2 = kdb2_c + kdb2_r * CDH1 + kdb2p * Cdc20;
Vdb5 = kdb5_c + kdb5_r * Cdc20;
Vkpc1 = kd1c1 + kd2c1 * ( ec1n3 * CLN3 + ec1k2 * BCK2 + ec1n2 * ...
                          CLN2 + ec1b2 * Clb2 + ec1b5 * Clb5 ) ...
        / ( Jd2c1 + Sic1T );
Vppc1 = kppc1 * Cdc14;
Vkpf6 = kd1f6 + kd2f6 * ( ef6n3 * CLN3 + ef6k2 * BCK2 + ef6n2 * ...
                          CLN2 + ef6b2 * Clb2 + ef6b5 * Clb5 ) ...
        / ( Jd2f6 + CDC6T );
Vppf6 = kppf6 * Cdc14;
Vaiep = kaiep * Clb2;
Vacdh = kacdh_c + kacdh_r * Cdc14;
Vicdh = kicdh_c + kicdh_r * ( eicdhn3 * CLN3 + eicdhn2 * CLN2 + ...
                              eicdhb5 * Clb5 + eicdhb2 * Clb2 );
Vppnet = kppnet_c + kppnet_r * PPX;
Vkpnet = ( kkpnet_c + kkpnet_r * Cdc15 ) * MASS;
% Vdpds = kd1pds_c + kd2pds_r * Cdc20 + kd3pds_r * CDH1;
Vdpds = GK( 1.0 + Cdc14, ( kkp1pds * Clb5 + kkp2pds * Clb2 ), ...
            0.1 / ( PDS1 + PE ), 0.1 / ( PDS1 + PE ) ) * 12 * Cdc20;
% Vdppx = kdppx_c + kdppx_r * ( J20ppx + Cdc20 ) * Jpds / ( Jpds + PDS1 );

SBF = SBFT * GK( Vasbf, kisbf_c + kisbf_r * Clb2, Jasbf, Jisbf );
MBF = MBFT * GK( Vasbf, kisbf_c + kisbf_r * Clb2, Jasbf, Jisbf );
MCM1 = MCM1T * GK( kamcm * Clb2, kimcm, Jamcm, Jimcm );

kg = log( 2 ) / mdt;
%% D = 1.026 / kg - 32;
%% f = exp( -kg * D );

% equations
MASS_dot = kg * MASS;

CLN2_dot = ( ksn2_c + ksn2_r * SBF )* MASS - kdn2 * CLN2;

Clb2_dot = ( ksb2_c + ksb2_r * MCM1 ) * MASS ...
    + ( kd3c1 * C2P + kd3f6 * F2P ) + ( kdib2 * C2 + kdif2 * F2 ) ...
    - ( Vdb2 + kasb2 * Sic1 + kasf2 * CDC6 ) * Clb2;

Clb5_dot = ( ksb5_c + ksb5_r * MBF ) * MASS ...
    + ( kd3c1 * C5P + kd3f6 * F5P ) + ( kdib5 * C5 + kdif5 * F5 ) ...
    - ( Vdb5 + kasb5 * Sic1 + kasf5 * CDC6 ) * Clb5;

Sic1_dot = ( ksc1_c + ksc1_r * Swi5 ) ...
    + ( Vdb2 * C2 + Vdb5 * C5 ) + ( kdib2 * C2 + kdib5 * C5 ) ...
    + ( Vppc1 * Sic1P ) - ( kasb2 * Clb2 + kasb5 * Clb5 + Vkpc1 ) * Sic1;

CDC6_dot = ( ksf6_c + ksf6_r * Swi5 + ksf6_r2 * SBF ) ...
    + ( Vdb2 * F2 + Vdb5 * F5 ) + ( kdif2 * F2 + kdif5 * F5 ) ...
    + Vppf6 * CDC6P-( kasf2 * Clb2 + kasf5 * Clb5 + Vkpf6 ) * CDC6;

C2_dot = kasb2 * Clb2 * Sic1 + Vppc1 * C2P - ( kdib2 + Vdb2 + Vkpc1 ) * C2;

C5_dot = kasb5 * Clb5 * Sic1 + Vppc1 * C5P - ( kdib5 + Vdb5 + Vkpc1 ) * C5;

F2_dot = kasf2 * Clb2 * CDC6 + Vppf6 * F2P - ( kdif2 + Vdb2 + Vkpf6 ) * F2;

F5_dot = kasf5 * Clb5 * CDC6 + Vppf6 * F5P - ( kdif5 + Vdb5 + Vkpf6 ) * F5;

Sic1P_dot = Vkpc1 * Sic1 - ( Vppc1 + kd3c1 ) * Sic1P ...
    + Vdb2 * C2P + Vdb5 * C5P;

C2P_dot = Vkpc1 * C2 - ( Vppc1 + kd3c1 + Vdb2 ) * C2P;

C5P_dot = Vkpc1 * C5 - ( Vppc1 + kd3c1 + Vdb5 ) * C5P;

CDC6P_dot = Vkpf6 * CDC6 - ( Vppf6 + kd3f6 ) * CDC6P ...
    + Vdb2 * F2P + Vdb5 * F5P;

F2P_dot = Vkpf6 * F2 - ( Vppf6 + kd3f6 + Vdb2 ) * F2P;

F5P_dot = Vkpf6 * F5 - ( Vppf6 + kd3f6 + Vdb5 ) * F5P;

Swi5T_dot = ksswi_c + ksswi_r * MCM1 - kdswi * Swi5T;

Swi5_dot = ksswi_c + ksswi_r * MCM1 ...
    + kaswi * Cdc14 * ( Swi5T - Swi5 ) - ( kiswi * Clb2 + kdswi ) * Swi5;

IEP_dot = Vaiep * ( 1 - IEP ) / ( Jaiep + 1 - IEP )...
          - kiiep * IEP / ( Jiiep + IEP );

Cdc20T_dot = ( ks20_c + ks20_r * MCM1 ) - kd20 * Cdc20T;

Cdc20_dot = ( ka20_c + ka20_r * IEP ) * ( Cdc20T-Cdc20 ) ...
    - ( Vi20 + kd20 ) * Cdc20;

CDH1T_dot = kscdh - kdcdh * CDH1T;

CDH1_dot = kscdh - kdcdh * CDH1 ...
    + Vacdh * ( CDH1T-CDH1 ) / ( Jacdh + CDH1T-CDH1 ) ...
    - Vicdh * CDH1 / ( Jicdh + CDH1  );

Cdc14T_dot = ks14 - kd14 * Cdc14T;

Cdc14_dot = ( kdirent * RENT + kdirentp * RENTP ) ...
    - ( kasrent * NET1 + kasrentp * NET1P ) * Cdc14 ...
    +  ks14 - kd14 * Cdc14 + kdnet * ( RENT + RENTP );

NET1T_dot = ksnet - kdnet * NET1T;

% NET1_dot = kdirent * RENT - kasrent * NET1 * Cdc14 ...
%     + Vppnet * NET1P - Vkpnet * NET1 ...
%     + ksnet - kdnet * NET1 + kd14 * RENT;
Jnet = 0.5;
NET1_dot = kdirent * RENT - kasrent * NET1 * Cdc14 ...
    + 10.0 * Vppnet * NET1P / ( NET1P + RENTP + Jnet ) ...
    - 10.0 * Vkpnet * NET1 / ( NET1 + RENT + Jnet ) ...
    + ksnet - kdnet * NET1 + kd14 * RENT;

% RENT_dot = -kdirent * RENT + kasrent * NET1 * Cdc14 ...
%     + Vppnet * RENTP - Vkpnet * RENT ...
%     - ( kd14 + kdnet ) * RENT;
RENT_dot = -kdirent * RENT + kasrent * NET1 * Cdc14 ...
    + 10.0 * Vppnet * RENTP / ( NET1P + RENTP + Jnet ) ...
    - 10.0 * Vkpnet * RENT / ( NET1 + RENT + Jnet ) ...
    - ( kd14 + kdnet ) * RENT;

Tem1_dot = Lte1 * ( Tem1T - Tem1 ) / ( JaTem + Tem1T-Tem1 ) ...
    - Bub2 * Tem1 / ( JiTem + Tem1 );

Cdc15_dot = ( ka15_c * ( Tem1T - Tem1 ) + ka15_r * Tem1 ...
              + ka15p * Cdc14 ) * ( Cdc15T - Cdc15 ) ...
    - ki15 * Cdc15;

% PPX_dot = ksppx - Vdppx * PPX;
PPX_dot = 0.4 - PPX;

% PDS1_dot = ( kspds_c + ks1pds_r * SBF + ks2pds_r * MCM1 ) ...
%     + kdiesp * PE - ( Vdpds + kasesp * ESP1 ) * PDS1;

% kspds_c = 0.07; ks1pds_r = 6.0;
PDS1_dot = ( kspds_c + ks1pds_r * MBF ) ...
    + kdiesp * PE - kasesp * ESP1 * PDS1 ...
    - Vdpds * PDS1;

ESP1_dot = -kasesp * PDS1 * ESP1 + kdiesp * PE ...
    + Vdpds * PE;

ORI_dot = ksori * ( eorib5 * Clb5 + eorib2 * Clb2 ) - kdori * ORI;

BUD_dot = ksbud * ( ebudn2 * CLN2 + ebudn3 * CLN3 + ebudb5 * Clb5 ) ...
          - kdbud * BUD;

SPN_dot = ksspn * Clb2 / ( Jspn + Clb2 ) - kdspn * SPN;

Vi20_dot = 0;

Lte1_dot = 0;

Bub2_dot = 0;

% Return dy / dt vector:
dydt = [ MASS_dot; CLN2_dot; Clb2_dot; Clb5_dot; Sic1_dot; ...
         CDC6_dot; C2_dot; C5_dot; F2_dot; F5_dot; ...
         Sic1P_dot; C2P_dot; C5P_dot; CDC6P_dot; F2P_dot; ...
         F5P_dot; Swi5T_dot; Swi5_dot; IEP_dot; Cdc20T_dot; ...
         Cdc20_dot; CDH1T_dot; CDH1_dot; Cdc14T_dot; Cdc14_dot; ...
         NET1T_dot; NET1_dot; RENT_dot; Tem1_dot; Cdc15_dot; ...
         PPX_dot; PDS1_dot; ESP1_dot; ORI_dot; BUD_dot; ...
         SPN_dot; Vi20_dot; Lte1_dot; Bub2_dot; ];

end
 
function x = BB( Va, Vi, Ja, Ji )

x = Vi - Va + Ja * Vi + Ji * Va;

end

function x = GK( Va, Vi, Ja, Ji )

x = 2 * Ji * Va ...
    / ( BB( Va, Vi, Ja, Ji ) ...
        + sqrt( BB( Va, Vi, Ja, Ji )^2 - 4 * ( Vi - Va )* Ji * Va ) );

end