Team:Colombia/Scripting

function y=CondIni(x)
%
global kcc kcd dsu duo fsu fuo gcs gcsa guf gu gof go gtr gta gr acs au ao ar atr ata btr bta br ho htr n
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%--------------------------------------------%
%                 VARIABLES                  %
%--------------------------------------------%
%
 C=0;                                           % Extracellular concentration of the cholerae autoinducer-1 (CAI-1)
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 CS=x(1);                                       % Concentration of the membrane bound CqsS protein (CAI-1 unbound=Inactive)
 CSa=x(2);                                      % Concentration of the membrane bound CqsS protein (CAI-1 bound=Active)
 Uf= x(3);                                      % Phosphorelay protein LuxU (phosphorylated) Concentration
 U=x(4);                                        % Phosphorelay protein LuxU (unphosphorylated) Concentration
 Of=x(5);                                       % Phosphorelay protein LuxO (phosphorylated) Concentration
 O=x(6);                                        % Phosphorelay protein LuxO (unphosphorylated) Concentration
 TR=x(7);                                       % Ptet Repressor protein concentration
 TA=x(8);                                       % Ptet Activator protein concentration
 R=x(9);                                        % Response molecule concentration
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%--------------------------------------------%
%                 PARAMETERS                 %
%--------------------------------------------%
%
kcc=1;                                          % CAI1 and CqsS coupling Rate
kcd=1;                                          % CAI1 and CqsS decoupling Rate
dsu=4;                                          % LuxU* dephosphorylation rate through CqsS*
duo=4;                                          % LuxO* dephosphorylation rate through LuxU
fsu=2;                                          % LuxU* phosphorylation rate through CqsS
fuo=2;                                          % LuxO* phosphorylation rate through LuxU*
%
gcs=1;                                          % CqsS protein decay rate
gcsa=1;                                         % CqsS* protein decay rate
guf=1;                                          % LuxU* protein decay rate
gu=1;                                           % LuxU protein decay rate
gof=1;                                          % LuxO* protein decay rate
go=1;                                           % LuxO protein decay rate
gtr=1;                                          % Ptet Repressor protein decay rate
gta=1;                                          % Ptet Activator protein decay rate
gr=1;                                           % Response molecule decay rate
%
acs=3;                                          % CS basal production rate
au=3;                                           % LuxU basal production rate
ao=3;                                           % LuxO basal production rate
ar=0.01;                                        % response molecule basal production rate
atr=0.01;                                       % TR basal production rate
ata=0.01;                                       % TA basal production rate
%
btr=5;                                          % Maximum rate of TR expression
bta=5;                                          % Maximum rate of TA expression
br=5;                                           % Maximum rate of response molecule expression
ho=1.5;                                         % LuxO*- DNA coupling rate
htr=2;                                          % TRdomain-DNA coupling rate
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n=1;                                            % Hill coefficient
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%--------------------------------------------%
%                 Equations                  %
%--------------------------------------------%
%
dCS = acs + kcd*CSa - C*CS*kcc - gcs*CS;                       % Differential equation governing the change in the concentration of the membrane bound CqsS protein (CAI-1 unbound=Inactive)through time
dCSa = -kcd*CSa + C*CS*kcc - gcsa*CSa;                         % Differential equation governing the change in the concentration of the membrane bound CqsS protein (CAI-1 bound=Active) through time
dUf = U*Of*duo-Uf*O*fuo-CSa*Uf*dsu + CS*U*fsu - guf*Uf;        % Differential equation governing the change in the phosphorelay protein LuxU (phosphorylated) Concentration through time
dU = au-U*Of*duo+Uf*O*fuo - CS*U*fsu + CSa*Uf*dsu -gu*U;       % Differential equation governing the change in the phosphorelay protein LuxU (unphosphorylated) Concentration through time
dOf = Uf*O*fuo - U*Of*duo - gof*Of;            			 % Differential equation governing the change in the phosphorelay protein LuxO (phosphorylated) Concentration through time
dO = ao - Uf*O*fuo + U*Of*duo - go*O;           		  % Differential equation governing the change in the phosphorelay protein LuxO (unphosphorylated) Concentration through time
dTR = atr + (btr*Of^n)/(ho^n+Of^n) - gtr*TR;                   % Differential equation governing the change in the ptet Repressor protein concentration through time
dTA = ata + bta/((1+TR/TA)+(htr/TA)) - gta*TA;                 % Differential equation governing the change in the ptet Activator protein concentration through time
dR = ar + br/((1+TR/TA)+(htr/TA)) - gr*R;                      % Differential equation governing the change in the response molecule concentration through time
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y(1)=dCS;                                       %
y(2)=dCSa;                                      %
y(3)=dUf;                                       %
y(4)=dU;                                        %
y(5)=dOf;                                       %
y(6)=dO;                                        %
y(7)=dTR;                                       %
y(8)=dTA;                                       %
y(9)=dR;                                        %
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y=y';                                           % Transposing the vector because of matlab language restrictions
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end
%";