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Scripting

RALSTONIA DIFFERENTIAL EQUATION SOLUTION

<textarea> 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 % %--------------------------------------------% % VARIABLES  % %--------------------------------------------% %

C=0;                                           % Extracellular concentration of the cholerae autoinducer-1 (CAI-1)

%

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

% %--------------------------------------------% % 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 % n=1;  % Hill coefficient % %--------------------------------------------% % 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 % 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;  % % y=y';  % Transposing the vector because of matlab language restrictions % end %"; </textarea>