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Team:Colombia/Scripting
From 2014.igem.org
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)
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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
% %--------------------------------------------% % 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>
