Team:Colombia/Scripting

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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 %

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 <br><br>
 <p>
-I smiled and shook my head. "I can quite understand your thinking so." I said. "Of course, in your position of unofficial adviser and helper to everybody who is absolutely puzzled, throughout three continents, you are brought in contact with all that is strange and bizarre. But here"--I picked up the morning paper from the ground--"let us put it to a practical test. Here is the first heading upon which I come. 'A husband's cruelty to his wife.' There is half a column of print, but I know without reading it that it is all perfectly familiar to me. There is, of course, the other woman, the drink, the push, the blow, the bruise, the sympathetic sister or landlady. The crudest of writers could invent nothing more crude."
+function y=CondIni(x)
+%
-"Indeed, your example is an unfortunate one for your argument," said Holmes, taking the paper and glancing his eye down it. "This is the Dundas separation case, and, as it happens, I was engaged in clearing up some small points in connection with it. The husband was a teetotaler, there was no other woman, and the conduct complained of was that he had drifted into the habit of winding up every meal by taking out his false teeth and hurling them at his wife, which, you will allow, is not an action likely to occur to the imagination of the average story-teller. Take a pinch of snuff, Doctor, and acknowledge that I have scored over you in your example."
+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
+%
-He held out his snuffbox of old gold, with a great amethyst in the centre of the lid. Its splendour was in such contrast to his homely ways and simple life that I could not help commenting upon it.
+%--------------------------------------------%
+%                 VARIABLES                  %
-"Ah," said he, "I forgot that I had not seen you for some weeks. It is a little souvenir from the King of Bohemia in return for my assistance in the case of the Irene Adler papers."
+%--------------------------------------------%
+%
-"And the ring?" I asked, glancing at a remarkable brilliant which sparkled upon his finger.
+ C=0;                                           % Extracellular concentration of the cholerae autoinducer-1 (CAI-1)
+%
-"It was from the reigning family of Holland, though the matter in which I served them was of such delicacy that I cannot confide it even to you, who have been good enough to chronicle one or two of my little problems."
+ 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
+%
 </p>
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