I'm trying to solve an equilibrium problem for the following competing chemical reaction:
AP + P -><- APa@P (K1 = APa@P/(AP*P) = 1e5)
AP + P -><- APp@P (K2 = APp@P/(AP*P) = 1e4)
That is; AP can bind in two ways to P and does so with two different association constants (K1 and K2). I will therefore have 4 species in solution: unbound AP, unbound P, APa@P and APp@P. Knowing the starting concentrations AP0 and P0, fsolve should easily be able to solve all the concentrations by solving the following four non-linear equations:
P0 - P - APa@P - APp@P = 0
AP0 - APa@P - APp@P = 0
APa@P/(P*AP) - K1 = 0
APp@P/(P*AP) - K2 = 0
My function file becomes:
function [Concentrations] = svdConcfunc(D)
global AP0 P0 K1 K2
Concentrations = [P0 - D(2) - D(3) - D(4);
AP0 - D(1) - D(3) - D(4);
D(3)./(D(1).*D(2)) - K1;
D(4)./(D(1).*D(2)) - K2];
My script, calling the above function looks like this:
global conc AP0 P0 K1 K2
options = optimset ('Tolfun', 1e-30, 'TolX', 1e-20, 'MaxFunEvals', 1e20, 'MaxIter', 1e20);
P0 = 2e-6;
K1 = 1e5;
K2 = 1e4;
for i = 1:length(conc);
AP0 = conc(i);
%format = [AP P APa@P APp@P ];
Guessconc = [AP0 P0 AP0 AP0 ];
CalcConc(i,:) = fsolve(@svdConcfunc, Guessconc, options);
test_should_be(i) = P0 + AP0;
test = sum(CalcConc, 2)
test_should_be = test_should_be'
the loaded "conc" becomes:
The output I get is the following:
So the sum of all calculated concentrations in solution is not the same (there is a difference between "test_should_be" and "test") as the sum of what I put in, which is physically impossible and I cannot for the life of me understand why it won't work. I have been able to solve far more complicated equilibrium problems (more equations, species and binding constants) before so this should be a walk in the park.
I have tried to play around with starting guesses and tolerance values but I can't seem to get a better solution.
Any help on this would be much appreciated!
"Jesper" wrote in message <firstname.lastname@example.org>...
> test_should_be(i) = P0 + AP0;
> test = sum(CalcConc, 2)
> So the sum of all calculated concentrations in solution is not the same (there is a difference between "test_should_be" and "test") as the sum of what I put in, which is physically impossible and I cannot for the life of me understand why it won't work. ....
- - - - - - - - -
Though I am not a chemist there seems to be something rather questionable with your test procedure. For every one mole of AP and one mole of P which is converted to APa@P or APp@P you have only one mole of result, but you appear to be requiring in "test=sum(CalcConc,2)" that the total number of moles should remain constant. In other words you may be obtaining perfectly valid solutions but your test looks invalid to me.
A better test would be to check whether your original four equations are satisfied or not for each of the AP0 concentrations.
There is a way you can avoid using 'fsolve' and I don't understand why you are not doing things this way. Your four equations can be reduced to the solution of simple quadratic equations in D1 and D2 (AP and P) in which one of the two roots gives positive values for the concentrations. D3 and D4 (APa@P and APp@P) are then readily found from D1 and D2. Do as follows:
T1 = (-1+sqrt(1+2*(K1+K2)*(P0+AP0)+((K1+K2)*(P0-AP0)).^2))/2/(K1+K2);
T2 = (P0-AP0)/2;
D1 = T1-T2;
D2 = T1+T2;
D3 = K1*D1.*D2;
D4 = K2*D1.*D2;
(These should be valid as vectorized solutions using a vector for AP0.)
I am assuming I have the correct equations to be solved:
D1 + D3 + D4 = AP0
D2 + D3 + D4 = P0
D3/(D1*D2) = K1
D4/(D1*D2) = K2
(You first wrote: "AP0-APa@P-APp@P=0" for that first equation but later added the obviously needed D1 (AP) term.)
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