Writing out a system of equations for an enzyme reaction

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Sergio
Sergio 2024년 3월 2일
댓글: Sam Chak 2024년 3월 2일
I have the given file, where the rate of reaction is evaluated and gives F as a function of the concentration of the product P. The file evaluates the function f (y, k) and computes the Jacobians ∇y f and ∇k f. y is the concentration of the enzyme while k is the reaction rate konstant.
We consider a system with the following reactions:
in which the constants μ and γ are unknown, and where ∅ → S denotes that substrates (S) are formed without using any products (P). A chemist has done a series of experiments with different initial concentrations (at time t0 = 0). At time T = 1, the chemist has measured the concentration of S and P again. The results of the measurements are summarized in Table 1
I have to write down the system of ordinary differential equations that describes system (2) (Notation: dydt = f (y, k)).
However, I am not sure, since the file uses dfdy and dfdk. What is the correct method to write up (2) in MATLAB code?
Thanks
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Sam Chak
Sam Chak 2024년 3월 2일
type enzymeRhs.m
function [f,dfdy,dfdk] = enzymeRhs(y,k) %ENZYMERHS evaluates the right hand side of the enzyme ODE system. % % [F,DFDY,DFDK] = ENZYMERHS(Y,K) evaluates the right hand side for the % enzyme system with rates K and current concentration Y and returns F, % the value of the right hand side as well as DFDY and DFDK, the % gradient of the right hand side function with respect to % concentrations Y and rates K, respectively. % C = 0.1; %constant creation of substrate f = zeros(2,1); f(1) = y(2) - k(1)*y(1)/(k(2)+y(1)) + C; f(2) = -y(2) + k(1)*y(1)/(k(2)+y(1)); if nargout>1 dfdy = [-k(1)/(k(2)+y(1))+k(1)*y(1)/(k(2)+y(1))^2 1; k(1)/(k(2)+y(1))-k(1)*y(1)/(k(2)+y(1))^2 -1]; dfdk = [-y(1)/(k(2)+y(1)) k(1)*y(1)/(k(2)+y(1))^2; y(1)/(k(2)+y(1)) -k(1)*y(1)/(k(2)+y(1))^2]; end Let y^T = ([S], [P]) and k^T = (μ, γ). Write down the system of ordinary differential equations that describes system (2) (Notation: dydt = f (y, k)). The file enzymeRhs.m contains the Matlab function enzymeRhs that evaluates the function f (y, k) and computes the Jacobians ∇y f and ∇k f. Verify the correctness of your derivation by comparing with the system in enzymeRhs.m!

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