Difference between revisions of "Team:Dundee/Modeling/Appendix2"
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$$ | $$ | ||
\begin{eqnarray*} | \begin{eqnarray*} | ||
− | LS(0)&=& | + | LS(0)&=&v_{0},\\ |
SE(0)&=&1,\\ | SE(0)&=&1,\\ | ||
PC(0)&=&0,\\ | PC(0)&=&0,\\ |
Revision as of 13:19, 13 August 2015
Dry Lab
Appendix 2: Fingerprint Aging Code
Principal Component Analysis Code
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Squalene Epoxide Model MATLAB Code
The figure shown in the squalene epoxide and lanosterol synthase were created using MATLAB. Before using MATLAB the original system of equations was non-dimensionalised to the system:
$$ \begin{eqnarray*} \frac{dLS}{d\tau}&=&PC-\lambda LS \cdot SE,\\ \frac{dSE}{d\tau}&=&PC-\lambda LS \cdot SE,\\ \frac{PC}{d\tau}&=&\lambda LS \cdot SE-PC-\gamma PC,\\ \frac{dLa}{d\tau}&=&\gamma PC. \end{eqnarray*} $$The initial conditions were also non-dimensionalised to become:
$$ \begin{eqnarray*} LS(0)&=&v_{0},\\ SE(0)&=&1,\\ PC(0)&=&0,\\ La(0)&=&0. \end{eqnarray*} $$Two files were written to perform sensitivity analysis; one to set the function (squalene.m) and one to solve the function and plot the results in Figure 1 (run_squalene.m). Both files are shown below, where the green is comments to aid in understanding of the scripts.
MATLAB code from squalene.m file
% File to solve the system of ODEs describing lanosterol synthase and squalene epoxide binding. % The vector u has 4 dimensions; % u(1) = Lanosterol synthase concentration, {non-dimensionalized A eqn} % u(2) = Squalene epoxide concentration, {" " " "} % u(3) = Protosterol cation (1st Intermediate), {" " " "} % u(4) = Lanosterol. {" " " "} % t is the time that the simulation is run over. % lambda is the 1st binding parameter ((k1/k2)B0). % gamma is the 2nd binding parameter (k3/k2). function f = squalene(t,u,lambda,gamma); % Then set f as the RHS of the system of ODEs. f = [u(3)-lambda.*u(1)*u(2); u(3)-lambda.*u(1)*u(2); lambda.*u(1)*u(2)-u(3)-gamma.*u(3); gamma.*u(3)]; % Then end the function. % This function can then be solved using ode23 in the file run_squalene.m % by using the @squalene command. % END OF FILE.
To see the MATLAB code for the BioSpray section of the project or the Chromate Biosensor section of the project use the following buttons.
Appendix 3: Chromate Biosensor Appendix 1: BioSpray