 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = Kierzek_LacZ 
 %  Accession Number = 29 
 %  Transcriber = Deepak Kumar Sinha, Jaffar Ali, Upinder S. Bhalla, NCBS 
 %  Developer = Kierzek, Zaim and Zielenkiewicz 
 %  Species = E. Coli 
 %  Tissue = - 
 %  Cell Compartment = Internal 
 %  Notes =  An approximation to the <a href= http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11062240 >Kierzek AM. et al. J Biol Chem. (2001) 276(11):8165-72</a> model of LacZ gene expression in E. coli. They use stochastic simulation and model cell growth. Despite these discrepancies, the continuous fixed size model is within a factor of 3 of their results. Parameter values are identical. 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Wed Feb  2 15:27:14 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 2000];
% Molecule names
molnames = {
'1 /kinetics/LacZ/Protein'
'2 /kinetics/LacZ/RBS'
'3 /kinetics/LacZ/RibRBS'
'4 /kinetics/LacZ/elRIB'
'5 /kinetics/LacZ/P_RNAP'
'6 /kinetics/LacZ/P'
'7 /kinetics/LacZ/ElRNAP'
'8 /kinetics/LacZ/TrRNAP'
};

bufnames = {
'1 /kinetics/LacZ/Ribosome'
'2 /kinetics/LacZ/AAs'
'3 /kinetics/LacZ/RNAP'
'4 /kinetics/LacZ/nucleotides'
};

sumtotnames = {
};

% Initial concs of 8 molecules
y0(1) = 0;
y0(2) = 0;
y0(3) = 0;
y0(4) = 0;
y0(5) = 0;
y0(6) = 0.00166672;
y0(7) = 0;
y0(8) = 0;
buff(1) = 0.583353;
buff(2) = 0;
buff(3) = 0.0583353;
buff(4) = 0;
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
plot(t,y(:,1));
plot(t,y(:,7));
plot(t,y(:,2));
plot(t,buff(:,3)*ones(size(t)));
plot(t,y(:,4));
plot(t,y(:,3));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 + 0.015 * y(4) - 6.42e-05 * y(1)
 + 1 * y(8) - 99.9927 * y(2) * buff(1) + 2.25 * y(3) + 0.5 * y(3) - 0.3 * y(2)
 + 99.9927 * y(2) * buff(1) - 2.25 * y(3) - 0.5 * y(3)
 + 0.5 * y(3) - 0.015 * y(4)
 + 99.9927 * y(6) * buff(3) - 10 * y(5) - 1 * y(5)
 - 99.9927 * y(6) * buff(3) + 10 * y(5) + 1 * y(8)
 + 1 * y(8) - 0.3 * y(7)
 + 1 * y(5) - 1 * y(8)
];

% end of model
