 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = Stuehr_NOS 
 %  Accession Number = 12 
 %  Transcriber = Sudhir Sivakumaran, NCBS 
 %  Developer = Santolini, Adak, Curran, Stuehr 
 %  Species = Generic mammalian 
 %  Tissue = Neuronal ; Expressioned in E.coli 
 %  Cell Compartment = Cytosol 
 %  Notes =  This is a model of neuronal Nitric Oxide Synthase expressed in Escherichia coli based on <a href= http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11038356 > Santolini J. et al.  J Biol Chem. (2001) 276(2):1233-43</a>. The rates have been converted by 2x for every 10 degrees C. The original temperature was 10 degree C, cell temperature is assumed 30 degree C, so the conversion factor is 4. 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Tue Feb  1 11:52:39 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 600];
% Molecule names
molnames = {
'1 /kinetics/NOS/FeIII_NO'
'2 /kinetics/NOS/FeII-O2_a'
'3 /kinetics/NOS/FeII_a'
'4 /kinetics/NOS/FeIII_a'
'5 /kinetics/NOS/CaM-Ca4'
'6 /kinetics/NOS/L-Arg'
'7 /kinetics/NOS/FeIII'
'8 /kinetics/NOS/FeII'
'9 /kinetics/NOS/FeII-O2'
'10 /kinetics/NOS/nNOS'
'11 /kinetics/NOS/Ca-CaM_nNOS'
'12 /kinetics/NOS/O2'
'13 /kinetics/NOS/NO3'
'14 /kinetics/NOS/FeII_NO'
};

bufnames = {
};

sumtotnames = {
};

% Initial concs of 14 molecules
y0(1) = 0;
y0(2) = 0;
y0(3) = 0;
y0(4) = 0;
y0(5) = 0;
y0(6) = 100;
y0(7) = 0;
y0(8) = 0;
y0(9) = 0;
y0(10) = 10;
y0(11) = 0;
y0(12) = 0.5;
y0(13) = 0;
y0(14) = 0;
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
plot(t,y(:,6));
plot(t,y(:,1));
plot(t,y(:,5));
plot(t,y(:,14));
plot(t,y(:,7));
plot(t,y(:,8));
plot(t,y(:,5));
plot(t,y(:,2));
plot(t,y(:,3));
plot(t,y(:,4));
plot(t,y(:,9));
plot(t,y(:,13));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 + 104 * y(2) - 10.4 * y(1) - 20 * y(1)
 + 3.6 * y(3) - 104 * y(2)
 + 10.4 * y(4) - 3.6 * y(3)
 + 104 * y(9) - 10.4 * y(4)
 - 3.25 * y(10) * y(5) + 0.05 * y(11)
 - 0.5 * y(6) * y(11) + 81 * y(7)
 - 10.4 * y(7) + 1.2 * y(14) * y(12) + 20 * y(1) + 0.5 * y(6) * y(11) - 81 * y(7)
 + 10.4 * y(7) - 3.6 * y(8) + 0.0004 * y(14)
 + 3.6 * y(8) - 104 * y(9)
 - 3.25 * y(10) * y(5) + 0.05 * y(11)
 - 0.5 * y(6) * y(11) + 81 * y(7) + 3.25 * y(10) * y(5) - 0.05 * y(11)
 - 1.2 * y(14) * y(12)
 + 1.2 * y(14) * y(12)
 + 10.4 * y(1) - 0.0004 * y(14) - 1.2 * y(14) * y(12)
];

% end of model
