 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = Kuroda_GC 
 %  Accession Number = 18 
 %  Transcriber = Sudhir Sivakumaran, NCBS 
 %  Developer = Shinya Kuroda, Nicolas Schweighofer and Mitsuo Kawato. 
 %  Species = Generic mammalian 
 %  Tissue = Neuronal 
 %  Cell Compartment = Synapse 
 %  Notes = This model of sGC is based on the paper by <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11466441>Kuroda S. et al. J Neurosci. (2001) 21(15):5693-702</a>. This models features the activation of sGC by NO, synthesis of cGMP, activity of PKG and PP2A in the synapse. The rates and concentrations have been taken from published literature. 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Tue Mar  1 14:07:47 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 1000];
% Molecule names
molnames = {
'1 /kinetics/NO'
'2 /kinetics/NO_GC'
'3 /kinetics/NO_GC/kenz/kenz_cplx'
'4 /kinetics/NOdegrade'
'5 /kinetics/GTP'
'6 /kinetics/cGMP'
'7 /kinetics/PDE'
'8 /kinetics/PDE/kenz/kenz_cplx'
'9 /kinetics/5_prime_GMP'
'10 /kinetics/PKG'
'11 /kinetics/cGMP.PKG'
'12 /kinetics/cGMP.PKG/kenz/kenz_cplx'
'13 /kinetics/Gsub'
'14 /kinetics/Gsub*'
'15 /kinetics/PP2A'
'16 /kinetics/PP2A_Gsub*'
};

bufnames = {
'1 /kinetics/GC'
};

sumtotnames = {
};

% Initial concs of 16 molecules
y0(1) = 0.1;
y0(2) = 0;
y0(3) = 0;
y0(4) = 0;
y0(5) = 10;
y0(6) = 0;
y0(7) = 5;
y0(8) = 0;
y0(9) = 0;
y0(10) = 2.5;
y0(11) = 0;
y0(12) = 0;
y0(13) = 10.7;
y0(14) = 0;
y0(15) = 2.7;
y0(16) = 0;
buff(1) = 3;
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
 plot(t,y(:,4));
 plot(t,y(:,11));
 plot(t,y(:,2));
 plot(t,y(:,6));
 plot(t,y(:,14));
 plot(t,y(:,16));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 - 0.01 * y(1) * buff(1) + 0.0025 * y(2) - 0.673 * y(1)
 + 0.01 * y(1) * buff(1) - 0.0025 * y(2) - 0.81667 * y(5) * y(2) + 29.4 * y(3) + 7.35 * y(3)
 + 0.81667 * y(5) * y(2) - 29.4 * y(3) - 7.35 * y(3)
 + 0.673 * y(1)
 - 0.81667 * y(5) * y(2) + 29.4 * y(3)
 + 7.35 * y(3) - 9.675 * y(6) * y(7) + 15.48 * y(8) - 10 * y(6) * y(10) + 0.5 * y(11)
 - 9.675 * y(6) * y(7) + 15.48 * y(8) + 3.87 * y(8)
 + 9.675 * y(6) * y(7) - 15.48 * y(8) - 3.87 * y(8)
 + 3.87 * y(8)
 - 10 * y(6) * y(10) + 0.5 * y(11)
 + 10 * y(6) * y(10) - 0.5 * y(11) - 18 * y(13) * y(11) + 2.88 * y(12) + 0.72 * y(12)
 + 18 * y(13) * y(11) - 2.88 * y(12) - 0.72 * y(12)
 - 18 * y(13) * y(11) + 2.88 * y(12) + 0.0001 * y(14)
 + 0.72 * y(12) - 1 * y(15) * y(14) + 0.27 * y(16) - 0.0001 * y(14)
 - 1 * y(15) * y(14) + 0.27 * y(16)
 + 1 * y(15) * y(14) - 0.27 * y(16)
];

% end of model
