# Times at which concentrations are printed out.  Can use alternatively set
# $n_steps and $step_length to do evenly spaced time sampling.
#$n_steps=60;
#$step_length=60;
@sample_times=(60, 180, 300, 600, 1200);

# Absolute and relative integration error tolerated
$atol_integ=1.0e-12; 
$rtol_integ=1.0e-10; 

# File containing the reaction network
$netfile="network.net";

# Group files.  netrun.pl assumes they end in suffix .groups
@groups=("rec","lyn","syk"); 


# Parameters used to set initial concentrations
$rtot=  4.0e5; # number of molecules per cell
$lyntot=2.8e4; # number of molecules per cell
$syktot=4.0e5; # number of molecules per cell
$ligtot=6e6; # 6e6 molecules per cell = 10 nM

$kpL= 5e-5;
$kmL= 20;
# equilibrium for constitutive Lyn association
$Klow= $kpL/$kmL;
$b= 1.0+($lyntot+$rtot)*$Klow;
$x= ($b - sqrt($b*$b - 4*($Klow*$Klow*$lyntot*$rtot)))/(2*$Klow);
$lynstart= 1.0 - $x/$lyntot;
$lynrecstart= $x/$rtot;
$recstart= 1.0 - $lynrecstart;

# Definition of rate parameters
# Unimolecular rates are s^(-1)
# Bimolecular rates are molecule^(-1) s^(-1)
# Cell volume is assumed to be  1.4x10^(-9) mL
# Cell density is assumed to be 10^6 cells/mL
$rates=<<"END_RATES";
    1                  kp1  1.328452377888242e-10
    2                  km1  0
    3                  kp2  2.5e-4
    4                  km2  0
    5                  kpL  $kpL
    6                  kmL  $kmL
    7                 kpL*  5e-5 
    8                 kmL*  0.12
    9                  kpS  6e-5
   10                  kmS  0.13
   11                 kpS*  6e-5
   12                 kmS*  0.13
   13                  pLb  30
   14                 pLb*  100
   15                  pLg    1
   16                 pLg*    3
   17                  pLS   30
   18                 pLS*  100
   19                  pSS  100
   20                 pSS*  200 
   21                   dm   20
   22                   dc   20 
END_RATES