glo_total.gro

////////////////////////////////////////////////////////////////////////////
//
//   gro
//
//   Copyright (c) 2011-2012 Eric Klavins, University of Washington
//   For more information, email klavins@uw.edu
//
//   This program is free software; you can redistribute it and/or
//   modify it under the terms of the GNU General Public License
//   as published by the Free Software Foundation; either version 2
//   of the License, or (at your option) any later version.
//
//   This program is distributed in the hope that it will be useful,
//   but WITHOUT ANY WARRANTY; without even the implied warranty of
//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
//   GNU General Public License for more details.
//
//   You should have received a copy of the GNU General Public License
//   along with this program; if not, write to the Free Software
//   Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
//
//

//////////////////////////////////////////////////////////////////////////////


include gro


chemostat(true);
set ( "chemostat_width", 400 );
set ( "chemostat_height", 400 );
set_theme ( dark_theme );
//set( "dt", 0.002);

// Initialize the simulation parameters
kdif := 10;      // signal diffusion rate
dS := 0.05;   // signal degradation rate
kS := 3.0;    // signal emission rate (use as reference for total population cap)
//kS0 := 1.0;    // signal emission rate
//kS1 := 1.0;    // signal emission rate
dC := 0.01;   // cell death rate; Figure 6 shows the parameter variation simulations of k4.
k_on := 1; // gp2 and RNAp annihilate each other with a really big rate.

//kdif := 2;      // slower signal diffusion rate


gG := 0.8; // growth-related chemical basal production (use as reference for total population cap)
//kG := 0.4; // growth-related chemical maximal production

gD := 0.0; // RNA antisense gp2 basal production
kD := 0.5; // RNA antisense gp2 maximal production


// Define a signal molecule
ahl := signal( kdif, dS );
//ahl0 := signal( kdif, dS );
//ahl1 := signal( kdif, dS );

red_total := 30;
green_total := 30;

program rk0() := {
  gfp := 100*volume;
  G := 100;
  D := 0;
  set ( "ecoli_growth_rate", 0.0346574*G/100 );   // reactions/min

  just_divided : {
      set ( "ecoli_growth_rate", 0.0346574*G/100 );   // reactions/min
      green_total := green_total + 0.5;
  };

  true  : {
    emit_signal( ahl, kS * dt );	// signal is emitted at every dt interval
    //emit_signal( ahl0, kS0 * dt);
    gfp := 100*volume;
  };

  // growth-related chemical production.
  rate( gG) : {
    //absorb_signal( ahl0, 1);
    G := G + 1;		      	// cell death
    set ( "ecoli_growth_rate", 0.0346574*G/100 );   // reactions/min
  };

  //Production of RNA antisense gp2.
  rate( gD + kD * get_signal( ahl) ) : {
    //absorb_signal( ahl1, 1);
    D := D + 1;           // make gp2
  };

  //Sequestering elimination of growth-related chemical and gp2
  rate( k_on *G/volume* D / volume) : {
    G := G - 1;
    D := D - 1;
    set ( "ecoli_growth_rate", 0.0346574*G/100 );   // reactions/min
  };


  // Amount of natural kills the cell.
  rate( dC  ) : {
    die();
    green_total := green_total - 1;
  };

};

program rk1() := {
  rfp := 100*volume;
  G := 100;
  D := 0;

  set ( "ecoli_growth_rate", 0.0346574*G/100 );   // reactions/min

  just_divided : {
      set ( "ecoli_growth_rate", 0.0346574*G/100 );   // reactions/min
      red_total := red_total + 0.5;
  };

  true  : {
    emit_signal( ahl, kS * dt );	// signal is emitted at every dt interval
    //emit_signal( ahl1, kS1 * dt);
    rfp := 100*volume;
  };

  // growth-related chemical production.
  rate( gG) : {
    //absorb_signal( ahl, 1);
    G := G + 1;		      	// cell death
    set ( "ecoli_growth_rate", 0.0346574*G/100 );   // reactions/min
  };

  //Production of RNA antisense gp2.
  rate( gD + kD * get_signal( ahl) ) : {
    //absorb_signal( ahl0, 1);
    D := D + 1;           // make gp2
  };

  //Sequestering elimination of growth-related chemical and gp2
  rate( k_on *G/volume* D / volume) : {
    G := G - 1;
    D := D - 1;
    set ( "ecoli_growth_rate", 0.0346574*G/100 );   // reactions/min
  };


  // Amount of natural kills the cell.
  rate( dC  ) : {
    die();
    red_total := red_total - 1;
  };


};


program main() := {

t := 0;
n := 0;
s := 0;
sn :=0;

true : {
t := t + dt;
n := n + 1;
s := s + dt;
};

(n = 100): {
  n := 0;
  fprint(fp, t , "," , red_total , "," , green_total, ",", red_total + green_total,"\n");
  print(t , "," , red_total , "," , green_total, ",", red_total + green_total,"\n");
}


t >400:{
  stop();
}

};



foreach q in range 30 do

ecoli( [x := rand(300) - 150, y := rand(300) - 150, theta := rand(360) ], program rk1() )

end;

foreach q in range 30 do

ecoli( [x := rand(300) - 150, y := rand(300) - 150, theta  := rand(360) ], program rk0() )

end;