%
% create_model_pop_ctrl
%
%  create the reactions for each cell and purely external reactions
%

% transcription
add_reaction({'P_luxR'},            {'P_luxR' 'LuxI' 'LuxR' 'Killer'},          0.1);
add_reaction({'P_luxR_LuxR_AHL'},   {'P_luxR_LuxR_AHL' 'LuxI' 'LuxR' 'Killer'}, 3.0);

% promoter regulation
add_reaction({'P_luxR' 'LuxR_AHL'}, {'P_luxR_LuxR_AHL'},                 0.1);
add_reaction({'P_luxR_LuxR_AHL'},   {'P_luxR' 'LuxR_AHL'},               0.3);
add_reaction({'P_luxR_LuxR_AHL'},   {'P_luxR'},                          0.3);

% AHL synthesis, binding, dissociation
add_reaction({'LuxI'},              {'LuxI' 'AHL'},                      0.4);
add_reaction({'LuxR' 'AHL'},        {'LuxR_AHL'},                        1.0);
add_reaction({'LuxR_AHL'},          {'LuxR' 'AHL'},                      0.4);

% decay
add_reaction({'LuxI'},              {},                                  1.0);
add_reaction({'LuxR'},              {},                                  1.0);
add_reaction({'AHL'},               {},                                  0.4);
add_reaction({'LuxR_AHL'},          {},                                  0.4);
add_reaction({'Killer'},            {},                                  2.0);

%
% AHL diffusion
%
%   ratio between diffusion in and out of the cell indicates ratio between 
%   a single cell volume and total volume of growth environment
%
add_reaction({'AHL'},               {'*external*_AHL'},                100.0);
add_reaction({'*external*_AHL'},    {'AHL'},                             1.0); 

% cell growth
add_reaction({'Alive'},             {'Alive' 'Volume'},                  2.0); 
add_reaction({'create_P_lux'},      {'P_lux'},                           1.0);
add_reaction({'create_P_luxR'},     {'P_luxR'},                          1.0);

%
% add reactions that take place completely outside the cell
%
add_external_reaction({'*external*_AHL'}, {},                            0.4); 

%
% special instructions for dealing with cell division
%
add_after_cell_division('create_P_lux',  10);
add_after_cell_division('create_P_luxR', 10);