# Simple bouncing molecules with surfaces define CARBOXY1 100 100 100 define CARBOXY2 200 120 100 define CARBOXY3 300 90 110 define CARBOXY4 400 90 80 graphics opengl_better graphic_iter 1 dim 3 species co2 glycerate max_mol 50000 ### Diffusion constants in px^2/ms difc co2 10 difc glycerate 10 color co2 1 0.2 0.2 # co2 is red color glycerate 0.5 0.5 1 # glycerate is blue display_size co2 1 display_size glycerate 1.5 light 0 position -50 50 0 light 0 diffuse 1 1 1 light 0 ambient 0.05 0.05 0.05 light 0 specular 0.9 0.9 0.9 background_color 0 0 0 frame_thickness 0 ### Length scale is pixel (10nm) - millisecond time_start 0 time_stop 1000 time_step 0.05 boundaries 0 0 500 boundaries 1 50 150 boundaries 2 50 150 max_surface 7 #### cell membrane surface start_surface cytoplasm action both all reflect color both 0.3 0.3 0.3 thickness 1 polygon front edge polygon back edge max_panels c 3 panel cyl 100 100 100 400 100 100 50 20 15 max_panels hemi 3 panel hemi 100 100 100 50 1 0 0 20 5 panel hemi 400 100 100 50 -1 0 0 20 5 end_surface #### carboxysome surface start_surface carb action both co2 transmit action both glycerate transmit color both 0 1 0 shininess both 20 thickness 1 polygon both face max_panels sph 4 panel sph CARBOXY1 7 20 20 panel sph CARBOXY2 7 20 20 panel sph CARBOXY3 7 20 20 panel sph CARBOXY4 7 20 20 end_surface ### Compartments max_compartment 3 start_compartment carbComp surface carb point CARBOXY1 point CARBOXY2 point CARBOXY3 point CARBOXY4 end_compartment start_compartment cytoplasmComp surface cytoplasm point 100 100 100 end_compartment compartment_mol 1000 co2 cytoplasmComp ### REACTIONS #reaction_surface cytoplasminside co2prod 0 -> co2 0.001 reaction_cmpt carbComp r1 co2 -> glycerate 1000 reaction_cmpt carbComp r2 glycerate -> co2 1 reaction_cmpt cytoplasmComp glycerateDegrade glycerate -> 0 0.001 end_file