# Simulation of diffusion in which half of the system is crowded and half is uncrowded, in 3D.
# Units are nanometers and microseconds
# Model HalfCrowd3D.txt by Steve Andrews, September 2023.
# Written for "Modeling diffusion between regions with different diffusion coefficients" for submission to IEEE Transactions on Molecular, Biological, and Multi-scale Communications

define Rb 0.5
define Rp 0.2
define PHI 0.2
define VOLHALF 10*10*10

#random_seed 1

graphics opengl_better

light room ambient 0 0 0
light 0 position -1 1 1 0
light 0 diffuse 0.5 0.5 0.5
light 0 ambient 0.5 0.5 0.5
light 0 specular 0.5 0.5 0.5

dim 3

boundaries x -10 10
boundaries y 0 10
boundaries z 0 10

time_start 0
time_stop 1000
time_step 0.001

species ball probe

difc ball 0.1
difc probe 1

display_size ball Rb
display_size probe Rp
color ball gray
color probe red

start_surface walls
color both black
polygon both edge
action both all reflect
panel rect +x -10 0 0  10 10
panel rect -x 10 0 0  10 10
panel rect +y -10 0 0  20 10
panel rect -y -10 10 0  20 10
panel rect +z -10 0 0  20 10
panel rect -z -10 0 10  20 10
end_surface

start_surface membrane
color both 0 0.5 0.5 0.2
action both ball reflect
action both probe transmit
panel rect +x 0 0 0  10 10
end_surface


reaction rxnbb ball + ball -> ball + ball
reaction rxnbp ball + probe -> ball + probe
reaction rxnpp probe + probe -> probe + probe
binding_radius rxnbb Rb+Rb
binding_radius rxnbp Rb+Rp
binding_radius rxnpp Rp+Rp
product_placement rxnbb bounce -2
product_placement rxnbp bounce -2
product_placement rxnpp bounce -2

mol PHI*VOLHALF/(4/3*3.14*Rb^3) ball -10-0 u u
mol 100 probe u u u


end_file