# Simulation of diffusion in which half of the system is crowded and half is uncrowded, in 2D.
# Units are nanometers and microseconds
# Model HalfCrowd.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 5
define Rp 2
define PHI 0.5
define VOLHALF 100*100

#random_seed 1

graphics opengl_good

dim 2

boundaries x -100 100
boundaries y 0 100

time_start 0
time_stop 11000
time_step 0.01

species ball probe

difc ball 1
difc probe 10

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 -100 0  100
panel rect -x 100 0  100
panel rect +y -100 0  200
panel rect -y -100 100  200
end_surface

start_surface innerwalls
color both black
polygon both none
action both ball reflect
action both probe transmit
panel rect +x -100+Rb 0+Rb  100-2*Rb
panel rect -x 0-Rb 0+Rb  100-2*Rb
panel rect +y -100+Rb 0+Rb  100-2*Rb
panel rect -y -100+Rb 100-Rb  100-2*Rb
end_surface


start_surface membrane
color both 0 0.5 0.5
action both ball reflect
action both probe transmit
panel rect +x 0 0  100
end_surface


reaction rxnbb ball + ball -> ball + ball
reaction rxnbp ball + probe -> ball + probe
binding_radius rxnbb Rb+Rb
binding_radius rxnbp Rb
product_placement rxnbb bounce -1
product_placement rxnbp bounce -1

mol PHI*VOLHALF/(3.14*Rb^2) ball -90--10 10-90
mol 200 probe u u

output_files stdout
cmd i 1000 11000 10 molcountspace probe x -100 100  2  0 100  100 stdout

end_file