# File Min1.txt, by Steve Andrews, 11/2009.
# E. coli Min system, based on Huang, Meir, Wingreen (HMW)
# This file is HMW system exactly, plus surface diffusion
# units are micron, second

define D_D		2.5	# MinD diffusion coefficient (um^2/s)
define D_E		2.5	# MinE diffusion coefficient (um^2/s)
define D_d		0.01	# MinD_ATP(front) diff. coeff. (um^2/s)
define D_de		0.01	# MinDMinE(front) diff. coeff. (um^2/s)
define SIGMA_D_D2T	1	# MinD phosphorylation rate (s^-1)
define SIGMA_D		0.025	# MinD_ATP adsorption coeff. (um/s)
define SIGMA_dD		0.0015	# cooperative adsorption coeff. (um^3/s)
define SIGMA_de		0.7	# desorption rate of MinDMinE (s^-1)
define SIGMA_E		0.093	# MinE binding to surface-bound MinD (um^3/s)

define UNBINDRAD	0.01	# MinD separation on surface (um)

define R		0.5	# cell radius
define L_PARAM		2	# half of cell length
define L_PARAM2		1.5	# half of cell length minus radius

define NUMBER_MIND	4000	# number of MinD in cell
define NUMBER_MINE	1400	# number of MinE in cell

define TIME_STOP	10	# stopping time

#define KICK_START	1	# start with MinD_ATP at an end

random_seed 1

#graphics opengl
#graphic_iter 100

#tiff_name movie/MinMovie
#tiff_iter 200
#tiff_min 1
#tiff_max 200

dim 3
boundaries 0 -L_PARAM L_PARAM
boundaries 1 -R R
boundaries 2 -R R
frame_thickness 0
time_start 0
time_stop TIME_STOP
time_step 0.002			# 2 millisecond time step

accuracy 5
molperbox 4

species MinD_ATP
species MinD_ADP
species MinE
species MinDMinE

molecule_lists list1 list2 list3 list4 list5
mol_list MinD_ATP(soln) list1
mol_list MinD_ATP(front) list2
mol_list MinD_ADP(all) list3
mol_list MinE(all) list4
mol_list MinDMinE(all) list5

difc MinD_ATP(solution) D_D
difc MinD_ATP(front) D_d
difc MinD_ADP(solution) D_D
difc MinE(solution) D_E
difc MinDMinE(front) D_de

color MinD_ATP(soln) 0 0 0.6	# MinD_ATP(solution) is dark blue
color MinD_ATP(front) 0 0.6 0	# MinD_ATP(front) is dark green
color MinD_ADP(soln) 0.4 0.6 1	# MinD_ADP is light blue
color MinE(soln) 1 0 0		# MinE is red
color MinDMinE(front) 0.2 1 0.2	# MinDMinE is bright green
display_size all(solution) 2
display_size all(front) 4

start_surface membrane
action both all reflect
rate MinD_ATP fsoln front SIGMA_D	# reaction 1a
polygon both edge
panel cylinder -L_PARAM2 0 0 L_PARAM2 0 0 -R 20 10 cyl0
panel hemi -L_PARAM2 0 0 -R 1 0 0 20 5 hemi0
panel hemi L_PARAM2 0 0 -R -1 0 0 20 5 hemi1
neighbors cyl0 hemi0 hemi1
neighbors hemi0 cyl0
neighbors hemi1 cyl0
end_surface

start_compartment cell
surface membrane
point 0 0 0
end_compartment

reaction rxn1b MinD_ATP(fsoln) + MinD_ATP(front) -> MinD_ATP(front) + MinD_ATP(front) SIGMA_dD
product_placement rxn1b unbindrad UNBINDRAD
reaction rxn1c MinD_ATP(fsoln) + MinDMinE(front) -> MinD_ATP(front) + MinDMinE(front) SIGMA_dD
product_placement rxn1c unbindrad UNBINDRAD
reaction rxn2 MinE(fsoln) + MinD_ATP(front) -> MinDMinE(front) SIGMA_E
reaction rxn3 MinDMinE(front) -> MinD_ADP(fsoln) + MinE(fsoln) SIGMA_de
reaction rxn4 MinD_ADP -> MinD_ATP SIGMA_D_D2T

ifundefine KICK_START
  surface_mol NUMBER_MIND MinD_ATP(front) membrane all all
else
  surface_mol NUMBER_MIND MinD_ATP(front) membrane hemi hemi1
endif
compartment_mol NUMBER_MINE MinE cell


output_files modelout.txt
cmd i 0 TIME_STOP 2 executiontime modelout.txt
cmd i 0 TIME_STOP 2 listmols modelout.txt

end_file