/* rat_nmj.main.mdl */

/* This is the main MDL file for this example (see book Boxes 4.1 
and 4.2 for general background on MDL files).  For readability, 
comments are shown in red and most input parameter values are 
included explicitly in the MDL statements.  The simulation 
would be run by typing "mcell rat_nmj.main.mdl <seed_index>" on 
the command line, with <seed_index> replaced by an integer 
(currently available range is from 1 to 3000) that specifies 
which pre-defined random number seed will be used. */

/* MDL keyword statements are used to specify the required Monte 
Carlo time-step and number of iterations. */
TIME_STEP = 0.5e-6	/* Simulation time-step is 0.5 microseconds */
ITERATIONS = 14000	/* Simulation will run for 14000 time-step 
iterations, i.e., for a total elapsed time of 7 milliseconds */

EFFECTOR_GRID_DENSITY = 10000	/* Barycentric subdivision of mesh 
elements will produce about 10000 effector tiles per square 
micron of surface area. */

/* The next 3 lines create spatial partitions (book Fig. 4.3, and 
Fig. 4.5 condition (c)) along the x, y, and z axes.  Partitions 
can be placed at arbitrary positions specified in a list 
(numerical array), and/or placed at regular intervals between 
lower and upper limits (as shown).  All spatial dimensions are 
given in microns. */
PARTITION_X = [ [ -1.576 TO 1.550 STEP 0.025 ] ]
PARTITION_Y = [ [ -1.026 TO 1.025 STEP 0.025 ] ]
PARTITION_Z = [ [ -0.926 TO 0.275 STEP 0.025 ] ]

/* MDL statement blocks are used to define diffusing molecules of 
acetylcholine and choline (named "ACh" and "Ch", respectively), 
with each required diffusion coefficient given in cm^2 per 
second. */
/* Logical Objects */
DEFINE_LIGAND ACh {
  DIFFUSION_CONSTANT = 2.1e-6
}
DEFINE_LIGAND Ch {
  DIFFUSION_CONSTANT = 2.1e-6
}

/* A list of additional MDL files is parsed here to specify AChR 
and AChE reaction mechanisms (book Fig. 4.1), ACh release (Fig. 
4.4F), surfaces for the nerve membrane, basal lamina, and 
muscle membrane (Fig. 4.4A), and a set of boxes in which to 
sample cleft ACh and Ch concentration (Fig. 4.6A). */
/* An include file that defines multiple logical objects. */
INCLUDE_FILE = "reaction_mechanisms.mdl"
/* An include file that contains a set of logical and physical 
objects to specify the timing and location of ACh release. */
INCLUDE_FILE = "release_sites.mdl"
/* Include files that create templates for physical objects */
INCLUDE_FILE = "nerve_membrane.mdl"
INCLUDE_FILE = "basal_lamina.mdl"
INCLUDE_FILE = "muscle_membrane.mdl"
INCLUDE_FILE = "ligand_sampling_boxes.mdl"

/* Logical objects and physical object templates next are 
instantiated for inclusion in the simulation.  Empty brackets 
following each subobject indicate that no geometric 
transformations are applied. */
INSTANTIATE nmj OBJECT {	/* Entire simulation object is named 
"nmj". */
  nerve_layer OBJECT nerve_membrane { }	/* The contents of the 
object template "nerve_membrane" (read from the include file 
"nerve_membrane.mdl") are copied into the "nmj" subobject 
named "nerve_layer". */
  lamina_layer OBJECT basal_lamina { }	/* The contents of 
template "basal_lamina" (read from "basal_lamina.mdl") are 
copied into "nmj" subobject "lamina_layer". */
  muscle_layer OBJECT postsynaptic_membrane { }	/* The contents 
of the metaobject template "postsynaptic_membrane" (read from 
"muscle_membrane.mdl") are copied into the "nmj" subobject 
"muscle_layer", which itself therefore includes 3 subobjects 
named "top", "middle", and "bottom" (each of which has a 
different density of AChR effector sites). */
  ACh_release OBJECT all_release_sites { }	/* The metaobject 
template "all_release_sites" (read from "release_sites.mdl"), 
which includes 303 separate ACh release events to simulate the 
time course of exocytosis, is copied into the "nmj" subobject 
"ACh_release". */
  sampling_boxes OBJECT all_sampling_boxes { }	/* The contents 
of the metaobject template "all_sampling_boxes" (read from 
"ligand_sampling_boxes.mdl") are copied into the "nmj" 
subobject "sampling_boxes", which itself therefore includes 5 
subobjects named "box_1", "box_2", "box_3", "box_4", and 
"box_5". */
}

/* Include file that specifies the format and content of 
simulation output files used for 3-D images and animations. */
INCLUDE_FILE = "visualization_output.mdl"

/* Include file that specifies the content of simulation output 
files used for 2-D plots of reaction data. */
INCLUDE_FILE = "reaction_output.mdl"