/* release_sites.mdl */

/* To reduce computation time many-fold, in this simulation 
explicit diffusion of ACh from a synaptic vesicle and fusion pore 
is replaced by a series of release events.  Each release occurs at 
a point in space where the pore opening would otherwise have been.  
The amount and timing of each release were determined by a 
function that reproduces the expected time course of ACh 
exocytosis (see book Fig. 4.4F). */

/* In general, a release pattern (logical object) can be used in 
conjunction with one or more release sites (physical objects).  
Each release pattern is like a stimulus generator, i.e., it 
initiates one or more trains of release events after some time 
delay. */
DEFINE_RELEASE_PATTERN release_pattern_1 {
  DELAY = 0.000000500000    /* The first release occurs after a 
0.5 microsecond delay. */
  RELEASE_INTERVAL = 2.0e-6    /* Time between release events 
within a train. */
  TRAIN_INTERVAL = 4.0e-6    /* Time between trains of release 
events. */
  TRAIN_DURATION = 1.0e-6    /* Length of each train.  In this 
case the train duration is shorter than the release interval, 
so only one release event occurs per train. */
  NUMBER_OF_TRAINS = 1    /* Only one train is generated, so in 
total only one release event occurs at time t = 0.5 
microseconds. */
}

release_site_1 SPHERICAL_RELEASE_SITE {    /* Generates an 
instantaneous spherical distribution of molecules at uniform 
concentration. */
  LOCATION = [0,0,0]    /* Molecules appear in the cleft diffusion 
space under the vesicle indicated in book Fig. 4.4A. */
  LIGAND = ACh    /* Any predefined molecule can be released. */
  NUMBER_TO_RELEASE = 18    /* 18 ACh molecules will appear at the 
specified location when the release site is triggered by a 
release pattern (but see RELEASE_PROBABILITY below). */
  SITE_DIAMETER = 0    /* Values >= 0 are valid; here a point 
source is used for simplicity. */
  RELEASE_PATTERN = release_pattern_1    /* References the above 
release pattern by name. */
  RELEASE_PROBABILITY = 1    /* When this release site is 
triggered by release_pattern_1, this probability value is 
tested against a random number to see if release occurs.  
Allowed values are from 0 (no release) to 1 (guaranteed 
release). */
}

/* From release_pattern_1 and release_site_1, 18 ACh molecules 
appear at time t = 0.5 microseconds (see leftmost open circle in 
book Fig. 4.4F).  Thereafter, differing amounts of ACh molecules 
are released at the same location at different times to obtain the 
desired time course of exocytosis.  The entire required (lengthy) 
MDL file was produced by a program that evaluates an analytic 
function for vesicle emptying (solid curve in book Fig. 4.4F; see 
Stiles et al., 1998 and MCell website for further details). */

/* (release patterns and sites numbered 2 – 88 omitted) */

/* Release number 89 occurs at 44.5 microseconds and is one of 
those that releases a maximal number of ACh molecules (40). */
DEFINE_RELEASE_PATTERN release_pattern_89 {
  DELAY = 0.000044500000
  RELEASE_INTERVAL = 2.0e-6
  TRAIN_INTERVAL = 4.0e-6
  TRAIN_DURATION = 1.0e-6
  NUMBER_OF_TRAINS = 1
}

release_site_89 SPHERICAL_RELEASE_SITE {
  LOCATION = [0,0,0]
  LIGAND = ACh
  NUMBER_TO_RELEASE = 40
  SITE_DIAMETER = 0
  RELEASE_PATTERN = release_pattern_89
  RELEASE_PROBABILITY = 1
}

/* (release patterns and sites numbered 90 – 302 omitted) */

/* the final release occurs at 192 microseconds and releases 1 ACh 
molecule. */
DEFINE_RELEASE_PATTERN release_pattern_303 {
  DELAY = 0.000192000000
  RELEASE_INTERVAL = 2.0e-6
  TRAIN_INTERVAL = 4.0e-6
  TRAIN_DURATION = 1.0e-6
  NUMBER_OF_TRAINS = 1
}

release_site_303 SPHERICAL_RELEASE_SITE {
  LOCATION = [0,0,0]
  LIGAND = ACh
  NUMBER_TO_RELEASE = 1
  SITE_DIAMETER = 0
  RELEASE_PATTERN = release_pattern_303
  RELEASE_PROBABILITY = 1
}

/* All of the release site templates are copied into one 
metaobject template named "all_release_sites", which then is 
instantiated in the main mdl file "rat_nmj.main.mdl". */
all_release_sites OBJECT {
  release_1 OBJECT release_site_1 { }
/* (objects release_2 through release_88 omitted) */
  release_89 OBJECT release_site_89 { }
/* (objects release_90 through release_302 omitted) */
  release_303 OBJECT release_site_303 { }
}