/* 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 { }
}