/* neuronal_epscs.main.mdl */
INCLUDE_FILE =
"input_parameter_values.mdl"
TIME_STEP
= dt /* numerical variable values are defined in the include file
"input_parameter_values.mdl" */
ITERATIONS = it
EFFECTOR_GRID_DENSITY = 10000
PARTITION_X = [[-0.26 TO 0.26 STEP 0.025]]
PARTITION_Y = [[-0.22 TO 0.22 STEP 0.025]]
PARTITION_Z = [[-0.33 TO 0.33 STEP 0.025]]
DEFINE_LIGAND Glu {
DIFFUSION_CONSTANT = D_Glu
}
/* AMPA Glu receptor reaction mechanism as shown in book Fig. 4.7A
(from Geiger et al., 1999). Positive
pole of effector sites faces diffusion space. */
DEFINE_REACTION AMPA {
C0 [>C1{AMPA_kC0C1:+Glu,POSITIVE_POLE}]
C1 [>C2{AMPA_kC1C2:+Glu,POSITIVE_POLE}]
[>C3{AMPA_kC1C3}][>C0{AMPA_kC1C0:-Glu,POSITIVE_POLE}]
C2 [>O{AMPA_kC2O}][>C4{AMPA_kC2C4}]
[>C1{AMPA_kC2C1:-Glu,POSITIVE_POLE}]
C3 [>C4{AMPA_kC3C4:+Glu,POSITIVE_POLE}]
[>C1{AMPA_kC3C1}]
C4 [>C5{AMPA_kC4C5}][>C2{AMPA_kC4C2}]
[>C3{AMPA_kC4C3:-Glu,POSITIVE_POLE}]
C5 [>C4{AMPA_kC5C4}]
[>O{AMPA_kC5O}]
O [>C2{AMPA_kOC2}]
[>C5{AMPA_kOC5}]
REFERENCE_STATE C0 {
Glu NUMBER_BOUND = 0
}
}
/* Glu reuptake reaction mechanism.
Positive pole of effector sites faces diffusion space. */
DEFINE_REACTION GluT {
T0 [>T1{GluT_kT0T1:+Glu,POSITIVE_POLE}]
T1 [>T2{GluT_kT1T2}][>T0{GluT_kT1T0:-Glu,POSITIVE_POLE}]
T2 [>T0{GluT_kT2T0:-Glu,NEGATIVE_POLE}]
REFERENCE_STATE T0 {
Glu NUMBER_BOUND = 0
}
}
/* Create release pattern to trigger Glu release at ~36 Hz, starting
immediately at time 0. */
DEFINE_RELEASE_PATTERN train_1 {
DELAY = 0 /* Initial release at time 0. */
RELEASE_INTERVAL = 0.028 /* 28
millisecond release interval. */
TRAIN_INTERVAL = 1 /* 1 second between trains. */
TRAIN_DURATION = 0.14 /*
Train lasts for entire simulation. */
NUMBER_OF_TRAINS = 1
}
/* Create release pattern to trigger Glu release at ~48 Hz, starting
after a delay of 1.5 milliseconds. */
DEFINE_RELEASE_PATTERN train_2 {
DELAY = 1.5e-3 /* Initial release at time 0.0015 seconds. */
RELEASE_INTERVAL = 0.021 /* 21
millisecond release interval. */
TRAIN_INTERVAL = 1 /* 1 second between trains. */
TRAIN_DURATION = 0.14 /*
Train lasts for entire simulation. */
NUMBER_OF_TRAINS = 1
}
/* Create release pattern to trigger Glu release at ~41 Hz, starting
after a delay of 3 milliseconds. */
DEFINE_RELEASE_PATTERN train_3 {
DELAY = 3.0e-3 /* Initial release at time 0.003 seconds. */
RELEASE_INTERVAL = 0.0245 /*
24.5 millisecond release interval. */
TRAIN_INTERVAL = 1 /* 1 second between trains. */
TRAIN_DURATION = 0.14 /* Train lasts for entire simulation. */
NUMBER_OF_TRAINS = 1
}
/* Spherical mesh templates are
read from include files. */
INCLUDE_FILE =
"cell_membrane.mdl"
INCLUDE_FILE =
"diffusion_space_boundary.mdl"
INSTANTIATE neuron OBJECT {
/* 3 release sites at
different locations are instantiated directly, rather than by referring to
templates. In each case, the default
(unspecified) release probability of 1 is used. */
Glu_release_site_1 SPHERICAL_RELEASE_SITE {
LOCATION = [0.227,0,0]
LIGAND = Glu
NUMBER_TO_RELEASE = n /*
Value of variable "n" defined in include file "input_parameter_values.mdl". */
SITE_DIAMETER = 0
RELEASE_PATTERN = train_1
}
Glu_release_site_2 SPHERICAL_RELEASE_SITE {
LOCATION = [0,0.227*0.8,0]
LIGAND = Glu
NUMBER_TO_RELEASE = n
SITE_DIAMETER = 0
RELEASE_PATTERN = train_2
}
Glu_release_site_3 SPHERICAL_RELEASE_SITE {
LOCATION = [0,0,0.227*1.3]
LIGAND = Glu
NUMBER_TO_RELEASE = n
SITE_DIAMETER = 0
RELEASE_PATTERN = train_3
}
/* An asymmetric scaling
transformation is used to convert spherical mesh templates into ellipsoidal
objects. */
cell_membrane OBJECT inner_sphere {SCALE = [1,0.8,1.3]}
diffusion_space_boundary OBJECT outer_sphere
{SCALE = [1,0.8,1.3]}
}
VIZ_DATA_OUTPUT {
MODE = DX
STATE_VALUES {
neuron.cell_membrane = 1
neuron.diffusion_space_boundary = 2
AMPA.C0 = 1
AMPA.C1 = 2
AMPA.C2 = 3
AMPA.C3 = 4
AMPA.C4 = 5
AMPA.C5 = 6
AMPA.O = 7
GluT.T0 = 8
GluT.T1 = 9
GluT.T2 = 10
Glu = 11
}
MOLECULE_FILE_PREFIX = "neuron"
OBJECT_FILE_PREFIXES {
neuron = "neuron"
}
ITERATION_FRAME_DATA {
SURFACE_POSITIONS = [0]
SURFACE_STATES = [0]
EFFECTOR_POSITIONS = [0]
EFFECTOR_STATES = [[0 TO 500 STEP 25]]
LIGAND_POSITIONS = [[0 TO 500 STEP 25]]
LIGAND_STATES = [[0 TO 500 STEP 25]]
/* To reproduce frame
data used for the "neuron" animation on CD-ROM, use the following 3 lines in
place of the above 3 lines.
CAUTION: Doing so will create
more than 7000 files that will require about 350 Mbytes of disk space!!
EFFECTOR_STATES = [[0 TO 140000 STEP 100]]
LIGAND_POSITIONS = [[0 TO 140000 STEP 100]]
LIGAND_STATES = [[0 TO 140000 STEP 100]]
*/
}
}
/* Reaction statistics output
for book Fig.’s 4.7B-E. */
REACTION_DATA_OUTPUT {
STEP = 1.0*dt /* Output values for each time-step iteration. */
{ COUNT[Glu,WORLD,FOR_EACH_TIME_STEP] }
=> INPUT_FILE & ".Glu"
/* INPUT_FILE keyword is a
placeholder for the name of the main MDL file used to run the simulation. In this case, the output file name will be
"neuronal_epscs.main.mdl.Glu". */
{
COUNT[AMPA.C0,WORLD,FOR_EACH_TIME_STEP] } => INPUT_FILE &
".AMPA.C0"
{
COUNT[AMPA.C1,WORLD,FOR_EACH_TIME_STEP] } => INPUT_FILE &
".AMPA.C1"
{
COUNT[AMPA.C2,WORLD,FOR_EACH_TIME_STEP] } => INPUT_FILE &
".AMPA.C2"
{
COUNT[AMPA.C3,WORLD,FOR_EACH_TIME_STEP] } => INPUT_FILE &
".AMPA.C3"
{
COUNT[AMPA.C4,WORLD,FOR_EACH_TIME_STEP] } => INPUT_FILE &
".AMPA.C4"
{
COUNT[AMPA.C5,WORLD,FOR_EACH_TIME_STEP] } => INPUT_FILE &
".AMPA.C5"
{
COUNT[AMPA.O,WORLD,FOR_EACH_TIME_STEP] } => INPUT_FILE &
".AMPA.O"
{
COUNT[GluT.T0,WORLD,FOR_EACH_TIME_STEP] } => INPUT_FILE &
".GluT.T0"
{
COUNT[GluT.T1,WORLD,FOR_EACH_TIME_STEP] } => INPUT_FILE & ".GluT.T1"
{
COUNT[GluT.T2,WORLD,FOR_EACH_TIME_STEP] } => INPUT_FILE &
".GluT.T2"
}