/* nerve_membrane.mdl */
/* The smoothly curved nerve
membrane surface (book Fig. 4.4A) is a polygon mesh that contains 1752 vertices
and 3363 triangular mesh elements. The
mesh is described by first listing all of the vertices, and then listing the
connections that exist between each set of 3 vertices that define a
triangle. In the list of connections,
the vertices are referenced by their position in the vertex list. By convention, numbering within the vertex
and connection lists begins at 0. */
nerve_membrane
POLYGON_LIST { /* This object named "nerve_membrane" is instantiated in the main
mdl file "rat_nmj.main.mdl". */
VERTEX_LIST {
[ -1.50190, -0.950832, 0.115681 ] /*
position 0 in the vertex list */
[ -1.47971, -0.999633, 0.125194 ] /* position 1 */
[ -1.53361, -0.999901, 0.128573 ]
/* position 2 */
[ -1.47569, -0.900435, 0.104002 ]
/* position 3 */
[ -1.42395, -0.937575, 0.112165 ]
/* position 4 */
/*
vertices 5 – 1750 omitted */
[ 1.364000, 0.9854670, 0.182298 ]
/* position 1751 */
}
ELEMENT_CONNECTIONS {
[ 0, 4, 3 ] /* Mesh element 0 (the first
mesh element) is created by connecting vertices 0, 4, and 3 from the above
list. Applying the right-hand-rule to
these vertices in this order determines the front and back faces of the mesh
element (see book Fig. 4.4C). */
/*
element connections for mesh elements 1 – 3362 omitted */
}
FULLY_CLOSED = NO /* The mesh does not encompass a
fully enclosed volume, so it does not define a space within which molecules
could be counted. */
ADD_EFFECTOR { /* Add Ch reuptake effector
sites to the mesh elements. */
STATE = ChR.R0 /* The "ChR.R0" molecule name
refers to the unbound "R0" state within the previously defined "ChR" reaction
mechanism. */
DENSITY = 1000 /* 1000 ChR.R0 molecules are
added per square micron of mesh element area, by choosing randomly among
available effector tiles. */
ELEMENT = ALL_ELEMENTS /* Add
the ChR.R0 molecules to all elements of the mesh. Could have specified a list of individual mesh elements using
their position numbers in the element connections list. */
POLE_ORIENTATION = POSITIVE_BACK /*
Orient the effector sites so that their positive pole is on the back face of
each mesh element. In this example,
this means that the Ch binding site faces the synaptic cleft diffusion space.
*/
}
}