Syntax:
permeable species-ID surface-ID flag keyword value ...
keywords = reflect or near or stick or far or thru or rsp or nsp or ssp or fsp or tsp
reflect, near, stick, far, thru value = probability
probability = value between 0.0 and 1.0 (inclusive)
rsp, nsp, ssp, fsp, tsp value = species-ID
species-ID = what the permeating particle will become if event takes place
Examples:
permeable A nucleus out reflect 0.9 thru 0.1 tsp A_nuc permeable Ca_cyto cell reflect 1.0
Description:
Set the permeability for a species when it encounters a surface (region or triangulated surface) during a move. The flag value in/out/both refers to which side of the surface. Each triangle in a triangulated surface has an "outside" determined by applying the right-hand rule to its 3 ordered vertices.
Each time a 3d particle hits a surface, there are 5 possibilities. It can reflect off and continue its move, end its move by being placed EPSILON away from the surface on the near side, stick to the surface and become a 2d species, end its move by being placed EPSILON away from the surface on the far side, or pass thru the surface unimpeded.
Each of the 5 cases is assigned a fractional probability P, the sum of which must be 1.0. When a particle moves and a surface is encountered, a random number is generated which is used to select which of the 5 cases occurs.
Each of the 5 surface interactions can also cause the particle to become a new species, if the corresponding keyword (rsp,nsp,ssp,fsp,tsp) is specified.
Restrictions:
This command cannot be used for 2d species. If the stick probability is non-zero, the ssp keyword must be specified, else the 3d species cannot become a 2d species.
This command can only be used for spatial simulations.
Related commands: none
Default:
By default, all 3d species interact with all surfaces with a reflection probability of 1.0 and with no species change.