ChemCell WWW Site - ChemCell Documentation - ChemCell Commands

permeable command


permeable species-ID surface-ID flag keyword value ... 


permeable A nucleus out reflect 0.9 thru 0.1 tsp A_nuc
permeable Ca_cyto cell reflect 1.0 


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.


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


By default, all 3d species interact with all surfaces with a reflection probability of 1.0 and with no species change.