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max_surface
int
name
start_surface
(optional) maximum number of surfaces
start of a surface block
optional statement for the surface name
action for when a molecule contacts surface
transition rate
name
species(state) face action
rate molec state1 state2 value [new_spec]
neighbor_action action
rate_internal molec state1 state2 value [new_spec]
color face color [alpha]
color face red green blue [alpha]
thickness float
polygon face drawmode
shininess face value
max_panels char int
(optional)
panel char float … float
panel char float … float name
jump name face -> name2 face2
jump name face <-> name2 face2
neighbors panel neigh1 neigh2 …
unbounded_diffusion face species amount pos0 pos1 … posdim-1
name
action
end_surface
Rates of surface interactions
For an interaction to occur between a solution-state molecule and a surface, the
molecule has to (1) contact the surface and (2) interact based on some probability. There
are subtleties both in the determination of contacts and in the calculation of these
probabilities.
Starting with the contacts, a molecule clearly contacted a surface during the
preceding time step if it ended up across the surface from where it began, which I’ll call a
direct collision. It is also possible for a molecule to start and end on the same side of a
surface, but to have contacted the surface at some point during the time step, labeled here
as an indirect collision. The probability of an indirect collision occurring is (Andrews
and Bray, Phys. Biol. 2004)
⎡ ll ⎤
exp ⎢ − 1 2 ⎥
⎣ DΔt ⎦
Here, l1 and l2 are the perpendicular distances to the surface before and after the time step,
D is the diffusion coefficient, and ∆t is the time step. These indirect collisions are
implemented in Smoldyn for simulating absorption of molecules to the bounding walls of
the system (the boundaries).
However, for interactions between diffusing molecules and all surfaces, Smoldyn
only accounts for direct collisions, thus ignoring the indirect collisions. This decreases
the accuracy of Smoldyn slightly but is done because indirect collisions were found to be
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