react_modify reaction-ID keyword value(s) ...
keywords = rate or loc or dist or prob or weight rate value = rate rate = reaction rate (same units as in reaction command) loc values = product styleflag whichflag dirflag product = which product (1-N) styleflag = def or at or near whichflag = def or 1 or 2 or 1/2 dirflag = def or in or out or in/out dist = R R = distance at which reactants will react (microns) prob = P P = probability (0-1) with which reactants react weight values = which index ratio which = reactant or product index = which reactant or product (1-N) ratio = weighting factor to apply
react_modify 1 dist 0.05 prob 1.0 react_modify channel 2 near 2 out
Reset one or more parameters of a specific reaction.
The rate keyword resets the reaction rate.
The loc keyword sets the location at which a product of the reaction is placed. The product setting determines which product (1 to N). A value of -1 means all products. The styleflag setting refers to placing the product at or near a reactant's location. The whichflag setting refers to which reactant (1 to N) to place the product at or near. A value of 1/2 means to randomly choose which reactant each time a reaction occurs. The dirflag setting only applies to 3d products placed near 2d reactants and refers to which side of the surface (inside or outside) to place the product on. A value of in/out means to randomly choose the side each time a reaction occurs. A value of def for default should be used if dirflag does not apply.
Depending on the kind of reaction (1 or 2 reactants) and whether the reactants are 3d diffusing species or 2d (on a surface), certain combinations of settings are invalid and will generate errors. Note that only 3d products can be placed at a 3d reactant's location. Only 2d products can be placed at a 2d reactant's location. And only 3d products can be placed near a 2d reactant's location, which means to place it a distance epsilon from the surface the 2d reactant is on.
These are the default rules for reactions with a single reactant:
These are the default rules for reactions with two reactants:
The dist keyword explicitly sets the cutoff distance for a binary reaction bewteen two reactants. Normally, ChemCell sets this distance itself (see the probability command for options). Setting the dist value to -1.0 turns off the explicit setting; ChemCell will again compute the reaction cutoff.
The prob keyword explicitly sets the probablility (from 0.0 to 1.0) for a binary reaction to take place (assuming the reactants are within the cutoff distance). Normally, ChemCell sets this probability itself (see the probability command for options). Setting the prob value to -1.0 turns off the explicit setting; ChemCell will again compute the probability.
Note that the dist and prob keywords give you the option of setting reaction parameters directly, using your own formulation or algorithms and settings from another code. For example, the Smoldyn simulator calculates a variety of reaction parameterizations for different kinds of reactions, as described in (Andrews). Essentially it computes reaction cutoff distances (binding radii in Smoldyn nomenclature) as a function of diffusion coefficients of the reactants, timestep, and reaction rate. The Smoldyn formulation spans the spectrum from diffusion-limited to reaction-limited reactions and thus produces reaction cutoff distances which are more accurate and complete than the simple heuristic that ChemCell uses by default.
The weight keyword sets a volume weighting factor for a specific reactant or product which adjusts its concentration the reaction occurs and the species is removed or produced. This can be used by non-spatial, continuum simulations (ODEs) to weight the effects of a reaction. The weighting factor can be thought of as a volume ratio between 2 compartments, so a factor can be set to enable a multi-compartment ODE solution where each compartment has its own volume.
The loc and dist and prob keywords only apply to spatial simulations. The weight keyword only applies to non-spatial, continuum (ODE) simulations.
(Andrews) Andrews and Bray, Phys Biol, 1, 137-151 (2004).