react_modify command

Syntax:

react_modify reaction-ID keyword value(s) ... 

• reaction-ID = ID of reaction to modify
• one or more keyword/value pairs can be specified

    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 
  

Examples:

react_modify 1 dist 0.05 prob 1.0
react_modify channel 2 near 2 out 

Description:

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:

• If the reactant and product are 3d, put the product at the location of the reactant.
• If the reactant and product are 2d, put the product at the location of the reactant.
• If the reactant is 3d and the product is 2d, this is an error.
• If the reactant is 2d and the product is 3d, put the product near the reactant on the inside of the surface.

These are the default rules for reactions with two reactants:

• If both reactants and the product are 2d, put the product at the location of the reactant with the smaller diffusion coeff.
• If both reactants and the product are 3d, put the product at the location of the reactant with the smaller diffusion coeff.
• If one reactant is 2d and the other 3d and the product is 3d, put the product at the 3d reactant's location.
• If one reactant is 2d and the other 3d and the product is 2d, put the product at the 2d reactant's location.
• If both reactants are 3d and the product is 2d, this is an error.
• If both reactants are 2d and the product is 3d, put the product a distance epsilon away from the reactant with the smaller diffusion coeff on the inside of the surface.
• In all cases where diffusion coeffs are used, if the diffusion coeffs of the 2 reactants are equal, the 1st reactant is used.

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.

Restrictions: none

The loc and dist and prob keywords only apply to spatial simulations. The weight keyword only applies to non-spatial, continuum (ODE) simulations.

Related commands:

probability, reaction

Default: none

(Andrews) Andrews and Bray, Phys Biol, 1, 137-151 (2004).