SCL involves three distinct chemical species (implemented as separate classes):
The SCL reaction scheme is implemented in a 2-D space. Subject to certain constraints, particles move around this space in random walks. The particles can undergo various transformations or reactions; where these involve more than one particle, the reacting particles must be adjacent to each other in the space.
The restriction to a 2-D space is important because it means that linear chains or polymers of L particles can actually serve as spatial separators or boundaries. It is stipulated that such chains are permeable to S particles, but impermeable to all others. In this way a closed chain of L particles can ``trap'' K and L particles inside, while still allowing S particles to move in (and out). These constraints on particle motion are critical to the intended autopoietic phenomena.
SCL supports six distinct reactions, as follows:
In essence, this is a reaction in which two particles of S combine to produce one particle of L. However, the reaction can occur only with the mediation of catalyst, K. The catalyst particle itself is unaffected by the reaction (hence its name).
This is a reverse reaction to production. It occurs spontaneously.
L chains can break down again either via spontaneous decay of individual bonds (see below), or if constituent L particles spontaneously disintegrate back to substrate (when any associated bonds will also undergo forced decay).
In this reaction, an L particle can spontaneously absorb an S particle. The absorbed S particle can subsequently be emitted again (see below). An L which has absorbed an S particle is denoted by L . An L particle can absorb at most one S particle--i.e. an L particle cannot undergo a further absorption reaction. The absorption and emission reactions together provide for the permeability of L chains to S particles.
This is a reverse reaction to absorption, in which a previously absorbed S particle is spontaneously re-emitted. An L particle which undergoes disintegration must necessarily first undergo a (forced) emission reaction.
Each of these reactions is controlled by a one or more, user configurable, rate parameters. Similarly, rates of random motion in the space are controlled by separate mobility parameters for each particle class. This parameters are all implemented as class variables of the relevant agent classes.
Of the six reactions, only the first three were present in the original model described by Varela et al. Furthermore, only disintegration was explicitly controlled by a rate parameter, and no explicit mobility parameters were defined, though there were implicit differences in mobility between the different particle classes. The implementation of bonding in SCL is quite different from the original.
Bond decay was added to SCL in the interests of making the reaction scheme somewhat more symmetrical. However, if desired, it can be ``switched off'' simply by setting its rate parameter to zero.
The original model implemented permeability of L chains as a special case of motion in the space, rather than using the explicit absorption and emission reactions introduced in SCL. However, that suffered from the drawbacks of requiring a neighborhood (for motion at least) extending two cells from any given cell, and also making it more difficult to control the rate at which permeation could occur separately from general mobility rates. I suggest that introducing the explicit absorption and emission reactions makes the model easier to understand and provides more intuitively tractable parameters.
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Timestamp: Tue Dec 31 19:40:38 GMT 1996