3.3.3 Bonding

Document: SCL: An Artificial Chemistry in Swarm

3.3.3 Bonding

Bonding is initiated by a primary L particle; however, in general, the various constraints or influences affecting bonding are evaluated symmetrically for both the primary and secondary L particle.

The factors influencing the bonding reaction are as follows:

Bonding is inhibited if an L particle has already formed two bonds. This sets the maximum number of bonds to any L particle as two, and ensures that the only particle aggregates or ``molecules'' which can form are linear ``chains'' rather than any more complex, branching, structures.
Two other mechanisms or interactions by which bonding can be inhibited are also provided. Each of these is qualified by a BOOL parameter whereby they can be enabled or disabled. These are essentially intended as alternative mechanisms for preventing ``premature'' bonding of free L particles that have been produced within the boundary of an autopoietic entity. However, even though the typical mode of operation would be with just one or the other of these interactions enabled, SCL will actually allow both to be simultaneously disabled, or both simultaneously enabled, if desired.
The need for some such form of inhibition interaction is quite subtle but, it transpires, quite crucial to the autopoietic phenomenology of the model; while no such effect was mentioned explicitly in (Varela et al. 1974), it is almost certain that it was present in their model. This is discussed further in (McMullin 1997).
- Inhibition by a neighboring L Chain: This interaction allows bonding to be inhibited to any L particle which is alongside (as opposed to, at the end of) an existing chain of L particles. This is implemented for any given L particle by checking whether there are any existing doubly bonded L particles in its (Moore) neighborhood. This interaction is qualified by the BOOL parameter, chainInhibitBondFlag. If this is YES this inhibition effect is enabled; if it is NO then it is disabled.
  As discussed in (McMullin 1997), this particular form of bond inhibition reaction was inspired by examination of the FORTRAN IV code for one early version of the model developed by Varela et al.
- Inhibition by a neighboring K particle: This is implemented for any given L particle by checking whether there are any K particles in its (Moore) neighborhood. This interaction is qualified by the BOOL parameter, catInhibitBondFlag. If this is YES this inhibition effect is enabled; if it is NO then it is disabled.
  This alternate form of bond inhibition reaction was inspired by (Lizana 1981).
A second bond to any particular L particle must form an angle of or more relative to the first bond. This rules out forming two bonds ``on top of each other'' (a double bond between the same two L particles), or with an angle of just between them.
Given that a new bond would satisfy the above constraints for both affected L particles, the formation of the bond is controlled by a reaction rate, or probability parameter. More precisely, one of three possible rate parameters is applied, depending on the exact conformation of the proposed new bond:
1. If neither L particle already has a bond, the new bond would initiate a new chain; in that case the probability is set by the parameter chainInitiateProbability.
2. If just one of the two L particles already has a bond, then the new bond would extend an already existing chain by one more particle; in that case the probability is set by the parameter chainExtendProbability.
3. If both of the L particles already have a bond, then the new bond would splice together two existing chains; in that case the probability is set by the parameter chainSpliceProbability.

The detailed implementation of the bonding reaction is as follows:

If bonding to the primary L is inhibited due to already having two bonds, or either of the inhibition interactions (an adjacent doubly bonded L particle, qualified by chainInhibitBondFlag, or an adjacent K particle, qualified by catInhibitBondFlag) the reaction is terminated.
A random neighbor (neighborParticle) is chosen from the default neighborhood.
If the primary L already has a bond to this neighbor, or to either of the neighbors at an angle of to this neighbor, the reaction is terminated.
If neighborParticle is not an L particle the reaction is terminated. Otherwise it becomes the secondary L particle in the reaction.
If bonding to the secondary L is inhibited due to already having two bonds, or either of the inhibition interactions, the reaction is terminated.
If the secondary L already has a bond to either of its neighbors at an angle of to the direction from it to the primary L particle, the reaction is terminated.
If neither the primary nor secondary L particles already have a bond, bondingProbability will be set to chainInitiateProbability; if just one of them already has a bond, bondingProbability will be set to chainExtendProbability; if both of them already have a bond, bondingProbability will be set to chainSpliceProbability.
A bernoulli random variable is evaluated with probability parameter bondingProbability; if this evaluates as NO, the reaction terminates.
The secondary L particle creates the bond to the primary L particle (and passes a pointer to it back to the latter).
The primary L particle records the presence of the new bond also. This completes the bonding reaction.

3.3.4 Bond Decay

3.3 Reactions

3.3.2 Disintegration

Document: SCL: An Artificial Chemistry in Swarm

mcmullin@eeng.dcu.ie