Presenting YAAC, yet another artificial chemistry based on petri nets.

A running simulation can be found here. Sources can be found here

Context

Multiple attempts have been made to create artificial chemistries that can support « life »; or, to be more precise, where evolution can take place (the Game of Life, Tierra, Avida, Hutton's chemistry to cite some of them).

YAAC is another attempt to tackle this challenge.

Presentation

YAAC takes it's inspiration from a (very simplified) vision of the operation of a biological cell, and especially of proteins :

  • A proteine is a string of aminate acids; this means it is easy to create one using a recipe (the DNA) : it is basically a linear read/write operation.
  • In its folded form, a proteine can perform functions on regular molecules or other proteines.

An artificial chemistry is a system that contains molecules, that live in a world, and that interact following chemical reaction. In this context, YAAC can be described as follow :

  • An atom is a letter in the range [A-F].
  • A molecule is a string of atoms.
  • Certain patterns in molecules are decoded as acids.
  • A proteine (a string of acids) can be folded to constuct a petri net, the functional form of a protein.
  • Chemical reactions are of two types :
    • some reactions are performed by the petri nets.
    • some reactions are statically defined.
  • Finally, the world is a dimensionless space.

We will talk more about YAAC's particular petri nets in the next section; let us say for now that they are extended versions of regular Petri Nets, in such a way that they provide the possibility to create a petri net that can duplicate an arbitrary molecule. In other words, the extensions are designed so that basic duplication can take place in YAAC's world.

More details

YAAC's petri nets

The extensions to petri nets provided by YAAC are as follow :

  • A token can hold a molecule, and then keeps a cursor to a position in the molecule.

  • A place can hold at most one token. It can be extended with properties that allow it to interact with the world :

    • catch another molecule from the world and create a token that contains it.
    • when it receives a token, release the molecule inside of it back to the world.

  • An arc can be extended with properties that allow it to modify the molecules present in the tokens that go through this arc. More precisely, the possible actions are :

    • move the cursor forward or backward.
    • cut the holded molecule at the position defined by the cursor. This will create a new token that will hold the dangling part of the molecule. This action is only available to arcs that lead to a transition.
    • take two tokens and create a new one : insert the molecule from the second token into the first token, at the position of the cursor.

YAAC's reactions

We call reaction anything that happens and modify the state of one or more of YAAC's entities. We define three types of reactions

  • Transition launch : firing of one of the transitions of one of the petri nets present inside the world, and the resulting effects.
  • Grab : one of the petri nets grabs another molecule present inside the world.
  • Breaks : one of the molecules breaks in two parts.

YAAC's world

The world is the entity that contains the molecules. It is here that we define when and how molecule interact with each other. In other word, is is here that we decide which reaction will happen next.

Since YAAC's world does not have any geometry, molecules collision is purely statistical.