chemart / flow-ac

hub:
  repo_type: generator
  builtin: flow-ac
  tags:
  - banzhaf-yamamoto
chemistries:
- id: flow-ac
  name: Flow artificial chemistry
  intuition: 'What happens when molecules are carried rather than stirred. An ordinary reaction network
    is placed in a two-dimensional domain and every molecule is advected along a vector field, reacting
    only with neighbours within a radius. Local reactions and transport then produce strongly inhomogeneous
    distributions - patches, and a shell of one species around a core of another - that the same network
    does not show when well mixed. The complement to swarm chemistry: here motion is imposed from outside
    rather than generated by the particles.

    '
  aliases:
  - reaction flow artificial chemistry
  origin: Kreyssig & Dittrich, 2011
  book: 11.4.3
  refs:
  - '[474]'
  family: spatial
  kind: generator
  constructive: false
  S:
    repr: ordinary molecular species placed in a 2D domain and moved along a vector field
    definition: explicit
  R:
    definition: explicit
    arity:
    - 1
    - 2
    - 3
    scheme: 'Book figure 11.23 network (a, b, c, d): a + b -> a + 2b ; a + d -> a + 2d ; b + c -> 2c ;
      c -> b ; b + d -> c ; b -> ; c -> ; d -> . Molecules move x -> x + V(x) each iteration and react
      only with neighbours within a radius.

      '
  A:
    reactor:
    - continuous-space
    dilution: none
    notes: stochastic particle simulation in discrete iterations (move every molecule, then apply randomly
      chosen rules to the neighbourhoods of a fraction of them; not the Gillespie algorithm), or the PDE
      d[m]/dt = -<grad([m] |V|), V>/|V| + reaction terms
  params:
  - name: example
    type: enum
    default: swirl
    choices:
    - swirl
    - radial
    - membrane
    - compartments
    role: structural
    meaning: 'which example of the paper: swirl (book figure 11.23) and radial use network R1; membrane
      is a membrane-forming core (R2); compartments is rock-scissors-paper (R3) in two stirred regions'
  - name: k
    type: float
    default: 1.0
    min: 0
    role: kinetic
    meaning: mass-action rate constant for every reaction (the paper's PDE example uses 1)
  provides:
  - topology
  - stoichiometry
  - catalysts
  - rate-constants
  - space
  fidelity: reconstructed
  sources:
  - 'Kreyssig, P. & Dittrich, P. (2011). Reaction flow artificial chemistries. Proc. ECAL 2011, MIT Press,
    431-437. Preprint: https://web.archive.org/web/2015/http://www.personal.uni-jena.de/~lo94wav/rfac.pdf'
  decisions:
  - The book gives no reactions. The networks R1, R2 and R3 are the paper's; R1's mass-action form is
    confirmed by the paper's PDE reaction terms (all k = 1), which the tests reproduce. The fourth example
    (E. coli central sugar metabolism, 92 species and 198 reactions) is not reproduced in the paper and
    is not offered.
  - R2 is printed as alpha p1 + beta p2 + gamma p3 -> m for alpha, beta, gamma in {0, 1}. The all-zero
    case (-> m) is excluded, because with it the empty set would not be closed, contradicting the paper's
    organisations O = {{}, {m}, {m, p1, p2, p3}}.
  - Vector fields and simulation settings (molecules n, initial radius rad, reaction radius r, reacting
    fraction u, iterations) are recorded per example in extras.space, as strings and numbers; Chemart
    does not simulate them. The swirl field's square roots were lost in the PDF text and are read as V1
    = (1/sqrt 2)((1 - sqrt 2) x - y, x + (1 - sqrt 2) y), an inward spiral. For the swirl example the
    paper states both 2500 starting molecules and n = 1600; 2500 is recorded.
  - 'The previous parameters reactions, flow_field, diffusion and n_species are replaced by `example`
    and `k`: the paper uses flow instead of diffusion, and the networks are fixed per example. R2 and
    R3 carry no rates in the paper; they use the same k.'
  phenomena:
  - strongly inhomogeneous species distributions that a well-stirred or diffusive system does not show
    (patches of b in the swirl)
  - a membrane of m around a producer core, matching the organisations {m} and {m, p1, p2, p3}
  - two compartments forming from rock-scissors-paper competitors
  notes: 'Complements Swarm Chemistry: here motion is external and passive. Together they cover the two
    ways space enters an AC.

    '