chemart / oregonator

hub:
  repo_type: generator
  builtin: oregonator
  tags:
  - banzhaf-yamamoto
chemistries:
- id: oregonator
  name: Oregonator (Belousov-Zhabotinsky)
  intuition: 'The reduced model of the Belousov-Zhabotinsky reaction - a real chemical oscillator, not
    an invented one. Five reactions couple an autocatalytic species, an inhibitor and an oxidised metal
    ion, with two reactants buffered; the autocatalysis fires, exhausts itself, regenerates the inhibitor
    and waits. Add diffusion and it becomes an excitable medium supporting target patterns and spiral
    waves, which is the basis of reaction-diffusion computing.

    '
  origin: Field & Noyes, 1974
  book: 19.3.3
  refs:
  - '[276]'
  - '[9]'
  - '[13]'
  - '[813]'
  - '[857]'
  family: wet
  kind: generator
  constructive: false
  S:
    repr: A, B (buffered reactants), X (autocatalyst, HBrO2), Y (inhibitor, Br-), Z (oxidised metal ion,
      e.g. Ce(IV)), P, Q (products)
    definition: explicit
  R:
    definition: explicit
    arity:
    - 1
    - 2
    scheme: A + Y --k1--> X ; X + Y --k2--> P ; B + X --k3--> 2X + Z ; 2X --k4--> Q ; Z --k5--> f Y
  A:
    reactor:
    - ode
    - lattice-2d
    dilution: A and B buffered; reaction-diffusion on a grid for spatial patterns
  params:
  - name: k1
    type: float
    default: 1.0
    min: 0
    role: kinetic
    meaning: A + Y -> X
  - name: k2
    type: float
    default: 10.0
    min: 0
    role: kinetic
    meaning: X + Y -> P
  - name: k3
    type: float
    default: 10.0
    min: 0
    role: kinetic
    meaning: B + X -> 2X + Z
  - name: k4
    type: float
    default: 2.5
    min: 0
    role: kinetic
    meaning: 2X -> Q
  - name: k5
    type: float
    default: 1.0
    min: 0
    role: kinetic
    meaning: Z -> f Y
  - name: f
    type: float
    default: 1.0
    min: 0
    role: kinetic
    meaning: stoichiometric factor of inhibitor regeneration; the key bifurcation parameter
  - name: A
    type: float
    default: 1.0
    min: 0
    role: population
    meaning: buffered concentration of A
  - name: B
    type: float
    default: 1.0
    min: 0
    role: population
    meaning: buffered concentration of B
  - name: D
    type: dict
    default:
      X: 1.0
      Y: 1.0
      Z: 1.0
    role: spatial
    meaning: diffusion coefficient per species for the reaction-diffusion setting
  - name: lattice
    type: enum
    default: hexagonal
    choices:
    - square
    - hexagonal
    role: spatial
    meaning: grid used for reaction-diffusion (the book's patterns use a hexagonal grid)
  provides:
  - topology
  - stoichiometry
  - catalysts
  - rate-constants
  - space
  - initial-state
  fidelity: book+decisions
  decisions:
  - Rate constants are the book's (figure 19.20). f, the buffered concentrations A and B, and the diffusion
    coefficients are not given; defaults are f = 1, A = B = 1, D = 1.
  - A real f cannot be an integer stoichiometric coefficient. Z -> f Y is emitted as Z -> floor(f) Y at
    rate k5 (1 - frac(f)) plus Z -> (floor(f)+1) Y at rate k5 frac(f), which gives exactly the same rate
    equations.
  - Space is recorded in extras.space (lattice, diffusion); A and B are listed in extras.buffered.
  reference_impl: an early PyCellChemistry variant on the Breve simulator
  phenomena:
  - target patterns and spiral waves
  - excitable medium supporting reaction-diffusion computing (logic gates, image processing, maze solving)