chemart / dorin-korb-ecosystem

hub:
  repo_type: generator
  builtin: dorin-korb-ecosystem
  tags:
  - banzhaf-yamamoto
chemistries:
- id: dorin-korb-ecosystem
  name: Dorin & Korb virtual ecosystem chemistry
  intuition: 'An ecosystem whose bookkeeping goes all the way down to atoms. Square atoms drift on a grid
    and bond covalently; each bond type stores or releases a definite energy, and four catalysts make
    or break specific bonds - one chlorophyll-like catalyst fixes sunlight into an A-B ''sugar'' bond,
    others decompose organic and inorganic matter. Because the atom inventory is closed and energy is
    tracked exactly, a trophic structure of producers and decomposers appears from conservation alone
    rather than being modelled.

    '
  origin: Dorin & Korb, 2007
  book: 8.2.3
  refs:
  - '[240]'
  - doi:10.1007/978-3-540-74913-4_11
  - https://bridges.monash.edu/articles/report/Building_Virtual_Ecosystems_from_Artificial_Chemistry/20365353
  family: spatial
  kind: generator
  constructive: true
  S:
    repr: molecules = covalently bonded clusters of square virtual atoms from {A, B, C, O} plus the four
      catalyst atoms {K, EAB, ECC, EO}, identified by the canonical (isomorphism-invariant) bond graph
    definition: implicit
    notes: 'valences come from the appendix''s electron shells (A:1, B:2:3, O:2:1, C:2:4:4, K:2:2, enzymes
      2:2) and rule 2 (a bond needs both a free outer electron and a free slot): A, B, O are monovalent,
      C tetravalent, every catalyst divalent'
  R:
    definition: implicit
    arity:
    - 1
    - 2
    scheme: 'One bond of table 1 made or broken per event, between two atoms that share a grid edge: A-B,
      C-C, A-O, B-O, C-O. Making a bond releases its bond energy and breaking it costs the same, so the
      negative bonds (A-B "sugar", C-C "biomass") are the ones that store energy. The paper''s three named
      reactions follow: AO + BO -(K, sunlight)-> AB + 2 O (photosynthesis), O + AB -(EAB)-> A + BO + energy
      (respiration), C + C -(energy)-> C2 (biosynthesis).

      '
    notes: 'a catalyst acts when one of the two reacting atoms neighbours it: K makes A-B and breaks A-O
      and B-O, EAB breaks A-B, ECC breaks C-C and makes C-O, EO breaks A-O and B-O; a reaction whose neighbourhood
      lacks the energy cannot proceed; released energy must be used in the same time step or is lost;
      energy can only be stored in complex molecules'
  A:
    reactor: lattice-2d
    dilution: 'none: the atom inventory is closed, so every atom count is conserved exactly'
    notes: 'each step: molecules drift one square (rigid, no collisions), then every adjacent pair is
      tried in random order; energy released is pooled in the spatially contiguous cluster of atoms around
      the site and sunlight (a sin function of time, per atom) is added to it for chlorophyll-catalysed
      reactions only'
  params:
  - name: width
    type: int
    default: 18
    min: 4
    max: 400
    range: paper-scale grids are hundreds of cells wide
    role: spatial
    meaning: grid width in cells (one square atom per cell)
  - name: height
    type: int
    default: 18
    min: 4
    max: 400
    role: spatial
    meaning: grid height in cells
  - name: steps
    type: int
    default: 150
    min: 0
    max: 100000
    range: long runs use thousands of steps
    role: population
    meaning: simulation time steps; one step is one movement phase followed by one reaction phase
  - name: atoms
    type: dict
    default:
      A: 28
      B: 28
      O: 36
      C: 24
    role: structural
    meaning: initial number of free atoms of each building block A, B, C, O
  - name: catalysts
    type: dict
    default:
      K: 4
      EAB: 4
      ECC: 4
      EO: 4
    role: structural
    meaning: 'initial number of free catalyst atoms: K chlorophyll, EAB sugar-breaker, ECC organic decomposer,
      EO inorganic decomposer'
  - name: structures
    type: enum
    default: all
    choices:
    - none
    - photoautotroph
    - decomposer
    - all
    role: structural
    meaning: 'which of the paper''s organism bodies to seed: the figure 5 photosynthetic autotroph (a
      C box with chlorophyll and the sugar enzyme on opposite inner walls around a vacuole) and the figure
      6 decomposer (a C-C body carrying ECC on a C-O spacer)'
  - name: light_amplitude
    type: float
    default: 8.0
    min: 0.0
    role: thermodynamic
    meaning: peak sunlight energy incident per atom per step; 0 switches the light off
  - name: light_period
    type: float
    default: 24.0
    min: 1.0
    role: thermodynamic
    meaning: period in steps of the sin function that governs incident sunlight
  - name: energy_high
    type: int
    default: 8
    min: 2
    max: 1000
    role: thermodynamic
    meaning: the magnitude table 1 calls 'high' (the A-B sugar bond energy)
  - name: energy_low
    type: int
    default: 1
    min: 1
    max: 999
    role: thermodynamic
    meaning: the magnitude table 1 calls 'low' (C-C, A-O, B-O and C-O bond energies)
  - name: p_low
    type: float
    default: 0.01
    min: 0.0
    max: 1.0
    role: kinetic
    meaning: per-step probability table 1 calls 'low'
  - name: p_moderate
    type: float
    default: 0.1
    min: 0.0
    max: 1.0
    role: kinetic
    meaning: per-step probability table 1 calls 'moderate'
  - name: p_high
    type: float
    default: 0.9
    min: 0.0
    max: 1.0
    role: kinetic
    meaning: per-step probability table 1 calls 'high', including every catalysed entry
  - name: move_probability
    type: float
    default: 0.8
    min: 0.0
    max: 1.0
    role: spatial
    meaning: probability that a molecule attempts a one-square move in a random direction in a step
  provides:
  - topology
  - stoichiometry
  - catalysts
  - energies
  - mass-conservation
  - space
  - initial-state
  fidelity: reconstructed
  sources:
  - Dorin, A. & Korb, K. B. (2007). Building Virtual Ecosystems from Artificial Chemistry. Advances in
    Artificial Life (ECAL 2007), LNCS 4648, 103-112. https://doi.org/10.1007/978-3-540-74913-4_11
  - 'Dorin, A. & Korb, K. B. (2007). Building Virtual Ecosystems from Artificial Chemistry. Monash University
    Technical Report 2007/212 (the full version, used here): table 1 (the bond table), sections 2.1-2.2
    (catalysts, energy neighbourhoods, sunlight, movement), sections 3.1.1-3.1.3 (photosynthesis, respiration,
    biosynthesis), figures 5-6 (autotroph and decomposer bodies) and the appendix (bonding rules, electron
    shells, known atoms and molecules). https://bridges.monash.edu/articles/report/Building_Virtual_Ecosystems_from_Artificial_Chemistry/20365353'
  decisions:
  - 'The paper gives no numbers: table 1 grades probabilities as low/moderate/high and bond energies as
    +/- low/high, and section 4 states that no run with all organism types had been performed, so nothing
    quantitative is published. The three levels are parameters (p_low 0.01, p_moderate 0.1, p_high 0.9)
    and so are the two magnitudes (energy_low 1, energy_high 8). Energies are integers so that the energy
    ledger balances exactly.'
  - 'Table 1 is implemented verbatim, including two entries the book''s summary omits: ECC also catalyses
    *making* C-O bonds (the spacer of the figure 6 decomposer), and the catalysed break of A-O and B-O
    is credited to chlorophyll as well as to the inorganic enzyme.'
  - Table 1 names enzAO and enzBO separately, but section 2.1 counts four catalyst types, so one inorganic
    decomposer EO covers both A-O and B-O. The appendix names four enzymes EA-ED without mapping them
    to functions; catalysts are named for their function here (K chlorophyll, EAB, ECC, EO).
  - 'Valences are derived, not assumed: appendix rule 2 (a bond needs a free outer-shell electron and
    a free slot) with shell capacities 2, 4, 8 gives A 1, B 1, O 1, C 4, K 2, enzymes 2, which is what
    the appendix''s known molecules (A-B, A-O, B-O ''one only since O has run out of electrons'', C chains,
    K-C-K) show.'
  - Only the five bonds of table 1 form or break. The appendix's K-C anchor bonds have no probabilities
    or energy, so bonds inside a seeded organism body are static anchors that never react ('any otherwise
    legal bond the Designer God doesn't want can simply be made to hurdle an absurd energy threshold').
  - 'Energy pools are spatial, not per molecule: section 2.1 says released energy reaches ''any continuous
    atomic structure that contacts directly or indirectly (through intermediate neighbours) the reaction
    site'', so the pool is the contact cluster of touching atoms. This is what lets respiration at an
    enzyme wall pay for biosynthesis elsewhere in the body. Atoms do not move during the reaction phase,
    so the clusters are fixed while reactions fire.'
  - 'Sunlight is ''incident on all atoms at a rate governed by a parameterized sin function'': each cluster
    receives floor(light_amplitude * max(0, sin(2 pi t / light_period)) * atoms) per step, spendable only
    by chlorophyll-catalysed reactions. Light is spent before the bond-energy pool, and anything left
    in either pool at the end of a step is dissipated.'
  - The grid is a torus and the neighbourhood is von Neumann (atoms are squares that bond along shared
    edges). Movement is per molecule, rigid, one square, rejected on any collision.
  - Species identity is the canonical bond graph, so lattice conformation (how a molecule is folded on
    the grid) is not part of it, while constitutional isomers with different bond graphs are different
    species. Ids are the atom formula for one- and two-atom molecules and formula plus a certificate hash
    beyond that.
  - The network is the set of reactions that fired in one run (status observed, with counts). Catalysts
    appear on both sides whenever the catalysing atom belongs to a molecule that is not itself a reactant.
  - 'Photosynthesis is three elementary bond events, not one: chlorophyll breaks A-O and breaks B-O, then
    makes A-B, so the freed A and B compete with the ''high'' probability of re-forming A-O and B-O. The
    sugar yield therefore turns on a ratio table 1 leaves unquantified. In the soup, where A and B are
    plentiful, sugar is made steadily; an isolated figure 5 autotroph, whose vacuole holds one A and one
    B, makes it only in some runs (seed 5 at the default parameters is one).'
  - 'A free C can only bond where a reaction has just released energy into its contact cluster, so biomass
    and its decomposition concentrate around the seeded bodies and dense patches. The default therefore
    seeds both organism bodies (structures: all); with structures: none the soup is lively but builds
    almost no C-C biomass.'
  phenomena:
  - 'a trophic structure emerges from atom-level bookkeeping: chlorophyll fixes sunlight into A-B sugar
    bonds, the sugar enzyme releases that energy again, the released energy pays for C-C biosynthesis,
    and the decomposers break C-C and A-O/B-O bonds to return atoms to the inorganic pool'
  - 'sugar is made only where energy is available: sunlight is the main source that can pay the high A-B
    bond energy, so with the light switched off no A-B bond forms at the default density; in denser soups
    the energy released by forming A-O and B-O bonds occasionally pays for one'
  - 'the figure 5 autotroph can make and respire sugar on its own: with nothing else on the grid, the
    chlorophyll on one inner wall turns the A-O and B-O trapped in its vacuole into A-B sugar, and the
    enzyme on the opposite wall respires that sugar again (in some runs; with no free C there is no biosynthesis)'
  - atoms are never created or destroyed, and every joule is either stored in a bond, spent on one, or
    dissipated in the step it was released
  notes: 'The paper is a feasibility argument rather than a results paper: it specifies the chemistry
    and hand-designs organism bodies, and states that a run with all organism types present had not yet
    been done.

    '