chemart / ono-ikegami-protocell

hub:
  repo_type: generator
  builtin: ono-ikegami-protocell
  tags:
  - banzhaf-yamamoto
chemistries:
- id: ono-ikegami-protocell
  name: Ono & Ikegami autopoietic protocells
  intuition: 'Protocells from nothing but hydrophobicity. Five particle types sit on a lattice - an autocatalyst,
    membrane particles, food, waste and water - with an autocatalyst that reproduces and also makes membrane
    material, and decay that returns everything to waste and back to food. Membrane particles repel water
    and so cluster; give them an orientation and the clusters become filaments that close into compartments.
    The enclosure retains the autocatalyst while food and waste pass through. There is no genetic material
    and no evolution mechanism (book 6.3.2), although the autocatalyst replicates and the published protocells
    grow and divide.

    '
  origin: Ono & Ikegami, 1999-2003
  book: 6.3.2
  refs:
  - '[637]'
  - '[639]'
  - '[641]'
  - '[538]'
  family: origin-of-life
  kind: generator
  constructive: false
  S:
    repr: five species A (autocatalyst, hydrophilic), M (membrane, hydrophobic, isotropic M_i or anisotropic
      M_a carrying one of the six lattice orientations), X (food, neutral), Y (waste, neutral), W (water,
      hydrophilic), one particle per cell of a hexagonal torus
    definition: explicit
  R:
    definition: explicit
    arity:
    - 1
    - 2
    scheme: A + X -> 2 A ; A + X -> A + M ; A -> Y, M -> Y, X -> Y (decay) ; Y -> X (recycling by an external
      energy source)
    notes: plus hydrophobic/hydrophilic repulsion; an anisotropic M_a spreads the same total repulsion
      unevenly over the six directions, which is what turns membrane clusters into filaments
  A:
    reactor: lattice-2d
    dilution: 'none: the lattice is closed and every cell holds exactly one particle; the external energy
      source enters as the recycling reaction Y -> X, whose rate X_supply is the food supply'
    notes: Kawasaki exchange with a neighbour plus rotation of M_a, both accepted with the Metropolis
      rule min(1, exp(-dE/T)); the reactions are then applied cell by cell
  params:
  - name: mode
    type: enum
    default: spatial
    choices:
    - spatial
    - reactions
    role: structural
    meaning: '''reactions'' returns the four-reaction network on its own; ''spatial'' runs the lattice
      and returns the reactions that fired with their counts, plus the lattice, the energies and the protocell
      measurements'
  - name: membrane
    type: enum
    default: anisotropic
    choices:
    - anisotropic
    - isotropic
    role: structural
    meaning: whether membrane particles are the anisotropic M_a or the isotropic M_i; the book's central
      result is that only M_a sustains protocells at low food supply
  - name: width
    type: int
    default: 24
    min: 6
    max: 200
    role: spatial
    meaning: lattice width in cells (axial r); the papers use a few hundred
  - name: height
    type: int
    default: 24
    min: 6
    max: 200
    role: spatial
    meaning: lattice height in cells (axial q)
  - name: steps
    type: int
    default: 100
    min: 1
    max: 20000
    role: population
    meaning: lattice sweeps; each sweep does six Metropolis exchange passes, one rotation pass and one
      chemistry pass
  - name: relaxation
    type: int
    default: 12
    min: 1
    max: 200
    role: spatial
    meaning: Metropolis exchange passes per chemistry pass; this is where the paper's separation between
      the mobility rates (7e-3) and the reaction rates (1e-4) enters, so particles demix long before they
      react
  - name: initial
    type: enum
    default: random
    choices:
    - random
    - cell
    role: population
    meaning: '''random'' is a well-mixed start (the papers'' homogeneous experiment); ''cell'' prepares
      a membrane ring around autocatalyst and food (their cell-like experiment)'
  - name: cell_radius
    type: int
    default: 5
    min: 1
    max: 60
    role: spatial
    meaning: radius in cells of the prepared membrane ring when initial = cell
  - name: A_fraction
    type: float
    default: 0.08
    min: 0
    max: 1
    role: population
    meaning: fraction of cells seeded with autocatalyst A when initial = random
  - name: X_fraction
    type: float
    default: 0.3
    min: 0
    max: 1
    role: population
    meaning: fraction of cells seeded with food X; the rest of the lattice is water W
  - name: M_fraction
    type: float
    default: 0.0
    min: 0
    max: 1
    role: population
    meaning: fraction of cells seeded with membrane M when initial = random; non-zero starts from dispersed
      membrane particles, so their self-assembly can be watched on its own
  - name: P_A
    type: float
    default: 0.03
    min: 0
    max: 1
    role: kinetic
    meaning: probability per sweep and per neighbouring A that a food particle replicates it (A + X ->
      2 A); the paper's reproduction rate of A
  - name: P_M
    type: float
    default: 0.03
    min: 0
    max: 1
    role: kinetic
    meaning: probability per sweep and per neighbouring A that a food particle becomes membrane (A + X
      -> A + M); the paper's production rate of M
  - name: P_decay
    type: float
    default: 0.01
    min: 0
    max: 1
    role: kinetic
    meaning: probability per sweep that an A, M or X particle decays to waste Y; water never decays
  - name: X_supply
    type: float
    default: 0.3
    min: 0
    max: 1
    role: kinetic
    meaning: probability per sweep that waste is recycled to food (Y -> X) by the external energy source;
      the decisive resource-supply parameter, low values being the regime where anisotropy pays off
  - name: anisotropy
    type: float
    default: 2.4
    min: 0
    max: 3
    role: spatial
    meaning: 'strength a of the directional part of the M_a repulsion field, F[k, o] = 1 + a cos(2 * 60deg
      * (k - o)): repulsion is strongest along the +-o axis and weakest on the four flanks, where it turns
      attractive once a > 2, so a membrane particle wants membrane neighbours along its axis and water
      on both flanks; 0 makes M_a behave like M_i'
  - name: repulsion
    type: float
    default: 1.0
    min: 0
    role: thermodynamic
    meaning: energy of one hydrophilic/hydrophobic neighbour pair, in units of the temperature
  - name: neutral_coupling
    type: float
    default: 0.25
    min: 0
    max: 1
    role: thermodynamic
    meaning: energy of a neutral/hydrophobic pair as a fraction of `repulsion`; this weak coupling is
      what lets X and Y cross a membrane that holds A back
  - name: temperature
    type: float
    default: 1.0
    min: 0.01
    role: thermodynamic
    meaning: Metropolis temperature T in min(1, exp(-dE/T))
  - name: mobility_ratio
    type: float
    default: 1.0
    min: 1
    role: spatial
    meaning: 'the paper''s m: exchanges involving A are attempted with probability 1/m, making the autocatalyst
      less mobile than membrane and food; the 1D paper needs m = 5 for a cell to divide'
  provides:
  - topology
  - stoichiometry
  - catalysts
  - space
  - energies
  - initial-state
  fidelity: reconstructed
  sources:
  - Ono, N. & Ikegami, T. (2000). Self-maintenance and self-reproduction in an abstract cell model. J.
    theor. Biol. 206:243-253, doi:10.1006/jtbi.2000.2121. Full text from the authors' lab archive, http://sacral.c.u-tokyo.ac.jp/pdf/ono_jtheorbiol_2000.pdf
    (via the Wayback Machine). Appendix A gives the reaction and mobility rules and every constant; appendix
    B the mean-field equations; figures 5, 7, 8 and 10 the phase diagram and the parameter values of each
    regime.
  - Banzhaf, W. & Yamamoto, L. (2015). Artificial Chemistries, MIT Press, section 6.3.2 and figures 6.13,
    6.14 - the five-species hexagonal model, the isotropic/anisotropic repulsion fields, and the low-supply
    result.
  decisions:
  - The book describes the two-dimensional hexagonal model of [639]/[641]; those papers, the BioSystems
    study [637] and the 3D extension [538] are all paywalled and were not obtainable (no open copy per
    OpenAlex/Unpaywall/Semantic Scholar, and the Internet Archive was offline during this work). The accessible
    primary source is the authors' 1D predecessor, Ono & Ikegami (2000), whose appendix A supplies the
    lattice algorithm reconstructed here.
  - That 1D model runs a different reaction scheme - it inserts an enzyme E (A + A -> A + E, E + R ->
    E + A, E + R -> E + M) and its resource/waste are R and W, whereas the book's 2D model has A act directly
    and names the five species A, M, X, Y, W. The implemented reaction set is the book's; the 1D constants
    (P_E = 0.5e-6, P_A' = 2e-6, P_R = P_W = 100e-6, P_D = 7e-3, P_R0 = 5e-3, P_R1 = 0.5 P_R0, m = 1 or
    5) therefore do NOT apply to it and are recorded, with the phase-diagram points of figures 4, 7 and
    10, in extras.reference_rates rather than used as rate constants.
  - 'Consequently every reaction carries rate = None: no accessible source publishes a rate for this scheme.
    P_A, P_M, P_decay and X_supply are simulation probabilities per sweep whose defaults were chosen so
    the zero-argument run is small and fast, and are not published values.'
  - Ono & Ikegami coarse-grain space into sites holding 100 particles each. Here each cell of the hexagonal
    torus holds exactly one particle, which is what lets M_a carry the orientation the book's figure 6.13
    requires, and particles move by Kawasaki exchange under the Metropolis rule instead of the paper's
    probability-proportional hopping. Both conserve the occupancy of every cell, which is the property
    the paper's swap rule exists to enforce.
  - 'The anisotropic field is nematic, F[k, o] = 1 + a cos(2 * 60deg * (k - o)), with mean 1 over the
    six directions, so M_i and M_a carry the same total repulsion and differ only in how it is distributed:
    strongest along the +-o axis, weakest on the four flanks. The book''s figure 6.13 shows a darker (more
    repulsive) direction around M_a and gives no formula; the 180-degree-symmetric form was chosen because
    a membrane has two equivalent sides. The default a = 2.4 is past the point where the flank term goes
    negative, which is what distinguishes a membrane from a droplet: a purely repulsive M_i minimises
    its water contact and collapses into a compact blob, whereas an amphiphilic M_a wants membrane neighbours
    along its axis and water on both flanks, giving the one-particle-thick filaments the book describes.'
  - 'Equation (A.8) of the 2000 paper appears to divide the membrane mobility by m as well, which contradicts
    its own section 3.3 and the caption of figure 10 (''A and E particles have lower diffusion and repulsion
    rates than M and R''). The prose is followed: mobility_ratio slows only A.'
  - Equations (B.1) and (B.2) write the spontaneous resource-to-autocatalyst term as P_A' W_0 although
    (A.2) makes it proportional to the local resource; that term is not part of the book's scheme, so
    the discrepancy is recorded but not implemented.
  - 'What this implementation does and does not reproduce. Reproduced and tested: membrane particles demix
    from water; isotropic M_i collapses into compact droplets while anisotropic M_a builds thin, orientationally
    ordered filaments (the contrast of figure 6.14); and the metabolism collapses when the recycling of
    waste into food is switched off. NOT reproduced: filaments closing into protocells, the osmotic permeability
    of a closed membrane to X and Y while it retains A, and growth followed by division. Prepared membrane
    rings dissolve rather than persisting, and no enclosed compartment ever retained autocatalyst. Those
    three phenomena are the results of [639]/[641], whose lattice rules were not obtainable, so they are
    listed in `phenomena` as published claims but are not asserted by the tests.'
  - 'The v1 parameters are replaced: grid becomes width/height, rate_constants becomes the four probabilities
    above, repulsion_strength becomes repulsion/neutral_coupling/temperature, anisotropy becomes the enum
    `membrane` plus the strength `anisotropy`, and dimensions is dropped because only the 2D model is
    implemented ([538]''s 3D lattice was not obtainable). The v1 claims of rate-constants and flow are
    dropped: no rate is published, and the lattice is closed rather than a flow reactor.'
  phenomena:
  - membrane particles demix from water into clusters; with anisotropic M_a the clusters are filaments
    that close into protocells
  - a closed membrane is osmotically permeable to the neutral X and Y but holds the hydrophilic A back,
    so a metabolism persists inside
  - a protocell grows and divides while its internal metabolism continues
  - isotropic M_i gives clusters that shrink and die out, anisotropic M_a gives dividing protocells; the
    advantage is clearest at low X supply (book figure 6.14)
  - without recycling of waste into food the cell starves and collapses
  - '3D: parallel membranes with tubular connections, and intertwined globular filaments (not implemented)'
  notes: 'No genetic material and no evolution mechanism - a self-maintenance model rather than a replicator
    model, which is why the book uses it to close the protocell discussion rather than the origin-of-information
    one.

    '