chemart / brane-calculi

hub:
  repo_type: generator
  builtin: brane-calculi
  tags:
  - banzhaf-yamamoto
chemistries:
- id: brane-calculi
  name: Brane calculi
  intuition: 'Membranes as the active element rather than the container. A system is a nest of membranes,
    and each membrane carries a program of actions: phagocytosis engulfs a neighbour, exocytosis expels
    contents and fuses, pinocytosis buds an empty vesicle inward, mating fuses two membranes. A reaction
    is one such rearrangement of the nesting. The payoff is that viral entry and reproduction - engulf,
    fuse with the endosome, release, re-envelope - become short derivations rather than special cases.

    '
  aliases:
  - Phago/Exo/Pino calculus
  - Mate/Bud/Drip calculus
  - Basic Brane Calculus
  origin: Cardelli, 2004
  book: '9.7'
  refs:
  - '[157]'
  - '[269]'
  - doi:10.1007/978-3-540-25974-9_24
  family: rewriting
  kind: formalism
  constructive: true
  S:
    repr: 'a system is a nest of membranes s[P] whose branes s are compositions of actions (s|t, !s, a.s),
      plus free molecules; ASCII notation with '','' for the composition of systems (paper ∘), [ ] for
      membranes, co-actions prefixed ''co'' (paper ⊥) and p1(p2)=>q1(q2) for bind&release. A species is
      a whole configuration: the canonical text of the system normalised under structural congruence;
      its structure is the indented membrane tree

      '
    definition: implicit
    notes: 'Actions: phago_n, cophago_n(r), exo_n, coexo_n, pino(r) (section 3.1); mate_n, comate_n, bud_n,
      cobud_n(r), drip(r) (section 3.2); p1(p2)=>q1(q2) (section 4.1). Other identifiers on a brane are
      inert placeholders (the paper''s metavariables X, σ0, ρ); in a system they are molecules. Programs
      are definitions ''name := term'' (paper ≜) with ''main'' the initial system.

      '
  R:
    definition: implicit
    arity: 1
    scheme: 'one reduction step of the whole configuration: phago_n.s|s0[P], cophago_n(r).t|t0[Q] -> t|t0[r[s|s0[P]],
      Q]; coexo_n.t|t0[exo_n.s|s0[P], Q] -> P, s|s0|t|t0[Q]; pino(r).s|s0[P] -> s|s0[r[], P]; mate_n.s|s0[P],
      comate_n.t|t0[Q] -> s|s0|t|t0[P, Q]; cobud_n(r).t|t0[bud_n.s|s0[P], Q] -> r[s|s0[P]], t|t0[Q]; drip(r).s|s0[P]
      -> r[], s|s0[P]; p1, (p1(p2)=>q1(q2)).s|s0[p2, P] -> q1, s|s0[q2, P]

      '
    notes: 'Reactions happen in any context (P->Q gives P,R->Q,R and s[P]->s[Q]) up to structural congruence:
      commutative monoids (systems '','' with unit 0; branes ''|'' with unit 0), replication !P ≡ P,!P
      and !s ≡ s|!s, and 0[0] ≡ 0. No reduction under ''!'' except on an unfolded copy. Phago, Exo, Pino,
      Mate, Bud and Drip preserve the nesting parity of P and Q (bitonality); bind&release moves molecules
      across a membrane.

      '
  A:
    reactor: compartments
    dilution: none; configurations can grow without bound (replicated actions), so the closure is truncated
      by max_species
    notes: 'The calculus is qualitative and nondeterministic: no rates (the paper only suggests stochastic
      pi-calculus rates as future work). Chemart returns the reduction graph (reachable configurations
      and one reaction per step) from the initial system.

      '
  params:
  - name: system
    type: enum
    default: viral-infection
    choices:
    - viral-infection
    - viral-reproduction
    - viral-replication
    - eat-me
    - seek-and-store
    - plant-vacuole
    - custom
    role: structural
    meaning: 'published system of Cardelli 2004: viral-infection (sec. 3.3, fig. 7: virus, cell), viral-reproduction
      (sec. 3.3, fig. 8: membrane[nucap, envelope-vesicle, Z'']), viral-replication (sec. 4.6, fig. 11:
      nucap, cytosol with vRNA replication, capsomer translation and ER), eat-me and seek-and-store (sec.
      4.5), plant-vacuole (sec. 4.4, fig. 10, with ATP, Cl-, Na+ outside), custom (program)'
  - name: program
    type: str
    default: ''
    range: 'e.g. ''A := =>n.phago[P]

      B := n=>.cophago(rho)[Q]

      main := A, B'''
    role: structural
    meaning: 'custom only: definitions ''name := term'' (one per line, continuation lines allowed, # comments)
      that must define main, the initial system; syntax in the module docstring'
  - name: max_species
    type: int
    default: 1000
    min: 1
    max: 100000
    range: viral-infection closes at 4 configurations, viral-reproduction 4, eat-me 4, seek-and-store
      5, plant-vacuole 5; viral-replication is infinite (vRNA replication) and truncated
    role: structural
    meaning: budget of configurations in the reduction closure; beyond it the network is truncated
  provides:
  - topology
  - stoichiometry
  - compartments
  - initial-state
  - sequence-structure-function
  fidelity: reconstructed
  sources:
  - 'Banzhaf, W. & Yamamoto, L. (2015). Artificial Chemistries, section 9.7 (one paragraph: brane calculi
    as process calculi on nested membranes; endocytosis, exocytosis, budding, mating; viral infections,
    molecular pumps, ion channels; Fellermann et al. [269]).'
  - 'Cardelli, L. (2005). Brane calculi: interactions of biological membranes. In V. Danos & V. Schachter
    (eds.), Computational Methods in Systems Biology (CMSB 2004), LNCS 3082, pp. 257-278, Springer (book
    [157]). Author''s copy dated 2004-06-01: syntax and structural congruence (sec. 2.1), Phago/Exo/Pino
    (sec. 3.1, fig. 3), Mate/Bud/Drip and their encodings with derivations (sec. 3.2), viral infection
    part 1 with figs. 7-8 (sec. 3.3), bind&release (sec. 4.1), chemical reactions (4.2), plant vacuole
    (4.4), Eat Me and Seek and Store (4.5), viral infection part 2 (4.6). http://lucacardelli.name/Papers/Brane%20Calculi.pdf'
  decisions:
  - 'Source copy: the author''s 2004-06-01 PDF was used; pdftotext loses every calculus glyph (∘ ◇ ⦇⦈
    ⟲ ⊚ ⇉ ⊥), so all rules, definitions and derivations were read from rendered page images. The two exocytosis-like
    glyphs were told apart by the derivations themselves (virus = phago.exo[nucap]: Phago fires first
    in fig. 7, Exo last).'
  - '[269] (Fellermann, Hadorn, Bönzli & Rasmussen, Living Machines 2012, LNCS 7375 pp. 343-344) is a
    two-page poster abstract with no open copy; its follow-up is a different formalism (the chemtainer
    calculus, Fellermann & Cardelli, J. R. Soc. Interface 11:20130987, 2014) and is not implemented here.'
  - 'Calculus offered: Phago/Exo/Pino, Mate/Bud/Drip as primitives (the paper says they should be primitives
    in practice and derives them from PEP; the derivations are reproduced in the tests), and bind&release
    of molecule multisets (sec. 4.1). Not offered: complexes m1:m2 (4.7), communication, choice, In/Out/Wrap
    (sec. 5 extensions), restriction.'
  - 'Species granularity: a species is a whole configuration and every step is a unimolecular reaction
    configuration -> configuration. Sub-membranes cannot be species because Phago, Mate and bind&release
    are contextual (they need a sibling or molecules outside the membrane) and every membrane interaction
    rebuilds the enclosing term, so reactions on parts do not compose into a multiset CRN.'
  - 'Structural congruence is decided by a normal form: compositions flattened and sorted by canonical
    text, units and 0[0] dropped, ! distributed over composition and !! collapsed, and a replicated element
    absorbs its plain copies (P,!P ≡ !P); replicated elements form a set. Reduction under ! happens only
    on an unfolded copy, which leaves the replicated term in place.'
  - 'Names: omitted subscripts match each other (''we omit them when there is no ambiguity''); pino and
    drip may carry a name, which has no effect. Metavariables of the paper (X, Z, Z'', σ0, ρ, P, Q, Nucleus)
    are inert placeholders: identifiers on a brane that are not actions, or molecules in a system.'
  - 'Errata in the derivations of sec. 3.2 (page 6): Mate''s second step prints ⟲⊥n''''.τ|τ0⦇⟲n''''|σ|σ0⦇◇⦈⦈
    P ∘ Q⦈, whose extra bracket must be removed (coexo_n''''.t|t0[exo_n''''|s|s0[], P, Q], what the Exo
    rule gives); the Drip definition prints an unbalanced ⊚(⊚(ρ).⟲n)).⟲⊥n.σ, read as pino(pino(r).exo_n).coexo_n.s
    as its derivation requires.'
  - viral-reproduction starts from membrane[nucap, envelope-vesicle, Z'] with the section 3.3 definitions
    (nucap = !bud|X[vRNA]); after budding, the new virus can be phagocytosed again by the same membrane,
    a branch the paper does not discuss (it is stuck without an endosome in Z').
  - viral-replication uses the section 4.6 definitions; vRNA-repl, written in the paper as the chemical
    reaction vRNA -> vRNA ∘ vRNA, is the section 4.2 encoding !vRNA=>vRNA,vRNA[] (an empty catalyst membrane).
    Its closure is infinite and truncated by max_species.
  - 'plant-vacuole: the paper defines the vacuole membrane (proton pump, ion channel, proton antiporter)
    but no environment; Chemart puts one ATP, one Cl- and one Na+ outside an empty vacuole. Ion names
    are ASCII (Cl- for Cl–).'
  - 'Rates: none; the calculus is qualitative. max_species replaces any simulation size. extras: system,
    program, definitions, main, reaction_rules (the rule of each reaction: phago, exo, pino, mate, bud,
    drip, bind&release), compartments (membrane tree of the initial configuration) and analysis (the published
    configurations with whether they are reached, terminal configurations of complete closures, and for
    viral-replication the largest numbers of nucap and envelope-vesicle copies).'
  phenomena:
  - 'viral infection (fig. 7): virus, cell -> Phago -> Mate with the endosome -> Exo, leaving membrane[nucap,
    cytosol]: the nucleocapsid reaches the cytosol'
  - 'viral reproduction (fig. 8): an envelope vesicle fuses by Exo with the cell membrane, which then
    buds the nucleocapsid out as a new virus'
  - 'nucleocapsid replication (sec. 4.6): disassembly releases vRNA, which is replicated, translated into
    capsomers that assemble new nucaps (B&R, Drip, B&R) and into envelope vesicles by the ER (B&R, Drip)'
  - Mate, Bud and Drip are derivable from Phago, Exo and Pino with the three-step encodings of sec. 3.2
  - 'bitonality: Phago, Exo, Pino, Mate, Bud and Drip preserve the nesting parity of every subsystem'
  - molecular pumps and channels (sec. 4.4) and molecularly triggered membrane interactions (Eat Me, Seek
    and Store, sec. 4.5)
  notes: 'Contrast with P systems: the membrane is the active element, not the container. The module exports
    parse_system, parse_brane, parse_program, steps (one-step reductions), reachable, layout, tree, membranes
    and molecule_parities for direct use.

    '