chemart / self-propelled-droplets

hub:
  repo_type: generator
  builtin: self-propelled-droplets
  tags:
  - banzhaf-yamamoto
chemistries:
- id: self-propelled-droplets
  name: Self-propelled oil droplets
  intuition: 'Chemistry that moves itself. An oil droplet carries a precursor that hydrolyses at the oil-water
    interface into surfactant and protons. The local pH drop changes the interfacial tension unevenly
    around the droplet, and that gradient drives a Marangoni flow which pushes the droplet along - and
    it will climb a pH gradient, which looks like chemotaxis. There is no genome, no replication and nothing
    being copied: what is ''processed'' is the chemistry and its own local environment.

    '
  origin: Hanczyc et al., 2007-2011
  book: 19.2.5
  refs:
  - '[363]'
  - '[364]'
  - '[365]'
  - '[403]'
  - '[858]'
  - '[483]'
  - '[885]'
  family: wet
  kind: wet
  constructive: false
  S:
    repr: an oil droplet carrying a precursor, in an aqueous surfactant phase; the species are the five
      or six chemicals of the published experiment (precursor, water, surfactant acid and anion, proton,
      inert oil solvent)
    definition: explicit
  R:
    definition: explicit
    arity:
    - 1
    - 2
    - 3
    scheme: oleic_anhydride + H2O -> 2 oleic_acid ; oleic_acid -> oleate + H (hydrolysis at the oil-water
      interface makes surfactant and protons; the local drop in pH raises the interfacial tension, which
      is the Marangoni force that propels the droplet)
    notes: 'the motion is not a reaction: the propulsion mechanism, the tension relation and the measured
      behaviour are recorded in extras.interaction_law, extras.analysis and extras.space. The `decanol-salt`
      system has no reactive chemistry at all and returns an empty reaction list.'
  A:
    reactor: continuous-space
    dilution: 'none: a shallow dish of aqueous surfactant, closed after the droplet is added. In the `fuel-surfactant`
      system the fuel is exogenous and the catalyst is not consumed, so the motion is not limited by the
      droplet''s own volume.'
    notes: Chemart returns the interfacial reaction network of the published experiment plus the published
      assay geometry; it does not integrate a droplet trajectory, because no accessible source publishes
      the force law (see decisions).
  params:
  - name: system
    type: enum
    default: oleic-anhydride
    choices:
    - oleic-anhydride
    - fuel-surfactant
    - maze-chemotaxis
    - decanol-salt
    role: structural
    meaning: 'which published droplet chemistry to return: `oleic-anhydride` is the canonical Hanczyc
      system (onboard fuel, refs [365] [364]), `fuel-surfactant` is Toyota et al.''s onboard-catalyst
      droplet fed by exogenous fuel ([858]), `maze-chemotaxis` is Lagzi et al.''s acid/base maze solver
      ([483]), and `decanol-salt` is Cejkova et al.''s decanol droplet in a NaCl gradient ([885]), which
      has no reactive chemistry and therefore no reactions'
  - name: droplet_volume_uL
    type: float
    default: 20.0
    min: 0.001
    max: 1000.0
    role: spatial
    meaning: volume of the droplet in microlitres (1 uL = 1 mm^3); it fixes the radius, the interfacial
      area and the surface-to-volume ratio, which is what sets the reaction rate because the reaction
      is interfacial, and it selects the published behavioural modes for that size
    range: Horibe et al. (2011) use 1, 3, 10, 20, 30 and 50 uL; Hanczyc & Ikegami (2010) show 1, 5, 10
      and 30 uL and report droplets from a few hundred microns to a few centimetres across
  - name: precursor_M
    type: float
    default: 0.5
    min: 0.0
    max: 20.0
    role: population
    meaning: concentration of the precursor in the oil phase, in mol/L; 0.5 M oleic anhydride in nitrobenzene
      is the published loading. Ignored by `decanol-salt`, which has no precursor.
    range: Hanczyc & Ikegami (2010) appendix A.2 use 0.5 M; Horibe et al. (2011) mix oleic anhydride with
      nitrobenzene 1:1 v/v
  - name: surfactant_mM
    type: float
    default: 10.0
    min: 0.0
    max: 1000.0
    role: population
    meaning: concentration of the surfactant already present in the aqueous phase, in mM (oleate micelles
      for the oleic-anhydride system, sodium decanoate for decanol-salt, the dispersed fuel precursor
      for fuel-surfactant)
    range: 10 mM oleate at pH 11 in every run of Hanczyc & Ikegami (2010) and Horibe et al. (2011)
  - name: pH
    type: float
    default: 11.0
    min: 0.0
    max: 14.0
    role: thermodynamic
    meaning: pH of the bulk aqueous phase, which fixes the proton concentration in the initial state;
      the published droplets run at pH 11, well above the pH 9 tension maximum, so it is the local acidification
      by the droplet's own protons that breaks the symmetry
    range: pH 11, NaOH-adjusted; the local pH around a moving droplet was measured to fall as low as 7
  provides:
  - topology
  - stoichiometry
  - catalysts
  - mass-conservation
  - space
  - initial-state
  fidelity: reconstructed
  sources:
  - 'M. M. Hanczyc and T. Ikegami (2010). Chemical basis for minimal cognition. Artificial Life 16(3):233-243,
    doi:10.1162/artl_a_00002. Recovered from the Wayback Machine: https://web.archive.org/web/2019id_/https://www.mitpressjournals.org/doi/pdf/10.1162/artl_a_00002
    - the full chemical system, the Marangoni mechanism step by step, the pendant-drop tensiometry of
    figure 2 (27 mN/m for bare nitrobenzene at pH 11, tension maximum at pH 9, local pH falling to 7),
    the droplet size range and the appendix''s materials and methods (0.5 M oleic anhydride in nitrobenzene;
    10 mM oleate at pH 11).'
  - N. Horibe, M. M. Hanczyc and T. Ikegami (2011). Mode switching and collective behavior in chemical
    oil droplets. Entropy 13(3):709-719, doi:10.3390/e13030709 (open access) - the four behavioural modes
    and which droplet sizes show them, the 1/3/10/20/30/50 uL size series, the coefficient-of-restitution
    measurements, the two-droplet attraction at 3 and 20 uL but not at 50 uL, and the experimental section's
    1:1 v/v oil and dish geometries.
  - 'M. M. Hanczyc (2014). Droplets: unconventional protocell model with life-like dynamics and room to
    grow. Life 4(4):1038-1049, doi:10.3390/life4041038 (open access, PMC4284481) - the three configurations
    of self-moving droplets (no reactive chemistry / onboard fuel / onboard catalyst), the identification
    of the maze-solving droplets as dichloromethane with 2-hexyldecanoic acid, and the statement that
    onboard-fuel droplets move for minutes to hours.'
  - 'M. M. Hanczyc, T. Toyota, T. Ikegami, N. Packard and T. Sugawara (2007). Fatty acid chemistry at
    the oil-water interface: self-propelled oil droplets. J. Am. Chem. Soc. 129(30):9386-9391, doi:10.1021/ja0706955
    - the primary paper. Paywalled and not obtainable (see decisions); used through its abstract (PubMed
    17616129) and through the two full-text papers above, which describe the same system.'
  - 'T. Toyota, N. Maru, M. M. Hanczyc, T. Ikegami and T. Sugawara (2009). Self-propelled oil droplets
    consuming ''fuel'' surfactant. J. Am. Chem. Soc. 131(14):5012-5013, doi:10.1021/ja806689p - abstract
    only (PubMed 19351200): a 4-octylaniline droplet with 5 mol % of an amphiphilic catalyst in an aqueous
    dispersion of an amphiphilic precursor of 4-octylaniline.'
  - 'I. Lagzi, S. Soh, P. J. Wesson, K. P. Browne and B. A. Grzybowski (2010). Maze solving by chemotactic
    droplets. J. Am. Chem. Soc. 132(4):1198-1199, doi:10.1021/ja9076793 - abstract only (PubMed 20063877):
    droplets emitting surface-active chemicals move toward low-pH regions and find the shortest path through
    a maze.'
  - 'J. Cejkova, M. Novak, F. Stepanek and M. M. Hanczyc (2014). Dynamics of chemotactic droplets in salt
    concentration gradients. Langmuir 30(40):11937-11944, doi:10.1021/la502624f - abstract only (PubMed
    25215439): decanol droplets in aqueous sodium decanoate migrating in NaCl gradients, with induction
    time and migration velocity as the measured parameters.'
  - W. Banzhaf and L. Yamamoto (2015). Artificial Chemistries, MIT Press, section 19.2.5 and figure 19.11
    - the droplet-based protocell section itself, and the statement that the droplet follows a pH gradient
    toward the highest pH.
  decisions:
  - 'The v1 entry pointed at book section 19.2.3, which is Szostak''s heterotrophic protocells and contains
    no droplet material at all. The self-propelled droplets are section 19.2.5, ''Droplet-Based Protocells''
    (page 416-417), and `book` has been corrected. The bibliography confirms the entry''s refs: [365]
    and [364] are the Hanczyc oil-droplet papers, [858] is Toyota et al.''s fuel-surfactant droplet, [483]
    Lagzi et al.''s maze, [885] Cejkova et al.''s salt gradients and [363] Hanczyc''s 2014 review; none
    of them is Szostak, whose refs are [754], [839] and [541].'
  - 'The primary paper [365] (JACS 2007) is paywalled and no open copy exists: Unpaywall, OpenAlex, Semantic
    Scholar and Europe PMC all report no OA location, pubs.acs.org returns 403, and the Internet Archive
    was intermittently offline during this work. The implementation is therefore reconstructed from its
    abstract plus two full-text papers by the same authors on the same system, Hanczyc & Ikegami (2010)
    and Horibe et al. (2011), both recovered in full.'
  - 'NO DROPLET SPEED IS ASSERTED. The one quantity the brief asked for that no accessible source supplies
    is the droplet velocity: [365], [858] and [885] are all paywalled, and the two full-text sources report
    velocity only as a relative quantity (it falls as the droplet ages, and it is anti-correlated with
    the turning angle). Rather than invent a number, the module records those qualitative findings in
    extras.analysis.measured_behaviour and the tests assert them as properties. The 6 mm/s figure sometimes
    quoted for self-propelled droplets belongs to Ban et al. (Langmuir 29:2554, ref [54]), a different
    chemistry (di-2-ethylhexyl phosphoric acid), and is deliberately not attached to this system.'
  - NO FORCE LAW IS INVENTED and no trajectory is integrated. The propulsion mechanism is published only
    qualitatively - an interfacial-tension gradient gives a Marangoni force tangential to the surface,
    which organises a pair of convective vortices - and the numerical study that would supply the equations
    (Matsuno, Hanczyc & Ikegami 2007, Springer LNCS 4828:179-188, ref [556]) has no open copy. The mechanism
    is therefore recorded as an ordered causal chain in extras.interaction_law, and extras.space holds
    the published assay geometry and the droplet's own geometry rather than positions.
  - Every reaction carries rate = None. No accessible source publishes a rate constant for the interfacial
    hydrolysis of oleic anhydride, or for any of the other three systems, so `rate-constants` is not claimed.
  - 'The hydrolysis is written as the two steps the sources describe rather than as one overall equation:
    oleic_anhydride + H2O -> 2 oleic_acid, then oleic_acid -> oleate + H. Hanczyc & Ikegami (2010) section
    3.1 state that the precursor ''is hydrolyzed at the oil-water interface to produce more oleate and
    protons'', which is the sum of the two, and splitting them keeps the proton release - the step that
    actually drives the motion by lowering the local pH - explicit and separately visible.'
  - 'The interfacial tension curves of Hanczyc & Ikegami''s figure 2 were published as pictures, so no
    tension function is fitted or invented. Only the values stated in the caption and prose are recorded:
    27 mN/m for a bare nitrobenzene droplet at pH 11 with no oleate, a tension maximum at pH 9, a bulk
    pH of 11, and a local pH falling as low as 7.'
  - 'Chemotaxis direction is asserted only where a source I read states the sign, and the two published
    systems disagree: the Hanczyc droplet moves toward the HIGHEST pH (book 19.2.5, and Hanczyc & Ikegami
    section 3.1), while Lagzi et al.''s maze-solving droplets move toward LOW pH. For `decanol-salt` the
    accessible abstract reports only that the droplets migrate in NaCl gradients, so the direction is
    recorded as null and is not tested.'
  - '`fuel-surfactant` and `maze-chemotaxis` are reconstructed from abstracts only. Toyota et al. name
    the droplet (4-octylaniline), the catalyst loading (5 mol %) and the fuel (''an amphiphilic precursor
    of 4-octylaniline'') but not the precursor''s identity or the other hydrolysis product, so the species
    are named as the abstract names them and the unnamed product is called `byproduct`. Lagzi et al.''s
    droplet composition (dichloromethane with 2-hexyldecanoic acid) comes from Hanczyc''s 2014 review
    rather than from their own paper.'
  - Two discrepancies in the sources are recorded rather than silently fixed. Horibe et al.'s experimental
    section says glass dishes of 35, 60 and 110 mm were purchased but then uses a '100 mm glass dish'
    for the mode experiments; the 100 mm figure, being the one actually used, is what extras.space records.
    Hanczyc & Ikegami's appendix writes the aqueous volumes as '100 mL' and '800 mL' on a 1.5 cm slide
    and a 35 mm dish, which are physically impossible and are plainly microlitres; they are recorded as
    100 uL and 800 uL.
  - The v1 parameters are replaced. `pH_gradient` was type `callable`, which schema v2 forbids and which
    would in any case have required the force law that is not published; the pH now enters as the scalar
    bulk `pH`, and the gradient response is recorded in extras.interaction_law.chemotaxis. `fuel_supply`
    becomes the two published concentrations `precursor_M` and `surfactant_mM`. `droplet_volume_uL` and
    `system` are new, and both change the network.
  - 'The v1 entry claimed `provides: [space]` only and declared the chemistry out of scope for generation.
    It is in scope: the interfacial chemistry is a genuinely specified reaction set, so the entry now
    provides topology, stoichiometry, catalysts (the amphiphilic catalyst of the fuel-surfactant system
    sits on both sides of its reaction), mass-conservation (the oleoyl moiety is conserved: one anhydride
    carries two), space and initial-state.'
  phenomena:
  - 'sustained self-propulsion: a droplet carrying its own precursor starts moving within seconds and
    keeps moving for minutes to hours, until the fuel is exhausted or waste slows the reaction'
  - chemotaxis up a pH gradient, self-generated or externally imposed, which the authors read as an elementary
    sensory-motor coupling
  - the droplet leaves a low-pH trail of expelled surfactant behind it and moves away from its own waste
  - four behavioural modes - directional, circular, fluctuating and vibrating - with spontaneous switching
    between them; which modes appear is set by droplet size, and only the largest droplets vibrate
  - 'velocity falls and turning angle rises as the droplet ages, the two being negatively correlated:
    droplets turn while stopped'
  - 'collective behaviour: two droplets of 3 or 20 uL stay closer together than two droplets in separate
    dishes, an attraction that fades over time and is absent for 50 uL droplets'
  - above a few hundred microns the mechanism shifts from convection-driven to shape-driven, and the droplet
    distorts into a horseshoe that supports straight motion
  - 'maze solving: chemotactic droplets find the shortest path through a maze to an acid source'
  - division and fusion of droplets, and extraction of rare-earth metal ions (other droplet chemistries,
    not implemented here)
  - some droplets transform into supramolecular aggregates resembling multilamellar vesicles as surfactant
    accumulates
  notes: 'Protocells with no information subsystem: there is no genome and no replication, and what is
    "processed" is the set of chemicals and their locations. The entry is the clean case of a wet chemistry
    whose interesting behaviour is motion rather than stoichiometry, so it returns the small interfacial
    reaction set that is genuinely published and keeps the physics as data: extras.interaction_law for
    the Marangoni mechanism, extras.analysis for the measured behaviour, extras.space for the geometry.
    The `decanol-salt` system is the limiting case with no reactions at all.

    '