chemart / dorin-korb-ecosystem

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"products": {"A": 1, "O": 1}, "rate": null, "count": 1}, {"reactants": {"C17KEAB_6b5f": 1, "C": 1}, "products": {"C18KEAB_48af": 1}, "rate": null, "count": 1}, {"reactants": {"AO": 1, "C18KEAB_48af": 1}, "products": {"A": 1, "O": 1, "C18KEAB_48af": 1}, "rate": null, "count": 3}, {"reactants": {"C2": 1, "ECC": 1}, "products": {"C": 2, "ECC": 1}, "rate": null, "count": 1}, {"reactants": {"C18KEAB_48af": 1}, "products": {"C17KEAB_6b5f": 1, "C": 1}, "rate": null, "count": 1}, {"reactants": {"CO2_4fc0": 1}, "products": {"CO": 1, "O": 1}, "rate": null, "count": 1}, {"reactants": {"C17KEAB_6b5f": 1, "C": 1}, "products": {"C18KEAB_2b8f": 1}, "rate": null, "count": 1}, {"reactants": {"AO": 1, "C18KEAB_2b8f": 1}, "products": {"A": 1, "O": 1, "C18KEAB_2b8f": 1}, "rate": null, "count": 3}, {"reactants": {"CO": 1, "C": 1}, "products": {"C2O_4137": 1}, "rate": null, "count": 1}, {"reactants": {"BO": 1, "C18KEAB_2b8f": 1}, "products": {"B": 1, "O": 1, "C18KEAB_2b8f": 1}, "rate": null, "count": 2}, {"reactants": {"C18KEAB_2b8f": 1, "C": 1}, "products": {"C19KEAB_7460": 1}, "rate": null, "count": 1}, {"reactants": {"C2O_4137": 1, "ECC": 1}, "products": {"CO": 1, "C": 1, "ECC": 1}, "rate": null, "count": 1}, {"reactants": {"BO": 1, "C19KEAB_7460": 1}, "products": {"B": 1, "O": 1, "C19KEAB_7460": 1}, "rate": null, "count": 1}, {"reactants": {"AO": 1, "C19KEAB_7460": 1}, "products": {"A": 1, "O": 1, "C19KEAB_7460": 1}, "rate": null, "count": 2}, {"reactants": {"C4OECC_5c53": 1, "CO": 1}, "products": {"C5O2ECC_3eff": 1}, "rate": null, "count": 1}], "status": "observed", "initial_state": {"A": 28.0, "AO": 1.0, "B": 28.0, "BO": 1.0, "C": 24.0, "C16KEAB_d33a": 1.0, "C4OECC_5c53": 1.0, "EAB": 4.0, "ECC": 4.0, "EO": 4.0, "K": 4.0, "O": 36.0}, "inflow": null, "outflow": null, "extras": {"energies": {"units": "integer energy units; energy_low and energy_high scale table 1", "convention": "a bond's energy is released when the bond is made and must be supplied to break it (table 1 caption), so negative bonds store energy", "bond_energy": {"A-B": -8, "C-C": -1, "A-O": 1, "B-O": 1, "C-O": 1}, "light": {"amplitude": 8.0, "period": 24.0, "law": "floor(amplitude * max(0, sin(2 pi t / period)) * atoms in the cluster)", "usable_by": "chlorophyll-catalysed reactions only (section 2.2)"}, "species_bonds": {"A": {}, "AB": {"A-B": 1}, "AO": {"A-O": 1}, "B": {}, "BO": {"B-O": 1}, "C": {}, "C16KEAB_d33a": {"C-C": 16, "C-K": 1, "C-EAB": 1}, "C16OKEAB_4e35": {"C-C": 16, "C-K": 1, "C-O": 1, "C-EAB": 1}, "C17KEAB_6b5f": {"C-C": 17, "C-K": 1, "C-EAB": 1}, "C17OKEAB_bda7": {"C-C": 17, "C-K": 1, "C-O": 1, "C-EAB": 1}, "C18KEAB_2b8f": {"C-C": 18, "C-K": 1, "C-EAB": 1}, "C18KEAB_48af": {"C-C": 18, "C-K": 1, "C-EAB": 1}, "C18KEAB_a92b": {"C-C": 18, "C-K": 1, "C-EAB": 1}, "C19KEAB_7460": {"C-C": 19, "C-K": 1, "C-EAB": 1}, "C2": {"C-C": 1}, "C2O_4137": {"C-C": 1, "C-O": 1}, "C4OECC_5c53": {"C-C": 3, "C-O": 1, "ECC-O": 1}, "C5O2ECC_3eff": {"C-C": 4, "C-O": 2, "ECC-O": 1}, "C5OECC_2ceb": {"C-C": 4, "C-O": 1, "ECC-O": 1}, "CO": {"C-O": 1}, "CO2_4fc0": {"C-O": 2}, "EAB": {}, "ECC": {}, "EO": {}, "K": {}, "O": {}}, "ledger": {"consumed": 271, "dissipated": 246, "light_incident": 62014, "light_lost": 61797, "light_spent": 217, "released": 300, "balanced": true}}, "conservation": [{"name": "atom A", "vector": {"A": 1, "AB": 1, "AO": 1}}, {"name": "atom B", "vector": {"AB": 1, "B": 1, "BO": 1}}, {"name": "atom C", "vector": {"C": 1, "C16KEAB_d33a": 16, "C16OKEAB_4e35": 16, "C17KEAB_6b5f": 17, "C17OKEAB_bda7": 17, "C18KEAB_2b8f": 18, "C18KEAB_48af": 18, "C18KEAB_a92b": 18, "C19KEAB_7460": 19, "C2": 2, "C2O_4137": 2, "C4OECC_5c53": 4, "C5O2ECC_3eff": 5, "C5OECC_2ceb": 5, "CO": 1, "CO2_4fc0": 1}}, {"name": "atom O", "vector": {"AO": 1, "BO": 1, "C16OKEAB_4e35": 1, "C17OKEAB_bda7": 1, "C2O_4137": 1, "C4OECC_5c53": 1, "C5O2ECC_3eff": 2, "C5OECC_2ceb": 1, "CO": 1, "CO2_4fc0": 2, "O": 1}}, {"name": "atom K", "vector": {"C16KEAB_d33a": 1, "C16OKEAB_4e35": 1, "C17KEAB_6b5f": 1, "C17OKEAB_bda7": 1, "C18KEAB_2b8f": 1, "C18KEAB_48af": 1, "C18KEAB_a92b": 1, "C19KEAB_7460": 1, "K": 1}}, {"name": "atom EAB", "vector": {"C16KEAB_d33a": 1, "C16OKEAB_4e35": 1, "C17KEAB_6b5f": 1, "C17OKEAB_bda7": 1, "C18KEAB_2b8f": 1, "C18KEAB_48af": 1, "C18KEAB_a92b": 1, "C19KEAB_7460": 1, "EAB": 1}}, {"name": "atom ECC", "vector": {"C4OECC_5c53": 1, "C5O2ECC_3eff": 1, "C5OECC_2ceb": 1, "ECC": 1}}, {"name": "atom EO", "vector": {"EO": 1}}], "space": {"dimensions": 2, "lattice": "torus", "width": 18, "height": 18, "neighbourhood": "von-neumann", "cell": "one square atom, bonds are shared edges", "motion": "each molecule moves one square in a random direction with probability 0.8; bonded atoms move identically", "collisions": "not permitted: a move is rejected if any target cell is occupied"}, "chemistry": {"valence": {"A": 1, "B": 1, "O": 1, "C": 4, "K": 2, "EAB": 2, "ECC": 2, "EO": 2}, "shells": {"A": [1], "B": [2, 3], "O": [2, 1], "C": [2, 4, 4], "K": [2, 2], "EAB": [2, 2], "ECC": [2, 2], "EO": [2, 2]}, "table": {"A-B": {"make": "low", "break": "low", "make_catalyst": {"K": "high"}, "break_catalyst": {"EAB": "high"}, "energy": "- high"}, "C-C": {"make": "moderate", "break": "low", "make_catalyst": null, "break_catalyst": {"ECC": "high"}, "energy": "- low"}, "A-O": {"make": "high", "break": "low", "make_catalyst": null, "break_catalyst": {"K": "high", "EO": "high"}, "energy": "+ low"}, "B-O": {"make": "high", "break": "low", "make_catalyst": null, "break_catalyst": {"K": "high", "EO": "high"}, "energy": "+ low"}, "C-O": {"make": "low", "break": "moderate", "make_catalyst": {"ECC": "high"}, "break_catalyst": null, "energy": "+ low"}}, "probabilities": {"low": 0.01, "moderate": 0.1, "high": 0.9}, "catalysts": {"K": "chlorophyll: makes A-B from sunlight, breaks A-O and B-O", "EAB": "sugar-breaking enzyme: breaks A-B and releases its stored energy", "ECC": "organic decomposer: breaks C-C, makes C-O", "EO": "inorganic decomposer: breaks A-O and B-O"}, "static_bonds": "bonds inside a seeded organism body are anchors and never react"}, "events": [{"action": "make", "bond": "B-O", "energy_released": 1, "catalysts": {}, "count": 93}, {"action": "make", "bond": "C-C", "energy_released": -1, "catalysts": {}, "count": 3}, {"action": "make", "bond": "A-O", "energy_released": 1, "catalysts": {}, "count": 90}, {"action": "break", "bond": "B-O", "energy_released": -1, "catalysts": {"K": 2}, "count": 2}, {"action": "break", "bond": "C-C", "energy_released": 1, "catalysts": {"ECC": 1}, "count": 1}, {"action": "break", "bond": "B-O", "energy_released": -1, "catalysts": {"EO": 12}, "count": 12}, {"action": "make", "bond": "A-B", "energy_released": -8, "catalysts": {"K": 13}, "count": 13}, {"action": "break", "bond": "A-O", "energy_released": -1, "catalysts": {"K": 47}, "count": 47}, {"action": "break", "bond": "A-B", "energy_released": 8, "catalysts": {"EAB": 7}, "count": 7}, {"action": "break", "bond": "A-O", "energy_released": -1, "catalysts": {"K": 3}, "count": 3}, {"action": "break", "bond": "B-O", "energy_released": -1, "catalysts": {"K": 52}, "count": 52}, {"action": "make", "bond": "C-O", "energy_released": 1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "A-O", "energy_released": -1, "catalysts": {"K": 4}, "count": 4}, {"action": "make", "bond": "C-O", "energy_released": 1, "catalysts": {"ECC": 3}, "count": 3}, {"action": "break", "bond": "B-O", "energy_released": -1, "catalysts": {}, "count": 5}, {"action": "break", "bond": "C-O", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "C-C", "energy_released": 1, "catalysts": {}, "count": 1}, {"action": "make", "bond": "C-C", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "C-C", "energy_released": 1, "catalysts": {"ECC": 1}, "count": 1}, {"action": "break", "bond": "C-O", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "make", "bond": "C-C", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "make", "bond": "C-C", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "A-B", "energy_released": 8, "catalysts": {}, "count": 6}, {"action": "break", "bond": "B-O", "energy_released": -1, "catalysts": {"K": 4}, "count": 4}, {"action": "break", "bond": "A-O", "energy_released": -1, "catalysts": {"K": 6}, "count": 6}, {"action": "make", "bond": "C-O", "energy_released": 1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "C-C", "energy_released": 1, "catalysts": {"ECC": 1}, "count": 1}, {"action": "make", "bond": "C-C", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "A-O", "energy_released": -1, "catalysts": {"K": 2}, "count": 2}, {"action": "break", "bond": "C-C", "energy_released": 1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "A-O", "energy_released": -1, "catalysts": {"EO": 3}, "count": 3}, {"action": "break", "bond": "A-O", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "make", "bond": "C-C", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "A-O", "energy_released": -1, "catalysts": {"K": 3}, "count": 3}, {"action": "break", "bond": "C-C", "energy_released": 1, "catalysts": {"ECC": 1}, "count": 1}, {"action": "break", "bond": "C-C", "energy_released": 1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "C-O", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "make", "bond": "C-C", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "A-O", "energy_released": -1, "catalysts": {"K": 3}, "count": 3}, {"action": "make", "bond": "C-C", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "B-O", "energy_released": -1, "catalysts": {"K": 2}, "count": 2}, {"action": "make", "bond": "C-C", "energy_released": -1, "catalysts": {}, "count": 1}, {"action": "break", "bond": "C-C", "energy_released": 1, "catalysts": {"ECC": 1}, "count": 1}, {"action": "break", "bond": "B-O", "energy_released": -1, "catalysts": {"K": 1}, "count": 1}, {"action": "break", "bond": "A-O", "energy_released": -1, "catalysts": {"K": 2}, "count": 2}, {"action": "make", "bond": "C-C", "energy_released": -1, "catalysts": {}, "count": 1}], "species_encoding": "id = atom formula for one- and two-atom molecules, else the formula and a hash of the certificate; structure = certificate, the canonical (isomorphism-invariant) bond graph as atom types in canonical order followed by the upper adjacency bits", "final_state": {"A": 12, "AO": 17, "B": 13, "BO": 16, "C": 19, "C19KEAB_7460": 1, "C5O2ECC_3eff": 1, "CO": 1, "EAB": 4, "ECC": 4, "EO": 4, "K": 4, "O": 3}, "analysis": {"steps": 150, "event_counts": {"break:A-B:none": 6, "break:A-B:EAB": 7, "break:A-O:none": 1, "break:A-O:EO": 3, "break:A-O:K": 70, "break:B-O:none": 5, "break:B-O:EO": 12, "break:B-O:K": 61, "break:C-C:none": 3, "break:C-C:ECC": 5, "break:C-O:none": 3, "make:A-B:K": 13, "make:A-O:none": 90, "make:B-O:none": 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