chemart / autopoiesis-vmu

{"species": [{"id": "S", "structure": "substrate O"}, {"id": "C", "structure": "catalyst *"}, {"id": "L0", "structure": "link [O], free (no bonds)"}, {"id": "L1", "structure": "link [O] with one bond (chain end)"}, {"id": "L2", "structure": "link [O] with two bonds (chain link, membrane constituent)"}, {"id": "L0S", "structure": "free link holding an absorbed substrate"}, {"id": "L1S", "structure": "singly bonded link holding an absorbed substrate"}, {"id": "L2S", "structure": "chain link holding an absorbed substrate"}], "reactions": [{"reactants": {"C": 1, "S": 2}, "products": {"C": 1, "L0": 1}, "rate": null, "count": 39}, {"reactants": {"L0": 1, "S": 1}, "products": {"L0S": 1}, "rate": null, "count": 45}, {"reactants": {"L0": 1, "L0S": 1}, "products": {"L1": 1, "L1S": 1}, "rate": null, "count": 5}, {"reactants": {"L1S": 1}, "products": {"L1": 1, "S": 1}, "rate": null, "count": 46}, {"reactants": {"L1": 1, "S": 1}, "products": {"L1S": 1}, "rate": null, "count": 52}, {"reactants": {"L1": 1, "L0": 1}, "products": {"L2": 1, "L1": 1}, "rate": null, "count": 5}, {"reactants": {"L0S": 1, "L1": 1}, "products": {"L1S": 1, "L2": 1}, "rate": null, "count": 5}, {"reactants": {"L2": 1, "S": 1}, "products": {"L2S": 1}, "rate": null, "count": 49}, {"reactants": {"L0S": 1}, "products": {"L0": 1, "S": 1}, "rate": null, "count": 24}, {"reactants": {"L2S": 1}, "products": {"L2": 1, "S": 1}, "rate": null, "count": 46}, {"reactants": {"L1S": 1}, "products": {"L2S": 1}, "rate": null, "count": 7}, {"reactants": {"L1S": 1, "L0S": 1}, "products": {"L2S": 1, "L1S": 1}, "rate": null, "count": 4}, {"reactants": {"L2": 2, "L1": 1}, "products": {"L0": 1, "L1": 1, "S": 2}, "rate": null, "count": 1}, {"reactants": {"L1": 1}, "products": {"L2": 1}, "rate": null, "count": 1}, {"reactants": {"L2S": 2, "L2": 1}, "products": {"L1S": 1, "L1": 1, "S": 1}, "rate": null, "count": 1}, {"reactants": {"L0": 1}, "products": {"L1": 1}, "rate": null, "count": 1}, {"reactants": {"L2": 1, "L2S": 1, "L1S": 1}, "products": {"L1S": 1, "L0S": 1, "S": 2}, "rate": null, "count": 1}, {"reactants": {"L1S": 1, "L0": 1}, "products": {"L2S": 1, "L1": 1}, "rate": null, "count": 4}, {"reactants": {"L2S": 1, "L2": 1, "L1S": 1}, "products": {"L1": 1, "L0S": 1, "S": 2}, "rate": null, "count": 1}, {"reactants": {"L0S": 1}, "products": {"L1S": 1}, "rate": null, "count": 2}, {"reactants": {"L1S": 1, "L1": 1}, "products": {"L2S": 1, "L2": 1}, "rate": null, "count": 2}, {"reactants": {"L1S": 1, "L2": 1}, "products": {"L1": 1, "S": 1}, "rate": null, "count": 1}, {"reactants": {"L0S": 1}, "products": {"S": 1}, "rate": null, "count": 1}, {"reactants": {"L2": 1, "L2S": 2}, "products": {"L1S": 2, "S": 2}, "rate": null, "count": 2}, {"reactants": {"L1S": 1, "L2S": 1}, "products": {"L1S": 1, "S": 2}, "rate": null, "count": 2}, {"reactants": {"L0S": 1}, "products": {"S": 3}, "rate": null, "count": 2}, {"reactants": {"L2S": 1, "L1": 1, "L2": 1}, "products": {"L0": 1, "L1": 1, "S": 3}, "rate": null, "count": 1}, {"reactants": {"L0": 1}, "products": {"S": 2}, "rate": null, "count": 2}, {"reactants": {"L2S": 2, "L2": 1}, "products": {"L1": 1, "L1S": 1, "S": 2}, "rate": null, "count": 2}, {"reactants": {"L1S": 2}, "products": {"L0S": 1, "S": 2}, "rate": null, "count": 1}, {"reactants": {"L2S": 3}, "products": {"L1S": 2, "S": 2}, "rate": null, "count": 1}, {"reactants": {"L1S": 1, "L2S": 1}, "products": {"L1S": 1, "S": 1}, "rate": null, "count": 1}, {"reactants": {"L0S": 1}, "products": {"S": 2}, "rate": null, "count": 1}], "status": "observed", "initial_state": {"C": 1.0, "S": 899.0}, "inflow": null, "outflow": null, "extras": {"space": {"dimensions": 2, "shape": [30, 30], "topology": "torus", "neighbourhood": {"interaction": "moore-8", "motion": "von-neumann-4"}, "grid": ["oooooooooooooooooooooooooooooo", ".ooooooooooooooooooooooooooooo", "oooooooooooooo.ooooooooooooooo", "oooooooooooooooooooooooooooooo", "oooooooooooooooooooooooooooooo", "ooooooooooooooooooo.oooooooooo", 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"one-bond link + absorbed substrate", "#": "chain link + absorbed substrate"}, "bonds": [[430, 459], [436, 437], [436, 467], [437, 467], [438, 469], [464, 495], [469, 499], [495, 525], [497, 527], [525, 556], [527, 556]], "mobility": {"substrate": 0.5, "catalyst": 0.1, "link": 0.1, "hole": 0.5}, "site_index": "i = y * width + x"}, "analysis": {"steps": 120, "events": {"absorption": 146, "bond": 36, "disintegration": 21, "emission": 116, "motion": 2851, "production": 39, "substrates_released": 41}, "membrane": {"closed_chains": 1, "chain_lengths": [3], "membranes": 0, "clusters": 1, "enclosed_catalysts": 0, "interior_sizes": [], "first_enclosure_step": null, "steps_enclosed": 0, "ruptures": 0, "repairs": 0}, "permeability": {"substrate_crossings": 0, "link_crossings": 0, "catalyst_crossings": 0}, "per_step": {"substrates": [899, 897, 895, 895, 893, 891, 891, 889, 887, 885, 883, 881, 881, 881, 881, 881, 881, 881, 879, 879, 877, 877, 875, 875, 875, 875, 875, 875, 875, 873, 871, 871, 871, 871, 871, 871, 871, 869, 867, 867, 867, 867, 869, 867, 865, 865, 865, 865, 863, 861, 859, 857, 857, 857, 857, 858, 858, 858, 856, 856, 856, 856, 856, 854, 854, 854, 852, 852, 852, 852, 852, 852, 852, 852, 852, 852, 852, 852, 852, 852, 852, 850, 850, 850, 848, 848, 848, 846, 844, 844, 844, 845, 843, 843, 845, 845, 847, 847, 847, 847, 845, 847, 847, 849, 849, 850, 850, 850, 851, 849, 849, 849, 850, 850, 850, 849, 851, 849, 849, 849, 847], "links": [0, 1, 2, 2, 3, 4, 4, 5, 6, 7, 8, 9, 9, 9, 9, 9, 9, 9, 10, 10, 11, 11, 12, 12, 12, 12, 12, 12, 12, 13, 14, 14, 14, 14, 14, 14, 14, 15, 16, 16, 16, 16, 15, 16, 17, 17, 17, 17, 18, 19, 20, 20, 20, 20, 20, 19, 19, 19, 20, 20, 20, 20, 20, 21, 21, 21, 22, 22, 22, 22, 22, 22, 20, 20, 20, 20, 20, 20, 20, 20, 20, 21, 21, 21, 22, 22, 22, 23, 24, 24, 24, 23, 24, 24, 23, 23, 22, 22, 22, 22, 23, 21, 21, 20, 20, 19, 19, 19, 18, 19, 18, 18, 17, 17, 17, 17, 16, 17, 17, 17, 18], "free_links": [0, 1, 2, 2, 3, 4, 2, 3, 4, 5, 6, 4, 3, 2, 2, 2, 2, 2, 3, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 8, 9, 9, 7, 7, 6, 5, 5, 5, 5, 5, 6, 7, 8, 7, 6, 5, 6, 5, 3, 3, 4, 4, 4, 4, 4, 5, 5, 5, 6, 6, 6, 6, 6, 6, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 6, 6, 7, 7, 7, 6, 7, 7, 6, 7, 4, 4, 5, 6, 6, 5, 5, 5, 5, 4, 3, 4, 4, 3, 3, 3, 3, 3, 2, 3, 3, 3, 4], "chain_links": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 8, 8, 8, 8, 8, 8, 5, 6, 7, 6, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 9, 9, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 12, 12, 12, 12, 12, 12, 9, 10, 11, 12, 10, 10, 12, 9, 10, 12, 12, 9, 9, 9, 9, 6, 6, 7, 7, 7, 6, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8], "closed_chains": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1], "enclosed_catalysts": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]}, "enclosed_per_step": [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false]}, "rules": "Lattice rules (McMullin's SCL reconstruction). Each time step every particle, in random order: (1) swaps with one random von Neumann neighbour with probability sqrt(m_i m_j) of the two mobility factors, bonded links being immobile; (2) a catalyst turns two substrates of its Moore neighbourhood into a link and a hole; (3) a link disintegrates, losing its bonds and becoming substrate; else it bonds to one random neighbouring link that has a free bond site, unless chain-based bond inhibition applies (a free link with a chain link in its Moore neighbourhood may not bond), and then absorbs a neighbouring substrate or emits the absorbed one into a hole."}, "chemistry": "autopoiesis-vmu", "params": {"mode": "lattice", "initial": "substrate", "width": 30, "height": 30, "steps": 120, "n_catalysts": 1, "substrate_density": 1.0, "production_probability": 1.0, "disintegration_probability": 0.01, "bond_probability": 1.0, "absorption_probability": 0.5, "emission_probability": 0.5, "bond_inhibition": true, "chain_inhibit_count": 1, "mobility": {"substrate": 0.5, "catalyst": 0.1, "link": 0.1, "hole": 0.5}}, "seed": 1}