chemart / ono-ikegami-protocell

{"species": [{"id": "A", "structure": "hydrophilic autocatalyst"}, {"id": "M_a", "structure": "hydrophobic membrane particle, anisotropic: one of six lattice orientations"}, {"id": "X", "structure": "neutral food"}, {"id": "Y", "structure": "neutral waste"}, {"id": "W", "structure": "hydrophilic water"}], "reactions": [{"reactants": {"A": 1, "X": 1}, "products": {"A": 2}, "rate": null, "count": 158}, {"reactants": {"A": 1, "X": 1}, "products": {"A": 1, "M_a": 1}, "rate": null, "count": 160}, {"reactants": {"A": 1}, "products": {"Y": 1}, "rate": null, "count": 106}, {"reactants": {"M_a": 1}, "products": {"Y": 1}, "rate": null, "count": 61}, {"reactants": {"X": 1}, "products": {"Y": 1}, "rate": null, "count": 46}, {"reactants": {"Y": 1}, "products": {"X": 1}, "rate": null, "count": 206}], "status": "observed", "initial_state": {"A": 48.0, "M_a": 0.0, "X": 178.0, "Y": 0.0, "W": 350.0}, "inflow": null, "outflow": null, "extras": {"space": {"dimensions": 2, "lattice": "hexagonal", "coordinates": "axial (q, r) on a torus", "shape": [24, 24], "boundary": "periodic", "occupancy": "one particle per cell", "neighbour_directions": [[0, 1], [1, 0], [1, -1], [0, -1], [-1, 0], [-1, 1]], "codes": {"A": "A", "M": "M_a", "X": "X", "Y": "Y", "W": "W"}, "final": ["WMAWWWWAWWWWWWWWWWWWMMWW", "MWWWWMWWWWAWWWWWWWWWWWXW", "MMAWAWWWWAWWWWWWWWWAAMAM", "XWWMWWAAWWAMAXWMWWMWWWAW", "MWWWAWMWYAWWWWWMWXWAAWWM", "WWWMYWMMMWWYWWWWMWWMWAWA", "WWWMAWMWWAWWMMAMWWWMAMWW", "WWMWWWWMMWWWAMXYWWWWWWWW", "WWWWWWWMWWWWWXWWWWWWAWMW", "AWAWWWMAAWXWWWWWWMWAWAMW", "AAWWWWAWAMYWWWWAMWMWWMWW", "AAMWWYWAXWWAWAMWWWWWWWAW", "WXAWAWAWWWMWWMWWXAWWWAWW", "WWXMWMMAWMMWMWWWAAMAMWWW", "AWWWAMWAAMWMWMYWMAAAMMMW", "WWWMMAMWAWAMAWWWAWWWMMAW", "WWWWWWAWAWMMWMAWWWMWMMMX", "WWWWAWAWWWMWWAWWWWWMXAWA", "WMWWWWWWAAWWMWWAWWWWWAWA", "MAAXWWWWWWWWWWAWMWWWWAAA", "WWWWWWWWAXAWWXWAAWAWAWWW", "WAWWWWWMMMWWMWMWWMWMWWWW", "WWWWXXAWWWWXWWWAMAAWAMWM", "WWWMWAAWWMWWAXWMMAMWWMMW"], "orientations": [".2..................53..", "5....5..................", "15...................1.0", "...3.......1...4..2.....", "4.....1........2.......3", "...0..130.......5..1....", "...2..0.....01.2...4.0..", "..5....43....0..........", ".......2..............4.", "......2..........3....3.", ".........2......3.1..2..", "..4...........2.........", "..........4..5..........", "...2.12..43.2.....0.1...", ".....2...1.3.4..1...435.", "...05.2....4........12..", "..........43.3....4.503.", "..........1........2....", ".5..........1...........", "2...............5.......", "........................", ".......123..2.2..3.1....", "................1....5.2", "...4.....5.....53.5..42."]}, "energies": {"law": "E = sum over neighbouring pairs; a hydrophilic/hydrophobic pair costs repulsion * F[k, o], a neutral/hydrophobic pair neutral_coupling * repulsion * F[k, o], every other pair 0", "repulsion": 1.0, "neutral_coupling": 0.25, "temperature": 1.0, "hydrophilic": ["A", "W"], "hydrophobic": ["M_a"], "neutral": ["X", "Y"], "anisotropy": 2.4, "anisotropy_field": "F[k, o] = 1 + anisotropy * cos(2 * 60deg * (k - o)); mean 1 over the six directions, so M_a redistributes the same total repulsion onto the two faces normal to its orientation o", "update": "Kawasaki exchange with a neighbour and (for M_a) rotation, both accepted with min(1, exp(-dE/temperature))", "reference_rates": {"source": "Ono & Ikegami, J. theor. Biol. 206:243-253 (2000), appendix A", "P_E": 5e-07, "P_A_spontaneous": 2e-06, "P_R_recycling": 0.0001, "P_W_decay": 0.0001, "P_D_diffusion": 0.007, "P_R0_repulsion_same_site": 0.005, "P_R1_repulsion_neighbour_site": 0.0025, "phase_points": {"fig4b_periodic_membranes": {"P_A": 9e-06, "P_M": 7e-06}, "fig7b_region_Ia_cell_dies": {"P_A": 5e-06, "P_M": 3e-06}, "fig7c_region_Ib_cell_stable": {"P_A": 7e-06, "P_M": 9e-06}, "fig7d_region_Ic_cell_reproduces": {"P_A": 1.1e-05, "P_M": 5e-06}, "fig10_recursive_division": {"P_A": 7e-06, "P_M": 5e-06, "m": 5}}}}, "analysis": {"counts": {"A": 100, "M": 99, "X": 20, "Y": 7, "W": 350}, "membrane_species": "M_a", "membrane_clusters": 43, "largest_membrane_cluster": 10, "membrane_cluster_sizes": [10, 8, 6, 5, 5, 5, 4, 4, 4, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1], "largest_cluster_gyration": 1.4283, "largest_cluster_elongation": 0.4517, "protocells": 0, "protocell_details": [], "enclosed_cells": 0, "enclosed_A": 0, "outside_cells": 477, "mean_membrane_coordination": 1.4545, "membrane_alignment": 0.2917, "history": {"A": [49, 52, 56, 56, 60, 65, 68, 73, 75, 80, 90, 93, 96, 97, 97, 99, 102, 104, 105, 106, 108, 110, 112, 113, 112, 112, 112, 112, 112, 112, 115, 115, 115, 118, 117, 118, 118, 119, 117, 118, 119, 116, 115, 114, 114, 114, 115, 117, 117, 117, 118, 116, 115, 118, 117, 117, 117, 116, 115, 117, 116, 118, 118, 117, 117, 117, 116, 115, 114, 110, 110, 110, 110, 106, 106, 105, 104, 103, 103, 102, 102, 104, 103, 102, 100, 104, 103, 101, 100, 98, 99, 99, 101, 100, 101, 103, 105, 104, 102, 100], "M": [1, 4, 7, 9, 11, 13, 16, 18, 22, 27, 27, 30, 32, 37, 40, 43, 45, 45, 45, 48, 52, 55, 59, 64, 67, 67, 67, 70, 69, 70, 71, 74, 74, 73, 72, 70, 69, 70, 70, 70, 69, 69, 65, 67, 69, 70, 70, 70, 70, 69, 68, 67, 67, 68, 70, 73, 73, 75, 74, 77, 77, 75, 77, 77, 77, 77, 78, 78, 79, 78, 79, 80, 82, 87, 89, 89, 89, 90, 90, 89, 88, 86, 87, 89, 90, 90, 90, 90, 92, 92, 91, 92, 92, 93, 94, 95, 96, 98, 99, 99], "X": [174, 170, 161, 156, 151, 143, 136, 130, 123, 113, 105, 97, 91, 82, 79, 77, 75, 70, 69, 65, 62, 58, 54, 47, 41, 39, 41, 37, 38, 33, 33, 31, 29, 27, 28, 27, 28, 27, 28, 31, 28, 28, 33, 35, 31, 34, 34, 35, 33, 32, 33, 32, 33, 35, 36, 32, 29, 28, 30, 25, 28, 28, 26, 26, 24, 23, 25, 26, 25, 27, 32, 32, 31, 27, 25, 27, 25, 24, 26, 26, 26, 28, 25, 25, 28, 26, 27, 27, 25, 26, 27, 29, 29, 30, 29, 26, 23, 21, 18, 20], "Y": [2, 0, 2, 5, 4, 5, 6, 5, 6, 6, 4, 6, 7, 10, 10, 7, 4, 7, 7, 7, 4, 3, 1, 2, 6, 8, 6, 7, 7, 11, 7, 6, 8, 8, 9, 11, 11, 10, 11, 7, 10, 13, 13, 10, 12, 8, 7, 4, 6, 8, 7, 11, 11, 5, 3, 4, 7, 7, 7, 7, 5, 5, 5, 6, 8, 9, 7, 7, 8, 11, 5, 4, 3, 6, 6, 5, 8, 9, 7, 9, 10, 8, 11, 10, 8, 6, 6, 8, 9, 10, 9, 6, 4, 3, 2, 2, 2, 3, 7, 7], "W": [350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350, 350]}}}, "chemistry": "ono-ikegami-protocell", "params": {"mode": "spatial", "membrane": "anisotropic", "width": 24, "height": 24, "steps": 100, "relaxation": 12, "initial": "random", "cell_radius": 5, "A_fraction": 0.08, "X_fraction": 0.3, "M_fraction": 0.0, "P_A": 0.03, "P_M": 0.03, "P_decay": 0.01, "X_supply": 0.3, "anisotropy": 2.4, "repulsion": 1.0, "neutral_coupling": 0.25, "temperature": 1.0, "mobility_ratio": 1.0}, "seed": 1}