chemart / bigan-conservative-crn

View on GitHub

Conservative random chemical reaction networks — A random reaction network built to be thermodynamically honest. Each abstract chemical gets a random free energy of formation; reactions are drawn as association, dissociation and transformation steps, and every backward…

chemistry official · built in network fidelity: reconstructed #banzhaf-yamamoto
files / preview.json · 6.9 KB · at 2c7cdd08db24 Raw
{"species": [{"id": "A0", "structure": null}, {"id": "A1", "structure": null}, {"id": "A2", "structure": null}, {"id": "A3", "structure": null}, {"id": "A4", "structure": null}, {"id": "A5", "structure": null}, {"id": "A6", "structure": null}, {"id": "A7", "structure": null}, {"id": "A8", "structure": null}, {"id": "A9", "structure": null}], "reactions": [{"reactants": {"A1": 1, "A3": 1}, "products": {"A5": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A5": 1}, "products": {"A1": 1, "A3": 1}, "rate": {"law": "mass-action", "k": 5852.229125020699}, "count": null}, {"reactants": {"A2": 1, "A5": 1}, "products": {"A0": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A0": 1}, "products": {"A2": 1, "A5": 1}, "rate": {"law": "mass-action", "k": 62.318124632246665}, "count": null}, {"reactants": {"A9": 1}, "products": {"A1": 1}, "rate": {"law": "mass-action", "k": 100.0}, "count": null}, {"reactants": {"A1": 1}, "products": {"A9": 1}, "rate": {"law": "mass-action", "k": 8.488690652415743}, "count": null}, {"reactants": {"A1": 2}, "products": {"A5": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A5": 1}, "products": {"A1": 2}, "rate": {"law": "mass-action", "k": 2865.976715541064}, "count": null}, {"reactants": {"A2": 1, "A5": 1}, "products": {"A4": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A4": 1}, "products": {"A2": 1, "A5": 1}, "rate": {"law": "mass-action", "k": 0.5376709375047533}, "count": null}, {"reactants": {"A3": 1, "A8": 1}, "products": {"A2": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A2": 1}, "products": {"A3": 1, "A8": 1}, "rate": {"law": "mass-action", "k": 808.6759781342932}, "count": null}, {"reactants": {"A5": 2}, "products": {"A8": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A8": 1}, "products": {"A5": 2}, "rate": {"law": "mass-action", "k": 0.616710046828746}, "count": null}, {"reactants": {"A7": 1}, "products": {"A6": 1}, "rate": {"law": "mass-action", "k": 100.0}, "count": null}, {"reactants": {"A6": 1}, "products": {"A7": 1}, "rate": {"law": "mass-action", "k": 16.955264910827832}, "count": null}, {"reactants": {"A4": 2}, "products": {"A6": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A6": 1}, "products": {"A4": 2}, "rate": {"law": "mass-action", "k": 0.8491098585962038}, "count": null}, {"reactants": {"A0": 2}, "products": {"A6": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A6": 1}, "products": {"A0": 2}, "rate": {"law": "mass-action", "k": 6.320744816337367e-05}, "count": null}, {"reactants": {"A5": 1}, "products": {"A3": 2}, "rate": {"law": "mass-action", "k": 100.0}, "count": null}, {"reactants": {"A3": 2}, "products": {"A5": 1}, "rate": {"law": "mass-action", "k": 83.68160770168583}, "count": null}, {"reactants": {"A1": 1, "A9": 1}, "products": {"A5": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A5": 1}, "products": {"A1": 1, "A9": 1}, "rate": {"law": "mass-action", "k": 243.28389755254622}, "count": null}, {"reactants": {"A9": 1}, "products": {"A3": 1}, "rate": {"law": "mass-action", "k": 100.0}, "count": null}, {"reactants": {"A3": 1}, "products": {"A9": 1}, "rate": {"law": "mass-action", "k": 4.157115047194698}, "count": null}, {"reactants": {"A3": 1, "A9": 1}, "products": {"A5": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A5": 1}, "products": {"A3": 1, "A9": 1}, "rate": {"law": "mass-action", "k": 496.7776266935832}, "count": null}, {"reactants": {"A1": 1}, "products": {"A3": 1}, "rate": {"law": "mass-action", "k": 100.0}, "count": null}, {"reactants": {"A3": 1}, "products": {"A1": 1}, "rate": {"law": "mass-action", "k": 48.972394182036204}, "count": null}, {"reactants": {"A0": 2}, "products": {"A7": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A7": 1}, "products": {"A0": 2}, "rate": {"law": "mass-action", "k": 0.0003727895051820068}, "count": null}, {"reactants": {"A4": 2}, "products": {"A7": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A7": 1}, "products": {"A4": 2}, "rate": {"law": "mass-action", "k": 5.007942152846884}, "count": null}, {"reactants": {"A9": 2}, "products": {"A5": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A5": 1}, "products": {"A9": 2}, "rate": {"law": "mass-action", "k": 20.651617470375662}, "count": null}, {"reactants": {"A1": 1, "A8": 1}, "products": {"A2": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A2": 1}, "products": {"A1": 1, "A8": 1}, "rate": {"law": "mass-action", "k": 396.02798766736356}, "count": null}, {"reactants": {"A0": 1, "A4": 1}, "products": {"A7": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A7": 1}, "products": {"A0": 1, "A4": 1}, "rate": {"law": "mass-action", "k": 0.04320773399681943}, "count": null}, {"reactants": {"A0": 1}, "products": {"A4": 1}, "rate": {"law": "mass-action", "k": 100.0}, "count": null}, {"reactants": {"A4": 1}, "products": {"A0": 1}, "rate": {"law": "mass-action", "k": 0.8627842071270123}, "count": null}, {"reactants": {"A0": 1, "A4": 1}, "products": {"A6": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A6": 1}, "products": {"A0": 1, "A4": 1}, "rate": {"law": "mass-action", "k": 0.00732598576112656}, "count": null}, {"reactants": {"A8": 1, "A9": 1}, "products": {"A2": 1}, "rate": {"law": "mass-action", "k": 10000.0}, "count": null}, {"reactants": {"A2": 1}, "products": {"A8": 1, "A9": 1}, "rate": {"law": "mass-action", "k": 33.61759077006963}, "count": null}], "status": "complete", "initial_state": {"A0": 0.001, "A1": 0.001, "A2": 0.001, "A3": 0.001, "A4": 0.001, "A5": 0.001, "A6": 0.001, "A7": 0.001, "A8": 0.001, "A9": 0.001}, "inflow": {"A5": 1.0}, "outflow": null, "extras": {"energies": {"formation_free_energy_RT": {"A0": 10.623821913719574, "A1": 4.624784258033708, "A2": 7.70201734906537, "A3": 3.910870827355746, "A4": 5.871061058886128, "A5": 7.999892628071283, "A6": 2.368215042393947, "A7": 4.1428068285780535, "A8": 6.306088578323105, "A9": 7.091219677922331}}, "conservation": [{"name": "mass", "vector": {"A0": 7, "A1": 1, "A2": 5, "A3": 1, "A4": 7, "A5": 2, "A6": 14, "A7": 14, "A8": 4, "A9": 1}, "unique": true}], "reaction_pairs": [[0, 1], [2, 3], [4, 5], [6, 7], [8, 9], [10, 11], [12, 13], [14, 15], [16, 17], [18, 19], [20, 21], [22, 23], [24, 25], [26, 27], [28, 29], [30, 31], [32, 33], [34, 35], [36, 37], [38, 39], [40, 41], [42, 43], [44, 45]]}, "chemistry": "bigan-conservative-crn", "params": {"N": 10, "max_reactions": 0, "kinetics": "mass-action", "k_avg_mono": 100.0, "k_avg_bi": 10000.0, "s": 0.0, "K_avg": 0.01, "p": 0.0, "G_max": 15.0, "nutrient": 5, "nutrient_flux": 1.0, "initial_concentration": 0.001}, "seed": 1}