{
	"Notes": "Notes fields replace commenting, which is not standard in JSON.",
	"Description": "This configuration demonstrates Michaelis-Menten chemical kinetics in the mesoscopic
		regime. We define a single subvolume so there is no diffusion. There are active actors
		to initialize the substrate and enzyme molecules and then all molecules are observed.
		This file has 2nd order reactions so it is not possible to run in the microscopic regime.
		This simulation with 100 repeats should take less than 1 second to
		execute on a personal computer.",
	"Output Filename": "accord_sample_reactor_2nd_order",
	"Warning Override": false,
	"Simulation Control": {
		"Number of Repeats": 1,
		"Final Simulation Time": 20,
		"Global Microscopic Time Step": 1,
		"Random Number Seed": 1,
		"Max Number of Progress Updates": 100
	},
	"Chemical Properties": {
		"Number of Molecule Types": 4,
		"Diffusion Coefficients": [0, 0, 0, 0],
		"Global Flow Type": "None",
		"Chemical Reaction Specification": [
			{							
				"Notes": "Enzyme binding.",
				"Label": "Binding",
				"Is Reaction Reversible?": true,
				"Reverse Reaction Label": "Unbinding",
				"Surface Reaction?": false,
				"Default Everywhere?": true,
				"Exception Regions": [],
				"Reactants": [1, 1, 0, 0],
				"Products": [0, 0, 1, 0],
				"Reaction Rate": 1e-14
			},
			{							
				"Notes": "Enzyme unbinding.",
				"Label": "Unbinding",
				"Is Reaction Reversible?": true,
				"Reverse Reaction Label": "Binding",
				"Surface Reaction?": false,
				"Default Everywhere?": true,
				"Exception Regions": [],
				"Reactants": [0, 0, 1, 0],
				"Products": [1, 1, 0, 0],
				"Reaction Rate": 0.3			
			},
			{							
				"Notes": "Degradation",
				"Label": "Degradation",
				"Is Reaction Reversible?": false,
				"Surface Reaction?": false,
				"Default Everywhere?": true,
				"Exception Regions": [],
				"Reactants": [0, 0, 1, 0],
				"Products": [0, 1, 0, 1],
				"Reaction Rate": 0.15			
			}
		]
	},
	"Environment":	{
		"Subvolume Base Size": 1e-6,
		"Region Specification": [
			{
				"Notes": "Single mesoscopic region with 1 subvolume.",
				"Label": "A",
				"Parent Label": "",
				"Shape": "Rectangular Box",
				"Type": "Normal",
				"Anchor Coordinate": [0, 0, 0],
				"Integer Subvolume Size": 100,
				"Is Region Microscopic?": false,
				"Number of Subvolumes Per Dimension": [1, 1, 1]
			}
		],
		"Actor Specification": [
		{
				"Notes": "Initialization of molecule 0",
				"Is Location Defined by Regions?": false,
				"Shape": "Rectangular Box",
				"Outer Boundary": [0e-6, 100e-6, 0e-6, 100e-6, 0e-6, 100e-6],
				"Is Actor Active?": true,
				"Start Time": 0,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e9999,
				"Is Actor Activity Recorded?": true,
				"Random Number of Molecules?": false,
				"Random Molecule Release Times?": false,
				"Release Interval": 0,
				"Slot Interval": 0,
				"Bits Random?": true,
				"Probability of Bit 1": 1,
				"Modulation Scheme": "CSK",
				"Modulation Bits": 1,
				"Modulation Strength": 100,
				"Is Molecule Type Released?": [true, false, false, false]
		},
		{
				"Notes": "Initialization of molecule 1",
				"Is Location Defined by Regions?": false,
				"Shape": "Rectangular Box",
				"Outer Boundary": [0e-6, 100e-6, 0e-6, 100e-6, 0e-6, 100e-6],
				"Is Actor Active?": true,
				"Start Time": 0,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e9999,
				"Is Actor Activity Recorded?": true,
				"Random Number of Molecules?": false,
				"Random Molecule Release Times?": false,
				"Release Interval": 0,
				"Slot Interval": 0,
				"Bits Random?": true,
				"Probability of Bit 1": 1,
				"Modulation Scheme": "CSK",
				"Modulation Bits": 1,
				"Modulation Strength": 100,
				"Is Molecule Type Released?": [false, true, false, false]
		},
		{
				"Notes": "Observer",
				"Is Location Defined by Regions?": true,
				"List of Regions Defining Location": ["A"],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 0.1,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true, true, true],
				"Is Molecule Position Observed?": [false, false, false, false]
		}
		]		
	}
}
