RSD_sim Class

RSD_sim is a Python class that gives access to all of the simulator’s built-in functions found here. To have access to the features of the class you must first instantiate an object of the class, directions for this can be found here.

This page gives info about the input of the object instantiation, and the initiaizations made for the class.

Class Object

__init__(domains=5)

Parameters:

domains: int, if NONE, default=5

The highest input or output index of the species indicated in molecular_species(). For example, if G{5,9} is specified, domains needs to be 9 or greater. This can be higher than the highest index in the system but it cannot be lower than the highest index in the system.

Initializations

All DNA template concentrations and initial conditions are initialized at 0.

Rate Constants:

self.ktxnO = 0.013 (1/s)

self.ktxnG = 0.013 (1/s)

self.ktxnTG = 0.013 (1/s)

self.ktxnF = 0.013 (1/s)

self.ktxnAG = 0.013 (1/s)

self.ktxnCG = 0.013 (1/s)

self.leak = 0.03

self.krz = 0.00417 (1/s)

self.krsd = 1e3/1e9 (1/nM-s)

self.krev = 270/1e9 (1/nM-s), 0 for inputs

self.krep = 1e4/1e9 (1/nM-s)

self.krepr = 0 (1/s)

self.kth = 1e5/1e9 (1/nM-s)

self.krzTG = 0.00417 (1/s)

self.krsdF = 1e3/1e9 (1/nM-s)

self.krevF = 1e3/1e9 (1/nM-s)

self.krzA = 0.00417 (1/s)

self.krsdA = 1e3/1e9 (1/nM-s)

self.leakA = 0.06

self.krzCG = 0.00417 (1/s)

self.krsdCGa = 1e5/1e9 (1/nM-s)

self.krsdCGb = 1e5/1e9 (1/nM-s)

self.krevCG = 1 (1/s)

self.kssdO = 0 (1/s)

self.kssdF = 0 (1/s)

self.kdsduG = 0 (1/s)

self.kdsdG = 0 (1/s)

self.kdsdGO = 0 (1/s)

self.kdsdGF = 0 (1/s)

self.kdsduTG = 0 (1/s)

self.kdsdTG = 0 (1/s)

self.kdsduAG = 0 (1/s)

self.kdsdAG = 0 (1/s)

self.kdsdAGOa = 0 (1/s)

self.kdsdAGOb = 0 (1/s)

self.kdsdAGFb = 0 (1/s)

self.kdsduCG = 0 (1/s)

self.kdsdCG = 0 (1/s)

self.kdsdCGOa = 0 (1/s)

self.kdsdCGOb = 0 (1/s)

self.kdrd = 0 (1/s)

self.khybO = 1e6/1e9 (1/nM-s)

self.khybR = 1e6/1e9 (1/nM-s)