Stochastic degradation model

class pints.toy.stochastic.DegradationModel(initial_molecule_count=20)

Stochastic degradation model of a single chemical reaction starting from an initial molecule count \(A(0)\) and degrading to 0 with a fixed rate \(k\):

\[A \xrightarrow{k} 0\]

Extends pints.MarkovJumpModel.

Parameters:

initial_molecule_count – The initial molecule count \(A(0)\).

interpolate_mol_counts(time, mol_count, output_times)

Takes raw times and inputs and mol counts and outputs interpolated values at output_times

mean(parameters, times)

Returns the deterministic mean of infinitely many stochastic simulations, which follows \(A(0) \exp(-kt)\).

n_outputs()

Returns the number of outputs this model has. The default is 1.

n_parameters()

See pints.ForwardModel.n_parameters().

simulate(parameters, times)

See pints.ForwardModel.simulate().

simulate_raw(rates, max_time)

Returns raw times, mol counts when reactions occur.

suggested_parameters()

See pints.toy.ToyModel.suggested_parameters().

suggested_times()

See “meth:pints.toy.ToyModel.suggested_times().

variance(parameters, times)

Returns the deterministic variance of infinitely many stochastic simulations, which follows \(\exp(-2kt)(-1 + \exp(kt))A(0)\).