deeptime.markov.tools.flux.rate

deeptime.markov.tools.flux.rate(totflux, pi, qminus)

Transition rate for reaction A to B.

Parameters:

  • totflux (float) – The total flux between reactant and product

  • pi ((M,) ndarray) – Stationary distribution

  • qminus ((M,) ndarray) – Backward comittor

Returns:

kAB – The reaction rate (per time step of the Markov chain)

Return type:

float

See also

committor, total_flux, flux_matrix

Notes

Computation of the rate relies on discrete transition path theory (TPT). The transition rate, i.e. the total number of reaction events per time step, is given in [1] as:

\[k_{AB}=\frac{1}{F} \sum_i \pi_i q_i^{(-)} \]

\(F\) is the total flux for the transition from \(A\) to \(B\).

References