msmtools.flux.tpt¶

msmtools.flux.tpt(T, A, B, mu=None, qminus=None, qplus=None, rate_matrix=False)

Computes the A->B reactive flux using transition path theory (TPT)

Parameters: T ((M, M) ndarray or scipy.sparse matrix) – Transition matrix (default) or Rate matrix (if rate_matrix=True) A (array_like) – List of integer state labels for set A B (array_like) – List of integer state labels for set B mu ((M,) ndarray (optional)) – Stationary vector qminus ((M,) ndarray (optional)) – Backward committor for A->B reaction qplus ((M,) ndarray (optional)) – Forward committor for A-> B reaction = False (rate_matrix) – By default (False), T is a transition matrix. If set to True, T is a rate matrix. tpt – A python object containing the reactive A->B flux network and several additional quantities, such as stationary probability, committors and set definitions. msmtools.flux.ReactiveFlux object

Notes

The central object used in transition path theory is the forward and backward comittor function.

TPT (originally introduced in ) for continous systems has a discrete version outlined in . Here, we use the transition matrix formulation described in .

References

  W. E and E. Vanden-Eijnden. Towards a theory of transition paths. J. Stat. Phys. 123: 503-523 (2006)
  P. Metzner, C. Schuette and E. Vanden-Eijnden. Transition Path Theory for Markov Jump Processes. Multiscale Model Simul 7: 1192-1219 (2009)
  F. Noe, Ch. Schuette, E. Vanden-Eijnden, L. Reich and T. Weikl: Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations. Proc. Natl. Acad. Sci. USA, 106, 19011-19016 (2009)