msmbuilder.tpt.fluxes

msmbuilder.tpt.fluxes(sources, sinks, msm, for_committors=None)

Compute the transition path theory flux matrix.

Parameters:
  • sources (array_like, int) – The set of unfolded/reactant states.
  • sinks (array_like, int) – The set of folded/product states.
  • msm (msmbuilder.MarkovStateModel) – MSM that has been fit to data.
  • for_committors (np.ndarray, optional) – The forward committors associated with sources, sinks, and tprob. If not provided, is calculated from scratch. If provided, sources and sinks are ignored.
Returns:

flux_matrix – The flux matrix
Return type:

np.ndarray

See also

net_fluxes()

References

[1]Weinan, E. and Vanden-Eijnden, E. Towards a theory of transition paths. J. Stat. Phys. 123, 503-523 (2006).
[2]Metzner, P., Schutte, C. & Vanden-Eijnden, E. Transition path theory for Markov jump processes. Multiscale Model. Simul. 7, 1192-1219 (2009).
[3]Berezhkovskii, A., Hummer, G. & Szabo, A. Reactive flux and folding pathways in network models of coarse-grained protein dynamics. J. Chem. Phys. 130, 205102 (2009).
[4]Noe, Frank, et al. “Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.” PNAS 106.45 (2009): 19011-19016.