.. currentmodule:: msmbuilder.tpt
Transition path theory (TPT) is a way to extract the highest-flux pathways
of your system from an estimated MSM.
These are some canonical references for TPT. Note that TPT is really a
specialization of ideas very familiar to the mathematical study of Markov
chains, and there are many books, manuscripts in the mathematical
literature that cover the same concepts.
| [1] | E, Weinan and Vanden-Eijnden, Eric 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] | Noé, Frank, et al. "Constructing the equilibrium ensemble of folding
pathways from short off-equilibrium simulations." PNAS 106.45 (2009):
19011-19016. |
.. autosummary::
:toctree: _tpt/
fluxes
net_fluxes
fraction_visited
hub_scores
paths
top_path
committors
conditional_committors
mfpts