Markov model lectures

Coordinate transforms

1 Time-lagged independent component analysis (TICA)

Coordinate clustering

2 Regular space clustering

Markov model estimation

3 Implied timescales

4 Nonreversible Markov model estimation

5 Reversible Markov model estimation

Markov model analysis

6 Perron-cluster cluster analysis (PCCA)

7 Computational spectroscopy / dynamical fingerprints

8 Transition path theory (TPT)

Multiple thermodynamic states

9 Thermodynamic reweighting principle

10 Discrete transition-based reweighting analysis method (dTRAM)