Add basic MSM theory

[cwehmeyer]

Rewrite Section 2.1 to include the basic MSM theory after the literature overview.

This needs to include (among other points):

• [x] lag times (#144)
• [x] transition matrix definition and properties
• [x] VAMP-2 score (#142, #144, #148)
• [x] TICA (#139, #146)
• [x] left/right eigenvectors (#145)
• [x] CK test (#140)

[brookehus]

Will aim to draft this tomorrow afternoon, US eastern time

[brookehus]

Most done in #150 ; more of the CK stuff is in the current PRs I think (e.g. #155).

[cwehmeyer]

@franknoe proposed additional changes to the theory section:

• [x] moving the literature overview into scope
• [x] focus on equilibrium simulations
• [x] removing left eigenvector text/equations beyond stationary distribution
• [x] remove broken line from Fig.2b and plot from y>2.5
• [x] replace sample density by sample free energy in Fig.2c (the reweighted plot is in Fig.4a)
• [x] use thinner lines in Fig.2d
• [x] add text on TICA
• [x] add text on HMMs

[cwehmeyer]

closed via #169