Theoretical Background

In this chapter, some necessary theoretical background is introduced which will inform the work in the remainder of this thesis. Section 2.1 begins with a review of stochastic dynamics, followed by some background into information theory in Sect. 2.1.2 and stochastic thermodynamics in Sect. 2.1.3. The fundamentals of transition-path theory are then reviewed in Sect. 2.2 and the utility of the committor as a reaction coordinate is discussed in more detail. In Sect. 2.3, the thermodynamics of control protocols are reviewed, followed by introduction of minimum-work protocols in the linear-response regime and the generalized friction.