Introduction

Quantifying the dynamics and energetics of a system as it undergoes a transition between stable conformations is central to the study of reaction mechanisms and the derivation of reaction rates. For conformational changes in biomolecules, the space the system navigates is high dimensional, presenting challenges to the observation of reactive events in simulation or experiment and obscuring dynamical details that are relevant to the reaction mechanism. Developments in recent decades in transition-path theory, transition-path sampling, and single-molecule experimental techniques have transformed our ability to observe biomolecular reactions in microscopic detail and extract general features of the mechanism. Nearly simultaneously, rapid developments in the field of stochastic thermodynamics have extended familiar notions of work, heat, and entropy to nonequilibrium contexts. One focus of these efforts is the design of protocols that dynamically manipulate the system’s conformation with minimal energetic cost. In this thesis, I investigate slow, energetically efficient driving protocols that drive a system between conformations corresponding to endpoints of a reaction, aiming to find connections between principles of efficient driving and the spontaneous transition mechanism in the absence of driving.