Titlebook: Efficient Control and Spontaneous Transitions; Miranda Louwerse Book 2024 The Editor(s) (if applicable) and The Author(s), under exclusive

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https://doi.org/10.1007/978-3-476-04170-8ics. These provide a thermodynamic measure of the relevance of a particular degree of freedom to the reaction, yielding an optimization criterion for selecting collective variables that describe a reaction. (Material in this chapter also appears in Louwerse and Sivak (Phys Rev Lett 128:170602, 2022).)

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Introduction,anisms 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 mecha

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Theoretical Background,th 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 mor

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Information Thermodynamics of Transition Paths,ermodynamics to describe flows of entropy, energy, and information during the reaction. The main result is a quantification of the irreversibility of system dynamics while a reaction occurs, with parallel definitions of an entropy production rate and mutual information flow for transition-path dynam

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Multidimensional Minimum-Work Protocols, and compared with naive protocols. Using multiple control parameters, which provide additional flexibility in manipulating the system conformation relative to a single control parameter, allows the system to be driven along a fast-relaxing pathway between reaction endpoints. An accounting of the wo

Concomitant

Connections Between Minimum-Work Protocols and Transition Paths,on inversion in a 3.3 Ising model is presented. Designed protocols are found to capture general features of the spontaneous mechanism and energetics given the constraints on the control parameters. Based on these results, the conditions under which a strong correspondence between efficient control p

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