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This thesis establishes a multifaceted extension of the
deterministic control framework that has been a workhorse of
nonequilibrium statistical mechanics, to stochastic, discrete, and
autonomous control mechanisms. This facilitates the application of
ideas from stochastic thermodynamics to the understanding of
molecular machines in nanotechnology and in living things. It also
gives a scale on which to evaluate the nonequilibrium energetic
efficiency of molecular machines, guidelines for designing
effective synthetic machines, and a perspective on the engineering
principles that govern efficient microscopic energy transduction
far from equilibrium. The thesis also documents the author's
design, analysis, and interpretation of the first experimental
demonstration of the utility of this generally applicable method
for designing energetically-efficient control in biomolecules.
Protocols designed using this framework systematically reduced
dissipation, when compared to naive protocols, in DNA hairpins
across a wide range of experimental unfolding speeds and between
sequences with wildly different physical characteristics.
This thesis establishes a multifaceted extension of the
deterministic control framework that has been a workhorse of
nonequilibrium statistical mechanics, to stochastic, discrete, and
autonomous control mechanisms. This facilitates the application of
ideas from stochastic thermodynamics to the understanding of
molecular machines in nanotechnology and in living things. It also
gives a scale on which to evaluate the nonequilibrium energetic
efficiency of molecular machines, guidelines for designing
effective synthetic machines, and a perspective on the engineering
principles that govern efficient microscopic energy transduction
far from equilibrium. The thesis also documents the author's
design, analysis, and interpretation of the first experimental
demonstration of the utility of this generally applicable method
for designing energetically-efficient control in biomolecules.
Protocols designed using this framework systematically reduced
dissipation, when compared to naive protocols, in DNA hairpins
across a wide range of experimental unfolding speeds and between
sequences with wildly different physical characteristics.
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