Honours Bachelor of Science
Molecular machines are stochastic systems that interconvert different forms of energy, such as chemical potential energy and mechanical energy. These machines are generally comprised of many subunits that each perform a specific function. We develop a novel model that captures some of the important behaviours of rotary stochastic coupled systems. This model contains an explicit reference to the degree of coupling between subunits and allows for the investigation of energy transduction as a function of coupling strength. Evolving the system using Fokker-Planck dynamics, we find that the efficiency of this energy transduction is tightly correlated with coupling strength. In addition, recent developments in theoretical studies have established links between information theory and stochastic thermodynamics. Prompted by these developments, we investigate the information-theoretic quantities of nostalgia and learning rate. We find that, in this model, these quantities lose their link to the thermodynamics of the system, as here we consider the case of symmetric coupling between subsystems whereas these quantities were originally derived for asymmetric coupling.
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Thesis advisor: Sivak, David A.
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