Nanothermodynamics for Molecular Machines

Nanothermodynamics give a unique insight into the transition between heat, energy, and work taking place on the nanoscale. A characteristic property of the small systems is the fact that their thermodynamic properties do not behave in the same way as those observed for macroscopic systems. Our systematic approach at mapping out, and describing changes in thermodynamic properties at different sizes have lead to new insights into the thermodynamic properties of small systems under various conditions. Systematic simulations of stretching of small RNA-strains have found a significant difference in thermodynamic properties due to size, and find that the interaction with water and co-solvents are detrimental for the thermodynamic properties. These descriptions will be of great importance in further studies of stability, and to understand the reversible stretching of polymer threads. We have in addition included non-equilibrium simulations of transport of ions in channels, and use this to understand how transport properties in small systems are evolving. This is of importance in how future energy materials are made, and which materials are utilised towards new energy-technology. In particular, the transport in solid-state electrolytes have proven to be a very interesting system, where ions are transported, and the interface between the electrolyte and the electrode determines the property of the material. The interfaces are small systems with changing properties due to the size.

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The aim of this project is to establish nanothermodynamics as a method to study molecular machines, and use it as the main method to describe thermodynamic behaviour of molecular machines in equilibrium and non-equilibrium. Based on previous experience with nanothermodynamics, we have established that the thermodynamic properties of systems that are on the nanoscale can deviate significantly from a macroscopic system. The effect is caused mainly by the difference in size and shape of the small system compared to the macroscopic system. Even with a thermodynamic description that has been shown to correctly describe small nanoscale isotropic systems, the difference between nano- and mesoscale is mostly due to size and shape effects, that are not understood at this point. A thorough understanding requires a computation effort to relate size and shape of small systems to the thermodynamic properties of these systems. Molecular machines are one of these types of systems where the small size is fundamental for the way the machine work. Molecular machines have been lifted out as one of the most promising new technologies for groundbreaking advances in energy, medicine, and electronics. To reach its potential, it is paramount that the fundamental thermodynamic laws governing molecular machines is established and understood. Even if molecular machines functions in a way resembling a classical machine, the way energy is converted and dissipated to the surroundings is not well understood, and based on the development of nanothermodynamics, we will explain this energy conversion, and use it to measure transport properties, as well as thermodynamic efficiency of molecular machines.