Non equilibrium thermodynamics of protein organization

Three quarters of the thesis will be devoted to the discussion of non equilibrium systems. We show how certain biological systems cannot be described by standard thermodynamics. The reason is that the energy consumption due to the hydrolysis of ATP imposes to the systems a directionality and therefore a chemical flux that is different from zero. More specifically, we will apply the formalism to molecular chaperones, that are proteins involved in a plethora of biological processes, with a particular in-depth analysis on the mechanisms of protein unfolding and refolding mediated by the two families of chaperones Hsp70 and GroEL. Moreover, with the same mathematical tools, we will provide a qualitative description of some phenomena regarding the Atp-binding cassette transporters, that are important membrane protein complexes used to translocate small molecules in and out of the cell. In the remaining quarter we will analyze the deformation of a polymer chain when it is pulled by an external force. We will explain how it is possible to quantify the orientation along the force and the shrinking along the other directions. It will be also shown that the transverse section shrinks isotropically once the orientation along the force is complete. The main quantities that are used to identify the shape and the orientation of a polymer chain can all be written as a function of a universal quantity that is independent, in first ap- proximation, by the number of monomers, by the rigidity, and even by the volume exclusion.