Classical thermodynamics is a theory for a collection of
molecules in equilibrium. What happens if the number of
molecules in the system becomes smaller and smaller, and the
system boundaries reflect conditions further and further
away from equilibrium? Can we still use thermodynamics? This
lecture aims to explain that the field of non-equilibrium
thermodynamics can be extended to describe in a systematic
manner even molecular behaviour far from equilibrium
conditions. We start introducing the concept of internal
variables, derive the law of mass action, and end
illustrating the theory by applications to RNA stretching
experiments and active transport by the Ca-ATPase. We
discuss that a thermodynamic theory is needed, also for
molecules.

References

S. Kjelstrup, D. Bedeaux, Isabella Inzoli, Jean-Marc Simon,
Criteria for validity of thermodynamic equations from
non-equilibrium molecular dynamics simulations, Energy, 33
(2008) 1185-1196  
J.M. Rubi, D. Bedeaux and S. Kjelstrup, Thermodynamics for
small molecule stretching experiments, J. Phys. Chem. B, 110
(2006) 12733-12737 
D. Bedeaux and S. Kjelstrup, The measurable heat flux that
accompanies active transport by the
Ca- ATPase. Phys. Chem. Chem. Phys. 48 (2008) 7304-7317.