Here are some recent applications of stochastic thermodynamics:
the first one concerns equilibrium systems with broken symmetries
[PDF], for a short version and
[PDF] for a long one.
the second one
is about non-markovian effects in an harmonic chain subject to a driving force
the last one is about kinetics and thermodynamics of reversible polymerization
in closed [PDF] or open systems [PDF].
We are proposing one internship/thesis in Non-equilibrium Statistical Physics to be started in the beginning of 2016,
which concerns a stochastic and thermodynamic approach to metabolism,
as described here.
Don't hesitate to get in touch with me to know more about this