  Structure-forming systems are ubiquitous in nature, ranging from atoms
building molecules to self-assembly of colloidal amphibolic particles. The
understanding of the underlying thermodynamics of such systems remains an
important problem. Here we derive the entropy for structure-forming systems
that differs from Boltzmann-Gibbs entropy by a term that explicitly captures
clustered states. For large systems and low concentrations, the approach is
equivalent to the grand-canonical ensemble; for small systems, we find
significant deviations. We derive the detailed fluctuation theorem and Crooks'
work fluctuation theorem for structure-forming systems. The connection to the
theory of particle self-assembly is discussed. We apply the results to several
physical systems. We present the phase diagram for patchy particles described
by the Kern-Frenkel potential. We show that the Curie-Weiss model with molecule
structures exhibits a first-order phase transition.
