  Large complexes of classical particles play central roles in biology, in
polymer physics, and in other disciplines. However, physics currently lacks
mathematical methods for describing such complexes in terms of component
particles, interaction energies, and assembly rules. Here we describe a Fock
space structure that addresses this need, as well as diagrammatic methods that
facilitate the use of this formalism. These methods can dramatically simplify
the equations governing both equilibrium and non-equilibrium stochastic
chemical systems. A mathematical relationship between the set of all complexes
and a list of rules for complex assembly is also identified.
