  Strand displacement and tile assembly systems are designed to follow
prescribed kinetic rules (i.e., exhibit a specific time-evolution). However,
the expected behavior in the limit of infinite time--known as thermodynamic
equilibrium--is often incompatible with the desired computation. Basic physical
chemistry implicates this inconsistency as a source of unavoidable error. Can
the thermodynamic equilibrium be made consistent with the desired computational
pathway? In order to formally study this question, we introduce a new model of
molecular computing in which computation is driven by the thermodynamic driving
forces of enthalpy and entropy. To ensure greatest generality we do not assume
that there are any constraints imposed by geometry and treat monomers as
unstructured collections of binding sites. In this model we design Boolean
AND/OR formulas, as well as a self-assembling binary counter, where the
thermodynamically favored states are exactly the desired final output
configurations. Though inspired by DNA nanotechnology, the model is
sufficiently general to apply to a wide variety of chemical systems.
