  We present a kinetic Monte Carlo method for simulating chemical
transformations specified by reaction rules, which can be viewed as generators
of chemical reactions, or equivalently, definitions of reaction classes. A rule
identifies the molecular components involved in a transformation, how these
components change, conditions that affect whether a transformation occurs, and
a rate law. The computational cost of the method, unlike conventional
simulation approaches, is independent of the number of possible reactions,
which need not be specified in advance or explicitly generated in a simulation.
To demonstrate the method, we apply it to study the kinetics of multivalent
ligand-receptor interactions. We expect the method will be useful for studying
cellular signaling systems and other physical systems involving aggregation
phenomena.
