Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems
Figure 2
Simple illustration of ambiguity in the products of reaction rules.
(A) A simple rule encodes the reversible binding of two molecule types, A and B. (B)–(D) If both molecules have multiple binding sites then they may be present within arbitrarily complex complexes. Breaking the bond between A and B thus produces a variety of product species, some of which may correspond to population species and others not. Dashed line represents a bond addition/deletion operation.