  The system-level dynamics of multivalent biomolecular interactions can be
simulated using a rule-based kinetic Monte Carlo method in which a rejection
sampling strategy is used to generate reaction events. This method becomes
inefficient when simulating aggregation processes with large biomolecular
complexes. Here, we present a rejection-free method for determining the
kinetics of multivalent biomolecular interactions, and we apply the method to
simulate simple models for ligand-receptor interactions. Simulation results
show that performance of the rejection-free method is equal to or better than
that of the rejection method over wide parameter ranges, and the rejection-free
method is more efficient for simulating systems in which aggregation is
extensive. The rejection-free method reported here should be useful for
simulating a variety of systems in which multisite molecular interactions yield
large molecular aggregates.
