Kinetic Monte Carlo Method for Rule-based Modeling of Biochemical Networks

摘要

We present a kinetic Monte Carlo method for simulating chemicaltransformations specified by reaction rules, which can be viewed as generatorsof chemical reactions, or equivalently, definitions of reaction classes. A ruleidentifies the molecular components involved in a transformation, how thesecomponents change, conditions that affect whether a transformation occurs, anda rate law. The computational cost of the method, unlike conventionalsimulation 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 multivalentligand-receptor interactions. We expect the method will be useful for studyingcellular signaling systems and other physical systems involving aggregationphenomena.