Implementation of a discrete event simulator for biological self-assembly systems

We have implemented a simulation tool for the study of computationally challenging biological self-assembly systems, particularly viral protein shells. The simulator implements a generic model of self-assembly based on simple local binding interactions to specify the behavior of complex self-assembly reactions. Developed discrete event methods allow for fast quantitative simulation of these systems. The new simulator uses the Java language to implement the model in a portable, interactive graphical tool. The Java libraries can also be used directly to build customized simulations. This paper discusses the simulator model, the theoretical basis for its efficient operation, and implementation issues in its design. It also discusses empirical validation of the simulator package and presents sample applications.