The local rules dynamics model for self-assembly simulation
The local rules dynamics model for self-assembly simulation
Queue-based method for efficient simulation of biological self-assembly systems
Journal of Computational Physics
Review: Stochastic approaches for modelling in vivo reactions
Computational Biology and Chemistry
Activation energy-based simulation for self-assembly of multi-shape tiles
Proceedings of the 9th annual conference companion on Genetic and evolutionary computation
CMC'10 Proceedings of the 11th international conference on Membrane computing
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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. Recently 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.