Analysis and optimization of DNA self-assembly in simulation

Efficient and useful simulations for problem solving in self-assembly of nanostructures require representations of complex DNA macromolecules far more complex than simple linear strands. We describe a model and data structure capable of compactly representing arbitrary DNA structures (herein referred to as DNA complexes.) This model is then used in Edna, our simulation environment for a test tube, to analyze the kinetics of self-assembly processes, predict concentrations of desirable products and not so desirable byproducts, optimize protocols, and verify their scalability We report thorough testing on two well known protocols, Adleman\u27s original HAMILTONIAN PATH experiment and 3-COLORABILITY. Preliminary results show the model is capable of capturing a good deal of the emerging complexity of interaction at the appropriate level of granularity to make it useful in design and analysis of experiments in self-assembly applications. Furthermore, the model shows that insight can be gained by analysis of simulation results that may be beyond reach with current technology in the wet lab