Tile Based Self-Assembly of the Rook\u27s Graph

The properties of DNA make it a useful tool for designing self-assembling nanostructures. Branched junction molecules provide the molecular building blocks for creating target complexes. We model the underlying structure of a DNA complex with a graph and we use tools from linear algebra to optimize the self-assembling process. Some standard classes of graphs have been studied in the context of DNA self-assembly, but there are many open questions about other families of graphs. In this work, we study the rook\u27s graph and its related design strategies