Using Automata to Describe Self-Assembled Nanostructures

There is an increased necessity for mathematical study of self-assembly of various phenomena ranging from nano-scale structures, material design, crystals, biomolecular cages such as viral capsids and for computing. We show an algebraic model for describing and characterizing nanostructures built by a set of molecular building blocks. This algebraic approach connects the classifcal view of crystal dissection with a more modern system based on algebraic automata theory.