Simulation of Self-Assembly in the Abstract Tile Assembly Model with ISU TAS (1101.5151v1)

Abstract: Since its introduction by Erik Winfree in 1998, the abstract Tile Assembly Model (aTAM) has inspired a wealth of research. As an abstract model for tile based self-assembly, it has proven to be remarkably powerful and expressive in terms of the structures which can self-assemble within it. As research has progressed in the aTAM, the self-assembling structures being studied have become progressively more complex. This increasing complexity, along with a need for standardization of definitions and tools among researchers, motivated the development of the Iowa State University Tile Assembly Simulator (ISU TAS). ISU TAS is a graphical simulator and tile set editor for designing and building 2-D and 3-D aTAM tile assembly systems and simulating their self-assembly. This paper reviews the features and functionality of ISU TAS and describes how it can be used to further research into the complexities of the aTAM. Software and source code are available at http://www.cs.iastate.edu/~lnsa.