A Domain-Specific Language for Programming in the Tile Assembly Model

Authors:
David Doty;Matthew J. Patitz
Affiliations:
Department of Computer Science, Iowa State University, Ames, USA 50011;Department of Computer Science, Iowa State University, Ames, USA 50011
Venue:
DNA Computing and Molecular Programming
Year:
2009

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Abstract

We introduce a domain-specific language (DSL) for creating sets of tile types for simulations of the abstract Tile Assembly Model. The language defines objects known as tile templates, which represent related groups of tiles, and a small number of basic operations on tile templates that help to eliminate the error-prone drudgery of enumerating such tile types manually or with low-level constructs of general-purpose programming languages. The language is implemented as a class library in Python (a so-called internal DSL), but is presented independently of Python or object-oriented programming, with emphasis on support for a visual editing tool for creating large sets of complex tile types.