Programming in Biomolecular Computation: Programs, Self-Interpretation and Visualisation

• Main Authors: L. Hartmann, N.D. Jones, J.G. Simonsen, S.B. Vrist
• Format: Article
• Language: English
• Published: Alexandru Ioan Cuza University of Iasi 2011-06-01
• Series: Scientific Annals of Computer Science
• Online Access: http://www.info.uaic.ro/bin/download/Annals/XXI1/XXI1_9.pdf

Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem conspicuously absent from the literature on biomolecular computing; to partially redress this absence, we introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm); it is also uniform: new ``hardware'' is not needed to solve new problems; and (last but not least) it is Turing complete in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient.