Programming in Biomolecular Computation

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Lars Hartmann, Neil D. Jones, Jakob Grue Simonsen
Department of Copmuter Science, University of Copenhagen(DIKU), Copenhagen, Denmark

Abstract

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 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.
A prototype model has been implemented (for now in silico on a conventional computer). This work opens new perspectives on just how computation may be specified at the biological level.

Keywords: biomolecular, computation, programmability, universality.

Presented at "1st International Workshop on Interactions between Computer Science and Biology"(CS2Bio) June 2010

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