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Efficient turing-universal computation with DNA polymers

by Lulu Qian, David Soloveichik, Erik Winfree
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) ()

Abstract

Bennett’s proposed chemical Turing machine is one of the most important thought experiments in the study of the thermodynam- ics of computation. Yet the sophistication of molecular engineering re- quired to physically construct Bennett’s hypothetical polymer substrate and enzymes has deterred experimental implementations. Here we pro- pose a chemical implementation of stack machines — a Turing-universal model of computation similar to Turing machines — using DNA strand displacement cascades as the underlying chemical primitive.More specif- ically, the mechanism described herein is the addition and removal of monomers from the end of a DNA polymer, controlled by strand displace- ment logic. We capture the motivating feature of Bennett’s scheme: that physical reversibility corresponds to logically reversible computation, and arbitrarily little energy per computation step is required. Further, as a method of embedding logic control into chemical and biological systems, polymer-based chemical computation is significantly more efficient than geometry-free chemical reaction networks.

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