Logic reversibility and thermodynamic irreversibility demonstrated by DNAzyme-based Toffoli and Fredkin logic gates

The Toffoli and Fredkin gates were suggested as a means to exhibit logic reversibility and thereby reduce energy dissipation associated with logic operations in dense computing circuits. We present a construction of the logically reversible Toffoli and Fredkin gates by implementing a library of pred...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2012-12, Vol.109 (52), p.21228-21233
Main Authors: Orbach, Ron, Remacle, Françoise, Levine, R. D., Willner, Itamar
Format: Article
Language:English
Subjects:
Abstract logic
Base Sequence
Correlation analysis
Deoxyribonucleic acid
DNA
DNA, Catalytic - metabolism
Energy dissipation
Enzymes
Fluorescence
Gels
Libraries
Logic
Logic circuits
Logic gates
Magnesium - pharmacology
MicroRNA
Nucleic acids
Physical Sciences
Physical, chemical, mathematical & earth Sciences
Physique, chimie, mathématiques & sciences de la terre
Protein Subunits - metabolism
Substrates
Thermodynamic irreversibility
Thermodynamics
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Summary:The Toffoli and Fredkin gates were suggested as a means to exhibit logic reversibility and thereby reduce energy dissipation associated with logic operations in dense computing circuits. We present a construction of the logically reversible Toffoli and Fredkin gates by implementing a library of predesigned Mg ²⁺-dependent DNAzymes and their respective substrates. Although the logical reversibility, for which each set of inputs uniquely correlates to a set of outputs, is demonstrated, the systems manifest thermodynamic irreversibility originating from two quite distinct and nonrelated phenomena. (i) The physical readout of the gates is by fluorescence that depletes the population of the final state of the machine. This irreversible, heat-releasing process is needed for the generation of the output. (ii) The DNAzyme-powered logic gates are made to operate at a finite rate by invoking downhill energy-releasing processes. Even though the three bits of Toffoli’s and Fredkin’s logically reversible gates manifest thermodynamic irreversibility, we suggest that these gates could have important practical implication in future nanomedicine.
ISSN:0027-8424
1091-6490
1091-6490
DOI:10.1073/pnas.1219672110