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Updated: Sep 25, 2025

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks
Published on: November 25, 2015
Exploring the symbol processing 'time interval' parametric constraint in a Belousov-Zhabotinsky operated chemical
Thomas C Draper1, Marta Dueñas-Díez1,2, Juan Pérez-Mercader1,3
1Department of Earth and Planetary Sciences and Origins of Life Initiative, Harvard University Cambridge Massachusetts 02138-1204 USA.
Abstract:
Chemical reactions are powerful molecular recognition machines. This power has been recently harnessed to build actual instances of each class of experimentally realizable computing automata, using exclusively small-molecule chemistry (i.e. without requiring biomolecules). The most powerful of them, a programmable Turing machine, uses the Belousov-Zhabotinsky oscillatory chemistry, and accepts/rejects input sequences through a dual oscillatory and thermodynamic output signature. The time interval between the aliquots representing each letter of the input is the parameter that determines the time it takes to run the computation. Here, we investigate this critical performance parameter, and its effect not only on the computation speed, but also on the robustness of the accept/reject oscillatory and thermodynamic criteria. Our work demonstrates that the time interval is a non-trivial design parameter, whose choice should be made with great care. The guidelines we provide can be used in the optimization of the speed, robustness, and energy efficiency of chemical automata computations.
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