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Reversible Bond Logic

Author Hannah Amelie Earley

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Author Details

Hannah Amelie Earley
  • Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK

Acknowledgements

The author would like to thank Gos Micklem, Jim Lathrop, William Poole, and three anonymous reviewers for their valuable comments and suggestions.

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Hannah Amelie Earley. Reversible Bond Logic. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 6:1-6:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
https://doi.org/10.4230/LIPIcs.DNA.29.6

Abstract

The field of molecular programming allows for the programming of the structure and behavior of matter at the molecular level, even to the point of encoding arbitrary computation. However, current approaches tend to be wasteful in terms of monomers, gate complexes, and free energy. In response, we present a novel abstract model of molecular programming, Reversible Bond Logic (RBL), which exploits the concepts of reversibility and reversible computing to help address these issues. RBL systems permit very general manipulations of arbitrarily complex "molecular" structures, and possess properties such as component reuse, modularity, compositionality. We will demonstrate the implementation of a common free-energy currency that can be shared across systems, initially using it to power a biased walker. Then we will introduce some basic motifs for the manipulation of structures, which will be used to implement such computational primitives as conditional branching, looping, and subroutines. Example programs will include logical negation, and addition and squaring of arbitrarily large numbers. As a consequence of reversibility, we will also obtain the inverse programs (subtraction and square-rooting) for free. Due to modularity, multiple instances of these computations can occur in parallel without cross-talk. Future work aims to further characterize RBL, and develop variants that may be amenable to experimental implementation.

Subject Classification

ACM Subject Classification
  • Computer systems organization → Molecular computing
  • Theory of computation → Models of computation
Keywords
  • Molecular Programming
  • Reversible Computing
  • Structural Manipulation

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