License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.DNA.29.6
URN: urn:nbn:de:0030-drops-187893
URL: https://drops.dagstuhl.de/opus/volltexte/2023/18789/
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Earley, Hannah Amelie

Reversible Bond Logic

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LIPIcs-DNA-29-6.pdf (4 MB)


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.

BibTeX - Entry

@InProceedings{earley:LIPIcs.DNA.29.6,
  author =	{Earley, Hannah Amelie},
  title =	{{Reversible Bond Logic}},
  booktitle =	{29th International Conference on DNA Computing and Molecular Programming (DNA 29)},
  pages =	{6:1--6:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-297-6},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{276},
  editor =	{Chen, Ho-Lin and Evans, Constantine G.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2023/18789},
  URN =		{urn:nbn:de:0030-drops-187893},
  doi =		{10.4230/LIPIcs.DNA.29.6},
  annote =	{Keywords: Molecular Programming, Reversible Computing, Structural Manipulation}
}

Keywords: Molecular Programming, Reversible Computing, Structural Manipulation
Collection: 29th International Conference on DNA Computing and Molecular Programming (DNA 29)
Issue Date: 2023
Date of publication: 04.09.2023


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