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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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References

  1. Leonard M Adleman. Molecular computation of solutions to combinatorial problems. science, 266(5187):1021-1024, 1994. Google Scholar
  2. Charles H Bennett. Logical reversibility of computation. IBM journal of Research and Development, 17(6):525-532, 1973. Google Scholar
  3. Charles H Bennett. The thermodynamics of computation—a review. International Journal of Theoretical Physics, 21:905-940, 1982. Google Scholar
  4. Tatiana Brailovskaya, Gokul Gowri, Sean Yu, and Erik Winfree. Reversible computation using swap reactions on a surface. In DNA Computing and Molecular Programming: 25th International Conference, DNA 25, Seattle, WA, USA, August 5-9, 2019, Proceedings 25, pages 174-196. Springer, 2019. Google Scholar
  5. Rory A Brittain, Nick S Jones, and Thomas E Ouldridge. What would it take to build a thermodynamically reversible universal turing machine? computational and thermodynamic constraints in a molecular design. arXiv preprint arXiv:2102.03388, 2021. Google Scholar
  6. Anne Condon, Alan J Hu, Ján Maňuch, and Chris Thachuk. Less haste, less waste: on recycling and its limits in strand displacement systems. Interface Focus, 2(4):512-521, 2012. Google Scholar
  7. Erica Del Grosso, Elisa Franco, Leonard J Prins, and Francesco Ricci. Dissipative DNA nanotechnology. Nature Chemistry, 14(6):600-613, 2022. Google Scholar
  8. David Doty, Trent A Rogers, David Soloveichik, Chris Thachuk, and Damien Woods. Thermodynamic binding networks. In DNA Computing and Molecular Programming: 23rd International Conference, DNA 23, Austin, TX, USA, September 24-28, 2017, Proceedings 23, pages 249-266. Springer, 2017. Google Scholar
  9. Hannah A Earley. On the performance and programming of reversible molecular computers. PhD thesis, University of Cambridge, 2021. Google Scholar
  10. Abeer Eshra, Shalin Shah, Tianqi Song, and John Reif. Renewable DNA hairpin-based logic circuits. IEEE Transactions on Nanotechnology, 18:252-259, 2019. Google Scholar
  11. Constantine G Evans and Erik Winfree. Physical principles for DNA tile self-assembly. Chemical Society Reviews, 46(12):3808-3829, 2017. Google Scholar
  12. Anthony J Genot, Jonathan Bath, and Andrew J Turberfield. Reversible logic circuits made of DNA. Journal of the American Chemical Society, 133(50):20080-20083, 2011. Google Scholar
  13. SJ Green, Jonathan Bath, and AJ Turberfield. Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion. Physical review letters, 101(23):238101, 2008. Google Scholar
  14. Hope A Johnson and Lulu Qian. Simplifying chemical reaction network implementations with two-stranded DNA building blocks. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Schloss Dagstuhl-Leibniz-Zentrum für Informatik, 2020. Google Scholar
  15. Hope A Johnson and Erik Winfree. Verifying polymer reaction networks using bisimulation. Theoretical Computer Science, 843:84-114, 2020. Google Scholar
  16. Hope Amber Johnson and Anne Condon. A coupled reconfiguration mechanism for single-stranded DNA strand displacement systems. In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Schloss Dagstuhl-Leibniz-Zentrum für Informatik, 2022. Google Scholar
  17. Jocelyn Y Kishi, Thomas E Schaus, Nikhil Gopalkrishnan, Feng Xuan, and Peng Yin. Programmable autonomous synthesis of single-stranded DNA. Nature chemistry, 10(2):155-164, 2018. Google Scholar
  18. Eric Klavins. Directed self-assembly using graph grammars. Foundations of nanoscience: self assembled architectures and devices, Snowbird, UT, 2004. Google Scholar
  19. Rolf Landauer. Irreversibility and heat generation in the computing process. IBM journal of research and development, 5(3):183-191, 1961. Google Scholar
  20. Christopher Lutz and Howard Derby. Janus: a time-reversible language. Letter to R. Landauer, 2, 1986. Google Scholar
  21. Kevin Montagne, Raphael Plasson, Yasuyuki Sakai, Teruo Fujii, and Yannick Rondelez. Programming an in vitro DNA oscillator using a molecular networking strategy. Molecular systems biology, 7(1):466, 2011. Google Scholar
  22. Jennifer E Padilla, Matthew J Patitz, Robert T Schweller, Nadrian C Seeman, Scott M Summers, and Xingsi Zhong. Asynchronous signal passing for tile self-assembly: Fuel efficient computation and efficient assembly of shapes. International Journal of Foundations of Computer Science, 25(04):459-488, 2014. Google Scholar
  23. Lulu Qian, David Soloveichik, and Erik Winfree. Efficient turing-universal computation with DNA polymers. In DNA Computing and Molecular Programming: 16th International Conference, DNA 16, Hong Kong, China, June 14-17, 2010, Revised Selected Papers 16, pages 123-140. Springer, 2011. Google Scholar
  24. Ian Seet, Thomas E Ouldridge, and Jonathan PK Doye. Simulation of reversible molecular mechanical logic gates and circuits. Physical Review E, 107(2):024134, 2023. Google Scholar
  25. Jong-Shik Shin and Niles A Pierce. A synthetic DNA walker for molecular transport. Journal of the American Chemical Society, 126(35):10834-10835, 2004. Google Scholar
  26. Friedrich C Simmel, Bernard Yurke, and Hari R Singh. Principles and applications of nucleic acid strand displacement reactions. Chemical reviews, 119(10):6326-6369, 2019. Google Scholar
  27. David Soloveichik, Matthew Cook, Erik Winfree, and Jehoshua Bruck. Computation with finite stochastic chemical reaction networks. natural computing, 7:615-633, 2008. Google Scholar
  28. David Soloveichik, Georg Seelig, and Erik Winfree. DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Sciences, 107(12):5393-5398, 2010. Google Scholar
  29. Leo Szilard. Über die Entropieverminderung in einem thermodynamischen System bei Eingriffen intelligenter Wesen. Zeitschrift für Physik, 53(11-12):840-856, 1929. Google Scholar
  30. Anupama J Thubagere, Wei Li, Hope A Johnson, Zibo Chen, Shayan Doroudi, Yae Lim Lee, Gregory Izatt, Sarah Wittman, Niranjan Srinivas, Damien Woods, et al. A cargo-sorting DNA robot. Science, 357(6356):eaan6558, 2017. Google Scholar
  31. Kohji Tomita, Haruhisa Kurokawa, and Satoshi Murata. Graph-rewriting automata as a natural extension of cellular automata. Adaptive Networks: Theory, Models and Applications, pages 291-309, 2009. Google Scholar
  32. Erik Winfree. Algorithmic self-assembly of DNA. California Institute of Technology, 1998. Google Scholar
  33. Peng Yin, Harry MT Choi, Colby R Calvert, and Niles A Pierce. Programming biomolecular self-assembly pathways. Nature, 451(7176):318-322, 2008. Google Scholar
  34. Tetsuo Yokoyama, Holger Bock Axelsen, and Robert Glück. Principles of a reversible programming language. In Proceedings of the 5th Conference on Computing Frontiers, pages 43-54, 2008. Google Scholar
  35. David Yu Zhang and Georg Seelig. Dynamic DNA nanotechnology using strand-displacement reactions. Nature chemistry, 3(2):103-113, 2011. Google Scholar
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