On Turedo Hierarchies and Intrinsic Universality

Authors Samuel Nalin, Guillaume Theyssier



PDF
Thumbnail PDF

File

LIPIcs.DNA.28.6.pdf
  • Filesize: 0.79 MB
  • 18 pages

Document Identifiers

Author Details

Samuel Nalin
  • Univ. Orléans, INSA Centre Val de Loire, LIFO EA 4022, FR-45067 Orléans, France
Guillaume Theyssier
  • I2M, CNRS, Université Aix-Marseille, France

Cite AsGet BibTex

Samuel Nalin and Guillaume Theyssier. On Turedo Hierarchies and Intrinsic Universality. In 28th International Conference on DNA Computing and Molecular Programming (DNA 28). Leibniz International Proceedings in Informatics (LIPIcs), Volume 238, pp. 6:1-6:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
https://doi.org/10.4230/LIPIcs.DNA.28.6

Abstract

This paper is about turedos, which are Turing machines whose head can move in the plane (or in a higher-dimensional space) but only in a self-avoiding way, by putting marks (letters) on visited positions and moving only to unmarked, therefore unvisited, positions. The turedo model has been introduced recently as a useful abstraction of oritatami systems, which where established a few years ago as a theoretical model of RNA co-transcriptional folding. The key parameter of turedos is their lookup radius: the distance up to which the head can look around in order to make its decision of where to move to and what mark to write. In this paper we study the hierarchy of turedos according to their lookup radius and the dimension of space using notions of simulation up to spatio-temporal rescaling (a standard approach in cellular automata or self-assembly systems). We establish that there is a rich interplay between the turedo parameters and the notion of simulation considered. We show in particular, for the most liberal simulations, the existence of 3D turedos of radius 1 that are intrinsically universal for all radii, but that this is impossible in dimension 2, where some radius 2 turedo are impossible to simulate at radius 1. Using stricter notions of simulation, intrinsic universality becomes impossible, even in dimension 3, and there is a strict radius hierarchy. Finally, when restricting to radius 1, universality is again possible in dimension 3, but not in dimension 2, where we show however that a radius 3 turedo can simulate all radius 1 turedos.

Subject Classification

ACM Subject Classification
  • Theory of computation → Models of computation
  • Theory of computation → Formal languages and automata theory
Keywords
  • Turedos
  • intrinsic universality
  • Higher-dimensional Turing machines
  • Oritatami systems

Metrics

  • Access Statistics
  • Total Accesses (updated on a weekly basis)
    0
    PDF Downloads

References

  1. Florent Becker, Diego Maldonado, Nicolas Ollinger, and Guillaume Theyssier. Universality in freezing cellular automata. In Sailing Routes in the World of Computation - 14th Conference on Computability in Europe, CiE 2018, Kiel, Germany, July 30 - August 3, 2018, Proceedings, pages 50-59, 2018. URL: https://doi.org/10.1007/978-3-319-94418-0_5.
  2. Laurent Boyer and Guillaume Theyssier. On factor universality in symbolic spaces. In Mathematical Foundations of Computer Science 2010, pages 209-220. Springer Berlin Heidelberg, 2010. URL: https://doi.org/10.1007/978-3-642-15155-2_20.
  3. Matthew Cook, Yunhui Fu, and Robert T. Schweller. Temperature 1 self-assembly: Deterministic assembly in 3D and probabilistic assembly in 2D. In SODA2011: Proceedings of the 22nd Annual ACM-SIAM Symposium on Discrete, pages 570-589, 2011. Google Scholar
  4. Marianne Delorme, Jacques Mazoyer, Nicolas Ollinger, and Guillaume Theyssier. Bulking ii: Classifications of cellular automata. Theor. Comput. Sci., 412(30):3881-3905, 2011. URL: https://doi.org/10.1016/j.tcs.2011.02.024.
  5. David Doty, Jack H. Lutz, Matthew J. Patitz, Robert T. Schweller, Scott M. Summers, and Damien Woods. The tile assembly model is intrinsically universal. In FOCS2012: Proceedings of the 53rd Annual IEEE Symposium on Foundations of Computer Science, pages 302-310, 2012. Google Scholar
  6. Pierre Étienne Meunier and Damien Woods. The non-cooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation. In STOC 2017: Proceedings of the 49th Annual ACM SIGACT Symposium on Theory of Computing, pages 328-341, 2017. Google Scholar
  7. Cody Geary, Guido Grossi, Ewan K. S. McRae, Paul W. K. Rothemund, and Ebbe S. Andersen. RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds. Nature Chemistry, 13:549-558, 2021. Google Scholar
  8. Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, and Shinnosuke Seki. Programming biomolecules that fold greedily during transcription. In MFCS2016: Proceedings of the 41st International Symposium on Mathematical Foundations of Computer Science, volume 58 of LIPIcs, pages 43:1-43:14, 2016. Google Scholar
  9. Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, and Shinnosuke Seki. Oritatami: A computational model for molecular co-transcriptional folding. International Jounal of Molecular Sciences, 9(2259), 2019. URL: https://doi.org/10.3390/ijms20092259.
  10. Cody Geary, Pierre-Étienne Meunier, Nicolas Schabanel, and Shinonsuke Seki. Proving the Turing universality of oritatami cotranscriptional folding. In ISAAC 2018: Proceedings of the 29th International Symposium on Algorithms and Computation, volume 123 of LIPIcs, pages 23:1-23:13, 2018. Google Scholar
  11. Cody Geary, Paul W. K. Rothemund, and Ebbe S. Andersen. A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Science, 345:799-804, 2014. Google Scholar
  12. Cody W. Geary, Pierre-Étienne Meunier, Nicolas Schabanel, and Shinnosuke Seki. Proving the turing universality of oritatami co-transcriptional folding. In Wen-Lian Hsu, Der-Tsai Lee, and Chung-Shou Liao, editors, 29th International Symposium on Algorithms and Computation, ISAAC 2018, December 16-19, 2018, Jiaoxi, Yilan, Taiwan, volume 123 of LIPIcs, pages 23:1-23:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. URL: https://doi.org/10.4230/LIPIcs.ISAAC.2018.23.
  13. Jacob Hendricks, Matthew J. Patitz, and Trent A. Rogers. Universal simulation of directed systems in the abstract tile assembly model requires undirectedness. In 2016 IEEE 57th Annual Symposium on Foundations of Computer Science (FOCS). IEEE, October 2016. URL: https://doi.org/10.1109/focs.2016.90.
  14. James I. Lathrop, Jack H. Lutz, Matthew J. Patitz, and Scott M. Summers. Computability and complexity in self-assembly. Theory Comput. Syst., 48(3):617-647, 2011. URL: https://doi.org/10.1007/s00224-010-9252-0.
  15. Ming Li and Paul Vitányi. Algorithmic complexity. In Texts in Computer Science, pages 101-195. Springer New York, 2008. URL: https://doi.org/10.1007/978-0-387-49820-1_2.
  16. Pierre-Etienne Meunier, Matthew J. Patitz, Scott M. Summers, Guillaume Theyssier, Andrew Winslow, and Damien Woods. Intrinsic universality in tile self-assembly requires cooperation. In Chandra Chekuri, editor, Proceedings of the Twenty-Fifth Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 2014, Portland, Oregon, USA, January 5-7, 2014, pages 752-771. SIAM, 2014. URL: https://doi.org/10.1137/1.9781611973402.56.
  17. Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, and Guillaume Theyssier. Oritatami Systems Assemble Shapes No Less Complex Than Tile Assembly Model (ATAM). In Petra Berenbrink and Benjamin Monmege, editors, 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022), volume 219 of Leibniz International Proceedings in Informatics (LIPIcs), pages 51:1-51:23, Dagstuhl, Germany, 2022. Schloss Dagstuhl - Leibniz-Zentrum für Informatik. URL: https://doi.org/10.4230/LIPIcs.STACS.2022.51.
  18. Paul W. K. Rothemund, Nick Papadakis, and Erik Winfree. Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biology, 2:2041-2053, 2004. Google Scholar
  19. Erik Winfree. Algorithmic Self-Assembly of DNA. PhD thesis, California Institute of Technology, 1998. Google Scholar
Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail