Skip to main content
SpringerLink
Log in

Counting Infinitely by Oritatami Co-transcriptional Folding

  • Conference paper
  • First Online:
SOFSEM 2020: Theory and Practice of Computer Science (SOFSEM 2020)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 12011))

Abstract

A fixed bit-width counter was proposed as a proof-of-concept demonstration of an oritatami model of cotranscriptional folding [Geary et al., Proc. MFCS 2016, LIPIcs 58, 43:1–43:14], and it was embedded into another oritatami system that self-assembles a finite portion of Heighway dragon fractal. In order to expand its applications, we endow this counter with capability to widen bit-width at every encounter with overflow.

This work is supported in part by KAKENHI Grant-in-Aid for Challenging Research (Exploratory) No. 18K19779 and JST Program to Disseminate Tenure Tracking System No. 6F36, both granted to S. S.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Adleman, L., Chang, Q., Goel, A., Huang, M.D.: Running time and program size for self-assembled squares. In: Proceedings of the STOC 2001, pp. 740–748. ACM (2001)

    Google Scholar 

  2. Bryans, N., Chiniforooshan, E., Doty, D., Kari, L., Seki, S.: The power of nondeterminism in self-assembly. Theory Comput. 9, 1–29 (2013)

    Article  MathSciNet  Google Scholar 

  3. Evans, C.G.: Crystals that count! Physical principles and experimental investigations of DNA tile self-assembly. Ph.D. thesis, Caltech (2014)

    Google Scholar 

  4. Geary, C., Étienne Meunier, P., Schabanel, N., Seki, S.: Proving the turing universality of oritatami co-transcriptional folding. In: Proceedings of the ISAAC 2018, pp. 23:1–23:13 (2018)

    Google Scholar 

  5. Geary, C., Étienne Meunier, P., Schabanel, N., Seki, S.: Oritatami: a computational model for molecular co-transcriptional folding. Int. J. Mol. Sci. 20(9), 2259 (2019)

    Article  Google Scholar 

  6. Geary, C., Rothemund, P.W.K., Andersen, E.S.: A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Science 345(6198), 799–804 (2014)

    Article  Google Scholar 

  7. Masuda, Y., Seki, S., Ubukata, Y.: Towards the algorithmic molecular self-assembly of fractals by cotranscriptional folding. In: Câmpeanu, C. (ed.) CIAA 2018. LNCS, vol. 10977, pp. 261–273. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-94812-6_22

    Chapter  MATH  Google Scholar 

  8. McClung, C.R.: Plant circadian rhythms. Plant Cell 18, 792–803 (2006)

    Article  Google Scholar 

  9. Minsky, M. (ed.): Computation: Finite and Infinite Machines. Prentice-Hall Inc., Upper Saddle River (1967)

    MATH  Google Scholar 

  10. Rothemund, P.W.K., Winfree, E.: The program-size complexity of self-assembled squares (extended abstract). In: Proceedings of the STOC 2000, pp. 459–468. ACM (2000)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo, 1828585, Japan

    Kohei Maruyama & Shinnosuke Seki

  2. École Normale Superiéure de Lyon, 46 allée d’Italie, 69007, Lyon, France

    Shinnosuke Seki

Authors
  1. Kohei Maruyama
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shinnosuke Seki
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kohei Maruyama .

Editor information

Editors and Affiliations

  1. University of Macedonia, Thessaloniki, Greece

    Alexander Chatzigeorgiou

  2. University of Bergamo, Bergamo, Italy

    Riccardo Dondi

  3. Cyprus University of Technology, Limassol, Cyprus

    Herodotos Herodotou

  4. Carnegie Mellon University Qatar, Doha, Qatar

    Christos Kapoutsis

  5. Open University of Cyprus, Nicosia, Cyprus

    Yannis Manolopoulos

  6. University of Cyprus, Nicosia, Cyprus

    George A. Papadopoulos

  7. Paris Dauphine University, Paris, France

    Florian Sikora

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Maruyama, K., Seki, S. (2020). Counting Infinitely by Oritatami Co-transcriptional Folding. In: Chatzigeorgiou, A., et al. SOFSEM 2020: Theory and Practice of Computer Science. SOFSEM 2020. Lecture Notes in Computer Science(), vol 12011. Springer, Cham. https://doi.org/10.1007/978-3-030-38919-2_46

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-38919-2_46

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-38918-5

  • Online ISBN: 978-3-030-38919-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation