Skip to main content

Turing Complete Catalytic Particle Computers

  • Conference paper
Advances in Artificial Life (ECAL 2007)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 4648))

Included in the following conference series:

Abstract

The Bare Bones language is a programming language with a minimal set of operations that exhibits universal computation. We present a conceptual framework, Chemical Bare Bones, to construct Bare Bones programs by programming the state transitions of a multi-functional catalytic particle. Molecular counts represent program variables, and are altered by the action of the catalytic particle. Chemical Bare Bones programs have unique properties with respect to correctness and time complexity. The Chemical Bare Bones implementation is naturally suited to parallel computation. Chemical Bare Bones programs are constructed and stochastically modeled to undertake computations such as multiplication.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bartel, D., Szostak, J.: Isolation of new ribozymes from a large pool of random sequences. Science 261, 1411–1418 (1991)

    Article  Google Scholar 

  2. Bray, D.: Signaling complexes: Biophysical constraints on intracellular communication. Ann. Rev. Biophys. Biomol. Struct. 27, 59–75 (1998)

    Article  Google Scholar 

  3. Bray, D., Duke, T.: Conformational spread: The propogation of allosteric states in large multiprotein complexes. Ann. Rev. Biophys. Biomol. Struct. 33, 53–73 (2004)

    Article  Google Scholar 

  4. Graham, I., Duke, T.: The logical repartoire of ligand-binding proteins. Phys. Biol. 2, 159–165 (2005)

    Article  Google Scholar 

  5. Seelig, G., Yurke, B., Winfree, E.: Dna hybrization catalysts and catalyst circuits. DNA, 329–343 (2004)

    Google Scholar 

  6. Bray, D.: Protein molecules as computational elements in living cells. Nature 376, 307–312 (2004)

    Article  Google Scholar 

  7. Arkin, A., Ross, J.: Computational functions in biochemical reaction networks. Biophys. J. 67, 560–578 (1994)

    Article  Google Scholar 

  8. Hjelmfelt, A., Weinburger, E.D., Ross, J.: Chemical implementation of neural networks and turing machines. Proc. Natl. Acad. Sci. USA 88, 10983–10987 (1991)

    Article  MATH  Google Scholar 

  9. Baron, R., Lioubashevski, O., Katz, E., Niazov, T., Willner, I.: Elementary arithmatic operations by enzymes: A paradigm for metabolic pathway-based computing. Angew. Chem. Int. Ed. (in press, 2006)

    Google Scholar 

  10. Magnasco, M.O.: Chemical kinetics is turing universal. Phys. Rev. Lett. 68, 1190–1193 (1997)

    Article  Google Scholar 

  11. Winfree, E.: Dna computing by self-assembly. The Bridge 33(4) (2003)

    Google Scholar 

  12. Sauro, H.M., Kholodenko, B.N.: Quantitative analysis of signaling networks. Prog. Biophys. Mol. Biol. 86, 5–43 (2004)

    Article  Google Scholar 

  13. Deckard, A., Sauro, H.M.: Preliminary studies on the in silico evolution of biochemical networks. Chembiochem. 5, 1423–1431 (2004)

    Article  Google Scholar 

  14. Brookshear, J.G.: Theory of Computation, Formal Languages, Automata and Complexity. Benjamin-Cummings, Redwood City (1989)

    MATH  Google Scholar 

  15. Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Chem. Phys. 81(25), 2340–2361 (1977)

    Article  Google Scholar 

  16. Sipper, M.: Evolution of Parallel Cellular Machines. Springer, Heidelberg (1997)

    Google Scholar 

  17. Adalsteinsson, D., McMillen, D., Elston, T.C.: Biochemical network stochastic simulator (bionets): software for stochastic modeling of biochemical networks. BMC Bioinformatics 5, 24 (2004)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Fernando Almeida e Costa Luis Mateus Rocha Ernesto Costa Inman Harvey António Coutinho

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Liekens, A.M.L., Fernando, C.T. (2007). Turing Complete Catalytic Particle Computers. In: Almeida e Costa, F., Rocha, L.M., Costa, E., Harvey, I., Coutinho, A. (eds) Advances in Artificial Life. ECAL 2007. Lecture Notes in Computer Science(), vol 4648. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74913-4_120

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-74913-4_120

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-74912-7

  • Online ISBN: 978-3-540-74913-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics