Skip to main content
SpringerLink
Log in

Peptide Computers

  • Chapter
Languages Alive

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7300))

Abstract

A peptide computer is a formal model for computations based on peptide-antibody interactions. We provide a rigorous detailed formal model and prove that this model leads to a well-defined computational behaviour. We review existing results concerning the power and limitations of peptide computers and the types of non-determinism arising in such computers on the basis of this formal model.

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 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adamatzky, A.: Physarum Machines, Computers from Slime Mold, Nonlinear Science, Series A, vol. 74. World Scientific, Singapore (2010)

    Book  Google Scholar 

  2. Balan, M.S., Krithivasan, K.: Modeling Boolean circuits using peptide-antibody interactions. In: Chandra, P., Rathish Kumar, B.V. (eds.) Mathematical Biology, pp. 187–193. Anamaya Publishers, New Delhi (2006), copublished by Anshan Ltd., Tunbridge Wells, UK

    Google Scholar 

  3. Balan, M.S.: Computational Models Using Peptide-Antibody Interactions. PhD Thesis, Indian Institute of Technology, Madras (2004)

    Google Scholar 

  4. Balan, M.S.: Non-determinism in peptide computer. In: Vaszil, G. (ed.) Proceedings of the International Workshop, Automata for Cellular and Molecular Computing, Budapest, Hungary, August 31, pp. 108–119. MTA, SZTAKI, Budapest (2007)

    Google Scholar 

  5. Balan, M.S.: A study on automation in peptide computing. In: Abraham, A., Carvalho, A., Herrera, F., Pai, V., Coelho, A., Menezes, R. (eds.) Proceedings of 2009 World Congress on Nature & and Biologically Inspired Computing, NABIC 2009, Coimbatore, India, December 9–11, pp. 128–133. IEEE (2009)

    Google Scholar 

  6. Balan, M.S.: Properties of binding-blocking automata: A study. In: Abdullah, R., Khader, A.T., Venkat, I., Wong, L.P., Subramanian, K.G. (eds.) Proceedings, Sixth International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2011, Penang, Malaysia, September 27–29, pp. 211–215. IEEE Computer Society, Los Alamitos (2011)

    Chapter  Google Scholar 

  7. Balan, M.S., Jürgensen, H.: Peptide Computing – Universality and Theoretical Model. In: Calude, C.S., Dinneen, M.J., Păun, G., Rozenberg, G., Stepney, S. (eds.) UC 2006. LNCS, vol. 4135, pp. 57–71. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  8. Balan, M.S., Jürgensen, H.: On the universality of peptide computing. Nat. Comput. 7, 71–94 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  9. Balan, M.S., Jürgensen, H., Krithivasan, K.: Peptide computing: A survey. In: Krithivasan, K., Rama, R. (eds.) Formal Language Aspects of Natural Computing, Proceedings of Research Level Discussion Meeting on Natural Computing Held at Indian Institute of Technology Madras, Chennai. Ramanujan Mathematical Society Lecture Notes Series, vol. 3, pp. 63–76. Ramanujan Mathematical Society, India (2006)

    Google Scholar 

  10. Balan, M.S., Krithivasan, K.: Realizing Switching Functions Using Peptide-Antibody Interactions. In: Jonoska, N., Păun, G., Rozenberg, G. (eds.) Aspects of Molecular Computing. LNCS, vol. 2950, pp. 353–360. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  11. Balan, M.S., Krithivasan, K.: Parallel computation of simple arithmetic using peptide-antibody interactions. BioSystems 76, 303–307 (2004)

    Article  MATH  Google Scholar 

  12. Balan, M.S., Krithivasan, K., Sivasubramanyam, Y.: Peptide Computing - Universality and Complexity. In: Jonoska, N., Seeman, N.C. (eds.) DNA 2001. LNCS, vol. 2340, pp. 290–299. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  13. Sakthi Balan, M., Seshan, P.: Incremental Building in Peptide Computing to Solve Hamiltonian Path Problem. In: Dediu, A.-H., Fernau, H., Martín-Vide, C. (eds.) LATA 2010. LNCS, vol. 6031, pp. 549–560. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  14. Bartha, M., Krész, M.: Soliton circuits and network-based automata: Review and perspectives. In: Martín-Vide, C. (ed.) Scientific Applications of Language Methods, Mathematics, Computing, Language, and Life: Frontiers in Mathematical Linguistics and Language Theory, vol. 2, pp. 585–631. Imperial College Press, London (2011)

    Chapter  Google Scholar 

  15. Blizard, W.D.: Multiset theory. Notre Dame J. Formal Logic 30, 36–66 (1989)

    Article  MathSciNet  MATH  Google Scholar 

  16. Calude, C.S., Păun, G.: Computing with Cells and Atoms: An Introduction to Quantum, DNA and Membrane Computing. Taylor & Francis, London (2001)

    MATH  Google Scholar 

  17. Cantor, C.R., Schimmel, P.R.: Biophysical Chemistry, vol. 3. W. H. Freeman, San Francisco (1980)

    Google Scholar 

  18. Czeizler, E., Czeizler, E.: On the power of parallel communicating Watson-Crick automata systems. Theoret. Comput. Sci. 358, 142–147 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  19. Czeizler, E., Czeizler, E.: Parallel communicating Watson-Crick automata systems. Acta Cybernet 17, 685–700 (2006)

    MathSciNet  MATH  Google Scholar 

  20. Czeizler, E., Czeizler, E.: A short survey on Watson-Crick automata. Bull. EATCS 88, 104–119 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  21. Dasgupta, D., Niño, L.F.: Immunological Computation: Theory and Applications. CRC Press, Boca Raton (2009)

    Google Scholar 

  22. Dassow, J., Jürgensen, H.: Soliton automata. J. Comput. System Sci. 40, 158–181 (1990)

    Article  MathSciNet  MATH  Google Scholar 

  23. Ehrenfeucht, A., Rozenberg, G.: Reaction systems. Fund. Inform. 75, 263–280 (2007)

    MathSciNet  MATH  Google Scholar 

  24. Gale, D., Shapley, L.S.: College admissions and the stability of marriage. Am. Math. Monthly 69, 9–15 (1962)

    Article  MathSciNet  MATH  Google Scholar 

  25. Gusfield, D., Irving, R.W.: The Stable Marriage Problem: Structure and Algorithms. MIT Press, Cambridge (1989)

    MATH  Google Scholar 

  26. Harada, K., Ishida, Y.: Antibody-based computing. Artif. Life Robotics 13, 180–183 (2008)

    Article  Google Scholar 

  27. Head, T.: Biomolecular realizations of a parallel architecture for solving combinatorial problems. New Generation Computing 19, 301–312 (2001)

    Article  MATH  Google Scholar 

  28. Heyting, A. (ed.): Constructivity in Mathematics, Proceedings of the Colloquium Held at Amsterdam 1957. Studies in Logic and the Foundations of Mathematics. North-Holland, Amsterdam (1959)

    MATH  Google Scholar 

  29. Hoeberechts, M.: On the Foundations of Computability Theory. PhD Thesis, The University of Western Ontario (2009)

    Google Scholar 

  30. Hug, H., Schuler, R.: Strategies for the development of a peptide computer. Bioinformatics 17, 364–368 (2001)

    Article  Google Scholar 

  31. Ishida, Y.: Immunity-Based Systems: A Design Perspective. Springer, Berlin (2004)

    Book  Google Scholar 

  32. Ishida, Y., Hayashi, T.: Asymmetric Phenomena of Segregation and Integration in Biological Systems: A Matching Automaton. In: Velásquez, J.D., Ríos, S.A., Howlett, R.J., Jain, L.C. (eds.) KES 2009, Part II. LNCS (LNAI), vol. 5712, pp. 789–796. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  33. Ishida, Y., Sasaki, K.: Asymmetric Structure between Two Sets of Adaptive Agents: An Approach Using a Matching Automaton. In: König, A., Dengel, A., Hinkelmann, K., Kise, K., Howlett, R.J., Jain, L.C. (eds.) KES 2011, Part IV. LNCS (LNAI), vol. 6884, pp. 357–365. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  34. Jürgensen, H.: Multisets, bags, families and crowds (2011) (manuscript)

    Google Scholar 

  35. Jürgensen, H., Konstantinidis, S.: Codes. In: Rozenberg, G., Salomaa, A. (eds.) Handbook of Formal Languages, vol. 1, pp. 511–607. Springer, Berlin (1997)

    Chapter  Google Scholar 

  36. Kalmár, L.: An argument against the plausibility of Church’s thesis. In: Heyting (ed.) [28], pp. 72–80

    Google Scholar 

  37. Knuth, D.E.: Mariages stables et leurs relations avec d’autres problèmes combinatoires: Introduction à l’analyse mathématique des algorithmes. Collection de la Chaire Aisenstadt, Les Presses de l’Université de Montréal, Montréal (1976), English translation: Stable Marriage and Its Relation to Other Combinatorial Problems: An Introduction to the Mathematical Analysis of Algorithms. Translated by M. Goldstein. CRM Proceedings & Lecture Notes, vol. 10. American Mathematical Society, Providence, Rhode Island (1997)

    Google Scholar 

  38. Păun, G., Rozenberg, G., Salomaa, A.: DNA Computing: New Computing Paradigms. Springer, Berlin (1998)

    Book  MATH  Google Scholar 

  39. Păun, G.: Membrane Computing. Springer, Berlin (2002)

    Book  MATH  Google Scholar 

  40. Péter, R.: Rekursivität und Konstruktivität. In: Heyting (ed.) [28], pp. 69–71

    Google Scholar 

  41. Rozenberg, G.: Computer science, informatics, and natural computing – personal reflections. In: Cooper, S.B., Löwe, B., Sorbi, A. (eds.) New Computational Paradigms. Changing Comceptions of What is Computable, pp. 373–379. Springer, New York (2008)

    Google Scholar 

  42. Surhone, L.M., Tennoe, M.T., Henssonow, S.F. (eds.): Peptide Computing. Betascript Publishing (August 2010), see footnote 1

    Google Scholar 

  43. Tarakanov, A.O., Skormin, V.A., Sokolova, S.P.: Immunocomputing, Principles and Applications. Springer, New York (2003)

    MATH  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. ECOM Research Lab, Education and Research, Infosys Limited, Bangalore, 560100, India

    M. Sakthi Balan

  2. Department of Computer Science, The University of Western Ontario, London, Ontario, Canada, N6A 5B7

    Helmut Jürgensen

Authors
  1. M. Sakthi Balan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Helmut Jürgensen
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Institut für Informatik, Universität Potsdam, August-Bebel-Straße 89, 14482, Potsdam, Germany

    Henning Bordihn

  2. Institut für Informatik, Universität Giessen, Arndtstraße 2, 35392, Giessen, Germany

    Martin Kutrib

  3. Fakultät für Informatik, Otto-von-Guericke-Universität Magdeburg, Universitätsplatz 2, 39016, Magdeburg, Germany

    Bianca Truthe

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Balan, M.S., Jürgensen, H. (2012). Peptide Computers. In: Bordihn, H., Kutrib, M., Truthe, B. (eds) Languages Alive. Lecture Notes in Computer Science, vol 7300. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31644-9_1

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-31644-9_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-31643-2

  • Online ISBN: 978-3-642-31644-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation