Natural Computing

, Volume 10, Issue 1, pp 407–428 | Cite as

Strand algebras for DNA computing

Article

Abstract

We present a process algebra for DNA computing, discussing compilation of other formal systems into the algebra, and compilation of the algebra into DNA structures.

Keywords

Process algebra DNA computing DNA strand displacement 

References

  1. Angluin D, Aspnes J, Diamadi Z, Fischer MJ, Peralta R (2006) Computation in networks of passively mobile finite-state sensors. Distrib Comput 18:235–253Google Scholar
  2. Benenson Y, Paz-Elizur T, Adar R, Keinan E, Livneh Z, Shapiro E (2001) Programmable and autonomous computing machine made of biomolecules. Nature 414:430–434Google Scholar
  3. Berry G, Boudol G (1989) The chemical abstract machine. In: Proceedings of the 17th POPL, ACM, pp 81–94Google Scholar
  4. Cardelli L (2009) Artificial biochemistry. In: Condon A, Harel D, Kok JN, Salomaa A, Winfree E (eds) Algorithmic bioprocesses. Springer, BerlinGoogle Scholar
  5. Cardelli L (2008) On process rate semantics. Theor Comput Sci 391(3):190–215MathSciNetMATHCrossRefGoogle Scholar
  6. Cardelli L (2009) Strand algebras for DNA computing (preliminary version). In: DNA computing and molecular programming, 15th International conference, DNA 15. LNCS 5877. Springer, pp 12–24Google Scholar
  7. Cardelli L, Zavattaro G (2010) Turing universality of the biochemical ground form. Math Struct Comput Sci 20(1):45–73MathSciNetMATHCrossRefGoogle Scholar
  8. Cardelli L, Qian L, Soloveichik D, Winfree E (2009) Personal communicationsGoogle Scholar
  9. Danos V, Laneve C (2004) Formal molecular biology. Theor Comput Sci 325(1):69–110MathSciNetMATHCrossRefGoogle Scholar
  10. Dirks RM, Bois JS, Schaeffer JM, Winfree E, Pierce NA (2007) Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev 49:65–88MathSciNetMATHCrossRefGoogle Scholar
  11. Fournet C, Gonthier G (2000) The join calculus: a language for distributed mobile programming. In: Proceedings of the Applied Semantics Summer School (APPSEM), Caminha, 9–15 SeptemberGoogle Scholar
  12. Hagiya M (2004) Towards molecular programming. In: Ciobanu G, Rozenberg G (eds) Modelling in molecular biology. Springer, HeidelbergGoogle Scholar
  13. Kari L, Konstantinidis S, Sosík P (2005) On properties of bond-free DNA languages. Theor Comput Sci 334(1–3):131–159MATHCrossRefGoogle Scholar
  14. Marathe A, Condon AE, Corn RM (2001) On combinatorial DNA word design. J Comp Biol 8(3):201–219CrossRefGoogle Scholar
  15. Milner R (1999) Communicating and mobile systems: the π-calculus. Cambridge University Press, CambridgeGoogle Scholar
  16. Phillips A, Cardelli L (2009) A programming language for composable DNA circuits. J R Soc Interface 6:S419–S436CrossRefGoogle Scholar
  17. Qian L, Winfree E (2008) A simple DNA gate motif for synthesizing large-scale circuits. In: Proceedings of the 14th international meeting on DNA computingGoogle Scholar
  18. Reisig W (1985) Petri nets: an introduction. Springer-Verlag, BerlinMATHGoogle Scholar
  19. Regev A, Panina EM, Silverman W, Cardelli L, Shapiro E (2004) BioAmbients: an abstraction for biological compartments. Theor Comput Sci 325(1):141–167MathSciNetMATHCrossRefGoogle Scholar
  20. Sakamoto K, Kiga D, Komiya K, Gouzu H, Yokoyama S, Ikeda S, Sugiyama H, Hagiya M (1999) State transitions by molecules. Biosystems 52:81–91CrossRefGoogle Scholar
  21. Seelig G, Soloveichik D, Zhang DY, Winfree E (2006) Enzyme-free nucleic acid logic circuits. Science 314:1585–1588Google Scholar
  22. Soloveichik D, Cook M, Winfree E, Bruck J (2008) Computation with finite stochastic chemical reaction networks. Nat Comput 7:615–633MathSciNetMATHCrossRefGoogle Scholar
  23. Soloveichik D, Seelig G, Winfree E (2010) DNA as a universal substrate for chemical kinetics. PNAS. doi:10.1073/pnas.0909380107
  24. Wolkenhauer O, Ullah M, Kolch W, Cho K (2004) Modelling and simulation of intracellular dynamics: choosing an appropriate framework. IEEE Trans Nanobiosci 3:200–207CrossRefGoogle Scholar
  25. Yin P, Choi HMT, Calvert CR, Pierce NA (2008) Programming biomolecular self-assembly pathways. Nature 451:318–322CrossRefGoogle Scholar
  26. Yurke B, Mills AP Jr (2003) Using DNA to power nanostructures. Genet Program Evolvable Mach 4(2):111–122Google Scholar
  27. Zavattaro G, Cardelli L (2008) Termination problems in chemical kinetics. In: van Breugel F, Chechik M (eds) CONCUR 2008—concurrency theory, 19th international conference. LNCS 5201. Springer, pp 477–491Google Scholar
  28. Zhang DY, Turberfield AJ, Yurke B, Winfree E (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318:1121–1125CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Microsoft ResearchCambridgeUK

Personalised recommendations