Modelling, simulating and verifying Turing-powerful strand displacement systems

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6937 LNCS, Issue , 2011, Pages 130-144

  Lakin, Matthew R ^a   Phillips, Andrew ^a  

^a MICROSOFT RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BINARY NUMBER; DNA POLYMERS; DNA STRANDS; KINETIC PROPERTIES; NON-TRIVIAL; PROGRAMMING LANGUAGE; RIPPLE CARRY ADDERS; STACK MACHINES; SUPPORT OPERATIONS; SYMBOLIC COMPUTATION;

ADDERS; CALCULATIONS; MACHINE DESIGN; MATHEMATICAL MODELS; MODEL CHECKING; SEMANTICS; TURING MACHINES;

DNA;

EID: 80053144639     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-23638-9_12     Document Type: Conference Paper

References (16)

1. Venkataraman, S., Dirks, R.M., Ueda, C.T., Pierce, N.A.: Selective cell death mediated by small conditional RNAs. Proc. Natl. Acad. Sci. U S A 107(39), 16777-16782 (2010)
2. Turing, A.M.: On computable numbers, with an application to the Entscheidungsproblem. Proc. London Mathematical Society s2-42(1), 230-265 (1937)
3. Zhang, D.Y., Seelig, G.: Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3, 103-113 (2011)
4. Qian, L., Soloveichik, D., Winfree, E.: Efficient turing-universal computation with DNA polymers. In: Sakakibara, Y., Mi, Y. (eds.) DNA 16 2010. LNCS, vol. 6518, pp. 123-140. Springer, Heidelberg (2011)
5. Phillips, A., Cardelli, L.: A programming language for composable DNA circuits. J. R. Soc. Interface 6(suppl 4), S419-S436 (2009)
6. Paulevé, L., Youssef, S., Lakin, M.R., Phillips, A.: A generic abstract machine for stochastic process calculi. In: Proc. CMSB 2010, pp. 43-54. ACM, New York (2010)
7. Zhang, D.Y.: Towards domain-based sequence design for DNA strand displacement reactions. In: Sakakibara, Y., Mi, Y. (eds.) DNA 16 2010. LNCS, vol. 6518, pp. 162-175. Springer, Heidelberg (2011)
8. Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 115, 1716-1733 (2001)
9. Hinton, A., Kwiatkowska, M., Norman, G., Parker, D.: PRISM: A tool for automatic verification of probabilistic systems. In: Hermanns, H., Palsberg, J. (eds.) TACAS 2006. LNCS, vol. 3920, pp. 441-444. Springer, Heidelberg (2006) (Pubitemid 44019387)
10. Bennett, C.H.: The thermodynamics of computation-a review. Int. J. Theor. Phys. 21(12), 905-939 (1982)
11. Cardelli, L., Zavattaro, G.: Turing universality of the biochemical ground form. Math. Struct. Comp. Sci. 20(1), 45-73 (2010)
12. Soloveichik, D., Cook, M., Winfree, E., Bruck, J.: Computation with finite stochastic chemical reaction networks. Nat. Comput. 7, 615-633 (2008)
13. Cook, M., Soloveichik, D., Winfree, E., Bruck, J.: Programmability of chemical reaction networks. In: Condon, A., Harel, D., Kok, J.N., Salomaa, A., Winfree, E. (eds.) Algorithmic Bioprocesses, pp. 543-584. Springer, Heidelberg (2009)
14. Jiang, H., Riedel, M.D., Parhi, K.K.: Synchronous sequential computation with molecular reactions. In: Design Automation Conference, San Diego, California, USA, June 5-10 (2011)
15. Rothemund, P.W.K.: A DNA and restriction enzyme implementation of Turing machines. In: Lipton, R.J., Baum, E.B. (eds.) DNA Based Computers: DIMACS Workshop, held April 4, pp. 75-120. American Mathematical Society, Providence (1996)
16. Kupferman, O., Vardi, M.Y.: An automata-theoretic approach to modular model checking. ACM T. Progr. Lang. Sys. 22(1), 87-128 (2000)