Efficient turing-universal computation with DNA polymers

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

Volumn 6518 LNCS, Issue , 2011, Pages 123-140

  Qian, Lulu ^a   Soloveichik, David ^c   Winfree, Erik ^a,b  

^a California Institute of Technology   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER CIRCUITS; DNA; MACHINERY; THERMODYNAMICS;

DNA POLYMERS; DNA STRANDS; MODEL OF COMPUTATION; MOLECULAR ENGINEERING; POLYMER SUBSTRATE; STACK MACHINES; THERMODYNAMICS OF COMPUTATION; THOUGHT EXPERIMENTS; UNIVERSAL COMPUTATIONS; UNIVERSAL MODEL;

TURING MACHINES;

EID: 79251560004     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-18305-8_12     Document Type: Conference Paper

References (30)

1. Adleman, L.: Molecular Computation of Solutions to Combinatorial Problems. Science 266(5187), 1021-1024 (1994)
2. Beaver, D.: A Universal Molecular Computer. In: Lipton, R., Baum, E. (eds.) DNA Based Computers, pp. 29-36. AMS, Providence (1996)
3. Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z., Shapiro, E.: Programmable and autonomous computing machine made of biomolecules. Nature 414(6862), 430-434 (2001) (Pubitemid 34173721)
4. Benenson, Y., Shapiro, E.: Molecular computing machines. In: Encyclopedia of Nanoscience and Nanotechnology, pp. 2043-2056 (2004)
5. Bennett, C.: Logical reversibility of computation. IBM Journal of Research and Development 17(6), 525-532 (1973)
6. Bennett, C.: The thermodynamics of computation - a review. International Journal of Theoretical Physics 21(12), 905-940 (1982)
7. Bennett, C.: Time/space trade-offs for reversible computation. SIAM Journal on Computing 18, 766-776 (1989)
8. Blinov, M., Faeder, J., Goldstein, B., Hlavacek, W.: BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 20(17), 3289-3291 (2004) (Pubitemid 39619231)
9. Cardelli, L.: Strand algebras for DNA computing. In: Deaton, R., Suyama, A. (eds.) DNA 15. LNCS, vol. 5877, pp. 12-24. Springer, Heidelberg (2009)
10. Cardelli, L.: Two-Domain DNA Strand Displacement. In: Developments in Computational Models (DCM), pp. 33-47 (2010)
11. Cardelli, L., Zavattaro, G.: On the computational power of biochemistry. In: Horimoto, K., Regensburger, G., Rosenkranz, M., Yoshida, H. (eds.) AB 2008. LNCS, vol. 5147, pp. 65-80. Springer, Heidelberg (2008)
12. Chen, H., De, A., Goel, A.: Towards Programmable Molecular Machines. In: Foundations of Nanoscience (FNANO) (2008)
13. Danos, V., Feret, J., Fontana, W., Harmer, R., Krivine, J.: Rule-based modelling of cellular signalling. In: Caires, L., Li, L. (eds.) CONCUR 2007. LNCS, vol. 4703, pp. 17-41. Springer, Heidelberg (2007)
14. Kurtz, S., Mahaney, S., Royer, J., Simon, J.: Biological computing. In: Complexity Theory Retrospective II, pp. 179-195 (1997)
15. Landauer, R.: Irreversibility and heat generation in the computing process. IBM Journal of Research and Development 5(3), 183-191 (1961)
16. Liekens, A.M.L., Fernando, C.T.: Turing complete catalytic particle computers. In: Almeida e Costa, F., Rocha, L.M., Costa, E., Harvey, I., Coutinho, A. (eds.) ECAL 2007. LNCS (LNAI), vol. 4648, pp. 1202-1211. Springer, Heidelberg (2007)
17. Minsky, M.L.: Computation: finite and infinite machines. Prentice-Hall, Englewood Cliffs (1967)
18. Morita, K., Shirasaki, A., Gono, Y.: A 1-tape 2-symbol reversible Turing machine. The Transactions of the IEICE E 72(3), 223-228 (1989)
19. Qian, L.,Winfree, E.: A simple DNA gate motif for synthesizing large-scale circuits. In: Goel, A., Simmel, F.C., Sosík, P. (eds.) DNA 14. LNCS, vol. 5347, pp. 70-89. Springer, Heidelberg (2009)
20. Rothemund, P.: A DNA and restriction enzyme implementation of Turing machines. In: Lipton, R., Baum, E. (eds.) DNA Based Computers. DIMACS, vol. 27, pp. 75-119. AMS, Providence (1996)
21. Rothemund, P., Papadakis, N., Winfree, E.: Algorithmic self-assembly of DNA sierpinski triangles. PLoS Biology 2(12), e424 (2004) (Pubitemid 40280512)
22. Seelig, G., Soloveichik, D., Zhang, D.Y., Winfree, E.: Enzyme-free nucleic acid logic circuits. Science 314(5805), 1585-1588 (2006) (Pubitemid 44907149)
23. Smith, W.: DNA computers in vitro and vivo. In: Lipton, R., Baum, E. (eds.) DNA Based Computers. DIMACS, vol. 27, pp. 121-185. AMS, Providence (1996)
24. Soloveichik, D., Cook, M., Winfree, E., Bruck, J.: Computation with finite stochastic chemical reaction networks. Natural Computing 7(4), 615-633 (2008) (Pubitemid 50052264)
25. Soloveichik, D., Seelig, G., Winfree, E.: DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Science 107(12), 5393-5398 (2010)
26. Winfree, E.: On the computational power of DNA annealing and ligation. In: Lipton, R., Baum, E. (eds.) DNA Based Computers. DIMACS, vol. 27, pp. 199-221. AMS, Providence (1996)
27. Winfree, E.: Simulations of computing by self-assembly. Technical Report CS-TR:1998.22, Caltech (1998)
28. Yin, P., Turberfield, A., Sahu, S., Reif, J.: Design of an autonomous DNA nanomechanical device capable of universal computation and universal translational motion. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA 10. LNCS, vol. 3384, pp. 426-444. Springer, Heidelberg (2005)
29. Zhang, D., Turberfield, A., Yurke, B., Winfree, E.: Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318(5853), 1121-1125 (2007) (Pubitemid 350134891)
30. Zhang, D., Winfree, E.: Control of DNA strand displacement kinetics using toehold exchange. Journal of the American Chemical Society 131(47), 17303-17314 (2009)