Abstract
Intelligent nanomechanical devices that operate in an autonomous fashion are of great theoretical and practical interest. Recent successes in building large scale DNA nano-structures, in constructing DNA mechanical devices, and in DNA computing provide a solid foundation for the next step forward: designing autonomous DNA mechanical devices capable of arbitrarily complex behavior. One prototype system towards this goal can be an autonomous DNA mechanical device capable of universal computation, by mimicking the operation of a universal Turing machine. Building on our prior theoretical design and prototype experimental construction of an autonomous unidirectional DNA walking device moving along a linear track, we present here the design of a nanomechanical DNA device that autonomously mimics the operation of a 2-state 5-color universal Turing machine. Our autonomous nanomechanical device, called an Autonomous DNA Turing Machine (ADTM), is thus capable of universal computation and hence complex translational motion, which we define as universal translational motion.
Extended abstract. For full version, see [41].
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Adleman, L.: Molecular computation of solutions to combinatorial problems. Science 266, 1021–1024 (1994)
Alberti, P., Mergny, J.L.: DNA duplex-quadruplex exchange as the basis for a nanomolecular machine. Proc. Natl. Acad. Sci. USA 100, 1569–1573 (2003)
Benenson, Y., Adar, R., Paz-Elizur, T., Livneh, Z., Shapiro, E.: DNA molecule provides a computing machine with both data and fuel. Proc. Natl. Acad. Sci. USA 100, 2191–2196 (2003)
Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., Shapiro, E.: An autonomous molecular computer for logical control of gene expression. Nature 429, 423–429 (2004)
Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z., Shapiro, E.: Programmable and autonomous computing machine made of biomolecules. Nature 414, 430–434 (2001)
Chen, Y., Wang, M., Mao, C.: An autonomous DNA nanomotor powered by a DNA enzyme. Angew. Chem. Int. Ed. 43, 3554–3557 (2004)
Faulhammer, D., Cukras, A.R., Lipton, R.J., Landweber, L.F.: Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. USA 97, 1385–1389 (2000)
Feng, L., Park, S.H., Reif, J.H., Yan, H.: A two-state DNA lattice switched by DNA nanoactuator. Angew. Chem. Int. Ed. 42, 4342–4346 (2003)
Henry, A.A., Romesberg, F.E.: Beyond A, C, G, and T: augmenting nature’s alphabet. Curr. Opin. Chem. Biol. 7, 727–733 (2003)
LaBean, T.H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H., Seeman, N.C.: The construction, analysis, ligation and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 122, 1848–1860 (2000)
Landweber, L.F., Lipton, R.J., Rabin, M.O.: DNA2 DNA computations: A potential ’Killer App’? In: Rubin, H., Wood, D.H. (eds.) DNA Based Computers III: DIMACS Workshop, University of Pennsylvania, June 23-27, pp. 161–172. American Mathematical Society, Providence, Rhode Island (1997)
Li, J., Tan, W.: A single DNA molecule nanomotor. Nano Lett. 2, 315–318 (2002)
Lipton, R.J.: DNA solution of hard computational problem. Science 268, 542–545 (1995)
Liu, D., Balasubramanian, S.: A proton fuelled DNA nanomachine. Angew. Chem. Int. Ed. 42, 5734–5736 (2003)
Liu, Q., Wang, L., Frutos, A.G., Condon, A.E., Corn, R.M., Smith, L.M.: DNA computing on surfaces. Nature 403, 175–179 (2000)
Mao, C., LaBean, T.H., Reif, J.H., Seeman, N.C.: Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000)
Mao, C., Sun, W., Seeman, N.C.: Designed two-dimensional DNA holliday junction arrays visualized by atomic force microscopy. J. Am. Chem. Soc. 121, 5437–5443 (1999)
Mao, C., Sun, W., Shen, Z., Seeman, N.C.: A DNA nanomechanical device based on the B-Z transition. Nature 397, 144–146 (1999)
Ouyang, Q., Kaplan, P.D., Liu, S., Libchaber, A.: DNA solution of the maximal clique problem. Science 278, 446–449 (1997)
Reif, J.H.: Parallel molecular computation: Models and simulations. In: Proceedings: 7th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA 1995), Santa Barbara,CA, pp. 213–223 (1995)
Reif, J.H.: Paradigms for biomolecular computation. In: Calude, C.S., Casti, J., Dinneen, M.J. (eds.) First International Conference on Unconventional Models of Computation, Auckland, New Zealand, pp. 72–93. Springer, Heidelberg (1998)
Reif, J.H.: Local parallel biomolecular computation. In: Rubin, H., Wood, D.H. (eds.) DNA-Based Computers 3. DIMACS, vol. 48, pp. 217–254. American Mathematical Society (1999)
Reif, J.H.: The design of autonomous DNA nanomechanical devices: Walking and rolling DNA. In: Hagiya, M., Ohuchi, A. (eds.) DNA 2002. LNCS, vol. 2568, pp. 22–37. Springer, Heidelberg (2003); Published in Natural Computing, DNA8 special issue, Vol. 2, p 439-461 (2003)
Rothemund, P.W.K.: A DNA and restriction enzyme implementation of Turing machines. In: Lipton, R.J., Baum, E.B. (eds.) DNA Based Computers: Proceedings of the DIMACS Workshop, April 4 (1995); vol. 27, pp. 75–119. Princeton University, American Mathematical Society (1996)
Ruben, A.J., Landweber, L.F.: The past, present and future of molecular computing. Nature Rev. Mol. Cell Biol. 1, 69–72 (2000)
Seeman, N.C.: DNA in a material world. Nature 421, 427–431 (2003)
Sherman, W.B., Seeman, N.C.: A precisely controlled DNA biped walking device. Nano Lett. 4, 1203–1207 (2004)
Simmel, F.C., Yurke, B.: Using DNA to construct and power a nanoactuator. Phys. Rev. EÂ 63, 41913 (2001)
Simmel, F.C., Yurke, B.: A DNA-based molecular device switchable between three distinct mechanical states. Appl. Phys. Lett. 80, 883–885 (2002)
Smith, W.D.: DNA computers in vitro and in vivo. In: Lipton, R.J., Baum, E.B. (eds.) DNA Based Computers: Proceedings of the DIMACS Workshop, April 4 (1995); pp. 121–186. Princeton University, American Mathematical Society, Providence, Rhode Island (1996):
Turberfield, A.J., Mitchell, J.C., Yurke Jr., B., Mills, A.P., Blakey, M.I., Simmel, F.C.: DNA fuel for free-running nanomachines. Phys. Rev. Lett. 90, 118102 (2003)
Turing, A.M.: On computable numbers, with an application to the Entscheidungs problem. Proc. London Math. Society Ser. II 42(2), 230–265 (1936)
Turing, A.M.: On computable numbers, with an application to the entscheidungsproblem. Proc. London Math. Society Ser. II 43, 544–546 (1937)
Winfree, E.: On the computational power of DNA annealing and ligation. In: Lipton, R.J., Baum, E.B. (eds.) DNA Based Computers 1. DIMACS, vol. 27, pp. 199–221. American Mathematical Society (1996)
Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998)
Wolfram, S.: A new kind of science. Wolfram Media, Inc., Champaign (2002)
Yan, H., LaBean, T.H., Feng, L., Reif, J.H.: Directed nucleation assembly of DNA tile complexes for barcode patterned DNA lattices. Proc. Natl. Acad. Sci. USA 100, 8103–8108 (2003)
Yan, H., Park, S.H., Finkelstein, G., Reif, J.H., LaBean, T.H.: DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301, 1882–1884 (2003)
Yan, H., Zhang, X., Shen, Z., Seeman, N.C.: A robust DNA mechanical device controlled by hybridization topology. Nature 415, 62–65 (2002)
Yin, P., Turberfield, A.J., Reif, J.H.: Designs of autonomous unidirectional walking DNA devices. DNA Based Computers 10 (2004)
Yin, P., Turberfield, A.J., Sahu, S., Reif, J.H.: Design of an autonomous DNA nanomechanical device capable of universal computation and universal translational motion. Technical Report CS-2004-07, Duke University, Computer Science Department (2004)
Yin, P., Yan, H., Daniell, X.G., Turberfield, A.J., Reif, J.H.: A unidirectional DNA walker moving autonomously along a linear track. Angew. Chem. Int. Ed. (2004) (in press)
Yurke, B., Turberfield Jr., A.J., Mills, A.P., Simmel, F.C., Neumann, J.L.: A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Yin, P., Turberfield, A.J., Sahu, S., Reif, J.H. (2005). Design of an Autonomous DNA Nanomechanical Device Capable of Universal Computation and Universal Translational Motion. In: Ferretti, C., Mauri, G., Zandron, C. (eds) DNA Computing. DNA 2004. Lecture Notes in Computer Science, vol 3384. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11493785_37
Download citation
DOI: https://doi.org/10.1007/11493785_37
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-26174-2
Online ISBN: 978-3-540-31844-6
eBook Packages: Computer ScienceComputer Science (R0)