Skip to main content
SpringerLink
Log in

Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface

  • Conference paper
DNA Computing and Molecular Programming (DNA 2014)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8727))

Included in the following conference series:

Abstract

We propose a theoretical framework that uses a novel DNA strand displacement mechanism to implement abstract chemical reaction networks (CRNs) on the surface of a DNA nanostructure, and show that surface CRNs can perform efficient algorithmic computation and create complex spatial dynamics. We argue that programming molecular behaviors with surface CRNs is systematic, parallel and scalable.

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 34.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 44.99
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. Beaver, D.: A universal molecular computer. DNA Based Computers, DIMACS 27, 29–36 (1996)

    Google Scholar 

  2. Bennett, C.H.: The thermodynamics of computation – a review. International Journal of Theoretical Physics 21, 905–940 (1982)

    Article  Google Scholar 

  3. Bennett, C.H.: Logical reversibility of computation. IBM Journal of Research and Development 17, 525–532 (1973)

    Article  MATH  Google Scholar 

  4. Boon, J.P., Dab, D., Kapral, R., Lawniczak, A.: Lattice gas automata for reactive systems. Physics Reports 273, 55–147 (1996)

    Article  MathSciNet  Google Scholar 

  5. Chandran, H., Gopalkrishnan, N., Phillips, A., Reif, J.: Localized hybridization circuits. In: Cardelli, L., Shih, W. (eds.) DNA 17. LNCS, vol. 6937, pp. 64–83. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  6. Chen, X.: Expanding the rule set of DNA circuitry with associative toehold activation. Journal of the American Chemical Society 134, 263–271 (2011)

    Article  Google Scholar 

  7. Chen, Y.J., Dalchau, N., Srinivas, N., Phillips, A., Cardelli, L., Soloveichik, D., Seelig, G.: Programmable chemical controllers made from DNA. Nature Nanotechnology 8, 755–762 (2013)

    Article  Google Scholar 

  8. Cook, M.: Universality in elementary cellular automata. Complex Systems 15, 1–40 (2004)

    MATH  MathSciNet  Google Scholar 

  9. Dabby, N.L.: Synthetic molecular machines for active self-assembly: prototype algorithms, designs, and experimental study. Ph.D. thesis, California Institute of Technology (2013)

    Google Scholar 

  10. Dannenberg, F., Kwiatkowska, M., Thachuk, C., Turberfield, A.J.: DNA walker circuits: Computational potential, design, and verification. In: Soloveichik, D., Yurke, B. (eds.) DNA 2013. LNCS, vol. 8141, pp. 31–45. Springer, Heidelberg (2013)

    Chapter  Google Scholar 

  11. Dirks, R.M., Pierce, N.A.: Triggered amplification by hybridization chain reaction. Proceedings of the National Academy of Sciences 101, 15275–15278 (2004)

    Article  Google Scholar 

  12. Douglas, S.M., Bachelet, I., Church, G.M.: A logic-gated nanorobot for targeted transport of molecular payloads. Science 335, 831–834 (2012)

    Article  Google Scholar 

  13. Ermentrout, G.B., Edelstein-Keshet, L.: Cellular automata approaches to biological modeling. Journal of Theoretical Biology 160, 97–133 (1993)

    Article  Google Scholar 

  14. Gács, P.: Reliable cellular automata with self-organization. Journal of Statistical Physics 103, 45–267 (2001)

    Article  MATH  MathSciNet  Google Scholar 

  15. Genot, A.J., Bath, J., Turberfield, A.J.: Combinatorial displacement of DNA strands: application to matrix multiplication and weighted sums. Angewandte Chemie International Edition 52, 1189–1192 (2013)

    Article  Google Scholar 

  16. Genot, A.J., Zhang, D.Y., Bath, J., Turberfield, A.J.: Remote toehold: a mechanism for flexible control of DNA hybridization kinetics. Journal of the American Chemical Society 133, 2177–2182 (2011)

    Article  Google Scholar 

  17. Greenberg, J.M., Hastings, S.: Spatial patterns for discrete models of diffusion in excitable media. SIAM Journal on Applied Mathematics 34(3), 515–523 (1978)

    Article  MATH  MathSciNet  Google Scholar 

  18. Gu, H., Chao, J., Xiao, S.J., Seeman, N.C.: A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202–205 (2010)

    Article  Google Scholar 

  19. Han, J., Jonker, P.: A defect-and fault-tolerant architecture for nanocomputers. Nanotechnology 14, 224 (2003)

    Article  Google Scholar 

  20. He, Y., Liu, D.R.: Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker. Nature Nanotechnology 5, 778–782 (2010)

    Article  Google Scholar 

  21. Jahnke, W., Winfree, A.T.: A survey of spiral-wave behaviors in the Oregonator model. International Journal of Bifurcation and Chaos 1, 445–466 (1991)

    Article  MATH  MathSciNet  Google Scholar 

  22. Jungmann, R., Steinhauer, C., Scheible, M., Kuzyk, A., Tinnefeld, P., Simmel, F.C.: Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Letters 10, 4756–4761 (2010)

    Article  Google Scholar 

  23. Kari, J.: Theory of cellular automata: A survey. Theoretical Computer Science 334, 3–33 (2005)

    Article  MATH  MathSciNet  Google Scholar 

  24. Lakin, M.R., Phillips, A., Stefanovic, D.: Modular verification of DNA strand displacement networks via serializability analysis. In: Soloveichik, D., Yurke, B. (eds.) DNA 19. LNCS, vol. 8141, pp. 133–146. Springer, Heidelberg (2013)

    Chapter  Google Scholar 

  25. Lee, J., Adachi, S., Peper, F., Mashiko, S.: Delay-insensitive computation in asynchronous cellular automata. Journal of Computer and System Sciences 70, 201–220 (2005)

    Article  MATH  MathSciNet  Google Scholar 

  26. Liu, W., Zhong, H., Wang, R., Seeman, N.C.: Crystalline two-dimensional DNA-origami arrays. Angewandte Chemie 123, 278–281 (2011)

    Article  Google Scholar 

  27. Muscat, R.A., Bath, J., Turberfield, A.J.: A programmable molecular robot. Nano Letters 11, 982–987 (2011)

    Article  Google Scholar 

  28. Muscat, R.A., Strauss, K., Ceze, L., Seelig, G.: DNA-based molecular architecture with spatially localized components. In: Proceedings of the 40th Annual International Symposium on Computer Architecture (ISCA), pp. 177–188 (2013)

    Google Scholar 

  29. Phillips, A., Cardelli, L.: A programming language for composable DNA circuits. Journal of The Royal Society Interface 6, S419–S436 (2009)

    Google Scholar 

  30. Qian, L., Soloveichik, D., Winfree, E.: Efficient turing-universal computation with DNA polymers. In: Sakakibara, Y., Mi, Y. (eds.) DNA 16. LNCS, vol. 6518, pp. 123–140. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  31. Qian, L., Winfree, E.: Scaling up digital circuit computation with DNA strand displacement cascades. Science 332, 1196–1201 (2011)

    Article  Google Scholar 

  32. Rothemund, P.W.K.: Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006)

    Article  Google Scholar 

  33. Rothemund, P.W.K., Papadakis, N., Winfree, E.: Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biology 2, e424 (2004)

    Google Scholar 

  34. Rothemund, P.W.K.: A DNA and restriction enzyme implementation of Turing machines. DNA Based Computers, DIMACS 27, 75–119 (1996)

    MathSciNet  Google Scholar 

  35. Smith, W.D.: DNA computers in vitro and in vivo. DNA Based Computers, DIMACS 27, 121–185 (1996)

    Google Scholar 

  36. Soloveichik, D., Seelig, G., Winfree, E.: DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Sciences 107, 5393–5398 (2010)

    Article  Google Scholar 

  37. Soloveichik, D., Cook, M., Winfree, E., Bruck, J.: Computation with finite stochastic chemical reaction networks. Natural Computing 7(4), 615–633 (2008)

    Article  MATH  MathSciNet  Google Scholar 

  38. Tan, S.J., Campolongo, M.J., Luo, D., Cheng, W.: Building plasmonic nanostructures with DNA. Nature Nanotechnology 6, 268–276 (2011)

    Article  Google Scholar 

  39. Toffoli, T., Margolus, N.: Cellular automata machines: a new environment for modeling. MIT Press (1987)

    Google Scholar 

  40. Venkataraman, S., Dirks, R.M., Rothemund, P.W.K., Winfree, E., Pierce, N.A.: An autonomous polymerization motor powered by DNA hybridization. Nature Nanotechnology 2, 490–494 (2007)

    Article  Google Scholar 

  41. Von Neumann, J.: Probabilistic logics and the synthesis of reliable organisms from unreliable components. Automata Studies 34, 43–98 (1956)

    Google Scholar 

  42. Wang, W.: An asynchronous two-dimensional self-correcting cellular automaton. In: Proceedings of 32nd Annual Symposium on Foundations of Computer Science, pp. 278–285. IEEE (1991)

    Google Scholar 

  43. Yin, P., Sahu, S., Turberfield, A.J., Reif, J.H.: Design of autonomous DNA cellular automata. In: Carbone, A., Pierce, N.A. (eds.) DNA 11. LNCS, vol. 3892, pp. 399–416. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  44. 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. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA 10. LNCS, vol. 3384, pp. 426–444. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  45. Yurke, B., Turberfield, A.J., Mills, A.P., Simmel, F.C., Neumann, J.L.: A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000)

    Article  Google Scholar 

  46. Zhang, D.Y., Winfree, E.: Control of DNA strand displacement kinetics using toehold exchange. Journal of the American Chemical Society 131, 17303–17314 (2009)

    Article  Google Scholar 

  47. Zhang, D.Y., Chen, S.X., Yin, P.: Optimizing the specificity of nucleic acid hybridization. Nature Chemistry 4, 208–214 (2012)

    Article  Google Scholar 

  48. Zhang, D.Y., Seelig, G.: Dynamic DNA nanotechnology using strand-displacement reactions. Nature Chemistry 3, 103–113 (2011)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Bioengineering, California Institute of Technology, Pasadena, CA, 91125, USA

    Lulu Qian & Erik Winfree

  2. Computer Science, California Institute of Technology, Pasadena, CA, 91125, USA

    Lulu Qian & Erik Winfree

  3. Computation and Neural Systems, California Institute of Technology, Pasadena, CA, 91125, USA

    Erik Winfree

Authors
  1. Lulu Qian
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Erik Winfree
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Graduate School of Engineering, Department of Bioengineering and Robotics, Tohoku University, 6-6-01 Aoba-yama, 980-8579, Sendai, Japan

    Satoshi Murata

  2. Graduate School of Informatics and Engineering, Department of Communication Engineering and Informatics, University of Electro-Communications, 1-5-1 Chofugaoka, 182-8585, Chofu, Tokyo, Japan

    Satoshi Kobayashi

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer International Publishing Switzerland

About this paper

Cite this paper

Qian, L., Winfree, E. (2014). Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface. In: Murata, S., Kobayashi, S. (eds) DNA Computing and Molecular Programming. DNA 2014. Lecture Notes in Computer Science, vol 8727. Springer, Cham. https://doi.org/10.1007/978-3-319-11295-4_8

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-11295-4_8

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-11294-7

  • Online ISBN: 978-3-319-11295-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation