From Reconfigurability to Evolution in Construction Systems: Spanning the Electronic, Microfluidic and Biomolecular Domains

  • John S. McCaskill
  • Patrick Wagler
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1896)

Abstract

This paper investigates configurability, reconfigurability and evolution of information processing hardware in conventional and unconventional media. Whereas current electronic systems have an advantage in terms of processing speed, they are at a definite disadvantage in terms of plasticity, true hardware reconfiguration and especially reconfiguration and evolution of the hardware construction system itself. Here molecular computers, including the control of chemical reaction synthesis, hold the promise of being able to achieve these properties. In particular, combinatorially complex families of molecules (such as DNA) can direct their own synthesis. The intermediate level of microfluidic systems is also open to reconfiguration and evolution and may play a vital role in linking up the electronic and molecular processing worlds. This paper discusses opportunities for and advantages of reconfiguration across these various levels and the possibility of integrating these technologies. Finally, the threshold level of construction control required for iterative bootstrapping of nanoscale construction is discussed.

Keywords

Microfluidic Device Field Programmable Gate Array Construction System IEEE International Workshop Evolvable Hardware 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    XC6200-field programmable gate arrays data sheet, Xilinx 11–73Google Scholar
  2. 2.
    Thompson, A. “An evolved circuit intrinsic in silicon, entwined with physics” Lect. Not. Comp. Sci. 1259 (1996) 390–405Google Scholar
  3. 3.
    Tangen, U, McCaskill, J.S. Hardware evolution with a massively parallel dynamically reconfigurable computer: Polyp. In Sipper, M., Mange, D. and Perez-Uribe, A., eds., ICES’98 Evolvable Systems: From Biology to Hardware, volume 1478, Springer-Verlag Heidelberg (1998) 364–371CrossRefGoogle Scholar
  4. 4.
    Tangen, U. “Self-Organisation in Micro-Configurable Hardware” to be published in Bedau, M.A., McCaskill, J.S., Packard, N., Rasmussen, S. eds. “Artificial Life VII: Proceedings of the 7. International Conference” Aug. 2–7 2000Google Scholar
  5. 5.
    Paun, G., Rozenberg, G., Salomaa, A. “DNA Computing — new computing paradigms” Springer-Verlag (1998) Berlin HeidelbergGoogle Scholar
  6. 6.
    von Neumann, J. (1956) “Theory of Self-Reproducing Automata” Urbana: Burks, A.W. University of Illinois Press.Google Scholar
  7. 7.
    Lecture Notes in Computer Science ICES 98 Sipper, M., Mange, D., Perez-Uribe, A. eds. (1998) and ICES 96 Higuchi, T., Iwata, M., Liu, W. (eds.) (1996) Springer-Verlag BerlinGoogle Scholar
  8. 8.
    Sanchez, E., Tomassini, M. eds. “Towards Evolvable Hardware — The Evolutionary Engineering Approach” (1996) Springer-Verlag HeidelbergGoogle Scholar
  9. 9.
    McCaskill, J.S., Maeke, T., Gemm, U., Schulte, L. and Tangen, U. “NGEN: A massively parallel reconfigurable computer for biological Simulation: Towards a self-organizing computer” Lect. Not. Comp. Sci. 1259 (1996) 260–276Google Scholar
  10. 10.
    Kenis, P.J.A., Ismagilov, R.F., Whitesides, G.M. “Microfabrication inside capillaries using multiphase laminar flow patterning” Science 285 (1999) 83–85CrossRefGoogle Scholar
  11. 11.
    Harrison, D.J., Fluri, K., Fan, Z., Effenhauser, C.S., Manz, A. Science 261 (1993) 895CrossRefGoogle Scholar
  12. 12.
    Manz, A., Becker, H. “Microsystem Technology in chemistry and Life Science”, Topics in Current Chemistry, Vol. 194, Springer-Verlag, Heidelberg (1998)Google Scholar
  13. 13.
    Köhler, M in ”Etching in Microsystem Technology” Wiley-VCH (1999)Google Scholar
  14. 14.
    Peterson, K.E. Proc. IEEE 70 (1982) 420CrossRefGoogle Scholar
  15. 15.
    Muller, R.S. Sensors and Actuators A21 (1990) 1Google Scholar
  16. 16.
    Dietrich, T.R., Abraham, M., Diebel, J., Lacher, M., Ruf, A. J. Micromech. Microeng. 3 (1993) 187CrossRefGoogle Scholar
  17. 17.
    Quin, D, Xia, Y., Whitesides, G.M. “Rapid prototyping of complex structures with feature sizes larger than 20 μm Adv. Mat. 8 (1996) 917–919CrossRefGoogle Scholar
  18. 18.
    Schuenemann, Bauer, G., Schaefer, W., Leutenbauer, Grosser, V., Reichl, H. Modularization of Microsystems and Standardization of Interfaces In Reichl, H., Obermeier, E. eds., Micro System Technologies 98 6th International conference on micro-, electro-, opto-Mechanical Systems an Components, VDE-Verlag GMbH Berlin (1998) 141–146Google Scholar
  19. 19.
    Ikuta, K., Hirowatari, K., Ogata, T. “Three Dimensional Micro Integrated Fluid System (MIFS) fabricated by stereo lithography” Proc. of. IEEE International Workshop on Micro Electro Mechanical Systems (MEMS’94) (1994) 1–9Google Scholar
  20. 20.
    Ikuta, K., Hirowatari, K. “Real three dimensional micro fabrication unsing stereo lithography and metal molding” Proc. of. IEEE International Workshop on Micro Electro Mechanical Systems (MEMS’93) (1993) 42–47Google Scholar
  21. 21.
    Ikuta, K., Maruo, S., Fukaya, Y and Fujisawa, T. “Biochemical IC chip toward cell free DNA protein synthesis” Proc. of. IEEE International Workshop on Micro Electro Mechanical Systems (MEMS’98) (1998) 131–136Google Scholar
  22. 22.
  23. 23.
    Bräutigam, R., Steen, D., Ehricht, McCaskill, J.S. Isothermal Biochemical Amplification in Miniaturized Reactors with integrated Micro Valves, Microreaction Technology, Proceedings of the third International Conference on Microreaction Technology, Frankfurt a.M., (1999) Springer-Verlag, BerlinGoogle Scholar
  24. 24.
    McCaskill, J.S. Schmidt, K. Patent PCT/EP98/03942 “Switchable dynamic micromixer with minimum dead volume” WO 99/01209Google Scholar
  25. 25.
    McCaskill, J.S. “Optically Programming DNA Computing in Microflow Reactors” Preprint GMD — German National Research Center for Information Technology Schloss Birlinghoven, St. Augustin March 2000Google Scholar
  26. 26.
    Asbury, C.L., van den Engh, G. “Trapping of DNA in non-uniform oscillating electric fields.” Biophys. J. 1 (1998) 1024–1030CrossRefGoogle Scholar
  27. 27.
    Manz, A. “The secret behind electrophoresis microstructure design” in Widmer, E., Verpoorte, Banard, S. eds. Proceedings of the 2nd International Symposium on μTAS (1996) pp. 28–30, BaselGoogle Scholar
  28. 28.
    Beebe, D.J., Moore, J.S, Bauer, J.M., Yu, Q., Liu, R.H., Devadoss, C., Jo, B.-H. Nature 404 (2000) 588–590CrossRefGoogle Scholar
  29. 29.
    Schueller, J.A., Duffy, D.C., Rogers, J.A., Brittain, S.T., Whitesides, G.M. “Reconfigurable diffraction gratings based on elastomeric microfluidic devices” Sens. Actuators 78 (1998) 149–159CrossRefGoogle Scholar
  30. 30.
    Kitano, H. “Morphogenesis for Evolvable Systems” In Sanchez, E., Tomassini, M. eds. “Towards Evolvable Hardware — The Evolutionary Engineering Approach” (1996) Springer-Verlag Heidelberg pp. 99–117.Google Scholar
  31. 31.
    Adleman, L.M. “Molecular computation of solutions to combinatorial problems” Science 266 (1994) 1021–1024CrossRefGoogle Scholar
  32. 32.
  33. 33.
    Landweber, L. F., Kuo, T.-C., Curtis, E.. Evolution and Assembly of an Extremely Scrambled Gene, Proc. Natl. Acad. Sci. (2000).Google Scholar
  34. 34.
    “DNA VI-Sixth International Meeting in DNA Based Computers” Conference Proceedings Condon, A., Rozenberg, G. eds. June 13–17 (2000) Leiden Center for Natural ComputingGoogle Scholar
  35. 35.
    McCaskill, J.S. “Spatially Resolved in vitro Molecular Ecology” Biophysical Chemistry 66 (1997) 145–158CrossRefGoogle Scholar
  36. 36.
    Wright, M. C., Joyce, G.F. “Continuous in vitro evolution of catalytic function.” Science 276(5312) (1997) 614–617CrossRefGoogle Scholar
  37. 37.
    Wlotzka, McCaskill, J.S. “A molecular predator and its prey: Coupled isothermal amplification of nucleic acids” Chemistry and Biology Vol. 4, No. 1 (1997) 25–33CrossRefGoogle Scholar
  38. 38.
    Ehricht, R., Ellinger, T., McCaskill, J.S. “Cooperative amplification of templates by cross hybridisation (CATCH)” European Journal of Biochemistry 243 (1997) 358–364CrossRefGoogle Scholar
  39. 39.
    Luther, A., Brandsch, R., von Kiedrowski, G. “Surface-promoted replication and exponential amplification of DNA analogues.” Nature 396 (1998) 245–248CrossRefGoogle Scholar
  40. 40.
    Alimov, A.P., Khmelnitsky, A.Yu, Simonenko, PN, Spirin AS, Chetverin AB “Cell-free synthesis and affinity isolation of proteins on a nanomole scale.” Biotechniques 28(2) (2000) 338–344Google Scholar
  41. 41.
    Doudna, J. A., Usman, N. et al. “Ribozyme-catalyzed primer extension by trinucleotides: a model for the RNA-catalyzed replication of RNA.” Biochemistry 32(8) (1993) 2111–2115CrossRefGoogle Scholar
  42. 42.
    McCaskill, J.S. Abschlussbericht BMBF Teilprojekt “In-vitro Evolution in Mikroreaktoren und Geräteentwicklungen” (1999) FKZ 0310799Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2000

Authors and Affiliations

  • John S. McCaskill
    • 1
  • Patrick Wagler
    • 1
  1. 1.GMDGerman National Research Center for Information TechnologySt. Augustin (Bonn)Germany

Personalised recommendations