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Nanocomputing

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NanoBioTechnology

Abstract

Nanocomputing encompasses any submicron devices and technologies applied to any computational or related tasks. A brief survey is given, and emphasis is placed on biomolecular devices that use nucleic acids as their substrate. Computational selfassembly of DNA and DNA-based enzymatic computing are surveyed in greater detail. The foremost implementation challenge for computation, namely, DNA word design, is also surveyed.

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References

  1. International Technology Roadmap for Semiconductors 2003, http://public. itrs.net.

    Google Scholar 

  2. Bennett CH. The thermodynamics of computation—a review. Int J Theor Phys 1982;21:905–940.

    CAS  Google Scholar 

  3. Zhirnov VV, Cavin RK III, Hutchby JA, Bourianoff GI. Limits to binary logic switching—a gedanken model. Proceedings of the IEEE 2003;91: 1934–1939.

    Google Scholar 

  4. Ball P. Chemistry meets computing. Nature 2000;406:118–120.

    CAS  Google Scholar 

  5. Reed M, Tour JM. Computing with molecules. Scientific American 2000; 2000:86–93.

    Google Scholar 

  6. Zhirnov VV, Herr DJC. New frontiers: self-assembly and nanoelectronics. IEEE Computer 2001;2001:34.

    Google Scholar 

  7. Hutchby JA, Bourianoff GI, Zhirnov VV, Brewer JE. Extending the road beyond CMOS. IEEE Circuits and Devices Magazine 2002;18:28–41.

    Google Scholar 

  8. Bourianoff G. The future of nanocomputing. IEEE Computer 2003;2003:36.

    Google Scholar 

  9. Stone NJ, Ahmed H. Silicon single electron memory cell. Appl Phys Lett 1998;73:2134–2136.

    CAS  Google Scholar 

  10. Mahapatra S, Vish V, Wasshuber C, Banerjee K, Ionescu AM. Analytical modeling of single electron transistor for hybrid CMOS-SET analog IC design. IEEE Transactions on Electron Devices 2004;51:1772–1782.

    Google Scholar 

  11. Bachtold A, Hadley P, Nakanishi T, Dekker C. Logic circuits with carbon nanotube transistors. Science 2001;294:1317–1320.

    CAS  Google Scholar 

  12. Chen Y, Ohlberg DAA, Medeiros-Ribeiro G, Chang YA, Williams RS. Self-assembled growth of epitaxial erbium disilicide nanowires. Appl Phys Lett 2000;76:4004–4006.

    CAS  Google Scholar 

  13. Cui Y, Wei Q, Park H, Lieber CM. Nanowire nanosensors for highly sensitive and selective detection of biological and chemical species. Science 2001;293:1289–1292.

    CAS  Google Scholar 

  14. Huang Y, Duan X, Cui Y, Lauhon LJ, Kim KH, Lieber CM. Logic gates and computation from assembled nanowire building blocks. Science 2001;294:1313–1317.

    CAS  Google Scholar 

  15. Reed MA, Zhou C, Muller CJ, Burgin TP. Conductance of a molecular junction. Science 1997;278:252–254.

    CAS  Google Scholar 

  16. Reed M, Chen J, Rawlett AM, Price DW, Tour JM. Molecular random access memory cell. Appl Phys Lett 2001;78:3735–3737.

    CAS  Google Scholar 

  17. Chen Y, Ohlberg DAA, Li X, et al. Nanoscale molecular-switch devices fabricated by imprint lithography. Appl Phys Lett 2003;82:1610–1612.

    CAS  Google Scholar 

  18. Csaba G, Imre A, Bernstein GH, Porod W, Metlushko V. Nanocomputing by field-coupled nanomagnets. IEEE Transactions on Nanotechnology 2002; 1: 209–213.

    Google Scholar 

  19. Porod W, Lent CS, Bernstein GH, et al. Quantum-dot cellular automata: computing with coupled quantum dots. International Journal of Electronics 1999;86:549–590.

    CAS  Google Scholar 

  20. Heath JR, Kuekes PJ, Snider GS, Williams RS. A defect-tolerant computer architecture: opportunities for nanotechnology. Science 1998;280:1716–1721.

    CAS  Google Scholar 

  21. Collier CP, Wong EW, Belohradsky M, et al. Electronically configurable molecular-based logic gates. Science 1999;285:391–394.

    CAS  Google Scholar 

  22. Metzger RM. Electrical rectification by a molecule: the advent of unimolecular electronic devices. Accounts Chem Res 1999;32:950–957.

    CAS  Google Scholar 

  23. Ellenbogen JC, Love JC. Architectures for molecular electronic computers: 1. Logic structures and an adder built from molecular electronic diodes. Proceedings of the IEEE 2000;88:386–426.

    CAS  Google Scholar 

  24. Joachim C, Gimzewski JK, Aviram A. Electronics using hybrid-molecular and monomolecular devices. Nature 2000;408:541–548.

    CAS  Google Scholar 

  25. Donhauser ZJ, Mantooth BA, Kelly KF, et al. Conductance switching in single molecules through conformational changes. Science 2001;292:2303–2307.

    CAS  Google Scholar 

  26. Goldstein SC, Budiu M. NanoFabrics: spatial computing using molecular electronics. In: Proceedings of the 28th International Symposium on Computer Architecture. New York: ACM Press, 2001:178–191.

    Google Scholar 

  27. Pease AR, Jeppesen JO, Stoddart JF, Luo Y, Collier CP, Heath JR. Switching devices based on interlocked molecules. Accounts Chem Res 2001;34: 433–444.

    CAS  Google Scholar 

  28. Postma HWC, Teepen T, Yao Z, Grifoni M, Dekker C. Carbon nanotube single-electron transistors at room temperature. Science 2001;293:76–79.

    CAS  Google Scholar 

  29. Mishra M, Goldstein SC. Scalable defect tolerance for molecular electronics. In: 1st Workshop on Non-Silicon Computing. Cambridge, MA, 2002.

    Google Scholar 

  30. de Silva AP, Gunaratne HQN, McCoy CP. A molecular photoionic AND gate based on fluorescent signalling. Nature 1993;364:42–44.

    Google Scholar 

  31. de Silva AP, Gunaratne HQN, McCoy CP. Molecular photoionic AND logic gates with bright fluorescence and “off-on” digital action. J Am Chem Soc 1997;119:7891–7892.

    Google Scholar 

  32. Credi A, Balzani V, Langford SJ, Stoddart JF. Logic operations at the molecular level. An XOR gate based on a molecular machine. J Am Chem Soc 1997;119:2679–2681.

    CAS  Google Scholar 

  33. Pina F, Melo MJ, Maestri M, Passaniti P, Balzani V. Artificial chemical systems capable of mimicking some elementary properties of neurons. J Am Chem Soc 2000; 122:4496–4498.

    CAS  Google Scholar 

  34. de Silva AP, McClenaghan ND. Proof-of-principle of molecular-scale arithmetic. J Am Chem Soc 2000;122:3965–3966.

    Google Scholar 

  35. Banerjee K, Soukri SJ, Kapur P, Saraswat K. 3-D ICs: A novel chip design for improving deep-submicrometer interconnect performance and systemson-chip integration. Proceedings of the IEEE 2001;89:602–633.

    CAS  Google Scholar 

  36. Bilardi G, Preparata FP. Horizons of parallel computation. Tech. Rep. CS-93-20, Department of Computer Science, Brown University, 1993.

    Google Scholar 

  37. Abelson H, Allen D, Coore D, et al. Amorphous computing. Communications of the ACM 2000;43:74–82.

    Google Scholar 

  38. Goldstein SC, Rosewater D. Digital logic using molecular electronics. In: IEEE International Solid-State Circuits Conference. San Francisco, CA, 2002;12:5.

    Google Scholar 

  39. Gruau F, Malbos P. The blob: a basic topological concept for hardware-free distributed computation. In: Calude C, Dinneen MJ, Peper F, eds. Unconventional Models of Computation, Third International Conference Proceedings, Lecture Notes in Computer Science, vol. 2509. Berlin, Heidelberg: Springer, 2002:151–163.

    Google Scholar 

  40. Gruau F, Lhuillier Y, Reitz P, Temam O. BLOB computing. In: Vassiliadis S, Gaudiot J-L, Piuri V, eds. Proceedings of the First Conference on Computing Frontiers. ACM SIGMICRO, 2004:125–139.

    Google Scholar 

  41. Durbeck LJK, Macias NJ. The cell matrix: an architecture for nanocomputing. Nanotechnology 2001; 12:217–230.

    Google Scholar 

  42. Munakata T, Sinha S, Ditto WL. Chaos computing: implementation of fundamental logic gates by chaotic elements. IEEE Transactions on Circuits and Systems—I: Fundamental Theory and Applications 2002;49:1629–1633.

    Google Scholar 

  43. Adleman LM. Molecular computation of solutions to combinatorial problems. Science 1994;266:1021–1024.

    CAS  Google Scholar 

  44. Deaton RJ, Garzon M, Rose JA, Franceschetti DR, Stevens SE Jr. DNA computing: a review. Fundamenta Informaticae 1998;35:231–245.

    Google Scholar 

  45. Lipton RJ. DNA solution of hard computational problems. Science 1995; 268:542–545.

    CAS  Google Scholar 

  46. Ruben AJ, Landweber LF. Timeline: the past, present and future of molecular computing. Nat Rev Mol Cell Biol 2000;1:69–72.

    CAS  Google Scholar 

  47. Wang L, Liu Q, Corn RM, Condon AE, Smith LM. Multiple word DNA computing on surfaces. J Am Chem Soc 2000; 122:7435–7440.

    CAS  Google Scholar 

  48. Winfree E. On the computational power of DNA annealing and ligation. In: Lipton RJ, Baum EB, eds. DNA Based Computers, DIMACS Workshop 1995, vol. 27 of Series in Discrete Mathematics and Theoretical Computer Science. Princeton University: American Mathematical Society, 1996:199–221.

    Google Scholar 

  49. Winfree E. Complexity of restricted and unrestricted models of molecular computation. In: Lipton RJ, Baum EB, eds. DNA Based Computers, DIMACS Workshop 1995, vol. 27 of Series in Discrete Mathematics and Theoretical Computer Science. Princeton University: American Mathematical Society, 1996:187–198.

    Google Scholar 

  50. Watson J, Crick FHC. A structure for deoxyribose nucleic acid. Nature 1953;171:737.

    CAS  Google Scholar 

  51. LaBean TH, Yan H, Kopatsch J, et al. Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. J Am Chem Soc 2000; 122:1848–1860.

    CAS  Google Scholar 

  52. Watson JD, Hopkins NH, Roberts JW, Steitz JA, Weiner AM. Molecular Biology of the Gene, 4th ed. Menlo Park, CA: Benjamin/Cummings, 1988.

    Google Scholar 

  53. Winfree E, Liu F, Wenzler LA, Seeman NC. Design and self-assembly of two-dimensional DNA crystals. Nature 1998;394:539–544.

    CAS  Google Scholar 

  54. Wang L, Hall JG, Lu M, Liu Q, Smith LM. A DNA computing readout operation based on structure-specific cleavage. Nat Biotechnol 2001;19:1053–1059.

    CAS  Google Scholar 

  55. Braich RS, Chelyapov N, Johnson C, Rothemund PWK, Adleman L. Solution of a 20variable 3-SAT problem on a DNA computer. Science 2002;296:499–502.

    CAS  Google Scholar 

  56. Morimoto N, Arita M, Suyama A. Solid phase DNA solution to the Hamiltonian path problem. In: Rubin H, Wood DH, eds. DNA Based Computers III, DIMACS Workshop 1997, vol. 48 of Series in Discrete Mathematics and Theoretical Computer Science. University of Pennsylvania: American Mathematical Society, 1999:193–206.

    Google Scholar 

  57. Ouyang Q, Kaplan PD, Liu S, Libchaber A. DNA solution of the maximal clique problem. Science 1997;278:446–449.

    CAS  Google Scholar 

  58. Pirrung MC, Connors RV, Odenbaugh AL, Montague-Smith MP, Walcott NG, Tollett JJ. The arrayed primer extension method for DNA microchip analysis. Molecular computation of satisfaction problems. J Am Chem Soc 2000;122:1873–1882.

    CAS  Google Scholar 

  59. Garzon M, Gao Y, Rose JA, et al. In vitro implementation of finite-state machines. In: Proceedings 2nd International Workshop on Implementing Automata WIA’97, Lecture Notes in Computer Science, vol. 1436. Berlin, Heidelberg: Springer Verlag, 1998:56–74.

    Google Scholar 

  60. Guarnieri F, Fliss M, Bancroft C. Making DNA add. Science 1996;273: 220–223.

    CAS  Google Scholar 

  61. Hug H, Schuler R. DNA-based parallel computation of simple arithmetic. In: Jonoska N, Seeman NC, eds. DNA Computing: 7th International Workshop on DNA-Based Computers, DNA 2001, Lecture Notes in Computer Science, vol. 2340. Berlin, Heidelberg: Springer, 2002.

    Google Scholar 

  62. Mao C, LaBean TH, Reif JH, Seeman NC. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 2000;407:493–496. Erratum, Nature 2000;408:750.

    CAS  Google Scholar 

  63. Rothemund PWK, Winfree E. The program-size complexity of self-assembled squares. In: The Thirty-Second Annual ACM Symposium on the Theory of Computing, 2000:459–468.

    Google Scholar 

  64. Faulhammer D, Cukras AR, Lipton RJ, Landweber LF. Molecular computation: RNA solutions to chess problems. Proc Natl Acad Sci USA 2000;97: 1385–1389. The PERMUTE Program is available at http://www.pnas.org/ cgi/content/full/97/4/1385/DC1.

    CAS  Google Scholar 

  65. Hartmanis J. On the weight of computation. Bulletin of the EATCS 1995;55:136–138.

    Google Scholar 

  66. Baum EB. DNA sequences useful for computation. In: Landweber LF, Baum EB, eds. DNA Based Computers II, DIMACS Workshop 1996, vol. 44 of Series in Discrete Mathematics and Theoretical Computer Science. University of Pennsylvania: American Mathematical Society, 1999:235–241.

    Google Scholar 

  67. Brenneman A, Condon AE. Strand design for bio-molecular computation. Tech. Rep., University of British Columbia, 2001.

    Google Scholar 

  68. Deaton RJ, Murphy RC, Garzon M, Franceschetti DR, Stevens SE Jr. Good encodings for DNA-based solutions to combinatorial problems. In: Landweber LF, Baum EB, eds. DNA Based Computers II, DIMACS Workshop 1996, vol. 44 of Series in Discrete Mathematics and Theoretical Computer Science. University of Pennsylvania: American Mathematical Society, 1999:247–258.

    Google Scholar 

  69. Frutos AG, Liu Q, Thiel AJ, et al. Demonstration of a word design strategy for DNA computing on surfaces. Nucl Acids Res 1997;25:4748–4757.

    CAS  Google Scholar 

  70. Garzon M, Deaton RJ, Niño LF, Stevens E, Wittner M. Encoding genomes for DNA computing. In: Gemetic Programming 1998: Proceedings 3rd Genetic Programming Conference. Morgan Kaufmann, 1998:684–690.

    Google Scholar 

  71. Garzon M, Neathery P, Deaton RJ, Murphy RC, Franceschetti DR, Stevens SE Jr. A new metric for DNA computing. In: Proceedings 2nd Genetic Programming Conference, 1997:472–478.

    Google Scholar 

  72. Marathe A, Condon AE, Corn RM. On combinatorial DNA word design. In: Winfree E, Gifford DK, eds. DNA Based Computers V, DIMACS Workshop 1999, vol. 54 of Series in Discrete Mathematics and Theoretical Computer Science. MIT: American Mathematical Society, 2000:75–89.

    Google Scholar 

  73. Reinert G, Schbath S, Waterman MS. Probabilistic and statistical properties of words: an overview. Journal of Computational Biology 2000;7:1–46.

    CAS  Google Scholar 

  74. Feldkamp U, Banzhaf W, Rauhe H. A DNA sequence compiler. Tech. Rep., University of Dortmund, 2000.

    Google Scholar 

  75. Hug H, Schuler R. Strategies for the development of a peptide computer. Bioinformatics 2001;17:364–368.

    CAS  Google Scholar 

  76. Sakamoto K, Gouzu H, Komiya K, et al. Molecular computation by DNA hairpin formation. Science 2000;288:1223–1226.

    CAS  Google Scholar 

  77. Winfree E. Simulations of computing by self-assembly. In: Kari L, Rubin H, Wood DH, eds. DNA Based Computers IV, DIMACS Workshop 1998, Biosystems, vol. 52, issues 1–3. Elsevier, 1999:213–242.

    Google Scholar 

  78. Basu S, Karig D, Weiss R. Engineering signal processing in cells: towards molecular concentration band detection. In: Hagiya M, Ohuchi A, eds. DNA Computing: 8th International Workshop on DNA-Based Computers, DNA 2002, Lecture Notes in Computer Science, vol. 2568. Berlin, Heidelberg: Springer, 2003.

    Google Scholar 

  79. Conrad M. On design principles for a molecular computer. Communications of the ACM 1985;28:464–480.

    Google Scholar 

  80. Guet CC, Elowitz MB, Wang W, Leibler S. Combinatorial synthesis of genetic networks. Science 2002;296:1466–1470.

    CAS  Google Scholar 

  81. Hayes B. Computing comes to life. American Scientist 2001;89:204–208.

    Google Scholar 

  82. Ji S. The cell as the smallest DNA-based molecular computer. BioSystems 1999;52:123–133.

    CAS  Google Scholar 

  83. Knight TF Jr, Sussman GJ. Cellular gate technology. In: Proceedings UMC98, First International Conference on Unconventional Models of Computation, 1998.

    Google Scholar 

  84. LaBean TH, Winfree E, Reif JH. Experimental progress in computation by self-assembly of DNA tilings. In: Winfree E, Gifford DK, eds. DNA Based Computers V, DIMACS Workshop 1999, vol. 54 of Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 2000:123–140.

    Google Scholar 

  85. Landweber LF, Kari L. The evolution of cellular computing: nature’s solution to a computational problem. BioSystems 1999;52:3–13.

    CAS  Google Scholar 

  86. Landweber LF, Kuo TC, Curtis EA. Evolution and assembly of an extremely scrambled gene. Proc Natl Acad Sci USA 2000;97:3298–3303.

    CAS  Google Scholar 

  87. Reif JH. Parallel biomolecular computation. In: Rubin H, Wood DH, eds. DNA Based Computers III, DIMACS Workshop 1997, vol. 48 of Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1999:217–254.

    Google Scholar 

  88. Saylor G. Construction of genetic logic gates for biocomputing. In: 101st General Meeting of the American Society for Microbiology, 2001.

    Google Scholar 

  89. Weiss R. Cellular Computation and Communication using Engineered Genetic Regulatory Networks. Ph.D. thesis, Massachusetts Institute of Technology, 2001.

    Google Scholar 

  90. Weiss R, Basu S. The device physics of cellular logic gates. In: First Workshop on Non-Silicon Computing, 2002.

    Google Scholar 

  91. Weiss R, Homsy G, Nagpal R. Programming biological cells. Tech. Rep., MIT Laboratory for Computer Science and Artificial Intelligence, 1998.

    Google Scholar 

  92. Weiss R, Homsy GE, Knight TF Jr. Towards in vivo digital circuits. In: DIMACS Workshop on Evolution as Computation, 1999.

    Google Scholar 

  93. Winfree E, Yang X, Seeman NC. Universal computation via self-assembly of DNA: some theory and experiments. In: Landweber LF, Baum EB, eds. DNA Based Computers II, DIMACS Workshop 1996, vol. 44 of Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1999:191–213. Errata: http://www.dna.caltech.edu/Papers/self-assem.errata.

    Google Scholar 

  94. Cox JC, Ellington AD. DNA computation function. Curr Biol 2001; 11:R336.

    CAS  Google Scholar 

  95. Yurke B, Mills Jr AP, Cheng SL. DNA implementation of addition in which the input strands are separate from the operator strands. BioSystems 1999;52: 165–174.

    CAS  Google Scholar 

  96. Reif JH. DNA lattices: a method for molecular scale patterning and computation. Computer and Scientific Engineering Magazine 2002;4:32–41.

    CAS  Google Scholar 

  97. Seeman NC. It started with Watson and Crick, but it sure didn’t end there: pitfalls and possibilities beyond the classic double helix. Natural Computing: an international journal 2002; 1:53–84.

    Google Scholar 

  98. Wang H. Proving theorems by pattern recognition I. Commun ACM 1960;3:220–234.

    Google Scholar 

  99. Jonoska N, Kephard DE, Lefevre J. Trends in computing with DNA. J Comput Sci Technol 2004; 19:98.

    Google Scholar 

  100. Carbone A, Mao C, Constantinou PE, et al. 3D fractal DNA assembly from coding, geometry and protection. Natural Computing 2004;3:235–252.

    CAS  Google Scholar 

  101. Barish RD, Rothemund PWK, Winfree E. Two computational primitives for algorithmic self-assembly: copying and counting. Nano Lett 2005;5: 2586–2592.

    CAS  Google Scholar 

  102. Winfree E. DNA computing by self-assembly. National Academy of Engineering’s The Bridge 2003;33:31–38.

    Google Scholar 

  103. Schulman R, Winfree E. Programmable control of nucleation for algorithmic self-assembly. In: Ferretti C, Mauri G, Zandron C, eds. DNA Computing: 10th International Workshop on DNA-Based Computers, DNA 2004, Lecture Notes in Computer Science, vol. 3384. Berlin: Springer, 2005:319–328.

    Google Scholar 

  104. Chen HL, Goel A. Error free self-assembly using error prone tiles. In: Ferretti C, Mauri G, Zandron C, eds. DNA Computing: 10th International Workshop on DNA-Based Computers, DNA 2004, Lecture Notes in Computer Science, vol. 3384. Berlin: Springer, 2005:62–75.

    Google Scholar 

  105. Winfree E, Bekbolatov R. Proofreading tile sets: Error-correction for algorithmic self-assembly. In: Chen J, Reif JH, eds. DNA Computing: 9th International Workshop on DNA-Based Computers, DNA 2003, Lecture Notes in Computer Science, vol. 2943. Berlin: Springer, 2004:126–144.

    Google Scholar 

  106. Reif JH, Sahu S, Yin P. Compact error-resilient computational DNA tiling assemblies. In: Ferretti C, Mauri G, Zandron C, eds. DNA Computing: 10th International Workshop on DNA-Based Computers, DNA 2004, Lecture Notes in Computer Science, vol. 3384. Berlin: Springer, 2005:293–307.

    Google Scholar 

  107. Stojanovic MN, de Prada P, Landry DW. Catalytic molecular beacons. ChemBioChem 2001;2:411–415.

    CAS  Google Scholar 

  108. Stojanovic MN, Mitchell TE, Stefanovic D. Deoxyribozyme-based logic gates. J Am Chem Soc 2002; 124:3555–3561.

    CAS  Google Scholar 

  109. Stojanovic MN, Kolpashchikov D. Modular aptameric sensors. J Am Chem Soc 2004; 126:9266–9270.

    CAS  Google Scholar 

  110. Stojanovic MN, Semova S, Kolpashchikov D, Morgan C, Stefanovic D. Deoxyribozymebased ligase logic gates and their initial circuits. J Am Chem Soc 2005;127:6914–6915.

    CAS  Google Scholar 

  111. Stojanovic MN, Stefanovic D. Deoxyribozyme-based half adder. J Am Chem Soc 2003; 125:6673–6676.

    CAS  Google Scholar 

  112. Stojanovic MN, Stefanovic D. A deoxyribozyme-based molecular automaton. Nature Biotechnology 2003;21:1069–1074.

    CAS  Google Scholar 

  113. Andrews B. Games, Strategies, and Boolean Formula Manipulation. Master’s thesis, University of New Mexico, 2005.

    Google Scholar 

  114. Epstein IR, Pojman JA. An Introduction to Nonlinear Chemical Dynamics. New York: Oxford University Press, 1998.

    Google Scholar 

  115. Field RJ, Körös E, Noyes R. Oscillations in chemical systems. II. Thorough analysis of temporal oscillation in the bromate-cerium-malonic acid system. J Am Chem Soc 1972;94:8649–8664.

    CAS  Google Scholar 

  116. Noyes R, Field RJ, Körös E. Oscillations in chemical systems. I. Detailed mechanism in a system showing temporal oscillations. J Am Chem Soc 1972; 94:1394–1395.

    CAS  Google Scholar 

  117. Tyson JJ. The Belousov-Zhabotinskii Reaction. In: Lecture Notes in Biomathematics, vol. 10. Berlin: Springer-Verlag, 1976.

    Google Scholar 

  118. Hjelmfelt A, Ross J. Chemical implementation and thermodynamics of collective neural networks. Proc Natl Acad Sci USA 1992;89:388–391.

    CAS  Google Scholar 

  119. Hjelmfelt A, Ross J. Pattern recognition, chaos, and multiplicity in neural networks of excitable systems. Proc Natl Acad Sci USA 1994;91:63–67.

    CAS  Google Scholar 

  120. Hjelmfelt A, Schneider FW, Ross J. Pattern recognition in coupled chemical kinetic systems. Science 1993;260:335–337.

    CAS  Google Scholar 

  121. Hjelmfelt A, Weinberger ED, Ross J. Chemical implementation of neural networks and Turing machines. Proc Natl Acad Sci USA 1991;88:10,983–10,987.

    CAS  Google Scholar 

  122. Hjelmfelt A, Weinberger ED, Ross J. Chemical implementation of finite-state machines. Proc Natl Acad Sci USA 1992;89:383–387.

    CAS  Google Scholar 

  123. Laplante JP, Pemberton M, Hjelmfelt A, Ross J. Experiments on pattern recognition by chemical kinetics. J Phys Chem 1995;99:10,063–10,065.

    CAS  Google Scholar 

  124. Rössler OE. A principle for chemical multivibration. J Theor Biol 1972;36:413–417.

    Google Scholar 

  125. Rössler OE, Seelig FF. A Rashevsky-Turing system as a two-cellular flipflop. Zeitschrift für Naturforschung 1972;27b:1444–1448.

    Google Scholar 

  126. Seelig FF, Rössler OE. Model of a chemical reaction flip-flop with one unique switching input. Zeitschrift für Naturforschung 1972;27b: 1441–1444.

    Google Scholar 

  127. Szilard L. über die Entropieverminderung in einem thermodynamischen System bei Eingriffen intelligenter Wesen. Zeitschrift für Physik 1929;53:840–856.

    CAS  Google Scholar 

  128. Matías MA, Güémez J. On the effects of molecular fluctuations on models of chemical chaos. J Chem Phys 1995;102:1597–1606.

    Google Scholar 

  129. Moore C. Unpredictability and undecidability in dynamical systems. Phys Rev Lett 1990;64:2354–2357.

    Google Scholar 

  130. Wolfram S. Undecidability and intractability in theoretical physics. Phys Rev Lett 1985;54:735–738.

    Google Scholar 

  131. Winfree AT. Spiral waves of chemical activity. Science 1972; 175:634–635.

    CAS  Google Scholar 

  132. Steinbock O, Kettunen P, Showalter K. Anisotropy and spiral organizing centers in patterned excitable media. Science 1995;269:1857–1860.

    CAS  Google Scholar 

  133. Steinbock O, Kettunen P, Showalter K. Chemical wave logic gates. J Phys Chem 1996;100:18,970–18,975.

    CAS  Google Scholar 

  134. Steinbock O, Toth A, Showalter K. Navigating complex labyrinths: optimal paths from chemical waves. Science 1995;267:868–871.

    CAS  Google Scholar 

  135. Yurke B, Turberfield AJ, Mills AP Jr, Neumann JL. A molecular machine made of and powered by DNA. In: The 2000 March Meeting of the American Physical Society, 2000.

    Google Scholar 

  136. Magnasco MO. Molecular combustion motors. Phys Rev Lett 1994;72: 2656–2659.

    Google Scholar 

  137. Magnasco MO. Chemical kinetics is Turing universal. Phys Rev Lett 1997; 78:1190–1193.

    CAS  Google Scholar 

  138. Homsy GE. Performance limits on biochemical computation. Tech. Rep., MIT Artificial Intelligence Laboratory, 2000.

    Google Scholar 

  139. Hiratsuka M, Aoki T, Higuchi T. Enzyme transistor circuits for reaction-diffusion computing. IEEE Transactions on Circuits and Systems—I: Fundamental Theory and Applications 1999;46:294–303.

    Google Scholar 

  140. Morgan C, Stefanovic D, Moore C, Stojanovic MN. Building the components for a biomolecular computer. In: Ferretti C, Mauri G, Zandron C, eds. Preliminary Proceedings of the 10th International Workshop on DNA-Based Computers, DNA 2004, 2004.

    Google Scholar 

  141. Farfel J, Stefanovic D. Towards practical biomolecular computers using microfluidic deoxyribozyme logic gate networks. In: Carbone A, Daley M, Kari L, McQuillan I, Pierce N, eds. Preliminary Proceedings of the 11th International Workshop on DNA-Based Computers, DNA 2005, 221–232.

    Google Scholar 

  142. Deaton RJ, Garzon M. Thermodynamic constraints on DNA-based computing. In: Paun G, ed. Computing with Bio-Molecules. Singapore: Springer-Verlag, 1998:138–152.

    Google Scholar 

  143. Mauri G, Ferretti C. Word design for molecular computing: a survey. In: Chen J, Reif JH, eds. DNA Computing: 9th International Workshop on DNA-Based Computers, Lecture Notes in Computer Science, vol. 2943. Berlin, Heidelberg: Springer, 2004:37–47.

    Google Scholar 

  144. Dirks RM, Lin M, Winfree E, Pierce NA. Paradigms for computational nucleic acid design. Nucl Acids Res 2004;32:1392–1403.

    CAS  Google Scholar 

  145. Seeman NC. De novo design of sequences for nucleic acid structural engineering. J Biomolecular Structure & Dynamics 1990;8:573–581.

    CAS  Google Scholar 

  146. Feldkamp U, Rauhe H, Banzhaf W. Software tools for DNA sequence design. Genetic Programming and Evolvable Machines 2003;4:153–171.

    Google Scholar 

  147. Tanaka F, Kameda A, Yamamoto M, Ohuchi A. Specificity of hybridization between DNA sequences based on free energy. In: Carbone A, Daley M, Kari L, McQuillan I, Pierce N, eds. Preliminary Proceedings of the 1 1th International Workshop on DNA-Based Computers, DNA, 2005:366–375.

    Google Scholar 

  148. Sen D, Gilbert W. Formation of parallel four-stranded complexes by guaninerich motifs in DNA and its implications for meiosis. Nature 1988;334: 364–366.

    CAS  Google Scholar 

  149. Mir KU. A restricted genetic alphabet for DNA computing. In: Landweber LF, Baum EB, eds. DNA Based Computers II, DIMACS Workshop 1996, vol. 44 of Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1999.

    Google Scholar 

  150. Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl Acids Res 1981;9: 133–148.

    CAS  Google Scholar 

  151. Andronescu M, Dees D, Slaybaugh L, et al. Algorithms for testing that sets of DNA word designs avoid unwanted secondary structure. In: Hagiya M, Ohuchi A, eds. DNA Computing: 8th International Workshop on DNA-Based Computers, Lecture Notes in Computer Science, vol. 2568. Berlin, Heidelberg: Springer, 2003:182–195.

    Google Scholar 

  152. Kobayashi S. Testing structure freeness of regular sets of biomolecular sequences (extended abstract). In: Ferretti C, Mauri G, Zandron C, eds. DNA Computing: 10th International Workshop on DNA-Based Computers, Lecture Notes in Computer Science, vol. 3384. Berlin, Heidelberg: Springer, 2005:192–201.

    Google Scholar 

  153. Kijima A, Kobayashi S. Efficient algorithm for testing structure freeness of finite set of biomolecular sequences. In: Carbone A, Daley M, Kari L, McQuillan I, Pierce N, eds. Preliminary Proceedings of the 11th International Workshop on DNA-Based Computers, DNA, 2005:278–288.

    Google Scholar 

  154. McCaskill JS. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 1990;29:1105–1119.

    CAS  Google Scholar 

  155. Dirks RM, Pierce NA. A partition function algorithm for nucleic acid secondary structure including pseudoknots. Journal of Computational Chemistry 2003;24:1664–1677. NUPACK is available at http://www.acm.caltech. edu/~niles/software.html.

    CAS  Google Scholar 

  156. Marathe A, Condon AE, Corn RM. On combinatorial DNA word design. Journal of Computational Biology 2001;8:201–220.

    CAS  Google Scholar 

  157. Leupold P. Partial words for DNA coding. In: Ferretti C, Mauri G, Zandron C, eds. Preliminary Proceedings of the 10th International Workshop on DNA-Based Computers, DNA, 2004.

    Google Scholar 

  158. Garzon M, Deaton RJ, Rose JA, Lu L, Franceschetti DR. Soft molecular computing. In: Winfree E, Gifford DK, eds. DNA Based Computers V, DIMACS Workshop 1999, vol. 54 of Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 2000:91–100. EdnaCo is available at http://zorro.cs.memphis.edu/~cswebadm/csweb/research/ pages/bmc/ or http://engronline.ee.memphis.edu/molec/demos.htm.

    Google Scholar 

  159. Penchovsky R, Ackermann J. DNA library design for molecular computation. Journal of Computational Biology 2003; 10:215–229.

    CAS  Google Scholar 

  160. D’yachkov AG, Macula AJ, Pogozelski WK, Renz TE, Rykov VV, Torney DC. A weighted insertion-deletion stacked pair thermodynamic metric. In: Ferretti C, Mauri G, Zandron C, eds. DNA Computing: 10th International Workshop on DNA-Based Computers, Lecture Notes in Computer Science, vol. 3384. Berlin, Heidelberg: Springer, 2005:90–103. Syn-DCode is available at http://cluster.ds.geneseo.edu:8080/ParallelDNA/.

    Google Scholar 

  161. Dimitrov RA, Zuker M. Prediction of hybridization and melting for doublestranded nucleic acids. Biophysical Journal 2004;87:215–226.

    CAS  Google Scholar 

  162. Rose JA, Deaton RJ, Franceschetti DR, Garzon M, Stevens SE Jr. A statistical mechanical treatment of error in the annealing biostep of DNA computation. In: Special Program in GECCO-99. 1999:1829–1834.

    Google Scholar 

  163. Rose JA, Deaton RJ. The fidelity of annealing-ligation: a theoretical analysis. In: Condon A, Rozenberg G, eds., DNA Computing: 6th International Workshop on DNA-Based Computers, DNA 2000, Lecture Notes in Computer Science, vol. 2054. Springer, 2001.

    Google Scholar 

  164. Rose JA, Deaton RJ, Hagiya M, Suyama A. The fidelity of the tag-antitag system. In: Jonoska N, Seeman NC, eds. DNA Computing: 7th International Workshop on DNA-Based Computers, DNA 2001, Lecture Notes in Computer Science, vol. 2340. Berlin, Heidelberg: Springer, 2002.

    Google Scholar 

  165. Rose JA, Deaton RJ, Hagiya M, Suyama A. An equilibrium analysis of the efficiency of an autonomous molecular computer. Physical Review E 2002;65.

    Google Scholar 

  166. Rose JA, Hagiya M, Suyama A. The fidelity of the tag-antitag system 2: identifying the regime of stringency. In: Sarker R, Reynolds R, Abbass H, et al., eds, Proceedings of the 2003 Congress on Evolutionary Computation CEC2003. New Jersey: IEEE Press, 2003:2740–2747. NucleicPark is available at http://hagi.is.s.u-tokyo.ac.jp/johnrose/ and http://engronline.ee.mem-phis. edu/molec/demos.htm.

    Google Scholar 

  167. Rose JA, Deaton RJ, Franceschetti DR, Garzon M, Stevens SE Jr. Hybridization error for DNA mixtures of N species, 1999. http://engronline.ee.memphis.edu/ molec/Misc/ci.pdf.

    Google Scholar 

  168. Rose JA, Suyama A. Physical modeling of biomolecular computers: models, limitations, and experimental validation. Natural Computing 2004;3:411–426.

    CAS  Google Scholar 

  169. SantaLucia J Jr, Hicks D. The thermodynamics of DNA structural motifs. Annual Review of Biophysics Biomolecular Structure 2004;33:415–440.

    CAS  Google Scholar 

  170. Hartemink AJ, Gifford DK. Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation. In: Rubin H, Wood DH, eds. Preliminary Proceedings of DNA Based Computers III, DIMACS Workshop, 1997:15–25.

    Google Scholar 

  171. Hartemink AJ, Gifford DK, Khodor J. Automated constraint-based nucleotide sequence selection for DNA computation. In: Kari L, Rubin H, Wood DH, eds. DNA Based Computers IV, DIMACS Workshop 1998, Biosystems, vol. 52, issues 1–3. Elsevier, 1999:227–235.

    Google Scholar 

  172. Nishikawa A, Yamamura M, Hagiya M. DNA computation simulator based on abstract bases. Soft Computing 2001;5:25–38.

    Google Scholar 

  173. Mathews DH, Turner DH. Dynalign: An algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol 2002;317:191–203.

    CAS  Google Scholar 

  174. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucl Acids Res 2003;31:3406–3415. Mfold is available at http://www.bioinfo. rpi.edu/applications/mfold.

    CAS  Google Scholar 

  175. Dirks RM, Pierce NA. An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. Journal of Computational Chemistry 2004;25:1295–1304.

    CAS  Google Scholar 

  176. Andronescu M, Aguirre-Hernandez R, Condon A, Hoos HH. RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucl Acids Res 2003;31:3416–3422. RNAsoft is available at http://www.rnasoft.ca/.

    CAS  Google Scholar 

  177. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zucker M, Turner DH. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 2004; 101:7287–7292. The free energy nearest neighbor parameters are available at http://rna.chem.rochester.edu/, RNAstructure is available at http://128.151.176.70/RNAstructure.html.

    CAS  Google Scholar 

  178. Hofacker IL. Vienna RNA secondary structure server. Nucl Acids Res 2003;31:3429–3431. Vienna Package is available at http://www.tbi.univie.ac. at/~ivo/RNA/.

    CAS  Google Scholar 

  179. Peyret N, Saro P, SantaLucia J Jr. HyTher server. HyTher Version 1.0 is available at http: //ozone2.chem.wayne.edu/.

    Google Scholar 

  180. SantaLucia J Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 1998;95: 1460–1465.

    CAS  Google Scholar 

  181. Peyret N, Seneviratne PA, Allawi HT, SantaLucia J Jr. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A-A, C-C, G-G, and T-T mismatches. Biochemistry 1999;38:3468–3477.

    CAS  Google Scholar 

  182. Novère NL. MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics 2001;17:1226–1227. Melting is available at http://www.ebi.ac.uk/~lenov/meltinghome.html.

    Google Scholar 

  183. Blake RD, Bizzaro JW, Blake JD, et al. Statistical mechanical simulation of polymeric DNA melting with MELTSIM. Bioinformatics 1999; 15: 370–375.

    CAS  Google Scholar 

  184. McDowell JA. MeltWin. MeltWin is available at http://www.meltwin.com/.

    Google Scholar 

  185. Flamm C, Fontana W, Hofacker IL, Schuster P. RNA folding at elementary step resolution. RNA 2000;6:325–338. Kinfold is available at http://www. tbi.univie.ac.at/~xtof/RNA/Kinfold/.

    CAS  Google Scholar 

  186. Visual OMP (Oligonucleotide Modeling Platform), DNA Software, Inc. Visual OMP is available at http://www.dnasoftware.com.

    Google Scholar 

  187. The DNA and Natural Algorithms Group. DNA design toolbox. DNA Design Toolbox is available at http://www.dna.caltech.edu/DNAdesign/.

    Google Scholar 

  188. Kim D, Shin SY, Lee IH, Zhang BT. NACST/Seq: A sequence design system with multiobjective optimization. In: Hagiya M, Ohuchi A, eds. DNA Computing: 8th International Workshop on DNA-Based Computers, DNA 2002, Lecture Notes in Computer Science, vol. 2568. Berlin: Springer, 2003:242–251.

    Google Scholar 

  189. Ruben AJ, Freeland SJ, Landweber LF. PUNCH: An evolutionary algorithm for optimizing bit set selection. In: Jonoska N, Seeman NC, eds. DNA Computing: 7th International Workshop on DNA-Based Computers, DNA 2001, Lecture Notes in Computer Science, vol. 2340. Berlin: Springer, 2002:150–160.

    Google Scholar 

  190. Bishop M, Macula AJ, Pogozelski WK, Renz TE, Rykov VV. SynDCode: Cooperative DNA code generating software. In: Carbone A, Daley M, Kari L, McQuillan I, Pierce N, eds. Preliminary Proceedings of the 11th International Workshop on DNA-Based Computers, DNA, 2005:391.

    Google Scholar 

  191. Pogozelski WK, Bernard MP, Priore SF, Macula AJ. Experimental validation of DNA sequences for DNA computing: Use of a SYBR green assay. In: Carbone A, Daley M, Kari L, McQuillan I, Pierce N, eds. Preliminary Proceedings of the 1 1th International Workshop on DNA-Based Computers, DNA, 2005:322–331.

    Google Scholar 

  192. Yin P, Guo B, Belmore C, et al. Tilesoft: Sequence optimization software for designing DNA secondary structures, 2004. http://www.cs.duke.edu/~reif/ paper/peng/TileSoft/TileSoft.pdf.

    Google Scholar 

  193. Kari L, Kitto R, Thierrin G. Codes, involutions and DNA encodings. In: Lecture Notes in Computer Science, vol. 2300. Berlin, Heidelberg: Springer, 2002:376.

    Google Scholar 

  194. Blain DR, Garzon M, Shin SY, et al. Development, evaluation and benchmarking of simulation software for biomolecule-based computing. Natural Computing 2004;3:427–442.

    CAS  Google Scholar 

  195. Arita M, Nishikawa A, Hagiya M, Komiya K, Gouzu H, Sakamoto K. Improving sequence design for DNA computing. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2000), 2000:875–882.

    Google Scholar 

  196. Hoos HH, Stutzle T. Stochastic Local Search: Foundations and Applications. Morgan Kaufmann, 2004.

    Google Scholar 

  197. Tulpan DC, Hoos HH, Condon A. Stochastic local search algorithms for DNA word design. In: DNA Computing: 8th International Workshop on DNA-Based Computers, DNA 2002, Lecture Notes in Computer Science, vol. 2568. Berlin: Springer, 2003:229–241.

    Google Scholar 

  198. Tulpan DC, Hoos HH. Hybrid randomised neighbourhoods improve stochastic local search for DNA code design. In: Canadian Conference on AI 2003, Lecture Notes in Computer Science, vol. 2671. Berlin: Springer-Verlag, 2003:418–433.

    Google Scholar 

  199. Tulpan D, Andronescu M, Change SB, et al. Thermodynamically based DNA strand design. Nucl Acids Res 2005;33:4951–4964.

    CAS  Google Scholar 

  200. Holland JH. Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control and Artificial Intelligence. Cambridge, MA: MIT Press, 1992.

    Google Scholar 

  201. Rechenberg I. Evolutionsstrategie—Optimierung technischer Systeme nach Prinzipien der biologischen Information. Freiburg, Germany: Fromman Verlag, 1973.

    Google Scholar 

  202. Schwefel HP. Numerical Optimization of Computer Models. New York: John Wiley & Sons, Inc., 1981.

    Google Scholar 

  203. Fogel LJ, Owens AJ, Walsh MJ. Artifical Intelligence Through Simulated Evolution. New York: John Wiley & Sons, 1966.

    Google Scholar 

  204. Deaton RJ, Murphy RC, Garzon M, Franceschetti DR, Stevens SE Jr. Genetic search of reliable encodings for DNA-based computation. In: First Genetic Programming Conference. Stanford University, 1996.

    Google Scholar 

  205. Deaton RJ, Rose JA. Simulations of statistical mechanical estimates of hybridization error. In: Condon A, Rozenberg G, eds. Preliminary Proceedings of the 6th International Workshop on DNA-Based Computers, DNA, 2000:251–252.

    Google Scholar 

  206. Shin SY, Kim DM, Lee IH, Zhang BT. Evolutionary sequence generation for reliable DNA computing. In: Proceedings of the 2002 Congress on Evolutionary Computation (CEC2002), vol. 1. 2002:79–84.

    Google Scholar 

  207. Shin SY, Kim DM, Lee IH, Zhang BT. Multiobjective evolutionary algorithms to design error-preventing dna sequences. Tech. Rep. BI-02-003, Biointelligence Lab (BI), School of Computer Science & Engineering, Seoul National University, 2002.

    Google Scholar 

  208. Smith WD. DNA computers in vitro and vivo. In: Lipton RJ, Baum EB, eds. DNA Based Computers, DIMACS Workshop 1995, vol. 27 of Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1995:121–185.

    Google Scholar 

  209. Tsaftaris SA, Katsaggelos AK, Pappas TN, Papoutsakis ET. DNA-based matching of digital signals. In: International Conference on Acoustics, Speech, and Signal Processing, vol. 5. Montreal, Quebec, Canada, 2004.

    Google Scholar 

  210. Tsaftaris SA, Katsaggelos AK, Pappas TN, Papoutsakis ET. How can DNA computing be applied to digital signal processing? IEEE Signal Processing Magazine 2004;21.

    Google Scholar 

  211. Benenson Y, Paz-Elizur T, Adar R, Keinan E, Livneh Z, Shapiro E. Programmable and autonomous computing machine made of biomolecules. Nature 2001;414:430–434.

    CAS  Google Scholar 

  212. 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 2003;100:2191–2196.

    CAS  Google Scholar 

  213. Stojanovic MN, Stefanovic D, LaBean T, Yan H. Computing with nucleic acids. In: Willner I, Katz E, eds. Bioelectronics: From Theory to Applications. Wiley-VCH, 2005.

    Google Scholar 

  214. Calude CS, Paun G. Computing with Cells and Atoms. London: Taylor & Francis, 2001.

    Google Scholar 

  215. Ehrenfeucht A, Harju T, Petre I, Prescott DM, Rozenberg G. Computation in Living Cells. Berlin: Springer-Verlag, 2004.

    Google Scholar 

  216. Paun G. Computing with Bio-Molecules. Singapore: Springer-Verlag, 1998.

    Google Scholar 

  217. Rothemund PWK. Folding DNA to create nanoscale shapes and patterns. Nature 2006;440:297–302.

    CAS  Google Scholar 

  218. Baron R, Lioubashevski O, Katz E, Niazov T, Willner I. Elementary arithmetic operations by enzymes: A model for metabolic pathway based computing. Angewandte Chemie International Edition 2006;45:1572–1576.

    CAS  Google Scholar 

  219. Pistol C, Lebeck AR, Dwyer C. Design automation for DNA self-assembled nanostructures. In: Design Automation Conference (DAC), 2006.

    Google Scholar 

  220. Patwardhan J, Johri V, Dwyer C, Lebeck AR. A defect tolerant self-organizing nanoscale simd architecture. In: Proceedings of the Twelth International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS XII), 2006.

    Google Scholar 

  221. Lipton RJ, Baum EB. DNA Based Computers, DIMACS Workshop 1995, vol. 27 of Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1996.

    Google Scholar 

  222. Rubin H, Wood DH. DNA Based Computers III, DIMACS Workshop 1997, vol. 48 of Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1999.

    Google Scholar 

  223. Jonoska N, Seeman NC. DNA Computing: 7th International Workshop on DNA-Based Computers, DNA 2001, Lecture Notes in Computer Science vol. 2340. Berlin, Heidelberg: Springer, 2002.

    Google Scholar 

  224. Landweber LF, Baum EB. DNA Based Computers II, DIMACS Workshop 1996, vol. 44 of Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1999.

    Google Scholar 

  225. Winfree E, Gifford DK. DNA Based Computers V, DIMACS Workshop 1999, vol. 54 of Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 2000.

    Google Scholar 

  226. Kari L, Rubin H, Wood DH. DNA Based Computers IV, DIMACS Workshop 1998, Biosystems, vol. 52, issues 1–3. Elsevier, 1999.

    Google Scholar 

  227. Hagiya M, Ohuchi A. DNA Computing: 8th International Workshop on DNA-Based Computers, DNA 2002, Lecture Notes in Computer Science, vol. 2568. Berlin, Heidelberg: Springer, 2003.

    Google Scholar 

  228. Ferretti C, Mauri G, Zandron C. DNA Computing: 10th International Workshop on DNA-Based Computers, DNA 2004, Lecture Notes in Computer Science, vol. 3384. Berlin, Heidelberg: Springer, 2005.

    Google Scholar 

  229. Chen J, Reif JH. DNA Computing: 9th International Workshop on DNA-Based Computers, DNA 2003, Lecture Notes in Computer Science, vol. 2943. Berlin, Heidelberg: Springer, 2004.

    Google Scholar 

  230. Ferretti C, Mauri G, Zandron C, eds. Preliminary Proceedings of the 10th International Workshop on DNA-Based Computers, DNA 2004.

    Google Scholar 

  231. Carbone A, Daley M, Kari L, McQuillan I, Pierce N. Preliminary Proceedings of the 1 1th International Workshop on DNA-Based Computers, DNA 2005.

    Google Scholar 

  232. Peyret N. Prediction of Nucleic Acid Hybridization: Parameters and Algorithms. Ph.D. thesis, Wayne State University, Dept. of Chemistry, 2000.

    Google Scholar 

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Sager, J., Farfel, J., Stefanovic, D. (2008). Nanocomputing. In: Shoseyov, O., Levy, I. (eds) NanoBioTechnology. Humana Press. https://doi.org/10.1007/978-1-59745-218-2_10

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