Abstract
Associative memories based on DNA-affinity have been proposed [2]. Here, the performance, efficiency, reliability of DNA-based memories is quantified through simulations in silico. Retrievals occur reliably (98%) within very short times (milliseconds) despite the randomness of the reactions and regardless of the number of queries. The capacity of these memories is also explored in practice and compared with previous theoretical estimates. Advantages of implementations of the same type of memory in special purpose chips in silico is proposed and discussed.
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References
L.M. Adleman: Molecular Computation of Solutions to Combinatorial Problems. Science 266 (1994) 1021–1024
E. Baum, Building An Associative Memory Vastly Larger Than The Brain. Science 268 (1995) 583–585.
A. Condon, G. Rozenberg (eds.): DNA Computing (Revised Papers). In: Proc. of the 6th International Workshop on DNA-based Computers, 2000. Springer-Verlag Lecture Notes in Computer Science 2054 (2001)
R. Deaton, R., J. Chen, H. Bi, M. Garzon, H. Rubin, D.H. Wood. A PCR-Based Protocol for In-Vitro Selection of Non-Crosshybridizing Oligonucleotides (2002). In [11], 105–114
R.J. Deaton, J. Chen, H. Bi, J.A. Rose: A Software Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides. In [11], pp. 211–220.
R. Deaton, M. Garzon, R. E. Murphy, J. A. Rose, D. R. Franceschetti, S.E. Stevens, Jr. The Reliability and Efficiency of a DNA Computation. Phys. Rev. Lett. 80 (1998) 417–420
M. Garzon, D. Blain, K. Bobba, A. Neel, M. West: Self-Assembly of DNA-like structures in silico. Journal of Genetic Programming and Evolvable Machines 4:2 (2003), in press.
M. Garzon: Biomolecular Computation in silico. Bull. of the European Assoc. For Theoretical Computer Science EATCS (2003), in press.
M. Garzon, C. Oehmen: Biomolecular Computation on Virtual Test Tubes. In: N. Jonoska and N. Seeman (eds.): Proc. of the 7th International Workshop on DNA-based Computers, 2001. Springer-Verlag Lecture Notes in Computer Science 2340 (2002) 117–128
M. Garzon, R. Deaton, P. Neathery, R.C. Murphy, D.R. Franceschetti, E. Stevens Jr.: On the Encoding Problem for DNA Computing. In: Proc. of the Third DIMACS Workshop on DNA-based Computing, U of Pennsylvania. (1997) 230–237
M. Hagiya, A. Ohuchi (eds.): Proceedings of the 8th Int. Meeting on DNA Based Computers, Hokkaido University, 2002, Springer-Verlag Lecture Notes in Computer Science 2568 (2003)
J. Lee, S. Shin, S.J. Augh, T.H. Park, B. Zhang: Temperature Gradient-Based DNA Computing for Graph Problems with Weighted Edges. In [11], pp. 41–50.
R. Lipton: DNA Solutions of Hard Computational Problems. Science 268 (1995) 542–544
A. Marathe, A. Condon, R. Corn: On Combinatorial Word Design. In: E. Winfree and D. Gifford (eds.): DNA Based Computers V, DIMACS Series in Discrete Mathematics and Theoretical Computer Science. 54 (1999) 75–89
J.H. Reif, T. LaBean. Computationally Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector Quantization In [3], pp. 145–172
K.A. Schmidt, C.V. Henkel, G. Rozenberg: DNA computing with single molecule detection. In [3], 336.
J.G. Wetmur: Physical Chemistry of Nucleic Acid Hybridization. In: H. Rubin and D.H. Wood (eds.): Proc. DNA-Based Computers III, U. of Pennsylvania, 1997. DIMACS series in Discrete Mathematics and Theoretical Computer Science 48 (1999) 1–23
E. Winfree, F. Liu, L.A. Wenzler, N.C. Seeman: Design and self-assembly of two-dimensional DNA crystals. Nature 394 (1998) 539–544
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Garzon, M.H., Neel, A., Chen, H. (2003). Efficiency and Reliability of DNA-Based Memories. In: Cantú-Paz, E., et al. Genetic and Evolutionary Computation — GECCO 2003. GECCO 2003. Lecture Notes in Computer Science, vol 2723. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45105-6_47
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DOI: https://doi.org/10.1007/3-540-45105-6_47
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