Abstract
The stickers model is a model of DNA computation that is computationally complete and universal. Many NP complete problems can be described by stickers programs that have polynomial runtime and are exponential in space. The stickers model can be viewed as a bit-vertically operating register machine. This makes it attractive for in silico implementation. This paper describes a stickers model for the maximum clique problem and its implementation by an FPGA architecture. The results show that the FPGA based algorithm is comparable with existing software algorithms for moderate problem sizes. More generally, the stickers model seems to be a well-suited programming model for dedicated hardware.
Similar content being viewed by others
References
Adleman, L. (1994). Molecular computation of solutions of combinatorial problems. Science 266, 1021–1023.
Garey, M. R., & Johnson D. S. (1979). Computers and intractability: A guide to the theory of NP-completeness. New York: W.H. Freeman.
Ignatova, Z., Martinez-Perez, I., & Zimmermann, K.-H. (2008). DNA computing models. Boston: Springer.
Kilts, S. (2007). Advanced FPGA design: Architecture, implementation, and optimization. New York: Wiley-IEEE.
Kendrew, J. (1998). Encyclopedia of molecular biology. Oxford: Blackwell.
Martinez-Perez, I. (2007). Biomolecular computing models for graph problems and finite state automata. Ph.D. thesis, Hamburg Univ Tech.
Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N., Goodman, M., Rothemund P., et al. (1996). A sticker based architecture for DNA computation. In E. B. Baum (Ed.), DNA based computers (pp. 1–27). Providence: AMS.
XILINX (2008). Virtex-4 FPGA user guide. http://www.xilinx.com/support/documentation/user_guides/ug070.pdf.
Zimmermann, K.-H. (2002). On applying molecular computation to binary linear codes. IEEE Transactions on Information Theory, 48, 505–510.
Zimmermann, K.-H. (2002). Efficient DNA sticker algorithms for NP-complete graph problems. Computer Physics Communications, 114, 297–309.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Martínez-Pérez, I., Brandt, W., Wild, M. et al. Bioinspired Parallel Algorithms for Maximum Clique Problem on FPGA Architectures. J Sign Process Syst Sign Image Video Technol 58, 117–124 (2010). https://doi.org/10.1007/s11265-008-0322-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11265-008-0322-3