Designing and Optimizing DNA Reversible Adders and Adder/Subtractors
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Abstract
The construction of new biological systems is a new field of biological science in which many fields of science, such as chemistry and engineering, are simultaneously applied. Reversible logic has shown its capabilities for DNA computing, quantum computing, low-power computing, and nano-technology. Due to its inherently reversible features, DNA technology can be used as a suitable alternative to traditional silicon technology to decrease power consumption. One area discussed in the context of DNA-based calculations is the design of DNA-based gates and circuits using related biochemical operations. The present study designs DNA-based reversible adder and subtractor circuits. Toffoli, Feynman, and Fredkin gates are used to demonstrate reversible DNA-based half adder, full adder, half adder/subtractor, full adder/subtractor, and switchable half adder/subtractor designs. An optimization method is used to optimize the proposed DNA-based circuits to have power and delay as low as possible. The novel circuits are then optimized in quantum merit criteria of quantum cost, constant inputs, garbage outputs, delay, and number of gates, using a combination of Toffoli and Feynman gates. The comparative results show that our proposed reversible DNA-based switchable half adder/subtractor is more optimized than existing circuit in terms of quantum merit criteria. For the comparison, the proposed full adder is implemented using CMOS and CNTFET technology as well.
Keywords
DNA Adder/subtractor Reversible gate Optimization Quantum merit criteriaReferences
- 1.Sarker, A., Babu, H. M. H., & Rashid, S. M. M. (2015). Design of a DNA-based reversible arithmetic and logic unit. IET Nanobiotechnology, 9, 226–238.CrossRefGoogle Scholar
- 2.Mardian, R., & Sekiyama, K. (2015). Ant systems-based DNA circuits. BioNanoScience, 4, 206–216.CrossRefGoogle Scholar
- 3.Kari, L., Daley, M., Gloor, G., Siromoney, R., Landweber, L. F., Rangan, C. P., Raman, V., Ramanujam, R. (1999). How to compute with DNA. FSTTCS’99, LNCS 1738. pp. 269–282.Google Scholar
- 4.Schaumann, H. C., Rief, M., Tolksdorf, C., & Gaub, H. E. (2000). Mechanical stability of single DNA molecule. Biophysical Journal, 78, 1997–2007.CrossRefGoogle Scholar
- 5.Fulekar, M. H. (2009). Bioinformatic in life and environmental sciences (pp. 200–206). New York: Springer.Google Scholar
- 6.Ryu, W. (2002). DNA computing: a primer. London: Ars Technica.Google Scholar
- 7.Yingwei, Y. (2002). DNA computing: DNA computers vs. conventional electronic computers, University of Stuttgart.Google Scholar
- 8.Echols, H., & Goodman, M. F. (1999). Fidelity mechanisms in DNA replication. Annual Review of Biochemistry, 60, 477–511.CrossRefGoogle Scholar
- 9.Karl, L. (1997). DNA computing: the arrival of biological mathematics. The Mathematical Intelligence, 19, 9–22.MathSciNetCrossRefGoogle Scholar
- 10.Hiasa, H., & Marians, K. J. (1994). Primase couples leading and lagging-strand DNA synthesis from oriC. The Journal of Biological Chemistry, 269, 6058–6063.Google Scholar
- 11.Sarker, A., Ahmed, T., Rashid, S. M, M., Anwar, S., Jaman, L., Tara, N., Alam, M. M., Babu, H. M. H. (2011). Realization of reversible logic in DNA computing. 11th IEEE International Conference on Bioinformatics and Bioengineering (BIBE). 24-26 Oct. 2011, Taichung, Taiwan, pp. 261–265.Google Scholar
- 12.Gupta, V., Parthasarathy, S., Zaki, M. J. (1997). Arithmetic and logic operations with DNA. 3rd Annual DIMACS Workshop on DNA Based Computers. University of Pennsylvania, 23-25 June 1997, pp. 212–220.Google Scholar
- 13.Stojanovic, M. N., & Stefanovic, D. (2003). Deoxyribozyme-based half-adder. Journal of the American Chemical Society, 125, 6673–6676.CrossRefGoogle Scholar
- 14.Lederman, H., Macdonald, J., Stefanovic, D., & Stojanovic, M. N. (2006). Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. Biochemistry, 45, 1194–1199.CrossRefGoogle Scholar
- 15.Inestrosa, E. P., Montenegro, J. M., Collado, D., Suau, R., & Casado, J. (2007). Molecules with multiple light-emissive electronic excited states as a strategy toward molecular reversible logic gates. The Journal of Physical Chemistry C, 111, 6904–6909.CrossRefGoogle Scholar
- 16.Zoraida, B. S. E., Arock, M., Ronald, B. S. M., Ponalagusamy, R. (2008). A novel generalized model for constructing reusable and reliable logic gates using DNA. Fourth International Conference on Natural Computation.18-20 Oct. 2008, Jinan, China pp. 533–537.Google Scholar
- 17.Song, T., Wang, S., Wang, X. (2008). The design of reversible gate and reversible sequential circuit based on DNA computing. IEEE 3rd International Conference on Intelligent System and Knowledge Engineering. ISKE, pp. 114–118.Google Scholar
- 18.Gearheart, C. M., Rouchka, E. C., Arazi, B. (2010). DNA-based dynamic logic circuitry. 53rd IEEE International Midwest Sympossium on Circuits and Systems (MWSCAS),1-4 Aug. 2010, Seattle, WA, USA, pp. 248–251.Google Scholar
- 19.Roy, P., Dey, D., Sinha, S., & De, D. (2013). Reversible OR Logic gate design using DNA. Proceedings of seventh international conference on bio-inspired computing, theories and applications (BIC-TA), advances in intelligent systems and computing (pp. 355–366). New Delhi: Springer.Google Scholar
- 20.Ahmed, T., Sarker, A., Sharif, M. I., Rashid, S. M. M., Rahman, M. A., Babo, H. M. H. (2013). A novel approach to design a reversible shifter circuit using DNA. IEEE 26th International SOC Conference (SOCC), 4-6 Sept. 2013, Erlangen, Germany, pp. 256–261.Google Scholar
- 21.Sarker A., Babu H. M. H., Islam M. S. (2014). A novel approach to perform reversible addition/subtraction operations using deoxyribonucleic acid. IEEE International Symposium on Circuits and Systems (ISCAS), 1-5 June 2014, Melbourne VIC, Australia, pp. 1828–1831.Google Scholar
- 22.Kari, L., Paun, G., Rozenberg, G., Salomaa, A., & Yu, S. (1998). DNA computing, sticker systems and universality. Acta Informatica, 35, 401–420.MathSciNetCrossRefMATHGoogle Scholar
- 23.Watson, J. D., & Crick, F. H. C. (1993). Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Journal of the American Medical Association., 269, 1966–1967.CrossRefGoogle Scholar
- 24.Liu, B., Wong, M. L., & Alberts, B. A. (1994). Transcribing RNA polymerase molecule survives DNA replication without aborting its growing RNA chain. Proceedings of the National Academy of Science, 91, 10660–10664.CrossRefGoogle Scholar
- 25.Hamilton, W. C., & Ibers, J. A. (1968). Hydrogen Bonding in Solids. In Methods of molecular structure determination. New York: W. A. Benjamin Inc..Google Scholar
- 26.Saenger, W. (1984). Principles of nucleic acid structure. New York: Springer-Verlag.CrossRefGoogle Scholar
- 27.Benenti G., Casati G., Strini G. (2004). Principles of quantum computation and information. Volume I: basic concepts. Singapore: World Scientific Publishing Company.Google Scholar
- 28.Wood, H., Junghuei Chen, D. J. (2004) Fredkin gate circuits via recombination enzymes, Proceedings Evolutionary Computation, CEC2004Google Scholar
- 29.Mohammadi, M., & Eshghi, M. (2009). On figures of merit in reversible and quantum logic designs. Quantum Information Processing., 8, 297–318.MathSciNetCrossRefMATHGoogle Scholar
- 30.Maslov, D.: Web Page: http://webhome.cs.uvic.ca/~dmaslov.
- 31.Barenco, A., Bennett, C. H., Cleve, R., Di Vincenzo, D. P., Margolus, N., Shor, P., Sleator, T., Smolin, J., & Weinfurter, H. (1995). Elementary gates for quantum computation. Physical Review A, 52, 3457–3467.CrossRefGoogle Scholar
- 32.Smolin, J. A., & DiVincenzo, D. P. (1996). Five two-bit quantum gates are sufficient to implement the quantum Fredkin gate. Physical Review A, 53, 2855–2856.CrossRefGoogle Scholar
- 33.Mano, M. M. (1984). Digital design. Prentice Hall, Canada, Incorporated: Englewood Cliffs.Google Scholar
- 34.Mathur, D., Singh, P., & Singh, S. (2013). Transcendental and optimized digital designing using reversible logic. International Journal of Emerging Science and Engineering (IJESE)., 1, 42–46.Google Scholar
- 35.Babu, H. M. H., Islam, M. R., Chowdhury, S. M. A., Chowdhury, A. R. (2004). Synthesis of full-adder circuit using reversible logic. Proceedings of the 17th International Conference on VLSI Design (VLSID’04), 9 Jan. 2004, Mumbai, India, pp. 757–760.Google Scholar
- 36.Adamatzky, A. (2017). Fredkin and Toffoli gates implemented in Oregonator model of Belousov-Zhabotinsky medium. International Journal Bifurcation and Chaos., 27, 1–15.CrossRefMATHGoogle Scholar
- 37.Mohammadi, M., Eshghi, M., Navi, K. (2007). Optimizing the reversible full adder circuit. IEEE EWDTS. 7-10 Sep. 2007, Yerevan, pp. 312–315.Google Scholar