Please use this identifier to cite or link to this item:
Design of Synthetic Genetic Logic Circuits Based on RSGA
|關鍵字:||基因演算法;Genetic algorithm;實數型結構基因演算法;多目標最佳化;基因震盪器;生物邏輯閘;順式規則輸入函數;Real structured genetic algorithm;Muliobjective optimization;genetic oscillator;biological logic gate;cis-regular input function||出版社:||電機工程學系所||引用:||References  J. Hasty, D. McMillen and J. J. Collins, “Engineered gene circuits,” Nature, vol. 420, pp. 224-230, 2002.  M. S. Dasika and C. D. Maranas, “OptCircuit: an optimization based method for computational design of genetic circuits,” BMC Systems Biology, vol. 2, 2008.  Holland J.H., “Adaptation in Natural and Artificial Systems,” Cambridge, MIT Press, MA,1975.  Goldberg D.E., “Real-Code Genetic Algorithm, Virtual Alphabets and Blocking, ” Coplex System, vol. 5, pp. 139-167, 1991.  Dasgupta D. and McGregor D. R., “A Structured Genetic Algorithm: the Model and the First Result, ” Univ. strathclyde, U.K., Res, Rep. IKBS-2-91, 1991.  Lai C.C., and Chang C.Y., “A Hierarchical Genetic Algorithm Based Approach for Image Segmentation,” in Proc. IEEE Int. Conf. on Networking, Sensing and Control, Taipei, Taiwan, pp. 1284-1288, 2004.  C. W. Tsai, C. H. Huang and C. L. Lin, “Structure-specified IIR filter and control design using real structured genetic algorithm,” Applied Soft Computing, vol. 9, pp. 1285-1295, 2009.  C. W. Tsai, C.L. Lin and C. H. Huang, “Microbrushless DC motor control design based on real coded structural genetic algorithm,” IEEE/ASME Transactions on Mechatronics, vol. 16, pp. 151-159, 2011.  M. B. Elowitz and S. Leibler, “A synthetic oscillatory network of transcriptional regulators,” Nature, vol. 403, pp. 335-338, 2000.  B. S. Chen and P. W. Chen, “GA-based design algorithms for the robust synthetic genetic oscillators with prescribed amplitude, period and phase,” Gene Regulation and Systems Biology, vol. 4, pp. 35-52, 2010.  Wang,B., Kitney, R. I., Joly, N., and Buck, M., “Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology,” Nat Commun, 2, 508, 2011.  Anderson, J.C., Voigt, C.A. and Arkin, A.P., “Environmental signal integration by a modular AND gate,” Mol. Syst. Biol. 3, 133, 2007.  Jan Halamek, et al, “Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Enzyme Inhibition by a Substrate,” J. Phys. Chem. B, 115(32), pp 9838–9845, 2011.  Vladimir Privman, et al, “Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Signal Change,” J. Phys.Chem.B, 114 (42), pp 13601–13608, 2010.  Vladimir Privman, “Error-Control and Digitalization Concepts for Chemical and Biomolecular Information Processing Systems,” Journal of Computational and Theoretical Nanoscience, Vol. 8,490-502, 2011.  Kaplan, S., Bren, A., Dekel, E. and Alon, U., “The incoherent feed-forward loop can generate non-monotonic input functions for genes,” Mol. Syst. Biol. 4, 203, 2008.  Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U, “Plasticity of the cis-regulatory input function of a gene,” PLoS Biol,4:e45, 2006.  Setty, Y., Mayo, A. E., Surette, M. G. and Alon, U., “Detailed map of a cis-regulatory input function,” Proc. Natl Acad. Sci. USA 100, 7702–7707 , 2003.  Kinkhabwala, A. Guet, C. C., “Uncovering cis regulatory codes using synthetic promoter shuffling,” PLoS ONE 3, e2030, 2008.  N. Zabet, A. Hone and D. Chu, , “Design principles of transcriptional logic circuits,” In: Artificial Life XII Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, MIT Press, August, pp. 186–193, 2010.  L., Mario, K. Bhalerao, M. M. Pugalanthiran, and Bo Yuan. “Building blocks of a biochemical CPU based on DNA transcription logic,” 3rd Workshop on Non-Silicon Computation (NSC-3), Munich, 2004.  N. Strelkowa and M. Barahona, “Switchable genetic oscillator operating in quasi-stable mode,” Journal of the Royal Society Interface, vol. 7, pp. 1071-1082, 2010.  Y. Hori, S. Hara and T. H. Kim, “Existence criteria of periodic oscillations incyclic gene regulatory networks,” Mathematical Engineering Technical Reports, The University of Tokyo, 2010.  S. Zeiser, J. Muller and V. Liebscher, “Modelling the Hes1 oscillator during somitogenesis,” Journal of Computational Biology, vol. 14, pp. 984-1000, 2007.  Y. Hori and S. Hara, “Oscillation pattern analysis for gene regulatory networks with negative cyclic feedback,” Mathematical Engineering Technical Reports, The University of Tokyo, 2010.  R. Wang, C. Li, L. N. Chen, and K. Aihara, “Modeling and analyzing biological oscillations in molecular networks,” Proceedings of the IEEE, vol. 96, pp. 1361-1385, 2008.  M. A. Marchisio and J. Stelling, “Automatic design of digital synthetic gene circuits,” PLoS Comput Biol, vol. 7, no. 2, Feb, 2011.  J Christopher, Christopher A Voigt and Adam P Arkin, “Environmental signal integration by a modular AND gate,” Molecular System Biology, 3:133, 2007.  Daniel J. Sayut, Yan Niu, and Lianhong Sun, “Construction and Enhancement of a Minimal Genetic AND Logic Gate,“ Applied and Environmental Microbiology, p.637-642, 2009.  Zhang, J.,Yuan, Z.and Zhou, T., ”Combinatorial regulation: characteristics of dynamic correlations,” Systems Biology, IET,Volume:3 Issue:6, 2009.  A.M. Chen and T.S. Zhou, “Sensitivity of Cis-Regulatory Input Function,” The Second International Symposium on Optimization and Systems Biology, 2008.  Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R,”Transcriptional regulation by the numbers: applications,” Curr Opin Genet, 15:125-135, 2005.  E. N. Buchler, U. Gerland and T. Hwa, “On schemes of combinatorial transcription logic,” Proc. Natl Acad. Sci. USA 100, 5136–5141, 2003.  Weiss R, Basu S, “The device physics of cellular logic gates,” NSC-1: The First Workshop of Non-Silicon Computing, Boston, MA , 2002.  Tamsir A, Tabor JJ, Voigt CA, “Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’,” Nature, 469:212–15, 2011.  Bintu, L. et al., “Transcriptional regulation by the numbers: models,” Curr. Opin, Genet, 116–124, 2005.||摘要:||
本論文結合了實數型基因演算法(real genetic algorithm)與結構型基因演算法(structured algorithm)的優點，發展出新穎的實數型結構基因演算法(real structured genetic algorithm)，並將其作為基因震盪器以及生物邏輯閘的最佳化設計策略。
This thesis develops a real structured genetic algorithm (RSGA) which combines advantages of the traditional real genetic algorithm (RGA) with those of the structured genetic algorithm (SGA) and applies it as an optimization strategy for genetic oscillator and biological logic gate design.
For the generalized genetic oscillator design, our proposed approach fulfills all types of genes by minimizing the order of oscillator while searching for the optimal network parameters. The design approach is shown to be capable of yielding genetic oscillators with a simple structure while searching for the optimal network parameters.
Furthermore, the proposed approach has also been applied to the biological logic gate design. For a nonlinear model with the cis-regular input function (CRIF), we define the multi-objective performance indices that are related to the accuracy of logic state and the difference between the high and low logic levels.
Simulation studies show the effectiveness of the proposed algorithm, when it is used to generate genetic oscillators, biological logic gates. For the genetic oscillator design, we show that our proposed approach performs better than traditional GAs in the sense that a cheaper structure can be obtained. For the logic gate design, we can establish a conceptualized design framework of steady-state combinational and sequential logic circuits.
|Appears in Collections:||電機工程學系所|
Show full item record
TAIR Related Article
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.