Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/98315
標題: 可編程之生物基因處理器
Programmable Biological Central Processing Unit
作者: 李威憲
Wei-Xian Li
關鍵字: 合成生物學;基因邏輯閘;基因震盪器;生物電腦;synthetic biology;genetic oscillator;genetic logic gate;biological computer
引用: [1] J. Hasty, D. McMillen, J. J. Collins, 'Engineered gene circuits.' Nature., vol. 420, pp. 224-230, 2002. [2] M. S. Dasika, C. D. Maranas, 'OptCircuit: an optimization based method for computational design of genetic circuits.' BMC systems biology., vol. 2, pp. 24-42, 2008. [3] J. M. Perkel, 'Cell engineering: How to hack the genome.' 2017. [4] J. Fernandez-Rodriguez, F. Moser, M. Song, et al. 'Engineering RGB color vision into Escherichia coli.' Nature chemical biology., vol.13, pp. 706-708, 2017. [5] T. S. Gardner, C. R. Cantor, J. J. Collins, 'Construction of a genetic toggle switch in Escherichia coli.' Nature., vol. 403, pp. 339-342, 2000. [6] M. B. Elowitz, S. Leibler, 'A synthetic oscillatory network of transcriptional regulators,' Nature., vol. 403, pp. 335-338, 2000. [7] B. Wang, R.I. Kitney, N. Joly et al., 'Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology.' Nature communications., vol.2, Article number: 508, 2011. [8] J. C. Anderson, C. A. Voigt, A. P. Arkin, 'Environmental signal integration by a modular AND gate.' Molecular systems biology., vol. 3, pp.133-140, 2007. [9] V. Privman, J. Zhou, J. Halámek et al., 'Realization and properties of biochemical-computing biocatalytic XOR gate based on signal change.' The Journal of Physical Chemistry B., vol. 114, pp. 13601-13608, 2010. [10] V. Privman, J. Zhou, J. Halámek et al., 'Realization and properties of biochemical-computing biocatalytic XOR gate based on enzyme inhibition by a substrate.' The Journal of Physical Chemistry B., vol. 115, pp. 9838-9845, 2011. [11] V. Privman, 'Error-control and digitalization concepts for chemical and biomolecular information processing systems.' Journal of Computational and Theoretical Nanoscience., vol. 8, pp. 490-502, 2011. [12] M. Lauria, K. Bhalerao, M. M. Pugalanthiran et al., 'Building blocks of a biochemical CPU based on DNA transcription logic.' 3rd Workshop on Non-Silicon Computation (NSC-3)., vol. 6, 2004. [13] M. A. Marchisio, J. Stelling, 'Automatic design of digital synthetic gene circuits.' PLoS computational biology., vol. 7, e1001083, 2011. [14] N. E. Buchler, U. Gerland, T. Hwa, 'On schemes of combinatorial transcription logic.' Proceedings of the National Academy of Sciences., vol. 100, pp. 5136-5141, 2003. [15] A. Tamsir, J. J. Tabor, C. A. Voigt, 'Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'.' Nature., vol. 469, pp. 212-215, 2011. [16] L. Bintu, N. E. Buchler, H. G. Garcia et al., 'Transcriptional regulation by the numbers: models.' Current opinion in genetics & development, vol. 15.2, pp.116-124, 2005. [17] J. Bonnet, P. Yin, M. E. Ortiz et al., 'Amplifying genetic logic gates.' Science., vol. 340, pp. 599-603, 2013. [18] B. H. Weinberg, N. T. H. Pham, L. D. Caraballo, 'Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells.' Nature biotechnology., vol. 35, pp. 453-462, 2017. [19] A. A. K. Nielsen, B. S. Der, J. Shin et al., 'Genetic circuit design automation.' Science., vol.352, aac7341, 2016. [20] C. H. Chuang, C. L. Lin, Y.C. Chang et al., 'Design of synthetic biological logic circuits based on evolutionary algorithm,' IET Systems Biology., vol. 7, no. 4, pp. 89-105, 2013. [21] C. H. Chuang, C. L. Lin, 'A novel synthesizing genetic logic circuit: frequency multiplier.' IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)., vol. 11, pp.702-713, 2014. [22] C. L. Lin, P. K. Chen, Y. Y. Cheng, 'Synthesising gene clock with toggle switch and oscillator.' IET systems biology. vol. 9, pp. 88-94, 2014. [23] C. H. Chuang, C. L. Lin, 'Synthesizing genetic sequential logic circuit with clock pulse generator.' BMC systems Biology., vol.8, pp. 63-77, 2014. [24] C. L. Lin, Y. C. Chang, 'Design of synthetic genetic logic circuits based on RSGA. ' Evol. Bioinf., vol. 9, pp. 137-150, 2013. [25] C. L. Lin, P. K. Chen, 'Synthesising periodic triggering signals with genetic oscillators.' IET systems biology., vol. 8, pp.1-12, 2014. [26] T. Y. Kuo, C. L. Lin, N. Charoenkit et al., 'Toward theoretical synthesis of biocomputer.' IET systems biology., vol. 11, pp. 36-43, 2017. [27] C. L. Lin, T. Y. Kuo, Y. Y. Chen, 'Implementation of a genetic logic circuit: bio-register.' Systems and synthetic biology., vol. 9, pp. 43-48, 2015. [28] J. H. Holland, 'Adaptation in natural and artificial systems: an introductory analysis with applications to biology, control, and artificial intelligence.' USA: University of Michigan., 1975. [29] C. W. Tsai, C. H. Huang, C. L. Lin, 'Structure-specified IIR filter and control design using real structured genetic algorithm.' Applied Soft Computing., vol. 9,pp. 1285-1295, 2009. [30] C. W. Tsai, C. L. Lin, 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. [31] D. C. Liebler, 'Introduction to proteomics: tools for the new biology.' Springer Science & Business Media, pp. 151-154, 2001. [32] R. Weiss, S. Basu, 'The device physics of cellular logic gates.' NSC-1: The First Workshop of Non-Silicon Computing. Boston., Massachusetts. 2002. [33] G. J. Myers, 'Advances in computer architecture.' John Wiley & Sons., 1982. [34] Michael Freeman, 'Simple CPU', https://www-users.cs.york.ac.uk/~mjf/simple_cpu/index.html, accessed at October 2017. [35] A. Lamaniya, B. Patel, 'Design of full adder and full subtractor using DNA computing.' Int J Latest Trends Eng Technol, vol. 3, pp. 12-16, 2014. [36] M. Kopniczky, 'Multilevel regulation and translational switches in synthetic biology.' 2015. [37] J. Li, H. W. Habbes, J. Eiberger, et al., 'Analysis of connexin expression during mouse Schwann cell development identifies connexin29 as a novel marker for the transition of neural crest to precursor cells.' Glia., vol. 55, pp. 93-103, 2007. [38] Davis, Penny K., Alan Ho, and Steven F. Dowdy. 'Biological methods for cell-cycle synchronization of mammalian cells.' Biotechniques., vol. 30, pp. 1322-1331, 2001. [39] C. T. Tu, B. S. Chen, 'On the increase in network robustness and decrease in network response ability during the aging process: a systems biology approach via microarray data,' IEEE/ACM Transactions on Computational Biology and Bioinformatics., vol. 10, no. 2, pp. 468-480, 2013. [40] S. S. Shen-Orr, R. Milo, S. Mangan, et al., 'Network motifs in the transcriptional regulation network of Escherichia coli.' Nature genetics., vol. 31, pp. 64-68, 2002. [41] MADAN BABU, M.; TEICHMANN, Sarah A. 'Evolution of transcription factors and the gene regulatory network in Escherichia coli.' Nucleic acids research., vol. 31, pp. 1234-1244, 2003.
摘要: 
隨著合成生物學的發展,諸多研究已證實使用基因表現的反應過程能夠表現電子電路中數位邏輯閘的角色。本研究利用實驗室研發的生物邏輯閘、生物時鐘產生器建立了許多不同的生物電路,分成生物循序邏輯電路及生物順向邏輯電路,我們用此建構許多不同的生物組件,包括生物暫存器、生物多工器、生物解碼器等。每樣生物組件在建立生物基因處理器中都是不可缺少的重要零件。
結構上,生物基因處理器中可以拆解成三大部分:記憶單元、控制單元、邏輯運算單元,本研究使用基本生物基因電路以建構組件並組成生物處理器的三大單元,將其整合,建立了一個4-bit架構的生物基因處理器。此生物處理器可以模擬電子電路處理器的操作動作,並完成預期的指令程式。該生物處理器係參照范紐曼架構來建構,因此本生物處理器是使用儲存程式架構來執行指令,其指令週期可細分為:提取、解碼、執行、寫回。
本論文詳細說明了建構四位元生物基因處理器的過程,從生物處理器記憶體指令取出,送入指令暫存器中解碼,並執行程式上所想表達的功能,最後將執行完成的生物資料再度存放回生物記憶單元,系統執行完成之前不斷循環:提取、解碼、執行、放回之動作。本論文進行了示範操作,並清楚地描繪每組生物單元的功能。

Along the development of the synthetic biological, the technology of the biological computer will be more mature in the future. In this paper, we present a Biological Central Processing Unit (Bio-CPU) structured that constructed by the biological logic gates and work in the Genetic clock generator devoted from our laboratory. We used it to construct the biological components, there are biological multiplexer, biological decoder, biological register, for used the biological component, it can used to construct the biological device for using in the Bio-CPU.
The Bio-CPU structure is following the silicon CPU, it can be decomposed into three cores: Biological Arithmetic Unit (Bio-ALU), Biological Control Unit (Bio-CU), and Biological Memory (Bio-Mem), every core has its specific function. For the Bio-CPU, we refer to the Von Neumann architecture for construction that it uses the prestored program to collect instructions to be executed. The instruction cycle is presented in the four function: fetch, decode, execute, store.
We let the executing instruction function from the electronics realized to the Bio-CPU and illustrate the procedure of constructing the 4-bit Bio-CPU in this paper. The Bio-CPU fetches the instruction from the biological instruction register, decodes and executes it, finally, stores the result back to the Bio-Mem, and keeps executing the instruction cycle until the project is completed. Details of the system function in the biological sense are explained. Demonstrative operation has been conducted and presented which clearly portraits function of each modules.
URI: http://hdl.handle.net/11455/98315
Rights: 同意授權瀏覽/列印電子全文服務,2018-08-15起公開。
Appears in Collections:電機工程學系所

Files in This Item:
File SizeFormat Existing users please Login
nchu-107-7105064022-1.pdf7.45 MBAdobe PDFThis file is only available in the university internal network    Request a copy
Show full item record
 

Google ScholarTM

Check


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.