面向组合逻辑的DNA计算
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摘要
随着半导体器件特征尺寸的快速减小,人们开始关注深度摩尔(more Moore)以及超越摩尔(more than Moore)的发展.为了实现取代传统硅基电路的技术,人们正在尝试将硅基计算转化到分子计算中.这种转化依赖于,以生物材料为基础的、具有类似于计算机逻辑的模块化编程,其目的是实现图灵机.为了达到这个目的,以DNA为基础的组合逻辑是我们首先需要考虑的.本文分别从模拟计算和数字计算两方面介绍了,基于DNA的组合逻辑实现.总结了最新的研究成果,为感兴趣的读者提供了快速理解DNA计算的渠道.同时,我们也希望启发读者对现有技术进行讨论,进而提出创新的解决方案.我们希望这篇文章能够为未来的DNA计算的发展铺平道路.
With the progressive scale-down of semiconductor feature size, people are looking forward to More Moore and More than Moore. Thus, people are trying to devise a feasible transfer from silicon to molecular computing to offer a possible alternative implementation process. Such a transfer is based on bio-based module programming with computer-like logic, aimed at realizing the Turing machine. DNA-based combinational logic is inevitably the first step that we have taken to accomplish this. This timely overview paper introduces combinational logic separately synthesized in DNA computing from both analog and digital perspectives. State-of-the-art research progress is summarized herein for interested readers to quickly understand DNA computing, initiate discussion on existing techniques, and inspire innovative solutions. We hope this review paves the way for future DNA computing synthesis.
With the progressive scale-down of semiconductor feature size, people are looking forward to More Moore and More than Moore. Thus, people are trying to devise a feasible transfer from silicon to molecular computing to offer a possible alternative implementation process. Such a transfer is based on bio-based module programming with computer-like logic, aimed at realizing the Turing machine. DNA-based combinational logic is inevitably the first step that we have taken to accomplish this. This timely overview paper introduces combinational logic separately synthesized in DNA computing from both analog and digital perspectives. State-of-the-art research progress is summarized herein for interested readers to quickly understand DNA computing, initiate discussion on existing techniques, and inspire innovative solutions. We hope this review paves the way for future DNA computing synthesis.
引文
1 Kish L B.End of Moore’s law:thermal(noise)death of integration in micro and nano electronics.Phys Lett A,2002,305:144-149
2 Desai S B,Madhvapathy S R,Sachid A B,et al.MoS2 transistors with 1-nanometer gate lengths.Science,2016,354:99-102
3 Yahiro W,Hagiya M.Implementation of Turing machine using DNA strand displacement.In:Proceedings of International Conference on Theory and Practice of Natural Computing,2016.161-172
4 Wikipedia.Combinational logic.2018.https://en.wikipedia.org/wiki/Combinational logic
5 Khalil A S,Collins J J.Synthetic biology:applications come of age.Nat Rev Genet,2010,11:367-379
6 Siuti P,Yazbek J,Lu T K.Synthetic circuits integrating logic and memory in living cells.Nat Biotechnol,2013,31:448-452
7 Andrianantoandro E,Basu S,Karig D K,et al.Synthetic biology:new engineering rules for an emerging discipline.Mol Syst Biol,2006,2:2006.0028
8 Green A A,Kim J,Ma D,et al.Complex cellular logic computation using ribocomputing devices.Nature,2017,548:117-121
9 Feynman R P.There’s plenty of room at the bottom.Eng Sci,1960,23:22-36
10 Adleman L M.Molecular computation of solutions to combinatorial problems.Science,1994,266:1021-1024
11 Paun G,Rozenberg G,Salomaa A.DNA Computing:New Computing Paradigms.Berlin:Springer,2005
12 Amos M.Theoretical and experimental DNA computation.Bull European Assoc Theor Comput Sci,1999,67:125-138
13 von Neumann J.First draft of a report on the EDVAC.IEEE Ann Hist Comput,1993,15:27-75
14 Backus J.Can programming be liberated from the von Neumann style?:a functional style and its algebra of programs.Commun ACM,1978,21:613-641
15 Deaton R,Murphy R C,Rose J A,et al.A DNA based implementation of an evolutionary search for good encodings for DNA computation.In:Proceedings of IEEE International Conference on Evolutionary Computation,1997.267-271
16 Tagore S,Bhattacharya S,Islam M,et al.DNA computation:application and perspectives.J Proteomics Bioinform,2010,3:234-343
17 Extance A.How DNA could store all the world’s data.Nature,2016,537:22-24
18 Hameed K.DNA computation based approach for enhanced computing power.Int J Emerging Sci,2011,1:23-30
19 Saxena S.Introduction to DNA Computing.Int Acadmey Eng Medical Res,2016,1:1-3
20 Kumar S N.A proper approach on DNA based computer.Am J Nanomater,2015,3:1-14
21 Ma S,Tang N,Tian J.DNA synthesis,assembly and applications in synthetic biology.Curr Opin Chem Biol,2012,16:260-267
22 Bornholt J,Lopez R,Carmean D M,et al.A DNA-based archival storage system.SIGOPS Oper Syst Rev,2016,50:637-649
23 Hughes R A,Ellington A D.Synthetic DNA synthesis and assembly:putting the synthetic in synthetic biology.Cold Spring Harb Perspect Biol,2017,9:a023812
24 Benenson Y,Gil B,Ben-Dor U,et al.An autonomous molecular computer for logical control of gene expression.Nature,2004,429:423-429
25 Landweber L F,Lipton R J,Rabin M O.DNA2DNA computations:a potential“killer app?”.In:Proceedings of a DIMACS Workshop on DNA Based Computers,Philadelphia,1997.161-172
26 Watada J,binti abu Bakar R.DNA computing and its applications.In:Proceedings of the 8th International Conference on Intelligent Systems Design and Applications,2008.288-294
27 Gehani A,LaBean T,Reif J.DNA-based cryptography.Lecture Notes Comput Sci,2003,2950:167-188
28 Miyamoto T,Razavi S,DeRose R,et al.Synthesizing biomolecule-based Boolean logic gates.ACS Synth Biol,2012,2:72-82
29 Jiang H,Riedel M D,Parhi K K.Digital logic with molecular reactions.In:Proceedings of International Conference on Computer-Aided Design(ICCAD),2013.721-727
30 Zhang C,Ge L,Zhong Z,et al.Karnaugh map-aided combinational logic design approach with bistable molecular reactions.In:Proceedings of IEEE International Conference on Digital Signal Processing(DSP),2015.1288-1292
31 Ge L,Zhong Z,Wen D,et al.A formal combinational logic synthesis with chemical reaction networks.IEEE Trans Mol Biol Multi-Scale Commun,2017,3:33-47
32 Wen D,Ge L,Lu Y,et al.A DNA strand displacement reaction implementation-friendly clock design.In:Proceedings of IEEE International Conference on Communications(ICC),2017.1-6
33 Zhang X,Ge L,You X,et al.Synthesizing LDPC belief propagation decoding with molecular reactions.In:Proceedings of IEEE International Conference on Communications(ICC),2018.1-6
34 Zhong Z,Li Z,Ge L,et al.Implementation of Mealy machine with molecular reactions.In:Proceedings of IEEEInternational Conference on Communications(ICC),2018.1-6
35 Lu X,Ge L,You X,et al.Implementation of sinusoids and pulse width modulation with chemical reactions.In:Proceedings of IEEE International Conference on Communications(ICC),2018.1-6
36 Li M,Ge L,You X,et al.Basic arithmetics based on analog signal with molecular reactions.In:Proceedings of IEEEInternational Conference on Communications(ICC),2018.1-6
37 Salehi S A,Riedel M D,Parhi K K.Molecular computation of complex Markov chains with self-loop state transitions.In:Proceedings of IEEE International Conference on Digital Signal Processing(DSP),2015.689-693
38 Salehi S A,Riedel M D,Parhi K K.Molecular computation of complex Markov chains with self-loop state transitions.In:Proceedings of the 51st Asilomar Conference on Signals,Systems,and Computers,2017.478-483
39 Shen Z,Ge L,Wei W,et al.Molecular synthesis for probability theory and stochastic process.J Sign Process Syst,2018,90:1479-1494
40 Fang C,Shen Z,Zhang Z,et al.Synthesizing a neuron using chemical reactions.In:Proceedings of IEEE International Workshop on Signal Processing Systems(SiPS),2018.1-6
41 Salehi S A,Liu X,Riedel M D,et al.Computing mathematical functions using DNA via fractional coding.2018,1:8321
42 Zhuang Y,Zhang Z,You X,et al.Arithmetic computations based on chemical reaction networks.In:Proceedings of IEEE International Workshop on Signal Processing Systems(SiPS),2018.1-6
43 Zhong Z,Ge L,Shen Z,et al.CRN-based design methodology for synchronous sequential logic.In:Proceedings of IEEE International Workshop on Signal Processing Systems(SiPS),2017.1-6
44 Shen Z,Ge L,Wei W,et al.Synthesizing Markov chain with reversible unimolecular reactions.In:Proceedings of International Conference on Wireless Communications and Signal Processing(WCSP),2017.1-6
45 Zhuang Y,Ge L,Shen Z,et al.A synthesis flow for fast convolution unit based on molecular reactions.In:Proceedings of International Conference on Wireless Communications and Signal Processing(WCSP),2017.1-6
46 Shen Z,Zhang C,Ge L,et al.Synthesis of probability theory based on molecular computation.In:Proceedings of IEEE International Workshop on Signal Processing Systems(SiPS),2016.1-6
47 Ge L,Zhang C,Zhong Z,et al.A formal design methodology for synthesizing a clock signal with an arbitrary duty cycle of M/N.In:Proceedings of IEEE International Workshop on Signal Processing Systems(SiPS),2015.1-6
48 Jiang H,Riedel M D,Parhi K K.Synchronous sequential computation with molecular reactions.In:Proceedings of the 48th Design Automation Conference(DAC),2011.836-841
49 Salehi S A,Riedel M D,Parhi K K.Asynchronous discrete-time signal processing with molecular reactions.In:Proceedings of the 48th Asilomar Conference on Signals,Systems and Computers,2014
50 Senum P,Riedel M D.Rate-independent constructs for chemical computation.PLoS ONE,2011,6:e21414
51 Howard P.Analysis of ODE models.2009.http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.441.4759&rep=rep1&type=pdf
52 Strogatz S H.Nonlinear Dynamics and Chaos:With Applications to Physics,Biology,Chemistry,and Engineering.Boulder:Westview Press,2014
53 Zauderer E.Partial Differential Equations of Applied Mathematics.Hoboken:John Wiley&Sons,2011
54 Hale J K,Lunel S M V.Introduction to Functional Differential Equations.Berlin:Springer,2013
55′Erdi P,T′oth J.Mathematical Models of Chemical Reactions:Theory and Applications of Deterministic and Stochastic Models.Manchester:Manchester University Press,1989
56 Horn F,Jackson R.General mass action kinetics.Arch Rational Mech Anal,1972,47:81-116
57 Crick F.Central dogma of molecular biology.Nature,1970,227:561-563
58 Soloveichik D,Seelig G,Winfree E.DNA as a universal substrate for chemical kinetics.Proc Natl Acad Sci USA,2010,107:5393-5398
59 Zhang D Y,Seelig G.Dynamic DNA nanotechnology using strand-displacement reactions.Nat Chem,2011,3:103-113
60 Zhang D Y,Winfree E.Control of DNA strand displacement kinetics using toehold exchange.J Am Chem Soc,2009,131:303-314
61 Phillips A,Cardelli L.A programming language for composable DNA circuits.J Royal Soc Inter,2009,6:419-436
62 Jr SantaLucia J,Hicks D.The thermodynamics of DNA structural motifs.Annu Rev Biophys Biomol Struct,2004,33:415-440
63 Shapiro E,Ran T.DNA computing:molecules reach consensus.Nat Nanotech,2013,8:703-705
64 Zhang D Y.Dynamic DNA strand displacement circuits.Dissertation for Ph.D.Degree.Los Angeles:California Institute of Technology,2010
65 Leavitt S.Deciphering the genetic code:marshall Nirenberg.Office of NIH History,2004
66 Sarpeshkar R.Analog versus digital:extrapolating from electronics to neurobiology.Neural Comput,1998,10:1601-1638
67 Sauro H M,Kim K.Synthetic biology:it’s an analog world.Nature,2013,497:572-573
68 Song T,Garg S,Mokhtar R,et al.Analog computation by DNA strand displacement circuits.ACS Synth Biol,2016,5:898-912
69 Yordanov B,Kim J,Petersen R L,et al.Computational design of nucleic acid feedback control circuits.ACS Synth Biol,2014,3:600-616
70 Chen Y J,Dalchau N,Srinivas N,et al.Programmable chemical controllers made from DNA.Nat Nanotech,2013,8:755-762
71 Sarpeshkar R.Analog synthetic biology.Philos Trans R Soc A-Math Phys Eng Sci,2014,372:20130110
72 Daniel R,Rubens J R,Sarpeshkar R,et al.Synthetic analog computation in living cells.Nature,2013,497:619-623
73 Salehi S A,Jiang H,Riedel M D,et al.Molecular sensing and computing systems.IEEE Trans Mol Biol Multi-Scale Commun,2015,1:249-264
74 Frezza B M,Cockroft S L,Ghadiri M R.Modular multi-level circuits from immobilized DNA-based logic gates.J Am Chem Soc,2007,129:875-879
75 Chiniforooshan E,Doty D,Kari L,et al.Scalable,time-responsive,digital,energy-efficient molecular circuits using DNA strand displacement.DNA,2010,16:25-36
76 Qian L,Winfree E.Scaling up digital circuit computation with DNA strand displacement cascades.Science,2011,332:1196-1201
77 Nielsen A A K,Der B S,Shin J,et al.Genetic circuit design automation.Science,2016,352:aac7341
78 Roquet N,Lu T K.Digital and analog gene circuits for biotechnology.Biotech J,2014,9:597-608
79 Weiss R,Basu S,Hooshangi S,et al.Genetic circuit building blocks for cellular computation,communications,and signal processing.Nat Comput,2003,2:47-84
80 Zadegan R M,Jepsen M D E,Hildebrandt L L,et al.Construction of a fuzzy and Boolean logic gates based on DNA.Small,2015,11:1811-1817
81 Zhang Y,Wirkert S J,Iszatt J,et al.Tissue classification for laparoscopic image understanding based on multispectral texture analysis.J Med Imag,2017,4:015001
82 Lu C H,Willner B,Willner I.DNA nanotechnology:from sensing and DNA machines to drug-delivery systems.ACSNano,2013,7:8320-8332
83 Li J,Pei H,Zhu B,et al.Self-assembled multivalent DNA nanostructures for noninvasive intracellular delivery of immunostimulatory CpG oligonucleotides.ACS Nano,2011,5:8783-8789
84 Qian L,Winfree E,Bruck J.Neural network computation with DNA strand displacement cascades.Nature,2011,475:368-372
85 Schneider G,Wrede P.Artificial neural networks for computer-based molecular design.Prog Biophys Mol Biol,1998,70:175-222
86 Noordewier M O,Towell G G,Shavlik J W.Training knowledge-based neural networks to recognize genes in DNAsequences.In:Proceedings of the 1990 Conference on Advances in Neural Information Processing Systems,1990.530-536
87 Zuber J,Sun H,Zhang X,et al.A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction.Nucleic Acids Res,2017,45:6168-6176
88 Brady M.Artificial intelligence and robotics.Artif Intell,1985,26:79-121
89 Ray K S,Mondal M.Similarity-based fuzzy reasoning by DNA computing.Int J Bio-Inspired Comput,2011,3:112-122
90 Jeng D J,Watada J,Wu B,et al.Fuzzy forecasting with DNA computing.In:Proceedings of International Workshop on DNA-Based Computers.Berlin:Springer,2006.324-336
1) http://www.cellocad.org/.
2 Desai S B,Madhvapathy S R,Sachid A B,et al.MoS2 transistors with 1-nanometer gate lengths.Science,2016,354:99-102
3 Yahiro W,Hagiya M.Implementation of Turing machine using DNA strand displacement.In:Proceedings of International Conference on Theory and Practice of Natural Computing,2016.161-172
4 Wikipedia.Combinational logic.2018.https://en.wikipedia.org/wiki/Combinational logic
5 Khalil A S,Collins J J.Synthetic biology:applications come of age.Nat Rev Genet,2010,11:367-379
6 Siuti P,Yazbek J,Lu T K.Synthetic circuits integrating logic and memory in living cells.Nat Biotechnol,2013,31:448-452
7 Andrianantoandro E,Basu S,Karig D K,et al.Synthetic biology:new engineering rules for an emerging discipline.Mol Syst Biol,2006,2:2006.0028
8 Green A A,Kim J,Ma D,et al.Complex cellular logic computation using ribocomputing devices.Nature,2017,548:117-121
9 Feynman R P.There’s plenty of room at the bottom.Eng Sci,1960,23:22-36
10 Adleman L M.Molecular computation of solutions to combinatorial problems.Science,1994,266:1021-1024
11 Paun G,Rozenberg G,Salomaa A.DNA Computing:New Computing Paradigms.Berlin:Springer,2005
12 Amos M.Theoretical and experimental DNA computation.Bull European Assoc Theor Comput Sci,1999,67:125-138
13 von Neumann J.First draft of a report on the EDVAC.IEEE Ann Hist Comput,1993,15:27-75
14 Backus J.Can programming be liberated from the von Neumann style?:a functional style and its algebra of programs.Commun ACM,1978,21:613-641
15 Deaton R,Murphy R C,Rose J A,et al.A DNA based implementation of an evolutionary search for good encodings for DNA computation.In:Proceedings of IEEE International Conference on Evolutionary Computation,1997.267-271
16 Tagore S,Bhattacharya S,Islam M,et al.DNA computation:application and perspectives.J Proteomics Bioinform,2010,3:234-343
17 Extance A.How DNA could store all the world’s data.Nature,2016,537:22-24
18 Hameed K.DNA computation based approach for enhanced computing power.Int J Emerging Sci,2011,1:23-30
19 Saxena S.Introduction to DNA Computing.Int Acadmey Eng Medical Res,2016,1:1-3
20 Kumar S N.A proper approach on DNA based computer.Am J Nanomater,2015,3:1-14
21 Ma S,Tang N,Tian J.DNA synthesis,assembly and applications in synthetic biology.Curr Opin Chem Biol,2012,16:260-267
22 Bornholt J,Lopez R,Carmean D M,et al.A DNA-based archival storage system.SIGOPS Oper Syst Rev,2016,50:637-649
23 Hughes R A,Ellington A D.Synthetic DNA synthesis and assembly:putting the synthetic in synthetic biology.Cold Spring Harb Perspect Biol,2017,9:a023812
24 Benenson Y,Gil B,Ben-Dor U,et al.An autonomous molecular computer for logical control of gene expression.Nature,2004,429:423-429
25 Landweber L F,Lipton R J,Rabin M O.DNA2DNA computations:a potential“killer app?”.In:Proceedings of a DIMACS Workshop on DNA Based Computers,Philadelphia,1997.161-172
26 Watada J,binti abu Bakar R.DNA computing and its applications.In:Proceedings of the 8th International Conference on Intelligent Systems Design and Applications,2008.288-294
27 Gehani A,LaBean T,Reif J.DNA-based cryptography.Lecture Notes Comput Sci,2003,2950:167-188
28 Miyamoto T,Razavi S,DeRose R,et al.Synthesizing biomolecule-based Boolean logic gates.ACS Synth Biol,2012,2:72-82
29 Jiang H,Riedel M D,Parhi K K.Digital logic with molecular reactions.In:Proceedings of International Conference on Computer-Aided Design(ICCAD),2013.721-727
30 Zhang C,Ge L,Zhong Z,et al.Karnaugh map-aided combinational logic design approach with bistable molecular reactions.In:Proceedings of IEEE International Conference on Digital Signal Processing(DSP),2015.1288-1292
31 Ge L,Zhong Z,Wen D,et al.A formal combinational logic synthesis with chemical reaction networks.IEEE Trans Mol Biol Multi-Scale Commun,2017,3:33-47
32 Wen D,Ge L,Lu Y,et al.A DNA strand displacement reaction implementation-friendly clock design.In:Proceedings of IEEE International Conference on Communications(ICC),2017.1-6
33 Zhang X,Ge L,You X,et al.Synthesizing LDPC belief propagation decoding with molecular reactions.In:Proceedings of IEEE International Conference on Communications(ICC),2018.1-6
34 Zhong Z,Li Z,Ge L,et al.Implementation of Mealy machine with molecular reactions.In:Proceedings of IEEEInternational Conference on Communications(ICC),2018.1-6
35 Lu X,Ge L,You X,et al.Implementation of sinusoids and pulse width modulation with chemical reactions.In:Proceedings of IEEE International Conference on Communications(ICC),2018.1-6
36 Li M,Ge L,You X,et al.Basic arithmetics based on analog signal with molecular reactions.In:Proceedings of IEEEInternational Conference on Communications(ICC),2018.1-6
37 Salehi S A,Riedel M D,Parhi K K.Molecular computation of complex Markov chains with self-loop state transitions.In:Proceedings of IEEE International Conference on Digital Signal Processing(DSP),2015.689-693
38 Salehi S A,Riedel M D,Parhi K K.Molecular computation of complex Markov chains with self-loop state transitions.In:Proceedings of the 51st Asilomar Conference on Signals,Systems,and Computers,2017.478-483
39 Shen Z,Ge L,Wei W,et al.Molecular synthesis for probability theory and stochastic process.J Sign Process Syst,2018,90:1479-1494
40 Fang C,Shen Z,Zhang Z,et al.Synthesizing a neuron using chemical reactions.In:Proceedings of IEEE International Workshop on Signal Processing Systems(SiPS),2018.1-6
41 Salehi S A,Liu X,Riedel M D,et al.Computing mathematical functions using DNA via fractional coding.2018,1:8321
42 Zhuang Y,Zhang Z,You X,et al.Arithmetic computations based on chemical reaction networks.In:Proceedings of IEEE International Workshop on Signal Processing Systems(SiPS),2018.1-6
43 Zhong Z,Ge L,Shen Z,et al.CRN-based design methodology for synchronous sequential logic.In:Proceedings of IEEE International Workshop on Signal Processing Systems(SiPS),2017.1-6
44 Shen Z,Ge L,Wei W,et al.Synthesizing Markov chain with reversible unimolecular reactions.In:Proceedings of International Conference on Wireless Communications and Signal Processing(WCSP),2017.1-6
45 Zhuang Y,Ge L,Shen Z,et al.A synthesis flow for fast convolution unit based on molecular reactions.In:Proceedings of International Conference on Wireless Communications and Signal Processing(WCSP),2017.1-6
46 Shen Z,Zhang C,Ge L,et al.Synthesis of probability theory based on molecular computation.In:Proceedings of IEEE International Workshop on Signal Processing Systems(SiPS),2016.1-6
47 Ge L,Zhang C,Zhong Z,et al.A formal design methodology for synthesizing a clock signal with an arbitrary duty cycle of M/N.In:Proceedings of IEEE International Workshop on Signal Processing Systems(SiPS),2015.1-6
48 Jiang H,Riedel M D,Parhi K K.Synchronous sequential computation with molecular reactions.In:Proceedings of the 48th Design Automation Conference(DAC),2011.836-841
49 Salehi S A,Riedel M D,Parhi K K.Asynchronous discrete-time signal processing with molecular reactions.In:Proceedings of the 48th Asilomar Conference on Signals,Systems and Computers,2014
50 Senum P,Riedel M D.Rate-independent constructs for chemical computation.PLoS ONE,2011,6:e21414
51 Howard P.Analysis of ODE models.2009.http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.441.4759&rep=rep1&type=pdf
52 Strogatz S H.Nonlinear Dynamics and Chaos:With Applications to Physics,Biology,Chemistry,and Engineering.Boulder:Westview Press,2014
53 Zauderer E.Partial Differential Equations of Applied Mathematics.Hoboken:John Wiley&Sons,2011
54 Hale J K,Lunel S M V.Introduction to Functional Differential Equations.Berlin:Springer,2013
55′Erdi P,T′oth J.Mathematical Models of Chemical Reactions:Theory and Applications of Deterministic and Stochastic Models.Manchester:Manchester University Press,1989
56 Horn F,Jackson R.General mass action kinetics.Arch Rational Mech Anal,1972,47:81-116
57 Crick F.Central dogma of molecular biology.Nature,1970,227:561-563
58 Soloveichik D,Seelig G,Winfree E.DNA as a universal substrate for chemical kinetics.Proc Natl Acad Sci USA,2010,107:5393-5398
59 Zhang D Y,Seelig G.Dynamic DNA nanotechnology using strand-displacement reactions.Nat Chem,2011,3:103-113
60 Zhang D Y,Winfree E.Control of DNA strand displacement kinetics using toehold exchange.J Am Chem Soc,2009,131:303-314
61 Phillips A,Cardelli L.A programming language for composable DNA circuits.J Royal Soc Inter,2009,6:419-436
62 Jr SantaLucia J,Hicks D.The thermodynamics of DNA structural motifs.Annu Rev Biophys Biomol Struct,2004,33:415-440
63 Shapiro E,Ran T.DNA computing:molecules reach consensus.Nat Nanotech,2013,8:703-705
64 Zhang D Y.Dynamic DNA strand displacement circuits.Dissertation for Ph.D.Degree.Los Angeles:California Institute of Technology,2010
65 Leavitt S.Deciphering the genetic code:marshall Nirenberg.Office of NIH History,2004
66 Sarpeshkar R.Analog versus digital:extrapolating from electronics to neurobiology.Neural Comput,1998,10:1601-1638
67 Sauro H M,Kim K.Synthetic biology:it’s an analog world.Nature,2013,497:572-573
68 Song T,Garg S,Mokhtar R,et al.Analog computation by DNA strand displacement circuits.ACS Synth Biol,2016,5:898-912
69 Yordanov B,Kim J,Petersen R L,et al.Computational design of nucleic acid feedback control circuits.ACS Synth Biol,2014,3:600-616
70 Chen Y J,Dalchau N,Srinivas N,et al.Programmable chemical controllers made from DNA.Nat Nanotech,2013,8:755-762
71 Sarpeshkar R.Analog synthetic biology.Philos Trans R Soc A-Math Phys Eng Sci,2014,372:20130110
72 Daniel R,Rubens J R,Sarpeshkar R,et al.Synthetic analog computation in living cells.Nature,2013,497:619-623
73 Salehi S A,Jiang H,Riedel M D,et al.Molecular sensing and computing systems.IEEE Trans Mol Biol Multi-Scale Commun,2015,1:249-264
74 Frezza B M,Cockroft S L,Ghadiri M R.Modular multi-level circuits from immobilized DNA-based logic gates.J Am Chem Soc,2007,129:875-879
75 Chiniforooshan E,Doty D,Kari L,et al.Scalable,time-responsive,digital,energy-efficient molecular circuits using DNA strand displacement.DNA,2010,16:25-36
76 Qian L,Winfree E.Scaling up digital circuit computation with DNA strand displacement cascades.Science,2011,332:1196-1201
77 Nielsen A A K,Der B S,Shin J,et al.Genetic circuit design automation.Science,2016,352:aac7341
78 Roquet N,Lu T K.Digital and analog gene circuits for biotechnology.Biotech J,2014,9:597-608
79 Weiss R,Basu S,Hooshangi S,et al.Genetic circuit building blocks for cellular computation,communications,and signal processing.Nat Comput,2003,2:47-84
80 Zadegan R M,Jepsen M D E,Hildebrandt L L,et al.Construction of a fuzzy and Boolean logic gates based on DNA.Small,2015,11:1811-1817
81 Zhang Y,Wirkert S J,Iszatt J,et al.Tissue classification for laparoscopic image understanding based on multispectral texture analysis.J Med Imag,2017,4:015001
82 Lu C H,Willner B,Willner I.DNA nanotechnology:from sensing and DNA machines to drug-delivery systems.ACSNano,2013,7:8320-8332
83 Li J,Pei H,Zhu B,et al.Self-assembled multivalent DNA nanostructures for noninvasive intracellular delivery of immunostimulatory CpG oligonucleotides.ACS Nano,2011,5:8783-8789
84 Qian L,Winfree E,Bruck J.Neural network computation with DNA strand displacement cascades.Nature,2011,475:368-372
85 Schneider G,Wrede P.Artificial neural networks for computer-based molecular design.Prog Biophys Mol Biol,1998,70:175-222
86 Noordewier M O,Towell G G,Shavlik J W.Training knowledge-based neural networks to recognize genes in DNAsequences.In:Proceedings of the 1990 Conference on Advances in Neural Information Processing Systems,1990.530-536
87 Zuber J,Sun H,Zhang X,et al.A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction.Nucleic Acids Res,2017,45:6168-6176
88 Brady M.Artificial intelligence and robotics.Artif Intell,1985,26:79-121
89 Ray K S,Mondal M.Similarity-based fuzzy reasoning by DNA computing.Int J Bio-Inspired Comput,2011,3:112-122
90 Jeng D J,Watada J,Wu B,et al.Fuzzy forecasting with DNA computing.In:Proceedings of International Workshop on DNA-Based Computers.Berlin:Springer,2006.324-336
1) http://www.cellocad.org/.
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