Abstract
With the progressive scale-down of semiconductor’s feature size, people are looking forward to More Moore and More than Moore. In order to offer a possible alternative implementation process, researchers are trying to figure out a feasible transfer from silicon to molecular computing. Such transfer lies on bio-based modules programming with computer-like logic, aiming at realizing the Turing machine. To accomplish this, the DNA-based combinational logic is inevitably the first step we have taken care of. This timely overview study introduces combinational logic synthesized in DNA computing from both analog and digital perspectives separately. State-of-the-art research progress is summarized for interested readers to quick understand DNA computing, initiate discussion on existing techniques and inspire innovation solutions. We hope this study can pave the way for the future DNA computing synthesis.
Similar content being viewed by others
References
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
Desai S B, Madhvapathy S R, Sachid A B, et al. MoS2 transistors with 1-nanometer gate lengths. Science, 2016, 354: 99–102
Yahiro W, Hagiya M, Implementation of Turing machine using DNA strand displacement. In: Proceedings of International Conference on Theory and Practice of Natural Computing. Berlin: Springer, 2016. 161–172
Wikipedia. Combinational logic. 2018. https://en.wikipedia.org/wiki/Combinational logic
Khalil A S, Collins J J. Synthetic biology: applications come of age. Nat Rev Genet, 2010, 11: 367
Siuti P, Yazbek J, Lu T K. Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol, 2013, 31: 448–452
Andrianantoandro E, Basu S, Karig D K, et al. Synthetic biology: new engineering rules for an emerging discipline. Molecular Syst Biol, 2006, 2: 28
Green A A, Kim J, Ma D, et al. Complex cellular logic computation using ribocomputing devices. Nature, 2017, 548: 117–121
Feynman R P. There’s plenty of room at the bottom. Eng Sci, 1960, 23: 22–36
Trautman J K, Macklin J J, Brus L E, et al. Near-field spectroscopy of single molecules at room temperature. Nature, 1994, 369: 40–42
Paun G, Rozenberg G, Salomaa A. DNA Computing: New Computing Paradigms. Berlin: Springer, 2005
Amos M. Theoretical and experimental DNA computation. Bull European Assoc Theor Comput Sci, 1999, 67: 125–138
von Neumann J. First draft of a report on the EDVAC. IEEE Ann Hist Comput, 1993, 15: 27–75
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
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, Indianapolis, 1997. 267–271
Tagore S, Bhattacharya S, Islam M, et al. DNA computation: application and perspectives. J Proteom Bioinform, 2010, 3: 234–343
Extance A. How DNA could store all the world’s data. Nature, 2016, 537: 22–24
Hameed K. DNA computation based approach for enhanced computing power. Int J Emerg Sci, 2011, 1: 23–30
Saxena S. Introduction to DNA computing. Int Acadmey Eng Medical Res, 2016, 1: 1–3
Kumar S N. A proper approach on DNA based computer. American Nanomater, 2015, 3: 1–14
Ma S, Tang N, Tian J. DNA synthesis, assembly and applications in synthetic biology. Curr Opin Chem Biol, 2012, 16: 260–267
Bornholt J, Lopez R, Carmean D M, et al. A DNA-based archival storage system. SIGOPS Oper Syst Rev, 2016, 50: 637–649
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
Benenson Y, Gil B, Ben-Dor U, et al. An autonomous molecular computer for logical control of gene expression. Nature, 2004, 429: 423–429
Landweber L F, Lipton R J, Rabin M O. DNA2DNA computations: a potential “killer app”? In: Proceedings of International Colloquium on Automata, Languages, and Programming (ICALP). Berlin: Springer, 1997. 56–64
Watada J, binti abu Bakar R. DNA computing and its applications. In: Proceedings of the 8th International Conference on Intelligent Systems Design and Applications, Kaohsiung, 2008. 288–294
Gehani A, LaBean T, Reif J. DNA-based cryptography. Asp Mol Comput, 2003, 2950: 167–188
Miyamoto T, Razavi S, DeRose R, et al. Synthesizing biomolecule-based Boolean logic gates. ACS Synth Biol, 2012, 2: 72–82
Jiang H, Riedel M D, Parhi K K. Digital logic with molecular reactions. In: Proceedings of International Conference on Computer-Aided Design (ICCAD), San Jose, 2013. 721–727
Zhang C, Ge L L, Zhong Z W, et al. Karnaugh map-aided combinational logic design approach with bistable molecular reactions. In: Proceedings of IEEE International Conference on Digital Signal Processing (DSP), Singapore, 2015. 1288–1292
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
Wen D L, Ge L L, Lu Y X, et al. A DNA strand displacement reaction implementation-friendly clock design. In: Proceedings of IEEE International Conference on Communications (ICC), Paris, 2017
Zhang X C, Ge L L, You X H, et al. Synthesizing LDPC belief propagation decoding with molecular reactions. In: Proceedings of IEEE International Conference on Communications (ICC), Kansas City, 2018
Zhong Z W, Li Z, Ge L L, et al. Implementation of Mealy machine with molecular reactions. In: Proceedings of IEEE International Conference on Communications (ICC), Kansas City, 2018
Lu Y X, Ge L L, You X H, et al. Implementation of sinusoids and pulse width modulation with chemical reactions. In: Proceedings of IEEE International Conference on Communications (ICC), Kansas City, 2018
Li M H, Ge L L, You X H, et al. Basic arithmetics based on analog signal with molecular reactions. In: Proceedings of IEEE International Conference on Communications (ICC), Kansas City, 2018
Shen Z, Ge L, Wei W, et al. Molecular synthesis for probability theory and stochastic process. J Sign Process Syst, 2018, 90: 1479–1494
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), Cape Town, 2018
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), Cape Town, 2018
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), Lorient, 2017
Shen Z Y, Ge L L, Wei W, et al. Synthesizing Markov chain with reversible unimolecular reactions. In: Proceedings of International Conference on Wireless Communications and Signal Processing (WCSP), Nanjing, 2017
Zhuang Y C, Ge L L, Wei W, 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), Nanjing, 2017
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), Dallas, 2016
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), Hangzhou, 2015
Jiang H, Riedel M D, Parhi K K. Synchronous sequential computation with molecular reactions. In: Proceedings of the 48th Design Automation Conference (DAC), San Diego, 2011. 836–841
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, Pacific Grove, 2014
Senum P, Riedel M D. Rate-independent constructs for chemical computation. PLoS ONE, 2011, 6: e21414
Howard P. Analysis of ODE models. 2009. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.441.4759& rep=rep1&type=pdf
Strogatz S H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering. Boulder: Westview Press, 2014
Zauderer E. Partial Differential Equations of Applied Mathematics. Hoboken: John Wiley & Sons, 2011
Hale J K, Lunel S M V. Introduction to Functional Differential Equations. Berlin: Springer, 2013
Érdi P, Tóth J. Mathematical Models of chemical Reactions: Theory and Applications of Deterministic and Stochastic Models. Manchester: Manchester University Press, 1989
Horn F, Jackson R. General mass action kinetics. Arch Rational Mech Anal, 1972, 47: 81–116
Crick F. Central dogma of molecular biology. Nature, 1970, 227: 561–563
Soloveichik D, Seelig G, Winfree E. DNA as a universal substrate for chemical kinetics. Proc Natl Acad Sci USA, 2010, 107: 5393–5398
Zhang D Y, Seelig G. Dynamic DNA nanotechnology using strand-displacement reactions. Nat Chem, 2011, 3: 103–113
Zhang D Y, Winfree E. Control of DNA strand displacement kinetics using toehold exchange. J Am Chem Soc, 2009, 131: 303–314
Phillips A, Cardelli L. A programming language for composable DNA circuits. J R Soc Interface, 2009, 6: S419–S436
SantaLucia Jr J, Hicks D. The thermodynamics of DNA structural motifs. Annu Rev Biophys Biomol Struct, 2004, 33: 415–440
Shapiro E, Ran T. DNA computing: molecules reach consensus. Nat Nanotech, 2013, 8: 703–705
Zhang D Y. Dynamic DNA strand displacement circuits. Dissertation for Ph.D. Degree. Pasadena: California Institute of Technology, 2010
Leavitt S. Deciphering the genetic code: Marshall Nirenberg. Office of NIH History, 2004
Sarpeshkar R. Analog versus digital: extrapolating from electronics to neurobiology. Neural Comput, 1998, 10: 1601–1638
Sauro H M, Kim K. Synthetic biology: It’s an analog world. Nature, 2013, 497: 572–573
Song T, Garg S, Mokhtar R, et al. Analog computation by DNA strand displacement circuits. ACS Synth Biol, 2016, 5: 898–912
Yordanov B, Kim J, Petersen R L, et al. Computational design of nucleic acid feedback control circuits. ACS Synth Biol, 2014, 3: 600–616
Chen Y J, Dalchau N, Srinivas N, et al. Programmable chemical controllers made from DNA. Nat Nanotech, 2013, 8: 755–762
Sarpeshkar R. Analog synthetic biology. Philos Trans R Soc A-Math Phys Eng Sci, 2014, 372: 20130110
Daniel R, Rubens J R, Sarpeshkar R, et al. Synthetic analog computation in living cells. Nature, 2013, 497: 619–623
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
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
Chiniforooshan E, Doty D, Kari L, et al. Scalable, time-responsive, digital, energy-efficient molecular circuits using DNA strand displacement. In: Proceedings of the 16th International Conference on DNA Computing and Molecular Programming, Hong Kong, 2010. 25–36
Qian L, Winfree E. Scaling up digital circuit computation with DNA strand displacement cascades. Science, 2011, 332: 1196–1201
Nielsen A A, Der B S, Shin J, et al. Genetic circuit design automation. Science, 2016, 352: aac7341
Roquet N, Lu T K. Digital and analog gene circuits for biotechnology. Biotech J, 2014, 9: 597–608
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
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
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
Lu C H, Willner B, Willner I. DNA nanotechnology: from sensing and DNA machines to drug-delivery systems. ACS Nano, 2013, 7: 8320–8332
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
Qian L, Winfree E, Bruck J. Neural network computation with DNA strand displacement cascades. Nature, 2011, 475: 368–372
Schneider G, Wrede P. Artificial neural networks for computer-based molecular design. Prog Biophys Mol Biol, 1998, 70: 175–222
Noordewier M O, Towell G G, Shavlik J W. Training knowledge-based neural networks to recognize genes in DNA sequences. In: Proceedings of Advances in Neural Information Processing Systems, Denver, 1991. 530–536
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
Brady M. Artificial intelligence and robotics. Artif Intell, 1985, 26: 79–121
Ray K S, Mondal M. Similarity-based fuzzy reasoning by DNA computing. Int J Bio-Inspired Comput, 2011, 3: 112–122
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
Acknowledgements
This work was supported in part by National Natural Science Foundation of China (Grant Nos. 61871115, 61501116), Jiangsu Provincial Natural Science Foundation for Excellent Young Scholars, Huawei HIRP Flagship under (Grant No. YB201504), the Fundamental Research Funds for the Central Universities, the SRTP of Southeast University, State Key Laboratory of ASIC & System (Grant No. 2016KF007), ICRI for MNC, and the Project Sponsored by the SRF for the Returned Overseas Chinese Scholars of MoE.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Zhang, C., Ge, L., Zhuang, Y. et al. DNA computing for combinational logic. Sci. China Inf. Sci. 62, 61301 (2019). https://doi.org/10.1007/s11432-018-9530-x
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11432-018-9530-x