基于DNA折纸基底的与非门计算模型

殷志祥; 唐震; 张强; 崔建中; 杨静; 王日晟; 赵寿为; 张居丽

doi:10.11999/JEIT190825

基于DNA折纸基底的与非门计算模型

doi: 10.11999/JEIT190825

殷志祥^{1, 2},
唐震^2, ,,
张强³,
崔建中⁴,
杨静²,
王日晟²,
赵寿为¹,
张居丽¹

1.
上海工程技术大学数理与统计学院上海 201620
2.
安徽理工大学数学与大数据学院淮南 232001
3.
大连理工大学计算机科学与技术学院大连 116024
4.
淮南联合大学计算机系淮南 232001

基金项目: 国家自然科学基金(61672001, 61702008, 11801362)，安徽省自然科学基金(1808085MF193)，安徽省高校自然科学研究项目(KJ2019A0538)

详细信息

作者简介:
殷志祥：男，1966年生，教授，研究方向为DNA计算和DNA自组装

唐震：男，1994年生，博士生，研究方向为DNA计算和DNA自组装

张强：男，1971年生，教授，研究方向为生物计算、智能机器人和医疗大数据处理

崔建中：男，1973年生，博士生，研究方向为DNA计算和DNA自组装

杨静：女，1980年生，副教授，研究方向为DNA计算和DNA自组装

王日晟：男，1993年生，博士生，研究方向为DNA计算和DNA自组装

赵寿为：女，1982年生，博士，研究方向为应用数学

张居丽：女，1982年生，博士，研究方向为计算数学

通讯作者:
唐震　1179145666@qq.com

中图分类号: TP301
计量
- 文章访问数: 3114
- HTML全文浏览量: 1137
- PDF下载量: 124
- 被引次数: 0
出版历程
- 收稿日期: 2019-10-28
- 修回日期: 2020-01-17
- 网络出版日期: 2020-02-19
- 刊出日期: 2020-06-22

NAND Gate Computational Model Based on the DNA Origami Template

1.
School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China
2.
School of Mathematics and Big Data, Anhui University of Science and Technology, Huainan 232001, China
3.
School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
4.
Department of Computer, Huainan Union University, Huainan 232001, China

Funds: The National Natural Science Foundation of China (61672001, 61702008, 11801362), The Natural Science Foundation of Anhui Province (1808085MF193), The Natural Science Research Project of Universities in Anhui Province (KJ2019A0538)

摘要

摘要: 与非门(NAND)的本质是与门(AND)和非门(NOT)的叠加，先进行与运算，再进行非运算，它是建立DNA计算机的基础。为了实现与非门的计算，该文在DNA折纸基底上建立了一个与非门计算模型，逻辑值的输入是通过在DNA折纸基底上发生有向的杂交链式反应(HCR)来完成的，输入链先经过与门区域再经过非门区域，最后通过DNA折纸基底上是否还保留纳米金颗粒来显示计算结果的真假。利用Visual DSD对该计算模型进行仿真模拟，显示该计算模型具有较好的可行性。
- DNA计算 /
- DNA折纸术 /
- 与非门
Abstract: The essence of NAND gate is the superposition of AND gate and NOT gate. The AND gate operation is performed first, and then the NOT gate is performed. It is the basis of the DNA computer. In order to realize the computing of NAND gate, a NAND gate computational model is established based on the DNA origami template. The inputs of the logic value are completed by the Hybridization Chain Reaction (HCR) on the DNA origami template. The input strands first react with the AND gate region and then react with the NOT gate region. The result of the reaction is shown by dynamically separation of the gold nanoparticles on the DNA origami template. The simulation of the model through Visual DSD shows that the system has the advantages of high feasibility.
- DNA computing /
- DNA origami /
- NAND gate

HTML全文

图 1 杂交链式反应基本反应原理

下载: 全尺寸图片幻灯片

图 2 构建好的折纸基底示意图

下载: 全尺寸图片幻灯片

图 3 输入链示意图

下载: 全尺寸图片幻灯片

图 4 输入A=0, B=0后的结果示意图

下载: 全尺寸图片幻灯片

图 5 输入A=1, B=0后的结果示意图

下载: 全尺寸图片幻灯片

图 6 输入A=0, B=1后的结果示意图

下载: 全尺寸图片幻灯片

图 7 输入A=1, B=1后的结果示意图

下载: 全尺寸图片幻灯片

图 8 仿真模拟数据图

下载: 全尺寸图片幻灯片

图 9 最终产物的DNA链示意图

下载: 全尺寸图片幻灯片

表 1 与非门真值表

A 0 0 1 1
B 0 1 0 1
F 1 1 1 0

下载: 导出CSV

参考文献(29)

ADLEMAN L M. Molecular computation of solutions to combinatorial problems[J]. Science, 1994, 266(5187): 1021–1024. doi: 10.1126/science.7973651

LIPTON R J. DNA solution of hard computational problems[J]. Science, 1995, 268(5210): 542–545. doi: 10.1126/science.7725098

SAKAMOTO K, GOUZU H, KOMIYA K, et al. Molecular computation by DNA hairpin formation[J]. Science, 2000, 288(5469): 1223–1226. doi: 10.1126/science.288.5469.1223

YIN Zhixiang, CUI Jianzhong, YANG Jing, et al. DNA computing model of the integer linear programming problem based on molecular beacon[C]. International Conference on Intelligent Computing, Kunming, China, 2006: 238–247.

GUO Ping and LIU Lili. A surface-based DNA algorithm for the 0–1 programming problem[C]. The 3rd International Conference on Innovative Computing Information and Control, Dalian, China, 2008.

QIAN Lulu and WINFREE E. Scaling up digital circuit computation with DNA strand displacement cascades[J]. Science, 2011, 32(6034): 1196–1201.

YANG Jing, ZHANG Cheng, LIU Shi, et al. A molecular computing model for 0-1 programming problem using DNA nanoparticles[J]. Journal of Computational and Theoretical Nanoscience, 2013, 10(10): 2380–2384. doi: 10.1166/jctn.2013.3218

LI Fei, LIU Jingming, and LI Zheng. DNA computation based on self-assembled nanoparticle probes for 0-1 integer programming problem[J]. Mathematics and Computers in Simulation, 2018, 151: 140–146. doi: 10.1016/j.matcom.2017.02.004

YIN Zhixiang, CUI Jianzhong, and YANG Jing. Integer programming problem based on plasmid DNA computing model[J]. Chinese Journal of Electronics, 2017, 26(6): 1284–1288. doi: 10.1049/cje.2017.07.013

XU Jin, QIANG Xiaoli, ZHANG Kai, et al. A DNA computing model for the graph vertex coloring problem based on a probe graph[J]. Engineering, 2018, 4(1): 61–77. doi: 10.1016/j.eng.2018.02.011

YURKE B, TURBERFIELD A J, MILLS JR A P, et al. A DNA-fuelled molecular machine made of DNA[J]. Nature, 2000, 406(6796): 605–608. doi: 10.1038/35020524

DIRKS R M and PIERCE N A. Triggered amplification by hybridization chain reaction[J]. Proceedings of the National Academy of Sciences of the United States of America, 2004, 101(43): 15275–15278. doi: 10.1073/pnas.0407024101

ROTHEMUND P W K. Folding DNA to create nanoscale shapes and patterns[J]. Nature, 2006, 440(7082): 297–302. doi: 10.1038/nature04586

LAKIN M R, PARKER D, CARDELLI L, et al. Design and analysis of DNA strand displacement devices using probabilistic model checking[J]. Journal of the Royal Society Interface, 2012, 9(72): 1470–1485. doi: 10.1098/rsif.2011.0800

CONDON A, KIRKPATRICK B, and MAŇUCH J. Reachability bounds for chemical reaction networks and strand displacement systems[J]. Natural Computing, 2014, 13(4): 499–516. doi: 10.1007/s11047-013-9403-8

MARDIAN R, SEKIYAMA K, and FUKUDA T. DNA strand displacement for stochastic decision making based on immune’s clonal selection algorithm[J]. Information Technologies Knowledge, 2013, 7(1): 34–45.

YANG Jing, DONG Chen, DONG Yafei, et al. Logic nanoparticle beacon triggered by the binding-induced effect of multiple inputs[J]. ACS Applied Materials & Interfaces, 2014, 6(16): 14486–14492.

YANG Jing, JIANG Shuoxing, LIU Xiangrong, et al. Aptamer-binding directed DNA origami pattern for logic gates[J]. ACS Applied Materials & Interfaces, 2016, 8(49): 34054–34060.

PAN Linqiang, WANG Zhiyu, LI Yifan, et al. Nicking enzyme-controlled toehold regulation for DNA logic circuits[J]. Nanoscale, 2017, 9(46): 18223–18228. doi: 10.1039/C7NR06484E

YANG Jing, WU Ranfeng, LI Yifan, et al. Entropy-driven DNA logic circuits regulated by DNAzyme[J]. Nucleic Acids Research, 2018, 46(16): 8532–8541. doi: 10.1093/nar/gky663

XU Fei, WU Tingfang, SHI Xiaolong, et al. A study on a special DNA nanotube assembled from two single-stranded tiles[J]. Nanotechnology, 2019, 30(11): 115602. doi: 10.1088/1361-6528/aaf9bc

PAN Linqiang, HU Yingxin, DING Taoli, et al. Aptamer-based regulation of transcription circuits[J]. Chemical Communications, 2019, 55(51): 7378–7381. doi: 10.1039/C9CC03141C

WANG Xiaolong, BAO Zhenmin, HU Jingjie, et al. Solving the SAT problem using a DNA computing algorithm based on ligase chain reaction[J]. Biosystems, 2008, 91(1): 117–125. doi: 10.1016/j.biosystems.2007.08.006

俞洋, 苏邵, 晁洁. 基于“DNA折纸术”设计哈密顿路径问题的解决方案[J]. 中国科学: 化学, 2015, 45(11): 1226–1230. doi: 10.1360/N032015-00035

YU Yang, SU Shao, and CHAO Jie. A "DNA origami"-based approach to the solution of Hamilton path problem[J]. Scientia Sinica Chimica, 2015, 45(11): 1226–1230. doi: 10.1360/N032015-00035

俞洋, 苏邵, 晁洁. 基于“DNA折纸术”设计图着色问题的解决方案[J]. 南京大学学报: 自然科学, 2016, 52(4): 656–661.

YU Yang, SU Shao, and CHAO Jie. A "DNA origami"-based approach to the solution of graph coloring problem[J]. Journal of Nanjing University:Natural Sciences, 2016, 52(4): 656–661.

YANG Jing, SONG Zhichao, LIU Shi, et al. Dynamically arranging gold nanoparticles on DNA origami for molecular logic gates[J]. ACS Applied Materials & Interfaces, 2016, 8(34): 22451–22456.

ZHANG Qiang, WANG Xiaobiao, Wang Xiaojun, et al. Solving probability reasoning based on DNA strand displacement and probability modules[J]. Computational Biology and Chemistry, 2017, 71: 274–279. doi: 10.1016/j.compbiolchem.2017.09.011

CHAO Jie, WANG Jianbang, WANG Fei, et al. Solving mazes with single-molecule DNA navigators[J]. Nature Materials, 2019, 18(3): 273–279. doi: 10.1038/s41563-018-0205-3

TANG Zhen, YIN Zhixiang, SUN Xia, et al. Dynamically NAND gate system on DNA origami template[J]. Computers in Biology and Medicine, 2019, 109: 112–120. doi: 10.1016/j.compbiomed.2019.04.026

施引文献

资源附件(0)

访问统计