Visual solution to minimum spanning tree problem based on DNA origami

2021 ◽  
Vol 11 (10) ◽  
pp. 1700-1706
Author(s):  
Jing Yang ◽  
Zhixiang Yin ◽  
Zhen Tang ◽  
Xue Pang ◽  
Jianzhong Cui ◽  
...  

DNA origami is a highly precise nanometer material based on DNA molecular. In the current study, we present a visual computing model of minimum spanning tree that combines advantages of DNA origami, hybridization chain reaction and nano-gold particles. Nano-gold particles were used to represent vertices and molecular beacons with fluorescent labels were used as anchor strands, which were fixed on origami substrate with staple strands according to the shape in graph. We then induced hybridization chain reaction using initiator strands and fuel strands. Lastly the problem was detected using fluorescence. The model provides a visualized calculation model of minimum spanning tree by using hybridization chain reaction and fluorescence labeling on origami bases. This model utilizes their advantages and demonstrates effectiveness of the model through case simulation. It also reduces computational complexity of the problem and improve the way of solution reading.

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Risheng Wang ◽  
Zhixiang Yin ◽  
Jianzhong Cui ◽  
Jing Yang ◽  
Zhen Tang ◽  
...  

DNA origami is the application of self-assembly in nanotechnology. The combination of DNA origami and hybridization chain reaction is one of the important application methods of DNA origami. In this paper, DNA origami is used to design the cipher pattern on the base of origami. The cipher chain, which is put into the reaction solution, hybridizes with the molecular beacon and the hairpin structure that form the cipher pattern to build a DNA origami model that can decode the pattern. The cipher chain consists of the starting chain and the intermediate chain. When the cipher is correct, the cipher chain can open the molecular beacon and the hairpin structure to display the cipher pattern on the origami base in the solution.


Author(s):  
Zhixiang Yin ◽  
Jing Yang ◽  
Qiang Zhang ◽  
Zhen Tang ◽  
Guoqiang Wang ◽  
...  

Satisfiability problem is a famous nondeterministic polynomial-time complete (NP-complete) problem, which has always been a hotspot in artificial intelligence. In this paper, by combining the advantages of DNA origami with hybridization chain reaction, a computing model was proposed to solve the satisfiability problem. For each clause in the given formula, a DNA origami device was devised. The device corresponding to the clause was capable of searching for assignments that satisfied the clause. When all devices completed the search in parallel, the intersection of these satisfying assignments found must satisfy all the clauses. Therefore, whether the given formula is satisfiable or not was decided. The simulation results demonstrated that the proposed computing model was feasible. Our work showed the capability of DNA origami in architecting automatic computing device. The paper proposed a novel method for designing functional nanoscale devices based on DNA origami.


2013 ◽  
Vol 411-414 ◽  
pp. 2056-2061
Author(s):  
Zhi Li Pei ◽  
Qing Hu Wang ◽  
Jie Lian ◽  
Bin Wu

Artificial intelligence based on the genetic algorithm and DNA computing based on the biological intelligence is two kinds of important intelligent computing model, Graph theory and combinatorial optimization problem is a hotspot of research on intelligent computing. This paper designs a coding space optimized by using genetic algorithm, and by using DNA computing to solve Minimum Spanning Tree Problem calculation model. Because MSTP (Minimum Spanning Tree Problem) refer to Weight, IMCE (Incompletion-Molecule Commixed Encoding) is used in vertex, edges and weights encoding. The calculation process of the MSTP solution has been detailed described detailed.


2019 ◽  
Vol 43 (24) ◽  
pp. 9458-9465
Author(s):  
Xiquan Yue ◽  
Lihong Su ◽  
Xu Chen ◽  
Junfeng Liu ◽  
Longpo Zheng ◽  
...  

The strategy is based on small molecule-mediated hybridization chain reaction.


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