DNA Computing Model for Satisfiability Problem Based on Hybridization Chain Reaction

2020 ◽  
pp. 2159010
Author(s):  
Zhixiang Yin ◽  
Jing Yang ◽  
Qiang Zhang ◽  
Zhen Tang ◽  
Guoqiang Wang ◽  
...  
Keyword(s):  
Dna Computing ◽  
Dna Origami ◽  
Satisfiability Problem ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Computing Device ◽  
Computing Model ◽  
Novel Method ◽  
Np Complete ◽  
The Given

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.

Search computing model for the knapsack problem based on DNA origami

2019 ◽  
Vol 9 (6) ◽  
pp. 553-562 ◽  
Author(s):  
Jing Yang ◽  
Zhixiang Yin ◽  
Zhen Tang ◽  
Kaifeng Huang ◽  
Jianzhong Cui ◽  
...  
Keyword(s):  
Combinatorial Optimization ◽  
Knapsack Problem ◽  
Simulation Software ◽  
Dna Origami ◽  
Directed Path ◽  
Chain Reaction ◽  
Detection Techniques ◽  
Complete Problem ◽  
Computing Model ◽  
Np Complete

The knapsack problem is an import NP-complete problem in combinatorial optimization. In order to reduce the complexity of the problem, we provide a search computing model based on DNA origami to solve it. In this paper, we map the choice of each item to the directed path on the origami base of DNA. Then the solution of the problem is mapped to find a directed path to maximize the total value of items in the knapsack. Hybrid chain reaction and fluorescence detection techniques are used to generate solutions satisfying constraints. Lastly, we use Visual DSD simulation software to verify the validity of the model. Compared with other models through simulation, this model can automatically search the solution of the problem, and really reduce the complexity of the problem to linear.

scholarly journals DNA Origami Model for Simple Image Decoding

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Risheng Wang ◽  
Zhixiang Yin ◽  
Jianzhong Cui ◽  
Jing Yang ◽  
Zhen Tang ◽  
...  
Keyword(s):  
Self Assembly ◽  
Molecular Beacon ◽  
Important Application ◽  
Dna Origami ◽  
Hairpin Structure ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Reaction Solution ◽  
Application Methods ◽  
Image Decoding

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.

A novel method for sensitive detection of Escherichia coli O157:H7 based on an aptamer and hybridization chain reaction

2020 ◽  
Vol 12 (29) ◽  
pp. 3734-3740
Author(s):  
Yuexin Liu ◽  
Ping Chen ◽  
Shuai Yuan ◽  
Bo Sun ◽  
Rui Sun ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sensitive Detection ◽  
Hybridization Chain Reaction ◽  
Escherichia Coli O157 ◽  
Chain Reaction ◽  
Bacterial Detection ◽  
E Coli ◽  
Novel Method

A novel assay for the sensitive detection of E. coli O157:H7 using an aptamer-based HCR, which provided a universal platform for other bacterial detection.

Molecular Beacon Based DNA Computing Model for General Satisfiability Problem

2009 ◽  
Vol 31 (12) ◽  
pp. 2200-2206 ◽  
Author(s):  
Zhi-Xiang YIN ◽  
Jian-Zhong CUI ◽  
Ling-Ying ZHI ◽  
Xia SUN ◽  
Xiao-Hui HUANG
Keyword(s):  
Dna Computing ◽  
Molecular Beacon ◽  
Satisfiability Problem ◽  
Computing Model

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 ◽  
...  
Keyword(s):  
Spanning Tree ◽  
Minimum Spanning Tree ◽  
Calculation Model ◽  
Dna Origami ◽  
Fluorescence Labeling ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Gold Particles ◽  
Visual Computing ◽  
Nano Gold

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.

A new method for the in situ assay of α-glucosidase activity and inhibitor screening through an enzyme substrate-mediated DNA hybridization chain reaction

2019 ◽  
Vol 43 (24) ◽  
pp. 9458-9465
Author(s):  
Xiquan Yue ◽  
Lihong Su ◽  
Xu Chen ◽  
Junfeng Liu ◽  
Longpo Zheng ◽  
...  
Keyword(s):  
Small Molecule ◽  
Dna Hybridization ◽  
New Method ◽  
Hybridization Chain Reaction ◽  
Chain Reaction ◽  
Inhibitor Screening ◽  
Glucosidase Activity ◽  
Enzyme Substrate ◽  
In Situ Assay

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

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