The Circular DNA Model of 0–1 Programming Problem Based on DNA Strand Displacement

Zhen, Tang; Yin, Zhixiang; Yang, Jing; Sun, Xuxu; Chen, Jianzhong

doi:10.1109/fskd.2018.8687233

Cited by 2 publications

(3 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Several studies have utilized DNA strand displacement to solve intractable combinational optimization problems. In 2018, Tang et al 22 applied DNA strand displacement to solve the 0-1 programming problem, where the model is built based on circular DNA. However, the method is impractical because the number of required species of fluorescence is equal to the number of variables.…”

Section: Introductionmentioning

confidence: 99%

A universal DNA computing model for solving NP-hard subset problems

Zhu¹,

Luo²,

Liu³

et al. 2022

Preprint

View full text Add to dashboard Cite

DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited to solve various intractable computational problems, such as the Hamiltonian path problem, SAT problem, and graph coloring problem, there has been little discussion of designing universal DNA computing-based models, which can solve a class of problems. In this paper, by leveraging the dynamic and enzyme-free properties of DNA strand displacement, we propose a universal model named DCMSubset for solving subset problems in graph theory. The model aims to find a minimum (or maximum) set satisfying given constraints. For each element x involved in a given problem, DCMSubset uses an exclusive single-stranded DNA molecule to model x as well as a specific DNA complex to model the relationship between x and other elements. Based on the proposed model, we conducted simulation and biochemical experiments on three kinds of subset problems, a minimum dominating set, maximum independent set, and minimum vertex cover. We observed that DCMSubset can also be used to solve the graph coloring problem. Moreover, we extended DCMSubset to a model for solving the SAT problem. The results of experiments showed the feasibility and university of the proposed method. Our results highlighted the potential for DNA strand displacement to act as a computation tool to solve NP-hard problems.

show abstract

Section: Introductionmentioning

confidence: 99%

A universal DNA computing model for solving NP-hard subset problems

Zhu¹,

Luo²,

Liu³

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Further, a DNA navigator system was developed by Chao et al 18 that can do a single-molecule parallel depth-first search on a two-dimensional DNA origami platform. Tang et al 19 used a circular DNA structure to solve the 0−1 programming problem using the DNA strand displacement method. In this method, the results were detected using the fluorescence color generated by DNA strand displacement.…”

Section: ■ Introductionmentioning

confidence: 99%

“…The existing structure assisted DNA computing models are prone to experimental errors, ,− as these are based on self-assembly of DNA molecules. Also, these are validated only for smaller size formulations.…”

Section: Introductionmentioning

confidence: 99%

In Vitro Identification of the Hamiltonian Cycle Using a Circular Structure Assisted DNA Computer

Sharma

Ramteke

2020

ACS Comb. Sci.

View full text Add to dashboard Cite

Adleman’s illustration of molecular computing using DNA paved the way toward an entirely new direction of computing (Science19942661021). The exponential time complex combinatorial problem on a traditional computer turns out to be a separation problem involving a polynomial number of steps in DNA computing experiments. Despite being a promising concept, the implementations of existing DNA computing procedures were restricted only to the smaller size formulations. In this work, we demonstrate a structure assisted DNA computing procedure on a bigger size Hamiltonian cycle problem involving 18 vertices. The developed model involves the formation and digestion of circular structure DNA, iteratively over multiple stages to eliminate the incorrect solutions to the given combinatorial problem. A high accuracy is obtained compared to other structure assisted models, which enable one to solve the bigger size problems.

show abstract

The Circular DNA Model of 0–1 Programming Problem Based on DNA Strand Displacement

Cited by 2 publications

References 12 publications

A universal DNA computing model for solving NP-hard subset problems

A universal DNA computing model for solving NP-hard subset problems

In Vitro Identification of the Hamiltonian Cycle Using a Circular Structure Assisted DNA Computer

Contact Info

Product

Resources

About