A New Solution for Maximal Clique Problem based Sticker Model

Darehmiraki, Majid

doi:10.1016/j.biosystems.2008.09.007

Cited by 21 publications

(8 citation statements)

References 7 publications

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“…In reference [ 29 ], the maximum clique problem for G can be solved using o ( n 3 ) operational time complexity, and o ( n 3 ) time complexity, where n is the number of edges of complement G .…”

Section: Resultsmentioning

confidence: 99%

Molecular Sticker Model Stimulation on Silicon for a Maximum Clique Problem

Ning

2015

IJMS

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Molecular computers (also called DNA computers), as an alternative to traditional electronic computers, are smaller in size but more energy efficient, and have massive parallel processing capacity. However, DNA computers may not outperform electronic computers owing to their higher error rates and some limitations of the biological laboratory. The stickers model, as a typical DNA-based computer, is computationally complete and universal, and can be viewed as a bit-vertically operating machine. This makes it attractive for silicon implementation. Inspired by the information processing method on the stickers computer, we propose a novel parallel computing model called DEM (DNA Electronic Computing Model) on System-on-a-Programmable-Chip (SOPC) architecture. Except for the significant difference in the computing medium—transistor chips rather than bio-molecules—the DEM works similarly to DNA computers in immense parallel information processing. Additionally, a plasma display panel (PDP) is used to show the change of solutions, and helps us directly see the distribution of assignments. The feasibility of the DEM is tested by applying it to compute a maximum clique problem (MCP) with eight vertices. Owing to the limited computing sources on SOPC architecture, the DEM could solve moderate-size problems in polynomial time.

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Section: Resultsmentioning

confidence: 99%

Molecular Sticker Model Stimulation on Silicon for a Maximum Clique Problem

Ning

2015

IJMS

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“…The advantage of the proposed sticker model is that it does not rely on short lived materials as enzymes and that it does not involve processes that are costly in terms of energy such as PCR. To put things in perspective, an opposite approach that relies only on PCR to solve problems has proved to be less error prone (Darehmiraki, 2009;Zhang et al, 2006).…”

Section: Implementation Techniquesmentioning

confidence: 99%

DNA Computation: Applications and Perspectives

Tagore¹,

Bhattacharya²,

Islam³

et al. 2010

J Proteomics Bioinform

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The computational capability of living systems has intrigued researchers for years. Primarily, the focus has been on implementing aspects of living systems in computational devices. Computer literal peoples expand their hand to the molecular biologist and chemist to explore the potential for computation of biological molecules line Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA) which are information carrying molecules. In this context, DNA computation is basically a collection of specially selected DNA strands whose combinations will result in the solution to some problems. DNA computation rather DNA-based computing is at the intersection of several threads of research. Main advantages of DNA computation are miniaturization and parallelism over conventional silicon-based machines. The informationbearing capability of DNA molecules is a cornerstone of modern theories of genetics and molecular biology. In this paper we have tried to focus on some key issues regarding the used and implementation DNA-based devices in life science fi eld. We have also tried to suggest its advantage over silicon computers.

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“…In 2009, a sticker model was used to carry out solving MCP by Majid. 8 In 2010, Yang solved the MCP by using circular DNA overcoming the problem of exponentialy increasing tubes. 9 However, there still are some deficiencies in these model, as the enzyme's incomplete cutting and the inaccurate selecting.…”

Section: Introductionmentioning

confidence: 99%

A Molecular Computing Model for Maximum Clique Problem Based on DNA Nanoparticles

Lingjing¹,

Song²,

Liuqing³

et al. 2014

Jnl of Comp & Theo Nano

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In this article, the maximum clique problem is solved based on a computing model using DNA/AuNP (gold nanoparticle). In this model, the DNA probes are used to link the specific DNA/AuNP structures in order to generate initial solution space, then specific recognizing DNA/AuNP structures are used to delete the false solutions. Finally, the true solution can be separated by electrophoresis. Different from conventional algorithm, the algorithm in this paper has high efficiency as its low time and space complexity (both are O(2n + m + 2)). What's more, the biological operation is convenient and fast for it doesn't need any enzyme. Both the operations of eliminating false solutions and obtaining the optimum solution only need to be carried out once. This model presents a different method to solve similar problems.

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A New Solution for Maximal Clique Problem based Sticker Model

Cited by 21 publications

References 7 publications

Molecular Sticker Model Stimulation on Silicon for a Maximum Clique Problem

Molecular Sticker Model Stimulation on Silicon for a Maximum Clique Problem

DNA Computation: Applications and Perspectives

A Molecular Computing Model for Maximum Clique Problem Based on DNA Nanoparticles

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