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The analysis of short tandem repeats (STRs) in DNA sequences has become an attractive method for determining the genetic profile of an individual. Here we focus on a more general and practical issue named short adjacent repeats identification problem (SARIP), which is extended from STR by allowing short gaps between neighboring units. Presently, the best available solution to SARIP is BASARD, which...
In this work, we propose a DNA hybridization detection platform with assembled magnetic beads and integrated photodiodes on a silicon chip. DNA targets labeled magnetic beads generate an opaque area after hybridization, and the fabricated photodiode is utilized to turn ordinary light into electricity. Compared with the detected photocurrent before hybridization, the signal of DNA hybridization can...
The solution space exponential explosion caused by the enumeration of the candidate solutions maybe is the biggest obstacle in DNA computing. In the paper, a new unenumerative DNA computing model for graph vertex coloring problem is presented based on two techniques: 1) ordering the vertex sequence for a given graph in such a way that any two consecutive labeled vertices and should be adjacent...
Evolutionary Monte Carlo (EMC) algorithm is an effective and powerful method to sample complicated distributions. Short adjacent repeats identification problem (SARIP), i.e., searching for the common sequence pattern in multiple DNA sequences, is considered as one of the key challenges in the field of bioinformatics. A recently proposed Markov chain Monte Carlo (MCMC) algorithm has demonstrated its...
A DNA computing model for solving graph vertex coloring problem is proposed in this article. To illustrate the capability of the DNA computing model, a 3-colorable graph with 61 vertices was constructed as an example. Using this model, more than 99% of false solutions were deleted when the initial solution space was established and finally all solutions of the graph were found. Because these operations...
Recent research has demonstrated that the ultra-scale computation by self-assembly DNA tiles could be implemented in the laboratory. One of the significant applications is the DNA-based cryptography systems. In this paper, we detail procedures for the DNA-based cryptography based on the One-Time-Pads (OTP) which is in principle unbreakable. In order to implement the whole encrypting and decrypting...
The data encryption standard (DES) is an algorithm with approximate 72 quadrillion possible keys. The security of the DES is based on the difficulty of picking out the right key after the 16-round nonlinear function operations. In this paper, we propose a concrete recursive sticker molecular algorithm to the DES. The molecular sticker algorithm includes three parts: initializing the key space with...
DNA tile self-assembly has been proved to enable programmable manipulation of biological systems as a tool of molecular computation. It is mainly based on the property that is the spontaneous self-ordering of substructure into superstructure driven by annealing of Watson-Crick base-pairing DNA sequences. We take full advantage of the superiority of DNA tile self-assembly to construct a molecular computing...
DNA tile self-assembly is a promising paradigm for nanotechnology. Recently, many researches show that computation by DNA tile self-assembly maybe scalable. In this paper, we propose the algorithm for elliptic curve Diffie-Hellman key exchange based on DNA tile self-assembly. First we give the DNA tile self-assembly model to compute the scalar multiplication, then we can successfully implement the...
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