Xuedong Zheng

Parallel DNA Arithmetic Operation With One Error Detection Based on 3-Moduli Set

The redundant residue number system is introduced into DNA computing in order to overcome the negative effect caused by the instability of the biochemical reactions and the error hybridizations. Based on the Adleman-Lipton model and a special 3-moduli set, the DNA encoding scheme for redundant residue numbers is presented and the DNA algorithm of one-digit error detection is proposed. The parallel DNA arithmetic operation can be realized in redundant residue number system with error detection, and which can improve the reliability of DNA computing and simplify the DNA encoding scheme.

Constructing DNA Barcode Sets Based on Particle Swarm Optimization

Following the completion of the human genome project, a large amount of high-throughput bio-data was generated. To analyze these data, massively parallel sequencing, namely next-generation sequencing, was rapidly developed. DNA barcodes are used to identify the ownership between sequences and samples when they are attached at the beginning or end of sequencing reads. Constructing DNA barcode sets provides the candidate DNA barcodes for this application. To increase the accuracy of DNA barcode sets, a particle swarm optimization (PSO) algorithm has been modified and used to construct the DNA barcode sets in this paper. Compared with the extant results, some lower bounds of DNA barcode sets are improved. The results show that the proposed algorithm is effective in constructing DNA barcode sets.

Correcting Errors in Image Encryption Based on DNA Coding

As a primary method, image encryption is widely used to protect the security of image information. In recent years, image encryption pays attention to the combination with DNA computing. In this work, we propose a novel method to correct errors in image encryption, which results from the uncertainty of DNA computing. DNA coding is the key step for DNA computing that could decrease the similarity of DNA sequences in DNA computing as well as correct errors from the process of image encryption and decryption. The experimental results show our method could be used to correct errors in image encryption based on DNA coding.

Splicing Model and Hyper–Chaotic System for Image Encryption

Abstract Encryption is an effective way to protect the image information from attacking by intruders in the transmission applications through the Internet. This study presents an image encryption scheme on the basics of the formal model of DNA computing-splicing system and hyper-chaotic system, which utilizes the instinct properties of hyper-chaotic system and splicing model while programming the method. In our proposed algorithm, the quaternary coding is used to split the plain image into four sub-sections so that we can’t get the cipher image without any one sub-section. This new method can be used to change the plain image information drastically. The experimental results and security analysis show that our method not only has a good security but also increases the resistance to common attacks such as exhaustive attacks, statistical attacks and differential attacks.

An Image Encryption Scheme Based on DNA Computing and Cellular Automata

Networks have developed very quickly, allowing the speedy transfer of image information through Internet. However, the openness of these networks poses a serious threat to the security of image information. The field of image encryption has drawn attention for this reason. In this paper, the concepts of 1-dimensional DNA cellular automata and T-DNA cellular automata are defined, and the concept of reversible T-DNA cellular automata is introduced. An efficient approach to encryption involving reversible T-DNA cellular automata as an encryption tool and natural DNA sequences as the main keys is here proposed. The results of a simulation experiment, performance analysis, and comparison to other encryption algorithms showed this algorithm to be capable of resisting brute force attacks, statistical attacks, and differential attacks. It also enlarged the key space enormously. It meets the criteria for one-time pad and resolves the problem that one-time pad is difficult to save.

Reversible Data Hiding Based on DNA Computing

Biocomputing, especially DNA, computing has got great development. It is widely used in information security. In this paper, a novel algorithm of reversible data hiding based on DNA computing is proposed. Inspired by the algorithm of histogram modification, which is a classical algorithm for reversible data hiding, we combine it with DNA computing to realize this algorithm based on biological technology. Compared with previous results, our experimental results have significantly improved the ER (Embedding Rate). Furthermore, some PSNR (peak signal-to-noise ratios) of test images are also improved. Experimental results show that it is suitable for protecting the copyright of cover image in DNA-based information security.

Improved Niche Genetic Algorithm for Protein Structure Prediction

Due to the complexity and variety of protein structure, the protein structure prediction (PSP) is a challenging problem in the field of bioinformatics. In this paper, we adopt an improved niche genetic algorithm for protein structure prediction, the niche genetic algorithm (NGA) bonds with some improvement strategies, which have a competitive selection, a random crossover and random linear mutation operator. These improvement strategies can maintain the population diversity and avoid the shortcomings of the Niche Genetic algorithm that stagnate evolution and be caught in local optimum. And our experiment gains some better results than other algorithms with the Fibonacci sequence and the real protein sequence. Finally, the experiment results illustrate the efficiency of this algorithm on the Fibonacci sequence and the real protein sequence.

Digital watermarking based on chaos game representation and discrete cosine transform

Digital watermarking is a means to protect multimedia copyright, and it will be subjected to various attacks. Therefore, the research on the robustness of watermarking algorithm is considered as a hot field. A digital image watermarking algorithm that can resist geometric attacks is proposed based on chaos game representation and normalization. Firstly, the original image is mapped to the geometrically invariant space using the image normalization. Then, according to the image characteristics and the human visual characteristics, the valid image is transformed by DCT transform and the embedding number is determined. At last, the embedding image and position are determined by chaos game representation and the embedding number, and the watermarking is embedded in the light of the embedding number and position into the embedding image. Analyzing experimental results, we can know that the algorithm is invisible, secure and robust against geometric attacks.

Logic Calculation Based on Two-Domain DNA Strand Displacement

DNA strand displacement technology has become one of the most commonly used in biological computing technology. In this paper, we design a calculation model of the basic logic unit based on two-domain DNA strand displacement and logical relation, including AND, OR logic gates. The calculation process is simple and easy to understand, because of the unified single strand structure. The process of the reaction is more thorough and more easy to control. The model is used to construct a converter of a four-bit binary into BCD code. The whole reaction process can be programmed and simulated in the software Visual DSD, and the result also verifies the correctness of the design of the basic logic calculation model.

IWO Algorithm Based on Niche Crowding for DNA Sequence Design

The design of DNA sequences is essential for the implementation of DNA computing, where the quantity and quality can directly affect the accuracy and efficiency of calculations. Many studies have focused on the design of good DNA sequences to make DNA computing more reliable. However, DNA sequence design needs to satisfy various constraints at the same time, which is an NP-hard problem. In this study, we specify appropriate constraints that should be satisfied in the design of DNA sequences and we propose evaluation formulae. We employ the Invasive Weed Optimization (IWO) algorithm and the niche crowding in the algorithm to solve the DNA sequence design problem. We also improve the spatial dispersal in the traditional IWO algorithm. Finally, we compared the sequences obtained with existing sequences based on the results obtained using a comprehensive fitness function, which demonstrated the efficiency of the proposed method.