Efficient DNA Coding Algorithm for Polymerase Chain Reaction Amplification Information Retrieval.

Polymerase Chain Reaction (PCR) amplification is widely used for retrieving information from DNA storage. During the PCR amplification process, nonspecific pairing between the 3' end of the primer and the DNA sequence can cause cross-talk in the amplification reaction, leading to the generation of interfering sequences and reduced amplification accuracy. To address this issue, we propose an efficient coding algorithm for PCR amplification information retrieval (ECA-PCRAIR). This algorithm employs variable-length scanning and pruning optimization to construct a codebook that maximizes storage density while satisfying traditional biological constraints. Subsequently, a codeword search tree is constructed based on the primer library to optimize the codebook, and a variable-length interleaver is used for constraint detection and correction, thereby minimizing the likelihood of nonspecific pairing. Experimental results demonstrate that ECA-PCRAIR can reduce the probability of nonspecific pairing between the 3' end of the primer and the DNA sequence to 2-25%, enhancing the robustness of the DNA sequences. Additionally, ECA-PCRAIR achieves a storage density of 2.14-3.67 bits per nucleotide (bits/nt), significantly improving storage capacity.

Medical video encryption using novel 2D Cosine-Sine map and dynamic DNA coding.

Modern healthcare systems contain a large amount of sensitive information related to a patient in textual and visual form. Surgical videos and diagnosis data such as ultrasound, Computed Tomography (CT) scan, and Magnetic Resonance Imaging (MRI) are examples of healthcare video data. The secure storage and transmission of medical data have become an important issue in medical applications. To handle this challenge, chaos based cryptosystems are widely used these days. The work in this paper proposes a novel 2D Cosine-Sine map that exploits the existing Sine map and cosine transformation in its mathematical computation. The performance assessment of the suggested map indicates that it possesses a broader chaotic range, more dynamic and hyperchaotic nature when compared to existing chaotic maps. The proposed work, also, combines this novel 2D Cosine-Sine map with dynamic DNA encoding to propose a new scheme to encrypt medical videos. The approach consists primarily of four distinct phases. In the initial stage, the video is divided into frames, and for each frame, a chaotic sequence is generated using a 2D Cosine-sine map. During the second stage, we proceed to pixel permutation for each frame by utilizing the chaotic sequence. The third step is diffusion, in this, we integrate the 2D Cosine-Sine map with dynamic DNA encoding and apply double DNA operations to substitute the pixel values. The last step is DNA decoding to get the frames back in binary format. DNA encoding/decoding rules and operands of DNA operations are not fixed. They are selected dynamically using a random key for each frame. The dynamic selection of encoding/decoding rules and operands is a unique feature that enhances the scheme's security. Simulation results and security analysis proves that the proposed medical video encryption scheme can resist different types of attacks.

An Image Encryption Algorithm Based on Improved Hilbert Curve Scrambling and Dynamic DNA Coding.

As an effective method for image security protection, image encryption is widely used in data hiding and content protection. This paper proposes an image encryption algorithm based on an improved Hilbert curve with DNA coding. Firstly, the discrete wavelet transform (DWT) decomposes the plaintext image by three-level DWT to obtain the high-frequency and low-frequency components. Secondly, different modes of the Hilbert curve are selected to scramble the high-frequency and low-frequency components. Then, the high-frequency and low-frequency components are reconstructed separately using the inverse discrete wavelet transform (IDWT). Then, the bit matrix of the image pixels is scrambled, changing the pixel value while changing the pixel position and weakening the strong correlation between adjacent pixels to a more significant correlation. Finally, combining dynamic DNA coding and ciphertext feedback to diffuse the pixel values improves the encryption effect. The encryption algorithm performs the scrambling and diffusion in alternating transformations of space, frequency, and spatial domains, breaking the limitations of conventional scrambling. The experimental simulation results and security analysis show that the encryption algorithm can effectively resist statistical attacks and differential attacks with good security and robustness.

Quantum Image Encryption Based on Quantum DNA Codec and Pixel-Level Scrambling.

In order to increase the security and robustness of quantum images, this study combined the quantum DNA codec with quantum Hilbert scrambling to offer an enhanced quantum image encryption technique. Initially, to accomplish pixel-level diffusion and create enough key space for the picture, a quantum DNA codec was created to encode and decode the pixel color information of the quantum image using its special biological properties. Second, we used quantum Hilbert scrambling to muddle the image position data in order to double the encryption effect. In order to enhance the encryption effect, the altered picture was then employed as a key matrix in a quantum XOR operation with the original image. The inverse transformation of the encryption procedure may be used to decrypt the picture since all the quantum operations employed in this research are reversible. The two-dimensional optical image encryption technique presented in this study may significantly strengthen the anti-attack of quantum picture, according to experimental simulation and result analysis. The correlation chart demonstrates that the average information entropy of the RGB three channels is more than 7.999, the average NPCR and UACI are respectively 99.61% and 33.42%, and the peak value of the ciphertext picture histogram is uniform. It offers more security and robustness than earlier algorithms and can withstand statistical analysis and differential assaults.

Research on Improved DNA Coding and Multidirectional Diffusion Image Encryption Algorithm.

In order to make the security and operating efficiency of an image encryption algorithm coexist, this study proposed a color image encryption algorithm with improved DNA coding and rapid diffusion. During the stage of improving DNA coding, the chaotic sequence was used to form a look-up table to complete the base substitutions. In the replacement process, several encoding methods were combined and interspersed to make the randomness higher, thereby improving the security performance of the algorithm. In the diffusion stage, three-dimensional and six-directional diffusion was performed on the three channels of the color image by taking the matrix and the vector as the diffusion unit successively. This method not only ensures the security performance of the algorithm, but also improves the operating efficiency in the diffusion stage. From the simulation experiments and performance analysis, it was shown that the algorithm has good encryption and decryption effects, large key space, high key sensitivity, and strong security. The algorithm can effectively resist differential attacks and statistical attacks, and has good robustness.

Evolutionary approach to construct robust codes for DNA-based data storage.

DNA is a practical storage medium with high density, durability, and capacity to accommodate exponentially growing data volumes. A DNA sequence structure is a biocomputing problem that requires satisfying bioconstraints to design robust sequences. Existing evolutionary approaches to DNA sequences result in errors during the encoding process that reduces the lower bounds of DNA coding sets used for molecular hybridization. Additionally, the disordered DNA strand forms a secondary structure, which is susceptible to errors during decoding. This paper proposes a computational evolutionary approach based on a synergistic moth-flame optimizer by Levy flight and opposition-based learning mutation strategies to optimize these problems by constructing reverse-complement constraints. The MFOS aims to attain optimal global solutions with robust convergence and balanced search capabilities to improve DNA code lower bounds and coding rates for DNA storage. The ability of the MFOS to construct DNA coding sets is demonstrated through various experiments that use 19 state-of-the-art functions. Compared with the existing studies, the proposed approach with three different bioconstraints substantially improves the lower bounds of the DNA codes by 12-28% and significantly reduces errors.

Construction of high-dimensional cyclic symmetric chaotic map with one-dimensional chaotic map and its security application.

Classical one-dimensional chaotic map has many ideal characteristics which is quite suitable for many different kinds of scientific fields, especially cryptography. In this paper, we propose an idea of constructing high-dimensional (HD) cyclic symmetric chaotic maps by using one-dimensional (1D) chaotic map. Two constructed 3D cyclic symmetric chaotic maps are taken as the examples, named three-dimensional cyclic symmetric logistic map (3D-CSLM) and three-dimensional cyclic symmetric Chebyshev map (3D-CSCM), respectively. Numerical experiments show that the new maps possesses better dynamical performances, and their parameters have a wider range, compared with the original map. Furthermore, to verify its effect in image encryption, a novel image encryption algorithm based on 3D-CSLM and DNA coding is proposed. DNA method for image encryption can improve the efficiency of permutation and diffusion. Firstly, the algorithm uses 3D-CSLM to generate chaotic sequences for DNA operation rule selection and pixel permutation. Then through the DNA XOR operation to achieve diffusion, and finally form an encrypted image. Several simulation tests results indicate that the proposal has a promising security performance and strong anti-attack ability.

FMG: An observable DNA storage coding method based on frequency matrix game graphs.

Using complex biomolecules for storage is a new carbon-based storage method. For example, DNA has the potential to be a good method for archival long-term data storage. Reasonable and efficient coding is the first and most important step in DNA storage. However, current coding methods, such as altruism algorithm, have the problem of low coding efficiency and high complexity, and coding constraints and sets make it difficult to see the coding results visually. In this study, a new DNA storage coding method based on frequency matrix game graph (FMG) is proposed to generate DNA storage coding satisfying combinatorial constraints. Compared with the randomness of the heuristic algorithm that satisfies the constraints, the coding method based on the FMG is deterministic and can clearly explain the coding process. In addition, the constraints and coding results have observable characteristics and are better than the previously published results for the size of the coding set. For example, when length of the code n = 10, hamming distance d = 4, the results obtained by proposed approach combining chaos game and graph are 24% better than the previous results. The proposed coding scheme successfully constructs high-quality coding sets with less complexity, which effectively promotes the development of carbon-based storage coding.

Design of DNA Storage Coding with Enhanced Constraints.

Traditional storage media have been gradually unable to meet the needs of data storage around the world, and one solution to this problem is DNA storage. However, it is easy to make errors in the subsequent sequencing reading process of DNA storage coding. To reduces error rates, a method to enhance the robustness of the DNA storage coding set is proposed. Firstly, to reduce the likelihood of secondary structure in DNA coding sets, a repeat tandem sequence constraint is proposed. An improved DTW distance constraint is proposed to address the issue that the traditional distance constraint cannot accurately evaluate non-specific hybridization between DNA sequences. Secondly, an algorithm that combines random opposition-based learning and eddy jump strategy with Aquila Optimizer (AO) is proposed in this paper, which is called ROEAO. Finally, the ROEAO algorithm is used to construct the coding sets with traditional constraints and enhanced constraints, respectively. The quality of the two coding sets is evaluated by the test of the number of issuing card structures and the temperature stability of melting; the data show that the coding set constructed with ROEAO under enhanced constraints can obtain a larger lower bound while improving the coding quality.

A Novel Color Image Encryption Scheme Based on Hyperchaos and Hopfield Chaotic Neural Network.

Problems such as insufficient key space, lack of a one-time pad, and a simple encryption structure may emerge in existing encryption schemes. To solve these problems, and keep sensitive information safe, this paper proposes a plaintext-related color image encryption scheme. Firstly, a new five-dimensional hyperchaotic system is constructed in this paper, and its performance is analyzed. Secondly, this paper applies the Hopfield chaotic neural network together with the novel hyperchaotic system to propose a new encryption algorithm. The plaintext-related keys are generated by image chunking. The pseudo-random sequences iterated by the aforementioned systems are used as key streams. Therefore, the proposed pixel-level scrambling can be completed. Then the chaotic sequences are utilized to dynamically select the rules of DNA operations to complete the diffusion encryption. This paper also presents a series of security analyses of the proposed encryption scheme and compares it with other schemes to evaluate its performance. The results show that the key streams generated by the constructed hyperchaotic system and the Hopfield chaotic neural network improve the key space. The proposed encryption scheme provides a satisfying visual hiding result. Furthermore, it is resistant to a series of attacks and the problem of structural degradation caused by the simplicity of the encryption system's structure.

An Efficient Chosen-Plaintext Attack on an Image Fusion Encryption Algorithm Based on DNA Operation and Hyperchaos.

This paper proposes a more efficient attack method on an image fusion encryption algorithm based on DNA operation and hyperchaos. Although several references have reported some methods to crack the image encryption algorithm, they are not the most efficient. The proposed chosen-plaintext attack method can break the encryption scheme with (4×N/M+1) or (M/(4×N)+1) chosen-plaintext images, which is much less than the number of chosen-plaintext images used in the previous cracking algorithms, where M and N represent the height and width of the target ciphertext image, respectively. The effectiveness of the proposed chosen-plaintext attack is supported by theoretical analysis, and verified by experimental results.

CLGBO: An Algorithm for Constructing Highly Robust Coding Sets for DNA Storage.

In the era of big data, new storage media are urgently needed because the storage capacity for global data cannot meet the exponential growth of information. Deoxyribonucleic acid (DNA) storage, where primer and address sequences play a crucial role, is one of the most promising storage media because of its high density, large capacity and durability. In this study, we describe an enhanced gradient-based optimizer that includes the Cauchy and Levy mutation strategy (CLGBO) to construct DNA coding sets, which are used as primer and address libraries. Our experimental results show that the lower bounds of DNA storage coding sets obtained using the CLGBO algorithm are increased by 4.3-13.5% compared with previous work. The non-adjacent subsequence constraint was introduced to reduce the error rate in the storage process. This helps to resolve the problem that arises when consecutive repetitive subsequences in the sequence cause errors in DNA storage. We made use of the CLGBO algorithm and the non-adjacent subsequence constraint to construct larger and more highly robust coding sets.

A New Image Encryption Algorithm Based on Composite Chaos and Hyperchaos Combined with DNA Coding.

In order to obtain chaos with a wider chaotic scope and better chaotic behavior, this paper combines the several existing one-dimensional chaos and forms a new one-dimensional chaotic map by using a modular operation which is named by LLS system and abbreviated as LLSS. To get a better encryption effect, a new image encryption method based on double chaos and DNA coding technology is proposed in this paper. A new one-dimensional chaotic map is combined with a hyperchaotic Qi system to encrypt by using DNA coding. The first stage involves three rounds of scrambling; a diffusion algorithm is applied to the plaintext image, and then the intermediate ciphertext image is partitioned. The final encrypted image is formed by using DNA operation. Experimental simulation and security analysis show that this algorithm increases the key space, has high sensitivity, and can resist several common attacks. At the same time, the algorithm in this paper can reduce the correlation between adjacent pixels, making it close to 0, and increase the information entropy, making it close to the ideal value and achieving a good encryption effect.

Secure Image Encryption Algorithm Based on Hyperchaos and Dynamic DNA Coding.

In this paper, we construct a five dimensional continuous hyperchaotic system and propose an image encryption scheme based on the hyperchaotic system, which adopts DNA dynamic coding mechanism and classical scrambling diffusion encryption structure. In the diffusion stage, two rounds of diffusion are adopted and the rules of DNA encoding (DNA decoding) are dynamically changed according to the pixel value of the plaintext image, that is, the rules of DNA encoding (DNA decoding) used to encrypt different images are different, which makes the algorithm can resist chosen-plaintext attack. The encryption (decryption) key is only the initial value of the chaotic system, which overcomes the difficulty of key management in the "one time pad" encryption system. The experimental results and security analysis show that the algorithm has some advantages of large key space, no obvious statistical characteristics of ciphertext, sensitivity to plaintext and key and able to resist differential attacks and chosen plaintext attack. It has good application prospects.

A Dynamic DNA Color Image Encryption Method Based on SHA-512.

This paper presents a dynamic deoxyribonucleic acid (DNA) image encryption based on Secure Hash Algorithm-512 (SHA-512), having the structure of two rounds of permutation-diffusion, by employing two chaotic systems, dynamic DNA coding, DNA sequencing operations, and conditional shifting. We employed the SHA-512 algorithm to generate a 512-bit hash value and later utilized this value with the natural DNA sequence to calculate the initial values for the chaotic systems and the eight intermittent parameters. We implemented a two-dimensional rectangular transform (2D-RT) on the permutation. We used four-wing chaotic systems and Lorentz systems to generate chaotic sequences and recombined three channel matrices and chaotic matrices with intermittent parameters. We calculated hamming distances of DNA matrices, updated the initial values of two chaotic systems, and generated the corresponding chaotic matrices to complete the diffusion operation. After diffusion, we decoded and decomposed the DNA matrices, and then scrambled and merged these matrices into an encrypted image. According to experiments, the encryption method in this paper not only was able to withstand statistical attacks, plaintext attacks, brute-force attacks, and a host of other attacks, but also could reduce the complexity of the algorithm because it adopted DNA sequencing operations that were different from traditional DNA sequencing operations.

An Intelligent Optimization Algorithm for Constructing a DNA Storage Code: NOL-HHO.

The high density, large capacity, and long-term stability of DNA molecules make them an emerging storage medium that is especially suitable for the long-term storage of large datasets. The DNA sequences used in storage need to consider relevant constraints to avoid nonspecific hybridization reactions, such as the No-runlength constraint, GC-content, and the Hamming distance. In this work, a new nonlinear control parameter strategy and a random opposition-based learning strategy were used to improve the Harris hawks optimization algorithm (for the improved algorithm NOL-HHO) in order to prevent it from falling into local optima. Experimental testing was performed on 23 widely used benchmark functions, and the proposed algorithm was used to obtain better coding lower bounds for DNA storage. The results show that our algorithm can better maintain a smooth transition between exploration and exploitation and has stronger global exploration capabilities as compared with other algorithms. At the same time, the improvement of the lower bound directly affects the storage capacity and code rate, which promotes the further development of DNA storage technology.

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.

Decoding DNA labels by melting curve analysis using real-time PCR.

Synthetic DNA has been used as an authentication code for a diverse number of applications. However, existing decoding approaches are based on either DNA sequencing or the determination of DNA length variations. Here, we present a simple alternative protocol for labeling different objects using a small number of short DNA sequences that differ in their melting points. Code amplification and decoding can be done in two steps using quantitative PCR (qPCR). To obtain a DNA barcode with high complexity, we defined 8 template groups, each having 4 different DNA templates, yielding 158 (>2.5 billion) combinations of different individual melting temperature (Tm) values and corresponding ID codes. The reproducibility and specificity of the decoding was confirmed by using the most complex template mixture, which had 32 different products in 8 groups with different Tm values. The industrial applicability of our protocol was also demonstrated by labeling a drone with an oil-based paint containing a predefined DNA code, which was then successfully decoded. The method presented here consists of a simple code system based on a small number of synthetic DNA sequences and a cost-effective, rapid decoding protocol using a few qPCR reactions, enabling a wide range of authentication applications.

DNA labelling of varieties covered by patent protection: a new solution for managing intellectual property rights in the seed industry.

Plant breeders' rights are undergoing dramatic changes due to changes in patent rights in terms of plant variety rights protection. Although differences in the interpretation of ¼breeder's exemption«, termed research exemption in the 1991 UPOV, did exist in the past in some countries, allowing breeders to use protected varieties as parents in the creation of new varieties of plants, current developments brought about by patenting conventionally bred varieties with the European Patent Office (such as EP2140023B1) have opened new challenges. Legal restrictions on germplasm availability are therefore imposed on breeders while, at the same time, no practical information on how to distinguish protected from non-protected varieties is given. We propose here a novel approach that would solve this problem by the insertion of short DNA stretches (labels) into protected plant varieties by genetic transformation. This information will then be available to breeders by a simple and standardized procedure. We propose that such a procedure should consist of using a pair of universal primers that will generate a sequence in a PCR reaction, which can be read and translated into ordinary text by a computer application. To demonstrate the feasibility of such approach, we conducted a case study. Using the Agrobacterium tumefaciens transformation protocol, we inserted a stretch of DNA code into Nicotiana benthamiana. We also developed an on-line application that enables coding of any text message into DNA nucleotide code and, on sequencing, decoding it back into text. In the presented case study, a short command line coding the phrase ¼Hello world« was transformed into a DNA sequence that was inserted in the plant genome. The encoded message was reconstructed from the resulting T1 seedlings with 100 % accuracy. The feasibility and possible other applications of this approach are discussed.

Color image encryption scheme using CML and DNA sequence operations.

In this paper, an encryption algorithm for color images using chaotic system and DNA (Deoxyribonucleic acid) sequence operations is proposed. Three components for the color plain image is employed to construct a matrix, then perform confusion operation on the pixels matrix generated by the spatiotemporal chaos system, i.e., CML (coupled map lattice). DNA encoding rules, and decoding rules are introduced in the permutation phase. The extended Hamming distance is proposed to generate new initial values for CML iteration combining color plain image. Permute the rows and columns of the DNA matrix and then get the color cipher image from this matrix. Theoretical analysis and experimental results prove the cryptosystem secure and practical, and it is suitable for encrypting color images of any size.