Chaos game representation （CGR）-walk model for DNA sequences

Chaos game representation (CGR) is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to determine the coordinates of their positions in a continuous space. This distribution of positions has two features: one is unique, and the other is source sequence that can be recovered from the coordinates so that the distance between positions may serve as a measure of similarity between the corresponding sequences. A CGR-walk model is proposed based on CGR coordinates for the DNA sequences. The CGR coordinates are converted into a time series, and a long-memory ARFIMA (p, d, q) model, where ARFIMA stands for autoregressive fractionally integrated moving average, is introduced into the DNA sequence analysis. This model is applied to simulating real CGR-walk sequence data of ten genomic sequences. Remarkably long-range correlations are uncovered in the data, and the results from these models are reasonably fitted with those from the ARFIMA (p, d, q) model.     

A novel chaotic based image encryption using a hybrid model of deoxyribonucleic acid and cellular automata

Currently, there are many studies have conducted on developing security of the digital image in order to protect such data while they are sending on the internet. This work aims to propose a new approach based on a hybrid model of the Tinkerbell chaotic map, deoxyribonucleic acid (DNA) and cellular automata (CA). DNA rules, DNA sequence XOR operator and CA rules are used simultaneously to encrypt the plain-image pixels. To determine rule number in DNA sequence and also CA, a 2-dimension Tinkerbell chaotic map is employed. Experimental results and computer simulations, both confirm that the proposed scheme not only demonstrates outstanding encryption, but also resists various typical attacks.     

Inference of DNA sequences from mechanical unzipping: an ideal-case study

The performances of Bayesian inference to predict the sequence of DNA molecules from fixed-force unzipping experiments are investigated. We show that the probability of misprediction decreases exponentially with the amount of collected data. The decay rate is calculated as a function of biochemical parameters (binding free energies), the sequence content, the applied force, the elastic properties of a DNA single strand, and time resolution.     

Investigation of a Kubo-formula-based approach to estimate DNA conductance in an atomistic model

A novel approach to estimate DNA conductance based upon Kubo formula is presented and discussed. Using this approach, the effects of base pair mismatches, different conformational changes and base pair sequence on DNA electrical properties were investigated. The results were compared with the data from other methods. The new approach makes possible very fast estimation of conductance spectra for oligonucleotides with hundreds of base pairs and can easily be extended to treat arbitrary chemical modifications of DNA.     

Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors

DNA melting under torsion plays an important role in a wide variety of cellular processes. In the present Letter, we have investigated DNA melting at the single-molecule level using an angular optical trap. By directly measuring force, extension, torque, and angle of DNA, we determined the structural and elastic parameters of torsionally melted DNA. Our data reveal that under moderate forces, the melted DNA assumes a left-handed structure as opposed to an open bubble conformation and is highly torsionally compliant. We have also discovered that at low forces melted DNA properties are highly dependent on DNA sequence. These results provide a more comprehensive picture of the global DNA force-torque phase diagram.     

Melting transition of directly linked gold nanoparticle DNA assembly

DNA melting and hybridization is a fundamental biological process as well as a crucial step in many modern biotechnology applications. DNA confined on surfaces exhibits a behavior different from that in free solutions. The system of DNA-capped gold nanoparticles exhibits unique phase transitions and represents a new class of complex fluids. Depending on the sequence of the DNA, particles can be linked to each other through direct complementary DNA sequences or via a ‘linker’ DNA, whose sequence is complementary to the sequence attached to the gold nanoparticles. We observed different melting transitions for these two distinct systems.     

DNA分子链的电子局域性质及电导的研究

将一维随机二元固体模型应用于DNA分子链，利用传输矩阵方法来研究系统电子态的局域性质并进而讨论系统的导电性质.对一个链长为50000个碱基对的DNA序列，数值分析了局域长度和电导随碱基对的摩尔百分数、本征能量和无序度的变化关系.结果表明，系统的局域长度和电导强烈地依赖于能量，在能带中心部分局域长度大于边沿部分.无序度也在一定程度上影响着局域长度，双方成反向变化的关系.对有限长度的DNA分子链，局域长度体现出明显的对碱基对摩尔百分数的依赖关系，对正常成分比例的随机DNA序列，在所有能量范围内系统的态都是局域的，系统的电导很小，系统呈现绝缘体行为.仅当一种碱基对在序列中所占比例很小时，系统中可以发现与特定分立能量值相对应的“扩展态”存在，处在这些态下的系统有较大的电导，但这些扩展态是不稳定的，在热力学极限之下会消失. 关键词： DNA分子链 电子局域 局域长度 电导     

Image Encryption Using a Spectrally Efficient Halton Logistics Tent (HaLT) Map and DNA Encoding for Secured Image Communication

With the advancement of technology worldwide, security is essential for online information and data. This research work proposes a novel image encryption method based on combined chaotic maps, Halton sequence, five-dimension (5D) Hyper-Chaotic System and Deoxyribonucleic Acid (DNA) encoding. Halton sequence is a known low-discrepancy sequence having uniform distribution in space for application in numerical methods. In the proposed work, we derived a new chaotic map (HaLT map) by combining chaotic maps and Halton sequence to scramble images for cryptography applications. First level scrambling was done by using the HaLT map along with a modified quantization unit. In addition, the scrambled image underwent inter- and intra-bit scrambling for enhanced security. Hash values of the original and scrambled image were used for initial conditions to generate a 5D hyper-chaotic map. Since a 5D chaotic map has complex dynamic behavior, it could be used to generate random sequences for image diffusion. Further, DNA level permutation and pixel diffusion was applied. Seven DNA operators, i.e., ADD, SUB, MUL, XOR, XNOR, Right-Shift and Left-Shift, were used for pixel diffusion. The simulation results showed that the proposed image encryption method was fast and provided better encryption compared to ‘state of the art’ techniques. Furthermore, it resisted various attacks.     

Current-voltage characteristics of double-strand DNA sequences

We use a tight-binding formulation to investigate the transmissivity and the current-voltage (I-V) characteristics of sequences of double-strand DNA molecules. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for the genomic DNA sequence with those of artificial sequences (the long-range correlated Fibonacci and Rudin-Shapiro one) and a random sequence, which is a kind of prototype of a short-range correlated system. The random sequence is presented here with the same first neighbors pair correlations of the human DNA sequence. We found that the long-range character of the correlations is important to the transmissivity spectra, although the I-V curves seem to be mostly influenced by the short-range correlations.     

A novel image fusion encryption algorithm based on DNA sequence operation and hyper-chaotic system

A new image fusion encryption algorithm based on image fusion and DNA sequence operation and hyper-chaotic system is presented. Firstly, two DNA sequences matrices are obtained by encoding the original image and the key image. Secondly, using the chaotic sequences generated by Chen's hyper-chaotic maps to scramble the locations of elements from the DNA sequence matrix which generated form original image. Thirdly, XOR the scrambled DNA matrix and the random DNA matrix by using DNA sequence addition operation. At last, decoding the DNA sequence matrix, we will get the encrypted image. The simulation experimental results and security analysis show that our algorithm not only has good encryption effect, but also has the ability of resisting exhaustive attack and statistical attack.     

Effects of cytosine methylation on DNA charge transport

The methylation of cytosine bases in DNA commonly takes place in the human genome and its abnormality can be used as a biomarker in the diagnosis of genetic diseases. In this paper we explore the effects of cytosine methylation on the conductance of DNA. Although the methyl group is a small chemical modification, and has a van der Waals radius of only 2 ?, its presence significantly changes the duplex stability, and as such may also affect the conductance properties of DNA. To determine if charge transport through the DNA stack is sensitive to this important biological modification we perform multiple conductance measurements on a methylated DNA molecule with an alternating G:C sequence and its non-methylated counterpart. From these studies we find a measurable difference in the conductance between the two types of molecules, and demonstrate that this difference is statistically significant. The conductance values of these molecules are also compared with a similar sequence that has been previously studied to help elucidate the charge transport mechanisms involved in direct DNA conductance measurements.     

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.     

Random coil carbon chemical shifts of deoxyribonucleic acids

The sequence and temperature effects on random coil DNA carbon chemical shifts have been investigated using sixteen 17-nucleotide sequences. Temperature effect correction parameters have been determined for the aromatic C6/C8 carbons and the deoxyribose C1', C2', and C3' carbons. The carbon chemical shifts of a specific nucleotide in a random coil sequence have been shown to depend mainly on the type of its nearest neighbors. A carbon chemical shift database containing all 64 different types of triplets has been established for predicting random coil DNA carbon chemical shifts. The use of this triplet database for carbon chemical shift predictions shows good accuracy with experimental data, with root-mean-square deviations of 0.09, 0.10, 0.10, and 0.10 ppm and correlation coefficients of 0.999, 0.996, 0.978, and 0.974 for C6/C8, C1', C2', and C3', respectively.     

单个人类端粒重复序列d(TTAGGG)对长链端粒DNA-d[AGGG(TTAGGG)6]结构影响的研究

本文使用超速离心沉降速度法、聚丙烯酰胺凝胶电泳和圆二色光谱和紫外吸收检测熔融实验研究了长序列端粒DNA-d[AGGG(TTAGGG)₆](G₆-DNA)的结构以及单个重复序列DNA-d(TTAGGG)(G₀₁-DNA)对G₆-DNA结构的影响. 结果表明G₆-DNA可以在水溶液中形成二聚体,并且G₀₁-DNA可以通过与G₆-DNA结合形成额外的G-四链体结构,从而改变单体与二聚体的平衡. 然而,G₀₁-DNA对序列为d[AGGG(TTAGGG)₃](G₃-DNA)的结构没有影响. 该研究为长序列单链端粒DNA的结构多样性提供了新的见解.     

脱氧核糖核酸单链序列的预测

利用Langevin动力学方法模拟了脱氧核糖核酸(DNA)单链在电场力作用下穿越纳米孔道的动力学过程.研究表明,不同种类的单体对应着不同的居留时间,相邻单体的居留时间随着孔道长度的增大而减小.在简化模型的基础上,可以从居留时间图中一次性地推测出一条DNA链的嘌呤和嘧啶的分布.应用该方法对17条不同序列的DNA链进行了预测,平均准确率为951%.在此方法的基础上做一些改进,可以为DNA链的测序提供一种高效的低成本方法. 关键词： Langevin动力学 脱氧核糖核酸单链 序列预测     

Thermal denaturation of DNA molecules: A comparison of theory with experiment

Experimental and theoretical results on the helix-coil transition of DNA are reviewed. The theoretical model of the transition is described, and the influence of heterogeneous base pair stacking, and strand dissociation on the predicted melting transition is examined. New experimental transition data on seven DNAs, 154–587 base pairs (bp) long, are reported and compared with theoretical calculations. We review and evaluate previous studies on long DNAs (≥1000 bp) as well as previous and recent results on short DNAs. The comparison of theory with equilibrium melting curves of short DNAs indicates that base pair sequence has a relatively small influence on the stacking free energy. Excellent agreement is obtained between theory and equilibrium transitions of 14 out of 15 fragments 80–587 pb. The deviation between theory and experiment for a 516 bp DNA can be attributed to the formation of stem-loop structures. This may provide the explanation for inconsistent results observed with long DNAs. The effect of single base pair changes on DNA transitions is discussed. Current views on fluctuational opening of base pairs at temperatures below the transition are described.     

Acceleration of the Smith–Waterman algorithm using single and multiple graphics processors

Finding regions of similarity between two very long data streams is a computationally intensive problem referred to as sequence alignment. Alignment algorithms must allow for imperfect sequence matching with different starting locations and some gaps and errors between the two data sequences. Perhaps the most well known application of sequence matching is the testing of DNA or protein sequences against genome databases. The Smith–Waterman algorithm is a method for precisely characterizing how well two sequences can be aligned and for determining the optimal alignment of those two sequences. Like many applications in computational science, the Smith–Waterman algorithm is constrained by the memory access speed and can be accelerated significantly by using graphics processors (GPUs) as the compute engine. In this work we show that effective use of the GPU requires a novel reformulation of the Smith–Waterman algorithm. The performance of this new version of the algorithm is demonstrated using the SSCA#1 (Bioinformatics) benchmark running on one GPU and on up to four GPUs executing in parallel. The results indicate that for large problems a single GPU is up to 45 times faster than a CPU for this application, and the parallel implementation shows linear speed up on up to 4 GPUs.     

DNA分子链电子结构特性研究

在单电子紧束缚近似下，建立了一维无序二元DNA分子链模型，计算了链长为2×10⁴个碱基对的DNA分子链的电子态密度、局域化特性，并探讨了碱基对的不同组分、格点能量无序度对电子局域态的影响.结果表明：由于DNA分子链中格点能量无序及碱基对的不同组分的存在，其电子波函数呈现出局域化的特性，而局域长度作为衡量电子局域化程度的一个尺度，受碱基对的组分及格点能量无序度的影响. 关键词： DNA分子链 电子结构 电子局域态 局域长度     

Spectrum of the Micromaser with Kerr Medium

We have established the master equation for the micromaser with Kerr medium field density operator,studied the spectrum of the micromaser with Kerr medium and analyzed the influence of Kerr effect and the detuning on the spectrum.In the thermal-atom regime,we find that Kerr effect broadens Linewidth D and increases frequency-shift S,and that the detuning Δ narrows linewidth D and increases frequency-shift S as a whole,Moreover Kerr effect leads to oscillatings more rapidly in the resonance peaks,which means that it causes quantum noise,As a whole,with the increase of cavity-length L,the linewidth D and frequency-shift S gradually increase.