Low frequency rhythms in human DNA sequences: a key to the organization of gene location and orientation?

We explore large-scale nucleotide compositional fluctuations of the human genome using multiresolution techniques. Analysis of the GC content and of the AT and GC skews reveals the existence of rhythms with two main periods of 110+/-20 kb and 400+/-50 kb that enlighten a remarkable cooperative gene organization. We show that the observed nonlinear oscillations are likely to display all the characteristic features of chaotic strange attractors which suggests a very attractive deterministic picture: gene orientation and location, in relation with the structure and dynamics of chromatin, might be governed by a low-dimensional nonlinear dynamical system.     

Electron–phonon coupling in DNA: a systematic study

The coupling of all twelve possible conformational modes of DNA duplexes and four pair-wise correlations among them to positive charge (hole) motion through these biopolymers has been systematically analysed in regular homogeneous B-DNA trimers and tetramers of adenosine–thymidine (AT) and guanosine–cytidine (GC) Watson–Crick pairs using PM3 semiempirical quantum chemistry. Of these only five modes have been found to be most strongly coupled to the electron motion in DNA, namely stretching of H-bonding both in AT and GC, correlated Buckle–Rise and Stagger–Tilt motions in GC and correlated Shear–Twist motion in AT. The parameters for the corresponding polaronic Hamiltonians have been estimated. The nature of these DNA polarons is discussed taking into account the relevant experimental results currently available.     

A novel image encryption method based on total shuffling scheme

In this paper, a novel image encryption method based on skew tent chaotic map and permutation-diffusion architecture is proposed. In the proposed method, the P-box is chosen as the same size of plain-image, which shuffles the positions of pixels totally. The keystream generated by skew tent chaotic map is related to the plain-image. Statistical analysis, information entropy analysis, and sensitivity analysis to plaintext and key on the proposed scheme are provided in this paper. It can be seen that this algorithm is efficient and reliable, with high potential to be adopted for network security and secure communications.     

Coherence and stacking interaction in DNA duplex

It is shown that a chaotic (deterministic) order, rather than a stochastic randomness, controls the energy minima positions of the stacking interactions in the DNA sequences on large-scales. The chaotic order results in a long-range chaotic coherence between the two complimentary DNA-duplex?s strands. A competition between this broad-band chaotic coherence and the resonance coherence produced by genetic code has been briefly discussed.     

From DNA sequence analysis to modeling replication in the human genome

We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward jumps, with a linear decreasing profile in between two successive jumps. We present a model of replication with well positioned replication origins and random terminations that accounts for the observed characteristic serrated skew profiles. We succeed in identifying 287 pairs of putative adjacent replication origins with an origin spacing approximately 1-2 Mbp that are likely to correspond to replication foci observed in interphase nuclei and recognized as stable structures that persist throughout subsequent cell generations.     

An Insight into the Helicase Functioning Through the Hydrogen Isotope Effects

The replacement of hydrogen atoms by deuterium in hydrogen bonds of base pairs AT and GC decreases the rate of unwinding DNA by more than 30% per each unzipped base pair. In active helicases this isotope effect refers to the ratio of the rate constants for unzipping closed base pairs in protiated and deuterated DNA. In passive helicases the effect is controlled by ratio of equilibrium constants for opening and closing base pairs in protiated and deuterated DNA. Hydrogen/deuterium isotope effects on the unwindening of double strand DNA seems to explain, at least partly, biological and pharmacological effects of heavy water on living organisms and may be used as a means to explore new facets of the helicase functioning.     

More complex DNA structures

Fibrous polynucleotide duplexes are very polymorphic. Detailed x-ray analysis of the D forms of poly d(AT) ·poly d(AT) and poly d(IC) ·poly d(IC) and of the B form of poly d(GC) ·poly d(GC) show that 5′RpY3′ dinucleoside monophosphates in these molecules have either t,t or t,g conformations at C3′–03′, 03′-P which lead to similar orientations of phosphate groups. On the other hand, 5′YpR3′ fragments commonly have g,t conformations and hence a markedly different orientation of the phosphate group. Studies of the more complex structures of the C form of poly d(ACC) ·poly d(GGT) and of a pleiomeric D form of poly d(AT) ·poly d(AT) where the repeated structural motifs are hexanucleotides reveal further details of the surface “wrinkles” on DNA. In the case of the H form of poly d(A) ·poly d(T), the sugar rings in each strand are puckered differently-C2′-endo in poly d(T) and C3′-endo in poly d(A). Such heteromerous duplexes have unusually pronounced directional properties. Similar structure ma be present in some DNA-RNA hybrids. These surface feature might enable regulatory proteins and enzymes to recognize their host DNA sequences more easily in the blinding process.     

The isolated critical value phenomenon in local－global riddling bifurcation

A chaotic synchronized system of two coupled skew tent maps is discussed in this paper. The locally and globally riddled basins of the chaotic synchronized attractor are studied. It is found that there is a novel phenomenon in the local－global riddling bifurcation of the attractive basin of the chaotic synchronized attractor in some specific coupling intervals. The coupling parameter corresponding to the locally riddled basin has a single value which is embedded in the coupling parameter interval corresponding to the globally riddled basin, just like a breakpoint. Also, there is no relation between this phenomenon and the form of the chaotic synchronized attractor. This phenomenon is found analytically. We also try to explain it in a physical sense. It may be that the chaotic synchronized attractor is in the critical state, as it is infinitely close to the boundary of its attractive basin. We conjecture that this isolated critical value phenomenon will be common in a system with a chaotic attractor in the critical state, in spite of the system being discrete or differential.     

A novel chaos-based image encryption algorithm using DNA sequence operations

An image encryption algorithm based on chaotic system and deoxyribonucleic acid (DNA) sequence operations is proposed in this paper. First, the plain image is encoded into a DNA matrix, and then a new wave-based permutation scheme is performed on it. The chaotic sequences produced by 2D Logistic chaotic map are employed for row circular permutation (RCP) and column circular permutation (CCP). Initial values and parameters of the chaotic system are calculated by the SHA 256 hash of the plain image and the given values. Then, a row-by-row image diffusion method at DNA level is applied. A key matrix generated from the chaotic map is used to fuse the confused DNA matrix; also the initial values and system parameters of the chaotic system are renewed by the hamming distance of the plain image. Finally, after decoding the diffused DNA matrix, we obtain the cipher image. The DNA encoding/decoding rules of the plain image and the key matrix are determined by the plain image. Experimental results and security analyses both confirm that the proposed algorithm has not only an excellent encryption result but also resists various typical attacks.     

Length and statistical weight of bubbles in DNA melting

We present measurements of the length of the bubble versus temperature in the melting transition of DNA oligomers. The sequences are clamped at the ends of GC pairs (strong binding), and have AT rich (weaker binding) middle regions of variable length B relative to the molecule size. We use a quenching technique to trap intermediate states. We find that the average relative bubble size grows from zero for increasing temperature, but reaches a plateau at a length of order B, producing a discontinuous transition with finite bubble size. The statistical weight of the bubble states decreases as B is reduced, the transition becoming more cooperative.     

混沌伪随机序列的谱熵复杂性分析

为了准确分析混沌伪随机序列的结构复杂性,采用谱熵算法对Logistic映射、Gaussian映射和TD-ERCS系统产生的混沌伪随机序列复杂度进行了分析.谱熵算法具有参数少、对序列长度N(惟一参数)和伪随机进制数K鲁棒性好的特点.采用窗口滑动法分析了混沌伪随机序列的复杂度演变特性,计算了离散混沌系统不同初值和不同系统参数条件下的复杂度.研究表明,谱熵算法能有效地分析混沌伪随机序列的结构复杂度;在这三个混沌系统中,TD-ERCS系统为广域高复杂度混沌系统,复杂度性能最好;不同窗口和不同初值条件下的混沌系统复杂度在较小范围内波动.为混沌序列在信息安全中的应用提供了理论和实验依据.     

Investigation of thionin-DNA interaction by satellite hole spectroscopy

The interactions of the two tautomers of thionin dye with DNA have been investigated by using satellite hole burning spectroscopy. Similar features in the absorption and satellite hole spectra of thionin in the presence of calf thymus (CT) DNA and polynucleotides [d(GC)₆]₂ (GC) suggested that thionin preferentially binds to GC rather than polynucleotides [d(AT)₆]₂ (AT). Different binding effects of the two tautomers to DNA could be observed. While the imino form fully intercalates into the DNA base pairs, the amino form is only partially intercalated. In addition, a broad hole associated with an antihole appeared in the presence of DNA, particularly in GC base pairs. The coincidence of the antihole with the absorption band of the amino form showed that the amino form is the photoproduct of the imino form. An increase in intensity of the broad hole and its antihole and the loss of nonresonant hole intensity upon interaction with CT DNA could be described by rapid ground state recovery resulting from fast charge transfer between the intercalated thionin and a guanine base quenching the internal conversion.     

贯流风机内动静干扰发声机理的研究

本文通过实验与数值计算方法,探讨了贯流风机内动静干扰的现象及其诱导的噪声特性.文中给出了贯流风机流场的三维大涡数值计算结果,分析了声源场的特性,指出贯流风机流场具有较强的随机性。分别对直叶轮及斜叶轮气动性能及远场噪声进行实验测量,讨论了两种叶轮的优劣性。使用微压传感器对蜗舌出口处边界层压力脉动进行采集,给出了此处边界层辐射噪声源的相关分析.通过对实验结果分析指出声源脉动的宽频特性是被测风机噪声呈现宽频的主要原因。     

CAPS satellite spread spectrum communication blind multi-user detecting system based on chaotic sequences

Multiple Path Interference (MPI) and Multiple Access Interference (MAI) are important factors that affect the performance of Chinese Area Positioning System (CAPS). These problems can be solved by using spreading sequences with ideal properties and multi-user detectors. Chaotic sequences based on Chebyshev map are studied and the satellite communication system model is set up to investigate the application of chaotic sequences for CAPS in this paper. Simulation results show that chaotic sequences have desirable correlation properties and it is easy to generate a large number of chaotic sequences with good security. It has great practical value to apply chaotic sequences to CAPS together with multi-user detecting technology and the system performance can be improved greatly. Supported by the National Basic Research Program of China (Grant No. 2007CB815500) and the National High Technology Research and Development Program of China (Grant No. 2007AA12z343)     

A new pseudorandom number generator based on a complex number chaotic equation

In recent years, various chaotic equation based pseudorandom number generators have been proposed. However, the chaotic equations are all defined in the real number field. In this paper, an equation is proposed and proved to be chaotic in the imaginary axis. And a pseudorandom number generator is constructed based on the chaotic equation. The alteration of the definitional domain of the chaotic equation from the real number field to the complex one provides a new approach to the construction of chaotic equations, and a new method to generate pseudorandom number sequences accordingly. Both theoretical analysis and experimental results show that the sequences generated by the proposed pseudorandom number generator possess many good properties.     

A new pseudorandom number generator based on complex number chaotic equation

In recent years, various chaotic equation based pseudorandom number generators have been proposed, however, the chaotic equations are all defined in the real number field. In this paper, an equation is proposed and proved to be chaotic in the imaginary axis. And a pseudorandom number generator is constructed based on the chaotic equation. The alteration of the definitional domain of the chaotic equation from the real number field to the complex one provides a new approach to the construction of chaotic equations, and a new method to generate pseudorandom number sequences accordingly. Both theoretical analysis and experimental results show that the sequences generated by the proposed pseudorandom number generator possess many good properties.     

Optimizing head/media electrical characterization in the presence of skew at high track density

The skew angle causes a discrepancy in determining the reader-to-writer offset (RWO) when using different periodical patterns in track profile tests. It also separates the peak overwrite (OW) from the peak high frequency amplitude HFA, (1 T periodical pattern) on corresponding track profiles. Furthermore, higher track density and larger skew angle exacerbate the skew effect and induce more RWO error, thus impacting the parametric performance optimization. Simulation studies are used to interpret the skew effect on the RWO determination and OW cross-track characteristics. Based on experimental investigations and simulation analyses, using the HFA, track profile for deriving the optimal RWO is proposed for spin-stand tests. Actual parametric characterization has proven that the optimal RWO minimized the skew effect and the RWO error, thus improving the parametric performance and reducing the test variation. The method is beneficial and necessary for the high track density characterization.     

基于新的五维多环多翼超混沌系统的图像加密算法

本文提出了一种基于新的五维多环多翼超混沌系统的数字图像加密方法.首先,将明文图像矩阵和五条混沌序列分别通过QR分解法分解成一个正交矩阵和一个上三角矩阵,将混沌系统产生的五条混沌序列分别通过LU分解法分解成一个上三角矩阵和一个下三角矩阵,分别将两个上三角矩阵和一个下三角矩阵相加,得到五个离散后的混沌序列;其次,将明文图像矩阵分解出来的正交矩阵与五个混沌序列分解出来的五个正交矩阵相乘,同时把明文图像矩阵分解出来的上三角矩阵中的元素通过混沌序列进行位置乱,再将操作后的两个矩阵相乘;最后,将相乘后的矩阵通过混沌序列进行比特位位置乱,再用混沌序列与其进行按位“异或”运算,得到最终加密图像.理论分析和仿真实验结果表明该算法的密钥空间远大于10^200,密钥敏感性强,能够有效地抵御统计分析和灰度值分析的攻击,对数字图像的加密具有很好的加密效果.     

级联混沌及其动力学特性研究

初值敏感性是混沌的本质,混沌的随机性来源于其对初始条件的高度敏感性,而Lyapunov指数又是这种初值敏感性的一种度量.本文的研究发现,混沌系统的级联可明显提高级联混沌的Lyapunov指数,改善其动力学特性.因此,本文研究了混沌系统的级联和级联混沌对动力学特性的影响,提出了混沌系统级联的定义及条件,从理论上证明了级联混沌的Lyapunov指数为各个级联子系统Lyapunov指数之和;适当的级联可增加系统参数、扩展混沌映射和满映射的参数区间,由此可提高混沌映射的初值敏感性和混沌伪随机序列的安全性.以Logistic映射、Cubic映射和Tent映射为例,研究了Logistic-Logistic级联、Logistic-Cubic级联和Logistic-Tent级联的动力学特性,验证了级联混沌动力学性能的改善.级联混沌可作为伪随机数发生器的随机信号源,用以产生初值敏感性更高、安全性更好的伪随机序列.     

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.