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.     

Chaos game representation of functional protein sequences, and simulation and multifractal analysis of induced measures

Investigating the biological function of proteins is a key aspect of protein studies. Bioinformatic methods become important for studying the biological function of proteins. In this paper, we first give the chaos game representation (CGR) of randomly-linked functional protein sequences, then propose the use of the recurrent iterated function systems (RIFS) in fractal theory to simulate the measure based on their chaos game representations. This method helps to extract some features of functional protein sequences, and furthermore the biological functions of these proteins. Then multifractal analysis of the measures based on the CGRs of randomly-linked functional protein sequences are performed. We find that the CGRs have clear fractal patterns. The numerical results show that the RIFS can simulate the measure based on the CGR very well. The relative standard error and the estimated probability matrix in the RIFS do not depend on the order to link the functional protein sequences. The estimated probability matrices in the RIFS with different biological functions are evidently different. Hence the estimated probability matrices in the RIFS can be used to characterise the difference among linked functional protein sequences with different biological functions. From the values of the D_q curves, one sees that these functional protein sequences are not completely random. The D_q of all linked functional proteins studied are multifractal-like and sufficiently smooth for the C_q (analogous to specific heat) curves to be meaningful. Furthermore, the D_q curves of the measure \mu based on their CGRs for different orders to link the functional protein sequences are almost identical if q\geq 0. Finally, the C_q curves of all linked functional proteins resemble a classical phase transition at a critical point.     

甲型流感病毒DNA序列的长记忆ARFIMA模型

流感病毒分为三类:甲型(A型),乙型(B型),丙型(C型).在这三种类型中甲型(A型)流感病毒是最致命的流感病毒,对人类引起了严重疾病.本文对甲型流感病毒DNA序列建立了一种新的时间序列模型,即CGR(Chaos Game Representation)弧度序列.利用CGR坐标将甲流病毒DNA序列转换成CGR弧度序列,且引入长记忆ARFIMA模型去拟合此类序列,发现随机找来的10条H1N1序列,10条H3N2序列都具有长相关性且拟合很好,并且还发现这两种序列可以尝试用不同的ARFIMA模型去识别,其中H1 关键词： 甲型流感 时间序列模型 CGR (p')" href="#">ARFIMA(p d 模型')" href="#">q)模型     

Wavelet-based multifractal analysis of DNA sequences by using chaos-game representation

Chaos game representation (CGR) is proposed as a scale-independent representation for DNA sequences and provides information about the statistical distribution of oligonucleotides in a DNA sequence. CGR images of DNA sequences represent some kinds of fractal patterns, but the common multifractal analysis based on the box counting method cannot deal with CGR images perfectly. Here, the wavelet transform modulus maxima (WTMM) method is applied to the multifractal analysis of CGR images. The results show that the scale-invariance range of CGR edge images can be extended to three orders of magnitude, and complete singularity spectra can be calculated. Spectrum parameters such as the singularity spectrum span are extracted to describe the statistical character of DNA sequences. Compared with the singularity spectrum span, exon sequences with a minimal spectrum span have the most uniform fractal structure. Also, the singularity spectrum parameters are related to oligonucleotide length, sequence component and species, thereby providing a method of studying the length polymorphism of repeat oligonucleotides.     

Early-warning signals for an outbreak of the influenza pandemic

Over the course of human history, influenza pandemics have been seen as major disasters, so studies on the influenza virus have become an important issue for many experts and scholars. Comprehensive research has been performed over the years on the biological properties, chemical characteristics, external environmental factors and other aspects of the virus, and some results have been achieved. Based on the chaos game representation walk model, this paper uses the time series analysis method to study the DNA sequences of the influenza virus from 1913 to 2010, and works out the early-warning signals indicator value for the outbreak of an influenza pandemic. The variances in the CGR walk sequences for the pandemic years (or + -1 to 2 years) are significantly higher than those for the adjacent years, while those in the non-pandemic years are usually smaller. In this way we can provide an influenza early-warning mechanism so that people can take precautions and be well prepared prior to a pandemic.     

Complete determination of the transition amplitudes from a comprehensive data analysis of the fusion reactions D(d,p)3H and D(d,n)3He for Ed<500 keV

All relevant low-energy transition amplitudes for the D(d,n)³He and D(d,p)³H reactions were determined from a fit to Legendre expansion coefficients of the available experimental data. A simple barrier penetrability model was used. Quintet S-wave transitions are found to contribute strongly thus obliterating the idea of neutron-lean “polarized” fusion energy production. The D+D interaction radius was determined with good accuracy for both reactions individually. The astrophysical S functions show a small S-wave enhancement and P-wave suppression of the D(d,p)³H branch.     

An adaptive high-dimensional stochastic model representation technique for the solution of stochastic partial differential equations

A computational methodology is developed to address the solution of high-dimensional stochastic problems. It utilizes high-dimensional model representation (HDMR) technique in the stochastic space to represent the model output as a finite hierarchical correlated function expansion in terms of the stochastic inputs starting from lower-order to higher-order component functions. HDMR is efficient at capturing the high-dimensional input–output relationship such that the behavior for many physical systems can be modeled to good accuracy only by the first few lower-order terms. An adaptive version of HDMR is also developed to automatically detect the important dimensions and construct higher-order terms using only the important dimensions. The newly developed adaptive sparse grid collocation (ASGC) method is incorporated into HDMR to solve the resulting sub-problems. By integrating HDMR and ASGC, it is computationally possible to construct a low-dimensional stochastic reduced-order model of the high-dimensional stochastic problem and easily perform various statistic analysis on the output. Several numerical examples involving elementary mathematical functions and fluid mechanics problems are considered to illustrate the proposed method. The cases examined show that the method provides accurate results for stochastic dimensionality as high as 500 even with large-input variability. The efficiency of the proposed method is examined by comparing with Monte Carlo (MC) simulation.     

(n,p)激发函数一种新的半经验计算方法

基于核反应蒸发模型和预平衡激子模型,在一些近似条件下得到了入射能量小于20MeV的(n,p)的激发函数解析半经验表达式,靶核在23≤A≤209的范围内,利用大量(n,p)反应的截面实验数据对可调参数进行了研究,得到了参数对靶核的N和Z以及中子入射能量的依赖关系,对得到的参数做了定性的解释,利用普适参数对(n,p)反应的激发函数做了预言,预言值在其误差范围内与实验数据一致。     

基于(p,γ)-(γ,p)平衡近似的快质子俘获过程模型及其应用

在(p,γ)-(γ,p)平衡近似下,本文建立了简化的快质子俘获(rp)过程模型, 讨论了天体物理条件输入量 (即质子辐照时间、质子数密度及温度) 对rp过程的影响. 结合中国科学院近代物理研究所等时性质谱仪 (IMS) 上的最新实验数据, 本文进而分析了新测的缺中子原子核质量对rp过程的影响; 发现利用新测的⁴¹Ti质量, A=41处的丰度相较之前的计算结果增大了两个数量级, 而计算的相对丰度误差减小了近两个量级. 关键词： 快质子俘获过程 γ)-(γ,p)平衡')" href="#">(p,γ)-(γ,p)平衡 原子核质量 缺中子原子核     

α螺旋蛋白质螺旋链模型的精确解组

文章运用Maple语言程序,在没有假设的条件下,得到了α螺旋蛋白质螺旋链运动模型方程组的行波精确解组,它涵盖了所有的耦合解组与非耦合解组,具有任意性.耦合解组的算例函数及其特性分析,解释了α螺旋蛋白质螺旋链运动模型的行波孤立子解的耦合效应,揭示了增加、稳定和控制蛋白质活性和功能的方向,文章的研究方法,为求解生物大分子螺旋链运动模型的行波精确解组探索了溪径.     

Validity of the two-term Boltzmann approximation employed in the fluid model for high-power microwave breakdown in gas

The electron energy distribution function （EEDF）, predicted by the Boltzmann equation solver BOLSIG＋ based on the two-term approximation, is introduced into the fluid model for simulating the high-power microwave （HPM） breakdown in argon, nitrogen, and air, and its validity is examined by comparing with the results of particle-in-cell Monte Carlo collision （PIC/MCC） simulations as well as the experimental data. Numerical results show that, the breakdown time of the fluid model with the Maxwellian EEDF matches that of the PIC/MCC simulations in nitrogen; however, in argon under high pressures, the results from the Maxwellian EEDF were poor. This is due to an overestimation of the energy tail of the Maxwellian EEDF in argon breakdown. The prediction of the fluid model with the BOLSIG＋ EEDF, however, agrees very well with the PIC/MCC prediction in nitrogen and argon over a wide range of pressures. The accuracy of the fluid model with the BOLSIG＋ EEDF is also verified by the experimental results of the air breakdown.     

On two-point boundary correlations of the gl(1|1) supersymmetric vertex model

The gl(1|1) supersymmetric vertex model with domain wall boundary conditions (DWBC) on an N ×N square lattice is considered. We obtain the reduction formulae for the two-point boundary correlation functions of the model.     

Okamoto model for necrosis and its expansions,CD38-cyclic ADP-ribose signal system for intracellular Ca2+ mobilization and Reg (Regenerating gene protein)-Reg receptor system for cell regeneration

In pancreatic islet cell culture models and animal models, we studied the molecular mechanisms involved in the development of insulin-dependent diabetes. The diabetogenic agents, alloxan and streptozotocin, caused DNA strand breaks, which in turn activated poly(ADP-ribose) polymerase/synthetase (PARP) to deplete NAD⁺, thereby inhibiting islet β-cell functions such as proinsulin synthesis and ultimately leading to β-cell necrosis. Radical scavengers protected against the formation of DNA strand breaks and inhibition of proinsulin synthesis. Inhibitors of PARP prevented the NAD⁺ depletion, inhibition of proinsulin synthesis and β-cell death. These findings led to the proposed unifying concept for β-cell damage and its prevention (the Okamoto model). The model met one proof with PARP knockout animals and was further extended by the discovery of cyclic ADP-ribose as the second messenger for Ca²⁺ mobilization in glucose-induced insulin secretion and by the identification of Reg (Regenerating gene) for β-cell regeneration. Physiological and pathological events found in pancreatic β-cells have been observed in other cells and tissues.     

Searching for a neutral top-Higgs in association with top-quark pairs at an e~+e~- collider in the TC2 model

We investigate the associated production of the neutral top-Higgs h_t⁰ with a pair of top-quarks in the context of the topcolor-assisted technicolor (TC2) model at the future e⁺e^- Linear Colliders (LC) i.e. e⁺e^- → tt h_t⁰. We calculate the production rate and present the distributions of the transverse momenta of top-Higgs and top-quarks. The results show that the total cross section is typically of the order of 1.0-7.5 fb in the energy range between 1000 GeV and 2000 GeV of the LC for the whole top-Higgs mass region of interest. It should be distinctly possible that hundreds or even thousands of h_t⁰ signals can be produced per year at the LC given the luminosity L=500 fb^-1.     

The importance of gold‐electrode‐adjacent stationary high‐field Böer domains for the photoconductivity of CdS

When the electron density decreases stronger than linearly with the electric field in photoconductive CdS due to field quenching, high‐field domains must occur that remain attached to either the cathode or anode in slit electrode geometry with blocking cathodes. These Böer domains¹ are easily seen by their shift in optical absorption due to the Franz‐Keldysh effect and offer unique opportunities to analyze field dependent parameters within the range of constant electron density and electric field, such as the carrier density or mobility as a function of the field, and give information of the light dependent work function. They also provide insight why a 200 Å thick cover layer of CdS on top of a CdTe solar cell increases its efficiency from 8 to 16% . The behavior of these Böer domains escapes conventional current voltage analyses except for their visual observation, while other high‐field domains with their current fluctuations or oscillations are easily observed and are the subjects of thousands of publications and many books. In this review we will exclude detailed discussion of dynamic domains, but include some new specifics that help to understand the mechanisms of the Böer domains and their applications. Only properties at low optical excitation intensities are discussed that exclude Joules heating. Within the p‐type regime of the anode‐adjacent domain extremely steep electronic quenching signal becomes visible that could signalize an intrinsic donor level slightly above the middle of the band gap that may be responsible for not allowing CdS to ever become p‐type by doping.