Entropy and Fractal Dimension Study of the TDP-43 Protein Low Complexity Domain Sequence in ALS Disease Severity and SARS-CoV-2 Gene Sequences in Virulence Variability

The low complexity domain (LCD) sequence has been defined in terms of entropy using a 12 amino acid sliding window along a protein sequence in the study of disease-related genes. The amyotrophic lateral sclerosis (ALS)-related TDP-43 protein sequence with intra-LCD structural information based on cryo-EM data was published recently. An application of entropy and Higuchi fractal dimension calculations was described using the Znf521 and HAR1 sequences. A computational analysis of the intra-LCD sequence entropy and Higuchi fractal dimension values at the amino acid level and at the ATCG nucleotide level were conducted without the sliding window requirement. The computational results were consistent in predicting the intermediate entropy/fractal dimension value produced when two subsequences at two different entropy/fractal dimension values were combined. The computational method without the application of a sliding-window was extended to an analysis of the recently reported virulent genes—Orf6, Nsp6, and Orf7a—in SARS-CoV-2. The relationship between the virulence functionality and entropy values was found to have correlation coefficients between 0.84 and 0.99, using a 5% uncertainty on the cell viability data. The analysis found that the most virulent Orf6 gene sequence had the lowest nucleotide entropy and the highest protein fractal dimension, in line with extreme value theory. The Orf6 codon usage bias in relation to vaccine design was discussed.     

Rescaled Range and Transition Matrix Analysis of DNA Sequences

We treat some fractal and statistical features of the DNA sequences. First, a fractal record model of DNA sequence is proposed by mapping,DNA sequences to integer sequences, followed by the R/S analysis of the model and computation of the Hurst exponents. Second, we consider the transition between the four kinds of bases within DNA. The transition matrix analysis of DNA sequences shows that some measures of complexity based on transition proportion matrices are of interest.     

KDP晶体单点金刚石车削表面形貌分形分析

 分别使用2维和3维分形方法对单点金刚石车削加工的KDP晶体表面形貌进行了分析，并对表面的3维分形维数和3维粗糙度表征参数进行了比较，分析了二者对表面形貌表征的差异。使用2维轮廓分形方法计算了KDP晶体表面圆周各方向上的分形维数。通过分析得出：3维分形维数与表面粗糙度值成反比关系；使用单点金刚石车削方法加工KDP晶体会形成各向异性特征明显的已加工表面，在一定程度上容易形成小尺度波纹；已加工表面是否具有明显的小尺度波纹特征与表面粗糙度值并无直接关系，但与其表面轮廓分形状态分布密切相关；KDP晶体表面2维功率谱密度与其分形状态具有相近的方向性特征。     

Statistical Dynamics of Clustering in the Genome Structure

Clustering and long-range correlations in the nucleotide sequences of different categories of organisms are discussed. Clustering, mostly observed in higher eucaryotes, can be found at different length scales in DNA and Central Limit Theorems are used as links between these length scales. Several dynamical, statistical, mean-field models are proposed based on biologically motivated dynamical mechanisms and they successfully reproduce both the short range behavior observed in coding DNA and the long range, out-of-equilibrium features of non-coding DNA. Such dynamical mechanisms include aggregation of oligonucleotides, influx and DNA length reduction schemes, transpositions, and fusions of large DNA macromolecules. Fractality can be inferred from the short and long range correlations observed in the sequence structure of higher eucaryotes, where the non-coding part is relatively extended. In these organisms the DNA coding/non-coding alternation has the characteristics of finite size, fractal, random sets.     

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.     

Laplacian growth and diffusion limited aggregation: different universality classes

It had been conjectured that diffusion limited aggregates and Laplacian growth patterns (with small surface tension) are in the same universality class. Using iterated conformal maps we construct a one-parameter family of fractal growth patterns with a continuously varying fractal dimension. This family can be used to bound the dimension of Laplacian growth patterns from below. The bound value is higher than the dimension of diffusion limited aggregates, showing that the two problems belong to two different universality classes.     

Effects of Different Connectivity Topologies in Small World Networks on EEG-Like Activities

Based on our previously pulse-coupled integrate-and-fire neuron model in small world networks, we investigate the effects of different connectivity topologies on complex behavior of electroencephalographic-like signals produced by this model. We show that several times series analysis methods that are often used for analyzing complex behavior of electroencephalographic-like signals, such as reconstruction of the phase space, correlation dimension, fractal dimension, and the Hurst exponent within the rescaled range analysis (R/S). We find that the different connectivity topologies lead to different dynamical behaviors in models of integrate-and-fire neurons.     

Mapping physical problems on fractals onto boundary value problems within continuum framework

In this Letter, we emphasize that methods of fractal homogenization should take into account a loop structure of the fractal, as well as its connectivity and geodesic metric. The fractal attributes can be quantified by a set of dimension numbers. Accordingly, physical problems on fractals can be mapped onto the boundary values problems in the fractional-dimensional space with metric induced by the fractal topology. The solutions of these problems represent analytical envelopes of non-analytical functions defined on the fractal. Some examples are briefly discussed. The interplay between effects of fractal connectivity, loop structure, and mass distributions on electromagnetic fields in fractal media is highlighted. The effects of fractal connectivity, geodesic metric, and loop structure are outlined.     

Fractal Aggregation Near the Threshold

In this papel, we present two fractal aggregation models, line pattern seed model (model 1) and point pattern seed model (model 2), which are particle-cluster models. Using the current models, we investigate the critical transition in fractal aggregation processes in two dimensions, and suggest a method for finding the critical transition point. The computer simulation results show that the critical concentration is P_ca=0.69±0.02 for model 1 and P_ca=0.72±0.01 for model 2, critical fractal dimension. D_c= 1.71±0.06 for model 1 and D_c=1.66±0.07 for model 2, which are in good agreement with those of DLA model (D=5/3) and experimental data. The results also show that the critical transition point in two dimensions seems to be inilependent of the size of lattices and the initial seed patterns. The results seem to belong to the same universality class.     

一种基于超复数系的数字全息图像生成方法

提出了一种基于超复数系的数字全息图像生成方法，通过定义超复数系，由此构成n维向量空间，然后采用分形迭代方法在n维向量空间中选择不同截面来绘制分形图像，因而能够在高维空间生成分形数字图像序列，并能够制作出具有动态效果和美感的激光全息图。由于分形数字全息图像生成具有较好的参数可控制性和不可逆转性，全盛的防伪标专难以仿制，在激光全息防伪领域有着良好的应用前景。     

Zipf’s law for fractal voids and a new void-finder

Voids are a prominent feature of fractal point distributions but there is no precise definition of what is a void (except in one dimension). Here we propose a definition of voids that uses methods of discrete stochastic geometry, in particular, Delaunay and Voronoi tessellations, and we construct a new algorithm to search for voids in a point set. We find and rank-order the voids of suitable examples of fractal point sets in one and two dimensions to test whether Zipf’s power-law holds. We conclude affirmatively and, furthermore, that the rank-ordering of voids conveys similar information to the number-radius function, as regards the scaling regime and the transition to homogeneity. So it is an alternative tool in the analysis of fractal point distributions with crossover to homogeneity and, in particular, of the distribution of galaxies.     

太阳高纬和低纬活动现象的混沌与分形特征

为了研究太阳高纬度和低纬度活动现象在南北半球的混沌与分形特征, 结合递归分析方法与Grassberger-Procaccia算法两种技术对1952年2月至1998年6月的极区光斑和黑子数目两种太阳磁活动指标进行了详细分析和比较. 主要结论如下: 1)由于太阳活动现象与磁场的时空演化密切相关, 导致太阳活动在南半球和北半球的混沌与分形特征具有不对称性, 太阳高纬度和低纬度活动现象的混沌与分形特征具有差异性; 2)太阳高纬度活动现象比低纬度活动现象具有更强的混沌程度和更复杂的分形结构, 其中太阳高纬度活动现象在北半球具有最强的混沌程度和最复杂的分形结构.     

An Extended Correlation Dimension of Complex Networks

Fractal and self-similarity are important characteristics of complex networks. The correlation dimension is one of the measures implemented to characterize the fractal nature of unweighted structures, but it has not been extended to weighted networks. In this paper, the correlation dimension is extended to the weighted networks. The proposed method uses edge-weights accumulation to obtain scale distances. It can be used not only for weighted networks but also for unweighted networks. We selected six weighted networks, including two synthetic fractal networks and four real-world networks, to validate it. The results show that the proposed method was effective for the fractal scaling analysis of weighted complex networks. Meanwhile, this method was used to analyze the fractal properties of the Newman–Watts (NW) unweighted small-world networks. Compared with other fractal dimensions, the correlation dimension is more suitable for the quantitative analysis of small-world effects.     

Regularity analysis of an individual-based ecosystem simulation

We analyze the results of a large simulation of an evolving ecosystem to evaluate its complexity. In particular, we are interested to know how close to a stochastic or a deterministic behavior our simulation is. Four methods have been used for this analysis: Higuchi fractal dimension, correlation dimension, largest Lyapunov exponent, and P&H method. Besides, we use a surrogate data test to reach a final decision about analysis. As we expect, our results show that there is a deterministic and chaotic behavior in ecosystem simulation.     

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.     

Fractal landscapes in biological systems: long-range correlations in DNA and interbeat heart intervals

Here we discuss recent advances in applying ideas of fractals and disordered systems to two topics of biological interest, both topics having common the appearance of scale-free phenomena, i.e., correlations that have no characteristic length scale, typically exhibited by physical systems near a critical point and dynamical systems far from equilibrium. (i) DNA nucleotide sequences have traditionally been analyzed using models which incorporate the possibility of short-range nucleotide correlations. We found, instead, a remarkably long-range power law correlation. We found such long-range correlations in intron-containing genes and in non-transcribed regulatory DNA sequences as well as intragenomic DNA, but not in cDNA sequences or intron-less genes. We also found that the myosin heavy chain family gene evolution increases the fractal complexity of the DNA landscapes, consistent with the intron-late hypothesis of gene evolution. (ii) The healthy heartbeat is traditionally thought to be regulated according to the classical principle of homeostasis, whereby physiologic systems operate to reduce variability and achieve an equilibrium-like state. We found, however, that under normal conditions, beat-to-beat fluctuations in heart rate display long-range power law correlations.     

Analysis of fractals with dependent branching by box counting, P-adic coverages, and systems of equations of P-adic coverages

Concept of the dimension of space-time in the general relativity theory and quantum theory is discussed. It is emphasized that the dimension of a discrete space can be defined based on the Hausdorff measure. The noninteger dimension is a typical characteristic of a fractal. The process of hadron formation in interactions between high-energy particles and nuclei is supposed to possess fractal properties. The following methods for analyzing fractals are considered: box counting (BC), method of P-adic coverages (PaC), and method of systems of equations of P-adic coverages (SePaC), for determining the fractal dimension. A comparative analysis of fractals with dependent branching is performed using these methods. We determine the optimum values of parameters permitting one to determine the fractal dimension D _F , number of levels N _lev, and the fractal structure with maximal efficiency. It is noted that the SePaC method has advantages in analyzing fractals with dependent branching.     

高光谱的矿区植物异常信息提取

白茎绢蒿是一种广泛分布于新疆富蕴县各个矿区的一种植物。在矿区进行矿产勘查时，由于植物等障碍信息的存在，传统的勘查方法已经难以发挥作用，急需一些新方法、新思路。遥感植物地球化学方法可以巧妙地利用植物这一天然的信息源，把植物从障碍信息转换为了有用信息。帮助人们快速、经济地获取植物屏障下的矿产有用信息。由于其具有大面积、快速、无损性等优点，受到了越来越多学者的关注，成为当下的研究热点。近些年虽然有学者综合考虑“吸收系数”和“衬度系数”这两个指标，证明了白茎绢蒿是对隐伏矿床的勘查具有较好指示性作用的植物，生在在矿床上部的植物可以较好的吸收土壤中的成矿元素，在其体内形成地球化学异常，相比于其他植物异常信息更加清晰可见。但是目前没有人研究是否可以从光谱的角度来发现白茎绢蒿体内的地球化学异常，进而为隐伏矿床的勘查提供参考。因此，本研究首次尝试从白茎绢蒿的光谱信息中寻找出与地球化学异常密切相关的特征波段或者特征值, 然后构建基于植物光谱的隐伏矿床预测模型。采取的方法是首先利用ASD FieldSpec3 型光谱仪分别对生长在矿床上部和背景区的植物进行光谱测定，然后从原始光谱、一阶导数光谱、二阶导数光谱、一阶导数的分形维数、二阶导数的分形维数五个层面对生长在这两个区域的植物光谱进行对比分析，最终优选出了10个差异显著的特征波段，分别为：R′₈₂₄，R′₈₃₄，R′_{1 533}，R′_{1 573}，R′_{1 633}，R′_{1 643}，R″_{1 284}，R″_{1 703}，一阶导数的分形维数以及二阶导数的分形维数。这些特征波段可以作为植物地区寻找隐伏矿床的植物地球化学标志。以优选出的10个特征波段作为输入参数，分别用随机森林 (RF)和偏最小二乘-支持向量机(PLS-SVM)构建了基于植物光谱数据的隐伏矿床预测模型。结果表明：(1)两种模型均可以取得较好的效果，但是相比于随机森林模型，偏最小二乘-支持向量机模型具有更好的鲁棒性，泛化能力也更强；(2)利用植物的光谱异常寻找隐伏矿床具有较大的潜力，因为相比于传统方法，更加简单、快速。课题组已经利用动力三角翼和HySpex成像高光谱传感器构建了“超低空探测平台”，可以实现对地“亚米级”的观测。但是如何有效的解决“空间尺度”和“光谱尺度”问题，如何把地面试验场建立的模型更好的应用于超低空探测平台，实现研究区大面积地、快速地植物异常信息提取将是我们下一步的研究重点。     

Random coil phosphorus chemical shift of deoxyribonucleic acids

Random coil phosphorus chemical shift has been studied using 16 17-nucleotide DNA sequences. Due to the presence of residual base stacking in these sequences, the temperature and sequence effects were investigated at 50 and 55 degrees C. The phosphorus chemical shifts of random coil DNA sequences have been found to be independent of temperature. Sequence effect analysis shows that the phosphorus chemical shift of a nucleotide in a random coil DNA sequence depends on both its 5'- and 3'-nearest neighbors. A trimer model has been used to establish the random coil 31P chemical shift prediction protocol which shows an accuracy of 0.02 ppm.