Fractal nature of protein surface roughness: a note on quantification of change of surface roughness in active sites,before and after binding

Year 2010 marked the 25th year since we came to know that roughness of a protein surface has fractal symmetry. Ever since the publication of Lewis and Rees' paper, hundreds of works from a spectrum of perspectives have established that fractal dimension (FD) can be considered as a reliable marker that describes roughness of protein surface objectively. In this article, we introduce readers to the fundamentals of fractals and present categorical biophysical and geometrical reasons as to why FD‐based constructs can describe protein surface roughness more accurately. We then review the commonality (and the lack of it) between numerous approaches that have attempted to investigate protein surface with fractal measures, before exploring the patterns in the results that they have produced. Apart from presenting the genealogy of approaches and results, we present an analysis that quantifies the difference in surface roughness in stretches of protein surface containing the active site, before and after binding to ligands, to underline the utility of FD‐based measures further. It has been found that surface stretches containing the active site, in general, undergo a significant increment in its roughness after binding. After presenting the entire repertoire of FD‐based surface roughness studies, we talk about two yet‐unexplored problems where application of FD‐based techniques can help in deciphering underlying patterns of surface interactions. Finally, we list the limitations of FD‐based constructs and put down several precautions that one must take while working with them. Copyright © 2013 John Wiley & Sons, Ltd.     

Nonlinear fractal dynamics of human colonic pressure activity based upon the box-counting method

The computational fractal dimension of human colonic pressure activity acquired by a telemetric capsule robot under normal physiological conditions was studied using the box-counting method. The fractal dimension is a numeric value that quantifies to measure how rough the signal is from nonlinear dynamics, rather than its amplitude or other linear statistical features. The colonic pressure activities from the healthy subject during three typical periods were analysed. The results showed that the activity might be fractal with a non-integer fractal dimension after it being integrated over time using the cumsum method, which was never revealed before. Moreover, the activity (after it being integrated) acquired soon after wakening up was the roughest (also the most complex one) with the largest fractal dimension, closely followed by that acquired during sleep with that acquired long time after awakening up (in the daytime) ranking third with the smallest fractal dimension. Fractal estimation might provide a new method to learn the nonlinear dynamics of human gastrointestinal pressure recordings.     

白音华矿区土壤重金属含量的空间异质性

为探讨开矿对白音华矿区土壤重金属空间分布的影响, 本研究以内蒙古西乌珠穆沁旗白音华煤矿区周边土壤为对象,分析了距离矿区8 km内的重金属Cu、Cr、Pb和Mn含量的空间异质性。结果表明: 土壤重金属Cu、Cr、Pb和Mn的平均含量分别为12.7、32.6、29.9和201.3 mg·kg^-1,其变异系数分别为26.8%、33.9%、27.1%和45.7%。采用半方差函数进行模型拟合, Cu、Cr、Pb和Mn空间分布分别符合高斯模型、高斯模型、高斯模型和线性模型。对其空间分布格局分析发现,Mn、Cr 和 Cu的空间自相关水平较高,主要受结构性因素影响,受随机性因素影响很小,Pb的空间相关性水平适中,同时受结构性因素和随机性因素影响。分形维数分析表明,4种土壤重金属含量空间分布简单,结合2D及3D图看,4种土壤重金属均呈现梯度分布,随着距离增加其含量逐步降低,Cu和Mn主要集中分布在距离矿区1.5 km内,Cr与Pb则分别集中分布在距离矿区2.0与3.0 km内。     

不同尺度下荒漠草原建群种短花针茅的空间分布对载畜率的响应

为探讨不同尺度下短花针茅种群密度空间分布对载畜率的响应特点及差异,本研究以内蒙古四子王旗短花针茅荒漠草原建群物种短花针茅为对象,分析了不同尺度(1 m×1 m小尺度和5 m×10 m中尺度)下对照、轻度放牧、中度放牧和重度放牧4种处理短花针茅种群的空间异质性。结果表明: 与小尺度相比,中尺度的对照与轻度放牧下短花针茅种群密度显著降低。在2种尺度下,与对照相比,放牧使得短花针茅种群密度显著增加。通过半方差函数进行模型拟合, 小尺度下,对照、轻度放牧、中度放牧及重度放牧样地短花针茅种群分布分别符合线性、指数、指数和指数模型,中尺度下分别为高斯、指数、高斯和指数模型。不同尺度和放牧强度下短花针茅种群空间结构发生改变,小尺度下,对照样地短花针茅分布格局较简单、空间结构较好;而重度放牧样地短花针茅分布格局较复杂、空间结构较差;中尺度下,重度放牧样地短花针茅分布格局较简单、空间结构较好,而中度放牧样地短花针茅分布格局较复杂、空间结构较差。中、小尺度下,中度和重度放牧使得短花针茅种群空间异质性降低且分布更为均匀;此外,对照、中度和重度放牧下中、小尺度短花针茅种群空间分布趋势基本一致,而轻度放牧则有所不同。     

分形理论及其在土壤空间变异研究中的应用

土壤具有不同程度的空间变异性,土壤空间变异研究对于土壤管理有重要意义.本文简要综述了分形理论及其在土壤空间变异研究中的应用,重点讨论了利用矩方法计算土壤属性分形维,多重分形分析土壤空间变异性及基于多重分形谱参数的土壤属性尺度转换.早期研究验证了分形理论在分析土壤空间变异中的有效性和应用潜力,国内外近期研究则报道了利用分形及多重分形理论分析土壤空间变异的最新进展.分形理论可以成为量化土壤属性空间变异性及尺度转换的重要工具.     

Computer Simulation of Vapor-Liquid Phase Separation

Abstract

A late-time growth law of domains undergoing vapor-liquid phase separation is studied for two- and three-dimensional Lennard-Jones fluids by molecular dynamics simulations. The characteristic domain size shows a power law growth in a late stage with the growth exponent of ½ for both two- and three-dimensional fluids. This study concerns also the relationship between statistical properties of domain patterns and temperatures. The asymptotic form factor of each system is obtained using scaling and the asymptotic tail of the form factor is analyzed. This tail is related to the domain-wall structure. At low system temperatures, the form factor satisfies Porod's law; the asymptotic tail decreases as S(k) ～ k ^{?(D+ 1)} where D is the system dimensionality. However, it is found that the decay of the asymptotic tail becomes slower than that of the Porod tail at higher temperatures in both two- and three-dimensional systems. This indicates that the dimension of the domain wall is fractal and increases with increasing system temperature.     

A Novel Reaction of Dehydroaltenusin with Diazomethane

Several fluorine- and bromine-containing BHC analogs having the γ-configuration were synthesized.