Self-Interactions of Strands and Sheets

Physical strands or sheets that can be modelled as curves or surfaces embedded in three dimensions are ubiquitous in nature, and are of fundamental importance in mathematics, physics, biology, and engineering. Often the physical interpretation dictates that self-avoidance should be enforced in the continuum model, i.e., finite energy configurations should not self-intersect. Current continuum models with self-avoidance frequently employ pairwise repulsive potentials, which are of necessity singular. Moreover the potentials do not have an intrinsic length scale appropriate for modelling the finite thickness of the physical systems. Here we develop a framework for modelling self-avoiding strands and sheets which avoids singularities, and which provides a way to introduce a thickness length scale. In our approach pairwise interaction potentials are replaced by many-body potentials involving three or more points, and the radii of certain associated circles or spheres. Self-interaction energies based on these many-body potentials can be used to describe the statistical mechanics of self-interacting strands and sheets of finite thickness.     

Thinking and Turing's test

The questions raised by A. M. Turing in his paper on thought and machines are discussed. Human thought is considered in turn as a concept of normal language usage, as a basic concept of psychology, and as the basis of intellectual activity. It is concluded that neither of these notions of thought identifies something specific that a human being can or cannot do. The imitation game proposed by Turing for deciding whether a machine can think is found to result from an arbitrary empoverishment of the channel of communication between the interrogator and the item under investigation. Turing's notions of thinking are shown to lead to logical difficulties. An alternative view of consciousness, that would place it beyond the reach of any finite test, is finally discussed.     

基于几何不变量的蛋白质三维分子结构比对

为了解决蛋白质三维结构比对需要处理大量的旋转、平移变换，直接用动态规划将变得十分繁琐这一问题，在保留蛋白质空间结构属性特征的基础上，对蛋白质三维数据进行了预先的处理．通过计算蛋白质结构在旋转和平移下的几何不变量，将蛋白质的三维结构坐标变换为具有旋转、平移不变性的一维序列．进一步给出了“距离”以及“相似得分”的定义．在此基础上采用动态规划方法给出了新的蛋白质结构比对算法．对专家分类的蛋白质结构数据库进行测试，结果显示准确、快速．     

Influence of organic modifiers on morphology and crystallization of poly(ϵ‐caprolactone)/synthetic clay intercalated nanocomposites

ε‐caprolactone was polymerized in the presence of neat montmorillonite or organomontmorillonites to obtain a variety of poly(ε‐caprolactone) (PCL)‐based systems loaded with 10 wt % of the silicates. The materials were thoroughly investigated by different X‐ray scattering techniques to determine factors affecting structure of the systems. For one of the nanocomposites it was found that varying the temperature in the range corresponding to crystallization of PCL causes reversible changes in the interlayer distance of the organoclay. Extensive experimental and literature studies on this phenomenon provided clues indicating that this effect might be a result of two‐dimensional ordering of PCL chains inside the galleries of the silicate. Small angle X‐ray scattering and wide angle X‐ray scattering investigation of filaments oriented above melting point of PCL revealed that polymer lamellae were oriented perpendicularly to particles of unmodified silicate, while in PCL/organoclay systems they were found parallel to clay tactoids. Calorimetric and microscopic studies shown that clay particles are effective nucleating agents. In the nanocomposites, PCL crystallized 20‐fold faster than in the neat polymer. The crystallization rate in nanocomposites was also significantly higher than in microcomposite. Further research provided an insight how the presence of the filler affects crystalline fraction and spherulitic structure of the polymer matrix in the investigated systems. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2350–2367, 2007     

现代优化计算方法在蛋白质结构预测中的应用

现代优化计算方法在蛋白质结构预测中占有重要地位.简要地介绍了模拟退火算法,遗传算法,人工神经网络和图论算法在蛋白质结构预测中的应用.对国内外近年来应用这些算法,特别是在蛋白质构象搜索问题中,解决蛋白质结构预测的研究作了回顾,并分析、比较了这几种算法的效果和特点.     

Photoelectron spectroscopic study of Li oxides on Li over-deposited V2O5 thin film surfaces

The Li oxides species formed on Li over-deposited V₂O₅ thin film surfaces have been studied by using X-ray and UV induced photoelectron spectroscopy (XPS and UPS). The photoelectron spectroscopic data show that the Li over-deposited V₂O₅ system itself is not stable. Further chemical decomposition reactions are taken place even under UHV conditions and lead to form Li₂O and Li₂O₂ compounds on the surface. The formation of Li₂O₂ causes to arise an emission line at about 11.3 eV in the valence band spectra.     

Kinetics of proton transfer in a green fluorescent protein: A laser-induced pH jump study

The sub-millisecond protonation dynamics of the chromophore in S65T mutant form of the green fluorescent protein (GFP) was tracked after a rapid pH jump following laser-induced proton release from the caged photolabile compoundo-nitrobenzaldehyde. Following a jump in pH from 8 to 5 (which is achieved within 2 μs), the fluorescence of S65T GFP decreased as a single exponential with a time constant of ∼90 μs. This decay is interpreted as the conversion of the deprotonated fluorescent GFP chromophore to a protonated non-fluorescent species. The protonation kinetics showed dependence on the bulk viscosity of the solvent, and therefore implicates bulk solvent-controlled protein dynamics in the protonation process. The protonation is proposed to be a sequential process involving two steps: (a) proton transfer from solvent to the chromophore, and (b) internal structural rearrangements to stabilize a protonated chromophore. The possible implications of these observations to protein dynamics in general is discussed     

Association Behavior of 4-Acylpyrazolone Derivative and Tertiary Amine of High Molecular Weight in Antagonistic Synergistic Extraction of Palladium

To find an effective extraction and removal method for palladium(II), which is one of the main fission products from an acidic nuclear spent fuel solution, the extraction behavior of palladium(II) from a nitric acid medium by an acidic chelating extractant, 1-phenyl-3-methyl-4-trifluoroacetylpyrazolone-5-one (HPMTP) and a tertiary amine of high molecular weight, tri-n-octylamine (TOA), has been studied by spectrophotometry. A noticeable antagonistic extraction effect was observed in the extraction system under the given conditions. To understand this phenomenon, a preliminary investigation was performed to explain the mechanism of this reaction. According to the theory of corresponding solutions (TCS), the association reaction between HPMTP and TOA is proposed in the organic phase. An associated species, HPMTP·TOA, formed through hydrogen bonding in a chloroform medium might be the main reason why an antagonistic extraction effect occurred. The association constant between HPMTP and TOA was calculated to be 2.86±0.05.     

Transition‐metal‐catalyzed reactions of 5‐methylene‐2‐oxazolidinone and 5‐methylene‐1,3‐thiazolidine‐2‐thione with isocyanates

5‐Methylene‐2‐oxazolidinone (1) and 5‐methylene‐1,3‐thiazolidine‐2‐thione (4) react with various isocyanates to give the corresponding urethanes 3 and 5 in high yields in the presence of palladium(0) or palladium(II) catalyst under mild reaction conditions. A mechanism is proposed. Copyright © 2003 John Wiley & Sons, Ltd.     

Intrinsic Fluorescence of Actin

In this work actin is used to illustrate connection of protein fluorescence characteristics with its structure. On one hand, it has been demonstrated what kind of information about the contribution of each tryptophan residues to the bulk fluorescence spectrum can be obtained from the special analysis of protein three-dimensional structure. On the other hand, potentials of intrinsic fluorescence for elucidation of proteins structure, dynamics and processes of folding-unfolding are shown. In particular, using this method a new essentially unfolded kinetic intermediate state of actin was detected and characterized, and the place of inactivated actin and its kinetic predecessor in the process of folding-unfolding was determined. It has been revealed that inactivated actin is not intermediate state between the native and completely unfolded states, as it has been accepted before, but a result of protein misfolding. On the basis of the obtained data a new model of actin folding-unfolding pathway has been proposed.