Numerical study on rainfall infiltration in rock-soil slop

A mathematical model for the rain infiltration in the rock-soil slop has been established and solved by using the finite element method. The unsteady water infiltrating process has been simulated to get water content both in the homogeneous and heterogeneous media. The simulated results show that the rock blocks in the rock-soil slop can cause the wetting front moving fast. If the rain intensity is increased, the saturated region will be formed quickly while other conditions are the same. If the rain intensity keeps a constant, it is possible to accelerate the generation of the saturated region by properly increasing the vertical filtration rate of the rock-soil slop. However, if the vertical filtration rate is so far greater than the rain intensity, it will be difficult to form the saturated region in the rock-soil slop. The numerical method was verified by comparing the calculation results with the field test data.

Analysis of critical excavation depth for a jointed rock slope using a face-to-face discrete element method

The critical excavation depth of a jointed rock slope is an important problem in rock engineering. This paper studies the critical excavation depth for two idealized jointed rock slopes by employing a face-to-face discrete element method (DEM). The DEM is based on the discontinuity analysis which can consider anisotropic and discontinuous deformations due to joints and their orientations. It uses four lump-points at each surface of rock blocks to describe their interactions. The relationship between the critical excavation depth D-s and the natural slope angle alpha, the joint inclination angle theta as well as the strength parameters of the joints c(r) ,phi(r) is analyzed, and the critical excavation depth obtained with this DEM and the limit equilibrium method (LEM) is compared. Furthermore, effects of joints on the failure modes are compared between DEM simulations and experimental observations. It is found that the DEM predicts a lower critical excavation depth than the LEM if the joint structures in the rock mass are not ignored.

Numerical Analyses of Transonic Fluid/Structure interaction in Aircraft Engineering

Through the coupling between aerodynamic and structural governing equations, a fully implicit multiblock aeroelastic solver was developed for transonic fluid/stricture interaction. The Navier-Stokes fluid equations are solved based on LU-SGS (lower-upper symmetric Gauss-Seidel) Time-marching subiteration scheme and HLLEW (Harten-Lax-van Leer-Einfeldt-Wada) spacing discretization scheme and the same subiteration formulation is applied directly to the structural equations of motion in generalized coordinates. Transfinite interpolation (TFI) is used for the grid deformation of blocks neighboring the flexible surfaces. The infinite plate spline (IPS) and the principal of virtual work are utilized for the data transformation between fluid and structure. The developed code was fort validated through the comparison of experimental and computational results for the AGARD 445.6 standard aeroelastic wing. In the subsonic and transonic range, the calculated flutter speeds and frequencies agree well with experimental data, however, in the supersonic range, the present calculation overpredicts the experimental flutter points similar to other computations. Then the flutter character of a complete aircraft configuration is analyzed through the calculation of the change of structural stiffness. Finally, the phenomenon of aileron buzz is simulated for the weakened model of a supersonic transport wing/body model at Mach numbers of 0.98 and l.05. The calculated unsteady flow shows, on the upper surface, the shock wave becomes stronger as the aileron deflects downward, and the flow behaves just contrary on the lower surface of the wing. Corresponding to general theoretical analysis, the flow instability referred to as aileron buzz is induced by a stronger shock alternately moving on the upper and lower surfaces of wing. For the rigid structural model, the flow is stable at all calculated Mach numbers as observed in experiment

三维离散元改进算法及其在三峡永久船闸高边坡工程中的应用

本文根据面－面接触模型，写出了三维离散元的物理方程及运动方程，对于接触刚度、阻尼系数、时步、计算控制及块体的滑动失稳判据等作了讨论。在NURBM－3D 长方体单元基础上改进了其划分单元的算法，依据岩体中三组真实的节理面划分平行六面体单元，实现了网格的自动剖分，从而可以将单元视为真实的岩块，更客观地体现了节理面对岩体稳定性的影响。运用改进后的三维离散元方法，编制了计算程序，对三峡工程永久船闸高连坡开挖进行了模拟。计算过程包括初始地应力场模拟、岩体开挖过程两个阶段。模拟计算首先给出了为水平、垂直节理面所切割的长方体单元情况下的应力场分析，考证了程序的可行性。将已有的三峡永久船闸实测节理简化为三组节理，完成了初始地应力场的模拟，给出了分四步开挖后的岩体位移场和应力场，计算出岩体开挖过程中产生滑动块体的位置，其结果可以定性地表明：沿节理面的块体滑动是边坡失稳的主要模式。编制的后处理程序提供了计算数据库与绘图软件Origin的接口，可以画出任意剖面或节理面上的应力等值线、位移矢量图及滑动块体分布图，由此可以直观判断岩体不稳定区域和高应力区范围。编制的计算程序在PC机上计算了10万块体单元，用于模拟大型工程，其计算结果与有限元及类似的连续介质模型相比更为合理，为用离散元法进一步研究可变形块体及岩体的蠕变提供了一种切实可行的工具。将离散元法应用于大型工程三维计算是可行的，但在本构模型建立、岩体破坏参数选择等方面均有等于更深入的研究，其结果也有待于更多工程的验证。

High-Strength Composite Fibers: Realizing True Potential of Carbon Nanotubes in Polymer Matrix through Continuous Reticulate Architecture and Molecular Level Couplings

Carbon nanotubes have unprecedented mechanical properties as defect-free nanoscale building blocks, but their potential has not been fully realized in composite materials due to weakness at the interfaces. Here we demonstrate that through load-transfer-favored three-dimensional architecture and molecular level couplings with polymer chains, true potential of CNTs can be realized in composites as Initially envisioned. Composite fibers with reticulate nanotube architectures show order of magnitude improvement in strength compared to randomly dispersed short CNT reinforced composites reported before. The molecular level couplings between nanotubes and polymer chains results in drastic differences in the properties of thermoset and thermoplastic composite fibers, which indicate that conventional macroscopic composite theory falls to explain the overall hybrid behavior at nanoscale.

Microstructures induced in the bulk of SrTiO3 crystal by a femtosecond laser

Microstructures with the total length of hundreds of mu m were induced by fixing the focal point of the femtosecond laser at a certain depth in the bulk of SrTiO3 crystal. By different combination of the focusing conditions with the laser parameters, different morphologies have been observed, such as void array, necklace-shaped structures, continuous/segmental filaments and etc. The possible mechanism of the formation of those diversiform structures is discussed.

Special effects of YbF3 on the structural changes for fluorophosphate glass

From Raman and IR spectra, obvious differences of the glass structure were observed in non-Yb3+-doped and Yb3+ -doped fluorophosphate glasses. Results showed that Yb3+ ions can induce, in a better glass, polymerization and network uniformity. Compared with the monophosphate-mastered Yb3+-free glass, Yb3+-doped glass has a pyrophosphate environment. The main building blocks in Yb3+ -doped samples are metaphosphate groups, pyrophosphate groups (P-2(O,F)(7),PO3F), Al[F-6]+Al[O,F](6) and F3Al-O-AlF3 while those of the Yb3+ -free glasses are monophosphate groups P(O,F)(4), little pyrophosphate groups, Al[F-4]+Al[F-6]+Al[O,F](4)+Al[O,F](6) and F3Al-O-AlF3. The DSC analysis also showed a slight increase in crystallization stability. (c) 2005 Elsevier B.V. All rights reserved.

Photonic nanowires directly drawn from bulk glasses

High-uniform nanowires with diameters down to 50 nm are directly taper-drawn from bulk glasses. Typical loss of these wires goes down to 0.1 dB/mm for single-mode operation. Favorable photonic properties such as high index for tight optical confinement in tellurite glass nanowires and photoluminescence for active devices in doped fluoride and phosphate glass nanowires are observed. Supporting high-index tellurite nanowires with solid substrates (such as silica glass and MgF2 crystal) and assembling low-loss microcoupler with these wires are also demonstrated. Photonic nanowires demonstrated in this work may open up vast opportunities for making versatile building blocks for future micro- and nanoscale photonic circuits and components. (c) 2006 Optical Society of America.

Anisotropic crystallographic properties, strain, and their effects on band structure of m -plane GaN on LiAlO2 (100)

The m-plane GaN films grown on LiAlO2(100) by metal-organic chemical vapor deposition exhibit anisotropic crystallographic properties. The Williamson-Hall plots point out they are due to the different tilts and lateral correlation lengths of mosaic blocks parallel and perpendicular to GaN[0001] in the growth plane. The symmetric and asymmetric reciprocal space maps reveal the strain of m-plane GaN to be biaxial in-plane compress epsilon(xx)=-0.79% and epsilon(zz)=-0.14% with an out-of-plane dilatation epsilon(yy)=0.38%. This anisotropic strain further separates the energy levels of top valence band at Gamma point. The energy splitting as 37 meV as well as in-plane polarization anisotropy for transitions are found by the polarized photoluminescence spectra at room temperature. (c) 2008 American Institute of Physics.

Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype

The Afrotheria, a supraordinal grouping of mammals whose radiation is rooted in Africa, is strongly supported by DNA sequence data but not by their disparate anatomical features. We have used flow-sorted human, aardvark, and African elephant chromosome painting probes and applied reciprocal painting schemes to representatives of two of the Afrotherian orders, the Tubulidentata (aardvark) and Proboscidea (elephants), in an attempt to shed additional light on the evolutionary affinities of this enigmatic group of mammals. Although we have not yet found any unique cytogenetic signatures that support the monophyly of the Afrotheria, embedded within the aardvark genome we find the strongest evidence yet of a mammalian ancestral karyotype comprising 2n = 44. This karyotype includes nine chromosomes that show complete conserved synteny to those of man, six that show conservation as single chromosome arms or blocks in the human karyotype but that occur on two different chromosomes in the ancestor, and seven neighbor-joining combinations (i.e., the synteny is maintained in the majority of species of the orders studied so far, but which corresponds to two chromosomes in humans). The comparative chromosome maps presented between human and these Afrotherian species provide further insight into mammalian genome organization and comparative genomic data for the Afrotheria, one of the four major evolutionary clades postulated for the Eutheria.

Cross-species chromosome painting in the golden mole and elephant-shrew: support for the mammalian clades Afrotheria and Afroinsectiphillia but not Afroinsectivora

Cross-species painting (fluorescence in situ hybridization) with 23 human (Homo sapiens (HSA)) chromosome-specific painting probes (HSA 1-22 and the X) was used to delimit regions of homology on the chromosomes of the golden mole (Ghrysochloris asiaticus) and elephant-shrew (Elephantulus rupestris). A cladistic interpretation of our data provides evidence of two unique associations, HSA 1/19p and 5/21/3, that support Afrotheria. The recognition of HSA 5/3/21 expands on the 3/21 synteny originally designated as an ancestral state for all eutherians. We have identified one adjacent segment combination (HSA2/8p/4) that is supportive of Afroinsectiphillia (aardvark, golden mole, elephant-shrew). Two segmental combinations (HSA 10q/17 and HSA 3/20) unite the aardvark and elephant-shrews as sister taxa. The finding that segmental syntenies in evolutionarily distant taxa can improve phylogenetic resolution suggests that they may be useful for testing sequence-based phylogenies of the early eutherian mammals. They may even suggest clades that sequence trees are not recovering with any consistency and thus encourage the search for additional rare genomic changes among afrotheres.

Characterization and Comparison of the Tissue-Related Modules in Human and Mouse

Background: Due to the advances of high throughput technology and data-collection approaches, we are now in an unprecedented position to understand the evolution of organisms. Great efforts have characterized many individual genes responsible for the interspecies divergence, yet little is known about the genome-wide divergence at a higher level. Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes. Hence, the comparative analysis between species at the module level would shed more light on the mechanisms underlying the evolution of organisms than the traditional comparative genomics approaches. Results: We systematically identified the tissue-related modules using the iterative signature algorithm (ISA), and we detected 52 and 65 modules in the human and mouse genomes, respectively. The gene expression patterns indicate that all of these predicted modules have a high possibility of serving as real biological modules. In addition, we defined a novel quantity, "total constraint intensity,'' a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context. We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity. Furthermore, there are modules coding the same essential biological processes, while their gene contents have diverged extensively between human and mouse. Conclusions: Our results suggest that unlike the composition of module, which exhibits a great difference between human and mouse, the functional organization of the corresponding modules may evolve in a more conservative manner. Most importantly, our findings imply that similar biological processes can be carried out by different sets of genes from human and mouse, therefore, the functional data of individual genes from mouse may not apply to human in certain occasions.

顶体反应抑制剂4'- 乙酰胺苯基4-胍基苯甲酸酯(AGB)具有阻断HIV-1进入细胞的作用

】目的: 研究4'- 乙酰胺苯基4- 胍基苯甲酸酯(AGB)抗 HIV-1 活性及作用靶点。方法: 通过 AGB对宿主细胞的毒性实验、合胞体抑制实验、融合阻断实验、对HIV-1感染细胞的保护作用实 验和对HIV-1急性感染细胞p24抗原产生的抑制作用等试验，观察AGB对HIV-1复制的影响和作 关键词: AGB; HIV-1; 病毒进入; 杀微生物剂; 杀精子活性 中图分类号: R967; 文献标识码: A 文章编号: 0253-357X(2005)11-0660-05 本研究为国家高技术研究发展计划(2003AA219142)、国 家科技攻关计划 (2004BA719A14)、中国科学院知识创新 工程重要方向(KSCX2-SW-216; KSCX12-SW-11)、云南 省科技攻关计划(2004NG12)和云南省生育调节与少数民 族优生研究重点实验室资助项目 通讯作者: 郑永唐; Tel: +86-871-5195684; Fax:+86-871-5191823; E-mail: zhengyt@mail.kiz.ac.cn 在我国, 人免疫缺陷病毒(human immunodeficiency virus, HIV)危害日趋严重，处在全国低流行 与局部地区及特定人群高流行并存的态势。卫生部 的数据显示，截止2005 年3 月底，全国累计报告 HIV 感染者114 703 例。专家估计我国实际HIV 感 染者超过100 万人。预计到2010 年, 全国HIV感染 者将突破千万。截止2004 年底, 云南省累计报告的 HIV 感染者已达28 391 人, 是全国流行最严重的地 区。艾滋病流行正由高危人群向一般人群传播。 新的证据显示近年来由性传播途径感染的比例有所 上升, 女性感染者的比例有较大幅度的上升, 迫切需 要发展一种女性可自主控制的方法 [1]。杀微生物剂 是可以局部用药于阴道和宫颈、能够杀灭或抑制 包括HIV等病毒性和细菌性病原体、人工合成或天 然的药物。具有避孕作用的杀微生物剂更是近年 来的研究热点，也具有广阔的应用前景[2,3]。 顶体酶是存在于精子顶体内的一种类胰蛋白 酶, 它是受精过程中的一种重要的蛋白水解酶, 此酶 能水解卵细胞的透明带, 使精子能够与卵细胞相融 合; 顶体酶还能促进生殖系统中激肽的释放, 后者能 够增强精子的活力和促进精子的运动, 顶体酶的失 活将导致不孕[4]。AGB(4'- 乙酰胺苯基 4- 胍基苯甲 酸酯)是顶体酶的抑制剂, 实验表明在多种动物中有 很好的杀精子作用[5-7]。Bourimbaiar等[8]曾报道AGB 还具有体外抗HIV-1的作用, 活性较N-9高, 且毒性 较小。在本实验中, 我们发现AGB 的体外抗HIV-1 活性主要是阻断HIV-1 进入细胞。 用机制。结果: AGB抑制HIV-1IIIB诱导C8166细胞形成合胞体, EC50为39.5 μg/ml; 抑制HIV-1感染 细胞上清中HIV-1 p24抗原的表达, EC50为33.36 μg/ml; 阻断HIV-1慢性感染H9细胞与正常C8166 细胞间融合的作用。结论: AGB具有阻断HIV-1 进入宿主细胞的作用，是一种有前景的具杀精子 作用的杀微生物剂。

The Genomes of Oryza sativa: A history of duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000 - 40,000. Only 2% - 3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism ( SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.