Additional angles to calculate the deformation of RNA helices induced by bulge loops

Bulges are common features of folded RNA structures. The RNA axial kinking caused by bulges has been confirmed by many experiments. Usually, a kinking angle zeta and a bending angle theta are used to describe the kinking and twisting of RNA molecules containing bulges. Here, we present two additional angles (twist angle zeta(1), twist angle zeta(2)) to describe the deformation of RNA helices induced by bulge loops because only two angles (a kinking angle zeta and a bending angle theta) are not enough to define the deformation of RNA induced by bulges. (C) 2002 Elsevier Science B.V. All rights reserved.

Dynamics of RNA with A6 bulge loop

In order to understand the behavior of RNAs with large bulges In solution, molecular dynamics was performed on the RNA molecule in water with A6 bulge. The result of simulation showed that nonstacked conformation Is the main conformation in large bulges, and the backbone of large bulge is of great conformational flexibility, but bulges-induced bends are relatively rigid. The fluctuation in bulge has little influence on the bend angle of RNAs.

Fracture properties of silicon carbide thin films by bulge test of long rectangular membrane

This paper reports the mechanical properties and fracture behavior of silicon carbide (3C-SiC) thin films grown on silicon substrates. Using bulge testing combined with a refined load-deflection model of long rectangular membranes, which takes into account the bending stiffness and prestress of the membrane material, the Young's modulus, prestress, and fracture strength for the 3C-SiC thin films with thicknesses of 0.40 and 1.42 mu m were extracted. The stress distribution in the membranes under a load was calculated analytically. The prestresses for the two films were 322 +/- 47 and 201 +/- 34 MPa, respectively. The thinner 3C-SiC film with a strong (111) orientation has a plane-gstrain moduli of 415 +/- 61 GPa, whereas the thicker film with a mixture of both (111) and (110) orientations exhibited a plane-strain moduli of 329 +/- 49 GPa. The corresponding fracture strengths for the two kinds of SiC films were 6.49 +/- 0.88 and 3.16 +/- 0.38 GPa, respectively. The reference stresses were computed by integrating the local stress of the membrane at the fracture over edge, surface, and volume of the specimens and were fitted with Weibull distribution function. For the 0.40-mu m-thick membranes, the surface integration has a better agreement between the data and the model, implying that the surface flaws are the dominant fracture origin. For the 1.42-mu m-thick membranes, the surface integration presented only a slightly better fitting quality than the other two, and therefore, it is difficult to rule out unambiguously the effects of the volume and edge flaws.

Bulge testing and fracture properties of plasma-enhanced chemical vapor deposited silicon nitride thin films

The mechanical properties and fracture behavior of silicon nitride (SiNx) thin film fabricated by plasma-enhanced chemical vapor deposition is reported. Plane-strain moduli, prestresses, and fracture strengths of silicon nitride thin film; deposited both oil a bare Si substrate and oil a thermally oxidized Si substrate were extracted using bulge testing combined with a refined load-deflection model of long rectangular membranes. The plane-strain modu i and prestresses of SiNx thin films have little dependence on the substrates, that is, for the bare Si substrate, they are 133 +/- 19 GPa and 178 +/- 22 MPa, respectively, while for the thermally oxidized substrate, they are 140 +/- 26 Gila and 194 +/- 34 MPa, respectively. However, the fracture strength values of SiNx films grown on the two substrates are quite different, i.e., 1.53 +/- 0.33 Gila and 3.08 +/- 0.79 GPa for the bare Si substrate a A the oxidized Si substrate, respectively. The reference stresses were computed by integrating the local stress of the membrane at the fracture over the edge, Surface, and volume of the specimens and fitted with the Weibull distribution function. For SiNx thin film produced oil the bare Si Substrate, the Volume integration gave a significantly better agreement between data and model, implying that the volume flaws re the dominant fracture origin. For SiNx thin film grown on the oxidized Si substrate, the fit quality of surface and edge integration was significantly better than the Volume integration, and the dominant surface and edge flaws could be caused by buffered HF attacking the SiNx layer during SiO2 removal. Crown Copyright (C) 2008 Published by Elsevier B.V. All rights reserved.

Fracture properties of PECVD silicon nitride thin films by long rectangular memrane bulge test

Bulge test combined with a refined load-deflection model for long rectangular membrane was applied to determine the mechanical and fracture properties of PECVD silicon nitride (SiNx) thin films. Plane-strain modulus E-ps prestress s(0), and fracture strength s(max) of SiNx thin films deposited both on bare Si substrate and on SiO2-topped Si substrate were extracted. The SiNx thin films on different substrates possess similar values of E-ps and s(0) but quite different values of s(max). The statistical analysis of fracture strengths were performed by Weibull distribution function and the fracture origins were further predicted.

Fracture properties of silicon carbide thin films charcterized by bulge test of long membranes

The mechanical properties and fracture behavior of silicon carbide (3C-SiC) thin films grown on silicon substrates were characterized using bulge testing combined with a refined load-deflection model for long rectangular membranes. Plane-strain modulus E-ps, prestress so, and fracture strength s(max) for 3C-SiC thin films with thickness of 0.40 mu m and 1.42 mu m were extracted. The E, values of SiC are strongly dependent on grain orientation. The thicker SIC film presents lower so than the thinner film due to stress relaxation. The s(max) values decrease with increasing film thickness. The statistical analysis of the fracture strength data were achieved by Weibull distribution function and the fracture origins were predicted.

神农架植被及其生物多样性与垂直分布格局-兼论中国中、北亚热带植被带的划分

本文主要通过样线法和样方法相结合，进行了大量的群落学调查和分析，分别从植物区系、物种多样性的垂直分布格局和森林群落类型三个方面分析了神农架植被的基本特征及其物种多样性，结果表明： 1．神农架地区具有很高的物种丰富度，有高等植物3，479种，隶属于1，010属，202科。 其中，蕨类植物305种，80属，32科;种子植物3，174种，930属，170科，其中裸子植物32种，19属，6科，被子植物3，142种，911属，164科;单子叶植物501种，175属，21科，双子叶植物2，641种，736属，143科。植物区系属的分布区类型中北温带分布型最多，其次为东亚分布、泛热带分布、东亚北美间断分布、旧世界温带分布以及热带亚洲分布。中国特有成分占5.65%，较全国的8.12%低。温热比(温带分布型(8-11)属数与热带分布型(2-7)属数的比值）为1.200，比全国(0.385)高。 调查样方中共出现高等植物784种，隶属于454属，144科，其中蕨类植物41种，32属，16科;种子植物743种，422属，128科，其中裸子植物20种，14属，5科，被子植物723种，408属，123科;单子叶植物86种，58属，11科，双子叶植物637种，350属，112科。属的分布区类型中北温带分布型最多，其次为东亚分布、泛热带分布、东亚北美间断分布、旧世界温带分布以及热带亚洲分布。温热比为1.52，草本层>乔木层>灌木层分别为2.18、1.76和1.14。 2．神农架植被类型多样，具有常绿阔叶林、常绿落叶阔叶混交林、落叶阔叶林、针阔混交林、亚高山针叶林、硬叶常绿阔叶林和亚高山灌丛草甸等自然植被类型。本文，依据乔木物种的重要值将神农架地区的森林植被划分出了69个类型。用Twinspan将调查的森林群落划分为32组，能基本上反映群落间相似的关系。 3．神农架地区具有完整的植被垂直带谱：海拔900 (1300) m以下为常绿阔叶林带;海拔900 (1300) m～1500 (1800)ⅡI为常绿落叶阔叶混交林带;海拔1500 (1800) m-2000 (2200)m为落叶阔叶林带;海拔2000 (2200) m～2400 (2600)m为针阔混交林带：海拔2400 (2600)m以上为亚高山针叶林带。神农架地区植被的垂直带的分化从总体上比较显著，但由于小生境的异质性和人为干扰，垂直带谱又具有一定的模糊性和次生性。南北坡具有一定的差异，但不十分明显，也说明神农架植被的过渡性。 4．神农架物种多样性的垂直分布格局。神农架的物种多样性与海拔的关系，类似于“中间膨胀”规律(mid-altitude bulge)，在中低海拔处生物多样性最高。通过二次多项式回归拟合，得到如下拟合曲线： 1)海拔与总体物种数：y= _14.445x2+ 34.74lx+42.07，Xd=1.203km; 2)海拔与乔木层物种数：y=-6.9707x2+ 21.334x+0.2004，Xdrl.530km; 3)海拔与灌木层物种数：y=-6.1599x2+ 9.9747x+30.991，Xd=0.8 lOkm: 4)海拔与草本层物种数：y= _3.9907x2+ 10.455x+15.35，Xd-1.308km; 5）海拔与乔木层Shannon-Wiener指数：y=_0.3337x2+ 0.9877x+0.2537，Xd' 1.480km; 6)海拔与灌木层Shannon-Wiener指数：y=-0.1938xz+ 0.422lx+1.2103，Xd=1.089km： 7)海拔与草本层Shannon-Wiener指数：y=_0.1072x2+ 0.294lx+0.9954，Xd=1.372km; x为海拔( km)，y为各物种多样性指标，Xd为物种多样性的最大时的海拔。 从这些拟合曲线中可以看出：总体物种多样性在海拔1200m左右的常绿落叶阔叶混交林带最高：乔木层物种多样性在海拔1500m左右的常绿落叶阔叶混交林带与落叶阔叶林的过渡带最高;灌木层物种多样性在海拔800-llOOm左右的常绿阔叶林与常绿落叶阔叶混交林带的过渡带最高;草本层物种多样性在海拔1300-1400m左右的常绿落叶阔叶混交林带最高。 但物种多样性随海拔变化有许多的起伏和波动。这些波动有些反映了群落的垂直带谱随海拔梯度变化的特点，在垂直带谱的过渡区物种多样性往往较高;有些波动反映了一些特殊的生境，有些反映了人为活动的影响，造成了神农架植被的次生性。因此，影响神农架物种多样性垂直分布的因素有：植被本身的性质和特点、过渡带的特点、生境的异质性和人为活动。 5．神农架植被水平地带性的过渡性。海拔1300m以下的植物属的分布区类型的温热比南坡总是比北坡小，而且相差十分显著，反映了神农架作为植被分界线的价值。神农架南坡的基带植被是常绿阔叶林，因此南坡属于中亚热带。北坡的基带植被，虽然也有常绿树种的零星分布，甚至有小块的常绿阔叶林，完全由于小生境所至，分布的主要类型是常绿落叶阔叶混交林，应属于北亚热带。因此，神农架是中、北亚热带重要的过渡地带。神农架地区中北亚热带的具体分界线宜按照分长江干流和汉水的水岭来划界，即猴子石、大窝坑、神农架、神农顶、老君山一线，南坡属于中亚热带，北坡属于北亚热带。 总之，神农架处于我国中、北亚热带的过渡带，具有过渡带的性质，具有很高的物种多样性，拥有完整的植被垂直带谱，具有多种多样的植物群落及其组成的生态系统。而且，具有我国许多特有植物和珍稀濒危保护植物和许多资源植物。因此，神农架植被在我国植被体系中具有重要的地位，是我国生物多样性最丰富的地区之一，是生物多样性保护的关键地区，也应是生物多样性研究的热点地区。 另外，调查分析了黄山和万朝山植被及其物种多样性与垂直分布格局，结果表明： 6．黄山样方中共出现高等植物259种，隶属于263属，110科，其中蕨类植物14种，II属，8科，种子植物345种，152属，105科，其中裸子植物9种，8属，6科，被子植物336种，144属，99科，其中单子叶植物37种，27属，6科，双子叶植物299种，117属，90科。属的分布区类型中北温带分布最多，其次为东亚分布和泛热带分布，再次为东亚北美间断分布、热带亚洲分布以及旧世界温带分布，与神农架和万朝山也较相似，但热带分布的属更多一些。温热比为1.1875，灌木层>草本层>乔木层，分别为1.3818、1.2609和1.2143。 黄山的森林植被类型有针叶林、常绿阔叶林、常绿落叶阔叶混交林、针阔混交林、落叶阔叶林和竹林。Twinspan将调查的森林群落划分为22组，反映群落间相似的关系，比较清楚和适用。依据乔木物种的重要值将森林植被划分出了34个类型。黄山物种多样性的与海拔的关系不十分明显。黄山植被的垂直带谱不是十分明显，将其垂直带谱划分为：海拔1300m(1500m)以下为常绿阔叶林带;海拔1300m(1500m)-1500m(1600m)常绿落叶阔叶混交林 带;1500m(1600m)以上为落叶阔叶林、黄山松林、山地灌木草丛带。垂直带谱在不同坡向上有差别，东、南、西坡的相似性较大，而北坡与其差别较大。 7．万朝山样方中共出现高等植物490种，隶属于339属，124科，其中蕨类植物21种，18属，11科，种子植物469种，321属，113科，其中裸子植物9种，7属，4科，被子植物460种，314属，109科，其中单子叶植物47种，37属，11科，双子叶植物413种，277属，98科。植物属的分布区类型中，北温带分布所占最多，其次为泛热带分布、东亚分布、东亚北美间断分布、旧世界温带分布以及热带亚洲分布，。温热比为1.3366，草本层>乔木层>灌木层，分别为1.5429、1.4063和1.0645。 万朝山的植被类型包括针叶林、落叶阔叶林、针阔混交林和常绿落时阔叶混交林，但没有典型的常绿阔叶林。依据乔木物种的重要值将森林植被划分出了20个类型。万朝山物种多样性与海拔的关系则不十分明显。万朝山的人为干扰比较强，植被的次生性很大，南、北坡物种多样性随海拔升高的起伏较大。

mRNA 很可能携带三维遗传信息

The forming mechanism of the three - dimensional structures of proteins，i.e.the mechanism of protein folding，is a basic problem in molecular biology which is still unsolved unitl now. In which a core problem is whether there is the three – dimensional genetic information that decide the three - dimensional structures of proteins. However, the research on this field has mot yet been reported. Recently，we made a comparative study on the folded structures of more than 70 mature messeneger RNAs (mRNAs) and the three - dimensional structures of the proteins encoded by them，it has been found that there exist marked correspondences between their featured structures in the following aspects: 1.The number of the structural units. An RNA molecule can form a secondary structure(stem and loop structure) by the folding and the base pairing of itself. The elementary structural unit of an RNA secondary structure is hairpin(or compound hair pin).The regular structural unit in the secondary structure of a protein is # alpha # - helix or #beta# - sheet . We have found that the hairpin number in the secondary structure of each mature mRNA is equal or approximately equal to the number of the regular secondary structural unis of the encoded protein. 2 .Turning region. Turn is a main structrual element in the secondary structure of a protein, which decides the backbone orientation of a protein molecule to some extent .Our analysis shows that the nucleotide sequence segments in an mRNA which encode the turns of the corresponding protein are overall situated in the turning regions of the mRNA secondary structure such as haipin，bulge loop or multibaranch loops. 3 .The arrangement of structural elements in space. In order to understand the backbone orientation of an RNA molecule and the arangement of its structural elements in space，we have modeled the three一dimensional structure of the mRNA molecule on SGI workstation based on its secondary structure.The result shows that the spatial arrangement of most of the nucleotide sequence segments encoding the structural elements of a protein is consistent with that of these stretural exements in the protein. For instance，the nucleotide sequences corresponding to each pleated sheet of a # beta # - sheet structure are close to each other in the mRNA secondary stucture and in the three - dimensional structure，although some of the nucleotide segments are far apart from each other in the one - dimensional sequence. For another instance，the two triplet codons of cysteines which form a disulphide bridge geneal1y are very close to each other in the mRNA folded structure. In addition，we also analyzed the locations of the codons proline - coding and the distrbution of the nucleotide sequences #alpha# - helix - coding in the folded structures of mRNAs . Some distribution laws have been found. All of these results suggest that the transfer of the genetic information from mRNA to protein not only is one – dimensional but also is three - dime ns ional. That is，there exists the genetic information that decide the three - dimensional structures of proteins. To a certain extent，we could say that the mRNA folding detemines the protein folding. Based on these results，it would be possible to predict the three - dimensional structures of proteins from the primary，secondary and tertiary structures of the m RNAs at a higher accuracy.And more important is that a new clue has been provided to uncover the“spatial coding" of the genetic information.

Fracture Properties of LPCVD Silicon Nitride and Thermally Grown Silicon Oxide Thin Films From the Load-Deflection of Long Si3N4 and SiO2/Si3N4 Diaphragms

The bulge test is successfully extended to the determination of the fracture properties of silicon nitride and oxide thin films. This is achieved by using long diaphragms made of silicon nitride single layers and oxide/nitride bilayers, and applying comprehensive mechanical model that describes the mechanical response of the diaphragms under uniform differential pressure. The model is valid for thin films with arbitrary z-dependent plane-strain modulus and prestress, where z denotes the coordinate perpendicular to the diaphragm. It takes into account the bending rigidity and stretching stiffness of the layered materials and the compliance of the supporting edges. This enables the accurate computation of the load-deflection response and stress distribution throughout the composite diaphragm as a function of the load, in particular at the critical pressure leading to the fracture of the diaphragms. The method is applied to diaphragms made of single layers of 300-nm-thick silicon nitride deposited by low-pressure chemical vapor deposition and composite diaphragms of silicon nitride grown on top of thermal silicon oxide films produced by wet thermal oxidation at 950 degrees C and 1050 degrees C with target thicknesses of 500, 750, and 1000 mn. All films characterized have an amorphous structure. Plane-strain moduli E-ps and prestress levels sigma(0) of 304.8 +/- 12.2 GPa and 1132.3 +/- 34.4 MPa, respectively, are extracted for Si3N4, whereas E-ps = 49.1 +/- 7.4 GPa and sigma(0) = -258.6 +/- 23.1 MPa are obtained for SiO2 films. The fracture data are analyzed using the standardized form of the Weibull distribution. The Si3N4 films present relatively high values of maximum stress at fracture and Weibull moduli, i.e., sigma(max) = 7.89 +/- 0.23 GPa and m = 50.0 +/- 3.6, respectively, when compared to the thermal oxides (sigma(max) = 0.89 +/- 0.07 GPa and m = 12.1 +/- 0.5 for 507-nm-thick 950 degrees C layers). A marginal decrease of sigma(max) with thickness is observed for SiO2, with no significant differences between the films grown at 950 degrees C and 1050 degrees C. Weibull moduli of oxide thin films are found to lie between 4.5 +/- 1.2 and 19.8 +/- 4.2, depending on the oxidation temperature and film thickness.

SELF-CONSISTENT TREATMENT OF 3-DIMENSIONAL - 2-DIMENSIONAL AND 2-DIMENSIONAL - 2-DIMENSIONAL RESONANT-TUNNELING IN DOUBLE-BARRIER STRUCTURES

By using a transfer-matrix method on the basis of two-dimensional (2D) Bloch sums in accordance with a tight-binding scheme, a self-consistent calculation on the resonant tunneling in asymmetric double-barrier structures is presented, in which contributions to resonant tunneling from both three-dimensional (3D) electrons in the contacts and 2D electrons in the spacer or accumulation layers are considered simultaneously. The charge buildup effect on the current versus voltage (I-V) curves is evaluated systematically, showing quantitatively how it results in the I-V bistability and enhanced differences between I-V curves for positive and negative bias in an asymmetric double-barrier structure. Special attention is focused on the interaction between 3D-2D and 2D-2D resonant-tunneling processes, including the suppression of 2D-2D resonant tunneling by the charge buildup in the well accompanying the 3D-2D resonant tunneling. The effects of the emitter doping condition (doping concentration, spacer thickness) on the presence of two types of quasi-2D levels in the emitter accumulation layers, and on the formation of a potential bulge in the emitter region, are discussed in detail in relation to the tunneling process.

Oscillation flow induced by underwater supersonic gas jets

This paper describes an experimental study on the oscillation flow characteristics of submerged supersonic gas jets issued from Laval nozzles. The flow pattern during the jet development and the jet expansion feedback phenomenon are studied using a high-speed camera and a pressure measurement system. The experimental results indicate that along the downstream distance, the jet has three flow regimes: (1) momentum jet; (2) buoyant jet; (3) plume. In the region near the nozzle exit a so-called bulge phenomenon is found. Bulging of the jet occurs many times before the more violent jet expansion feedback occurs. During the feedback process, the jet diameter can become several times that of the original one depending on the jet Mach number. The frequencies of the jet bulging and the jet expansion feedback are measured.

Dynamics of the buoyant plume off the Pearl River Estuary in summer

Field measurements of salinity, wind and river discharge and numerical simulations of hydrodynamics from 1978 to 1984 are used to investigate the dynamics of the buoyant plume off the Pearl River Estuary (PRE), China during summer. The studies have shown that there are four major horizontal buoyant plume types in summer: Offshore Bulge Spreading (Type I), West Alongshore Spreading (Type II), East Offshore Spreading (Type III), and Symmetrical Alongshore Spreading (Type IV). River mouth conditions, winds and ambient coastal currents have inter-influences to the transport processes of the buoyant plume. It is found that all of the four types are surface-advected plumes by analysing the vertical characteristic of the plumes, and the monthly variations of the river discharge affect the plume size dominantly. The correlation coefficient between the PRE plume size and the river discharge reaches 0.85 during the high river discharge season. A wind strength index has been introduced to examine the wind effect. It is confirmed that winds play a significant role in forming the plume morphology. The alongshore wind stress and the coastal currents determine the alongshore plume spreading. The impact of the ambient currents such as Dongsha Current and South China Sea (SCS) Warm Current on the plume off the shelf has also assessed. The present study has demonstrated that both the river discharge and wind conditions affect the plume evolution.

The Apertospathulidae, a new family of haptorid ciliates (Protozoa, Ciliophora)

We studied the morphology of three rare haptorid ciliates, using live observation and silver impregnation: Apertospathula verruculifera n. sp., Longispatha elegans n. gen., n. sp., and Rhinothrix porculus (Penard, 1922) n. gen., n. comb. Simple ethanol fixation (50-70%, v/v) is recommended to reveal the ciliary pattern of "difficult" ciliates, such as R. porculus, by protargol impregnation. The three genera investigated have a distinct feature in common, viz., a lasso-shaped oral bulge and circumoral kinety, where the right half is slightly to distinctly longer than the left and the circumoral kinety is open ventrally. Thus, they are united in a new spathidiid family, the Apertospathulidae n. fam., which probably evolved from a Bryophyllum-like ancestor by partial reduction of the oral bulge and circumoral kinety. Apertospathula verruculifera has a wart-like process, the palpus dorsalis, at the anterior end of the dorsal brush. The right branch of the circumoral kinety is only slightly longer than the left one. Longispatha elegans has a straight oral bulge and circumoral kinety, the right branch of which extends to the posterior end of the body while the left branch ends in the anterior third of the body. Rhinothrix porculus, a curious ciliate with a snout-like dorsal elongation of the oral bulge, the palpus oralis, has a highly characteristic ciliary pattern: the oral pattern is as in Longispatha, but the bulge and circumoral kinety extend spirally to the posterior end of the body while the somatic kinetics course meridionally. This is achieved by inserting some shortened kinetics in the curves of the oral bulge.