Recent advance in the study of ribosomal model.

With the technological developments of cryoelectron microscope, X-ray diffraction and the growing data available on various components of ribosome, some marvelously intricate structural models of the Escherichia coli 70S ribosome have been reconstructed. The picture of the ribosomal model are detailed, including the placement of the mRNA, the arrangement of the A-site and P-site tRNAs and the peptidyltransferase within the interface gap as well as the path of nascent polypeptide chain, which results in a better understanding of the structure and function of ribosome as well as the translational process.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Adlayer Structures of DL-Homocysteine and L-Homocysteine Thiolactone on Au(111) Surface: an in situ STM Study

The adsorption Of DL-homocysteine (Hcy) and L-homocysteine thiolactone (HTL) on Au(1 1 1) electrode was investigated in 0.1 M HClO4 by cyclic voltammetry and in situ scanning tunneling microscopy (STM). Hcy and HTL molecules formed highly ordered adlayers on Au(1 1 1) surface. High-resolution STM images revealed the orientation and packing arrangement in the ordered adlayers. Hcy molecules formed (2root3 x 3root3)R30degrees adlayer structure and H-bonds between carboxyl groups were assumed to be responsible for the origin of tail-to-tail or head-to-head molecular arrangement, while HTL molecules formed (4 x 6) adlayer structure, and two different orientations and appearances in the ordered adlayer were found. Structural models were proposed for the two adlayers.

Deformation Twinning In Bulk Nanocrystalline Metals: Experimental Observations

Deformation twins have been observed in nanocrystalline (nc) fcc metals with medium-to-high stacking fault energies such as aluminum, copper, and nickel. These metals in their coarse-grained states rarely deform by twining at room temperature and low strain rates. Several twinning mechanisms have been reported that are unique to nc metals. This paper reviews experimental evidences on deformation twinning and partial dislocation. emissions from grain boundaries, twinning mechanisms, and twins with zero-macro-strain. Factors that affect the twinning propensity and recent analytical models on the critical grain sizes for twinning are also discussed. The current issues on deformation twinning in nanocrystalline metals are listed.

太阳辐射对热层和电离层变化性的影响

Solar ultraviolet (UV) radiation at wavelengths less than 400 nm is an important source of energy for aeronomic processes throughout the solar system. Solar UV photons are absorbed in planetary atmospheres, as well as throughout the heliosphere, via photodissociation of molecules, photoionization of molecules and atoms, and photoexcitation toexcitation including resonance scattering. In this paper, the solar irradiances data measured by TIMED SEE, as well as the solar proxies such as F10.7 and Mg II, thermosphere neutral density of CHAMP measurements and topside ionospheric plasmas densities from DMSP, are used to analyze solar irradiance effects on the variabilities of the thermosphere and the ionosphere. First, thermosphere densities near 410 km altitude are analyzed for solar irradiance variability effects during the period 2002-2004. Correlations between the densities and the solar irradiances for different spectral lines and wavelength ranges reveal significantly different characteristics. The density correlates remarkably well with all the selected solar irradiances except the lower chromospheric O I (130.4 nm) emission. Among the chosen solar proxies, the Mg II core-to-wing ratio index, EUV (30-120 nm) and F10.7 show the highest correlations with the density for short-term (< ~27 days) variations. For both long- (> ~27 days) and short-term variations, linear correlation coefficients exhibit a decreasing trend from low latitudes towards high latitudes. The density variability can be effectively modeled (capturing 71% of the variance) using multiple solar irradiance indices, including F10.7, SEUV (the EUV 30-120 nm index), and SFUV (the FUV 120-193 nm index), in which a lag time of 1 day was used for both F10.7 and SEUV, and 5 days for SFUV. In our regression formulation SEUV has the largest contribution to the density variation (40%), with the F10.7 having the next largest contribution (32%) and SFUV accounting for the rest (28%). Furthermore, a pronounced period of about 27.2 days (mean period of the Sun's rotation) is present in both density and solar irradiance data of 2003 and 2004, and a pronounced period of about 54.4 days (doubled period of the solar rotation) is also revealed in 2004. However, soft X-ray and FUV irradiances did not present a pronounced 54.4 day period in 2004, in spite of their high correlation with the densities. The Ap index also shows 54-day periodicities in 2004, and magnetic activity, together with solar irradiance, affects the 54-day variation in density significantly. In addition, NRLMSISE00, DTM-2000 and JB2006 model predictions are compared with density measurements from CHAMP to assess their accuracy, and the results show that these models underestimate the response of the thermosphere to variations induced by solar rotation. Next, the equatorial topside ionospheric plasmas densities Ni are analyzed for solar irradiance variability effects during the period 2002-2005. Linear correlations between Ni and the solar irradiances for different wavelength ranges reveal significantly different characteristics. XUV (0-35 nm) and EUV (115-130 nm) show higher correlation with Ni for the long-term variations, whereas EUV (35-115 nm) show higher correlation for the short-term variations. Moreover, partial correlation analysis shows that the long-term variations of Ni are affected by both XUV (0-35 nm) and EUV (35-115 nm), whereas XUV (0-35 nm) play a more important role; the short-term variations of Ni are mostly affected by EUV (35-115 nm). Furthermore, a pronounced period of about 27 days is present in both Ni and solar irradiance data of 2003 and 2004, and a pronounced period of about 54 days is also revealed in 2004. Finally, prompted by previous studies that have suggested solar EUV radiation as a means of driving the semiannual variation, we investigate the intra-annual variation in thermosphere neutral density near 400 km during 2002-2005. The intra-annual variation, commonly referred to as the ‘semiannual variation’, is characterized by significant latitude structure, hemispheric asymmetries, and inter-annual variability. The magnitude of the maximum yearly difference, from the yearly minimum to the yearly maximum, varies by as much as 60% from year to year, and the phases of the minima and maxima also change by 20-40 days from year to year. Each annual harmonic of the intra-annual variation, namely, annual, semiannual, ter-annual and quatra-annual, exhibits a decreasing trend from 2002 through 2005 that is correlated with the decline in solar activity. In addition, some variations in these harmonics are correlated with geomagnetic activity, as represented by the daily mean value of Kp. Recent empirical models of the thermosphere are found to be deficient in capturing most of the latitude dependencies discovered in our data. In addition, the solar flux and geomagnetic activity proxies that we have employed do not capture some latitude and inter-annual variations detected in our data. It is possible that these variations are partly due to other effects, such as seasonal-latitudinal variations in turbopause altitude (and hence O/N2 composition) and ionosphere coupling processes that remain to be discovered in the context of influencing the intra-annual variations depicted here. Our results provide a new dataset to challenge and validate thermosphere-ionosphere general circulation models that seek to delineate the thermosphere intra-annual variation and to understand the various competing mechanisms that may contribute to its existence and variability. We furthermore suggest that the term “intra-annual” variation be adopted to describe the variability in thermosphere and ionosphere parameters that is well-captured through a superposition of annual, semiannual, ter-annual, and quatra-annual harmonic terms, and that “semiannual’ be used strictly in reference to a pure 6-monthly sinusoidal variation. Moreover, we propose the term “intra-seasonal” to refer to those shorter-term variations that arise as residuals from the above Fourier representation.

焦虑的因素结构及其在中学生中的验证

Since anxiety exists as a certain kind of relation between the subject and his stimuli, present study proposed the criterion that every one of the anxiety’s structural components had to manifest the properties of the relation, not the subject’s properties, and not the stimuli’s properties, too; and that every component must be a bridge from the subject to the object. Several structural models on anxiety were judged by the criterion, and three suited factors were drawn out, which were controllability, importance and urgency. Then through various methods of interview, questionnaire, laboratorial experiment, events graded, the research examined the relations between the three factors and normal anxiety, and explored the interaction of controllability, importance and urgency when they worked together. The results were as the following: 1. The hypothesis that controllability, importance and urgency were the structural components of normal anxiety sounds reasonable, which was supported in different degrees by the results of several secondary research with various methods. 2. With a totally different method of constructing items from the prevalent integrative anxiety inventory, an effective normal anxiety inventory of middle school students was developed based on this theoretical consideration. Reliability and validity research showed that the coefficient of homogeneity and test-retest reliability were high. The construct validity and criterion validity were good enough. The inventory was a useful scale to measure the normal anxiety for middle school students. 3. It’s through their interaction that controllability and importance effect on the level of anxiety which was produced by the relevant event. 4. Anxiety arises with the increasing of importance or urgency. Though there’s a very close connection between controllability and anxiety, the concrete situation is very complicated. Not only is the level of anxiety affected by the interaction of controllability and importance, but when controllability tends to be extremely high or extremely low, importance may also begin to vary with controllability. What’s more, dispositional optimism and self-efficacy still exert influences that cannot be ignored on the relationship between controllability and anxiety. All the results indicated that it was reasonable to regard and study anxiety as a kind of relation between the subject and his environment, and to some extent it’s even necessary if the intention was to clarify the structure of anxiety. Since all the other emotion also exists as a kind of relation between the subject and his stimuli, the wholeness principle which was first proposed and recommended in this study will be of great value to the related researchers. And the interaction between controllability and importance may suggest a valid coping strategy of anxiety.

Comparison of existing poroelastic models for wave damping in a porous seabed

Mechanism of wave-seabed interaction has been extensively studied by coastal geotechnical engineers in recent years. Numerous poro-elastic models have been proposed to investigate the mechanism of wave propagation on a seabed in the past. The existing poro-elastic models include drained model, consolidation model, Coulomb-damping model, and full dynamic model. However, to date, the difference between the existing models is unclear. In this paper, the fully dynamic poro-elastic model for the wave-seabed interaction will be derived first. Then, the existing models will be reduced from the proposed fully dynamic model. Based on the numerical comparisons, the applicable range of each model is also clarified for the engineering practice.

Influences of Structural Damping and Buoyancy-Weight Ratio on Dynamic Responses of Submerged Floating Tunnel

The recent progress of submerged floating tunnel (SFT) investigation and SFT prototype (SFTP) project in Qiandao Lake (Zhejiang Province, P.R. China) is the background of this research. Structural damping effect is brought into present computation model in terms of Rayleigh damping. Based on the FEM computational results of SFTPs as a function of buoyancy-weight ratio (BWR) under hydrodynamic loads, the effect of BWR on the dynamic response of SFT is illustrated. In addition, human comfort index is adopted to discuss the comfort status of the SFTP.

Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by h

A Review of Active Appearance Models

Active appearance model (AAM) is a powerful generative method for modeling deformable objects. The model decouples the shape and the texture variations of objects, which is followed by an efficient gradient-based model fitting method. Due to the flexible and simple framework, AAM has been widely applied in the fields of computer vision. However, difficulties are met when it is applied to various practical issues, which lead to a lot of prominent improvements to the model. Nevertheless, these difficulties and improvements have not been studied systematically. This motivates us to review the recent advances of AAM. This paper focuses on the improvements in the literature in turns of the problems suffered by AAM in practical applications. Therefore, these algorithms are summarized from three aspects, i.e., efficiency, discrimination, and robustness. Additionally, some applications and implementations of AAM are also enumerated. The main purpose of this paper is to serve as a guide for further research.

Structural selectivity of aromatic diamidines

Competition dialysis was used to study the interactions of 13 substituted aromatic diamidine compounds with 13 nucleic acid structures and sequences. The results show a striking selectivity of these compounds for the triplex structure poly dA:(poly dT)(2), a novel aspect of their interaction with nucleic acids not previously described. The triplex selectivity of selected compounds was confirmed by thermal denaturation studies. Triplex selectivity was found to be modulated by the location of amidine substiuents on the core phenyl-furan-phenyl ring scaffold. Molecular models were constructed to rationalize the triplex selectivity of DB359, the most selective compound in the series. Its triplex selectivity was found to arise from optimal ring stacking on base triplets, along with proper positioning of its amidine substituents to occupy the minor and the major-minor grooves of the triplex. New insights into the molecular recognition of nucleic acid structures emerged from these studies, adding to the list of available design principles for selectively targeting DNA and RNA.

Impacts of anthropogenic activity on the recent evolution of the Huanghe (Yellow) River delta

Hydrological statistical data, remote sensing images, and bathymetric charts were used to study the recent evolution of the Huanghe (Yellow) River delta under human-induced interventions. It was clear that water and sediment discharge from the Huanghe River had dropped rapidly since 1970, particularly after 1986. The water and sediment discharges for the period of 1986-2000 were found to have been reduced to only 29.2% and 31.2% of those in the period of 1950-69. This was caused by human factors in the upper and middle reaches of the Huanghe River, including water diversion, damming and reservoir construction, and water and soil conservation. Based on the results from visual interpretation of processed Landsat (MSS or TMJETM+) images dated from 1976 to 2001 and two digital elevation models generated from bathymetric charts surveyed in 1976 and 1992, we found that human-induced reduction of water and sediment discharge led to coastline retrogradation, with the maximum mean recession rate of -0.51 km yr-1 over the period of 1976-98, and seabed erosion beyond the -20 m isobath between 1976 and 1992. Other impacts of human activities on the recent evolution of the Huanghe River delta, including tidal flats shrinking, artificial coastline increasing, land surface sinking and so on, were also analyzed. We found that: (i) the whole delta, including subaerial and subaqueous, has turned from a highly constructive period to a destructive phase; (ii) channelization and dredging were two of the main causes of delta destruction; (iii) land loss in the Huanghe River delta caused by submersion will be increased in the near future; (iv) the Huanghe River delta was becoming more fragile and susceptible to natural hazards.

东海陆架盆地西南部烟囱构造与油气运聚关系研究

In recent years, chimney structure has been proved one of important indicators and a useful guide to major petroleum fields exploration through their exploration history both at home and abroad. Chimney structure, which has been called "gas chimney" or "seismic chimney", is the special fluid-filled fracture swarm, which results from the boiling of active thermal fluid caused by abruptly decreasing of high pressure and high temperature in sedimentary layers of upper lithosphere. Chimney structure is well developed in continental shelf basin of East China Sea, which indicates the great perspectives of petroleum resources there. However, the chimney structure also complicated the petroleum accumulation. So the study of chimney structure on its formation, its effect on occurrence and distribution of petroleum fields is very important not only on theoretical, but also on its applied research. It is for the first time to make a clear definition of chimney structure in this paper, and the existence and practical meaning of chimney structure are illustrated. Firstly, on the viewpoint of exploration, this will amplify exploration area or field, not only in marine, but also on continent. Secondly, this is very important to step-by-step exploration and development of petroleum fields with overpressure. Thirdly, this will provide reference for the study on complex petroleum system with multi-sources, commingled sources and accumulation, multi-stage accumulations, and multi-suits petroleum system in the overlay basin. Fourthly, when the thermal fluid enters the oceanic shallow layer, it can help form gas hydrate under favorable low-temperature and high-pressure conditions. Meanwhile, the thermal fluid with its particular component and thermal content will affect the physical, chemical and ecological environments, which will help solving the problem of global resources and environment. Beginning from the regional tectonic evolution characteristics, this paper discussed the tectonic evolution history of the Taibei depression, then made an dynamical analysis of the tectonic-sedimentary evolution during the Mesozoic and Cenozoic for the East China Sea basin. A numerical model of the tectonic-thermal evolution of the basin via the Basin-Mod technique was carried out and the subsidence-buried history and thermal history of the Taibei depression were inverse calculated: it had undergone a early rapid rift and sag, then three times of uplift and erosion, and finally depressed and been buried. The Taibei depression contains a huge thick clastic sedimentary rock of marine facies, transitional facies and continental facies on the complex basement of ante-Jurassic. It is a part of the back-arc rifting basins occurred during the Mesozoic and Cenozoic. The author analyzed the diagenesis and thermal fluid evolution of this area via the observation of cathodoluminescence, scanning electron microscope and thin section, taking advantage of the evidences of magma activities, paleo-geothermics and structural movement, the author concluded that there were at least three tectonic-thermal events and three epochs of thermal-fluid activities; and the three epochs of thermal-fluid activities were directly relative to the first two tectonic-thermal events and were controlled by the generation and expulsion of hydrocarbon in the source rock simultaneously. Based on these, this paper established the corresponding model between the tectonic-thermal events and the thermal-fluid evolution of the Taibei Depression, which becomes the base for the study on the chimney structures. According to the analyses of the gas-isotope, LAM spectrum component of fluid inclusion, geneses of CO_2 components and geneses of hydrocarbon gases, the author preliminarily verified four sources of the thermal fluid in the Taibei Depression: ① dehydration of mud shale compaction, ② expulsion of hydrocarbon in the source rock; ③ CO_2 gas hydro-thermal decomposition of carbonatite; ④magma-derived thermal fluid including the mantle magma water and volatile components (such as H_2O, CO_2, H_2S, SO_2, N_2 and He etc.). On the basis of the vitrinite reflectance (Ro), homogenization temperature of fluid inclusion, interval transit time of major well-logging, mud density of the wells, measured pressure data and the results of previous studies, this paper analyzed the characteristics of the geothermal fields and geo-pressure fields for the various parts in this area, and discussed the transversal distribution of fluid pressure. The Taibei depression on the whole underwent a temperature-loss process from hot basin to cold basin; and locally high thermal anomalies occurred on the regional background of moderate thermal structure. The seal was primarily formed during the middle and late Paleocene. The overpressured system was formed during the middle and late Eocene. The formation of overpressured system in Lishui Sag underwent such an evolutionary process as "form-weaken-strengthen-weaken". Namely, it was formed during the middle and late Eocene, then was weakened in the Oligocene, even partly broken, then strengthened after the Miocene, and finally weakened. The existence of the thermal fluid rich in volatile gas is a physical foundation for the boiling of the fluid, and sharply pressure depletion was the major cause for the boiling of the fluid, which suggests that there exists the condition for thermal fluid to boil. According to the results of the photoelastic simulation and similarity physical experiments, the geological condition and the formation mechanism of chimnestructures are summarized: well compartment is the prerequisite for chimney formation; the boiling of active thermal fluid is the original physical condition for chimney formation; The local place with low stress by tension fault is easy for chimney formation; The way that thermal fluid migrates is one of the important factors which control the types of chimney structures. Based on where the thermal fluid come from and geometrical characteristics of the chimney structures, this paper classified the genetic types of chimney structures, and concluded that there existed three types and six subtypes chimney structures: organic chimney structures generated by the hydrocarbon-bearing thermal fluid in middle-shallow layers, inorganic and commingling-genetic chimney structures generated by thermal fluid in middle-deep layers. According to the seismic profiles interpretations, well logging response analysis and mineralogical and petrological characteristics in the study area, the author summarized the comprehensive identification marks for chimney structures. Especially the horizon velocity analysis method that is established in this paper and takes advantage of interval velocity anomaly is a semi-quantitative and reliable method of chimney structure s identification. It was pointed out in this paper that the occurrence of the chimney structures in the Taibei depression made the mechanism of accumulation complicated. The author provided proof of episodic accumulation of hydrocarbon in this area: The organic component in the boiling inclusion is the trail of petroleum migration, showing the causality between the boiling of thermal fluid and the chimney structures, meanwhile showing the paroxysmal accumulation is an important petroleum accumulation model. Based on the evolutionary characteristics of various types of chimney structures, this paper discussed their relationships with the migration-accumulation of petroleum respectively. At the same time, the author summarized the accumulating-dynamical models associated with chimney structures. The author analyzed such accumulation mechanisms as the facies state, direction, power of petroleum migration, the conditions of trap, the accumulation, leakage and reservation of petroleum, and the distribution rule of petroleum. The author also provides explanation for such practical problems the existence of a lot of mantle-derived CO_2, and its heterogeneous distribution on plane. By study on and recognition for chimney structure, the existence and distribution of much mantle-derived CO_2 found in this area are explained. Caused by tectonic thermal activities, the deep magma with much CO_2-bearing thermal fluid migrate upward along deep fault and chimney structures, which makes two wells within relatively short distance different gas composition, such as in well LF-1 and well LS36-1-1. Meanwhile, the author predicted the distribution of petroleum accumulation belt in middle-shallow layer for this area, pointed out the three favorable exploration areas in future, and provided the scientific and deciding references for future study on the commingling-genetic accumulation of petroleum in middle-deep layer and the new energy-gas hydrate.