Interaction between human interleukin-16 and CD4 receptor of HIV-1

AIM: To study the interaction between human interleukin-16 (IL-16) and the receptor CD4 (T-lymphocyte differentiation antigen) of human immunodeficiency virus type 1 (HIV-1). METHODS: Two structurally con served regions (SCRs) of human IL-16 were built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of human interleukin-1 (HIL-4) and HIL-2 as the templates. The coordinates for amino-terminal residue sequence, carboxyl-terminal residue sequences, and cytoplasm loops were generated using Biopolymer's LOOP SEARCH algorithm. RESULTS: HIL-16 first formed a homodimer, then contacted with CD4 dimer further forming a dimeric complex. Subsequently, the dimeric complex constructed the tetrameric complex by two disulfide bridges between the cysteines of HIL-16 (Cys31-Cys31). CONCLUSION: The interaction model is useful to propose the action mechanism of HIL-16 and is beneficial for rational designing of novel anti-HIV drugs.

Improved Analysis Method for Wave-Induced Pipeline Stability on Sandy Seabed

The existing Det Norske Veritas DNV Recommended Practice RP E305 for pipeline on-bottom stability is mainly based on the pipe–soil interaction model reported by Wagner et al. in 1987, and the wake model reported by Lambrakos et al. in 1987, to calculate the soil resistance and the hydrodynamic forces upon pipeline, respectively. Unlike the methods in the DNV Practice, in this paper, an improved analysis method is proposed for the on-bottom stability of a submarine pipeline, which is based on the relationships between Um/ gD 0.5 and Ws / D2 for various restraint conditions obtained by the hydrodynamic loading experiments, taking into account the coupling effects between wave, pipeline, and sandy seabed. The analysis procedure is illustrated with a detailed flow chart. A comparison is made between the submerged weights of pipeline predicted with the DNV Practice and those with the new method. The proposed analysis method may provide a helpful tool for the engineering practice of pipeline on-bottom stability design.

Molecular modeling on human CCR5 receptors and complex with CD4 antigens and HIV-1 envelope glycoprotein gp120

AIM: To investigate the interaction between human CCR5 receptors (CCR5) and HIV-1 envelope glycoprotein gp120 (HIV-1 gp120) and HIV-1 receptor CD4 antigens (CD4). METHODS: The structurally con served regions (SCR) of human CCR5 was built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of bacteriorhodopsin (bR) as the template. The coordinates for amino-ter minal residue sequence, and carboxyl-terminal residue sequence, extracellular and cytoplasmic loops were generated using LOOP SEARCH algorithm. Subsequently the structural model was merged into the complex with HIV-1 gp120 and CD4. RESULTS: Human CCR5 interacted with both an HIV-1 gp120 and CD4. The N-terminal residues (especially Met1 and Gln4) of human CCR5, contacted with CD4 residues, mainly 7Nith one span (56 - 59) of CD4 in electrostatic interaction and hydrogen-bonds. The binding sites of human CCR5 were buried in a hydrophobic center surrounded by a highly basic periphery. On the other hand, direct interatomic contacts were made between ? CCR5 residues and 6 gp120 amino-acid residues, which included van der Waals contacts, hydrophobic interaction, and hydrogen bonds. CONCLUSION: The interaction model should be helpful for rational design of novel anti-HIV drugs.

Soil microbial community analysis using terminal restriction fragment length polymorphisms

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a polymerase chain reaction (PCR)-fingerprinting method that is commonly used for comparative microbial community analysis. The method can be used to analyze communities of bacteria, archaea, fungi, other phylogenetic groups or subgroups, as well as functional genes. The method is rapid, highly reproducible, and often yields a higher number of operational taxonomic units than other, commonly used PCR-fingerprinting methods. Sizing of terminal restriction fragments (T-RFs) can now be done using capillary sequencing technology allowing samples contained in 96- or 384-well plates to be sized in an overnight run. Many multivariate statistical approaches have been used to interpret and compare T-RFLP fingerprints derived from different communities. Detrended correspondence analysis and the additive main effects with multiplicative interaction model are particularly useful for revealing trends in T-RFLP data. Due to biases inherent in the method, linking the size of T-RFs derived from complex communities to existing sequence databases to infer their taxonomic position is not very robust. This approach has been used successfully, however, to identify and follow the dynamics of members within very simple or model communities. The T-RFLP approach has been used successfully to analyze the composition of microbial communities in soil, water, marine, and lacustrine sediments, biofilms, feces, in and on plant tissues, and in the digestive tracts of insects and mammals. The T-RFLP method is a user-friendly molecular approach to microbial community analysis that is adding significant information to studies of microbial populations in many environments.

地质导向钻井关键技术及方法

On the basis of analyzing the principle and realization of geo-steering drilling system, the key technologies and methods in it are systematically studied in this paper. In order to recognize lithology, distinguish stratum and track reservoirs, the techniques of MWD and data process about natural gamma, resistivity, inductive density and porosity are researched. The methods for pre-processing and standardizing MWD data and for converting geological data in directional and horizontal drilling are discussed, consequently the methods of data conversion between MD and TVD and those of formation description and adjacent well contrast are proposed. Researching the method of identifying sub-layer yields the techniques of single well explanation, multi-well evaluation and oil reservoir description. Using the extremum and variance clustering analysis realizes logging phase analysis and stratum subdivision and explanation, which provides a theoretical method and lays a technical basis for tracing oil reservoirs and achieving geo-steering drilling. Researching the technique for exploring the reservoir top with a holdup section provides a planning method of wellpath control scheme to trace oil and gas reservoir dynamically, which solves the problem of how to control well trajectory on condition that the layer’s TVD is uncertain. The control scheme and planning method of well path for meeting the demands of target hitting, soft landing and continuous steering respectively provide the technological guarantee to land safely and drill successfully for horizontal, extended-reach and multi-target wells. The integrative design and control technologies are researched based on geology, reservoir and drilling considering reservoir disclosing ratio as a primary index, and the methods for planning and control optimum wellpath under multi-target restriction, thus which lets the target wellpath lie the favorite position in oil reservoir during the process of geo-steering drilling. The BHA (bottomhole assembly) mechanical model is discussed using the finite element method, and the BHA design methods are given on the basis of mechanical analyses according to the shape of well trajectory and the characteristics of BHA’s structure and deformation. The methods for predicting the deflection rate of bent housing motors and designing their assemblies are proposed based on the principle of minimum potential energy, which can clearly show the relation between the BHA’s structure parameters and deflection rate, especially the key factors’ effect to the deflection rate. Moreover, the interaction model between bit and formation is discussed through the process of equivalent formation and equivalent bit considering the formation anisotropy and bit anisotropy on the basis of analyzing the influence factors of well trajectory. Accordingly, the inherence relationship among well trajectory, formation, bit and drilling direction is revealed, which lays the theory basis and technique for predicting and controlling well trajectory.

Quantum Monte Carlo study of the CO interaction with a dimer model surface for Cr(110)

The chemisorption of CO on a Cr( 110) surface is investigated using the quantum Monte Carlo method in the diffusion Monte Carlo (DMC) variant and a model Cr2CO cluster. The present results are consistent with the earlier ab initio HF study with this model that showed the tilted/ near-parallel orientation as energetically favoured over the perpendicular arrangement. The DMC energy difference between the two orientations is larger (1.9 eV) than that computed in the previous study. The distribution and reorganization of electrons during CO adsorption on the model surface are analysed using the topological electron localization function method that yields electron populations, charge transfer and clear insight on the chemical bonding that occurs with CO adsorption and dissociation on the model surface.

On the interaction of water waves and seabed by the porous medium model

The interaction of water waves and seabed is studied by using Yamamoto's model, which takes into account the deformation of soil skeletal frame, compressibility of pore fluid flow as well as the Coulumb friction. When analyzing the propagation of three kinds of stress waves in seabed, a simplified dispersion relation and a specific damping formula are derived. The problem of seabed stability is further treated analytically based on the Mohr-Coulomb theory. The theory is finally applied to the coastal problems in the Lian-Yun Harbour and compared with observations and measurements in soil-wave tank with satisfactory results.

Interplay between the Dzyaloshinskii-Moriya anisotropic antisymmetric interaction and the SWAP operation in a two-qubit Heisenberg model

The SWAP operation in a two-qubit Heisenberg model in the presence of Dzyaloshinskii-Moriya (DM) anisotropic antisymmetric interaction is investigated. 1t is shown that the SWAP operation can be implemented for some kinds of DM coupling and the influence of DM couplings is divided into different cases. The conditions of the DM coupling under which the SWAP operation is feasible are established. (C) 2007 Elsevier B.V. All rights reserved.

Hyperon-hyperon interaction in relativistic mean field model

By using the new experimental data of Lambda Lambda potential, this paper has performed a full calculation for strange hadronic matter with different strangeness contents as well as its consequences on the global properties of neutron star matter in relativistic mean field model. It finds that the new weak hyperon - hyperon interaction makes the equations of state much stiffer than the result of the previous strong hyperon-hyperon interaction, and even stiffer than the result without consideration of hyperon -hyperon interaction. This new hyperon -hyperon interaction results in a maximum mass of 1.75M(circle dot) ( where M-circle dot stands for the mass of the Sun), about 0.2-0.5M(circle dot) larger than the previous prediction with the presence of hyperons. After examining carefully the onset densities of kaon condensation it finds that this new weak version of hyperon -hyperon interaction favours the occurrence of kaons in comparison with the strong one.

Analytical Interaction of the Acoustic Wave and Turbulent Flame

A modified resonance model of a weakly turbulent flame in a high-frequency acoustic wave is derived analytically. Under the mechanism of Darrieus-Landau instability, the amplitude of flame wrinkles, which is as functions of the expansion coefficient and the perturbation wave number, increases greatly independent of the 'stationary' turbulence. The high perturbation wave number makes the resonance easier to be triggered but weakened with respect to the extra acoustic wave. In a closed burning chamber with the acoustic wave induced by the flame itself, the high perturbation wave number is to restrain the resonance for a realistic flame.

Correlative reference model and molecular dynamics simulation of dislocation emission process

A correlative reference model for computer molecular dynamics simulations is proposed. Based on this model, a flexible displacement boundary scheme is introduced and the dislocations emitted from a crack tip can continuously pass through the border of the inner discrete atomic region and pile up at the outer continuum region. The effect of the emitted dislocations within the plastic zone on the inner atomistic region can be clearly demonstrated. The simulations for a molybdinum crystal show that a full dislocation in a bcc crystal is dissociated into three partial dislocations and interaction between the crack and the emitted dislocations results in gradual decrease of the local stress intensity factor.

Conjugate Model for Heat and Mass Transfer of Porous Wall in the High Temperature Gas Flow

Heat and mass transfer of a porous permeable wall in a high temperature gas dynamical flow is considered. Numerical simulation is conducted on the ground of the conjugate mathematical model which includes filtration and heat transfer equations in a porous body and boundary layer equations on its surface. Such an approach enables one to take into account complex interaction between heat and mass transfer in the gasdynamical flow and in the structure subjected to this flow. The main attention is given to the impact of the intraporous heat transfer intensity on the transpiration cooling efficiency.

Evolution induced catastrophe in a nonlinear dynamical model of material failure

In order to study the failure of disordered materials, the ensemble evolution of a nonlinear chain model was examined by using a stochastic slice sampling method. The following results were obtained. (1) Sample-specific behavior, i.e. evolutions are different from sample to sample in some cases under the same macroscopic conditions, is observed for various load-sharing rules except in the globally mean field theory. The evolution according to the cluster load-sharing rule, which reflects the interaction between broken clusters, cannot be predicted by a simple criterion from the initial damage pattern and even then is most complicated. (2) A binary failure probability, its transitional region, where globally stable (GS) modes and evolution-induced catastrophic (EIC) modes coexist, and the corresponding scaling laws are fundamental to the failure. There is a sensitive zone in the vicinity of the boundary between the GS and EIC regions in phase space, where a slight stochastic increment in damage can trigger a radical transition from GS to EIC. (3) The distribution of strength is obtained from the binary failure probability. This, like sample-specificity, originates from a trans-scale sensitivity linking meso-scopic and macroscopic phenomena. (4) Strong fluctuations in stress distribution different from that of GS modes may be assumed as a precursor of evolution-induced catastrophe (EIC).

Experiments on interaction between current-induced vibration and scour of submarine pipelines on sandy bottom

In order to understand the dynamic behavior of submarine pipelines exposed to current and the mechanism of the interaction between current-induced vibration and scour of pipelines on a sandy bottom, an experimental investigation is conducted with a small scale model A test model which can be tested in the flume is set up by taking into account the typical working conditions of the pipelines and by applying the similarity theory. The interactions between the shape of the scour hole and the behavior of the pipeline as well as the flow patterns of the current are detailed, and the interaction mechanism outlined. The effect of vibration of the pipeline on the development of dynamic scour at different stages is found out. The proposed experimental method and test results provide an effective means for design of marine pipelines against scouring.