Air flow over a mountain and the convective boundary-layer

In this paper, the analytical model coupling the convective boundary layer (CBL) with the free atmosphere developed by Qi and Fu (1992) is improved. And by this improved model, the interaction between airflow over a mountain and the CBL is further discussed. The conclusions demonstrate: (1) The perturbation potential temperatures in the free atmosphere can counteract the effect of orographic thermal forcing through entraining and mixing in the CBL. If u(M)BAR > u(F)BAR, the feedback of the perturbation potential temperatures in the free atmosphere is more important than orographic thermal forcing, which promotes the effect of interfacial waves. If u(M)BAR < u(F)BAR, orographic thermal forcing is more important, which makes the interfacial height and the topographic height identical in phase, and the horizontal speeds are a maximum at the top of the mountain. (2) The internal gravity waves propagating vertically in the free atmosphere cause a strong downslope wind to become established above the lee slope in the CBL and result in the hydraulic jump at the top of the CBL. (3) With the CBL deepening, the interfacial gravity waves induced by the potential temperature jump at the top of the CBL cause the airflow in the CBL to be subcritical.

Mechanics of a grip system of three-key-board hydraulic tongs developed for offshore oil pipe lines

This paper carries out the analysis of mechanics of a grip system of three-key-board hydraulic tongs developed for offshore oil pipe lines which has been successfully used in oil fields in China. The main improvement of this system is that a lever frame structure is used in the structural design, which reduces greatly the stresses of the major components of the oil pipe tongs. Theoretical analysis and numerical calculation based on thirteen basic equations developed Show that the teeth board of the tongs is not easy to slip as frequently happens to other systems and is of higher reliability.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

A stochastic jump and deterministic dynamics model of impact failure evolution with rate effect

Motivated by the observation of the rate effect on material failure, a model of nonlinear and nonlocal evolution is developed, that includes both stochastic and dynamic effects. In phase space a transitional region prevails, which distinguishes the failure behavior from a globally stable one to that of catastrophic. Several probability functions are found to characterize the distinctive features of evolution due to different degrees of nucleation, growth and coalescence rates. The results may provide a better understanding of material failure.

The concentration-jump coefficient in a rarefied binary gas-mixture

The results presented are obtained from sound velocity measurements, uniaxial compression tests, Brazilian tests and three-point bending tests. The density of microcracks in the heated rock is studied by means of optical microscopy, SEM and differential strain analysis (DSA).

The concentration-jump coefficient in a rarefied binary gas-mixture

The problem of the concentration jump of a vapour in the vicinity of a plane wall, which consists of the condensed phase of the vapour, in a rarefied gas mixture of that vapour (A) and another 'inert' gas (B), is considered. The general formulation of the problem of determining the concentration-jump coefficient for dA is given. In the Knudsen layer the simplest model of Boley-Yip theory is used to simplify the Boltzmann equations for the binary gas mixture. The numerical calculation of the concentration jump coefficient for dA for various values of evaporation coefficient of A is illustrated for the case of the equilibrium concentration of B being much greater than that of A, for which experimental data are available.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by "GAMESS", and the rest atoms are treated as MM part calculated by "TINKER". The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(100) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the in-tidazole rings are attached to the substrate more tightly than other bases in this peptide.

A numerical model for predicting the jump of lift force on an oscillating cylinder

The fluid force coefficients on a transversely oscillating cylinder are calculated by applying two- dimensional large eddy simulation method. Considering the ‘‘jump’’ phenomenon of the amplitude of lift coefficient is harmful to the security of the submarine slender structures, the characteristics of this ‘‘jump’’ are dissertated concretely. By comparing with experiment results, we establish a numerical model for predicting the jump of lift force on an oscillating cylinder, providing consultation for revising the hydrodynamic parameters and checking the fatigue life scale design of submarine slender cylindrical structures.

Resolution and noise in ghost imaging with classical thermal light

The resolution and classical noise in ghost imaging with a classical thermal light are investigated theoretically. For ghost imaging with a Gaussian Schell model source, the dependences of the resolution and noise on the spatial coherence of the source and the aperture in the imaging system are discussed and demonstrated by using numerical simulations. The results show that an incoherent source and a large aperture will lead to a good image quality and small noise.

Classical correlated imaging from the perspective of coherent-mode representation

We use coherent-mode representation of partially coherent fields to analyze correlated imaging with classical light sources. This formalism is very useful to study the imaging quality. By decomposing the unknown object as the superposition of different coherent modes, the components corresponding to small eigenvalues cannot be well imaged. The generated images depend crucially on the distribution of the eigenvalues of the coherent-mode representation of the source and the decomposition coefficients of the objects. Three kinds of correlated imaging schemes are analyzed numerically.

De novo RNA synthesis and homology modeling of the classical swine fever virus RNA polymerase

Classical swine fever virus (CSFV) non-structural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp), a key enzyme which initiates RNA replication by a de novo mechanism without a primer and is a potential target for anti-virus therapy. We expressed the NS5B protein in Escherichia coli. The rGTP can stimulate de novo initiation of RNA synthesis and mutation of the GDD motif to Gly-Asp-Asp (GAA) abolishes the RNA synthesis. To better understand the mechanism of viral RNA synthesis in CSFV, a three-dimensional model was built by homology modeling based on the alignment with several virus RdRps. The model contains 605 residues folded in the characteristic fingers, palm and thumb domains. The fingers domain contains an N-terminal region that plays an important role in conformational change. We propose that the experimentally observed promotion of polymerase efficiency by rGTP is probably due to the conformational changes of the polymerase caused by binding the rGTP. Mutation of the GDD to GAA interferes with the interaction between the residues at the polymerase active site and metal ions, and thus renders the polymerase inactive. (c) 2005 Elsevier B.V. All rights reserved.

Classical two-site fidelity and quantum phase transitions in the Ising model and the extended Hubbard model

In this Letter, the classical two-site-ground-state fidelity (CTGF) is exploited to identify quantum phase transitions (QPTs) for the transverse field Ising model (TFIM) and the one-dimensional extended Hubbard model (EHM). Our results show that the CTGF exhibits an abrupt change around the regions of criticality and can be used to identify QPTs in spin and fermionic systems. The method is especially convenient when it is connected with the density-matrix renormalization group (DMRG) algorithm. (C) 2008 Elsevier B.V. All rights reserved.