A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Direct patterning of negative nanostructures on self-assembled monolayers of 16-mercaptohexadecanoic acid on Au(111) substrate via dip-pen nanolithography

Both bare and self-assembled monolayer (SAM) protected gold substrate could be etched by allyl bromide according to atomic force microscopy (AFM), x-ray photoelectron spectroscopy (XPS) and inductively coupled plasma mass spectrometric (ICPMS) analysis results. With this allyl bromide ink material, negative nanopatterns could be fabricated directly by dip-pen nanolithography (DPN) on SAMs of 16-mercaptohexadecanoic acid (MHA) on Au(111) substrate. A tip-promoted etching mechanism was proposed where the gold-reactive ink could penetrate the MHA resist film through tip-induced defects resulting in local corrosive removal of the gold substrate. The fabrication mechanism was also confirmed by electrochemical characterization, energy dispersive spectroscopy (EDS) analysis and fabrication of positive nanopatterns via a used DPN tip.

飞行器多任务在线实时航迹规划

针对不确定环境中的飞行器多任务航迹规划问题展开研究,提出了一种基于飞行路线图的两阶段航迹规划框架,航迹规划分成学习和查询两个阶段,环境信息和飞行器约束条件分阶段体现.在该框架下,通过采用一种混合多任务动态航迹规划方法,分别在稀疏路线图上实时搜索初始航迹和在精细路线图上启发式搜索后备航迹,能够在具有预先未知威胁、可变飞行任务的战场环境中实时生成三维航迹.

Negative refraction in a honeycomb-lattice photonic crystal

In this paper we theoretically investigate a photonic crystal with dielectric rods in a honeycomb lattice. Two left-handed frequency regions are found in the second and third photonic band by using the plane wave expansion method to analyze the photonic band structure and equifrequency contours. Subwavelength imaging by the photonic crystal flat lens are systematically studied by numerical simulations using the multiple scattering method. Different from the photonic crystals with noncircular dielectric rods in air, this structure is almost isotropic at the optimal frequency for superlensing. As a comparison, flat slab focusing is also demonstrated at other frequencies in the two left-handed regions. (c) 2006 Elsevier Ltd. All rights reserved.

Numerical solution of the incompressible Navier-Stokes equations with an upwind compact difference scheme

A new finite difference method for the discretization of the incompressible Navier-Stokes equations is presented. The scheme is constructed on a staggered-mesh grid system. The convection terms are discretized with a fifth-order-accurate upwind compact difference approximation, the viscous terms are discretized with a sixth-order symmetrical compact difference approximation, the continuity equation and the pressure gradient in the momentum equations are discretized with a fourth-order difference approximation on a cell-centered mesh. Time advancement uses a three-stage Runge-Kutta method. The Poisson equation for computing the pressure is solved with preconditioning. Accuracy analysis shows that the new method has high resolving efficiency. Validation of the method by computation of Taylor's vortex array is presented.

Combined Effects of Silica Filler and Its Interface in Epoxy Resin

In this paper, mechanical properties of silica-filled epoxy resin are tested. The tests show that at elevated temperatures, the material’s properties (e.g. yield stress, flow stress, etc.) vary immonotonically with filler volume fraction. Nanoindentation test results suggest that an interface region, stronger than the matrix, is formed in the materials. The formation of the interface has positive effects on the yield strengths of materials. The addition of particles in the matrix produces a large disturbance in stress distribution, leading to stress concentration in the matrix. The stress concentration has negative effects on the yield strengths of materials. The calculation demonstrates that the maximum stress in samples varies immonotonically with particulate concentration. So, the immonotonic variation of mechanical behavior of materials may be rooted in the contradictory effects of the interface region and the stress concentration caused by particulate addition.

3D Finite Volume Scheme for Czochralski Crystal Growth

A general three-dimensional model is developed for simulation of the growth process of silicon single crystals by Czochralski technique. The numerical scheme is based on the curvilinear non-orthogonal finite volume discretization. Numerical solutions show that the flow and temperature fields in the melt are asymmetric and unsteady for 8’’ silicon growth. The effects of rotation of crystal on the flow structure are studied. The rotation of crystal forms the Ekman layer in which the temperature gradient along solid/melt surface is small.

A CE/SE Scheme for Flows in Porous Media and Its Applications

In this paper, a new computational scheme for solving flows in porous media was proposed. The scheme was based on an improved CE/SE method (the space-time Conservation Element and Solution Element method). We described porous flows by adopting DFB (Brinkman-Forchheimer extended Darcy) equation. The comparison between our computational results and Ghia's confirmed the high accuracy, resolution, and efficiency of our CE/SE scheme. The proposed first-order CE/SE scheme is a new reliable way for numerical simulations of flows in porous media. After investigation of effects of Darcy number on porous flow, it shows that Darcy number has dominant influence on porous flow for the Reynolds number and porosity considered.

Negative effects of Microcystis blooms on the crustacean plankton in an enclosure experiment in the subtropical China

Effects of Microcystis blooms on the crustacean plankton were studied using enclosure experiments during July-September, 2000. Eight enclosures were set in the hypereutrophic Donghu Lake. Different nutrient concentrations through additional nutrient and sediment in enclosures were expected to result in different abundance of Micropystis. From July to early August, the phytoplankton community was dominated by Chlorophyta, Cryptophyta, Bacillariophyta and Cyanophyta other than Microcystis aeruginosa. M. aeruginosa showed a rapid increase during early August in all enclosures and predominated. Crustacean plankton was dominated by the herbivorous Moina micrura, Diaphanosoma brachyurum and Ceriodaphnia cornuta, and the predaceous Mesocyclops sp. and Thermocyclops taihokuensis. During the pre-bloom period, the dynamics of M. micrura population appeared to be mainly affected by the predaceous cyclopoids. With the development of Microcystis blooms, such interaction between M. micrura and cyclopoids seemed weakened, especially when the Microcystis biomass was high. But there was no apparent influence on the interaction between Leptodora kindti and its zooplanktonic prey. The density of two cyclopoids decreased with the enhancement of Microcystis. The density decline of M. micrura was caused by both predation and inhibition by Micropystis. The low food availability of other edible phytoplankton during the blooms led to low densities of both C. cornuta and D. brachyurum by late August. It appears that dense Microcystis blooms exert strong negative effects on the herbivorous cladocerans and the predaceous cyclopoids.

Origin of the blueshift in the infrared absorbance of intersubband transitions in AlxGa1-x/GaN multiple quantum wells

A self-consistent calculation of the subband energy levels of n-doped quantum wells is studied. A comparison is made between theoretical results and experimental data. In order to account for the deviations between them, the ground-state electron-electron exchange interactions, the ground-state direct Coulomb interactions, the depolarization effect, and the exciton-like effect are considered in the simulations. The agreement between theory and experiment is greatly improved when all these aspects are taken into account. The ground-to-excited-state energy difference increases by 8 meV from its self-consistent value if one considers the depolarization effect and the exciton-like effect only. It appears that the electron-electron exchange interactions account for most of the observed residual blueshift for the infrared intersubband absorbance in AlxGa1-xN/GaN multiple quantum wells. It seems that electrons on the surface of the k-space Fermi gas make the main contribution to the electron-electron exchange interactions, while for electrons further inside the Fermi gas it is difficult to exchange their positions. (C) 2004 Elsevier B.V. All rights reserved.

Effect of an indium-doped barrier on enhanced near-ultraviolet emission from InGaN/AlGaN: In multiple quantum wells grown on Si(111)

Low indium content InGaN/AlGaN multiple quantum wells (MQWs) have been grown on Si(111) substrate by metal-organic chemical vapour deposition (MOCVD). A new method of using an isoelectronic indium-doped AlGaN barrier has been found to be very effective in improving the crystalline quality and interfacial abruptness of InGaN quantum well layers. We grew five periods of In0.06Ga0.94N/Al0.20Ga0.80N:In MQWs with In-doped barrier layers and obtained strong near-ultraviolet (UV) emission (similar to 400 nm) at room temperature. An In-doped AlGaN barrier improves the room-temperature PL intensity of InGaN/AlGaN MQWs, making it a candidate barrier for a near-UV source on Si substrate.

The effect of Be-doping structure in negative electron affinity GaAs photocathodes on integrated photosensitivity

A new structure of GaAs photocathode was introduced. The Be-doping concentration is variable in the new structure compared with the constant concentration of Be in the normal photocathode. Negative electron affinity GaAs photocathodes were fabricated by alternate input of Cs and O. The spectral response results measured by the on-line spectral response measurement system show that the integrated photosensitivity of the photocathodes with the new structure is enhanced by at least 50% as compared to those with the monolayer structure. Accordingly, two main factors leading to the enhanced photosensitivity of the photocathodes were discussed. (c) 2005 Elsevier B.V. All rights reserved.

A power-saving scheme for IEEE 802.11 Ad hoc networks

In the Wireless Local Area Networks (WLANs), the terminals are often powered by battery, so the power-saving performance of the wireless network card is a very important issue. For IEEE 802.11 Ad hoc networks, a power-saving scheme is presented in Medium Access Control (MAC) layer to reduce the power consumption by allowing the nodes enter into the sleep mode, but the scheme is based on Time-Drive Scheme (TDS) whose power-saving efficiency becomes lower and lower with the network load increasing. This paper presented a novel energy-saving mechanism, called as Hybrid-Drive Scheme (HDS), which introduces into a Message.-Drive Scheme (MDS) and combines MDS with the conventional TDS. The MDS, could obtain high efficiency when the load is heavy; meanwhile the TDS has high efficiency when the network load is small. The analysis shows that the proposed HDS could obtain high energy-efficiency whether the network load is light or heavy and have higher energy-saving efficiency than conventional scheme in the IEEE 802.11 standard.

High-Integrated-Photosensitivity Negative-Electron-Affinity GaAs Photocathodes with Multilayer Be-Doping Structures

The effect of changing Be doping concentration in GaAs layer on the integrated photosensitivity for nega- tive-electron-affinity GaAs photocathodes is investigated. Two GaAs samples with the monolayer structure and the muhilayer structure are grown by molecular beam epitaxy. The former has a constant Be concentration of 1 × 10^19 cm^-3, while the latter includes four layers with Be doping concentrations of 1 × 10^19, 7 × 10^18, 4 × 10^18, and 1 × 10^18 cm^-3 from the bottom to the surface. Negative-electron-affinity GaAs photocathodes are fabricated by exciting the sample surfaces with alternating input of Cs and O in the high vacuum system. The spectral response results measured by the on-line spectral response measurement system show that the integrated photosensitivity of the photocathode with the muhilayer structure enhanced by at least 50% as compared to that of the monolayer structure. This attributes to the improvement in the crystal quality and the increase in the surface escape probability. Different stress situations are observed on GaAs samples with monolayer structure and muhilayer structure, respectively.

Formation of Fullerooxazoles from C61HPh3-: The Regioselectivity of Heteroatom Additions

The formation of fullerooxazoles from C61HPh3- has been examined in benzonitrile (PhCN), m-methoxybenzonitrile (m-OCH3PhCN), m-tolunitrile (m-CH3PhCN), and o-tolunitrile (o-CH3PhCN), where cis-1 bisadducts wit h Ph-, m-OCH3Ph-, m-CH3Ph-, and o-CH3Ph-substituted cyclic imidate next to the phenylmethano are formed its evidenced by various characterizations. Interestingly, only regioisomers 2a-d with the oxygen atom bonded to C4/C5 and the nitrogen atom bonded to C3/C6 are generated its demonstrated by heteronuclear multiple bond coherence (HMBC) NMR, while the alternative regioisomers 3a-d, which have the oxygen and nitrogen atoms at C3/C6 and C4/C5, respectively, are not formed from the reactions, even though the DFT (density functional theory) calculations have predicted that the energy differences between the two types of regioisomers are very small, with regioisomers 3a-d actually having lower energies than 2a-d The results are rationalized by the charge distributions Of C61HPh3-, where computational calculations have shown that the negative charges on C4 and C5 are greater than those on C3 and C6, indicating that the exhibited site selectivity of heteroatoms is a result of the charge-directed addition process