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.

An Improved Ce/Se Scheme For Multi-Material Elastic-Plastic Flows And Its Applications

In this paper, a new definition of SE and CE, which is based on the hexahedron mesh and simpler than Chang's original CE/SE method (the space-time Conservation Element and Solution Element method), is proposed and an improved CE/SE scheme is constructed. Furthermore, the improved CE/SE scheme is extended in order to solve the elastic-plastic flow problems. The hybrid particle level set method is used for tracing the interfaces of materials. Proper boundary conditions are presented in interface tracking. Two high-velocity impact problems are simulated numerically and the computational results are carefully compared with the experimental data, as well as the results from other literature and LS-DYNA software. The comparisons show that the computational scheme developed currently is clear in physical concept, easy to be implemented and high accurate and efficient for the problems considered. (C) 2008 Elsevier Ltd. All rights reserved.

A Hybrid Scheme Based on Finite Element/Volume Methods for Two Immiscible Fluid Flows

We have successfully extended our implicit hybrid finite element/volume (FE/FV) solver to flows involving two immiscible fluids. The solver is based on the segregated pressure correction or projection method on staggered unstructured hybrid meshes. An intermediate velocity field is first obtained by solving the momentum equations with the matrix-free implicit cell-centered FV method. The pressure Poisson equation is solved by the node-based Galerkin FE method for an auxiliary variable. The auxiliary variable is used to update the velocity field and the pressure field. The pressure field is carefully updated by taking into account the velocity divergence field. This updating strategy can be rigorously proven to be able to eliminate the unphysical pressure boundary layer and is crucial for the correct temporal convergence rate. Our current staggered-mesh scheme is distinct from other conventional ones in that we store the velocity components at cell centers and the auxiliary variable at vertices. The fluid interface is captured by solving an advection equation for the volume fraction of one of the fluids. The same matrix-free FV method, as the one used for momentum equations, is used to solve the advection equation. We will focus on the interface sharpening strategy to minimize the smearing of the interface over time. We have developed and implemented a global mass conservation algorithm that enforces the conservation of the mass for each fluid.

An Improved CE/SE Scheme for Numerical Simulation of Gaseous and Two-Phase Detonations

A new structure of solution elements and conservation elements based on rectangular mesh was pro- posed and an improved space-time conservation element and solution element (CE/SE) scheme with sec- ond-order accuracy was constructed. Furthermore, the application of improved CE/SE scheme was extended to detonation simulation. Three models were used for chemical reaction in gaseous detonation. And a two-fluid model was used for two-phase (gas–droplet) detonation. Shock reflections were simu- lated by the improved CE/SE scheme and the numerical results were compared with those obtained by other different numerical schemes. Gaseous and gas–droplet planar detonations were simulated and the numerical results were carefully compared with the experimental data and theoretical results based on C–J theory. Mach reflection of a cellular detonation was also simulated, and the numerical cellular pat- terns were compared with experimental ones. Comparisons show that the improved CE/SE scheme is clear in physical concept, easy to be implemented and high accurate for above-mentioned problems.

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.

Electronic entanglement purification scheme enhanced by charge detections

We present an entanglement purification scheme for the mixed entangled states of electrons with the aid of charge detections. Our scheme adopts the electronic polarizing beam splitters rather than the controlled-NOT (CNOT) operations, but the total successful probability of our scheme can reach the quantity as large as that of the the CNOT-operation-based protocol and twice as large as that of linear-optics-based protocol for the purification of photonic entangled states. Thus our scheme can achieve a high successful prabability without the usage of CNOT operations.

A plasma channel scheme for the interaction of an intense femtosecond laser pulse with a deuterium cluster jet

We propose a plasma channel scheme to obtain an improved table-top laser driven fusion neutron yield as a result of explosions of large deuterium clusters irradiated by an intense laser pulse. A cylindrical plasma channel is created by two moderate intensity laser prepulses at the edge of a deuterium cluster jet along which an intense main laser pulse propagates several nanoseconds later. With the aid of this plasma channel, the main laser pulse will be allowed to deposit its energy into the central region of the deuterium gas jet where the cluster sizes are larger and the atomic density is higher. The plasma channel formation and its impact on the deuterium ion energy spectrum and the consequent fusion neutron yield have been investigated. The calculated results show that a remarkable increase of the table-top laser driven fusion neutron yield would be expected.

Enhancement of Kerr nonlinearity with vanishing absorption in a tripod scheme

The giant enhancement of Kerr nonlinearity in a four-level tripod type system is investigated theoretically. By tuning the value of the Rabi frequency of the coherent control field, owing to the double dark resonances, the giant-enhanced Kerr nonlinearity can be achieved within the right transparency window. The in fluence of Doppler broadening is also discussed.

Routing scheme, permutation properties, and optical implementation of a four-shuffle-exchange-based Omega network

The routing scheme and some permutation properties of a four-shuffle-exchange-based Omega network are discussed. The corresponding optical setup, which is composed of 2-D phase spatial light modulators and calcite plates, is proposed and demonstrated through mapping the inputs to a 2-D array. Instead of one shuffle-exchange followed by one switching operation as in ordinary Omega networks, in our presented system, the shuffle interconnection embraced in the switches is accomplished simply by varying the switching structure of each stage. For the proposed polarization-optical modules, the system is compact in structure, efficient in performance, and insensitive to the environment. (C) 1997 Society of Photo-Optical Instrumentation Engineers.

基于法布里-珀罗干涉仪的毫米波副载波光学产生方法

在光纤无线电系统(ROF)中，提出了一种利用法布里-珀罗干涉仪来实现将一个光学脉冲转换为毫米波频率调制的光学脉冲的方法。在这种方法中，毫米波调制的频率是由法布里-珀罗干涉仪的腔长来决定的，而脉冲序列振幅衰减和能量转移效率则是由法布里-珀罗干涉仪的腔镜反射率决定的。同时，文中对输出脉冲宽度的扩展所导致的脉冲间的干涉问题也进行了详细阐述。

Investigation on nonradiative decay of the (Er3+I13/2)-I-4 -> I-4(15/2) transition in different tellurite glass matrix

Three kinds of Er3+-doped tellurite glasses with different hydroxyl groups are prepared by the conventional melt-quenching method. Infrared spectra are measured to estimate the exact content of OH- groups in samples. The maximum phonon energy in glasses are obtained by measuring the Raman scattering spectra. The strength parameters Omega(t) (t = 2, 4, 6) for all the samples are calculated and compared. The nonradiative decay rate of the Er3+ I-4(13/2) -> I-4(15/2) transition are calculated for the glass samples with different phonon energy and OH- group contents. Finally, the effect of OH- groups on fluorescence decay rate of Er3+ is analysed, the constant KOH-Er Of TWN, TZPL and TZL glasses are calculated to be 9.2 x 10(-19) cm(4)s(-1), 5.9 x 10(-19) cm(4)s(-1), and 3.5 x 10(-19) cm(4)s(-1), respectively.

Effect of hydroxyl groups on nonradiative decay of Er3+: I-4(13/2)-> I-4(15/2) transition in zinc tellurite glasses

A series of zinc tellurite glasses of 75TeO(2)-20ZnO-(5-x)La2O3-xEr(2)O(3) (x=0.02, 0.05, and 0.1 mol%) with the different hydroxl groups were prepared by the conventional melt-quenching method. Infrared spectra were measured in order to estimate the exact content of OH- groups in samples. The observed increase of the fluorescence lifetime with the oxygen bubbling time has been related to the reduction in the OH- content concentration as evidenced by IR transmission spectra. Various nonradiative decay rates from I-4(13/2) of Er3+ with. the change of OH content were determined from the fluorescence lifetime and radiative decay rates were calculated on the basis of Judd-Ofelt theory. (c) 2005 Elsevier B.V. All rights reserved.

Spectroscopic and fluorescence decay behaviors of Yb3+ -doped SiO2-PbO-Na2O-K2O glass

The spectroscopic and fluorescent decay behaviors of Yb3+-doped SiO2-PbO-Na2O-K2O glass is reported in this work. Yb2O3 contents of 1, 1.5 and 2mol% are added into the glass. Through the measurement of absorption and fluorescence spectra, and fluorescent decay rate at room temperature and at low temperature (18 K), it is found that the nonradiative decay rate of Yb3+ ions is mainly determined by the interaction between residual hydroxyl groups and Yb3+ ions. Concentration quenching effect can be omitted in this glass up to the Yb3+ ion concentration of 8.98 x 10(20)/cm(3). Multiphonon decay rate is also very small because of the large energy gap between F-2(5/2) and F-2(7/2) levels of Yb3+ ions. (c) 2004 Elsevier B.V. All rights reserved.

Growth and spectroscopic characteristics of Yb : GSO single crystal

For the first time, a high optical quality 10 at.% Yb3+-doped gadolinium oxyorthosilicate laser crystal Gd2SiO5 (GSO) was grown by the Czochralski (Cz) method. The segregation coefficient of Yb3+ was studied by the inductively coupled plasma atomic emission spectrometer (ICP-AES) method. The crystal structure has monoclinic symmetry with space group P2(1)/c; this was determined by means of an x-ray diffraction analysis. The absorption spectra, fluorescence spectra and fluorescence decay curves of Yb3+ ions in a GSO crystal at room temperature were also studied. Then, the spectroscopic parameters of Yb:GSO were calculated. The advantages of the Yb:GSO crystal include high crystal quality, quasi-four-level laser operating scheme, high absorption cross-sections and particularly broad emission bandwidth (similar to 72 nm). The results indicated that the Yb:GSO crystal seemed to be a very promising laser gain medium in diode-pumped femtosecond laser and tunable solid state laser applications when LD pumped at 940 and 980 nm.

Efficient diode-pumped Tm : YALO(3) laser with a pump recycling scheme

By using a pump recycling configuration, the maximum power of 8.1 W in the wavelength range 1.935-1.938 mu m is generated by a 5-mm long Tm:YAlO3 (4 at. %) laser operating at 18 degrees C with a pump power of 24 W. The highest slope efficiency of 42% is attained, and the pump quantum efficiency is up to 100%. The Tm:YAlO3 laser is employed as a pumping source of singly-doped Ho(l%):GdVO4 laser operating at room temperature, in which continuous wave output power of greater than 0.2 W at 2.05 mu m is achieved with a slope efficiency of 9%.