Numerical analysis of spatial evolution of the small signal gain in a chemical oxygen-iodine laser operating without primary buffer gas

A chemical oxygen iodine laser (COIL) that operates without primary buffer gas has become a new way of facilitating the compact integration of laser systems. To clarify the properties of spatial gain distribution, three-dimensional (3-D) computational fluid dynamics (CFD) technology was used to study the mixing and reactive flow in a COIL nozzle with an interleaving jet configuration in the supersonic section. The results show that the molecular iodine fraction in the secondary flow has a notable effect on the spatial distribution of the small signal gain. The rich iodine condition produces some negative gain regions along the jet trajectory, while the lean iodine condition slows down the development of the gain in the streamwise direction. It is also found that the new configuration of an interleaving jet helps form a reasonable gain field under appropriate operation conditions. (c) 2007 Elsevier Ltd. All rights reserved.

Vibration analysis of laminated plates using a refined shear deformation-theory

A previously published discrete-layer shear deformation theory is used to analyze free vibration of laminated plates. The theory includes the assumption that the transverse shear strains across any two layers are linearly dependent on each other. The theory has the same dependent variables as first order shear deformation theory, but the set of governing differential equations is of twelfth order. No shear correction factors are required. Free vibration of simply supported symmetric and antisymmetric cross-ply plates is calculated. The numerical results are in good agreement with those from three-dimensional elasticity theory.

Parametric Analysis for Monitoring 2D Kinetics of Receptor-Ligand binding

Thermal fluctuation approach is widely used to monitor association kinetics of surface-bound receptor-ligand interactions. Various protocols such as sliding standard deviation (SD) analysis (SSA) and Page's test analysis (PTA) have been used to estimate two-dimensional (2D) kinetic rates from the time course of displacement of molecular carrier. In the current work, we compared the estimations from both SSA and modified PTA using measured data from an optical trap assay and simulated data from a random number generator. Our results indicated that both SSA and PTA were reliable in estimating 2D kinetic rates. Parametric analysis also demonstrated that such the estimations were sensitive to parameters such as sampling rate, sliding window size, and threshold. These results furthered the understandings in quantifying the biophysics of receptor-ligand interactions.

Analysis of an ultrashort pulsed finite beam diffracted by volume gratings

We obtain analytical solutions of the coupled wave equations that describe the Bragg diffraction of ultrashort pulsed finite beams by a thick planar grating, using two-dimensional coupled wave theory. The diffraction properties for the case of an ultrashort pulsed finite beam with Gaussian profiles in both the time and spatial domains are investigated. The spectral bandwidth of the diffracted beam, the Bragg selectivity bandwidth and the diffraction efficiency of the volume grating are influenced by the geometry parameter and the input bandwidth. Therefore extra attention should be paid to designing optical elements based on volume gratings for use with ultrashort pulsed waves in applications of pulse shaping and processing.

Structure analysis of CCR5 from human and primates

It is well known that the chemokine receptor CCR5 plays very important roles in HIV-1 virus infection. A three-dimensional molecular model of human CCR5 was generated by SYBYL, a distance geometry-based homologous modeling package, using the corresponding transmembrane domain of bacteriorhodopsin as the template. On the basis of human CCR5 model, we also built 18 3D molecular models of CCR5 in primates from Pongo pygmaeus, Pygathrix nemaeus, Macaca assameniss, Trachy-pithecus phayrei, T. francoisi, M. arotoides, Rhinopithecus roxellance, R, bieti, R. avunculus, Hylobates leucogenys, Pan troglodytes, Gorilla gorilla, Cercopithecus aethiops 1, C. aethiops 2, Papio hamadryas M. mulatta, M. fascicularis and M. nemestrina. Structural analyses and statistics results suggested that the main-chains of the primate CCR5 were similar to that of the human CCR5 and that the fit-RMS deviation values of these primate CCR5 were less than 0.1 Angstrom. Moreover, the structures of these CCR5 proteins, except those of the African green monkey 1 (C.aet1), do not have a remarkable difference. It is proved that the 14th residue is possibly very important in the inhibition infections by M-tropic HIV-1, and it is also demonstrated that the 13th residue of human CCR5 was changed from asparagine into aspartic acid in all these primates. It means that the primate CCR5 no longer depend on CD4 for efficient entry, but human CCR5 may have evolved subsequently due to the use of CD4 as a receptor, allowing the high-affinity chemokine receptor-binding site of HIV to be sequestered from host immune surveillance. (C) 2000 Elsevier Science B.V. All rights reserved.

Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water-K+-TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT. (C) 2002 Elsevier Science B.V. All rights reserved.

NK-lysin of channel catfish: Gene triplication, sequence variation, and expression analysis

Antimicrobial peptides (AMPs) are important components of the host innate immune response against microbial invasion. In addition to the previously known four classes of antimicrobial peptides, a fifth class of antimicrobial peptides has been recently identified to include NK-lysins that have a globular three-dimensional structure and are larger with 74-78 amino acid residues. NK-lysin has been shown to harbor antimicrobial activities against a wide spectrum of microorganisms including bacteria, fungi, protozoa, and parasites. To date, NK-lysin genes have been reported from only a limited number of organisms. We previously identified a NK-lysin cDNA in channel catfish. Here we report the identification of two noveltypes of NK-lysin transcripts in channel catfish. Altogether, three distinct NK-lysin transcripts exist in channel catfish. In this work, their encoding genes were identified, sequenced, and characterized. We provide strong evidence that the catfish NK-lysin gene is tripled in the same genomic neighborhood. All three catfish NK-lysin genes are present in the same genomic region and are tightly linked on the same chromosome, as the same BAC clones harbor all three copies of the NK-lysin genes. All three NK-lysin genes are expressed, but exhibit distinct expression profiles in various tissues. In spite of the existence of a single copy of NK-lysin gene in the human genome, and only a single hit from the pufferfish,genome, there are two tripled clusters of NK-lysin genes on chromosome 17 of zebrafish in addition to one more copy on its chromosome 5. The similarity in the genomic arrangement of the tripled NK-lysin genes in channel catfish and zebrafish suggest similar evolution of NK-lysin genes. (c) 2005 Elsevier Ltd. All rights reserved.

Microstructure and strain analysis of GaN epitaxial films using in-plane grazing incidence x-ray diffraction

This paper investigates the major structural parameters, such as crystal quality and strain state of (001)-oriented GaN thin films grown on sapphire substrates by metalorganic chemical vapour deposition, using an in-plane grazing incidence x-ray diffraction technique. The results are analysed and compared with a complementary out-of-plane x-ray diffraction technique. The twist of the GaN mosaic structure is determined through the direct grazing incidence measurement of (100) reflection which agrees well with the result obtained by extrapolation method. The method for directly determining the in-plane lattice parameters of the GaN layers is also presented. Combined with the biaxial strain model, it derives the lattice parameters corresponding to fully relaxed GaN films. The GaN epilayers show an increasing residual compressive stress with increasing layer thickness when the two dimensional growth stage is established, reaching to a maximum level of -0.89 GPa.

Analysis of lateral current spreading in solar cell devices by spatially-resolved electroluminescence

Spatially-resolved electroluminescence (EL) images from solar cells contain information of local current distribution. By theoretical analysis of the EL intensity distribution, the current density distribution under a certain current bias and the sheet resistance can be obtained quantitatively. Two-dimensional numerical simulation of the current density distribution is employed to a GaInP cell, which agrees very well with the experimental results. A reciprocity theorem for current spreading is found and used to interpret the EL images from the viewpoint of current extraction. The optimization of front electrodes is discussed based on the results. (C) 2010 American Institute of Physics. [doi:10.1063/1.3431390]

Mode Analysis and Design of a Low-Loss Photonic Crystal 60 degrees Waveguide Bend

The guided modes of a two-dimensional photonic crystal straight waveguide and a waveguide bend are studied in order to find the high transmission mechanism for the waveguide bend. We find that high transmission occurs when the mode patterns and wave numbers match, while the single-mode condition in the waveguide bend is not necessarily required. According to the mechanism, a simply modified bend structure with broad high transmission band is proposed. The bandwidth is significantly increased from 19 to 116 nm with transmission above 90%, and covers the entire C band of optical communication.

The impact of imperfect symmetry on band edge modes of a two-dimensional photonic crystal with square lattice

A theoretical analysis has been performed by means of the plane-wave expansion method to examine the dispersion properties of photons at high symmetry points of an InP based two-dimensional photonic crystal with square lattice. The Q factors are compared qualitatively. The mechanism of surface-emitting is due to the photon manipulation by periodic dielectric materials in terms of Bragg diffraction. A surface-emitting photonic crystal resonator is designed based on the phenomenon of slow light. Photonic crystal slabs with different unit cells are utilized in the simulation. The results indicate that the change of the air holes can affect the polarization property of the modes. So we can find a way to improve the polarization by reducing the symmetry of the structure.

Distinct two dimensional lateral ordering of self-assembled quantum dots

We report a quantum dot (QD) ensemble structure in which the in-plane arrangements of the dots are in a hexagonal way while the dots are also vertically aligned. Such a distinct lateral ordering of QDs is achieved on a planar GaAs(l 0 0) rather than on a prepatterned substrate by strain-mediated multilayer vertical stacking of the QDs. The analysis indicates that the strain energy of the lateral island-island interaction is minimum for arrangement of the hexagonal ordering. The ordered dots demonstrate strong photoluminescence (PL) emission at room temperature (RT) and the full width at half maximum of PL peak at RT is only 50 meV. (C) 2007 Elsevier B.V. All rights reserved.

Spin precession induced by an effective magnetic field in a two-dimensional electron gas

We theoretically study the spatial behaviors of the spin precession in a two-dimensional electron system with spin-orbit interaction. Through analysis of interaction between the spin and the effective magnetic field in the system, we obtain the general conditions to generate a persistent spin helix and predict a persistent spin helix pattern in [001]-grown quantum wells. Particularly, we demonstrate that the phase of spin can be locked to propagate in a quantum well with SU(2) symmetry.

Theoretical analysis of gate voltage-controlled subband states in an AlxGa1-xN/GaN heterostructure

The subband structure and inter-subband transition as a function of gate voltage are determined by solving the Schrodinger and Poisson equations self-consistently in an AlxGa1-xN/GaN heterostructure. Different aluminum mole fraction and thickness of AlxGa1-xN barrier are considered. Calculation results show that energy difference between the first and second subband covers a wide range (from several tens to hundreds milli-electron volt) by applying different gate voltage, which corresponds to the midinfrared and long-wave infrared wavelength scope. Furthermore, such a modulation on the subband transition energy is much more pronounced for the structure with thin barrier. When the applied positive gate voltage is increased, the triangle well formed at the interface turns to be deeper and narrower, which enhances the confinement for electrons. As a result, the overlap between electron wave function at two subbands increases, and thus the optical intersubband transition also enhances its intensity. This tendency is in good agreement with the available data in the literature. (c) 2005 Elsevier B.V. All rights reserved.

Analysis of modes in a freestanding microsquare resonator by 3-D finite-difference time-domain

Modes in a microsquare resonator slab with strong vertical waveguide consisting of air/semiconductor/air are analyzed by three-dimensional (3-D) finite-difference time-domain simulation, and compared with that of two-dimensional (2-D) simulation under effective index approximation. Mode frequencies and field distributions inside the resonator obtained by the 3-D simulation are in good agreement with those of the 2-D approximation. However, field distributions at the boundary of the resonator obtained by 3-D simulation are different from that of the 2-D simulation, especially the vertical field distribution near the boundary is great different from that of the slab waveguide, which is used in the effective index approximation. Furthermore the quality factors obtained by 3-D simulation are much larger. than that by 2-D simulation for the square resonator slab with the strong vertical waveguide.