Mode of operation and low-resolution structure of a multi-domain and hyperthermophilic endo-beta-1,3-glucanase from Thermotoga petrophila

1,3-beta-Glucan depolymerizing enzymes have considerable biotechnological applications including biofuel production, feedstock-chemicals and pharmaceuticals. Here we describe a comprehensive functional characterization and low-resolution structure of a hyperthermophilic laminarinase from Thermotoga petrophila (TpLam). We determine TpLam enzymatic mode of operation, which specifically cleaves internal beta-1,3-glucosidic bonds. The enzyme most frequently attacks the bond between the 3rd and 4th residue from the non-reducing end, producing glucose, laminaribiose and laminaritriose as major products. Far-UV circular dichroism demonstrates that TpLam is formed mainly by beta structural elements, and the secondary structure is maintained after incubation at 90 degrees C. The structure resolved by small angle X-ray scattering, reveals a multi-domain structural architecture of a V-shape envelope with a catalytic domain flanked by two carbohydrate-binding modules. Crown Copyright (C) 2011 Published by Elsevier Inc. All rights reserved.

Optical waveguide and cavity effects on whispering-gallery mode resonances in a ZnO nanonail

Spatially resolved cathodoluminescence (CL) study of a ZnO nanonail, having thin shank, tapered neck, and hexagonal head sections, is reported. Monochromatic imaging and line scan profiling indicate that the wave guiding and leaking from growth imperfections in addition to the oxygen deficiency variation determine the spatial contrast of CL emissions. Occurrence of resonance peaks at identical wavelengths regardless of CL-excitation spots is inconsistent with the whispering-gallery mode (WGM) resonances of a two-dimensional cavity in the finite difference time domain simulation. However, three dimensioanl cavity simulation produced WGM peaks that are consistent with the experimental spectra, including transverse-electric resonances that are comparable to transverse-magnetic ones.

Development of a switch mode assisted linear amplifier for use as a high fidelity voltage source

Frequency Domain Spectroscopy (FDS) is one of the major techniques used for determining the condition of the cellulose based paper and pressboard components in large oil/paper insulated power transformers. This technique typically makes use of a sinusoidal voltage source swept from 0.1 mHz to 1 kHz. The excitation test voltage source used must meet certain characteristics, such as high output voltage, high fidelity, low noise and low harmonic content. The amplifier used; in the test voltage source; must be able to drive highly capacitive loads. This paper proposes that a switch-mode assisted linear amplifier (SMALA) can be used in the test voltage source to meet these criteria. A three level SMALA prototype amplifier was built to experimentally demonstrate the effectiveness of this proposal. The developed SMALA prototype shows no discernable harmonic distortion in the output voltage waveform, or the need for output filters, and is therefore seen as a preferable option to pulse width modulated digital amplifiers. The lack of harmonic distortion and high frequency switching noise in the output voltage of this SMALA prototype demonstrates its feasibility for applications in FDS, particularly on highly capacitive test objects such as transformer insulation systems.

The C-terminal domain is sufficient for endonuclease activity of Neisseria gonorrhoeae MutL

The mutL gene of Neisseria gonorrhoeae has been cloned and the gene product purified. We have found that the homodimeric N. gonorrhoeae MutL (NgoL) protein displays an endonuclease activity that incises covalently closed circular DNA in the presence of Mn2+, Mg2+ or Ca2+ ions, unlike human MutL alpha which shows endonuclease activity only in the presence of Mn2+. We report in the present paper that the C-terminal domain of N. gonorrhoeae MutL (NgoL-CTD) consisting of amino acids 460-658 exhibits Mn2+-dependent endonuclease activity. Sedimentation velocity, sedimentation equilibrium and dynamic light scattering experiments show NgoL-CTD to be a dimer. The probable endonucleolytic active site is localized to a metal-binding motif, DMHAX(2)EX(4)E, and the nicking endonuclease activity is dependent on the integrity of this motif. By in vitro comparison of wild-type and it mutant NgoL-CTD protein, we show that the latter protein exhibits highly reduced endonuclease activity. We therefore suggest that the mode of excision initiation in DNA mismatch repair may be different in organisms that lack MutH protein, but have MutL proteins that harbour the D[M/Q]HAX(2)EX(4)E motif.

Joint Performance Analysis of Channel Quality Indicator Feedback Schemes and Frequency-Domain Scheduling for LTE

Frequency-domain scheduling and rate adaptation enable next-generation orthogonal frequency-division multiple access (OFDMA) cellular systems such as Long-Term Evolution (LTE) to achieve significantly higher spectral efficiencies. LTE uses a pragmatic combination of several techniques to reduce the channel-state feedback that is required by a frequency-domain scheduler. In the subband-level feedback and user-selected subband feedback schemes specified in LTE, the user reduces feedback by reporting only the channel quality that is averaged over groups of resource blocks called subbands. This approach leads to an occasional incorrect determination of rate by the scheduler for some resource blocks. In this paper, we develop closed-form expressions for the throughput achieved by the feedback schemes of LTE. The analysis quantifies the joint effects of three critical components on the overall system throughput-scheduler, multiple-antenna mode, and the feedback scheme-and brings out its dependence on system parameters such as the number of resource blocks per subband and the rate adaptation thresholds. The effect of the coarse subband-level frequency granularity of feedback is captured. The analysis provides an independent theoretical reference and a quick system parameter optimization tool to an LTE system designer and theoretically helps in understanding the behavior of OFDMA feedback reduction techniques when operated under practical system constraints.

Frequency Domain Based Solution for Certain Class of Wave Equations: An exhaustive study of Numerical Solutions

The paper discusses the frequency domain based solution for a certain class of wave equations such as: a second order partial differential equation in one variable with constant and varying coefficients (Cantilever beam) and a coupled second order partial differential equation in two variables with constant and varying coefficients (Timoshenko beam). The exact solution of the Cantilever beam with uniform and varying cross-section and the Timoshenko beam with uniform cross-section is available. However, the exact solution for Timoshenko beam with varying cross-section is not available. Laplace spectral methods are used to solve these problems exactly in frequency domain. The numerical solution in frequency domain is done by discretisation in space by approximating the unknown function using spectral functions like Chebyshev polynomials, Legendre polynomials and also Normal polynomials. Different numerical methods such as Galerkin Method, Petrov- Galerkin method, Method of moments and Collocation method or the Pseudo-spectral method in frequency domain are studied and compared with the available exact solution. An approximate solution is also obtained for the Timoshenko beam with varying cross-section using Laplace Spectral Element Method (LSEM). The group speeds are computed exactly for the Cantilever beam and Timoshenko beam with uniform cross-section and is compared with the group speeds obtained numerically. The shear mode and the bending modes of the Timoshenko beam with uniform cross-section are separated numerically by applying a modulated pulse as the shear force and the corresponding group speeds for varying taper parameter in are obtained numerically by varying the frequency of the input pulse. An approximate expression for calculating group speeds corresponding to the shear mode and the bending mode, and also the cut-off frequency is obtained. Finally, we show that the cut-off frequency disappears for large in, for epsilon > 0 and increases for large in, for epsilon < 0.

Docking, molecular dynamics and QM/MM studies to delineate the mode of binding of CucurbitacinE to F-actin

CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the beta-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable ``tense'' state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin. (C) 2015 Elsevier Inc. All rights reserved.

Nonlinear phenomena in thermoacoustics: A comparison between single-mode and multi-mode methods

Nonlinear analysis of thermoacoustic instability is essential for prediction of frequencies and amplitudes of limit cycles. In frequency domain analyses, a quasi-linear transfer function between acoustic velocity and heat release rate perturbations, called the flame describing function (FDF), is obtained from a flame model or experiments. The FDF is a function of the frequency and amplitude of velocity perturbations but only contains the heat release response at the forcing frequency. While the gain and phase of the FDF provide insight into the nonlinear dynamics of the system, the accuracy of its predictions remains to be verified for different types of nonlinearity. In time domain analyses, the governing equations of the fully coupled problem are solved to find the time evolution of the system. One method is to discretize the governing equations using a suitable basis, such as the natural acoustic modes of the system. The number of modes used in the discretization alters the accuracy of the solution. In our previous work we have shown that predictions using the FDF are almost exactly the same as those obtained from the time-domain using only one mode for the discretization. We call this the single-mode method. In this paper we compare results from the single-mode and multi-mode methods, applied to a thermoacoustic system of a premixed flame in a tube. For some cases, the results differ greatly in both amplitude as well as frequency content. This study shows that the contribution from higher and subharmonics to the nonlinear dynamics can be significant and must be considered for an accurate and comprehensive analysis of thermoacoustic systems. Hence multi-mode simulations are necessary, and the single-mode method or the FDF may be insufficient to capture some of the complex nonlinear behaviour in fhermoacoustics.

Theory of high-power mode-locked lasers with a slow absorber

We develop an analytical theory of high-power passively mode-locked lasers with a slow absorber; the theory is valid at pulse energies well exceeding the saturation energy. We analyze the Haus modelocking master equation in the pulse-energy-domain representation, approximating the intensity profile function by a series in the vicinity of its peak value. We consider the high-power operation regime of subpicosecond blue-violet GaN mode-locked diode lasers, using the approach developed. © 2010 Springer Science+Business Media, Inc.

Mode Simulation for Midinfrared Microsquare Resonators With Sloped Sidewalls and Confined Metals

EQUILATERAL-TRIANGLE; MU-M; LASERS; MICROLASERS; MICRODISK Abstract: Mode characteristics for midinfrared microsquare resonators with sloped sidewalls and confined metal layers are investigated by finite-difference time-domain (FDTD) techniques. For a microsquare with a side length of 10 mu m, the mode quality (Q)-factors of 8329, 4772, and 2053 are obtained for TM5,7 mode at wavelength 7.1 mu m by three-dimensional FDTD simulations, as the tilting angles of the side walls are 90 degrees, 88 degrees, and 86 degrees, respectively. Furthermore, microsquare resonators laterally surrounded by SiO2 and metal layers are investigated by the two-dimensional FDTD technique for the metal layers of Au, Ti-Au, Ag-Au, and Ti-Ag-Au, respectively.

Mode Characteristics for Square Resonators With a Metal Confinement Layer

Microsquare resonators laterally confined by SiO2/Au/air multilayer structure are investigated by light ray method with reflection phase-shift of the multiple layers and two-dimensional (2-D) finite-difference time-domain (FDTD) technique. The reflectivity and phase shift of the mode light ray on the sides of the square resonator with the semiconductor/SiO2/Au/air multilayer structure are calculated for TE and TM modes by transfer matrix method. Based on the reflection phase shift and the reflectivity, the mode wavelength and factor are calculated by the resonant condition and the mirror loss, which are in agreement well with that obtained by the FDTD simulation. We find that the mode factor increases greatly with the increase of the SiO2 layer thickness, especially as d < 0.3 mu m. For the square resonator with side length 2 mu m and refractive index 3.2, anticrossing mode couplings are found for confined TE modes at wavelength about 1.6 mu m at d = 0.11 mu m, and confined TM modes at d = 0.71 mu m, respectively.

Investigation of mode radiation loss for microdisk resonators with pedestals by FDTD technique

Mode radiation loss for microdisk resonators with pedestals is investigated by three-dimensional (3D) finite-difference time-domain (FDTD) technique. For the microdisk with a radius of 1 mu m, a thickness of 0.2 mu m, and a refractive index of 3.4, on a pedestal with a refractive index of 3.17, the mode quality (Q) factor of the whispering-gallery mode (WGM) quasi-TE7,1 first increases with the increase of the radius of the pedestal, and then quickly decreases as the radius is larger than 0.75 mu m. The mode radiation loss is mainly the vertical radiation loss induced by the mode coupling between the WGM and vertical radiation mode in the pedestal, instead of the scattering loss around the perimeter of the round pedestal. The WG M can keep the high Q factor when the mode coupling is forbidden.

Mode characteristics of metallically coated square microcavity connected with an output waveguide

Mode characteristics of a square microcavity with an output waveguide on the middle of one side, laterally confined by an insulating layer SiO2 and a p-electrode metal Au, are investigated by two-dimensional finite-difference time-domain technique. The mode quality (Q) factors versus the width of the output waveguide are calculated for Fabry-Peacuterot type and whispering-gallery type modes in the square cavity. Mode coupling between the confined modes in the square cavity and the guided modes in the output waveguide determines the mode Q factors, which is greatly influenced by the symmetry behaviors of the modes. Fabry-Peacuterot type modes can also have high Q factors due to the high reflectivity of the Au layer for the vertical incident mode light rays. For the square cavity with side length 4 mu m and refractive index 3.2, the mode Q factors of the Fabry-Peacuterot type modes can reach 10(4) at the mode wavelength of 1.5 mu m as the output waveguide width is 0.4 mu m.

Mode coupling and vertical radiation loss for whispering-gallery modes in 3-D microcavities

The characteristics of whispering-gallery modes (WGMs) in 3-D cylindrical, square, and triangular microcavities with vertical optical confinement of semiconductors are numerically investigated by the finite-difference time-domain (FDTD) technique. For a microcylinder with a vertical refractive index 3.17/3.4/3.17 and a center layer thickness 0.2 mu m, Q-factors of transverse electric (TE) WGMs around wavelength 1550 nm are smaller than 10(3), as the radius R < 4 mu m and reach the orders of 10(4) and 10(6) as R = 5 and 6 mu m, respectively. However, the Q-factor of transverse magnetic (TM) WGMs at wavelength 1.659 mu m reaches 7.5 x 10(5) as R = 1 mu m. The mode coupling between the WGMs and vertical radiation modes in the cladding layer results in vertical radiation loss for the WGMs. In the microcylinder, the mode wavelength of TM WGM is larger than the cutoff wavelength of the vertical radiation mode with the same mode numbers, so TM WGMs cannot couple with the vertical radiation mode and have high Q-factor. In contrast, TE WGMs can couple with the corresponding vertical radiation mode in the 3-D microcylinder as R < 5 mu m. However, the mode wavelength of the TE WGM approaches (is larger than) the cutoff wavelength of the corresponding radiation modes at R = 5 mu m (6 mu m), so TE WGMs have high Q-factors in such microcylinders too. The results show that a critical lateral size is required for obtaining high, Q-factor TE WGMs in the 3-D microcylinder. For 3-D square and triangular microcavities, we also find that the Q-factor of TM WGM is larger than that of TE WGM.

Analysis of mode characteristics for equilateral-polygonal resonators with a center hole

Mode characteristics for equilateral triangles, squares, and hexagonal resonators with a center hole are numerically simulated by the finite-different time domain (FDTD) technique. The center hole does not break the symmetry behavior of the original resonators and can result in modification of the mode field patterns and mode Q factors. In an equilateral triangle resonator the center hole can suppress the symmetry state of degenerate states with the merit of single mode operation. In a square resonator, the Q factor can be enhanced for some modes with a suitable size of the hole. For a hexagonal resonator with a side length of 1 mu m and a refractive index of 3.2, the mode Q factors first gradually decrease with the increase of the hole diameter for modes at a wavelength of about 1500 nm, then the modes transform to that of a microdisk with a jump of the mode wavelength as the hole diameter approaches 0.7 mu m. Finally, the mode Q factors greatly enhance as the hole diameter reaches about 1 mu m. The results indicate that the center hole can greatly modify mode characteristics, especially that of the mode Q factor. (C) 2009 Optical Society of America