Simulated pathogenic conformational switch regions matched well with the biochemical findings

Pathogenic conformational conversion is a general causation of many disease, such as transmissible spon- giform encephalopathy (TSE) caused by misfolding of prion, sickle cell anemia, and etc. In such structural changes, misfolding occurs in regions important for the stability of native structure firstly. This destabi- lizes the normal conformation and leads to subsequent errors in folding pathway. Sites involved in the first stage can be deemed switch regions of the protein, and are vital for conformational conversion. Namely it could be a switch of disease at residue level. Here we report an algorithm that can identify such sites computationally with an accuracy of 93%, by calculating the probability of the native structure of a short segment jumping to a mistake one. Knowledge of such switch sites could be used to target clinical therapy, study physiological and pathologic mechanism of protein, and etc.

Switch Region for Pathogenic Structural Change in Conformational Disease and Its Prediction

Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs) and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1) influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1) it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2) it provides an ideal target for clinical treatment.

Acoustic Calculation for Supersonic Turbulent Boundary Layer Flow

An approach which combines direct numerical simulation (DNS) with the Lighthill acoustic analogy theory is used to study the potential noise sources during the transition process of a Mach 2.25 flat plate boundary layer. The quadrupole sound sources due to the flow fluctuations and the dipole sound sources due to the fluctuating surface stress are obtained. Numerical results suggest that formation of the high shear layers leads to a dramatic amplification of amplitude of the fluctuating quadrupole sound sources. Compared with the quadrupole sound source, the energy of dipole sound source is concentrated in the relatively low frequency range.

A Wide Band Strong Acoustic Absorption in a Locally Network Anechoic Coating

Composite materials with interpenetrating network structures usually exhibit unexpected merit due to the cooperative interaction. Locally resonant phononic crystals (LRPC) exhibit excellent sound attenuation performance based on a periodical arrangement of sound wave scatters. Inspired by the interpenetrating network structure and the LRPC concept, we develop a locally network anechoic coating (LNAC) that can achieve a wide band of underwater strong acoustic absorption. The experimental results show that the LNAC possesses an excellent underwater acoustic absorbing capacity in a wide frequency range. Moreover, in order to investigate the impact of the interpenetrating network structure, we fabricate a faultage structure sample and the network is disconnected by hard polyurethane (PU). The experimental comparison between the LNAC and the faultage structure sample shows that the interpenetrating network structure of the LNAC plays an important role in achieving a wide band strong acoustic absorption.

Locally resonant phononic woodpile: A wide band anomalous underwater acoustic absorbing material

To meet the demand of modern acoustic absorbing material for which acoustic absorbing frequency region can be readily tailored, we introduced woodpile structure into locally resonant phononic crystal (LRPC) and fabricated an underwater acoustic absorbing material, which is called locally resonant phononic woodpile (LRPW). Experimental results show that LRPW has a strong capability of absorbing sound in a wide frequency range. Further theoretical research revealed that LRPC units and woodpile structure in LRPW play an important role in realization of wide band underwater strong acoustic absorption.

Electro-optic integration of embedded electrodes and waveguides in LiNbO3 using a femtosecond laser

We describe the fabrication of a Mach-Zehnder optical modulator in LiNbO3 by femtosecond laser micormachining, which is composed of optical waveguides inscripted by a femtosecond laser and embedded microelectrodes subsequently using femtosecond laser ablation and selective electroless plating. A half-wave voltage close to 19 V is achieved at a wavelength of 632.8 nm with an interaction length of 2.6 mm. This simple and cost-effective technique opens up new opportunities for fabricating integrated electro-optic devices. (C) 2008 Optical Society of America

Pulse compression by filamentation in argon with an acoustic optical programmable dispersive filter for predispersion compensation

We have experimentally demonstrated pulses 0.4 mJ in duration smaller than 12 fs; with an excellent spatial beam profile by self-guided propagation in argon. The original 52 fs pulses from the chirped pulsed amplification laser system are first precompressed to 32 fs by inserting an acoustic optical programmable dispersive filter instrument into the laser system for spectrum reshaping and dispersion compensation, and the pulse spectrum is subsequently broadened by filamentation in an argon cell. By using chirped mirrors for post-dispersion compensation, the pulses are successfully compressed to smaller than 12 fs.

Quantum computation based on a quantum switch in cavity QED

A feasible scheme for constructing quantum logic gates is proposed on the basis of quantum switches in cavity QED. It is shown that the light field which is fed into the cavity due to the passage of an atom in a certain state can be used to manipulate the conditioned quantum logical gate. In our scheme, the quantum information is encoded in the states of Rydberg atoms and the cavity mode is not used as logical qubits or as a communicating "bus"; thus, the effect of atomic spontaneous emission can be neglected and the strict requirements for the cavity can be relaxed.

A new method of measuring the waveguide dispersion factor and the thermo-optic coefficient of long-period fiber gratings

Based on the Mach-Zehnder effect between the core mode and the cladding modes, the interference fringes are formed by a pair of cascaded long-period fiber gratings (CLPFGs). Theoretical analyses show that the spectral spacing and the wavelength of these fringes are functions of the waveguide dispersion factor gamma, which is a characterizing parameter to LPFG and with theoretical and applicational significance. By measuring the characteristics of the transmission spectra of CLPFGs, the absolute value of gamma can be obtained. At the same time, the thermo-optic coefficient of effective refractive index difference between core and cladding modes, p, can also be obtained by measured the temperature sensitivity of these fringes. In the experiments, \gamma\ and mu were measured by this method to be 0.874 and 4.08 x 10(-5) degreesC(-1), respectively, for LPFGs with period of 450 mum and with a HE14 resonant peak at 1554 nm. (C) 2004 Elsevier B.V. All rights reserved.

Polarization analysis and experimental implementation of PLZT electro-optical switch using fiber Sagnac interferometers

The polarization characteristics of electro-optical (EO) switches using fiber Sagnac interferometer (FSI) structures are theoretically investigated. Analytical solutions of output fields are presented when the twists and birefringence in a Sagnac loop are considered. Numerical calculations show that the twists of fiber, the orientation of the inserted phase retarder, and the splitting ratio of the coupler will influence both the output intensity and the output polarization properties of the proposed switch. A polarization-independent EO switch based on a Sagnac interferometer and a PUT bar was experimentally implemented, which showed good coincidence with the analytical results. The experiment showed a switch with 22 dB extinction ratio and less than 31.1 ns switching time. (c) 2006 Optical Society of America.

Electro-optic modulation of light propagating near the optic axis with any polarization in uniaxial crystals

The electro-optic effect in uniaxial crystals for light propagating near the optic axis with any polarization has been analyzed. The passive and the electrically induced birefringences and the rotation of polarization direction in crystals have been calculated, and the conoscopic interference figures under orthogonal polariscopes for different polarizer directions have been plotted. The extinction areas caused by the rotation of polarization direction in crystals change with the polarizer direction, but the two heads of the induced optical axes do not vary, which are always on the induced principal axis with bigger refractive index. The directions of polariscopes are always extinction, and the +/- 45 degrees directions with polarizer are always complete transmission. The conoscopic interference figures for LiNbO3 crystals have been demonstrated experimentally by rotating polariscopes directions, which accord with the theoretically calculating plots. (c) 2006 Elsevier GmbH. All rights reserved.

Experimental investigation of optical beam deflection based on PLZT electro-optic ceramic

Based on the optical characteristics of PLZT electro-optic ceramic, two kinds of electro-optic deflectors, triangular electrode structure and optical phased array technology, are studied in detail by using transverse electro-optic effect. Theoretically, the electro-optic deflection characteristics and mechanisms of the deflectors are analyzed. Experimentally, the optical characteristics of ceramic wafer, such as the phase modulation, the hysteresis and the electro-induced loss characteristics, are measured firstly, and then the beam deflection experiments are designed to verify the theoretical results. Moreover, the effect of temperature on the performance of triangular electrode deflector is investigated. The characteristics of both deflectors are also compared and illuminated. (c) 2007 Optical Society of America.

Laser diode array side-pumped acousto-optic induced unidirectional operation Q-switched Nd : YAG slab ring laser

A laser-diode array (LDA) side-pumped Nd:YAG slab ring laser is described that incorporates a prism-shaped acousto-optic modulator to enforce unidirectional operation and Q-switching. When pumped by the maximum power of 50 W, Q-switched energies of 3.6 mJ and 50 ns duration, corresponding to a peak power of 72 kW, are obtained. (C) 1999 Society of Photo-Optical Instrumentation Engineers. [S0091-3286(99)01306-9].

Focal switch in unapertured converging Hermite-cosh-Gaussian beams

Based on the Huygens-Fresnel diffraction integral, analytical representation of unapertured converging Hermite-cosh-Gaussian beams is derived. Focal switch of Hermite-cosh-Gaussian beams is studied detailedly with numerical calculation examples and a physical interpretation of focal switch is presented. It is found that decentered parameter is the dominant factor for the emergence of focal switch, and Fresnel number affects the amplitude of focal switch and the value of critical decentered parameter to determine emergence of focal switch. Physically, the emergence of focal switch of Hermite-cosh-Gaussian beams is resulted from competition between two major maximum intensities and switch of the absolute maximum intensity from a point to another when decentered parameter increases. (C) 2005 Elsevier Ltd. All rights reserved.