A combined statistical model for multiple motifs search

Transcription factor binding sites (TFBS) play key roles in genebior 6.8 wavelet expression and regulation. They are short sequence segments with de¯nite structure and can be recognized by the corresponding transcription factors correctly. From the viewpoint of statistics, the candidates of TFBS should be quite di®erent from the segments that are randomly combined together by nucleotide. This paper proposes a combined statistical model for ¯nding over- represented short sequence segments in di®erent kinds of data set. While the over-represented short sequence segment is described by position weight matrix, the nucleotide distribution at most sites of the segment should be far from the background nucleotide distribution. The central idea of this approach is to search for such kind of signals. This algorithm is tested on 3 data sets, including binding sites data set of cyclic AMP receptor protein in E.coli, PlantProm DB which is a non-redundant collection of proximal promoter sequences from di®erent species, collection of the intergenic sequences of the whole genome of E.Coli. Even though the complexity of these three data sets is quite di®erent, the results show that this model is rather general and sensible.

Plasma channeling by multiple short-pulse lasers

Channeling by a train of laser pulses into homogeneous and inhomogeneous plasmas is studied using particle-in-cell simulation. When the pulse duration and the interval between the successive pulses are appropriate, the laser pulse train can channel into the plasma deeper than a single long-pulse laser of similar peak intensity and total energy. The increased penetration distance can be attributed to the repeated actions of the ponderomotive force, the continuous between-pulse channel lengthening by the inertially evacuating ions, and the suppression of laser-driven plasma instabilities by the intermittent laser-energy cut-offs.

Ultrafast control of multiple filamentation by ultrafast laser pulses

Control of multiple filamentation by laser-induced microlens effect due to a nonlinear interaction of two overlapping laser beams inside a glass plate was demonstrated. Individual or multiple spots on the white light pattern which is a product of multiple filamentation through a mesh can be switched on and off with a very high contrast ratio on a femtosecond time scale. This phenomenon can find applications such as ultrafast optical switch and high-speed sampling. (C) 2005 American Institute of Physics.

Long lifetime plasma channel in air generated by multiple femtosecond laser pulses and an external electrical field

The lifetime of a plasma channel produced by self-guiding intense femtosecond laser pulses in air is largely prolonged by adding a high voltage electrical field in the plasma and by introducing a series of femtosecond laser pulses. An optimal lifetime value is realized through adjusting the delay among these laser pulses. The lifetime of a plasma channel is greatly enhanced to 350 ns by using four sequential intense 100fs( FWHM) laser pulses with an external electrical field of about 350kV/m, which proves the feasibility of prolonging the lifetime of plasma by adding an external electrical field and employing multiple laser pulses. (c) 2006 Optical Society of America.

Self-induced transmission on intersubband resonance in multiple quantum wells

We investigate the nonlinear propagation of ultrashort pulses on resonant intersubband transitions in multiple semiconductor quantum wells. It is shown that the nonlinearity rooted from electron-electron interactions destroys the condition giving rise to self-induced transparency. However, by adjusting the area of input pulse, we find the signatures of self-induced transmission due to a full Rabi flopping of the electron density, and this phenomenon can be approximately interpreted by the traditional standard area theorem via defining the effective area of input pulse.

Spatiotemporal evolution and multiple self-focusing of ultrashort pulses in a resonant two-level medium

The spatiotemporal evolutions of ultrashort pulses in two dimensions are investigated numerically by solving the coupled Maxwell-Bloch equations without invoking the slowly varying envelope approximation and rotating-wave approximation. For an on-axis 2n pi sech pulse, local delay makes the temporal split 2 pi sech pulses crescent-shaped in the transverse distribution. Due to the transverse effect, the temporal split 2 pi sech pulses become unstable and experience reshaping during the propagation process. Then, interference occurs between the successive crescent-shaped pulses and multiple self-focusing can form.

Multiple quasi-phase-matching for enhanced generation of selected high harmonics in aperiodic modulated fibers

A technique for enhanced generation of selected high harmonics in a gas medium, in a high ionization limit, is proposed in this paper. An aperiodically corrugated hollow-core fiber is employed to modulate the intensity of the fundamental laser pulse along the direction of propagation, resulting in multiple quasi-phase-matched high harmonic emissions at the cutoff region. Simulated annealing (SA) algorithm is applied for optimizing the aperiodic hollow-core fiber. Our simulation shows that the yield of selected harmonics is increased equally by up to 2 orders of magnitude compared with no modulation and this permits flexible control of the quasi-phase-matched emission of selected harmonics by appropriate corrugation. (c) 2007 Optical Society of America.

Coma measurement of projection optics in lithographic tools based on relative image displacements at multiple illumination settings

In this paper, we propose a novel method for measuring the coma aberrations of lithographic projection optics based on relative image displacements at multiple illumination settings. The measurement accuracy of coma can be improved because the phase-shifting gratings are more sensitive to the aberrations than the binary gratings used in the TAMIS technique, and the impact of distortion on displacements of aerial image can be eliminated when the relative image displacements are measured. The PROLITH simulation results show that, the measurement accuracy of coma increases by more than 25% under conventional illumination, and the measurement accuracy of primary coma increases by more than 20% under annular illumination, compared with the TAMIS technique. (c) 2007 Optical Society of America.

Specklegram in a multiple-mode fiber and its dependence on longitudinal modes of the laser source

A specklegram in a multimode fiber (MMF) has successfully been used as a sensor for detecting external disturbance. Our experiments showed that the sensitivity in the sensor with a multiple longitudinal-mode laser as its source was much higher than that with a single longitudinal-mode laser. In addition, the near-field pattern observations indicated that the coupling between different transverse modes in the MMF is quite weak. Based on the experimental results, a theoretical model for the speckle formation is proposed, taking a bend-caused phase factor into consideration. It is shown in the theoretical analysis that the interferences between different longitudinal modes make a larger contribution to the specklegram signals. (C) 2007 Optical Society of America.

Specklegram in a grapefruit fiber and its response to external mechanical disturbance in a single-multiple-single mode fiber structure

Specklegram in multimode fiber has successfully been used as a sensor for detecting mechanical disturbance. Speckles in a multimode pure silica grapefruit fiber are observed and compared to that of a step-index multimode fiber, showing different features between them. The sensitivities to external disturbance of two kinds of fiber were measured, based on single-multiple-single mode (SMS) fiber structure. Experimental results show that the grapefruit fiber shows higher sensitivity than does the step-index multimode fiber. The transmission spectrum of the grapefruit fiber was measured as well, showing some oscillation features that are significantly different from that of a step-index multimode fiber. The experiments may provide suggestions to understand the mechanisms of light propagation in grapefruit fibers. (D 2008 Optical Society of America.

Damage on HfO2/SiO2 high-reflecting coatings under single and multiple Nd:YAG laser pulse irradiation

The single- and multi-shot damage behaviors of HfO2/SiO2 high-reflecting (HR) coatings under Nd:YAG laser exposure were investigated. Fundamental aspects of multi-shot laser damage, such as the instability due to pulse-to-pulse accumulation of absorption defect and structural defect effect, and the mechanism of laser induced defect generation, are considered. It was found in multi-shot damage, the main factors influencing laser-induced damage threshold (LIDT) are accumulation of irreversible changes of structural defects and thermal stress that induced by thermal density fluctuations.

Guided-mode resonant grating filter with an antireflective surface for the multiple channels

In this paper, a new type of guided-mode resonant grating (GMRG) filter with an antireflective surface called the 'moth-eye structure' for the multiple channels is presented by using rigorous coupled-wave analysis (RCWA) and the S-matrix method. Long range, low sidebands and multiple channels are found when the GMRG filters with antireflective surface are illuminated with incident polarization light. It is calculated that the multiple channel phenomenon can be shown when the depth of antireflective surface is increased. Moreover, the wavelengths of the multiple channels can be easily shifted by changing the depth of the homogenous layer which is under the antireflective surface, and the optical properties of GMRG filters such as low sideband reflection and narrow band are not badly spoiled when the depth is changed.

Surface relief resonant Brewster niters with multiple channels

In this paper, a new type of resonant Brewster filters (RBF) with surface relief structure for the multiple channels is first presented by using the rigorous coupled-wave analysis and the S-matrix method. By tuning the depth of homogeneous layer which is under the surface relief structure, the multiple channels phenomenon is obtained. Long range, extremely low sidebands and multiple channels are found when the RBF with surface relief structure is illuminated with Transverse Magnetic incident polarization light near the Brewster angle calculated with the effective media theory of sub wavelength grating. Moreover, the wavelengths of RBF with surface relief structure can be easily shifted by changing the depth of homogeneous layer while its optical properties such as low sideband reflection and narrow band are not spoiled when the depth is changed. Furthermore, the variation of the grating thickness does not effectively change the resonant wavelength of RBF, but have a remarkable effect on its line width, which is very useful for designing such filters with different line widths at desired wavelength.