Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Triangle Evolution-A Hybrid Heuristic for Global Optimization

Abstract This paper presents a hybrid heuristic{triangle evolution (TE) for global optimization. It is a real coded evolutionary algorithm. As in di®erential evolution (DE), TE targets each individual in current population and attempts to replace it by a new better individual. However, the way of generating new individuals is di®erent. TE generates new individuals in a Nelder- Mead way, while the simplices used in TE is 1 or 2 dimensional. The proposed algorithm is very easy to use and e±cient for global optimization problems with continuous variables. Moreover, it requires only one (explicit) control parameter. Numerical results show that the new algorithm is comparable with DE for low dimensional problems but it outperforms DE for high dimensional problems.

MODELING EVOLUTION OF INTERNAL WAVES IN SOUTH CHINA SEA

Internal waves are an important factor in the design of drill operations and production in deep water, because the waves have very large amplitude and may induce large horizontal velocity. How the internal waves occur and propagate over benthal terrain is of great concern for ocean engineers. In the present paper, we have formulated a mathematical model of internal wave propagation in a two-layer deep water, which involves the effects of friction, dissipation and shoaling, and is capable of manifesting the variation of the amplitude and the velocity pattern. After calibration by field data measured at the Continental Slope in the Northern South China Sea, we have applied the model to the South China Sea, investigating the westward propagation of internal waves from the Luzon Strait, where internal waves originate due to the interaction of benthal ridge and tides. We find that the internal wave induced velocity profile is obviously characterized by the opposite flow below and above the pycnocline, which results in a strong shear, threatening safety of ocean structures, such as mooring system of oil platform, risers, etc. When internal waves propagate westwards, the amplitude attenuates due to the effects of friction and dissipation. The preliminary results show that the amplitude is likely to become half of its initial value at Luzon Strait when the internal waves propagate about 400 kilometers westwards.

Femtosecond laser-induced damage in reflector

We have investigated the damage for ZrO2/SiO2 800 nm 45 degrees high-reflection mirror with femtosecond pulses. The damage morphologies and the evolution of ablation crater depths with laser fluences are dramatically different from that with pulse longer than a few tens of picoseconds. The ablation in multilayers occurs layer by layer, and not continuously as in the case of bulk single crystalline or amorphous materials. The weak point in damage is the interface between two layers. We also report its single-short damage thresholds for pulse durations ranging from 50 to 900 fs, which departs from the diffusion-dominated tau(1/2)(p) scaling. A developed avalanche model, including the production of conduction band electrons (CBE) and laser energy deposition, is applied to study the damage mechanisms. The theoretical results agree well with our measurements. (c) 2005 Elsevier B.V. All rights reserved.

Nonlinear propagation of fs laser pulses in liquids and evolution of supercontinuum generation

Nonlinear propagation of fs laser pulses in liquids and the dynamic processes of filamentation such as self-focusing, intensity clamping, and evolution of white light production have been analyzed by using one- and two-photon fluorescence. The energy losses of laser pulses caused by multiphoton absorption and conical emission have been measured respectively by z-scan technique. Numerical simulations of fs laser propagation in water have been made to explain the evolution of white light production as well as the small-scale filaments in liquids we have observed by a nonlinear fluorescence technique. (c) 2005 Optical Society of America.

Effect of phases on the dynamic evolution of a Lambda system with spontaneously generated coherence

The dynamic evolution of a A system coupled by two strong coherent fields is investigated by taking spontaneously generated coherence (SGC) into account. By numericaly simulation, it is shown that the relative phase of the two coherent fields affects significantly the time scale to the coherent population trapping state. In addition, an analytical expression to the evolution rate which is consistent with the numerical results is given. (c) 2005 Elsevier B.V. All rights reserved.

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.

Spectral evolution of angularly resolved third-order harmonic generation by infrared femtosecond laser-pulse filamentation in air

We experimentally investigate the evolution of an angularly resolved spectrum of third harmonic generated by infrared femtosecond laser pulse filamentation in air. We show that at low pump intensity, phase matching between the fundamental and third-harmonic waves dominates the nonlinear optical effect and induces a ring structure of the third-harmonic beam, whereas at high pump intensity, the dispersion properties of air begin to affect the angular spectrum, leading to the formation of a nonlinear X wave at third harmonic.

Transverse evolution of a plasma channel in air induced by a femtosecond laser

We investigate the evolution of filamentation in air by using a longitudinal diffraction method and a plasma fluorescence imaging technique. The diameter of a single filament in which the intensity is clamped increases as the energy of the pump light pulse increases, until multiple filaments appear. (c) 2006 Optical Society of America.

Polarization evolution of a few-cycle ultrashort laser pulse propagating in a degenerate three-level medium

The propagation of an arbitrary polarized few-cycle ultrashort laser pulse in a degenerate three-level medium is investigated by using an iterative predictor-corrector finite-difference time-domain method. It is found that the polarization evolution of the ultrashort laser pulse is dependent not only on the initial atomic coherence of the medium but also on the polarization condition of the incident laser pulse. When the initial effective area is equal to 2 pi, complete linear-to-circular and circular-to-linear polarization conversion of few-cycle ultrashort laser pulses can be achieved due to the quantum interference effects between the two different transition paths.

Thickness dependence of structure and optical properties of silver films deposited by magnetron sputtering

A series of silver films with different thickness were prepared under identical conditions by direct current magnetron sputtering. The optical properties of the silver films were measured using spectrophotometric techniques and the optical constants were calculated from reflection and transmission measurements made at near normal incidence. The results show that the optical properties and constants are affected by films' thickness. Below the critical thickness of 17 nm at which Ag film forms a continuous film, the optical properties and constants vary significantly as the thickness of films increases and then tends to a stable value which is reached at 41 nm. X-ray diffraction measurements were carried out to examine the structure and stress evolution of the Ag films as a function of films' thickness. It was found that the interplanar distance of (111) orientation decreases when the film thickness increases and tends to be close to that of bulk material. The compressive strains also decrease with increasing thickness. (C) 2007 Published by Elsevier B.V.