Statistical correlation between protein secondary structure and messenger RNA stem-loop structure

Anew integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect. (C) 2003 Wiley Periodicals, Inc.

The dynamical process of a coronal transient associated with an eruptive prominence .1. Basic mechanism

The statistical correlation between an eruptive prominence and the coronal transient associated with this prominence implies that there should be a relationship between these two kinds of dynamical processes. This paper analyzes the dynamical effect of a plasma

Statistical modeling of damage evolution in spallation

In order to understand the mechanism of the incipient spallation in rolled metals, a one dimensional statistical mode1 on evolution of microcracks in spallation was proposed. The crack length appears to be the fundamental variable in the statistical description. Two dynamic processes, crack nucleation and growth, were involved in the model of damage evolution. A simplified case was examined and preliminary correlation to experimental observations of spallation was made.

Absolute measurement of roughness and lateral-correlation length of random surfaces by use of the simplified model of image-speckle contrast

We present a method of image-speckle contrast for the nonprecalibration measurement of the root-mean-square roughness and the lateral-correlation length of random surfaces with Gaussian correlation. We use the simplified model of the speckle fields produced by the weak scattering object in the theoretical analysis. The explicit mathematical relation shows that the saturation value of the image-speckle contrast at a large aperture radius determines the roughness, while the variation of the contrast with the aperture radius determines the lateral-correlation length. In the experimental performance, we specially fabricate the random surface samples with Gaussian correlation. The square of the image-speckle contrast is measured versus the radius of the aperture in the 4f system, and the roughness and the lateral-correlation length are extracted by fitting the theoretical result to the experimental data. Comparison of the measurement with that by an atomic force microscope shows our method has a satisfying accuracy. (C) 2002 Optical Society of America.

Ultrafast sum-frequency polarization beats in twin Markovian stochastic correlation

An analytic closed form for the second- order or fourth- order Markovian stochastic correlation of attosecond sum- frequency polarization beat ( ASPB) can be obtained in the extremely Doppler- broadened limit. The homodyne detected ASPB signal is shown to be particularly sensitive to the statistical properties of the Markovian stochastic light. fields with arbitrary bandwidth. The physical explanation for this is that the Gaussian- amplitude. field undergoes stronger intensity. fluctuations than a chaotic. field. On the other hand, the intensity ( amplitude). fluctuations of the Gaussian- amplitude. field or the chaotic. field are always much larger than the pure phase. fluctuations of the phase-diffusion field. The field correlation has weakly influence on the ASPB signal when the laser has narrow bandwidth. In contrast, when the laser has broadband linewidth, the ASPB signal shows resonant- nonresonant cross correlation, and the sensitivities of ASPB signal to three Markovian stochastic models increase as time delay is increased. A Doppler- free precision in the measurement of the energy- level sum can be achieved with an arbitrary bandwidth. The advantage of ASPB is that the ultrafast modulation period 900as can still be improved, because the energy- level interval between ground state and excited state can be widely separated.

Twin Markovian field correlation on four-level attosecond polarization beats

Based on the phase-conjugate polarization interference between two two-photon processes, we obtained an analytic closed form for the second-order or fourth-order Markovian stochastic correlation of the four-level attosecond sum-frequency polarization beat (FASPB) in the extremely Doppler-broadened limit. The homodyne-detected FASPB signal is shown to be particularly sensitive to the statistical properties of the Markovian stochastic light fields with arbitrary bandwidth. The different roles of the amplitude fluctuations and the phase fluctuations can be understood physically in the time-domain picture. The field correlation has a weak influence on the FASPB signal when the laser has narrow bandwidth. In contrast, when the laser has broadband linewidth, the FASPB signal shows resonant-nonresonant cross-correlation, and drastic difference for three Markovian stochastic fields. The maxima of the two two-photon signals are shifted from zero time delay to the opposite direction, and the signal exhibits damping oscillation when the laser frequency is off-resonant from the two-photon transition. A Doppler-free precision in the measurement of the energy-level sum can be achieved with an arbitrary bandwidth. As an attosecond ultrafast modulation process, it can be extended intrinsically to any sum frequency of energy levels.

Statistical analysis of microscale gas flows and stock price changes

First, recent studies on the information preservation (IP) method, a particle approach for low-speed micro-scale gas flows, are reviewed. The IP method was validated for benchmark issues such as Couette, Poiseuille and Rayleigh flows, compared well with measured data for typical internal flows through micro-channels and external flows past micro flat plates, and combined with the Navier-Stokes equations to be a hybrid scheme for subsonic, rarefied gas flows. Second, the focus is moved to the microscopic characteristic of China stock market, particularly the price correlation between stock deals. A very interesting phenomenon was found that showed a reverse transition behaviour between two neighbouring price changes. This behaviour significantly differs from the transition rules for atomic and molecular energy levels, and it is very helpful to understand the essential difference between stock markets and nature.

Cross-correlation of excitation functions for different fragments and different scattering angles in Al-27(F-19, x)y reactions

Excitation functions have been measured for different projectile-like fragments produced in Al-27(F-19,x)y reactions at incident energies from 110.25 to 118.75 MeV in 250 keV steps. Strong cross section fluctuations of the excitation functions are observed. The cross- correlation coefficients of the excitation functions for different atomic number Z and for different scattering angle theta(cm) have been deduced. These coefficients are much larger than the statistical theoretical calculated ones. This indicates that there are strong correlations between different exit channels in the dissipative heavy ion Collision of Al-27(F-19,x)y.

Surface sediment diatoms from the western Pacific marginal seas and their correlation to environmental variables

Diatom data of 192 surface sediment samples from the marginal seas in the western Pacific together with modern summer and winter sea surface temperature and salinity data were analyzed. The results of canonical correspondence analysis show that summer sea-surface salinity (SSS) is highly positively correlated with winter SSS and so is summer sea-surface temperature (SST) with winter SST. The correlations between SSSs and SSTs are less positively correlated, which may be due to interactions of regional current pattern and monsoon climate. The correlations between diatom species, sample sites and environmental variables concur with known diatom ecology and regional oceanographic characters. The results of forward selection of the environmental variables and associated Monte Carlo permutation tests of the statistical significance of each variable suggest that summer SSS and winter SST are the main environmental factors affecting the diatom distribution in the area and therefore preserved diatom data from down core could be used for reconstructions of summer SSS and winter SST in the region.

Correlation between Discharging Property and Coatings Microstructure during Plasma Electrolytic Oxidation

The voltage-current properties during plasma electrolytic discharge were determined by measuring the current density and cell voltage as functions of processing time and then by mathematical transformation. Correlation between discharge I-V property and the coatings microstructure on aluminum alloy during plasma electrolfic oxidation was determined by comparing the voltage-current properties at different process stages with SEM results of the corresponding coatings. The results show that the uniform passive film corresponds to a I-V property with one critical voltage, and a compound of porous layer and shred ceramic particles corresponds to a I-Vproperty with two critical voltages. The growth regularity of PEO cermet coatings was also studied.

A generalized self-consistent method accounting for fiber section shape

A three-phase confocal elliptical cylinder model is proposed for fiber-reinforced composites, in terms of which a generalized self-consistent method is developed for fiber-reinforced composites accounting for variations in fiber section shapes and randomness in fiber section orientation. The reasonableness of the fiber distribution function in the present model is shown. The dilute, self-consistent, differential and Mori-Tanaka methods are also extended to consider randomness in fiber section orientation in a statistical sense. A full comparison is made between various micromechanics methods and with the Hashin and Shtrikman's bounds. The present method provides convergent and reasonable results for a full range of variations in fiber section shapes (from circular fibers to ribbons), for a complete spectrum of the fiber volume fraction (from 0 to 1, and the latter limit shows the correct asymptotic behavior in the fully packed case) and for extreme types of the inclusion phases (from voids to rigid inclusions). A very different dependence of the five effective moduli on fiber section shapes is theoretically predicted, and it provides a reasonable explanation on the poor correlation between previous theory and experiment in the case of longitudinal shear modulus.

Statistical Simulation of Rarefied Gas Flows in Micro-Channels

Rarefied gas flows through micro-channels are simulated using particle approaches, named as the information preservation (IP) method and the direct simulation Monte Carlo (DSMC) method. In simulating the low speed flows in long micro-channels the DSMC method encounters the problem of large sample size demand and the difficulty of regulating boundary conditions at the inlet and outlet. Some important computational issues in the calculation of long micro-channel flows by using the IP method, such as the use the conservative form of the mass conservation equation to guarantee the adjustment of the inlet and outlet boundary conditions and the super-relaxation scheme to accelerate the convergence process, are addressed. Stream-wise pressure distributions and mass fluxes through micro-channels given by the IP method agree well with experimental data measured in long micro-channels by Pong et al. (with a height to length ratio of 1.2:3000), Shih et al. (l.2:4800), Arkilic et al. and Arkilic (l.3:7500), respectively. The famous Knudsen minimum of normalized mass flux is observed in IP and DSMC calculations of a short micro-channel over the entire flow regime from continuum to free molecular, whereas the slip Navier-Stokes solution fails to predict it.

Statistical and stochastic description of microvoid evolution observed in dynamic failure of ductile materials

A brief review is presented of statistical approaches on microdamage evolution. An experimental study of statistical microdamage evolution in two ductile materials under dynamic loading is carried out. The observation indicates that there are large differences in size and distribution of microvoids between these two materials. With this phenomenon in mind, kinetic equations governing the nucleation and growth of microvoids in nonlinear rate-dependent materials are combined with the balance law of void number to establish statistical differential equations that describe the evolution of microvoids' number density. The theoretical solution provides a reasonable explanation of the experimentally observed phenomenon. The effects of stochastic fluctuation which is influenced by the inhomogeneous microscopic structure of materials are subsequently examined (i.e. stochastic growth model). Based on the stochastic differential equation, a Fokker-Planck equation which governs the evolution of the transition probability is derived. The analytical solution for the transition probability is then obtained and the effects of stochastic fluctuation is discussed. The statistical and stochastic analyses may provide effective approaches to reveal the physics of damage evolution and dynamic failure process in ductile materials.

Molecular/Cluster Statistical Thermodynamics Methods To Simulate Quasi-Static Deformations At Finite Temperature

The rapid evolution of nanotechnology appeals for the understanding of global response of nanoscale systems based on atomic interactions, hence necessitates novel, sophisticated, and physically based approaches to bridge the gaps between various length and time scales. In this paper, we propose a group of statistical thermodynamics methods for the simulations of nanoscale systems under quasi-static loading at finite temperature, that is, molecular statistical thermodynamics (MST) method, cluster statistical thermodynamics (CST) method, and the hybrid molecular/cluster statistical thermodynamics (HMCST) method. These methods, by treating atoms as oscillators and particles simultaneously, as well as clusters, comprise different spatial and temporal scales in a unified framework. One appealing feature of these methods is their "seamlessness" or consistency in the same underlying atomistic model in all regions consisting of atoms and clusters, and hence can avoid the ghost force in the simulation. On the other hand, compared with conventional MD simulations, their high computational efficiency appears very attractive, as manifested by the simulations of uniaxial compression and nanoindenation. (C) 2008 Elsevier Ltd. All rights reserved.