80 resultados para Similarity, Protein Function, Empirical Mode Decomposition

em Chinese Academy of Sciences Institutional Repositories Grid Portal


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The dynamics of phase separation in a binary polymer blend of poly(vinyl acetate) with poly(methyl methacrylate) was investigated by using a time-resolved light-scattering technique. In the later stages of spinodal decomposition, a simple dynamic scaling law was found for the scattering function S(q, t)(S(q, t) approximately I(q, t)): S(q, t)q(m)-3 S approximately (q/q(m)). The scaling function determined experimentally was in good agreement with that predicted by Furukawa, S approximately (X) approximately X2/(3 + X8) for critical concentration, and approximately in agreement with that predicted by Furukawa, S approximately (X) approximately X2/(3 + X6) for non-critical mixtures. The light-scattering invariant shows that the later stages of the spinodal decomposition were undergoing domain ripening.

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Acoustic Gravity waves (AGW) play an important role in balancing the atmospheric energy and momentum budget. Propagation of gravity wave in the atmosphere is one of the important factors of changing middle and upper atmosphere and ionosphere. The purpose of this dissertation is to study the propagation of gravity wave in a compression atmosphere whit means of numerical simulation and to analyze the response of middle and upper atmosphere to pulse disturbance from lower atmosphere. This work begins with the establishment of 2-D fully nonlinear compressible atmospheric dynamic model in polar coordinate, which is used ton numerically study gravity wave propagation. Then the propagation characteristics of acoustic gravity wave packets are investigated and discussed. We also simulate the response of middle and upper atmosphere to pulse disturbance of lower atmosphere in background winds or without background winds by using this model and analyze the data we obtained by using Fourier Transform (FT), Short-time Fourier Transform (STFT) and Empirical Mode Decomposition (EMD) method which is an important part of Hilbert-Huang Transform (HHT). The research content is summarized in the following: 1. By using a two-dimensional full-implicit-continuous-Eulerian (FICE) scheme and taking the atmospheric basic motion equations as the governing equations, a numerical model for nonlinear propagation of acoustic gravity wave disturbance in two-dimensional polar coordinates is solved. 2. Then the propagation characteristics of acoustic gravity wave packets are investigated and discussed. Results of numerical simulation show that the acoustic gravity wave packets propagate steadily upward and keep its shape well after several periods. 3. We simulate the response of middle and upper atmosphere to pulse disturbance of lower atmosphere in background winds or without background winds by using this model, and obtain the distribution of a certain physical quantity in time and space from earth’s surface to 300km above. The results reveal that the response of ionosphere occurs at a large horizontal distance from the source and the disturbance becomes greater with increasing of height. The situation when the direction of the background wind is opposite to or the same as the direction of disturbed velocity of gravity-wave is studied. The results show that gravity wave propagating against winds is easier than those propagating along winds and the background wind can accelerate gravity wave propagation. Just upon the source, an acoustic wave component with period of 6 min can be found. These images of simulation are similar to observations of the total electron content (TEC) disturbances caused by the great Sumatra-Andaman earthquake on December 26 in 2004. 4. Using the EMD method the disturbed velocity data of a certain physical quantity in time and space can be decomposed into a series of intrinsic mode function (IMF) and a trend mode respectively. The results of EMD reveal impact of the gravity wave frequency under the background winds.

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In modem signal Processing,non-linear,non-Gaussian and non-stable signals are usually the analyzed and Processed objects,especially non-stable signals. The convention always to analyze and Process non-stable signals are: short time Fourier transform,Wigner-Ville distribution,wavelet Transform and so on. But the above three algorithms are all based on Fourier Transform,so they all have the shortcoming of Fourier Analysis and cannot get rid of the localization of it. Hilbert-Huang Transform is a new non-stable signal processing technology,proposed by N. E. Huang in 1998. It is composed of Empirical Mode Decomposition (referred to as EMD) and Hilbert Spectral Analysis (referred to as HSA). After EMD Processing,any non-stable signal will be decomposed to a series of data sequences with different scales. Each sequence is called an Intrinsic Mode Function (referred to as IMF). And then the energy distribution plots of the original non-stable signal can be found by summing all the Hilbert spectrums of each IMF. In essence,this algorithm makes the non-stable signals become stable and decomposes the fluctuations and tendencies of different scales by degrees and at last describes the frequency components with instantaneous frequency and energy instead of the total frequency and energy in Fourier Spectral Analysis. In this case,the shortcoming of using many fake harmonic waves to describe non-linear and non-stable signals in Fourier Transform can be avoided. This Paper researches in the following parts: Firstly,This paper introduce the history and development of HHT,subsequently the characters and main issues of HHT. This paper briefly introduced the basic realization principles and algorithms of Hilbert-Huang transformation and confirms its validity by simulations. Secondly, This paper discuss on some shortcoming of HHT. By using FFT interpolation, we solve the problem of IMF instability and instantaneous frequency undulate which are caused by the insufficiency of sampling rate. As to the bound effect caused by the limitation of envelop algorithm of HHT, we use the wave characteristic matching method, and have good result. Thirdly, This paper do some deeply research on the application of HHT in electromagnetism signals processing. Based on the analysis of actual data examples, we discussed its application in electromagnetism signals processing and noise suppression. Using empirical mode decomposition method and multi-scale filter characteristics can effectively analyze the noise distribution of electromagnetism signal and suppress interference processing and information interpretability. It has been founded that selecting electromagnetism signal sessions using Hilbert time-frequency energy spectrum is helpful to improve signal quality and enhance the quality of data.

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Offshore seismic exploration is full of high investment and risk. And there are many problems, such as multiple. The technology of high resolution and high S/N ratio on marine seismic data processing is becoming an important project. In this paper, the technology of multi-scale decomposition on both prestack and poststack seismic data based on wavelet and Hilbert-Huang transform and the theory of phase deconvolution is proposed by analysis of marine seismic exploration, investigation and study of literatures, and integration of current mainstream and emerging technology. Related algorithms are studied. The Pyramid algorithm of decomposition and reconstruction had been given by the Mallat algorithm of discrete wavelet transform In this paper, it is introduced into seismic data processing, the validity is shown by test with field data. The main idea of Hilbert-Huang transform is the empirical mode decomposition with which any complicated data set can be decomposed into a finite and often small number of intrinsic mode functions that admit well-behaved Hilbert transform. After the decomposition, a analytical signal is constructed by Hilbert transform, from which the instantaneous frequency and amplitude can be obtained. And then, Hilbert spectrum. This decomposition method is adaptive and highly efficient. Since the decomposition is based on the local characteristics of the time scale of data, it is applicable to nonlinear and non-stationary processes. The phenomenons of fitting overshoot and undershoot and end swings are analyzed in Hilbert-Huang transform. And these phenomenons are eliminated by effective method which is studied in the paper. The technology of multi-scale decomposition on both prestack and poststack seismic data can realize the amplitude preserved processing, enhance the seismic data resolution greatly, and overcome the problem that different frequency components can not restore amplitude properly uniformly in the conventional method. The method of phase deconvolution, which has overcome the minimum phase limitation in traditional deconvolution, approached the base fact well that the seismic wavelet is phase mixed in practical application. And a more reliable result will be given by this method. In the applied research, the high resolution relative amplitude preserved processing result has been obtained by careful analysis and research with the application of the methods mentioned above in seismic data processing in four different target areas of China Sea. Finally, a set of processing flow and method system was formed in the paper, which has been carried on in the application in the actual production process and has made the good progress and the huge economic benefit.

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An equivalent-barotropic (EB) description of the tropospheric temperature field is derived from the geostrophic empirical mode (GEM) in the form of a scalar function Gamma(p, phi), where p is pressure and phi is 300-850-mb thickness. Baroclinic parameter phi plays the role of latitude at each longitudinal section. Compared with traditional Eulerian-mean methods, GEM defines a mean field in baroclinic streamfunction space with a time scale much longer than synoptic variability. It prompts an EB concept that is only based on a baroclinic field. Monthly GEM fields are diagnosed from NCEP-NCAR reanalysis data and account for more than 90% of the tropospheric thermal variance. The circumglobal composite of GEM fields exhibits seasonal, zonal, and hemispheric asymmetries, with larger rms errors occurring in winter and in the Northern Hemisphere (NH). Zonally asymmetric features and planetary deviation from EB are seen in the NH winter GEM. Reconstruction of synoptic sections and correlation analysis reveal that the tropospheric temperature field is EB at the leading order and has a 1-day phase lag behind barotropic variations in extratropical regions.

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To extend the cross-hole seismic 2D data to outside 3D seismic data, reconstructing the low frequency data to high frequency data is necessary. Blind deconvolution method is a key technology. In this paper, an implementation of Blind deconvolution is introduced. And optimized precondition conjugate gradient method is used to improve the stability of the algorithm and reduce the computation. Then high-frequency retrieved Seismic data and the cross-hole seismic data is combined for constraint inversion. Real data processing proved the method is effective. To solve the problem that the seismic data resolution can’t meet the request of reservoir prediction in the river face thin-layers in Chinese eastern oil fields, a high frequency data reconstruction method is proposed. The extrema of the seismic data are used to get the modulation function which operated with the original seismic data to get the high frequency part of the reconstruction data to rebuild the wide band data. This method greatly saves the computation, and easy to adjust the parameters. In the output profile, the original features of the seismic events are kept, the common feint that breaking the events and adding new zeros to produce alias is avoided. And the interbeded details are enhanced compared to the original profiles. The effective band of seismic data is expended and the method is approved by the processing of the field data. Aim to the problem in the exploration and development of Chinese eastern oil field that the high frequency log data and the relative low frequency seismic data can’t be merged, a workflow of log data extrapolation constrained by time-phase model based on local wave decomposition is raised. The seismic instantaneous phase is resolved by local wave decomposition to build time-phase model, the layers beside the well is matched to build the relation of log and seismic data, multiple log info is extrapolated constrained by seismic equiphase map, high precision attributes inverse sections are produced. In the course of resolve the instantaneous phase, a new method of local wave decomposition --Hilbert transform mean mode decomposition(HMMD) is raised to improve the computation speed and noise immunity. The method is applied in the high resolution reservoir prediction in Mao2 survey of Daqing oil field, Multiple attributes profiles of wave impedance, gamma-ray, electrical resistivity, sand membership degree are produced, of which the resolution is high and the horizontal continuous is good. It’s proved to be a effective method for reservoir prediction and estimation.

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Dynamic properties of proteins have crucial roles in understanding protein function and molecular mechanism within cells. In this paper, we combined total internal reflection fluorescence microscopy with oblique illumination fluorescence microscopy to observe directly the movement and localization of membrane-anchored green fluorescence proteins in living cells. Total internal reflect illumination allowed the observation of proteins in the cell membrane of living cells since the penetrate depth could be adjusted to about 80 nm, and oblique illumination allowed the observation of proteins both in the cytoplasm and apical membrane, which made this combination a promising tool to investigate the dynamics of proteins through the whole cell. Not only individual protein molecule tracks have been analyzed quantitatively but also cumulative probability distribution function analysis of ensemble trajectories has been done to reveal the mobility of proteins. Finally, single particle tracking has acted as a compensation for single molecule tracking. All the results exhibited green fluorescence protein dynamics within cytoplasm, on the membrane and from cytoplasm to plasma membrane.

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Analytical expression of signal bandwidth of general straight and tapered N x N multimode interference (MMI) couplers is presented. The signal bandwidth is characterized as a function of mode relative energy, mode propagation delay time, and mode pulse broadening in the multimode section of MMI coupler. The model is used to evaluate the signal bandwidth of specific couplers. Results indicate that the signal bandwidth decreases seriously with the increase of channel number and channel guide space. Compared with the straight MMI coupler, the tapered MMI coupler has an improved signal bandwidth.

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The relationships between ecological diversity and ecosystem functions such as stability and productivity have long been debated and have no final conclusion until now. It is ignored that the debate should be firstly based on the same diversity index, which should be theoretically complete, and on same observation scale. For the issue on the scale of ecotope observation, ecosystems should be distinguished according to intensity of human disturbance. For the issue on the scale of species observation, either number diversity or biomass diversity should be identified. This paper takes grassland ecosystems located within the Bayin Xile grassland of Xilin Gol League of Inner Mongolia Autonomous Region as an example to analyze effects of different diversity indices and spatial scales on the conclusions of ecological diversity and its relationships with ecosystem functions. The analysis results both on the scale of ecotope observation and on the scale of species observation show that different diversity indices might give different conclusions and spatial resolution has a great effect on the relative conclusions. (c) 2005 Elsevier B.V. All rights reserved.

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The identification of kinetic pathways is a central issue in understanding the nature of flexible binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

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We investigate the influence of low-frequency Rossby waves on the thermal structure of the upper southwestern tropical Indian Ocean (SWTIO) using Argo profiles, satellite altimetric data, sea surface temperature, wind field data and the theory of linear vertical normal mode decomposition. Our results show that the SWTIO is generally dominated by the first baroclinic mode motion. As strong downwelling Rossby waves reach the SWTIO, the contribution of the second baroclinic mode motion in this region can be increased mainly because of the reduction in the vertical stratification of the upper layer above thermocline, and the enhancement in the vertical stratification of the lower layer under thermocline also contributes to it. The vertical displacement of each isothermal is enlarged and the thermal structure of the upper level is modulated, which is indicative of strong vertical mixing. However, the cold Rossby waves increase the vertical stratification of the upper level, restricting the variability related to the second baroclinic mode. On the other hand, during decaying phase of warm Rossby waves, Ekman upwelling and advection processes associated with the surface cyclonic wind circulation can restrain the downwelling processes, carrying the relatively colder water to the near-surface, which results in an out-of-phase phenomenon between sea surface temperature anomaly (SSTA) and sea surface height anomaly (SSHA) in the SWTIO.

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基于东海PN断面近五十年的历史水文数据,本文应用一种斜压流函数空间投影的方法分析冲绳海槽北部黑潮水团的水文结构及其季节性和年代际变异。通过将历史数据投影到一个斜压流函数空间中,GEM方法能很好地消除黑潮中尺度变异引起的噪音。诊断生成的东海黑潮温度和盐度GEM场以压力和斜压流函数为参数,能反映黑潮基本的温盐结构。通过分析1987年之后黑潮季节平均的温盐GEM场,结果显示黑潮中层水的盐度在夏季相对较低, 在春季达到最高。通过比较1987年之后温盐深仪(CTD)数据生成的GEM场与1987年之前南森瓶(Bottle)数据生成的GEM场,我们证实黑潮的年代际变化特征,即黑潮表层水近二十年来温度升高而盐度减小,同时发现黑潮中层水具有盐度减小而黑潮热带水具有盐度增加的趋势。进一步通过对PN断面上黑潮水团来源的分析讨论,得出中层水盐度最小值靠近黑潮左侧的现象是由于冲绳岛-宫古岛之间入侵的北太平洋中层水受黑潮主轴的平流作用所致。

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Here we attempt to characterize protein evolution by residue features which dominate residue substitution in homologous proteins. Evolutionary information contained in residue substitution matrix is abstracted with the method of eigenvalue decomposition. Top eigenvectors in the eigenvalue spectrums are analyzed as function of the level of similarity, i.e. sequence identity (SI) between homologous proteins. It is found that hydrophobicity and volume are two significant residue features conserved in protein evolution. There is a transition point at SI approximate to 45%. Residue hydrophobicity is a feature governing residue substitution as SI >= 45%. Whereas below this SI level, residue volume is a dominant feature. (C) 2007 Elsevier B.V. All rights reserved.

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CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

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We introduce a conceptual model for the in-plane physics of an earthquake fault. The model employs cellular automaton techniques to simulate tectonic loading, earthquake rupture, and strain redistribution. The impact of a hypothetical crustal elastodynamic Green's function is approximated by a long-range strain redistribution law with a r(-p) dependance. We investigate the influence of the effective elastodynamic interaction range upon the dynamical behaviour of the model by conducting experiments with different values of the exponent (p). The results indicate that this model has two distinct, stable modes of behaviour. The first mode produces a characteristic earthquake distribution with moderate to large events preceeded by an interval of time in which the rate of energy release accelerates. A correlation function analysis reveals that accelerating sequences are associated with a systematic, global evolution of strain energy correlations within the system. The second stable mode produces Gutenberg-Richter statistics, with near-linear energy release and no significant global correlation evolution. A model with effectively short-range interactions preferentially displays Gutenberg-Richter behaviour. However, models with long-range interactions appear to switch between the characteristic and GR modes. As the range of elastodynamic interactions is increased, characteristic behaviour begins to dominate GR behaviour. These models demonstrate that evolution of strain energy correlations may occur within systems with a fixed elastodynamic interaction range. Supposing that similar mode-switching dynamical behaviour occurs within earthquake faults then intermediate-term forecasting of large earthquakes may be feasible for some earthquakes but not for others, in alignment with certain empirical seismological observations. Further numerical investigation of dynamical models of this type may lead to advances in earthquake forecasting research and theoretical seismology.