Probing the kinetics of single molecule protein folding

We propose an approach to integrate the theory, simulations, and experiments in protein-folding kinetics. This is realized by measuring the mean and high-order moments of the first-passage time and its associated distribution. The full kinetics is revealed in the current theoretical framework through these measurements. In the experiments, information about the statistical properties of first-passage times can be obtained from the kinetic folding trajectories of single molecule experiments ( for example, fluorescence). Theoretical/simulation and experimental approaches can be directly related. We study in particular the temperature-varying kinetics to probe the underlying structure of the folding energy landscape. At high temperatures, exponential kinetics is observed; there are multiple parallel kinetic paths leading to the native state. At intermediate temperatures, nonexponential kinetics appears, revealing the nature of the distribution of local traps on the landscape and, as a result, discrete kinetic paths emerge. At very low temperatures, exponential kinetics is again observed; the dynamics on the underlying landscape is dominated by a single barrier.

Shear induced molecular alignments of a side-chain liquid crystalline polyacetylene containing biphenyl mesogens

Mesomorphic properties of a side chain liquid crystalline polyacetylene, poly(11-{[(4'-heptyloxy-4-biphenylyl)carbonyl]oxy}-1-undecyne) (PA9EO7), are investigated using polarized optical microscope, X-ray diffraction, and transmission electron microscope. Polymer PA9EO7 forms enantiotropic smectic A and smectic B phases. It also exhibits an additional high order smectic phase, a sandwich structure consisting of different molecular packing of biphenyl mesogenic moieties from that of alkyl spacers and terminals, when it is prepared from its toluene solution. Shearing the polymer film at its smectic A phase generates banded texture with the alignment of the backbones parallel to the direction of shear force. While at its high order smectic phase, the mesogen pendants of the polymer are arranged parallel to the direction of shear. The different mesomorphic behaviors arise from different molecular alignments influenced by the fluidity.

Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Go-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T-opt*. The optimal folding temperature T-opt* is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T-opt* and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T-opt* and start to diverge when the temperature is lower than T-opt*. The distribution of FPT is close to a log-normal-like distribution at T* greater than or equal to T-opt*. At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.

Monitoring and simulation of water, heat,and CO2 fluxes in terrestrial ecosystems based on the APEIS-FLUX system

The Integrated Environmental Monitoring (IEM) project, part of the Asia-Pacific Environmental Innovation Strategy (APEIS) project, developed an integrated environmental monitoring system that can be used to detect, monitor, and assess environmental disasters, degradation, and their impacts in the Asia-Pacific region. The system primarily employs data from the moderate resolution imaging spectrometer (MODIS) sensor on the Earth Observation System- (EOS-) Terra/Aqua satellite,as well as those from ground observations at five sites in different ecological systems in China. From the preliminary data analysis on both annual and daily variations of water, heat and CO2 fluxes, we can confirm that this system basically has been working well. The results show that both latent flux and CO2 flux are much greater in the crop field than those in the grassland and the saline desert, whereas the sensible heat flux shows the opposite trend. Different data products from MODIS have very different correspondence, e.g. MODIS-derived land surface temperature has a close correlation with measured ones, but LAI and NPP are quite different from ground measurements, which suggests that the algorithms used to process MODIS data need to be revised by using the local dataset. We are now using the APEIS-FLUX data to develop an integrated model, which can simulate the regional water,heat, and carbon fluxes. Finally, we are expected to use this model to develop more precise high-order MODIS products in Asia-Pacific region.

基于LMI全方位移动机器人H_∞鲁棒控制

针对机器人控制领域中一类多输入多输出(MIMO)高阶线性时不变系统,根据模型自身的结构特点,给出了基于线性矩阵不等式(LMI)的通过局部反馈H∞控制实现整个系统对不确定扰动具有鲁棒性的充分条件及相关推论,并在此基础上提出了一种解决该类型系统H∞控制问题的新算法。通过对一完整约束移动机器人系统的局部输出反馈H∞控制仿真,说明了此算法具有良好的控制效果和实用性。

基于独立成分分析和模糊支持向量机的人脸识别方法

成分分析(PCA)只能从2阶上去消除数据的相关性，传统支持向量机在解决多类问题时会出现分类的盲区问题，针对这两种情况，首先采用独立成分分析(ICA)方法解决了高阶上的数据相关性问题；同时在传统支持向量机中引入模糊隶属度函数，用模糊支持向量机解决了传统支持向量机在多类数据识别中的盲区问题。通过实验证明了该方法在人脸识别率上取得了显著提高。

高阶无静差采样控制系统的动态综合

本文利用“最小响应法”给出了 N≥2阶无静差采样控制系统的设计公式.作者指出:对于某类闭环控制系统,在给定阶跃响应最大超调量σ_(max)的条件下,可以找出最佳比值T/T_(T 为系统的采样周期,T_(?)为对象的不便克服的等效小时间常数之和),使系统获得相应阶最大误差系数 K_(N+1),从而可使系统达到快速精密的控制指标。为了在工程设计中应用方便,文中还给出了二至六阶无静差的σ_(max),T/T_(?),K_(N+1)T(?)最佳参数组,使得这类闭环控制系统的设计最佳化和简易化.

高阶广义屏波动方程叠前深度偏移

Attaining sufficient accuracy and efficiency of generalized screen propagator and improving the quality of input gathers are often problems　of wave equation presack depth migration,　in this paper,a high order formula of generalized screen propagator　for one-way wave equation is proposed by using the asymptotic expansion of single-square-root operator. Based on the formula，a new generalized screen propagator is developed ,which is composed of split-step Fourier propagator and high order correction terms，the new generalized screen propagator not only improving calculation precision without sharply increasing the quantity of computation，facilitates the suitability of generalized screen propagator to the media with strong lateral velocity variation.　As wave-equation prestack depth migration is sensitive to the quality of input gathers, which greatly affect the output，and the available seismic data processing system has inability to obtain traveltimes corresponding to the multiple arrivals, to estimate of great residual statics， to merge seismic datum from different projects and to design inverse Q filter, we establish　difference equations with an embodiment of Huygens’s principle for obtaining traveltimes corresponding to the multiple arrivals,bring forward a time variable matching filter for seismic datum merging by using the fast algorithm called Mallat tree for wavelet transformations， put forward a method for estimation of residual statics by applying the optimum model parameters estimated by iterative inversion with three organized algorithm,i.e,the CMP intertrace cross-correlation algorithm,the Laplacian image edge extraction algorithm,and the DFP algorithm, and present phase-shift inverse Q filter based on Futterman’s amplitude and phase-velocity dispersion formula and wave field extrapolation theory. All of their numerical and real data calculating results shows that our theory and method are practical and efficient. Key words: prestack depth migration, generalized screen propagator, residual statics，inverse Q filter ,traveltime，3D seismic datum mergence

层析静校正技术研究和应用

Static correction is one of the indispensable steps in the conventional onshore seismic data processing, particularly in the western part of China; it is theoretically and practically significant to resolve the issue of static correction. Conventional refraction static correction is put forward under the assumption that layered medium is horizontal and evenly distributed. The complicated nature of the near surface from western part of China is far from the assumption. Therefore, the essential way to resolve the static correction problem from the complex area is to develop a new theory. In this paper, a high-precision non-linear first arrival tomography is applied to solve the problem, it moved beyond the conventional refraction algorithm based on the layered medium and can be used to modeling the complex near surface. Some of the new and creative work done is as follows: One. In the process of first arrival tomographic image modeling, a fast high-order step algorithm is used to calculate the travel time for first arrival and ray path and various factors concerning the fast step ray tracing algorithm is analyzed. Then the second-order and third-order differential format is applied to the step algorithm which greatly increased the calculation precision of the ray tracing and there is no constraint to the velocity distribution from the complex areas. This method has very strong adaptability and it can meet the needs of great velocity variation from the complicated areas. Based on the numerical calculation, a fast high-order step is a fast, non-conditional and stable high-precision tomographic modeling algorithm. Two, in the tomographic inversion, due to the uneven fold coverage and insufficient information, the inversion result is unstable and less reliable. In the paper, wavelet transform is applied to the tomographic inversion which has achieved a good result. Based on the result of the inversion from the real data, wavelet tomographic inversion has increased the reliability and stability of the inversion. Three. Apply the constrained high-precision wavelet tomographic image to the static correction processing from the complex area. During tomographic imaging, by using uphole survey, refraction shooting or other weathering layer method, weathering layer can be identified before the image. Because the group interval for the shot first arrival is relatively big, there is a lack of precision for the near surface inversion. In this paper, an inversion method of the layer constraint and well constraint is put forward, which can be used to compensate the shallow velocity of the inversion for the shot first arrival and increase the precision of the tomographic inversion. Key words: Tomography ，Fast marching method，Wavelet transform, Static corrections, First break

基于广义正交多项式迭积微分算子的地震波场数值模拟研究

Seismic Numerical Modeling is one of bases of the Exploratory Seismology and Academic Seismology, also is a research field in great demand. Essence of seismic numerical modeling is to assume that structure and parameters of the underground media model are known, simulate the wave-field and calculate the numerical seismic record that should be observed. Seismic numerical modeling is not only a means to know the seismic wave-field in complex inhomogeneous media, but also a test to the application effect by all kinds of methods. There are many seismic numerical modeling methods, each method has its own merits and drawbacks. During the forward modeling, the computation precision and the efficiency are two pivotal questions to evaluate the validity and superiority of the method. The target of my dissertation is to find a new method to possibly improve the computation precision and efficiency, and apply the new forward method to modeling the wave-field in the complex inhomogeneous media. Convolutional Forsyte polynomial differentiator (CFPD) approach developed in this dissertation is robust and efficient, it shares some of the advantages of the high precision of generalized orthogonal polynomial and the high speed of the short operator finite-difference. By adjusting the operator length and optimizing the operator coefficient, the method can involve whole and local information of the wave-field. One of main tasks of the dissertation is to develop a creative, generalized and high precision method. The author introduce convolutional Forsyte polynomial differentiator to calculate the spatial derivative of seismic wave equation, and apply the time staggered grid finite-difference which can better meet the high precision of the convolutional differentiator to substitute the conventional finite-difference to calculate the time derivative of seismic wave equation, then creating a new forward method to modeling the wave-field in complex inhomogeneous media. Comparing with Fourier pseudo-spectral method, Chebyshev pseudo-spectral method, staggered- grid finite difference method and finite element method, convolutional Forsyte polynomial differentiator (CFPD) method has many advantages: 1. Comparing with Fourier pseudo-spectral method. Fourier pseudo-spectral method (FPS) is a local operator, its results have Gibbs effects when the media parameters change, then arose great errors. Therefore, Fourier pseudo-spectral method can not deal with special complex and random heterogeneous media. But convolutional Forsyte polynomial differentiator method can cover global and local information. So for complex inhomogeneous media, CFPD is more efficient. 2. Comparing with staggered-grid high-order finite-difference method, CFPD takes less dots than FD at single wave length, and the number does not increase with the widening of the studying area. 3. Comparing with Chebyshev pseudo-spectral method (CPS). The calculation region of Chebyshev pseudo-spectral method is fixed in , under the condition of unchangeable precision, the augmentation of calculation is unacceptable. Thus Chebyshev pseudo-spectral method is inapplicable to large area. CFPD method is more applicable to large area. 4. Comparing with finite element method (FE), CFPD can use lager grids. The other task of this dissertation is to study 2.5 dimension (2.5D) seismic wave-field. The author reviews the development and present situation of 2.5D problem, expatiates the essentiality of studying the 2.5D problem, apply CFPD method to simulate the seismic wave-field in 2.5D inhomogeneous media. The results indicate that 2.5D numerical modeling is efficient to simulate one of the sections of 3D media, 2.5D calculation is much less time-consuming than 3D calculation, and the wave dispersion of 2.5D modeling is obviously less than that of 3D modeling. Question on applying time staggered-grid convolutional differentiator based on CFPD to modeling 2.5D complex inhomogeneous media was not studied by any geophysicists before, it is a fire-new creation absolutely. The theory and practices prove that the new method can efficiently model the seismic wave-field in complex media. Proposing and developing this new method can provide more choices to study the seismic wave-field modeling, seismic wave migration, seismic inversion, and seismic wave imaging.

离散裂缝诱导各向异性粘弹性地震波模拟与特征分析

The real media always attenuate and distort seismic waves as they propagate in the earth. This behavior can be modeled with a viscoelastic and anisotropic wave equation. The real media can be described as fractured media. In this thesis, we present a high-order staggered grid finite-difference scheme for 2-D viscoelastic wave propagation in a medium containing a large number of small finite length fractures. We use the effective medium approach to compute the anisotropic parameters in each grid cell. By comparing our synthetic seismogram by staggered-grid finite-difference with that by complex-ray parameter ray tracing method, we conclude that the high-order staggered-grid finite-difference technique can effectively used to simulate seismic propagation in viscoelastic-anisotropic media. Synthetic seismograms demonstrate that strong attenuation and significant frequency dispersion due to viscosity are important factors of reducing amplitude and delaying arrival time varying with incidence angle or offset. On the other hand, the amount of scattered energy not only provides an indicator of orientation of fracture sets, but can also provide information about the fracture spacing. Analysis of synthetic seismograms from dry- and fluid-filled fractures indicates that dry-filled fractures show more significant scattering on seismic wavefields than fluid-filled ones, and offset-variations in P-wave amplitude are observable. We also analyze seismic response of an anticlinal trap model that includes a gas-filled fractured reservoir with high attenuation, which attenuates and distorts the so-called bright spot.

全局优化的Fourier有限差分偏移方法研究

Seismic exploration is the main method of seeking oil and gas. With the development of seismic exploration, the target becomes more and more complex, which leads to a higher demand for the accuracy and efficiency in seismic exploration. Fourier finite-difference (FFD) method is one of the most valuable methods in complex structure exploration, which has obtained good effect. However, in complex media with wider angles, the effect of FFD method is not satisfactory. Based on the FFD operator, we extend the two coefficients to be optimized to four coefficients, then optimize them globally using simulated annealing algorithm. Our optimization method select the solution of one-way wave equation as the objective function. Except the velocity contrast, we consider the effects of both frequency and depth interval. The proposed method can improve the angle of FFD method without additional computation time, which can reach 75° in complex media with large lateral velocity contrasts and wider propagation angles. In this thesis, combinating the FFD method and alternative-direction-implicit plus interpolation(ADIPI） method, we obtain 3D FFD with higher accuracy. On the premise of keeping the efficiency of the FFD method, this method not only removes the azimuthal anisotropy but also optimizes the FFD mehod, which is helpful to 3D seismic exploration. We use the multi-parameter global optimization method to optimize the high order term of FFD method. Using lower-order equation to obtain the approximation effect of higher-order equation, not only decreases the computational cost result from higher-order term, but also obviously improves the accuracy of FFD method. We compare the FFD, SAFFD（multi-parameter simulated annealing globally optimized FFD）, PFFD, phase-shift method(PS）, globally optimized FFD （GOFFD）, and higher-order term optimized FFD method. The theoretical analyses and the impulse responses demonstrate that higher-order term optimized FFD method significantly extends the accurate propagation angle of the FFD method, which is useful to complex media with wider propagation angles.

指数矩阵近似计算在地震波场延拓中的应用

Seismic wave field numerical modeling and seismic migration imaging based on wave equation have become useful and absolutely necessarily tools for imaging of complex geological objects. An important task for numerical modeling is to deal with the matrix exponential approximation in wave field extrapolation. For small value size matrix exponential, we can approximate the square root operator in exponential using different splitting algorithms. Splitting algorithms are usually used on the order or the dimension of one-way wave equation to reduce the complexity of the question. In this paper, we achieve approximate equation of 2-D Helmholtz operator inversion using multi-way splitting operation. Analysis on Gauss integral and coefficient of optimized partial fraction show that dispersion may accumulate by splitting algorithms for steep dipping imaging. High-order symplectic Pade approximation may deal with this problem, However, approximation of square root operator in exponential using splitting algorithm cannot solve dispersion problem during one-way wave field migration imaging. We try to implement exact approximation through eigenfunction expansion in matrix. Fast Fourier Transformation (FFT) method is selected because of its lowest computation. An 8-order Laplace matrix splitting is performed to achieve a assemblage of small matrixes using FFT method. Along with the introduction of Lie group and symplectic method into seismic wave-field extrapolation, accurate approximation of matrix exponential based on Lie group and symplectic method becomes the hot research field. To solve matrix exponential approximation problem, the Second-kind Coordinates (SKC) method and Generalized Polar Decompositions (GPD) method of Lie group are of choice. SKC method utilizes generalized Strang-splitting algorithm. While GPD method utilizes polar-type splitting and symmetric polar-type splitting algorithm. Comparing to Pade approximation, these two methods are less in computation, but they can both assure the Lie group structure. We think SKC and GPD methods are prospective and attractive in research and practice.

工作幸福感的结构、测量及作用机制

With the emergence and development of positive psychology, happiness has been the focus of academia and business. However, there is no uniform measure of happiness, because of many different theories of happiness, which are not compatible with others. It bounds the further development of happiness theory. It is also the same with the research of work well-being, which refers to the emotional experience and quality of psychological functioning of employee in the workplace. Subjective well-being (SWB) and psychological well-being (PWB) are two major theories of happiness. Prior research has demonstrated the integration of these two theories theoretically, but still needs more empirical support. Besides, in line with the development of positive psychology, a body of knowledge about positive leadership is advocated. Transformational leadership is treated as one kind of positive leadership, since it emphasizes the leader’s motivational and elevating effect on followers. But the extent to which the transformational leadership can enhance work well-being, and what the mechanism is, these are the questions need to be explored. Based on the integration of SWB and PWB, this research tried to investigate the structure, measurement and mechanism of work well-being, and combining with the theory of transformational leadership, this study also tried to investigate the relationship between transformational leadership and work well-being. The structure and measurement of work well-being, the relationships between work well-being and job characteristics (including job resources and job demands), the relationships among transformational leadership, job resources, work well-being and corresponding outcomes, the relationships among transformational leadership, job demands, work well-being and corresponding outcomes, and the relationships among transformational leadership, group job characteristics, group work well-being and corresponding group outcomes were explored by using content analysis, Subject Matter Experts (SMEs) discussion, and structural questionnaire surveys. More than 7000 subjects were surveyed, and Explore Factor Analysis (EFA), Confirm Factor Analysis (CFA), Structural Equation Modeling (SEM), Hierarchical Linear Modeling (HLM) and other statistics methods were used. The following is the major conclusions. Firstly, work well-being is a two high-order factors structure, which includes affective well-being (AWB) and cognitive well-being (CWB). AWB is similar to SWB, and CWB is similar to PWB. Besides, the construct of AWB includes sub-dimensions of positive emotional experience and negative emotional experience. And the construct of CWB consists of work autonomy, personal growth, work competent, and work significance. Secondly, the relationships between job characteristics and AWB and CWB are different. On one hand job demands are directly related to AWB, and are indirectly related to CWB through the full mediation of AWB, on the other job resources are directly related to CWB, and are indirectly related to AWB through the full mediation of CWB, which means AWB and CWB reciprocally influences each other in the model of job demands-resources. These results were concluded as the process model of work well-being. Thirdly, AWB and CWB are positively related to many workplace outcomes, including job satisfaction, group satisfaction, organizational commitment, turnover intention, job performance, organizational citizenship behavior (OCB), and general psychological health and general physiological health. Fourthly, transformational leadership is indirectly related to CWB through the full mediation of job resources, and is related to AWB through the partial mediation of job demands. Meanwhile, transformational leadership is related to many workplace outcomes through the mediation of job characteristics and work well-being. These results implied that transformational leadership is indeed one kind of positive leadership. Fifthly, in the group level, transformational leadership is indirectly related to group CWB through the full mediation of group job resources, and is related to group AWB through the full mediation of group job demands. Group AWB has positive influence on group CWB, but not vice versa. Group job characteristics and group work well-being fully mediate the relationships between transformational leadership and intragroup cooperation and group performance.