改进的势能曲面变平法在二维非格点模型中的应用

蛋白质结构预测问题是生物信息学中的一个重要问题。缺少一种有效的全局寻优方法是阻碍这一问题解决的关键。势能曲面变平(ELP)法是一种启发式的全局优化方法,是一种推广的Monte Carlo方法,已成功地应用于许多优化问题。在ELP法的基础上,提出了改进的势能曲面变平(ELP+)算法。将ELP+算法应用于二维非格点的蛋白质AB模型,预测和发现四条链长分别为13,21,34和55的氨基酸序列的蛋白质结构。数值实验表明,ELP+算法是一种预测蛋白质结构的有效算法。

免疫算法在蛋白质折叠模拟中的应用

利用免疫算法 ,结合非格模型 ,对于长度为 12～ 2 0的氨基酸序列的折叠进行预测 ,并与标准的遗传算法和模拟退火算法进行对比 ,该算法有更强的全局搜索能力 ,对减轻遗传算法后期波动性有明显效果 。

人口迁移算法在蛋白质折叠模拟中的应用

PMA(population migration algorithm)算法具有较强的全局搜索能力和稳定性.针对PMA算法的思想,首次提出将人口迁移算法应用于蛋白质的折叠模拟中,并使用该算法求解蛋白质折叠构形预测的二维AB模型,对计算结果进行了分析.

用于真实蛋白质结构预测的一种新的优化方法

用“相对熵”作为优化函数 ,提出了一个有效快速的折叠预测优化算法 .使用了非格点模型 ,预测只关心蛋白质主链的走向 .其中只用到了蛋白质主链上的两两连续的Cα 原子间的距离信息以及 2 0种氨基酸的接触势的一个扩展形式 .对几个真实蛋白质做了算法测试 ,预测的初始结构都为比较大的去折叠态 ,预测构象相对于它们天然结构的均方根偏差 (RMSD)为 5～ 7 .从原理上讲 ,该方法是对能量优化的改进 .

势能曲面变平法的改进及其在三维非格点模型中的应用

根据蛋白质的氨基酸序列预测其空间结构可以归纳为一个多极值的全局优化问题,缺少一种有效的全局寻优方法是阻碍这一难题解决的一个关键。势能曲面变平(ELP)法是一种启发式的全局优化算法,是一种推广的蒙特卡罗(MC)法,已被成功地应用于蛋白质结构预测问题。本文在ELP法的基础上,提出改进的势能曲面变平(ELP+)算法。将ELP+算法应用于三维非格点的蛋白质AB模型,预测和发现蛋白质结构,数值实验表明ELP+算法是一种预测蛋白质结构的有效算法,计算结果优于ELP和MC算法。

Velocity of a Liquid Drop with a Sorption-Controlled Surfactant

The terminal velocity of a liquid droplet settling in a sulfactant solution has been studied for the non-linear adsorption Langmuir frameworks accounting for monolayer saturation and non-ideal surfactant interactions. Most prior research uses a linear adsorption model which cannot capture these effects, The Maragoni migration of a liquid drop settling through a surfactant solution is examined by using Langmuir framework. The solution concentration Ceq is assumed large enough for the surfactant mass transfer to be adsorption-controlled. Langmuir model generates non-linear Marangoni stresses which diverge in the limit of approaching ∝, strongly retarding U'.

A FVCOM-Based Unstructured Grid Wave, Current,Sediment Transport Model,I.Model Description and Validation

An effort was made to couple FVCOM (a three-dimensional (3D),unstructured grid,Finite Volume Coastal Ocean Model) and FVCOM-SWAVE (an unstructured grid,finite-volume surface wave model) for the study of nearshore ocean processes such as tides,circulation,storm surge,waves,sediment transport,and morphological evolution.The coupling between FVCOM and FVCOM-SWAVE was achieved through incorporating 3D radiation stress,wave-current-sediment-related bottom boundary layer,sea surface stress parameterizations,and morphology process.FVCOM also includes a 3D sediment transport module.With accurate fitting of irregular coastlines,the model provides a unique tool to study sediment dynamics in coastal ocean,estuaries,and wetlands where local geometries are characterized by inlets,islands,and intertidal marsh zones.The model was validated by two standard benchmark tests: 1) spectral waves approaching a mild sloping beach and 2) morphological changes of seabed in an idealized tidal inlet.In Test 1,model results were compared with both analytical solutions and laboratory experiments.A further comparison was also made with the structured grid Regional Ocean Model System (ROMS),which provides an insight into the performance of the two models with the same open boundary forcing.

The Partition of Unity Method for High-Order Finite Volume Schemes Using Radial Basis Functions Reconstruction

This paper introduces the use of partition of unity method for the development of a high order finite volume discretization scheme on unstructured grids for solving diffusion models based on partial differential equations.The unknown function and its gradient can be accurately reconstructed using high order optimal recovery based on radial basis functions.The methodology proposed is applied to the noise removal problem in functional surfaces and images.Numerical results demonstrate the effectiveness of the new numerical approach and provide experimental order of convergence.

A Three-dimensional Heterogeneous Mass Transfer Model for the Absorption of Gas into Multiphase System

A three-dimensional heterogeneous mass transfer model was proposed to investigate the enhancement of dispersed particles on gas absorption. The strategy to calculate local and overall enhancement factors is proposed. Instead of a global grid, the composite overlapping grid is adopted, which simplifies the setup and solution of the three-dimensional model equations. It is found that dispersed particle hold-up, particle size, liquid-solid partition coefficient of transported component, characteristic contact time, and the shortest distance between particles and gas-liquid interface have major influence on absorption enhancement factor. The particle-particle interaction on gas absorption and the lateral diffusion of transported component in liquid film were studied with the multi-particle simulation. The proposed model predicted the experimental data from the literature reasonably well.

Improved Crude Oil Price Forecasting With Statistical Learning Methods

Reliable forecasts of the price of oil are of interest for a wide range of applications. For example, central banks and private sector forecasters view the price of oil as one of the key variables in generating macroeconomic projections and in assessing macroeconomic risks. Of particular interest is the question of the extent to which the price of oil is helpful in predicting recessions. This paper presents a statistical learning method （SLM） based on combined fuzzy system （FS）, artificial neural network （ANN）, and support vector regression （SVR） to cope with optimum long-term oil price forecasting in noisy, uncertain, and complex environments. A number of quantitative factors were discovered from this model and used as the input. For verification and testing, the West Texas Intermediate （WT1） crude oil spot price is used to test the effectiveness of the proposed learning methodology. Empirical results reveal that the proposed SLM-based forecasting can model the nonlinear relationship between the input variables and price very well. Furthermore, in-sample and out-of-sample prediction performance also demonstrates that the proposed SLM model can produce more accurate prediction results than other nonlinear models.

Non-Linear Dependence in Oil Price Behavior

In this paper, the authors analyze the adequacy of GARCH-type models to analyze oil price behavior by applying two types of non-parametric tests, the Hinich portmanteau test for non-linear dependence and a frequency-dominant test of time reversibility, the reverse test based on the bispectrum, to explore the high-order spectrum properties of the Mexican oil price series. The results suggest strong evidence of a non-linear structure and time irreversibility. Therefore, it does not comply with the i.i.d （independent and identically distributed） property. The non-linear dependence, however, is not consistent throughout the sample period, as indicated by a windowed test, suggesting episodic nonlinear dependence. The results imply that GARCH models cannot capture the series structure.

New Positive and Negative Hierarchies of Integrable Differential-Difference Equations and Conservation Laws

Two hierarchies of nonlinear integrable positive and negative lattice equations are derived from a discrete spectrak problem. The two lattice hierarchies are proved to have discrete zero curvature representations associated with a discrete spectral problem, which also shows that the positive and negative hierarchies correspond to positive and negative power expansions of Lax operators with respect to the spectral parameter, respectively. Moreover, the integrable lattice models in the positive hierarchy are of polynomial type, and the integrable lattice models in the negative hierarchy are of rational type. Further, we construct infinite conservation laws about the positive hierarchy.

Numerical Study on Inter-Tidal Transports in Coastal Seas

Inter-tidal(subtidal) transport processes in coastal sea depend on the residual motion, turbulent dispersion and relevant sources/sinks. In Feng et al.(2008), an updated Lagrangian inter-tidal transport equation, as well as new concept of Lagrangian in- ter-tidal concentration(LIC), has been proposed for a general nonlinear shallow water system. In the present study, the LIC is nu- merically applied for the first time to passive tracers in idealized settings and salinity in the Bohai Sea, China. Circulation and tracer motion in the three idealized model seas with different topography or coastline, termed as ‘flat-bottom', ‘stairs' and ‘cape' case, re- spectively, are simulated. The dependence of the LIC on initial tidal phase suggests that the nonlinearities in the stairs and cape cases are stronger than that in the flat-bottom case. Therefore, the ‘flat-bottom' case still meets the convectively weakly nonlinear condi- tion. For the Bohai Sea, the simulation results show that most parts of it still meet the weakly nonlinear condition. However, the de- pendence of the LIS(Lagrangian inter-tidal salinity) on initial tidal phase is significant around the southern headland of the Liaodong Peninsula and near the mouth of the Yellow River. The nonlinearity in the former region is mainly related to the complicated coast- lines, and that in the latter region is due to the presence of the estuarine salinity front.

Numerical Simulation of Seawater Intrusion from Estuary into River Using a Coupled Modeling System

One of the most important causes of the freshwater shortage in estuarine area is the increasing seawater intrusion into the river.To simulate seawater intrusion properly,two important factors should be considered.One is the bidirectional and time-dependent coupling effects between river discharges and tidal forces.The other is the three-dimensional and stratified structure of dynamic processes involved.However,these two factors have rarely been investigated simultaneously,or they were often simplified in previous researches,especially for the estuary connected with an upstream river network through multiple outlets such as the Pearl River Estuary(PRE).In order to consider these two factors,a numerical modeling system,which couples a one-dimensional river network model with a three-dimensional unstructured-grid Finite-Volume Coastal Ocean Model(FVCOM),has been developed and successfully applied to the simulation of seawater intrusion into rivers emptying into the PRE.By treating the river network with a one-dimensional model,computational efficiency has been improved.With coupling 1D and 3D models,the specification of upstream boundary conditions becomes more convenient.Simulated results are compared with field measured data.Good agreement indicates that the modeling system may correctly capture the physical processes of seawater intrusion into rivers.

Numerical research on lid-driven cavity flows using a three-dimensional lattice Boltzmann model on non-uniform meshes

A lattice Boltzmann model combined with curvilinear coordinate is proposed for lid-driven cavity three-dimensional (3D) flows. For particle velocity distribution, the particle collision process is performed in physical domain, and the particle streaming process is carried out in the corresponding computational domain, which is transferred from the physical domain using interpolation method. For the interpolation calculation, a second-order upwind interpolation method is adopted on internal lattice nodes in flow fields while a second-order central interpolation algorithm is employed at neighbor-boundary lattice nodes. Then the above-mentioned model and algorithms are used to numerically simulate the 3D flows in the lid-driven cavity at Reynolds numbers of 100, 400 and 1000 on non-uniform meshes. Various vortices on the x-y, y-z and x-z symmetrical planes are successfully predicted, and their changes in position with the Reynolds number increasing are obtained. The velocity profiles of u component along the vertical centerline and w component along the horizontal centerline are both in good agreement with the data in literature and the calculated results on uniform meshes. Besides, the velocity vector distributions on various cross sections in lid-driven cavity predicted on non-uniform meshes are compared with those simulated on uniform meshes and those in the literature. All the comparisons and validations show that the 3D lattice Boltzmann model and all the numerical algorithms on non-uniform meshes are accurate and reliable to predict effectively flow fields.

Coupling of wave and current numerical model with unstructured quadtree grid for nearshore coastal waters

This paper presents 2D wave-current interaction model for evaluating nearly horizontal wave-induced currents in the surf-zone and coastal waters.The hydrodynamic model is the two-dimensional depth-averaged nonlinear shallow water equations by using an unstructured non-staggered and multiple-level quadtree rectangular mesh,this mesh information is stored in simple data structures and it is easy to obtain a locally high resolution for important region.The intercell fluxes are computed based on the HLL(Harten-Lax-van Leer) approximate Riemann solver with shock capturing capability for computing the dry-to-wet interface of coastal line.The effects of pressure and gravity are included in source term in the model,this treatment can simplify the computation and eliminate numerical imbalance between source and flux terms.The wave model readily provides the radiation stresses that represent the shortwave-averaged forces in a water column for the hydrodynamic model and the wave model takes into account the effect of wave-induced nearshore currents and water level.The coupling model is applied to verify different experimental cases and real life case of considering the wave-current interaction.The calculated results agree with analytical solution,experimental and field data.The results show that the modeling approach presented herein should be useful in simulating the nearshore processes in complicated natural coastal domains.

Development and validation of a three-dimensional,wave-current coupled model on unstructured meshes

Using unstructured meshes provides great flexibility for modeling the flow in complex geomorphology of tidal creeks,barriers and islands,with refined grid resolution in regions of interest and not elsewhere.In this paper,an unstructured three-dimensional fully coupled wave-current model is developed.Firstly,a parallel,unstructured wave module is developed.Variations in wave properties are governed by a wave energy equation that includes wave-current interactions and dissipation representative of wave breaking.Then,the existing Finite-Volume Coastal Ocean Model(FVCOM) is modified to couple with the wave module.The couple procedure includes depth dependent wave radiation stress terms,Stokes drift,vertical transfer of wave-generated pressure transfer to the mean momentum equation,wave dissipation as a source term in the turbulence kinetic energy equation,and mean current advection and refraction of wave energy.Several applications are presented to evaluate the developed model.In particular the wind and wave-induced storm surge generated by Hurricane Katrina is investigated.The obtained results have been compared to the in situ measurements with respect to the wave heights and water level elevations revealing good accuracy of the model in reproduction of the investigated events.In a comparison to water level measurements at Dauphin Island,inclusion of the wave induced water level setup reduced the normalized root mean square error from 0.301 to 0.257 m and increased the correlation coefficient from 0.860 to 0.929.Several runs were carried out to analyze the effects of waves.The experiments show that among the processes that represent wave effects,radiation stress and wave-induced surface stress are more important than wave-induced bottom stress in affecting the water level.The Hurricane Katrina simulations showed the importance of the inclusion of the wave effects for the hindcast of the water levels during the storm surge.

Conductance Spectra in Graphene-Superconductor Junctions

The conductance spectra of a graphene ribbon and graphene-superconductor （G-S） junctions are investi- gated, using the tight-binding model and non-equilibrium Green＇s function formalism. It is found that the quantized conductance related to graphene＇s edge-states is robust against perturbations in the model parameters for a graphene monolayer ribbon with the zigzag boundary. With appropriate a new bound state with odd-frequency symmetry is found in conductance amplitude is followed model parameter of the spin-orbit interaction strength, the G-S junction. An enhancement in the zero-energy

Initial-boundary value problem of three phase flow in porous media

We study the mathematical model of three phase compressible flows through porous media. Under the condition that the rock, water and oil are incompressible, and the compressibility of gas is small, we present a finite element scheme to the initial-boundary value problem of the nonlinear system of equations, then by the convergence of the scheme we prove that the problem admits a weak solution.

Effects of Unintended Dopants on I-V Characteristics of the Double-Gate MOSFETs,a Simulation Study

In this paper, we study the effects of an unintended dopant in the channel on the current-voltage char-acteristics of a Double-Gate (DG) Metal-Oxide-Semiconductor Field-Effect Transistor (MOSFET). Non-Equilibrium Green's Function (NEGF) approach is used. A quantum transport model to calculate the drain current is presented and subthreshold swing and drain induced barrier lowering (DIBL) effect are studied.