Modal reduction of mathematical models of biological molecules

This paper reports a detailed study of modal reduction based on either linear normal mode (LNM) analysis or proper orthogonal decomposition (POD) for modeling a single α-d-glucopyranose monomer as well as a chain of monomers attached to a moving atomic force microscope (AFM) under harmonic excitations. Also a modal reduction method combining POD and component modal synthesis is developed. The accuracy and efficiency of these methods are reported. The focus of this study is to determine to what extent these methods can reduce the time and cost of molecular modeling and simultaneously provide the required accuracy. It has been demonstrated that a linear reduced order model is valid for small amplitude excitation and low frequency excitation. It is found that a nonlinear reduced order model based on POD modes provides a good approximation even for large excitation while the nonlinear reduced order model using linear eigenmodes as the basis vectors is less effective for modeling molecules with a strong nonlinearity. The reduced order model based on component modal synthesis using POD modes for each component also gives a good approximation. With the reduction in the dimension of the system using these methods the computational time and cost can be reduced significantly.     

飞行器大攻角复杂流动的POD和DMD对比分析

基于非结构/混合网格、耗散自适应2阶混合格式以及脱体涡模拟（detached eddy simulation,DES）方法开展了现代战斗机模型复杂分离流动的数值模拟,并与有限的平均气动力试验数据进行了对比,结果表明计算具有合理性,在此基础上进一步应用本征正交分解（proper orthogonal decomposition,POD）和动力学模态分解（dynamic mode decomposition,DMD）方法对数值模拟流场的非定常特性进行了对比分析.研究表明飞行器背风区流场由一对边条涡的螺旋运动主导,旋涡破裂前在横向空间截面上流场是中性稳定的,同时主涡核的运动是多频耦合的.POD和DMD的对比分析则表明:两者模态配对的方式不同,但主要模态之间具有一定相关性;POD模态中包含多种频率的运动,而且能量较集中于主模态,流场重构效率更高;DMD则将流场的主要特征运动提取为一些单频模态的组合,同时能够给出模态的稳定性.      

A new measure of efficiency for model reduction: Application to a vibroimpact system

The aim of this paper is to propose a new way to measure the efficiency of the proper orthogonal decomposition (POD) to construct a reduced-order model in Structural Dynamics. It investigates the efficiency of three reduced-order models for a vibroimpact problem: (1) POD_dir-basis, which is the basis constructed using the direct method of the proper orthogonal decomposition; (2) POD_snap-basis, which is the basis constructed using the snapshot method of the POD; and (3) LIN-basis, which is the basis composed by the normal modes of the associated linear (LIN) conservative system. The efficiency is measured in terms of (1) number of elements to represent the dynamics with a given precision and (2) computational cost to simulate the time response within a given precision.     

风力机翼型气动计算的降阶模型研究

将基于POD的降阶模型应用于风力机翼型的气动研究。首先应用CFD数值模拟得到一系列快照结果;应用基于本征正交分解(POD)的方法得到流场的一组基模态,认为对于所研究的问题,任一流场可以由这些基模态通过线性表达得到;对控制方程进行Galerkin投影,得到降阶模型,将离散求解N-S方程的问题转化为一组只有十几个自由度的常微分方程,从而减少计算时间,提高计算效率。并对二维翼型的绕流的定常和非定常问题进行了分析,计算结果表明,降阶模型可以较好地捕捉流动的特征,与直接CFD模拟相比计算精度相当,但大幅有效地提高了计算效率。     

Enablers for robust POD models

This paper focuses on improving the stability as well as the approximation properties of reduced order models (ROMs) based on proper orthogonal decomposition (POD). The ROM is obtained by seeking a solution belonging to the POD subspace and that at the same time minimizes the Navier–Stokes residuals. We propose a modified ROM that directly incorporates the pressure term in the model. The ROM is then stabilized making use of a method based on the fine scale equations. An improvement of the POD solution subspace is performed, thanks to a hybrid method that couples direct numerical simulations and reduced order model simulations. The methods proposed are tested on the two-dimensional confined square cylinder wake flow in laminar regime.     

Predictive flow-field estimation

We are considering the problem of real-time prediction of 3D turbulent velocity fields based on a small number of scalar measurements. The method of proper orthogonal decomposition (POD) allows for the decomposition of an ensemble of velocity fields into a set of spatial basis functions and a set of temporal coefficients. The computation of the temporal coefficients is by no means a trivial matter, especially when one is faced with a large number of modes. In this paper we discuss the use of radial basis function (RBF) models to capture the discrete time evolution and nonlinear dynamics of the POD coefficients. Further, we propose the use of regularized regression techniques to generate models that provide mappings between the POD coefficients and scalar measurements. As a final step towards real-time prediction, the state-space RBF models and regression measurement models are combined using unscented Kalman filters to produce optimal solutions such that a balance between the state models and measurement models is achieved.The proposed methods are tested for two specific cases. The classical Lorenz model is chosen to demonstrate the use and effectiveness of RBF models as a potential candidate for state models. Flow around a wall-mounted cube in a channel at Re=20,000 is considered as the second case. The aim for the second case is to be able to accurately predict the POD coefficients outside the ensemble. It is shown that a large number of POD coefficients is required to approximate the velocity fields with sufficient accuracy. The RBF models are created based on only the temporal information available from the initial ensemble, and it is shown that the RBF model is able to correctly approximate the high-dimensional phase space. Combined with the unscented Kalman filter it is indeed possible to track the evolution of the POD coefficients for a long time. The robustness of the filter is demonstrated by considering the presence of noise in measurements and using measurement information at time steps greater than the evolution time step.     

Lie symmetry analysis,new group invariant for the (3 + 1)-dimensional and variable coefficients for liquids with gas bubbles models

The explored solutions described some different solutions as, Lump soliton, a solitary wave and exponential solutions. These solutions are investigated through some new Lie infinitesimals for the (3 + 1) dimensional variable coefficients Kudryashov-Sinelshchikov (VCKS). We used the fourth prolongation to investigate fifteen cases of Lie vectors. In each case, there is an infinite number of possibilities of vectors due to the unknown arbitrary functions and the variable coefficients for the considered model. We selected one case and examined the commutative product between multi unknown Lie infinitesimals for the (3 + 1) dimensional (VCKS) equation and this complicated process resulted from some new Lie vectors. The commutative product generates a system of nonlinear ODEs which had been solved manually. Through three stages of Lie symmetry reduction using the equivalence transformation, (VCKS) equation is reduced to solvable nonlinear ODEs using various combinations of optimal Lie vectors. By solving these ODEs, we investigate new analytical solutions for these ODEs. Back substituting to the original variables generates new solutions for (VCKS). Some selected solutions are illustrated through three-dimensional plots.     

Projection-free proper orthogonal decomposition method for a cantilever plate in supersonic flow

This paper explores the use of the proper orthogonal decomposition (POD) method for supersonic nonlinear flutter of a cantilever plate or wing. The aeroelastic equations are constructed using von Karman plate theory and first-order piston theory. The two-dimensional POD modes (POMs) in xy plane are determined from the chaotic results given by the traditional Rayleigh–Ritz (RR) approach. For a specific structure, the POMs need to be calculated once and then can be used for various parameters of interest. The derivatives of the POMs are calculated numerically to avoid the complex projection from the POMs to the Rayleigh–Ritz modes (RRMs). Numerical examples demonstrate that the POD method using 4 POMs can obtain accurate limit cycle oscillation (LCO) results with substantial computational cost savings, compared with 12 RRMs by the Rayleigh–Ritz method. The POD method is employed for the analysis of the chaotic oscillations. It is also demonstrated that the POD modes are robust over a range of flight parameters.     

抛物化Navier-Stokes方程的降维仿真模型

利用特征投影分解技术和奇值分解方法,建立抛物化Navier-Stokes方程的降维仿真模型,讨论降维仿真模型解的稳定性和误差,并利用误差估计指导特征投影分解基函数的选取及特征投影分解基函数的更新.最后,用数值试验验证降维仿真模型的有效性和可行性.     

Geodesics on a supermanifold and projective equivalence of superconnections

We investigate the concept of projective equivalence of connections in supergeometry. To this aim, we propose a definition for (super) geodesics on a supermanifold in which, as in the classical case, they are the projections of the integral curves of a vector field on the tangent bundle: the geodesic vector field associated with the connection. Our (super) geodesics possess the same properties as in the classical case: there exists a unique (super) geodesic satisfying a given initial condition and when the connection is metric, our supergeodesics coincide with the trajectories of a free particle with unit mass. Moreover, using our definition, we are able to establish Weyl’s characterization of projective equivalence in the super context: two torsion-free (super) connections define the same geodesics (up to reparametrizations) if and only if their difference tensor can be expressed by means of a (smooth, even, super) 1-form.     

盐碱胁迫下杨树叶片MDA含量与各抗氧化酶的相关性

在前人的基础上,从利用偏相关分析和多元线性回归分析的方法深入分析了盐碱胁迫环境下杨树叶丙二醛(MDA)含量与超氧化物歧化酶(Superoxide dismutase,SOD)、过氧化物酶(Peroxidase,POD)、过氧化氢酶(Catalase,CAT)活性之间,以及各抗氧化酶之间的内在相关性.研究结果表明,在盐碱...     

A Tensor Product of Representations of Cuntz Algebras

We introduce a nonsymmetric and associative tensor product among representations of Cuntz algebras by using embeddings. Since the tensor product of permutative representations is also a permutative representation, the decomposition of such a tensor product is unique up to unitary equivalence. We show the decomposition formulae explicitly. As an application, we show properties of concrete endomorphisms.      

DMD和POD对超燃冲压发动机凹腔流动的稳定性分析

开式凹腔作为超燃冲压发动机中增加掺混和稳焰的装置, 其流动稳定性的研究对深入理解凹腔增加掺混和稳焰机理以及凹腔的设计有着重要的学术意义和工程应用价值.基于大涡模拟方法对超燃冲压发动机开式凹腔流动进行数值模拟, 分别采用动力学模态分解(dynamic mode decomposition, DMD)和本征正交分解方法(proper orthogonal decomposition, POD)对自激振荡流动进行稳定性分析. DMD方法可准确提取凹腔的振荡频率, 与Rossiter模型以及压力脉动FFT分析得到的频率吻合较好, 且DMD中对应Rossiter前3阶频率的模态在流动中的主导作用顺序也与FFT分析结果一致, 自激振荡中RossiterⅢ模态占据主导作用, 同时DMD方法对Rossiter 3阶以上模态频率的预测能力明显强于FFT分析方法.在对低频的提取方面, DMD方法比Rossiter模型更具有优势.与前6阶Rossiter模态对应DMD模态均缓慢收敛, 主要表现为剪切层中的分离涡结构和中部及下游区域中的涡结构.前3阶不稳定模态中的分离涡结构主要集中在中部剪切层以及后缘附近区域. POD方法中较少的模态包含流场绝大部分的能量.但是, 通过POD方法提取的模态频率在分辨率上效果不佳, 提取到最低频率为Rossiter 3阶模态对应的频率, 且模态中均存在次频, 次频与主频之间的耦合导致模态的形态相差较大.另外, 与DMD方法相比POD方法无法判断所提取的模态的稳定性.      

Reliable reduced-order models for time-dependent linearized Euler equations

Development of optimal reduced-order models for linearized Euler equations is investigated. Recent methods based on proper orthogonal decomposition (POD), applicable for high-order systems, are presented and compared. Particular attention is paid to the link between the choice of the projection and the efficiency of the reduced model. A stabilizing projection is introduced to induce a stable reduced-order model at finite time even if the energy of the physical model is growing. The proposed method is particularly well adapted for time-dependent hyperbolic systems and intrinsically skew-symmetric models. This paper also provides a common methodology to reliably reduce very large nonsymmetric physical problems.     

Proper orthogonal decomposition of solar photospheric motions

The spatiotemporal dynamics of the solar photosphere is studied by performing a proper orthogonal decomposition (POD) of line of sight velocity fields computed from high resolution data coming from the MDI/SOHO instrument. Using this technique, we are able to identify and characterize the different dynamical regimes acting in the system. Low-frequency oscillations, with frequencies in the range 20-130 microHz, dominate the most energetic POD modes (excluding solar rotation), and are characterized by spatial patterns with typical scales of about 3 Mm. Patterns with larger typical scales of approximately 10 Mm, are associated to p-modes oscillations at frequencies of about 3000 microHz.     

A spectral method for the wave equation of divergence-free vectors and symmetric tensors inside a sphere

The wave equation for vectors and symmetric tensors in spherical coordinates is studied under the divergence-free constraint. We describe a numerical method, based on the spectral decomposition of vector/tensor components onto spherical harmonics, that allows for the evolution of only those scalar fields which correspond to the divergence-free degrees of freedom of the vector/tensor. The full vector/tensor field is recovered at each time-step from these two (in the vector case), or three (symmetric tensor case) scalar fields, through the solution of a first-order system of ordinary differential equations (ODE) for each spherical harmonic. The correspondence with the poloidal–toroidal decomposition is shown for the vector case. Numerical tests are presented using an explicit Chebyshev-tau method for the radial coordinate.     

Deformation measurement by holographic interferometry. Analysis on curved surfaces. General aspects

Holographic Interferometry is briefly outlined in the case of large deformations. Modifications at the reconstruction are necessary to recover the previously invisible fringes. The spacing and contrast are characterized by the fringe and visibility vectors. The relevant first derivative of the path difference involves the polar decomposition of the deformation gradient and some affine connections. Owing to the modification, one must consider the aberration together with changes of geodesic curvatures and of surface curvatures. This leads to similar aspects for hypersurfaces with remarks concerning the general problem of the gravitational lens.     

多类运动想象脑电信号特征提取与分类

针对多类运动想象情况下存在的脑电信号识别正确率比较低的问题,提出了一种将小波包方差,小波包熵和共同空间模式相结合的脑电信号特征提取,输入到支持向量机达到分类目的。首先选择小波包去噪后重要导联的脑电信号,进行小波包分解;然后对通道优化选取的重要导联的每个通道信号计算方差和熵值,对重要导联的每个通道信号的子带系数进行重构后,进行共同空间模式特征提取;最后结合2种不同导联方式所获取的特征向量进行分类。采用BCI2005desc_IIIa中l1b数据,该算法的分类正确率最高达到88.75%,相对2种单一的提取方法分别提高28.27%和6.55%。结果表明该算法能够有效提取特征向量,进而改善多类识别正确率较低的问题。