Pairwise decomposition of an MMGBSA energy function for computational protein design

Computational protein design (CPD) aims at predicting new proteins or modifying existing ones. The computational challenge is huge as it requires exploring an enormous sequence and conformation space. The difficulty can be reduced by considering a fixed backbone and a discrete set of sidechain conformations. Another common strategy consists in precalculating a pairwise energy matrix, from which the energy of any sequence/conformation can be quickly obtained. In this work, we examine the pairwise decomposition of protein MMGBSA energy functions from a general theoretical perspective, and an implementation proposed earlier for CPD. It includes a Generalized Born term, whose many‐body character is overcome using an effective dielectric environment, and a Surface Area term, for which we present an improved pairwise decomposition. A detailed evaluation of the error introduced by the decomposition on the different energy components is performed. We show that the error remains reasonable, compared to other uncertainties. © 2014 Wiley Periodicals, Inc.     

Chemical depth profiling and 3D reconstruction of III–V heterostructures selectively grown on non‐planar Si substrates by MOCVD

The chemical characterization of novel 3D architectures with nanometre‐scale dimensions is extremely challenging. The chemical composition of InGaAs/AlAs quantum wells selectively grown in SiO₂ trenches, 100–300 nm wide, is studied. Combining high lateral resolution 3D ToF‐SIMS analysis and Auger measurements, the chemical composition of individual trenches was obtained confirming the uniformity of these III–V heterostructures. These results correlate well with an average approach using SIMS depth profiling. The effects of ion beam orientation on the surface topography of confined structures were highlighted. (© 2015 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

Qualitative spectroscopic characterization of the matrix–silane coupling agent interface across metal fibre reinforced ion exchange resin composite membranes

The characterization of novel metal reinforced electro-dialysis ion exchange membranes, for water desalination, by attenuated total reflectance Fourier transform infrared spectroscopy mapping is presented in this paper. The surface of the porous stainless steel fibre meshes was treated in order to enhance the amount of surface oxide groups and increase the material hydrophilicity. Then, the metal membranes were functionalized through a sol–gel reaction with silane coupling agents to enhance the affinity with the ion exchange resins and avoid premature metal oxidation due to redox reactions at the metal–polymer interface. Polished cross sections of the composite membranes embedded into an epoxy resin revealed interfaces between metallic frameworks and the silane layer at the interface with the ion exchange material. The morphology of the metal–polymer interface was investigated with scanning electron microscopy and Fourier transform infrared micro-spectroscopy. Fourier transform infrared mapping of the interfaces was performed using the attenuated total reflectance mode on the polished cross-sections at the Australian Synchrotron. The nature of the interface between the metal framework and the ion exchange resin was shown to be homogeneous and the coating thickness was found to be around 1 μm determined by Fourier transform infrared micro-spectroscopy mapping. The impact of the coating on the properties of the membranes and their potential for water desalination by electro-dialysis are also discussed.     

关于《线性代数》教材改革的几点想法

随着现代科学技术的迅猛发展,尤其是计算机技术的广泛应用,我们应当在工科数学课程的教学内容、教学方法和教学手段上积极改革,与时俱进,以改进教学方法,提高教学质量,使得工科学生能借助于计算机,学好本专业所需的数学知识.在这篇短文中,我们想就《线性代数》的教学内容的改革     

序线性空间中向量优化问题的K-T型定理

本文在广义凸性条件下,研究实线性空间中一类向量优化问题的最优性条件,我们引入F ritz-John鞍点,、“K-T鞍点”讨论它们与有效解、弱有效解之间的关系.     

一种大视场相位测量轮廓术系统标定方法

在进行大视场相位测量轮廓术系统参量标定时需要大的标定平面和精密移动台,由于携带不方便,不易进行现场标定。提出了一种用于相位测量轮廓术系统参量的高精度、现场标定方法,采用一块较小的平面标定靶在有效测量体积内不同位置多次摆放,以获取密集的数据点。先标定出摄像机的内参量和外参量,再指定一个全局参考平面和若干辅助参考平面,然后在图像平面上分区计算出每个位置标定靶上每点相对辅助参考平面的高度差和相位差,最后应用极大似然估计法估计出相位高度映射参量。实验中平面高度测量的标准偏差达到0.0433 mm。这种方法只需要较小的平面标定靶,标定过程方便、精度高,完全适合大视场三维测量相位测量轮廓术系统现场标定要求。     

A general modal frequency-domain vortex lattice method for aeroelastic analyses

The generalized aerodynamic force (GAF) matrix is derived for the Unsteady Vortex Lattice Method (UVLM) without the assumption of out-of-plane dynamics. As a result, the approach naturally includes in-plane motion and forces unlike the doublet lattice method (DLM). The derived UVLM GAF is therefore applicable to industry-standard techniques for aeroelastic stability analyses, such as the p–k method. In this work, the fluid–structure interpolation is performed with radial basis functions for surface interpolation. The generalized aerodynamic forces computed with the UVLM are verified against the DLM from NASTRAN on a simple flat plate configuration. The ability of the UVLM to include steady loads is verified with a T-tail flutter case and the results confirm the importance of including steady loads for T-tail flutter analysis. The modal frequency domain VLM therefore provides the same level of efficiency and accuracy than the DLM, but without the restrictions and with the ability to handle complex geometries. It is therefore a viable replacement to the DLM.     

若干高维可积和不可积模型的严格解

可积和不可积模型可以描述自然科学中的诸多现象, 寻找高维非线性模型的严格解已成为可积系统的一个重要研究内容. 结合达布变换法和多线性分离变量法, 可以得到多个(2+1)维非线性模型包含任意函数的严格解, 通过选取不同的任意函数, 构造这些非线性模型新的相互激发模式. 进一步推广了形变映射理论, 建立了变系数 场和sine-Gordon以及双sine-Gordon场的形变映射关系, 从而得到高维不可积模型包含任意函数的新严格解. 对任意函数的不同选择, 构造了sine-Gordon和双sine-Gordon可积模型丰富的局域解和周期解, 如多solitoff解及其周期波推广、周期形变的蛇形孤波解以及变模的拟周期解等.     

Symmetry classification of quasi-linear PDE’s containing arbitrary functions

We consider the problem of performing the preliminary “symmetry classification” of a class of quasi-linear PDE’s containing one or more arbitrary functions: we provide an easy condition involving these functions in order that nontrivial Lie point symmetries be admitted, and a “geometrical” characterization of the relevant system of equations determining these symmetries. Two detailed examples will elucidate the idea and the procedure: the first one concerns a nonlinear Laplace-type equation, the second a generalization of an equation (the Grad–Schlüter–Shafranov equation) which is used in magnetohydrodynamics.     

Generalized Einstein manifolds

A Finslerian manifold is called a generalized Einstein manifold (GEM) if the Ricci directional curvature R(u,u) is independent of the direction. Let F⁰(M, g_t) be a deformation of a compact n-dimensional Finslerian manifold preserving the volume of the unitary fibre bundle W(M). We prove that the critical points g₀ F⁰(g_t) of the integral I(g_t) on W(M) of the Finslerian scalar curvature (and certain functions of the scalar curvature) define a GEM. We give an estimate of the eigenvalues of Laplacian Δ defined on W(M) operating on the functions coming from the base when (M, g) is of minima fibration with a constant scalar curvature H admitting a conformal infinitesimal deformation (CID). We obtain λ ≥ H/(n − 1) (Δf = λf). If M is simply connected and λ = H/(n − 1), then (M, g) is Riemannian and is isometric to an n-sphere. We first calculate, in the general case, the formula of the second variationals of the integral I (g_t) for G = g₀, then for a CID we show that for certain Finslerian manifolds, I″(g₀) > 0. Applications to the gravitation and electromagnetism in general relativity are given. We prove that the spaces characterizing Einstein-Maxwell equations are GEMs.