Multiscale geometric modeling of macromolecules II: Lagrangian representation

Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics, and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as that from X‐ray, NMR, and cryo‐electron microscopy, and theoretical/mathematical models, such as molecular dynamics, the Poisson–Boltzmann equation, and the Nernst–Planck equation. In this work, we present a family of variational multiscale geometric models for macromolecular systems. Our models are able to combine multiresolution geometric modeling with multiscale electrostatic modeling in a unified variational framework. We discuss a suite of techniques for molecular surface generation, molecular surface meshing, molecular volumetric meshing, and the estimation of Hadwiger's functionals. Emphasis is given to the multiresolution representations of biomolecules and the associated multiscale electrostatic analyses as well as multiresolution curvature characterizations. The resulting fine resolution representations of a biomolecular system enable the detailed analysis of solvent–solute interaction, and ion channel dynamics, whereas our coarse resolution representations highlight the compatibility of protein‐ligand bindings and possibility of protein–protein interactions. © 2013 Wiley Periodicals, Inc.     

Construction of conformal mappings by generalized polarization tensors

We present a new systematic method to compute the Riemann mapping from the outside of the unit disc to the outside of a simply connected domain. We derive explicit relations between the coefficients of the Riemann mapping and the generalized polarization tensors associated with the domain. Because the generalized polarization tensors can be computed numerically, we are able to compute the coefficients of the Riemann mapping using these relations. Effectiveness of the method is validated by numerical examples. Copyright © 2014 John Wiley & Sons, Ltd.     

复射影空间CP~((n+p)/2)中具有2-调和的一般子流形

本文研究了复射影空间中具有2-调和的一般子流形问题.利用活动标架法,获得了这类子流形成为极小子流形的Pinching定理和Simons型积分不等式,此外还得到关于2-调和伪脐一般子流形的一个刚性定理,推广了复射影空间中具有2-调和全实子流形的一些相应结果.     

Multilevel preconditioning and low‐rank tensor iteration for space–time simultaneous discretizations of parabolic PDEs

This paper addresses the solution of parabolic evolution equations simultaneously in space and time as may be of interest in, for example, optimal control problems constrained by such equations. As a model problem, we consider the heat equation posed on the unit cube in Euclidean space of moderately high dimension. An a priori stable minimal residual Petrov–Galerkin variational formulation of the heat equation in space–time results in a generalized least squares problem. This formulation admits a unique, quasi‐optimal solution in the natural space–time Hilbert space and serves as a basis for the development of space–time compressive solution algorithms. The solution of the heat equation is obtained by applying the conjugate gradient method to the normal equations of the generalized least squares problem. Starting from stable subspace splittings in space and in time, multilevel space–time preconditioners for the normal equations are derived. In order to reduce the complexity of the full space–time problem, all computations are performed in a compressed or sparse format called the hierarchical Tucker format, supposing that the input data are available in this format. In order to maintain sparsity, compression of the iterates within the hierarchical Tucker format is performed in each conjugate gradient iteration. Its application to vectors in the hierarchical Tucker format is detailed. Finally, numerical results in up to five spatial dimensions based on the recently developed htucker toolbox for MATLAB are presented. Copyright © 2014 John Wiley & Sons, Ltd.     

计算富勒烯结构的新方法:曲率定理*

介绍了利用曲率定理计算富勒烯结构的方法,证明了富勒烯结构中五元环数恒为12,与传统的欧拉定理法进行了对比,凸显了曲率定理法在研究多面体结构时直观形象的特点,强调了数学方法对解决化学问题和认识化学模型的重要性。     

脑胶质瘤磁共振弥散张量成像定量参数与VEGF、MMP-9表达的相关性

本研究旨在分析脑胶质瘤患者的磁共振弥散张量成像(DTI)参数与病变组织血管内皮生长因子(VEGF)和基质金属蛋白酶-9(MMP-9)表达的相关性,以及DTI参数对脑胶质瘤进行分级诊断的价值。根据病理分级将102例脑胶质瘤患者分为低级别组(47例)和高级别组(55例),均行MRI和DTI检查,定量测定表观弥散系数(ADC)、各向异性分数(FA)、相对ADC(rADC)、相对FA(rFA)值及相对轴向扩散系数(rAD)值;用免疫组化法检测VEGF和MMP-9表达情况。结果显示,高级别组患者的rADC、ADC、rAD、FA、rFA均低于低级别组(P<0.05);高级别组患者的VEGF和MMP-9阳性表达均高于低级别组(P<0.05)。rADC、ADC、rAD、FA、rFA与VEGF和MMP-9表达均呈负相关(P<0.05);rADC、ADC、rAD、FA、rFA对脑胶质瘤分级诊断的AUC均具有一定诊断价值(P<0.05)。本研究结果提示DTI定量参数与脑胶质瘤VEGF和MMP-9表达具有相关性,且有助于脑胶质瘤的分级诊断。     

Optimal estimation of the diffusion coefficient from non-averaged and averaged noisy magnitude data

The magnitude operation changes the signal distribution in MRI images from Gaussian to Rician. This introduces a bias that must be taken into account when estimating the apparent diffusion coefficient. Several estimators are known in the literature. In the present paper, two novel schemes are proposed. Both are based on simple least squares fitting of the measured signal, either to the median (MD) or to the maximum probability (MP) value of the Probability Density Function (PDF). Fitting to the mean (MN) or a high signal-to-noise ratio approximation to the mean (HS) is also possible. Special attention is paid to the case of averaged magnitude images. The PDF, which cannot be expressed in closed form, is analyzed numerically. A scheme for performing maximum likelihood (ML) estimation from averaged magnitude images is proposed. The performance of several estimators is evaluated by Monte Carlo (MC) simulations. We focus on typical clinical situations, where the number of acquisitions is limited. For non-averaged data the optimal choice is found to be MP or HS, whereas uncorrected schemes and the power image (PI) method should be avoided. For averaged data MD and ML perform equally well, whereas uncorrected schemes and HS are inadequate. MD provides easier implementation and higher computational efficiency than ML. Unbiased estimation of the diffusion coefficient allows high resolution diffusion tensor imaging (DTI) and may therefore help solving the problem of crossing fibers encountered in white matter tractography.     

基于Demons算法改进的图像去噪模型研究

在Demons算法的基础上, 将扩散过程看作图像配准, 建立一种新的基于图像配准的Demons 去噪模型. 实验表明, 该模型去噪效果优于经典的Perona-Malik模型, 排除了模型的病态性. 考虑到新模型在图像去噪过程中仅靠梯度信息表示图像的局部特征还不完善, 故将水平集曲率作为控制图像结构的驱动力因素引入到此模型中, 提出了一种新的梯度和曲率双重驱动力的图像去噪模型. 分析和仿真结果表明, 两种新模型都可有效抑制噪声, 清晰度也有明显的提高, 其中双重驱动力的图像去噪模型去噪效果更具优越性.     

An explanation of the unusual strength of the hydrogen bond in small water clusters

We seek to explain why the hydrogen bond possesses unusual strength in small water clusters that account for many of the complex behaviors of water. We have investigated and visualized the donation of covalent character from covalent (sigma) to hydrogen bonds by calculating the eigenvector coupling properties of quantum theory of atoms in molecules (QTAIM), stress tensor σ ( r ), and Ehrenfest Force F ( r ) on the F ( r ) molecular graph. The next-generation three-dimensional (3-D) bond-path framework sets are presented, and only the F ( r ) bond-path framework sets reproduce the earlier finding on the coupling between covalent (sigma) and hydrogen bonds that possess a degree of covalent character. Exploration of the bond-path between the covalent (sigma) and hydrogen bond's critical points provides an explanation for the previously obtained coupling results. The directional character of the covalent (sigma) and hydrogen bonds' 3-D bond-path framework sets for the F ( r ) explains differences found in the earlier results from QTAIM and the stress tensor σ ( r ).     

基于支座反力影响线曲率差分的等截面连续梁损伤识别方法

为了实现仅采用损伤状态信息对等截面连续梁进行损伤识别,通过推导三跨不等跨连续梁在移动荷载作用下的支座反力影响线,发现支座反力影响线求曲率并作差分后的曲线在损伤位置会发生突变,基于该现象提出了一种损伤定位方法,进一步建立了损伤程度计算方法,可对损伤程度进行较精确的定量。通过一三跨连续梁和一四跨连续梁工程实例的仿真分析,证明了支座反力影响线曲率差分指标损伤定位和相应的损伤程度定量方法对等截面连续梁损伤识别具有可行性。