A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

A simple method to simulate shrinkage-induced cracking in cement-based composites by lattice-type modeling

A new numerical procedure is proposed to investigate cracking behaviors induced by mismatch between the matrix phase and aggregates due to matrix shrinkage in cement-based composites. This kind of failure processes is simplified in this investigation as a purely spontaneous mechanical problem, therefore, one main difficulty during simulating the phenomenon lies that no explicit external load serves as the drive to propel development of this physical process. As a result, it is different from classical mechanical problems and seems hard to be solved by using directly the classical finite element method (FEM), a typical kind of "load -> medium -> response" procedures. As a solution, the actual mismatch deformation field is decomposed into two virtual fields, both of which can be obtained by the classical FEM. Then the actual response is obtained by adding together the two virtual displacement fields based on the principle of superposition. Then, critical elements are detected successively by the event-by-event technique. The micro-structure of composites is implemented by employing the generalized beam (GB) lattice model. Numerical examples are given to show the effectiveness of the method, and detailed discussions are conducted on influences of material properties.

Numerical investigation of crack growth in concrete subjected to compression by the generalized beam lattice model

The beam lattice-type models, such as the Euler-Bernoulli (or Timoshenko) beam lattice and the generalized beam (GB) lattice, have been proved very effective in simulating failure processes in concrete and rock due to its simplicity and easy implementation. However, these existing lattice models only take into account tensile failures, so it may be not applicable to simulation of failure behaviors under compressive states. The main aim in this paper is to incorporate Mohr-Coulomb failure criterion, which is widely used in many kinds of materials, into the GB lattice procedure. The improved GB lattice procedure has the capability of modeling both element failures and contact/separation of cracked elements. The numerical examples show its effectiveness in simulating compressive failures. Furthermore, the influences of lateral confinement, friction angle, stiffness of loading platen, inclusion of aggregates on failure processes are respectively analyzed in detail.

The elasto-damage theory of the components assembling model

The potential energy in materials is well approximated by pair functional which is composed of pair potentials and embedding energy. During calculating material potential energy, the orientational component and the volumetric component are derived respectively from pair potentials and embedding energy. The sum of energy of all these two kinds of components is the material potential. No matter how microstructures change, damage or fracture, at the most level, they are all the changing and breaking atomic bonds. As an abstract of atomic bonds, these components change their stiffness during damaging. Material constitutive equations have been formulated by means of assembling all components' response functions. This material model is called the component assembling model. Theoretical analysis and numerical computing indicate that the proposed model has the capacity of reproducing some results satisfactorily, with the advantages of great conceptual simplicity, physical explicitness, and intrinsic induced anisotropy, etc.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Micro-scale Plasticity Mechanics=微尺度塑性力学

本书系统地介绍了材料微尺度力学行为的尺寸效应实验现象，重点介绍了几种代表性的微尺度应变梯度塑性理论及对微尺度实验现象的解释；以及对裂纹尖端微尺度范围内解理断裂的应用。融会贯通的介绍了国内外学者的原创性工作和创新性学术思想。 全书共8章。第1章介绍了应变梯度塑性理论的应用背景及经典微极理论；第2章介绍了金属材料典型的微尺度力学实验现象；第3～7章介绍了几种典型的应变梯度理论及其应用；第8章介绍了应变梯度理论在微观断裂力学中的应用。 本书适合从事固体微尺度力学、先进材料的微结构设计与力学性能优化、微机电和微电子元件力学行为研究的科技工作者及工程师使用和参考，也可供力学专业及材料专业的高年级本科生和研究生阅读参考。

Researches on essential mechanics issues for submerged floating tunnel

Since 2001, a research group in the Institute of Mechanics, Chinese Academy of Sciences, has been devoted to the research of essential mechanics issues for submerged floating tunnel (SFT). In addition to the structural design of the SFT prototype in Qiandao Lake, the relevant researches cover a number of topics. This paper briefly describes the research procedure and results, including dynamic response of SFT due to surface wave, vortex-induced vibration of anchoring system, structural analysis of curved SFT, temperature effects of curved SFT, structural dynamic response due to accidental load, and effects of structural parameters (buoyancy-weight ratio, tunnel length，tether stiffness，etc.) on dynamic response.

New Numerical Algorithms in SUPER CE/SE and Their Applications in Explosion Mechanics

The new numerical algorithms in SUPER/CESE and their applications in explosion mechanics are studied. The researched algorithms and models include an improved CE/SE (space-time Conservation Element and Solution Element) method, a local hybrid particle level set method, three chemical reaction models and a two-fluid model. Problems of shock wave reflection over wedges, explosive welding, cellular structure of gaseous detonations and two-phase detonations in the gas-droplet system are simulated by using the above-mentioned algorithms and models. The numerical results reveal that the adopted algorithms have many advantages such as high numerical accuracy, wide application field and good compatibility. The numerical algorithms presented in this paper may be applied to the numerical research of explosion mechanics.

在役设备材料断裂力学参数测定方法综述——小冲杆实验力学研究进展之二

20多年以来, 用小型试件的小冲杆实验技术来测量在役设备材料的各种力学参数已经取得了很大进展. 小冲杆实验的试样虽然还没有标准, 但一般均采用直径为3～10mm,厚度为0.1～0.5mm的圆片试样.这个方法已经用来确定材料的弹性模量、屈服强度、塑性性能、抗拉强度、断裂形态转变温度、断裂韧性、蠕变性能以及表示塑性硬化和韧性损伤的微观力学参数和黏塑性性能等各种力学性能.该方法兼具取样方便和几乎无损的优点,非常适用于那些无法取出传统试样或取样不经济的场合,因此引起科技界和工业界的关注.本文综述了小冲杆试验的测量技术及从测量数据来确定材料断裂形态转变温度、断裂韧性和主曲线的移动温度的各种计算方法研究进展.

Interface Fracture Behavior Of Electroplated Coating On Metal Substrate Under Compressive Strain

The inducement of interface fracture is crucial to the analysis of interfacial adhesion between coating and substrate. For electroplated coating/metal substrate adhering materials with strong adhesion, interface cracking and coating spalling are difficult to be induced by conventional methods. In this paper an improved bending test named as T-bend test was conducted on a model coating system, i.e. electroplated chromium on a steel substrate. After the test, cross-sections of the coated materials were prepared to compare the failure behaviors under tensile strain and compressive strain induced by T-bend test. And the observation results show that coating cracking, interface cracking and partial spalling appear step by step. Based on experimental results, a new method may be proposed to rank the coated materials with strong inter-facial adhesion. (C) 2008 Elsevier B.V. All rights reserved.

Part I. On the breaking of nonlinear dispersive waves. Part II. Variational principles in continuum mechanics

A model equation for water waves has been suggested by Whitham to study, qualitatively at least, the different kinds of breaking. This is an integro-differential equation which combines a typical nonlinear convection term with an integral for the dispersive effects and is of independent mathematical interest. For an approximate kernel of the form e^(-b|x|) it is shown first that solitary waves have a maximum height with sharp crests and secondly that waves which are sufficiently asymmetric break into "bores." The second part applies to a wide class of bounded kernels, but the kernel giving the correct dispersion effects of water waves has a square root singularity and the present argument does not go through. Nevertheless the possibility of the two kinds of breaking in such integro-differential equations is demonstrated.

Difficulties arise in finding variational principles for continuum mechanics problems in the Eulerian (field) description. The reason is found to be that continuum equations in the original field variables lack a mathematical "self-adjointness" property which is necessary for Euler equations. This is a feature of the Eulerian description and occurs in non-dissipative problems which have variational principles for their Lagrangian description. To overcome this difficulty a "potential representation" approach is used which consists of transforming to new (Eulerian) variables whose equations are self-adjoint. The transformations to the velocity potential or stream function in fluids or the scaler and vector potentials in electromagnetism often lead to variational principles in this way. As yet no general procedure is available for finding suitable transformations. Existing variational principles for the inviscid fluid equations in the Eulerian description are reviewed and some ideas on the form of the appropriate transformations and Lagrangians for fluid problems are obtained. These ideas are developed in a series of examples which include finding variational principles for Rossby waves and for the internal waves of a stratified fluid.