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.

An extension of the two dimensional JKR theory to the case with a large contact width

In the Hertz and JKR theories, parabolic assumptions for the rounded profiles of the sphere or cylinder are adopted under the condition that the contact radius (width) should be very small compared to the radius of the sphere or cylinder. However, a large contact radius (width) is often found in experiments even under a zero external loading. We aim at extending the plane strain JKR theory to the case with a large contact width. The relation between the external loading and the contact width is given. Solutions for the Hertz, JKR and rounded-profile cases are compared and analyzed. It is found that when the ratio of a/R is approximately larger than about 0.4, the parabolic assumptions in the Hertz and JKR theories are no longer valid and the exact rounded profile function should be used.

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.

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.

Influence of Contact Angle and Tube Size on Capillary-Driven Flow Under Microgravity

The influence of contact angle and tube radius on the capillary-driven flow for circular cylindrical tubes is studied systematically by microgravity experiments using the drop tower. Experimental results show that the velocity of the capillary flow decreases monotonically with an increase in the contact angle. However, the time-evolution of the velocity of the capillary flow is different for different sized tubes. At the beginning of the microgravity period, the capillary flow in a thinner tube moves faster than that in a thicker tube, and then the latter overtakes the former. Therefore, there is an intersection between the curves of meniscus velocity vs microgravity time for two differently sized tubes. In addition, for two given sized tubes this intersection is delayed when the contact angle increases. The experimental results are analyzed theoretically and also supported by numerical computations.

Sessile Drop in Microgravity: Creation, Contact Angle and Interface

We present in this paper the results obtained from a parabolic flight campaign regarding the contact angle and the drop interface behavior of sessile drops created under terrestrial gravity (1g) or in microgravity (mu g). This is a preliminary study before further investigations on sessile drops evaporation under microgravity. In this study, drops are created by the mean of a syringe pump by injection through the substrate. The created drops are recorded using a video camera to extract the drops contact angles. Three fluids have been used in this study : de-ionized water, HFE-7100 and FC-72 and two heating surfaces: aluminum and PTFE. The results obtained evidence the feasibility of sessile drop creation in microgravity even for low surface tension liquids (below 15 mN m (-aEuro parts per thousand 1)) such as FC-72 and HFE-7100. We also evidence the contact angle behavior depending of the drop diameter and the gravity level. A second objective of this study is to analyze the drop interface shape in microgravity. The goal of the these experiments is to obtain reference data on the sessile drop behavior in microgravity for future experiments to be performed in an French-Chinese scientific instrument (IMPACHT).

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.

Topics in gravitational-wave science : macroscopic quantum mechanics and black hole physics

The theories of relativity and quantum mechanics, the two most important physics discoveries of the 20th century, not only revolutionized our understanding of the nature of space-time and the way matter exists and interacts, but also became the building blocks of what we currently know as modern physics. My thesis studies both subjects in great depths --- this intersection takes place in gravitational-wave physics.

Gravitational waves are "ripples of space-time", long predicted by general relativity. Although indirect evidence of gravitational waves has been discovered from observations of binary pulsars, direct detection of these waves is still actively being pursued. An international array of laser interferometer gravitational-wave detectors has been constructed in the past decade, and a first generation of these detectors has taken several years of data without a discovery. At this moment, these detectors are being upgraded into second-generation configurations, which will have ten times better sensitivity. Kilogram-scale test masses of these detectors, highly isolated from the environment, are probed continuously by photons. The sensitivity of such a quantum measurement can often be limited by the Heisenberg Uncertainty Principle, and during such a measurement, the test masses can be viewed as evolving through a sequence of nearly pure quantum states.

The first part of this thesis (Chapter 2) concerns how to minimize the adverse effect of thermal fluctuations on the sensitivity of advanced gravitational detectors, thereby making them closer to being quantum-limited. My colleagues and I present a detailed analysis of coating thermal noise in advanced gravitational-wave detectors, which is the dominant noise source of Advanced LIGO in the middle of the detection frequency band. We identified the two elastic loss angles, clarified the different components of the coating Brownian noise, and obtained their cross spectral densities.

The second part of this thesis (Chapters 3-7) concerns formulating experimental concepts and analyzing experimental results that demonstrate the quantum mechanical behavior of macroscopic objects - as well as developing theoretical tools for analyzing quantum measurement processes. In Chapter 3, we study the open quantum dynamics of optomechanical experiments in which a single photon strongly influences the quantum state of a mechanical object. We also explain how to engineer the mechanical oscillator's quantum state by modifying the single photon's wave function.

In Chapters 4-5, we build theoretical tools for analyzing the so-called "non-Markovian" quantum measurement processes. Chapter 4 establishes a mathematical formalism that describes the evolution of a quantum system (the plant), which is coupled to a non-Markovian bath (i.e., one with a memory) while at the same time being under continuous quantum measurement (by the probe field). This aims at providing a general framework for analyzing a large class of non-Markovian measurement processes. Chapter 5 develops a way of characterizing the non-Markovianity of a bath (i.e.,whether and to what extent the bath remembers information about the plant) by perturbing the plant and watching for changes in the its subsequent evolution. Chapter 6 re-analyzes a recent measurement of a mechanical oscillator's zero-point fluctuations, revealing nontrivial correlation between the measurement device's sensing noise and the quantum rack-action noise.

Chapter 7 describes a model in which gravity is classical and matter motions are quantized, elaborating how the quantum motions of matter are affected by the fact that gravity is classical. It offers an experimentally plausible way to test this model (hence the nature of gravity) by measuring the center-of-mass motion of a macroscopic object.

The most promising gravitational waves for direct detection are those emitted from highly energetic astrophysical processes, sometimes involving black holes - a type of object predicted by general relativity whose properties depend highly on the strong-field regime of the theory. Although black holes have been inferred to exist at centers of galaxies and in certain so-called X-ray binary objects, detecting gravitational waves emitted by systems containing black holes will offer a much more direct way of observing black holes, providing unprecedented details of space-time geometry in the black-holes' strong-field region.

The third part of this thesis (Chapters 8-11) studies black-hole physics in connection with gravitational-wave detection.

Chapter 8 applies black hole perturbation theory to model the dynamics of a light compact object orbiting around a massive central Schwarzschild black hole. In this chapter, we present a Hamiltonian formalism in which the low-mass object and the metric perturbations of the background spacetime are jointly evolved. Chapter 9 uses WKB techniques to analyze oscillation modes (quasi-normal modes or QNMs) of spinning black holes. We obtain analytical approximations to the spectrum of the weakly-damped QNMs, with relative error O(1/L^2), and connect these frequencies to geometrical features of spherical photon orbits in Kerr spacetime. Chapter 11 focuses mainly on near-extremal Kerr black holes, we discuss a bifurcation in their QNM spectra for certain ranges of (l,m) (the angular quantum numbers) as a/M → 1. With tools prepared in Chapter 9 and 10, in Chapter 11 we obtain an analytical approximate for the scalar Green function in Kerr spacetime.

Coupled effects of mechanics, geometry, and chemistry on bio-membrane behavior

Lipid bilayer membranes are models for cell membranes--the structure that helps regulate cell function. Cell membranes are heterogeneous, and the coupling between composition and shape gives rise to complex behaviors that are important to regulation. This thesis seeks to systematically build and analyze complete models to understand the behavior of multi-component membranes.

We propose a model and use it to derive the equilibrium and stability conditions for a general class of closed multi-component biological membranes. Our analysis shows that the critical modes of these membranes have high frequencies, unlike single-component vesicles, and their stability depends on system size, unlike in systems undergoing spinodal decomposition in flat space. An important implication is that small perturbations may nucleate localized but very large deformations. We compare these results with experimental observations.

We also study open membranes to gain insight into long tubular membranes that arise for example in nerve cells. We derive a complete system of equations for open membranes by using the principle of virtual work. Our linear stability analysis predicts that the tubular membranes tend to have coiling shapes if the tension is small, cylindrical shapes if the tension is moderate, and beading shapes if the tension is large. This is consistent with experimental observations reported in the literature in nerve fibers. Further, we provide numerical solutions to the fully nonlinear equilibrium equations in some problems, and show that the observed mode shapes are consistent with those suggested by linear stability. Our work also proves that beadings of nerve fibers can appear purely as a mechanical response of the membrane.