Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

Research Progress On Thermal Protection Materials And Structures Of Hypersonic Vehicles

Hypersonic vehicles represent future trends of military equipments and play an important role in future war. Thermal protection materials and structures, which relate to the safety of hypersonic vehicles, are one of the most key techniques in design and manufacture of hypersonic vehicles. Among these materials and structures, such as metallic temperature protection structure, the temperature ceramics and carbon/carbon composites are usually adopted in design. The recent progresses of research and application of ultra-high temperature materials in preparation, oxidation resistance, mechanical and physical characterization are summarized.

Tuning The Geometrical Parameters Of Biomimetic Fibrillar Structures To Enhance Adhesion

Fibrillar structures are common features on the feet of many animals, such as geckos, spiders and flies. Theoretical analyses often use periodical array to simulate the assembly, and each fibril is assumed to be of equal load sharing (ELS). On the other hand, studies on a single fibril show that the adhesive interface is flaw insensitive when the size of the fibril is not larger than a critical one. In this paper, the Dugdale Barenblatt model has been used to study the conditions of ELS and how to enhance adhesion by tuning the geometrical parameters in fibrillar structures. Different configurations in an array of fibres are considered, such as line array, square and hexagonal patterns. It is found that in order to satisfy flaw-insensitivity and ELS conditions, the number of fibrils and the pull-off force of the fibrillar interface depend significantly on the fibre separation, the interface interacting energy, the effective range of cohesive interaction and the radius of fibrils. Proper tuning of the geometrical parameters will enhance the pull-off force of the fibrillar structures. This study may suggest possible methods to design strong adhesion devices for engineering applications.

Crack propagation in structures subjected to periodic excitation

In the present paper, a simple mechanical model is developed to predict the dynamic response of a cracked structure subjected to periodic excitation, which has been used to identify the physical mechanisms in leading the growth or arrest of cracking. The structure under consideration consists of a beam with a crack along the axis, and thus, the crack may open in Mode I and in the axial direction propagate when the beam vibrates. In this paper, the system is modeled as a cantilever beam lying on a partial elastic foundation, where the portion of the beam on the foundation represents the intact portion of the beam. Modal analysis is employed to obtain a closed form solution for the structural response. Crack propagation is studied by allowing the elastic foundation to shorten (mimicking crack growth) if a displacement criterion, based on the material toughness, is met. As the crack propagates, the structural model is updated using the new foundation length and the response continues. From this work, two mechanisms for crack arrest are identified. It is also shown that the crack propagation is strongly influenced by the transient response of the structure.

Snap-through and pull-in instabilities of an arch-shaped beam under an electrostatic loading

The snap-through and pull-in instabilities of the micromachined arch-shaped beams under an electrostatic loading are studied both theoretically and experimentally. The pull-in instability that results in a system collision with an electrode substrate may lead to a system failure and, thus, limits the system maximum displacement. The beam/plate structure with a flat initial configuration under an electrostatic loading can only experience the pull-in instability. With the different arch configurations, the structure may experience either only the pull-in instability or the snap-through and pull-in instabilities together. As shown in our computation and experiment, those arch-shaped beams with the snap-through instability have the larger maximum displacement compared with the arch-shaped beams with only the pull-in stability and those with the flat initial configuration. The snap-through occurs by exerting a fixed load, and the structure experiences a discontinuous displacement jump without consuming power. Furthermore, after the snap-through jump, the structures are demonstrated to have the capacity to withstand further electrostatic loading without pull-in. Those properties of consuming no power and increasing the structure deflection range without pull-in is very useful in microelectromechanical systems design, which can offer better sensitivity and tuning range.

Deflections and curvatures of a film-substrate structure with the presence of gradient stress in MEMS applications

The close form solutions of deflections and curvatures for a film-substrate composite structure with the presence of gradient stress are derived. With the definition of more precise kinematic assumption, the effect of axial loading due to residual gradient stress is incorporated in the governing equation. The curvature of film-substrate with the presence of gradient stress is shown to be nonuniform when the axial loading is nonzero. When the axial loading is zero, the curvature expressions of some structures derived in this paper recover the previous ones which assume the uniform curvature. Because residual gradient stress results in both moment and axial loading inside the film-substrate composite structure, measuring both the deflection and curvature is proposed as a safe way to uniquely determine the residual stress state inside a film-substrate composite structure with the presence of gradient stress.

An improvement on the theoretical model for the large-scale coherent structures in the outer region of a turbulent boundary layer

According to the experimental results, there exist large-scale coherent structures in the outer region of a turbulent boundary layer, which have been studied by many authors.As experimental results, Antonia (1990) showed the phase- aver aged streamlines and isovorticity lines of the large-scale coherent structures in a turbulent boundary layer for different Reynolds numbers. Based on the hydrodynamic stability theory, the 2-D theoretical model for the large-scale structures was proposed by Luo and Zhou, in which the eddy viscosity was defined as a complex function of the position in the normal direction. The theoretical results showed in ref. were in agreement with those in ref. However, there were two problems in the results. One is that in the experimental results, there were divergent focuses between two saddle points in the streamlines, but in the theoretical results, there were centers. The other is that the stretched parts of the isovorticity lines appear at the location of centers in the theoretical results, while in the experimental results they located somewhere between the focuses and saddle points. The reason is that the computations were based on a 2-D model.

An optimal theory for an expansion of flow quantities to capture the flow structures

An optimal theory on how database analysis to capture the flow structures has been developed in this paper, which include the POD method as its special case. By means of the remainder minimization method in the Sobolev space, for more general optimal conditions the new theory has the potential to overcome an inherent limitation of the POD method, i.e., it cannot be used to the situations in which the optimal condition is other than the inner product global one. As an example, using the new theory, the database of a two-dimensional flow over a backward-facing step is analyzed in detail, with velocity and vorticity bases.

Saturation impulses for dynamically loaded structures with finite-deflections

The concept of ''Saturation Impulse'' for rigid, perfectly plastic structures with finite-deflections subjected to dynamic loading was put forward by Zhao, Yu and Fang (1994a). This paper extends the concept of Saturation Impulse to the analysis of structures such as simply supported circular plates, simply supported and fully clamped square plates, and cylindrical shells subjected to rectangular pressure pulses in the medium load range. Both upper and lower bounds of nondimensional saturation impulses are presented.

Symmetry of chaotic attractors and kink-antikink structures in CMLs

In this paper the symmetries of coupled map lattices (CMLs) and their attractors are investigated by group and dynamical system theory, as well as numerical simulation, by means of which the kink-antikink patterns of CMLs in space-amplitude plots are discussed.

Numerical study of bluff body flow structures

Our recent progress in numerical studies of bluff body flow structures and a new method for the numerical analysis of near wake flow field for high Reynolds number flow are introduced. The paper consists of three parts. In part one, the evolution of wake vortex structure and variation of forces on a flat plate in harmonic oscillatory flows and in in-line steady-harmonic combined flows are presented by an improved discrete vortex method, as the Keulegan-Carpenter number (KC) varies from 2 to 40 and ratios of U-m to U-0 are of O(10(-1)), O(10) and O(10), respectively. In part 2, a domain decomposition hybrid method, combining the finite-difference and vortex methods for numerical simulation of unsteady viscous separated flow around a bluff body, is introduced. By the new method, some high resolution numerical visualization on near wake evolution behind a circular cylinder at Re = 10(2), 10(3) and 3 x 10(3) are shown. In part 3, the mechanism and the dynamic process for the three-dimensional evolution of the Karman vortex and vortex filaments in braid regions as well as the early features of turbulent structure in the wake behind a circular cylinder are presented numerically by the vortex dynamics method.

Orthotropy rescaling and implications for fracture in composites

For most practically important plane elasticity problems of orthotropic materials, stresses depend on elastic constants through two nondimensional combinations. A spatial rescaling has been found to reduce the orthotropic problems to equivalent problems in materials with cubic symmetry. The latter, under favorable conditions, may be approximated by isotropic materials. Consequently, solutions for orthotropic materials can be constructed approximately from isotropic material solutions or rigorously from cubic ones. The concept is developed to gain insight into the interplay between anisotropy and finite geometry. The inherent simplicity of the solutions allows a variety of technical problems to be addressed efficiently. Included are stress concentration related cracking, effective contraction of orthotropic material specimens, crack deflection onto easy fracture planes, and surface flaw induced delamination.

Structures on sliding base subject to horizontal and vertical motions

In this paper particular investigation is directed towards the combined effects of horizontal and vertical motions of real earthquakes to structures resting on sliding base. A simplified method is presented to treat the nonlinear effects of time dependent frictional force of the sliding base as a function of the vertical reaction produced by the foundation. As an example, the El Centro 1940 earthquake record is used on a structural model to show the structural responses due to a sliding base with different frictional and stiffness characteristics. The study shows that vertical ground motion does affect both the superstructure response and the base sliding displacement. Nevertheless, the sliding base isolator is shown to be effective for the reduction of seismic response of a superstructure.

Experimental Study and Numerical Simulation of Cellular Structures and Mach Reflection of Gaseous Detonation Wave

In this paper the Deflagration to Detonation Transition (DDT) process of gaseous H-2-O-2 mixture and Mach reflection of gaseous detonation wave on a wedge have been conducted experimentally. The cellular pattern of DDT process and Mach reflection were obtained from experiments with wedge angle theta = 10(0) similar to 40(0) and initial pressure of gaseous mixture 16kPa similar to 26.7kPa. The 2-D numerical simulations of DDT process and Mach reflection of detonation wave were performed by using the simplified ZND model and improved space-time conservation element and solution element (CE/SE) method. The numerical cellular structures were compared with the cellular patterns of soot track. Compared results were shown that it is satisfactory. The characteristic comparisons on Mach reflection of air shock wave and detonation wave were carried also out and their differences were given.

The effects of surface tension on the elastic properties of nano structures

In the absence of external loading, surface tension will induce a residual stress field in the bulk of nano structures. However, in the prediction of mechanical properties of nano structures, the elastic response of the bulk is usually described by classical Hooke’s law, in which the aforementioned residual stress was neglected in the existing literatures. The present paper investigates the influences of surface tension and the residual stress in the bulk induced by the surface tension on the elastic properties of nano structures. We firstly present the surface elasticity in the Lagrangian and the Eulerian descriptions and point out that even in the case of infinitesimal deformations the reference and the current configurations should be discriminated; otherwise the out-plane terms of surface displacement gradient, associated with the surface tension, may sometimes be overlooked in the Eulerian descriptions, particularly for curved and rotated surfaces. Then, the residual stress in the bulk is studied through the non-classical boundary conditions and used to construct the linear elastic constitutive relations for the bulk material. Finally, these relations are adopted to analyze the size-dependent properties of pure bending of Al nanowires. The present results show that surface tension will considerably affect the effective Young’s modulus of Al nanowires, which decrease with either the decrease of nanowires thickness or the increase of the aspect ratio.