Analysis Of Two-dimensional Structures Research Articles

IMGT/DomainGapAlign: IMGT Standardized Analysis of Amino Acid Sequences of Variable, Constant, and Groove Domains (IG, TR, MH, IgSF, MhSF)

INTRODUCTIONIMGT/DomainGapAlign is the IMGT online tool for the analysis of amino acid (AA) sequences and two-dimensional (2D) structures of domains. The use of this tool is described here. Three domain types can be analyzed: the variable (V) and constant (C) domains of the immunoglobulins (IG) and T cell receptors (TR) and other immunoglobulin superfamily (IgSF) proteins, and the groove (G) domain of major histocompatibility (MH) and other MH superfamily (MhSF) proteins. IMGT/DomainGapAlign creates gaps in the user amino acid sequences and delimits, for the V and C domains, the framework regions (FR-IMGT) and complementarity determining regions (CDR-IMGT), and, for the G domains, the strands and helix, according to the IMGT unique numbering. The tool provides alignments with the closest sequences from the IMGT domain directory of IMGT/DomainDisplay. For the IG and TR V domains that result from V-(D)-J rearrangement, the tool provides alignments with the translation of the IMGT/GENE-DB germline V and joining (J) genes. IMGT/DomainGapAlign displays the amino acid changes, highlights them in IMGT Colliers de Perles, and provides tables with their detailed description, according to the IMGT rules. Several amino acid sequences can be analyzed simultaneously, provided that they belong to the same domain type.

An efficient meshfree method for analysis of two-dimensional piezoelectric structures

Further application of an efficient novel meshfree technique based on the moving kriging(MK) interpolation for static and dynamic analyses of two-dimensional piezoelectricstructures is presented. The MK scheme is used for constructing the shape functions whichsatisfy the Kronecker delta property. Hence, the burdensome task of enforcing the essentialboundary conditions as in the moving least-squares approximation is avoided. Themechanical displacements, electric potential and natural frequencies of structures areinvestigated in detail through a series of numerical examples that are to demonstrate theapplicability and the efficiency of the proposed method. The results obtained are thencompared with those of other available reference solutions with very good agreement.

Finite-Element Models for Slender, Posttensioned Masonry Walls Loaded Out-of-Plane

Nonlinear finite-element models were developed, verified, and used to simulate the measured response of twelve 3.54 m (11.6 ft) tall posttensioned masonry walls with 810×100 mm (32×4 in.) cross sections that were tested to failure under uniform lateral loading in a laboratory. Variables included masonry type, wall slenderness, degree of tendon restraint, and prestress magnitude. The force-displacement relations obtained from the experimental tests of the walls were simulated using models developed by using an extended version of the program Dynamic Response Analysis of Inelastic Two-Dimensional Structures (DRAIN-2DX), and the results illustrate the influence of tensile strength, masonry type, magnitude of prestress, and tendon restraint on wall response to out-of-plane lateral loading. The computations indicate that load-displacement response of posttensioned masonry (PTM) walls is influenced by masonry tensile strength and that the stiffness and number of tendon restraints have a direct effect on peak ...

Two-dimensional analysis of the semidiurnal tide in some regions of the white sea

An improved method of two-dimensional kinematical structural analysis of tides (the “method of the orbits”) is presented. This method allows us to determine the parameters of the primary tidal waves shaping the observed tidal structure. The construction of the vertical orbits for the individual tidal harmonics is performed along the horizontal coordinate axes; one of them is oriented along the so-called “reactive azimuth,” which coincides with the direction of the tidal current at the instant of the zero tidal level. In this case, the orbit parameters include information on the amplitude-phase relations of the interfering waves and allow us to determine the angle of the waves crossing. The suggested method enables us to quantitatively describe the mechanism of the tidal formation with oblique interference both close to the shore and in the open sea. We tested the new method in two local zones of the White Sea (Morzhovets Island and in the vicinity of the entrance to Kandalaksha Gulf) where the presence of rotating semidiurnal tidal currents evidences the significant role of oblique interference of tidal waves. In these zones, the developed method made it possible to perform a detailed quantitative analysis of the local tide structure caused by the M2 tidal wave, which plays the dominant role in the White Sea. The result describes the structure of the propagation of the primary tidal waves better than the field of “pure” energy fluxes that was used earlier.

Neutron and X-Ray Studies of Advanced Materials

The selection of articles in the special topic 'Neutron and X-Ray Studies of Advanced Materials' is based on the materials presented during the TMS 2009 annual meeting in San Francisco, CA, February 15-19, 2009. The development of ultrabrilliant third-generation synchrotron X-ray sources, together with advances in X-ray optics, has created intense X-ray microbeams, which provide the best opportunities for in-depth understanding of mechanical behavior in a broad spectrum of materials. Important applications include ultrasensitive elemental detection by X-ray fluorescence/absorption and microdiffraction to identify phase and strain with submicrometer spatial resolution. X-ray microdiffraction is a particularly exciting application compared with alternative probes of crystalline structure, orientation, and strain. X-ray microdiffraction is nondestructive with good strain resolution, competitive or superior spatial resolution in thick samples, and with the ability to probe below the sample surface. Moreover, the high-energy X-ray diffraction technique provides an effective tool for characterizing the mechanical and functional behavior in various environments (temperature, stress, and magnetic field). At the same time, some neutron diffraction instruments constructed mainly for the purpose of engineering applications can be found at nearly all neutron facilities. The first generation-dedicated instruments designed for studying in-situ mechanical behavior have been commissioned and used, and industrial standardsmore » for reliable and repeatable measurements have been developed. Furthermore, higher penetration of neutron beams into most engineering materials provides direct measurements on the distribution of various stresses (i.e., types I, II, and III) beneath the surface up to several millimeters, even tens of millimeters for important industrial components. With X-ray and neutron measurements, it is possible to characterize material behavior at different length scales. It is predicted that the application of these techniques, in combination with theoretical simulations and numerical modeling, will lead to major breakthroughs in materials science in the foreseeable future, which will contribute to the development of materials technology and industrial innovation. Specifically, the use of these techniques provides bulk material properties that further augment new characterization tools including the increased use of atom probe tomography and high-resolution transmission electron microscopy systems. The combination of these techniques greatly assists the material property models that address multi-length-scale mechanisms. Different applications of diffuse scattering for understanding the fundamental materials properties are illustrated in the articles of Welberry et al., Goossens and Welberry, Campbell, Abe et al., Gilles et al., and Zhang et al. Analysis of thin films and two-dimensional structures is described in the articles of Gramlich et al., Brock et al., Vigliante et al., Kuzel et al., and Davydok et al. Recent advances in the line profile analysis are represented by the the articles of Scardi et al., Ungar et al., and Woo et al. Characterization of modern alloys is presented by the articles of Wollmershauser et al., Eidenberger et al., Garlea et al., Jia et al., Soulami et al., Wilson et al., and Wang et al. The collected articles are written by different scientific X-ray and neutron research groups. They represent a general trend in the development and application of diffraction techniques all over the world.« less

Model based atomic resolution tomography

Electron tomography is a valuable three-dimensional characterization method, but the technique has so far been limited to a nanometer scale resolution, and therefore complementary two-dimensional structural analysis is generally performed using other techniques. In this paper, computer simulations of the latest transmission electron microscope technologies are performed on a CeO2 supercell to investigate the extension of electron tomography to the atomic scale resolution, from a tilt series of high resolution electron microscopy (HREM) images. We showed that high-voltage and aberration-corrected microscopes were both capable of retrieving adjacent oxygen and Ce atoms for a thickness up to 2.5 nm. In the case where only a few tilt angle projections are in zone-axis orientations, we introduced a hybrid tomography method, whereby a lattice-resolved tomogram obtained from a few zone-axis projections is combined with the external shape reconstruction of the crystal from binary projections. Finally, we discussed some experimental challenges related to the proposed HREM tomography technique.

Static analysis of two-dimensional elastic structures using global collocation

Based on previous findings concerning the numerical solution of one-dimensional elastodynamical problems [Provatidis in Arch Appl Mech 78(4):241–250, 2008] this paper extends the methodology to the static analysis of two-dimensional problems in quadrilateral domains. This target is achieved by replacing the Galerkin/Ritz procedure involved in Lagrangian (or Gordon–Coons) type finite elements by a global collocation scheme. In brief, the boundary conditions are fulfilled at all boundary nodes, while the governing equation is fulfilled at internal points. The theory is supported by four test cases concerning rectangular and curvilinear structures under plane-stress or plane-strain conditions, where the convergence rate is successfully compared with that of conventional bilinear finite elements with the same mesh density.

Isogeometric analysis using T-splines

We explore T-splines, a generalization of NURBS enabling local refinement, as a basis for isogeometric analysis. We review T-splines as a surface design methodology and then develop it for engineering analysis applications. We test T-splines on some elementary two-dimensional and three-dimensional fluid and structural analysis problems and attain good results in all cases. We summarize the current status of T-splines, their limitations, and future possibilities.

Comparative Study of Different Hierarchical Bases of Finite Element Method: Application to Elastostatic Analysis of Two-Dimensional Structures

Comparative Study of Different Hierarchical Bases of Finite Element Method: Application to Elastostatic Analysis of Two-Dimensional Structures

An adaptive strategy for elastic-plastic analysis of structures with cracks

This work presents a methodology for self-adaptive finite element analysis of two-dimensional elastic-plastic structures. The self-adaptive process is based on an h-type refinement, with a posteriori error estimation. Two types of error estimators are available. The first is based on effective stress (Lee and Bathe, 1994) and the second is based on a ratio of plastic work (Peric et al., 1994). In the non-linear adaptive process for incremental plasticity analysis, a technique for interpolating analysis variables across distinct meshes (Lee and Bathe, 1994) is adopted. The von Mises yield criterion, with isotropic hardening, is adopted. Fracture problems are used to evaluate the performance of the adaptive process.

Free vibration multiquadric boundary elements applied to plane elasticity

This paper presents a new boundary element formulation for free vibration analysis of two-dimensional elastic structures. The dual reciprocity method (DRM) is introduced using the multiquadric radial basis functions (MQ). The required particular solution kernels for displacement and traction are derived and smoothed using simple mathematical trick; hence the limiting values of these kernels are computed. The eigen-problem of displacement is formulated and solved to obtain the required frequencies of different vibration modes. Finally, several numerical problems are studied to demonstrate the validity and accuracy of the developed formulation. The results are compared to those obtained from other interpolation functions, and finite element analysis to demonstrate the validity and superiority of the present formulation.

Shape sensitivity analysis of composites in contact using the boundary element method

This paper presents the application of the boundary element method to the shape sensitivity analysis of two-dimensional composite structures in contact. A directly differentiated form of boundary integral equation with respect to geometric design variables is used to calculate shape design sensitivities for anisotropic materials with frictionless contact. The selected design variables are the coordinates of the boundary points either in the contact or non-contact area. Three example problems with anisotropic material properties are presented to validate the applications of this formulation.

A smoothed four-node piezoelectric element for analysis of two-dimensional smart structures

This paper reports a study of linear elastic analysis of two-dimensional piezoelectric structures using a smoothed four-node piezoelectric element. The element is built by incorporating the strain smoothing method of mesh-free conforming nodal integration into the standard four-node quadrilateral piezoelectric finite element. The approximations of mechanical strains and electric potential fields are normalized using a constant smoothing function. This allows the field gradients to be directly computed from shape functions. No mapping or coordinate transformation is necessary so that the element can be used in arbitrary shapes. Through several examples, the simplicity, efficiency and reliability of the element are demonstrated. Numerical results and comparative studies with other existing solutions in the literature suggest that the present element is robust, computationally inexpensive and easy to implement.

Molecular cloning and characterization of 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase gene from Ginkgo biloba

Ginkgo biloba contains terpene triclactones of high pharmaceutical value such as ginkgolides. 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate (HMBPP) reductase (HDR) is proved to be the terminal-acting enzyme in the plastid MEP pathway which provides isoprenoid precursors for the biosynthesis of ginkgolides. The full-length cDNA encoding HDR, designated as GbHDR (Genbank Accession Number DQ364231), was isolated for the first time from G. biloba by RACE method. GbHDR contained a 1,422-bp open reading frame encoding 474 amino acids. The deduced GbHDR protein, showing high identity to HDRs of other plant species, was predicted to possess a chloroplast transit peptide at the N-terminal and four conserved cysteine residues. Two-dimensional structural analysis showed that GbHDR had a similar secondary structure with HDR from Arabidopsis thaliana. Southern blot analysis indicated that GbHDR belonged to a small gene family. Transcription pattern analysis revealed that GbHDR had high transcription in roots, and low in leaves and stems. The cloning of GbHDR gene will enable us to further understand the role of GbHDR involved in terpene triclatones biosynthetic pathway in G. biloba at molecular level.

β‐strand recombination in tricalbin evolution and the origin of synaptotagmin‐like C2 domains

Two protein families involved in membrane traffic, tricalbins and synaptotagmins, contain several copies of C2 domains and are related based on their sequence and domain architecture. Paradoxically, tricalbin and synaptotagmin C2 domains belong to different structural types with apparent circular permutation of terminal beta-strands. To understand whether a topological switch took place, we analyzed tricalbin and synaptotagmin-like C2 domains using two-dimensional structural analysis. We found that yeast tricalbins contain five to six C2 domains. One of these C2 domains possesses many features of synaptotagmin-like C2 domains and also carries a conserved C-terminal strand that is similar to its structural equivalent in synaptotagmin-like C2 domains, suggesting a structural permutation event. Indeed, among higher eukaryotes, animal tricalbins have evolved a C2 domain with synaptotagmin-like topology indicating that the structural conversion has taken place. Investigation of plant synaptotagmins, however, proves that they are direct tricalbin orthologs. Our analysis shows that beta-strand recombination is a possible evolutionary mechanism to generate new structural topologies with altered functional properties.

Transient elastodynamic analysis of two-dimensional structures using Coons-patch macroelements

Recently, Coons’ interpolation was used for the construction of large finite elements with degrees of freedom appearing mostly along the boundaries of a structure. So far, these so-called Coons-patch macroelements were successfully applied to the analysis of two-dimensional and axisymmetric elastic structures as well as potential problems including Poisson equation and acoustics. Now, this paper continues the research by investigating their applicability and performance in calculating the propagation of elastic waves within continua due to sudden loads. Explicit (central difference) and implicit ( θ-Wilson) time-integration schemes have been successfully applied to four typical model problems in conjunction with the proposed Coons-patch macroelements—without and with substructuring—and the results are successfully compared with conventional finite elements having the same number of nodes along the boundary. Finally, theoretical issues between the proposed global technique and well-established computational methods are discussed.

Free vibration analysis of two-dimensional structures using Coons-patch macroelements

Recently, Coons’ interpolation was used for the construction of large finite elements with degrees of freedom appearing mostly along the boundaries of a structure. In the regime of elasticity problems, these so-called “Coons-patch macroelements” were successfully applied to the static analysis of plane structures [C.G. Provatidis, Analysis of axisymmetric structures using Coons’ interpolation, Finite Elem. Anal. Des. 39 (2003) 535–558.] while this paper continues the research by investigating their performance in the extraction of natural frequencies and mode shapes. Apart from the piecewise-linear and cubic B-splines interpolation previously used, the performance of Lagrange polynomials and the role of additional internal nodes is studied here. Relationships with classical Serendipity and Lagrangian type elements are discussed. Moreover, the capability of Coons-patch macroelements to couple with conventional finite elements is investigated. The proposed method was applied to three illustrative examples and it was successfully compared with conventional bilinear finite elements.

GC-IR based two-dimensional structural group analysis of petroleum products

To characterize petroleum products, a method based on the combination of IR-spectrometric structural group analysis, GC-simulated boiling analysis and multivariate regression techniques (PLS, PCR) has been developed. The best performance was achieved by a PLS regression model with six aliphatic and aromatic structural groups. Thereby, structural group distribution related to the boiling temperature could be obtained in order to quantify product-specific distribution parameters and to control material-conversion processes caused by biodegradation.

A novel meshless approach ? Local Kriging (LoKriging) method with two-dimensional structural analysis

This paper develops a novel meshless approach, called Local Kriging (LoKriging) method, which is based on the local weak form of the partial differential governing equations and employs the Kriging interpolation to construct the meshless shape functions. Since the shape functions constructed by this interpolation have the delta function property based on the randomly distributed points, the essential boundary conditions can be implemented easily. The local weak form of the partial differential governing equations is obtained by the weighted residual method within the simple local quadrature domain. The spline function with high continuity is used as the weight function. The presently developed LoKriging method is a truly meshless method, as it does not require the mesh, either for the construction of the shape functions, or for the integration of the local weak form. Several numerical examples of two-dimensional static structural analysis are presented to illustrate the performance of the present LoKriging method. They show that the LoKriging method is highly efficient for the implementation and highly accurate for the computation.

Statistical analysis of two-dimensional cluster structures composed of ferromagnetic particles based on a flexible chain model.

We investigate two-dimensional cluster structures composed of ferromagnetic colloidal particles, based on a flexible chain model, by the configurational-bias Monte Carlo method. We clarify the dependence of the probabilities of the creation of different types of clusters on the dipole-dipole interactive energy and the cluster size.