Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A > T, C > G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA. (c) 2008 Published by Elsevier Inc.

Orientation-based Continuum Damage Models for Rocks

A general formulation of the Helmholtz free energy used in thermodynamics of damage process of rocks is derived within a multi-scale framework. Such a physically-based thermodynamic state potential has a hybrid, discrete/continuum, nature in the sense tha

Modeling Nonlinear Peeling of Ductile Thin Films-Critical Assessment of Analytical Bending Models Using FE Simulations

Three analytical double-parameter criteria based on a bending model and a two-dimensional finite element analysis model are presented for the modeling of ductile thin film undergoing a nonlinear peeling process. The bending model is based on different governing parameters: (1) the interfacial fracture toughness and the separation strength, (2) the interfacial fracture toughness and the crack tip slope angle, and (3) the interfacial fracture toughness and the critical Mises effective strain of the delaminated thin film at the crack tip. Thin film nonlinear peeling under steady-state condition is solved with the different governing parameters. In addition, the peeling test problem is simulated by using the elastic-plastic finite element analysis model. A critical assessment of the three analytical bending models is made by comparison of the bending model solutions with the finite element analysis model solutions. Furthermore, through analyses and comparisons for solutions based on both the bending model and the finite element analysis model, some connections between the bending model and the finite element analysis model are developed. Moreover, in the present research, the effect of different selections for cohesive zone shape on the ductile film peeling solutions is discussed.

Peeling Experiments Of Ductile Thin Films Along Ceramic Substrates - Critical Assessment Of Analytical Models

Two types of peeling experiments are performed in the present research. One is for the Al film/Al2O3 substrate system with an adhesive layer between the film and the substrate. The other one is for the Cu film/Al2O3 substrate system without adhesive layer between the film and the substrate, and the Cu films are electroplated onto the Al2O3 substrates. For the case with adhesive layer, two kinds of adhesives are selected, which are all the mixtures of epoxy and polyimide with mass ratios 1:1.5 and 1:1, respectively. The relationships between energy release rate, the film thickness and the adhesive layer thickness are measured during the steady-state peeling process. The effects of the adhesive layer on the energy release rate are analyzed. Using the experimental results, several analytical criteria for the steady-state peeling based on the bending model and on the two-dimensional finite element analysis model are critically assessed. Through assessment of analytical models, we find that the cohesive zone criterion based on the beam bend model is suitable for a weak interface strength case and it describes a macroscale fracture process zone case, while the two-dimensional finite element model is effective to both the strong interface and weak interface, and it describes a small-scale fracture process zone case. (C) 2007 Elsevier Ltd. All rights reserved.

Study of three elastic-plastic constitutive models by non-proportional finite deformations of OFHC copper

Experimental stress-strain data of OFHC copper first under torsion to 13% and then under torsion-tension to about 10% are used to study the characteristics of three elastic-plastic constitutive models: Chaboche's super-positional nonlinear model, Dafalias and Popov's two surface model and Watanabe and Atluri's version of the endochronic model. The three models, originally oriented for infinitesimal deformation, have been extended for finite deformation. The results show (a) the Mises-type yield surface used in the three models brings about significant departure of the predictions from the experimental data; (b) Chaboche's and Dafalias' models are easier than Watanabe and Atluri's model in determining the material parameters in them, and (c) Chaboche's and Watanabe & Atluri's models produce almost the same prediction to the data, while Dafalias' model cannot accurately predict the plastic deformations when a loading path changes in its direction. Copyright (C) 1996 Elsevier Science Ltd

Numerical Analysis of the Effects of Free-Stream Thermo-Chemical State on the Test Model Flow Field in High-Enthalpy Tunnel

The effects of the free-stream thermo-chemical state on the test model flow field in the high-enthalpy tunnel are studied numerically. The properties of the free-stream, which is in thermo-chemical non-equilibrium, are determined by calculating the nozzle flow field. A free-stream with total enthalpy equal to the real one in the tunnel while in thermo-chemical equilibrium is constructed artificially to simulate the natural atmosphere condition. The flow fields over the test models (blunt cone and Apollo command capsule model) under both the non-equilibrium and the virtual equilibrium free-stream conditions are calculated. By comparing the properties including pressure, temperature, species concentration and radiation distributions of these two types of flow fields, the effects of the non-equilibrium state of the free-stream in the high-enthalpy shock tunnel are analyzed.

CFD study of a sudden-expanding coal combustor using Euler-Euler and Euler-Lagrange models

In this study, the Euler-Euler (E-E) and Euler-Lagrange (E-L) models designed for the same chemical mechanism of heterogeneous reactions were used to predict the performance of a typical sudden-expanding coal combustor. The results showed that the current E-E model underestimated the coal burnout rate because the particle temperature fluctuation on char combustion is not adequately considered. A comparison of the E-E and E-L simulations showed the underestimation of heterogeneous chemical reaction rates by the E-E model. (C) 2010 Elsevier Ltd. All rights reserved.

Gound State Properties of Nuclei in (295)118 alpha-Decay Chain

The properties of nuclei belonging to the alpha-decay chain of superheavy element (295)118 have been studied in the framework of axially deformed relativistic mean field (RMF) theory with the parameter set of NL-Z2 in the blocked BCS approximation. Some ground state properties such as binding energies, deformations, and alpha-decay energies Q(alpha) have been obtained and agree well with those from finite-range droplet model (FRDM). The single-particle spectra of nuclei in (295)118 alpha-decay chain show that the shell gaps present obviously nucleon number dependence. The root-mean-square (rms) radii of proton, neutron and matter distributions change slowly from (283)112 to (295)118 but dramatically from (279)110 to (283)112, which may be due to the subshell closure at Z = 110 in (279)110. The alpha-decay half-lives in (295)118 decay chain are evaluated by employing the cluster model and the generalized liquid drop model (GLDM), and the overall agreement is found when they are compared with the known experimental data. The alpha-decay lifetimes obtained from the cluster model are slightly larger than those of GLDM ones. Finally, we predict the alpha-decay half-lives of Z = 118, 116, 114, 112 isotopes using the cluster model and GLDM, which also indicate these two models can corroborate each other in studies on superheavy nuclei. The results from GLDM are always lower than those obtained from the cluster model.

Electron impact excitation of xenon from the metastable state to the excited states

The electron impact excitation cross sections from the lowest metastable state 5p(5)6sJ = 2 to the six lowest excited states of the 5p(5)6p configuration of xenon are calculated systematically by using the fully relativistic distorted wave method. In order to discuss the effects of target state descriptions on the electron impact excitation cross sections, two correlation models are used to describe the target states based on the multiconfiguration Dirac-Fock (MCDF) method. It is found that the correlation effects play a very important role in low energy impact. For high energy impact, however, the cross sections are not sensitive to the description of the target states, but many more partial waves must be included.

COASTAL SEA-LEVEL AND THE LARGE-SCALE CLIMATE STATE - A DOWNSCALING EXERCISE FOR THE JAPANESE ISLANDS

A major problem which is envisaged in the course of man-made climate change is sea-level rise. The global aspect of the thermal expansion of the sea water likely is reasonably well simulated by present day climate models; the variation of sea level, due to variations of the regional atmospheric forcing and of the large-scale oceanic circulation, is not adequately simulated by a global climate model because of insufficient spatial resolution. A method to infer the coastal aspects of sea level change is to use a statistical ''downscaling'' strategy: a linear statistical model is built upon a multi-year data set of local sea level data and of large-scale oceanic and/or atmospheric data such as sea-surface temperature or sea-level air-pressure. We apply this idea to sea level along the Japanese coast. The sea level is related to regional and North Pacific sea-surface temperature and sea-level air pressure. Two relevant processes are identified. One process is the local wind set-up of water due to regional low-frequency wind anomalies; the other is a planetary scale atmosphere-ocean interaction which takes place in the eastern North Pacific.