MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes

The annotation of newly sequenced bacterial genomes begins with running several automatic analysis methods, with major emphasis on the identification of protein-coding genes. DNA sequences are heterogeneous in local nucleotide composition and this leads sometimes to sequences being annotated as authentic genes when they are not protein-coding genes or are true but uncharacterized protein-coding genes. This first annotation step is generally followed by an expert manual annotation of the predicted genes. The genomic data (sequence and annotations) organized in an appropriate databank file format is subsequently submitted to an entry point of the International Nucleotide Sequence Database. These procedures are inevitably subject to mistakes, and this can lead to unintentional syntactic annotation errors being stored in public databanks. Here, we present a new web program, MICheck (MIcrobial genome Checker), that enables rapid verification of sets of annotated genes and frameshifts in previously published bacterial genomes. The web interface allows one easily to investigate the MICheck results, i.e. inaccurate or missed gene annotations: a graphical representation is drawn, in which the genomic context of a unique coding DNA sequence annotation or a predicted frameshift is given, using information on the coding potential (curves) and annotation of the neighbouring genes. We illustrate some capabilities of the MICheck site through the analysis of 20 bacterial genomes, 9 of which were selected for their ‘Reviewed’ status in the National Center for Biotechnology Information (NCBI) Reference Sequence Project (RefSeq). In the context of the numerous re-annotation projects for microbial genomes, this tool can be seen as a preliminary step before the functional re-annotation step to check quickly for missing or wrongly annotated genes. The MICheck website is accessible at the following address:

Combined effects of temperature and of high hydrogen and oxygen contents on the mechanical behavior of a zirconium alloy upon cooling from the βZr phase temperature range

International audienceDuring hypothetical loss-of-coolant accidents (LOCA), zirconium-based nuclear fuel claddings can be exposed to high temperatures in the βZr phase domain and absorb substantial amounts of hydrogen (up to about 3000 weight ppm) and oxygen (up to about 1 weight %). This paper provides novel data about the combined effects of high hydrogen and oxygen contents on the mechanical behavior of the (prior-)βZr phase, as a function of temperature, upon cooling from the βZr phase temperature range. A protocol was developed to homogeneously charge Zircaloy-4 cladding tubes at different hydrogen contents, up to 3200 weight ppm, and oxygen contents, between 0.13 and 0.9 weight %. Tensile tests were then performed at various temperatures between 700 and 30°C upon cooling from the βZr domain. The results show that the mechanical behavior strongly depends on the testing temperature and the hydrogen and oxygen contents. Relationships are proposed to describe the macroscopic ductile-to-brittle transition and the mechanical behavior of the material as a function of temperature, hydrogen and oxygen contents. The predictions based on these relationships are compared to selected data from the literature obtained on claddings oxidized at high temperature, including results from semi-integral LOCA tests. Also, it is shown that considering the combined effects of hydrogen and oxygen is necessary to interpret the mechanical behavior of the material, in particular the embrittlement of claddings subjected to LOCA-relevant secondary hydriding

A model to describe the cyclic anisotropic mechanical behavior of short fiber-reinforced thermoplastics

International audienceDue to the injection molding process, short fiber-reinforced thermoplastic composites show a complex fiber orientation distribution and, as a consequence, an overall anisotropic mechanical behavior. The monotonic and cyclic mechanical behavior of PolyEtherEtherKetone thermoplastic reinforced with 30 wt.% of short carbon fibers was characterized through a series of tests generating various complex loading histories (loading–unloading with creep or recovery steps, cyclic loading with various stress amplitudes) performed at room temperature on samples with various homogeneous and heterogeneous fiber orientation distributions. A three-dimensional model relying on a thermodynamic framework was then developed to represent the anisotropic mechanical behavior of the material, including elastic, viscoelastic, and plastic phenomena. Relevant constitutive laws were defined to describe the phenomena within wide ranges of loading rates and levels, with a limited number of parameters. Elastic anisotropy and plastic anisotropy were naturally described by using a two-step homogenization method and a Hill-like equivalent stress taking into account the fiber orientation distribution. The model was implemented into a finite element code to be able to simulate the response of complex parts with a heterogeneous fiber orientation distribution subjected to a heterogeneous loading. Model parameters were identified by applying a robust and original approach relying on a limited number of relevant experiments. The prediction capability of the model was demonstrated by simulating several types of tests not used for the identification, covering a wide range of monotonic and cyclic, homogeneous and heterogeneous, loading conditions, for various simple and complex fiber orientation distributions. In particular, the model is shown to be able to predict the energy dissipated in the material when subjected to cyclic loading

1D and 3D modelling of PCMI during a RIA with ALCYONE v1.1

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Constitutive equations for the cyclic behaviour of short carbon fibre-reinforced thermoplastics and identification on a uniaxial database

International audienceA constitutive model for the cyclic behaviour of short carbon fibre-reinforced thermoplastics for aeronautical applications is proposed. First, an extended experimental database is generated in order to highlight the specificities of the studied material. This database is composed of complex tests and is used to design a relevant constitutive model able to capture the cyclic behaviour of the material. A general 3D formulation of the model is then proposed, and an identification strategy is defined to identify its parameters. Finally, a validation of the identification is performed by challenging the prediction of the model to the tests that were not used for the identification. An excellent agreement between the numerical results and the experimental data is observed revealing the capabilities of the model

Fast screening of the fatigue properties of thermoplastics reinforced with short carbon fibers based on a heat build-up protocol

This study deals with the characterization of the fatigue lifetime of a short carbon fiber reinforced PEEK matrix thermoplastic composite using a heat build-up protocol. Several commercial grades and fillers ratios are considered in order to challenge the ability of the technique to capture the influence of these variations. First, the materials investigated and the experimental protocols are described. The way to build the heat build-up curves is outlined. Then the results obtained from the heat build-up and the fatigue experiments are presented. Finally these results are used to discuss two main points. The first one is the validity of the hypotheses needed to apply the approach, ranging from the evaluation of the dissipation to the response during the fatigue tests. The second one is the capability to predict the fatigue curves accurately throughout an energetic criterion and to catch the influence of the variation of material on the fatigue properties. The results presented here are published with more details in [47]

Fast screening of the fatigue properties of thermoplastics reinforced with short carbon fibers based on a heat build-up protocol

International audienceThis study deals with the characterization of the fatigue lifetime of a short carbon fiber reinforced PEEK matrix thermoplastic composite using a heat build-up protocol. Several commercial grades and fillers ratios are considered in order to challenge the ability of the technique to capture the influence of these variations. First, the materials investigated and the experimental protocols are described. The way to build the heat build-up curves is outlined. Then the results obtained from the heat build-up and the fatigue experiments are presented. Finally these results are used to discuss two main points. The first one is the validity of the hypotheses needed to apply the approach, ranging from the evaluation of the dissipation to the response during the fatigue tests. The second one is the capability to predict the fatigue curves accurately throughout an energetic criterion and to catch the influence of the variation of material on the fatigue properties. The results presented here are published with more details in [47]

Constitutive equations for the cyclic behaviour of short carbon fibre-reinforced thermoplastics and identification on a uniaxial database

International audienceA constitutive model for the cyclic behaviour of short carbon fibre-reinforced thermoplastics for aeronautical applications is proposed. First, an extended experimental database is generated in order to highlight the specificities of the studied material. This database is composed of complex tests and is used to design a relevant constitutive model able to capture the cyclic behaviour of the material. A general 3D formulation of the model is then proposed, and an identification strategy is defined to identify its parameters. Finally, a validation of the identification is performed by challenging the prediction of the model to the tests that were not used for the identification. An excellent agreement between the numerical results and the experimental data is observed revealing the capabilities of the model

Mechanical behavior at high temperatures of highly oxygen- or hydrogen-enriched α and (Prior-) β phases of zirconium alloys

International audienceMechanical behavior at high temperature of highly oxygen-or hydrogen-enriched α and (prior-) β phases of zirconium alloys ABSTRACT: During a hypothetical loss-of-coolant accident (LOCA), zirconium alloy fuel claddings can be loaded by internal pressure and exposed to steam at high temperature (HT, potentially up to 1200°C), then cooled and water quenched. A significant fraction of the oxygen reacting with the cladding during HT oxidation diffuses beneath the oxide through the metallic substrate. This induces a progressive transformation of the metallic βZr phase layer into an intermediate layer of αZr(O) phase containing up to 7 wt.% of oxygen. Furthermore, in some specific conditions, the cladding may rapidly absorb a significant amount of hydrogen during steam exposition at HT. Being a βZr-stabilizer, hydrogen would mainly diffuse and concentrate up to several thousands of wt.ppm into the inner βZr phase layer. Oxygen and hydrogen are known to modify the metallurgical and mechanical properties of zirconium alloys but data are scarce for high contents, especially at HT. However, such data are important basic components to improve the assessment of the oxidized cladding mechanical behavior and integrity during and after LOCA-like thermal-mechanical transients. This study intended to provide new, more comprehensive data on the HT mechanical behavior of the αZr(O) and the (prior-) βZr phases containing high contents of oxygen and hydrogen, respectively. Model samples, produced from M5® 5 and Zircaloy-4 cladding tubes, homogeneously charged in oxygen (≤6 wt.%) and in hydrogen (≤3000 wt.ppm) respectively, were prepared. Their mechanical behavior was determined under vacuum between 800 and 1100°C for the oxygen-enriched αZr phase, and in air between 700 and 20°C, after cooling from the βZr temperature domain, for the hydrogen-enriched (prior-) βZr phase. The αZr phase is substantially strengthened and embrittled by oxygen. Power-law and nearly linear creep regimes are observed and were modelled for stress levels beyond and below 15 MPa, respectively. The model αZr(O) material experiences a ductile-to-brittle transition at 1000-1100°C for oxygen contents between 3.4 and 4.3 wt.%. The viscoplastic behavior of the αZr(O) phase was used to evaluate the contribution of the αZr(O) layer to the HT creep behavior of an oxidized fuel cladding tube subjected to internal pressure. The model (prior-) βZr phase becomes macroscopically brittle at temperatures ≤135°C and ≤350-400°C for average hydrogen content