Mechanical effects of the self-organization of dislocations and related critical characteristics

The effects of the dislocation pattern formed due to the self-organization of the dislocations in crystals on the macroscopic hardening and dynamic internal friction (DIF) during deformation are studied. The classic dislocation models for the hardening and DIF corresponding to the homogeneous dislocation configuration are extended to the case for the non-homogeneous one. In addition, using the result of dislocation patterning deduced from the non-linear dlislocation dynamics model for single slip, the correlation between the dislocation pattern and hardening as well as DIF is obtained. It is shown that in the case of the tension with a constant strain rate, the bifurcation point of dislocation patterning corresponds to the turning point in the stress versus strain and DIF versus strain curves. This result along with the critical characteristics of the macroscopic behavior near the bifurcation point is microscopically and macroscopically in agreement with the experimental findings on mono-crystalline pure aluminum at temperatures around 0.5T(m). The present study suggests that measuring the DIF would be a sensitive and useful mechanical means in order to study the critical phenomenon of materials during deformation.

The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia : Anura): a new gene order in the vertebrate mtDNA

The mitochondrial DNA of the rice frog, Fejervarya limnocharis (Amphibia, Anura), was obtained using long-and-accurate polymerase chain reaction (LA-PCR) combining with subcloning method. The complete nucleotide sequence (17,717 bp) of mitochondrial genome was determined subsequently. This mitochondrial genome is characterized by four distinctive features: the translocation of ND5 gene, a cluster of rearranged tRNA genes (tRNA(Thr), tRNA(Pro), tRNA(Leu) ((CUN))) a tandem duplication of tRNA(Mer) gene, and eight large 89-bp tandem repeats in the control region, as well as three short noncoding regions containing two repeated motifs existing in the gene cluster of ND5/tRNA(Thr)/tRNA(Pro)/tRNA(Leu)/tRNA(Phe). The tandem duplication of gene regions followed by deletions of supernumerary genes can be invoked to explain the shuffling of tRNAM(Met) and a cluster of tRNA and ND5 genes, as observed in this study. Both ND5 gene translocation and tandem duplication of tRNA(Met) were first observed in the vertebrate mitochondrial genomes. (c) 2004 Elsevier B.V. All rights reserved.

Self-organization of the InGaAs GaAs quantum dots superlattice

The mechanism of self-organization of quantum dots (QDs) during the growth of InGaAs/GaAs multilayers on GaAs (1 0 0) was investigated with cross-sectional transmission electron microscopy (XTEM), and double-crystal X-ray diffraction (DCXD). We found that the QDs spacing in the first layer can affect the vertical alignment of QDs. There seems to exist one critical lateral QD spacing, below which merging of QDs with different initial size is found to be the dominant mechanism leading to perfect vertical alignment. Once the critical value of QDs spacing is reached, the InGaAs QDs of the first layer are simply reproduced in the upper layers. The X-ray rocking curve clearly shows two sets of satellite peaks, which correspond to the QDs superlattice, and multi-quantum wells (QW) formed by the wetting layers around QDs. (C) 1999 Elsevier Science B.V. All rights reserved.

Self-organization of the InGaAs GaAs quantum dots superlattice

The mechanism of self-organization of quantum dots (QDs) during the growth of InGaAs/GaAs multilayers on GaAs (1 0 0) was investigated with cross-sectional transmission electron microscopy (XTEM), and double-crystal X-ray diffraction (DCXD). We found that the QDs spacing in the first layer can affect the vertical alignment of QDs. There seems to exist one critical lateral QD spacing, below which merging of QDs with different initial size is found to be the dominant mechanism leading to perfect vertical alignment. Once the critical value of QDs spacing is reached, the InGaAs QDs of the first layer are simply reproduced in the upper layers. The X-ray rocking curve clearly shows two sets of satellite peaks, which correspond to the QDs superlattice, and multi-quantum wells (QW) formed by the wetting layers around QDs. (C) 1999 Elsevier Science B.V. All rights reserved.

Genomic organization, nucleotide sequence analysis of the core histone genes cluster in Chlamys farreri and molecular evolution assessment of the H2A and H2B

This work represents the nucleotide sequence of the core histone gene cluster from scallop Chlamys farreri. The tandemly repeated unit of 5671 bp containing a copy of the four core histone genes H4, H2B, H2A and H3 was amplified and identified by the techniques of homology cloning and genomic DNA walking. All the histone genes in the cluster had the structures in their 3' flanking region which related to the evolution of histone gene expression patterns throughout the cell cycle, including two different termination signals, the hairpin structure and at least one AATAAA polyadenylation signal. In their 5' region, the transcription initiation sites with a conserved sequence of 5'-PyATTCPu-3' known as the CAP site were present in all genes except to H2B, generally 37-45 bp upstream of the start code. Canonical TATA and CAAT boxes were identified only in certain histone genes. In the case of the promoters of H2B and H2A genes, there was a 5'-GATCC-3' element, which had been found to be essential to start transcription at the appropriate site. After this element, in the promoter of H2B, there was another sequence, 5'-GGATCGAAACGTTC-3', which was similar to the consensus sequence of 5'-GGAATAAACGTATTC-3' corresponding to the H2B-specific promoter element. The presence of enhancer sequences (5'-TGATATATG-3') was identified from the H4 and H3 genes, matching perfectly with the consensus sequence defined for histone genes. There were several slightly more complex repetitive DNA in the intergene regions. The presence of the series of conserved sequences and reiterated sequences was consistent with the view that mollusc histone gene cluster arose by duplicating of an ancestral precursor histone gene, the birth-and-death evolution model with strong purifying selection enabled the histone cluster less variation and more conserved function. Meanwhile, the H2A and the H2B were demonstrated to be potential good marks for phylogenetic analysis. All the results will be contributed to the characterization of repeating histone gene families in molluscs.

Complex organization of the Streptomyces avermitilis genes encoding the avermectin polyketide synthase

The avermectin (Av) polyketide synthase (PKS) and erythromycin (Er) PKS are encoded by modular repeats of DNA, but the genetic organization of the modules encoding Av PKS is more complex than Er PKS. Sequencing of several related DNA fragments from Streptomyces avermitilis that are part of the Av biosynthetic gene cluster, revealed that they encode parts of large multifunctional PKS proteins. The Av PKS proteins show strong similarity to each other, as well as similarity to Er PKS proteins [Donadio et al., Science 252 (1991) 675–679] and fatty acid synthases. Partial DNA sequencing of the 65-kb region containing all the related sequence elements in the avr genes provides evidence for twelve modular repeats encoding FAS-like domains. The genes encoding the Av PKS are organized as two sets of six modular repeats which are convergently transcribed.