Large-scale pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing

Pyrosequencing is a relatively recent method for sequencing short stretches of DNA. Because both Pyrosequencing and Sanger dideoxy sequencing were recently used to characterize and validate DNA molecular barcodes in a large yeast gene-deletion project, a meta-analysis of those data allow an excellent and timely opportunity for evaluating Pyrosequencing against the current gold standard, Sanger dideoxy sequencing. Starting with yeast genomic DNA, parallel PCR amplification methods were used to prepared 4747 short barcode-containing constructs from 6000 Saccharomyces cerevisiae gene-deletion strains. Pyrosequencing was optimized for average read lengths of 25-30 bases, which included in each case a 20-mer barcode sequence. Results were compared with sequence data obtained by the standard Sanger dideoxy chain termination method. In most cases, sequences obtained by Pyrosequencing and Sanger dideoxy sequencing were of comparable accuracy, and the overall rate of failure was similar. The DNA in the barcodes is derived from synthetic oligonucleotide sequences that were inserted into yeast-deletion-strain genomic DNA by homologous recombination and represents the most significant amount of DNA from a synthetic source that has been sequenced to date. Although more automation and quality control measures are needed, Pyrosequencing was shown to be a fast and convenient method for determining short stretches of DNA sequence.     

Numerical analysis of the stress concentration near holes originating in previously loaded viscoelastic bodies at finite strains

The state of stress and strain of previously loaded viscoelastic bodies with holes originating in them, successively or simultaneously, is analyzed under finite plane deformations. The problem statement and solution are based on the theory of repeatedly superimposed large deformations. The material mechanical properties are described using integral relations of the convolution type over time with a weakly singular kernel. The problem solving is based on the finite-element method. To calculate the integral of the convolution type, a recurrence formula is used that can be obtained by approximating the initial kernel with a linear combination of exponential functions (the truncated Prony’s series). The nonlinear effects and the effect of the interaction between holes on the stress concentration are analyzed. For the dynamic problems, the results for incompressible and weakly compressible materials are compared.     

Switching the direction of spin accumulation in the spin Hall effect of light by adjusting the optical axis of an uniaxial crystal

We theoretically and experimentally investigate a switchable spin Hall effect (SHE) of light in reflection near the Brewster angle at an air-uniaxial crystal interface. We find a large transverse spin splitting near the Brewster angle, whose sign can be altered by rotating the optical axis. As an analogy of the SHE in an electronic system, a switchable spin accumulation in the SHE of light is detected. We are able to switch the direction of the spin accumulation by adjusting the optical axis angle of the uniaxial crystal. These findings may give opportunities for photon spin manipulating and developing a new generation of nano-photonic devices.     

Orientation dependence of structural transition in fcc Al driven under uniaxial compression by atomistic simulations

By molecular dynamics simulations employing an embedded atom method potential,we have investigated structural transformations in single crystal Al caused by uniaxial strain loading along the [001],[011] and [111] directions. We find that the structural transition is strongly dependent on the crystal orientations. The entire structure phase transition only occurs when loading along the [001] direction,and the increased amplitude of temperature for [001] loading is evidently lower than that for other orientations. The morphology evolutions of the structural transition for [011] and [111] loadings are analysed in detail. The results indicate that only 20% of atoms transit to the hcp phase for [011] and [111] loadings,and the appearance of the hcp phase is due to the partial dislocation moving forward on {111} fcc family. For [011] loading,the hcp phase grows to form laminar morphology in four planes,which belong to the {111} fcc family; while for [111] loading,the hcp phase grows into a laminar structure in three planes,which belong to the {111} fcc family except for the (111) plane. In addition,the phase transition is evaluated by using the radial distribution functions.     

Lattice stability and the effect of Co and Re on the ideal strength of Ni:First-principles study of uniaxial tensile deformation

Using first-principles density functional calculations, lattice stability of γ-Ni under [001], [110], and [111] uniaxial tensions and the effect of alloying elements Co and Re on the uniaxial tensile behavior of γ-Ni were studied in this paper.With elastic constants and phonon spectra calculations, we examined the mechanical stability and phonon stability of Ni during the uniaxial tensions along the three characteristic directions. The results show that the mechanical stability and phonon stability of a lattice occurs before the maximum stress–strain point under the [001] and [111] tension, respectively.The effects of Co and Re on the ideal tensile strength of γ-Ni show a significant directivity: Co and Re have little effect on the stresses in [001] and [111] directions, but increases the ideal strength of the system in the weakest uniaxial tensile direction. Moreover, the strengthening effect of Re is significantly better than that of Co. By further analyzing electronic structure, it is found that the effect of alloying elements on the uniaxial tensile behavior of γ-Ni comes from their interactions with host atoms.     

厚板的高阶剪切变形理论研究

已有多种厚板理论和高阶剪切变形模型,但仍需要进一步研究以更加完善.首先根据平均转角及上下表面剪应力自由这两个条件,提出了具有统一高阶剪切变形模型的中面位移模式,并将之表示为正交分解形式.根据正交特性,定义了板的广义应力;运用板问题应变能密度表示的等价性,提出了与广义应力功共轭的广义应变表示形式,建立了板的本构关系.证明了不同转角定义时虚功原理板理论表示的客观性,以及与三维弹性理论表示的等价性.运用虚功原理,建立了变分自洽的高阶厚板理论和变分渐近的低阶厚板理论,推导了相应的平衡方程及边界条件,分析了与已有板理论的异同.以广义应力形式建立了厚板理论的平衡方程,厘清了不同转角表示时板理论间的关系、低阶厚板理论与高阶厚板理论间的关系以及剪切系数计算等若干基本问题.对圣维南扭转问题的求解证明了该理论的正确性.      

Enhancement of ferromagnetic resonance in Al203-doped CozFeAI Heusler alloy film prepared by oblique sputtering

Large and variable in-plane uniaxial magnetic anisotropy in a nanocrystalline （Co2FeA1）97.8（Al2O3）2.2 soft magnetic thin film is obtained by an oblique sputtering method without being induced by magnetic field or post anneaiing. The in-plane uniaxiai magnetic anisotropy varies from 50 Oe to 180 Oe （1 Oe=79.5775 A·m-1） by adjusting the sample＇s position. As a result, the ferromagnetic resonance frequency of the film increases from 1.9 GHz to 3.75 GHz.     

基于$lt;i$gt;J$lt;/i$gt;积分的颗粒煤岩单轴压缩下裂纹扩展研究

颗粒煤岩是由众多离散的煤岩颗粒组成的固态多层次多结构物质,具有煤岩与颗粒物质的双重性质,其裂纹扩展规律可以从煤岩力学特性和颗粒物质多尺度特性进行研究. 首先,从能量角度对线弹性材料受压破坏,裂纹扩展产生原因进行了阐述,指出线弹性阶段裂纹的扩展动力源自应变能的释放. 然后,通过物理实验和数值试验从宏观和细观两方面对颗粒煤岩受压破裂过程中裂纹扩展做了进一步研究,结果表明:颗粒煤岩完全破裂后,底部会形成一个锥形堆,裂纹的扩展随着煤岩颗粒粒径的减小而减缓,部分裂纹扩展会出现突变点,且裂纹无光滑性;由于煤岩颗粒粒径等引起介质的非均匀性对裂纹扩展有重要的影响,均质度系数越大裂纹起裂时间越晚,声发射能量释放在裂纹扩展的轻度、中度和深度三个不同阶段逐渐变得频繁、剧烈. 研究结果将有利于进一步研究岩土类颗粒材料受压破裂过程的裂纹扩展规律. 关键词： J积分')" href="#">J积分 颗粒煤岩 单轴压缩 裂纹扩展     

Strain-modulated anisotropic Andreev reflection in a graphene-based superconducting junction

We investigate the Andreev reflection across a uniaxial strained graphene-based superconducting junction. Compared with pristine graphene-based superconducting junction, three opposite properties are found. Firstly, in the regime of the interband conversion of electron-hole, the Andreev retro-reflection happens. Secondly, in the regime of the intraband conversion of electron-hole, the specular Andreev reflection happens. Thirdly, the perfect Andreev reflection, electron-hole conversion with unit efficiency, happens at a nonzero incident angle of electron. These three exotic properties arise from the strain-induced anisotropic band structure of graphene, which breaks up the original relation between the direction of velocity of particle and the direction of the corresponding wavevector. Our finding gives an insight into the understanding of Andreev reflection and provides an alternative method to modulate the Andreev reflection.     

On the Elastic Modulus of Powders

For the design of silos and similar equipment for storage, handling and processing of particulate materials, a thorough understanding of the mechanical behaviour of powders is of great importance. Whereas strength properties of powders have been investigated by many workers, the elastic behaviour at small deformations has been much less in focus. In that respect, a simple preliminary theory of uniaxial elasticity has been derived for particles, based on a simple system of spherical and monosized particles of a homogenous and elastically isotropic material. The equation σ = E_p?_el² gives the relationship between stress, elastic modulus and elastic deformation for the unloading of a given powder at a specific consolidation stress/ compression level. Comparisons with experimental results of real powders in a uniaxial tester show surprisingly good agreement in many cases. The equation seems to describe the elasticity of powders fairly well, although it is only a preliminary derivation based on simple considerations.