A proteome-wide analysis of domain architectures of prokaryotic single-spanning transmembrane proteins

We performed a proteome-wide survey of the domain architectures in single-spanning transmembrane (TM) proteins (single-spannings) from 87 sequenced prokaryotic (Bacterial and Archaean) genomes by assigning Pfam domains to their N-tail and C-tail loops. Out of 14,625 single-spannings, 3,516 sequences have at least one domain assigned, and no domains were assigned to 7,850, with the remaining 3,259 with less reliable assignment. In the domain-assigned sequences, 3116 sequences are with at most two domains, and the other 400 sequences with more than two. The assigned domains distribute over 651 Pfam families, which account for 11.4% of the total Pfam-A families. Among the 651 families are mostly soluble-protein-originated ones, but only 21 families are unique to TM proteins. The occurrence frequency of the individual domain families follows a power-law, that is, 264 families occur only once, 106 just twice, and the families appeared more than 30 times are counted by only 39. It is found that the great majority of the sequences having one or two domains are of the type II topology with the C-tail loop containing domains on it. On the contrary, the N-tail loop of the same type topology seldom carries domains. Importantly, the assigned domains are always found on the tail loops longer than 60 residues, even for the small domains with less than 30 residues. There are still as many as 5,800 sequences without assigned domains in spite of having at least one long tail, on which no less than 1,000 novel domain families are expected most likely to lie concealed unknown yet. We also investigated the domain arrangement preference and the domain family combination patterns in 'singlets' (single-spannings with one assigned domain) and 'doublets' (with two domains).     

Single domain wall dynamics in ferromagnetic lamination with variable conductivity

The influence of variable conductivity and thickness of two outer non-ferromagnetic layers on magnetization reversal of one central ferromagnetic layer is theoretically investigated. The model of a thin rigid 180°$180°$ domain wall moving transversely through the axially magnetized ferromagnetic layer is used to calculate induced eddy currents in lamination from which the domain wall mobility is determined. The effect of asymmetric distribution of eddy currents around moving domain wall results in acceleration of the wall near the edge of the lamination. The known domain wall mobility in ferromagnetic lamination can then be used to determine either the conductivity or the thickness of deposited outer non-ferromagnetic layers as proposed in discussion.     

金银三层纳米管局域表面等离激元共振特性研究

相对于单一金属纳米材料,二金属复合纳米材料具有更大的潜在应用价值.基于时域有限差分方法,研究了SiO₂-Ag-Au和SiO₂-Au-Ag二金属三层纳米管的消光光谱,并对其局域表面等离激元共振(Localized Surface Plasmon Resonance,LSPR)特性进行了分析.研究发现,内核尺寸变大将导致上述两种金属纳米管LSPR峰红移;内层金属及外层金属壳层厚度增大均会导致其LSPR峰蓝移.银壳厚度变化对纳米管LSPR的调制作用大于金壳厚度变化造成的影响.上述现象可以利用等离激元杂化理论及自由电子和振荡电子变化的竞争机制进行分析.     

食用香料的太赫兹时域光谱

食用香料是人们在烹饪过程中必不可少的调味品,对食用香料的鉴别和食用安全性检测也尤为重要.本文利用太赫兹时域光谱技术对食用香料进行测试,得到了黑胡椒、白胡椒、花椒、大料、姜粉、甘草、香叶以及五香粉、十三香等香料在太赫波段的吸收谱和折射率谱.结果表明,不同种类的香料都有其独特的特征吸收光谱,样品的吸收谱在0.2～1.25THz频段内以不同的斜率单调递增,在1.25～2.0THz频段呈现出不同的吸收峰.样品的折射率值在1.3～1.8之间变化,并且,样品的折射率在其吸收峰所对应的频率处出现了反常色散.通过对吸收系数的斜率、峰值位置以及折射率进行定标分析,太赫兹时域光谱技术可以用于不同种香料的定性检测.实验数据为食用香料的鉴别提供了依据,可以用于建立食用香料的太赫兹波谱数据库.     

Influence of Pt thickness on magnetization reversal processes in (Pt/Co)3 multilayers with perpendicular anisotropy

We present a detailed study of the magnetization reversal in perpendicularly magnetized (Pt/Co)₃ multilayers with different values of the platinum interlayer thickness t_Pt. To study the magnetization reversal in our samples we combined measurements of relaxation curves with the direct visualization of domain structures. Magnetization reversal was dominated by domain wall propagation for t_Pt=1 nm and by domain nucleation for t_Pt=0.2 nm, while a mixed process was observed for t_Pt=0.8 nm. We interpret our results within the framework of a model of thermally activated reversal where a distribution of activation energy barriers is taken into account. The reversal process was correlated with the energy barrier distribution.     

Role of anisotropy on the domain wall properties of ferromagnetic nanotubes

In this paper we investigate the role of magneto-crystalline anisotropy on the domain wall (DW) properties of tubular magnetic nanostructures. Based on a theoretical model and micromagnetic simulations, we show that either cubic or uniaxial magneto-crystalline anisotropies have some influence on the domain wall properties (wall size, propagation velocity and energy barrier) and then on the overall magnetization reversal mechanism. Besides the characterization of the transverse and vortex domain wall sizes for different anisotropies, we predict an anisotropy dependent transition between the occurrence of transverse and vortex domain walls in tubular nanowires. We also discuss the dynamics of the vortex DW propagation gradually increasing the uniaxial anisotropy constant and we found that the average velocity is considerably reduced. Our results show that different anisotropies can be considered in real samples in order to manipulate the domain wall behavior and the magnetization reversal process.     

Two-scale micromechanics-based probabilistic modeling of domain switching in ferroelectric ceramics

A two-scale micromechanics model is developed in this paper to analyze domain switching in ferroelectric ceramics, using a probabilistic domain switching criterion based on energetic analysis. The microstructure of ferroelectric ceramics at two distinct length scales, domains and grains, has been carefully analyzed. The interaction at domain level is accounted for by energy minimization theory, while the fluctuation at grain level is analyzed using ellipsoidal two-point correlation function. The model has been implemented by Monte Carlo method, and applied to simulate the electric poling and mechanical depoling of Pb(Zr_xTi_1-x)O₃ (PZT) ceramics across morphotropic phase boundary (MPB). The drastically different switching characteristics of PZT ceramics across MPB has been captured, and good agreement with experiments has been observed. The effects of the transformation strains and spontaneous polarizations are highlighted, confirming the proposition of Li et al. [2005. Domain switching in polycrystalline ferroelectric ceramics. Nature Materials 4, 776–781] that the strain compatibility plays a dominant role in domain switching in ferroelectric ceramics.     

Thermodynamic driving force in ferroelectric crystals with a rank-2 laminated domain pattern, and a study of enhanced electrostriction

The thermodynamic driving force for domain growth in a rank-2 laminated ferroelectric crystal is derived in this article, and we used it, together with a homogenization theory, to study the issue of enhanced electrostrictive actuation recently reported by Burcsu et al. [2004. Large electrostrictive actuation of barium titanate single crystals. J. Mech. Phys. Solids 52, 823-846]. We derived this force from the reduction of Gibbs free energy with respect to the increase of domain concentration. It is shown that both the free energy and the thermodynamic force consist of three parts: the first arises from the difference in M₀ and M₁, the linear electromechanical compliances of the parent and product domains, respectively, at a given level of applied stress and electric field, the second stems from the electromechanical work associated with the change of spontaneous strain and spontaneous polarization during domain switch, and the third from the internal energy due to the distribution of polarizations strain and electric polarization inside the crystal. We prove that the first term is substantially lower than the second one, and the third one is identically zero with compatible domain pattern. The second one is, however, not exactly equal to the commonly written sum of the products of stress with strain, and electric field with polarization during switch, unless both domains have identical moduli in the common global axes. We also show that, with compatible domain patterns and when M₁=M₀, this driving force is identical to Eshelby's driving force acting on a flat interface due to the jump of energy-momentum tensor. Applications of the theory to a BaTiO₃ crystal subjected to a fixed axial compression and decreasing electric field from the [0 0 1] state reveal that the crystal undergoes a three-stage switching process: (i) the 0→90° switch to form a rank-1 laminate, (ii) the 0→180° switch inside the 0° domain to form a laminate I with a concurrent 90°→−90° switch inside the 90° domain to form laminate II, creating a rank-2-laminated domain pattern, and (iii) finally the 90→180° switch. It is the exchange of stability between the 0, 90°, and 180° domains under compression and electric field that is the origin of the enhanced actuation. We illustrate these intrinsic features by showing the evolution of these domains, and demonstrate how the reported large actuation strain can be attained with a rank-2 laminate.     

Aerodynamic and aeroacoustic analysis of a pulsating internal flow by a multidomain weak collocation spectral method

A numerical methodology is presented for the coupled aerodynamic and aeroacoustic analysis of time dependent laminar viscous flows in general two-dimensional geometries. The overall procedure is constituted firstly by the solution of the incompressible Navier-Stokes equations and secondly by the solution of a linear evolution equation of second order in space and time which originates from Lighthill's acoustic analogy. A semi-implicit projection method is utilized for the time integration of the incompressible Navier-Stokes system, while a choice between a second order implicit Newmark scheme and a fourth order explicit Runge-Kutta-Nyström method is offered for the temporal discretization of the wave equation. The multidomain weak Legendre collocation spectral method on quadrilateral subdomain topologies is employed for the spatial approximation of both the fluid dynamic and the acoustic problems. A specific pulsating internal flow inside a plane constricted channel is selected as a representative application for the assessment of the capabilities of the proposed discrete algorithm. Numerous results are presented and discussed, so as to thoroughly demonstrate the behavior of the numerical procedure.     

Magnetic behavior and role of the antiphase boundaries in Fe3O4 epitaxial films sputtered on MgO (001)

Magnetite Fe₃O₄ films were grown on single crystal MgO (001) substrates using facing target sputtering technique. Conversion Electron M?ssbauer Spectroscopy and magneto optical polar Kerr spectra have confirmed the stoichiometric repartition of Fe cations corresponding to the inverse spinel structure and the electronic structure characteristic of bulk Fe₃O₄. Hysteresis loops carried out at room temperature show that, in a 1 T applied magnetic field, only 60% of the saturation magnetization is detected. This behavior is discussed in correlation to the antiphase boundaries (APBs) observed by electron microscopy. Magnetic force microscopy studies show that magnetic domains are larger than the mean distance between APBs. Received 2 July 2001