A new method for assigning common spot boundaries for multiple gels in two-dimensional gel electrophoresis

The benefits of defining common spot boundaries when several gels from 2-DE are compared and analyzed have lately been stressed by both commercial software producers and users of this software. Though the importance of common spot boundaries is clearly stated, few reports exist that target this issue explicitly. In this study a method for defining common spots boundaries is developed, called the spot density method. The method consists of the following steps: segmentation and spot identification on each individual gel, transferring the spot-center coordinates for all gels onto a single new gel, collecting spot centers clustered together in the new gel and finally assigning pixels and new spot boundaries based on the spots in each cluster. The method is compared to a synthetic gel approach, and validated by visual inspection of three representative areas in the gels. The gel images need to be aligned prior to segmentation and spot identification, but the method can be used regardless of the choice of segmentation procedure. This makes the method an easy extension to existing methods for spot identification and matching. Conclusions based on the visual inspection are that the spot density method identifies partly overlapping spots and low-intensity spots better than the synthetic gel approach.     

The microstructure of hydrogen- and deuterium-doped nanocrystalline palladium studied by small-angle neutron scattering

By means of small-angle neutron scattering the microstructure of two nanocrystalline Pd samples (prepared by inert gas condensation) has been studied at room temperature in a Q-range from [0pt] to [0pt] . An additional subsequent doping of the two samples with H as well as with D (concentrations < 4 at%) caused contrast variations that provided more detailed structural information. The measured scattering intensity was modeled by a Porod contribution from large heterogenities (e.g. pores) and a contribution from spherical grains with a log-normal distribution of their radii. To account for the presence of grain boundaries, the grains were considered to be surrounded by a shell with a reduced Pd density and a thickness half as large as the thickness of the grain boundaries. For the above model, the data of the H-doped, D-doped and undoped sample were simultaneously fitted with one single set of adjustable parameters. The fits yielded for the two samples volume-weighted mean grain radii of 10 nm and 13 nm. The values for the grain boundary thickness lie between 0.2 and 0.8 nm. Almost all of the H- and D-atoms are, at low hydrogen concentrations, located in the grain boundaries. Received 1 May 2000     

Spin-ordering in S = 1 anisotropic Heisenberg models with nondiagonal spin exchange

The properties of S = 1 anisotropic Heisenberg models with nondiagonal exchange between axial and planar spin components are investigated using Monte Carlo techniques. The quantum nature is taken into account in a semi-classical approximation. The ordering of the spins when applying an external field with axial and planar components is discussed. It is argued that the quantum nature of the spins and the nondiagonal exchange may explain the peculiar shape of the magnetic specific heat of FeBr₂ as well as the weakly first-order phase transition observed in the same compound when a tilted field is applied. Received 24 January 1999     

正交曲线坐标系下紊流数学模型的曲率修正

考虑弯曲边界曲率效应对水流水力特性的影响,建立了正交曲线坐标系下的素流数学模型。通过计算实例说明,该数学模型能够很好地帷有复杂边界的流线弯曲水流的水力特性。     

Anisotropy of Interfaces in an Ordered HCP Binary Alloy

A multiple-order-parameter mean-field theory of ordering on a binary hexagonal- close-packed (HCP) crystal structure is developed, and adapted to provide a continuum formulation that incorporates the underlying symmetries of the HCP crystal in both the bulk and gradient energy terms of the free energy. The work is an extension of the previous treatment by Braun et al. [Phil. Trans. Roy. Soc. Lond. A 355:1787 (1997)] of order–disorder transitions on a face-centered-cubic crystal (FCC) lattice. The theory is used to compute the orientation dependence of the structure and energy of interphase and antiphase boundaries in ordering to the Cd₃Mg and CdMg structures, which are the HCP analogs of Cu₃Au and CuAu structures in FCC. As in the corresponding FCC case, the multiple order parameters do not form a vector. Anisotropy is a natural consequence of the underlying crystal symmetries and the multiple-order-parameter continuum formation presented here. The isotropy transverse to the sixfold axis expected for a scalar order parameter is not found.     

钢中小角度晶界区的电子结构及掺杂效应

根据位错的弹性理论,建立了9Ni钢中53°掺杂小角度晶界的原子模型,利用Recursion方法,计算了杂质在53°小角度晶界典型环境中的能量和电子结构,由此得出,钢中小角度晶界的强度敏感地依赖于隔离杂质的类型,S,P杂质使晶粒间结合减弱,从而导致晶界疏松 ;相反,B,C,N则会使晶界间的结合加强.在所有的杂质中,B显示出独特的性质,在钢中B 不仅能增强晶界的结合,而且由于占位竞争效应会使其他杂质远离晶界,具有净化晶界的作用. 关键词： 小角晶界 杂质 占位竞争 晶界隔离     

Considerations on the spring analogy

This paper presents an investigation on the spring analogy. The spring analogy serves for deformation in a moving boundary problem. First, two different kinds of springs are discussed: the vertex springs and the segment springs. The vertex spring analogy is originally used for smoothing a mesh after mesh generation or refinement. The segment spring analogy is used for deformation of the mesh in a moving boundary problem. The difference between the two methods lies in the equilibrium length of the springs. By means of an analogy to molecular theory, the two theories are generalized into a single theory that covers both. The usual choice of the stiffness of the spring is clarified by the mathematical analysis of a representative one‐dimensional configuration. The analysis shows that node collision is prevented when the stiffness is chosen as the inverse of the segment length. The observed similarity between elliptic grid generation and the spring analogy is also investigated. This investigation shows that both methods update the grid point position by a weighted average of the surrounding points in an iterative manner. The weighting functions enforce regularity of the mesh. Based on these considerations, several improvements on the spring analogy are developed. The principle of Saint Venant is circumvented by a boundary correction. The prevention of inversion of triangular elements is improved by semi‐torsional springs. The numerical results show the superiority of the segment spring analogy over the vertex one for a small rotation of an NACA0012 mesh. The boundary correction allows for large deformation of the mesh, where the standard spring analogy fails. The final test is performed on a Navier–Stokes mesh. This mesh contains high aspect ratio mesh cells near the boundary. Large deformation of this mesh shows that the semi‐torsional spring improvement is imperative to retain the validity of this mesh. Copyright © 2000 John Wiley & Sons, Ltd.     

Using fractal to solve the multiple minima problem in molecular mechanics calculation

This article presents an approach using fractal to solve the multiple minima problem. We use the Newton–Raphson method of the MM3 molecular mechanics program to scan the conformational spaces of a model molecule and a real molecule. The results show each energy minimum, maximum point, and saddle point has a basin of initial points converging to it in conformational spaces. Points converging to different extrema are mixed, and form fractal structures around basin boundaries. Singular points seem to involve in the formation of fractal. When searching within a small region of fractal basin boundaries, the self‐similarity of fractal makes it possible to find all energy minima, maxima, and saddle points from which global minimum may be extracted. Compared with other methods, this approach is efficient, accurate, conceptually simple, and easy to implement. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1101–1108, 2000