Significant Residue Features Revealed By Eigenvalue Decomposition Analysis Of Blosum Matrices

Here we attempt to characterize protein evolution by residue features which dominate residue substitution in homologous proteins. Evolutionary information contained in residue substitution matrix is abstracted with the method of eigenvalue decomposition. Top eigenvectors in the eigenvalue spectrums are analyzed as function of the level of similarity, i.e. sequence identity (SI) between homologous proteins. It is found that hydrophobicity and volume are two significant residue features conserved in protein evolution. There is a transition point at SI approximate to 45%. Residue hydrophobicity is a feature governing residue substitution as SI >= 45%. Whereas below this SI level, residue volume is a dominant feature. (C) 2007 Elsevier B.V. All rights reserved.

RESONANT TUNNELING, EIGENVALUE AND ENERGY-BAND CALCULATION FOR POTENTIAL AND PERIODIC POTENTIAL STRUCTURES

Recursion formulae for the reflection and the transmission probability amplitudes and the eigenvalue equation for multistep potential structures are derived. Using the recursion relations, a dispersion equation for periodic potential structures is presented. Some numerical results for the transmission probability of a double barrier structure with scattering centers, the lifetime of the quasi-bound state in a single quantum well with an applied field, and the miniband of a periodic potential structure are presented.

Influence Of Rayleigh Effect Combined With Marangoni Effect On The Onset Of Convection In A Liquid Layer Overlying A Porous Layer

The coupling mechanism of Rayleigh effect and Marangoni effect in a liquid-porous system is investigated using a linear stability analysis. The eigenvalue problem is solved by means of a Chebyshev tau method. Results indicate that there are three coupling modes between the Rayleigh effect and the Marangoni effect for different depth ratios. (C) 2008 Elsevier Ltd. All rights reserved.

Instability Of Plane Poiseuille Flow In A Fluid-Porous System

The instability of Poiseuille flow in a fluid-porous system is investigated. The system consists of a fluid layer overlying porous media and is subjected to a horizontal plane Poiseuille flow. We use Brinkman's model instead of Darcy's law to describe the porous layer. The eigenvalue problem is solved by means of a Chebyshev collocation method. We study the influence of the depth ratio (d) over cap and the Darcy number delta on the instability of the system. We compare systematically the instability of Brinkman's model with the results of Darcy's model. Our results show that no satisfactory agreement between Brinkman's model and Darcy's model is obtained for the instability of a fluid-porous system. We also examine the instability of Darcy's model. A particular comparison with early work is made. We find that a multivalued region may present in the (k, Re) plane, which was neglected in previous work. Here k is the dimensionless wavenumber and Re is the Reynolds number. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.3000643]

Semi-weight function method on computation of stress intensity factors in dissimilar materials

Semi-weight function method is developed to solve the plane problem of two bonded dissimilar materials containing a crack along the bond. From equilibrium equation, stress and strain relationship, conditions of continuity across interface and free crack surface, the stress and displacement fields were obtained. The eigenvalue of these fields is lambda. Semi-weight functions were obtained as virtual displacement and stress fields with eigenvalue-lambda. Integral expression of fracture parameters, K-I and K-II, were obtained from reciprocal work theorem with semi-weight functions and approximate displacement and stress values on any integral path around crack tip. The calculation results of applications show that the semi-weight function method is a simple, convenient and high precision calculation method.

Stress intensity factors calculation in anti-plane fracture problem by orthogonal integral extraction method based on femol

For an anti-plane problem, the differential operator is self-adjoint and the corresponding eigenfunctions belong to the Hilbert space. The orthogonal property between eigenfunctions (or between the derivatives of eigenfunctions) of anti-plane problem is exploited. We developed for the first time two sets of radius-independent orthogonal integrals for extraction of stress intensity factors (SIFs), so any order SIF can be extracted based on a certain known solution of displacement (an analytic result or a numerical result). Many numerical examples based on the finite element method of lines (FEMOL) show that the present method is very powerful and efficient.

Note on the instability of capillary jet with thermocapillarity

In this paper, we examine a new basic state of long axisymmetric liquid zone, subjected to axial temperature gradients which induce steady viscous flow driven by thermocapillarity. Axial velocity 1/4S-1/2R(B) of liquid zone connects pulling velocity of single crystal. The stability of liquid zone with pulling velocity 1/4S-1/2R(B) to small axisymmetric disturbance is examined The eigenvalue problems on the stability are derived. A special case (eta = 0) is discussed.

The thermal and mechanical structure of a two-dimensional plume in the earths mantle

On the condition that the distribution of velocity and temperature at the mid-plane of a mantle plume has been obtained (pages 213–218, this issue), the problem of determining the lateral structure of the plume at a given depth is reduced to solving an eigenvalue problem of a set of ordinary differential equations with five unknown functions, with an eigenvalue being related to the thermal thickness of the plume at this depth. The lateral profiles of upward velocity, temperature and viscosity in the plume and the thickness of the plume at various depths are calculated for two sets of Newtonian rheological parameters. The calculations show that the precondition for the existence of the plume, δT/L 1 (L = the height of the plume, δT = lateral distance from the mid-plane), can be satisfied, except for the starting region of the plume or near the base of the lithosphere. At the lateral distance, δT, the upward velocity decreases to 0.1 – 50% of its maximum value at different depths. It is believed that this model may provide an approach for a quantitative description of the detailed structure of a mantle plume.

Instabilities of a liquid film flowing down an inclined porous plane

The problem of a film flowing down an inclined porous layer is considered. The fully developed basic flow is driven by gravitation. A careful linear instability analysis is carried out. We use Darcy's law to describe the porous layer and solve the coupling equations of the fluid and the porous medium rather than the decoupled equations of the one-sided model used in previous works. The eigenvalue problem is solved by means of a Chebyshev collocation method. We compare the instability of the two-sided model with the results of the one-sided model. The result reveals a porous mode instability which is completely neglected in previous works. For a falling film on an inclined porous plane there are three instability modes, i.e., the surface mode, the shear mode, and the porous mode. We also study the influences of the depth ratio d, the Darcy number delta, and the Beavers-Joseph coefficient alpha(BJ) on the instability of the system.

Some new bounds on eigenvalues of the Hadamard product and the Fan product of matrices

Let A and B be nonsingular M-matrices. A lower bound on the minimum eigenvalue q(B circle A(-1)) for the Hadamard product of A(-1) and B, and a lower bound on the minimum eigenvalue q(A star B) for the Fan product of A and B are given. In addition, an upper bound on the spectral radius rho(A circle B) of nonnegative matrices A and B is also obtained. These bounds improve several existing results in some cases and the estimating formulas are easier to calculate for they are only depending on the entries of matrices A and B. (C) 2009 Elsevier Inc. All rights reserved.

Optical analysis of AlGaInP laser diodes with real refractive index guided self-aligned structure

Optical modes of AlGaInP laser diodes with real refractive index guided self-aligned (RISA) structure were analyzed theoretically on the basis of two-dimension semivectorial finite-difference methods (SV-FDMs) and the computed simulation results were presented. The eigenvalue and eigenfunction of this two-dimension waveguide were obtained and the dependence of the confinement factor and beam divergence angles in the direction of parallel and perpendicular to the pn junction on the structure parameters such as the number of quantum wells, the Al composition of the cladding layers, the ridge width, the waveguide thickness and the residual thickness of the upper P-cladding layer were investigated. The results can provide optimized structure parameters and help us design and fabricate high performance AlGaInP laser diodes with a low beam aspect ratio required for optical storage applications.

Eigenmode confinement in semiconductor microcavity lasers with an equilateral triangle resonator

We analyze the mode behaviors for semiconductor lasers with an equilateral triangle resonator by deriving the mode field distribution and the eigenvalue equation. The eigenvalue equation shows that the longitudinal mode wavelength interval is equivalent to that of a Fabry-Perot cavity with the cavity length of 1.5a, where a is the side length of the equilateral triangle resonator. The transverse waveguiding is equivalent to as a strip waveguide with the width of root 3a/ 2, and the number of transverse modes supported by the resonator is limited by the total reflection condition on the sides of the equilateral triangle. Semiconductor microcavity laser with an equilateral triangle resonator is suitable to realize single mode operation, and the mode wavelength can be adjusted by changing the side length.

Study on tapered crossed subwavelength gratings by Fourier modal method

Fourier modal method incorporating staircase approximation is used to study tapered crossed subwavelength gratings in this paper. Three intuitive formulations of eigenvalue functions originating from the prototype are presented, and their convergences are compared through numerical calculation. One of them is found to be suitable in modeling the diffraction efficiency of the circular tapered crossed subwavelength gratings without high absorption, and staircase approximation is further proven valid for non-highly-absorption tapered gratings. This approach is used to simulate the "moth-eye" antireflection surface on silicon, and the numerical result agrees well with the experimental one.

Non-modal instabilities of two-dimensional disturbances in plane Couette flow of a power-law fluid

Instabilities of fluid flows have traditionally been investigated by normal mode analysis, i.e. by linearizing the equations of flow and testing for unstable eigenvalues of the linearized problem. However, the results of eigenvalue analysis agree poorly in many cases with experiments, especially for shear flows. In this paper we study the instabilities of two-dimensional Couette flow of a polymeric fluid in the framework of non-modal stability theory rather than normal mode analysis. A power-law model is used to describe the polymeric liquid. We focus on the response to external excitations and initial conditions by examining the pseudospectra structures and the transient energy growths. For both Newtonian and non-Newtonian flows, the results show that there can be a rather large transient growth even though the linear operator of Couette flow has no unstable eigenvalue. The effects of non-Newtonian viscosity on the transient behaviors are examined in this study. The results show that the "shear-thinning/shear-thickening" effect increases/decreases the amplitude of responses to external excitations and initial conditions. (C) 2010 Elsevier B.V. All rights reserved.

Instabilities and transient behaviors of a liquid film flowing down a porous inclined plane

The nonmodal linear stability of a falling film over a porous inclined plane has been investigated. The base flow is driven by gravity. We use Darcy's law to describe the flow in the porous medium. A simplified one-sided model is used to describe the fluid flow. In this model, the influence of the porous layer on the flow in the film can be identified by a parameter beta. The instabilities of a falling film have traditionally been investigated by linearizing the governing equations and testing for unstable eigenvalues of the linearized problem. However, the results of eigenvalue analysis agree poorly in many cases with experiments, especially for shear flows. In the present paper, we have studied the linear stability of three-dimensional disturbances using the nonmodal stability theory. Particular attentions are paid to the transient behavior rather than the long time behavior of eigenmodes predicted by traditional normal mode analysis. The transient behaviors of the response to external excitations and the response to initial conditions are studied by examining the pseudospectral structures and the energy growth function G(t) Before we study the nonmodal stability of the system, we extend the results of long-wave analysis in previous works by examining the linear stabilities for streamwise and spanwise disturbances. Results show that the critical conditions of both the surface mode and the shear mode instabilities are dependent on beta for streamwise disturbances. However, the spanwise disturbances have no unstable eigenvalue. 2010 American Institute of Physics. [doi:10.1063/1.3455503]