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.

Eigenvalue problems associated with Korn's inequalities in the theory of elasticity

Interest in the possible applications of a priori inequalities in linear elasticity theory motivated the present investigation. Korn's inequality under various side conditions is considered, with emphasis on the Korn's constant. In the "second case" of Korn's inequality, a variational approach leads to an eigenvalue problem; it is shown that, for simply-connected two-dimensional regions, the problem of determining the spectrum of this eigenvalue problem is equivalent to finding the values of Poisson's ratio for which the displacement boundary-value problem of linear homogeneous isotropic elastostatics has a non-unique solution.

Previous work on the uniqueness and non-uniqueness issue for the latter problem is examined and the results applied to the spectrum of the Korn eigenvalue problem. In this way, further information on the Korn constant for general regions is obtained.

A generalization of the "main case" of Korn's inequality is introduced and the associated eigenvalue problem is a gain related to the displacement boundary-value problem of linear elastostatics in two dimensions.

Fast numerical methods for mixed, singular Helmholtz boundary value problems and Laplace eigenvalue problems - with applications to antenna design, sloshing, electromagnetic scattering and spectral geometry

This thesis presents a novel class of algorithms for the solution of scattering and eigenvalue problems on general two-dimensional domains under a variety of boundary conditions, including non-smooth domains and certain "Zaremba" boundary conditions - for which Dirichlet and Neumann conditions are specified on various portions of the domain boundary. The theoretical basis of the methods for the Zaremba problems on smooth domains concern detailed information, which is put forth for the first time in this thesis, about the singularity structure of solutions of the Laplace operator under boundary conditions of Zaremba type. The new methods, which are based on use of Green functions and integral equations, incorporate a number of algorithmic innovations, including a fast and robust eigenvalue-search algorithm, use of the Fourier Continuation method for regularization of all smooth-domain Zaremba singularities, and newly derived quadrature rules which give rise to high-order convergence even around singular points for the Zaremba problem. The resulting algorithms enjoy high-order convergence, and they can tackle a variety of elliptic problems under general boundary conditions, including, for example, eigenvalue problems, scattering problems, and, in particular, eigenfunction expansion for time-domain problems in non-separable physical domains with mixed boundary conditions.

Shock transmission and eigenvalue veering within a coupled system.

The operation of dynamical systems in harsh environments requires continuous monitoring. Internal sensors may be used to monitor the conditions in real time. A typical example is the sensor and electronic components used in space structures which, especially during launch, are subject to huge g force. The paper will present an experimental and theoretical study on a simplified model used to analyze the possible cause of high acceleration on the enclosed sensors and equipments due to impulsive loading. The model system consists of two beams coupled using compliant connections. An impulse hammer excites one beam, and vibrations are transmitted to the indirectly driven beam. A theoretical model is developed using a Rayleigh-Ritz approach and validated using experimental results in both the frequency and time domains. Monto Carlo simulation was done with random masses positioned on the indirectly driven beam to determine the worst-case conditions for maximum peak acceleration. Highest acceleration levels were found when mode matching in the two beams led to veering behavior in the coupled modes. The results suggest guidelines for the detailed design of internal components of a structure exposed to shock loading from its environment. [The authors thank Schlumberger Cambridge Research for financial support.].

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.

On the Performance of Eigenvalue-Based Cooperative Spectrum Sensing for Cognitive Radio

In this paper, the distribution of the ratio of extreme eigenvalues of a complex Wishart matrix is studied in order to calculate the exact decision threshold as a function of the desired probability of false alarm for the maximum-minimum eigenvalue (MME) detector. In contrast to the asymptotic analysis reported in the literature, we consider a finite number of cooperative receivers and a finite number of samples and derive the exact decision threshold for the probability of false alarm. The proposed exact formulation is further reduced to the case of two receiver-based cooperative spectrum sensing. In addition, an approximate closed-form formula of the exact threshold is derived in terms of a desired probability of false alarm for a special case having equal number of receive antennas and signal samples. Finally, the derived analytical exact decision thresholds are verified with Monte-Carlo simulations. We show that the probability of detection performance using the proposed exact decision thresholds achieves significant performance gains compared to the performance of the asymptotic decision threshold.

A recursive construction of the regular exceptional graphs with least eigenvalue -2

In spectral graph theory a graph with least eigenvalue 2 is exceptional if it is connected, has least eigenvalue greater than or equal to 2, and it is not a generalized line graph. A ðk; tÞ-regular set S of a graph is a vertex subset, inducing a k-regular subgraph such that every vertex not in S has t neighbors in S. We present a recursive construction of all regular exceptional graphs as successive extensions by regular sets.

Finding the smallest eigenvalue by the inverse Monte Carlo method with refinement

Finding the smallest eigenvalue of a given square matrix A of order n is computationally very intensive problem. The most popular method for this problem is the Inverse Power Method which uses LU-decomposition and forward and backward solving of the factored system at every iteration step. An alternative to this method is the Resolvent Monte Carlo method which uses representation of the resolvent matrix [I -qA](-m) as a series and then performs Monte Carlo iterations (random walks) on the elements of the matrix. This leads to great savings in computations, but the method has many restrictions and a very slow convergence. In this paper we propose a method that includes fast Monte Carlo procedure for finding the inverse matrix, refinement procedure to improve approximation of the inverse if necessary, and Monte Carlo power iterations to compute the smallest eigenvalue. We provide not only theoretical estimations about accuracy and convergence but also results from numerical tests performed on a number of test matrices.