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.

MILU-CG method and the numerical study on the flow around a rotating circular cylinder

A hybrid finite difference method and vortex method (HDV), which is based on domain decomposition and proposed by the authors (1992), is improved by using a modified incomplete LU decomposition conjugate gradient method (MILU-CG), and a high order implicit difference algorithm. The flow around a rotating circular cylinder at Reynolds number R-e = 1000, 200 and the angular to rectilinear speed ratio alpha is an element of (0.5, 3.25) is studied numerically. The long-time full developed features about the variations of the vortex patterns in the wake, and drag, lift forces on the cylinder are given. The calculated streamline contours agreed well with the experimental visualized flow pictures. The existence of critical states and the vortex patterns at the states are given for the first time. The maximum lift to drag force ratio can be obtained nearby the critical states.

Proper orthogonal decomposition of oscillatory Marangoni flow in half-zone liquid bridges of low-Pr fluids

Proper orthogonal decomposition (POD) using method of snapshots was performed on three different types of oscillatory Marangoni flows in half-zone liquid bridges of low-Pr fluid (Pr = 0.01). For each oscillation type, a series of characteristic modes (eigenfunctions) have been extracted from the velocity and temperature disturbances, and the POD provided spatial structures of the eigenfunctions, their oscillation frequencies, amplitudes, and phase shifts between them. The present analyses revealed the common features of the characteristic modes for different oscillation modes: four major velocity eigenfunctions captured more than 99% of the velocity fluctuation energy form two pairs, one of which is the most energetic. Different from the velocity disturbance, one of the major temperature eigenfunctions makes the dominant contribution to the temperature fluctuation energy. On the other hand, within the most energetic velocity eigenfuction pair, the two eigenfunctions have similar spatial structures and were tightly coupled to oscillate with the same frequency, and it was determined that the spatial structures and phase shifts of the eigenfunctions produced the different oscillatory disturbances. The interaction of other major modes only enriches the secondary spatio-temporal structures of the oscillatory disturbances. Moreover, the present analyses imply that the oscillatory disturbance, which is hydrodynamic in nature, primarily originates from the interior of the liquid bridge. (C) 2007 Elsevier B.V. All rights reserved.