Metric representation of DNA sequences

A metric representation of DNA sequences is borrowed from symbolic dynamics. In view of this method, the pattern seen in the chaos game representation of DNA sequences is explained as the suppression of certain nucleotide strings in the DNA sequences. Frequencies of short nucleotide strings and suppression of the shortest ones in the DNA sequences can be determined by using the metric representation.

Recurrence plot analysis of DNA sequences

Recurrence plot technique of DNA sequences is established on metric representation and employed to analyze correlation structure of nucleotide strings. It is found that, in the transference of nucleotide strings, a human DNA fragment has a major correlation distance, but a yeast chromosome's correlation distance has a constant increasing. (C) 2004 Elsevier B.V All rights reserved.

Transient effect on ideally plastic stationary crack-tip fields

This paper analyses the transient effect on ideally plastic stationary crack-tip fields under mode I plane strain conditions, when the inertial forces are not negligible. It is shown that the governing equation for such a problem can be expressed in formal simplicity when referred to a system of moving curvilinear coordinates, which is a generalization of the system defined by the slip-line field in quasi-static plasticity. A perturbation method of solving the equations is described and illustrated by application to problems of ideally plastic stationary crack-tip fields when the inertia forces are not negligible.

Transient effect on ideally plastic stationary crack-tip fields

This paper analyses the transient effect on ideally plastic stationary crack tip fields under mode I plane strain conditions, when the inertial forces are not negligible. It is shown that the governing equation for such a problem can be expressed in formal simplicity when referred to a system of moving curvilinear coordinates, which is a generalization of the system defined by the slip-line field in quasi-static plasticity. A perturbation method of solving the equations is described and illustrated by application to problems of ideally plastic stationary crack tip fields when the inertial forces are not negligible.

A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Scale-similarity model for Lagrangian velocity correlations in isotropic and stationary turbulence

A scale-similarity model for Lagrangian two-point, two-time velocity correlations LVCs in isotropic turbulence is developed from the Kolmogorov similarity hypothesis. It is a second approximation to the isocontours of LVCs, while the Smith-Hay model is only a first approximation. This model expresses the LVC by its space correlation and a dispersion velocity. We derive the analytical expression for the dispersion velocity from the Navier-Stokes equations using the quasinormality assumption. The dispersion velocity is dependent on enstrophy spectra and shown to be smaller than the sweeping velocity for the Eulerian velocity correlation. Therefore, the Lagrangian decorrelation process is slower than the Eulerian decorrelation process. The data from direct numerical simulation of isotropic turbulence support the scale-similarity model: the LVCs for different space separations collapse into a universal form when plotted against the separation axis defined by the model.