An Amino Acid Substitution Matrix for Protein Conformation Identification

Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived from limited data of structure alignment. Using databases PDB_SELECT and DSSP, we create a database of sequence-conformation blocks which explicitly represent sequence-structure relationship. Members in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.

Identification of Nonlinear Systems Through Time-Frequency Filtering Technique

In the previous paper, a class of nonlinear system is mapped to a so-called skeleton linear model (SLM) based on the joint time-frequency analysis method. Behavior of the nonlinear system may be indicated quantitatively by the variance of the coefficients of SLM versus its response. Using this model we propose an identification method for nonlinear systems based on nonstationary vibration data in this paper. The key technique in the identification procedure is a time-frequency filtering method by which solution of the SLM is extracted from the response data of the corresponding nonlinear system. Two time-frequency filtering methods are discussed here. One is based on the quadratic time-frequency distribution and its inverse transform, the other is based on the quadratic time-frequency distribution and the wavelet transform. Both numerical examples and an experimental application are given to illustrate the validity of the technique.

Continuous spectrum growth and modal instability in swirling duct flow

We present results on the stability of compressible inviscid swirling flows in an annular duct. Such flows are present in aeroengines, for example in the by-pass duct, and there are also similar flows in many aeroacoustic or aeronautical applications. The linearised Euler equations have a ('critical layer') singularity associated with pure convection of the unsteady disturbance by the mean flow, and we focus our attention on this region of the spectrum. By considering the critical layer singularity, we identify the continuous spectrum of the problem and describe how it contributes to the unsteady field. We find a very generic family of instability modes near to the continuous spectrum, whose eigenvalue wavenumbers form an infinite set and accumulate to a point in the complex plane. We study this accumulation process asymptotically, and find conditions on the flow to support such instabilities. It is also found that the continuous spectrum can cause a new type of instability, leading to algebraic growth with an exponent determined by the mean flow, given in the analysis. The exponent of algebraic growth can be arbitrarily large. Numerical demonstrations of the continuous spectrum instability, and also the modal instabilities are presented.

Modal scattering at an impedance transition in a lined flow duct

An explicit Wiener-Hopf solution is derived to describe the scattering of duct modes at a hard-soft wall impedance transition in a circular duct with uniform mean flow. Specifically, we have a circular duct r = 1, - ∞ < x < ∞ with mean flow Mach number M > 0 and a hard wall along x < 0 and a wall of impedance Z along x > 0. A minimum edge condition at x = 0 requires a continuous wall streamline r = 1 + h(x, t), no more singular than h = Ο(x1/2) for x ↓ 0. A mode, incident from x < 0, scatters at x = 0 into a series of reflected modes and a series of transmitted modes. Of particular interest is the role of a possible instability along the lined wall in combination with the edge singularity. If one of the "upstream" running modes is to be interpreted as a downstream-running instability, we have an extra degree of freedom in the Wiener-Hopf analysis that can be resolved by application of some form of Kutta condition at x = 0, for example a more stringent edge condition where h = Ο(x3/2) at the downstream side. The question of the instability requires an investigation of the modes in the complex frequency plane and therefore depends on the chosen impedance model, since Z = Z (ω) is essentially frequency dependent. The usual causality condition by Briggs and Bers appears to be not applicable here because it requires a temporal growth rate bounded for all real axial wave numbers. The alternative Crighton-Leppington criterion, however, is applicable and confirms that the suspected mode is usually unstable. In general, the effect of this Kutta condition is significant, but it is particularly large for the plane wave at low frequencies and should therefore be easily measurable. For ω → 0, the modulus fends to |R001| → (1 + M)/(1 -M) without and to 1 with Kutta condition, while the end correction tends to ∞ without and to a finite value with Kutta condition. This is exactly the same behaviour as found for reflection at a pipe exit with flow, irrespective if this is uniform or jet flow.

Some advances in study of crack identification problems

In the present paper, the crack identification problems are investigated. This kind of problems belong to the scope of inverse problems and are usually ill-posed on their solutions. The paper includes two parts: (1) Based on the dynamic BIEM and the optimization method and using the measured dynamic information on outer boundary, the identification of crack in a finite domain is investigated and a method for choosing the high sensitive frequency region is proposed successfully to improve the precision. (2) Based on 3-D static BIEM and hypersingular integral equation theory, the penny crack identification in a finite body is reduced to an optimization problem. The investigation gives us some initial understanding on the 3-D inverse problems.