Rapid protein domain assignment from amino acid sequence using predicted secondary structure

The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (±20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed

Modal coupling in linear control systems using robust eigenstructure assignment

Eigenvalue assignment methods are used widely in the design of control and state-estimation systems. The corresponding eigenvectors can be selected to ensure robustness. For specific applications, eigenstructure assignment can also be applied to achieve more general performance criteria. In this paper a new output feedback design approach using robust eigenstructure assignment to achieve prescribed mode input and output coupling is described. A minimisation technique is developed to improve both the mode coupling and the robustness of the system, whilst allowing the precision of the eigenvalue placement to be relaxed. An application to the design of an automatic flight control system is demonstrated.

Robust pole assignment in linear state feedback

Numerical methods are described for determining robust, or well-conditioned, solutions to the problem of pole assignment by state feedback. The solutions obtained are such that the sensitivity of the assigned poles to perturbations in the system and gain matrices is minimized. It is shown that for these solutions, upper bounds on the norm of the feedback matrix and on the transient response are also minimized and a lower bound on the stability margin is maximized. A measure is derived which indicates the optimal conditioning that may be expected for a particular system with a given set of closed-loop poles, and hence the suitability of the given poles for assignment.

Some necessary and sufficient conditions for eigenstructure assignment

Some necessary and sufficient conditions for closed-loop eigenstructure assignment by output feedback in time-invariant linear multivariable control systems are presented. A simple condition on a square matrix necessary and sufficient for it to be the closed-loop plant matrix of a given system with some output feedback is the basis of the paper. Some known results on entire eigenstructure assignment are deduced from this. The concept of an inner inverse of a matrix is employed to obtain a condition concerning the assignment of an eigenstructure consisting of the eigenvalues and a mixture of left and right eigenvectors.

Robust pole assignment in systems subject to structured perturbations

The problem of robust pole assignment by feedback in a linear, multivariable, time-invariant system which is subject to structured perturbations is investigated. A measure of robustness, or sensitivity, of the poles to a given class of perturbations is derived, and a reliable and efficient computational algorithm is presented for constructing a feedback which assigns the prescribed poles and optimizes the robustness measure.

Robust eigenstructure assignment in quadratic matrix polynomials: nonsingular case

Feedback design for a second-order control system leads to an eigenstructure assignment problem for a quadratic matrix polynomial. It is desirable that the feedback controller not only assigns specified eigenvalues to the second-order closed loop system but also that the system is robust, or insensitive to perturbations. We derive here new sensitivity measures, or condition numbers, for the eigenvalues of the quadratic matrix polynomial and define a measure of the robustness of the corresponding system. We then show that the robustness of the quadratic inverse eigenvalue problem can be achieved by solving a generalized linear eigenvalue assignment problem subject to structured perturbations. Numerically reliable methods for solving the structured generalized linear problem are developed that take advantage of the special properties of the system in order to minimize the computational work required. In this part of the work we treat the case where the leading coefficient matrix in the quadratic polynomial is nonsingular, which ensures that the polynomial is regular. In a second part, we will examine the case where the open loop matrix polynomial is not necessarily regular.

Robust pole assignment and optimal stability margins

A robust pole assignment by linear state feedback is achieved in state-space representation by selecting a feedback which minimises the conditioning of the assigned eigenvalues of the closed-loop system. It is shown here that when this conditioning is minimised, a lower bound on the stability margin in the frequency domain is maximised.

Comments, with reply, on "Computational algorithms for pole assignment" by N.K. Nichols

Some points of the paper by N.K. Nichols (see ibid., vol.AC-31, p.643-5, 1986), concerning the robust pole assignment of linear multiinput systems, are clarified. It is stressed that the minimization of the condition number of the closed-loop eigenvector matrix does not necessarily lead to robustness of the pole assignment. It is shown why the computational method, which Nichols claims is robust, is in fact numerically unstable with respect to the determination of the gain matrix. In replying, Nichols presents arguments to support the choice of the conditioning of the closed-loop poles as a measure of robustness and to show that the methods of J Kautsky, N. K. Nichols and P. VanDooren (1985) are stable in the sense that they produce accurate solutions to well-conditioned problems.

Eigenstructure assignment in descriptor systems

Coordinate free conditions are given for pole assignment by feedback in linear descriptor (singular) systems which guarantee closed-loop regularity. These conditions are shown to be both necessary and sufficient for assignment of the maximum possible number of finite poles. Transformation to special coordinates are not used and the results provide a robust algorithm for the computation of the required feedback.

On computational algorithms for pole assignment

A number of computationally reliable direct methods for pole assignment by feedback have recently been developed. These direct procedures do not necessarily produce robust solutions to the problem, however, in the sense that the assigned poles are insensitive to perturbalions in the closed-loop system. This difficulty is illustrated here with results from a recent algorithm presented in this TRANSACTIONS and its causes are examined. A measure of robustness is described, and techniques for testing and improving robustness are indicated.

Bifurcation Analysis of Eigenstructure Assignment Control in a Simple Nonlinear Aircraft Model

Aircraft systems are highly nonlinear and time varying. High-performance aircraft at high angles of incidence experience undesired coupling of the lateral and longitudinal variables, resulting in departure from normal controlled � ight. The construction of a robust closed-loop control that extends the stable and decoupled � ight envelope as far as possible is pursued. For the study of these systems, nonlinear analysis methods are needed. Previously, bifurcation techniques have been used mainly to analyze open-loop nonlinear aircraft models and to investigate control effects on dynamic behavior. Linear feedback control designs constructed by eigenstructure assignment methods at a � xed � ight condition are investigated for a simple nonlinear aircraft model. Bifurcation analysis, in conjunction with linear control design methods, is shown to aid control law design for the nonlinear system.