Mode matches and their locations in the hydrophobic free energy sequences of peptide ligands and their receptor eigenfunctions

Patterns in sequences of amino acid hydrophobic free energies predict secondary structures in proteins. In protein folding, matches in hydrophobic free energy statistical wavelengths appear to contribute to selective aggregation of secondary structures in “hydrophobic zippers.” In a similar setting, the use of Fourier analysis to characterize the dominant statistical wavelengths of peptide ligands’ and receptor proteins’ hydrophobic modes to predict such matches has been limited by the aliasing and end effects of short peptide lengths, as well as the broad-band, mode multiplicity of many of their frequency (power) spectra. In addition, the sequence locations of the matching modes are lost in this transformation. We make new use of three techniques to address these difficulties: (i) eigenfunction construction from the linear decomposition of the lagged covariance matrices of the ligands and receptors as hydrophobic free energy sequences; (ii) maximum entropy, complex poles power spectra, which select the dominant modes of the hydrophobic free energy sequences or their eigenfunctions; and (iii) discrete, best bases, trigonometric wavelet transformations, which confirm the dominant spectral frequencies of the eigenfunctions and locate them as (absolute valued) moduli in the peptide or receptor sequence. The leading eigenfunction of the covariance matrix of a transmembrane receptor sequence locates the same transmembrane segments seen in n-block-averaged hydropathy plots while leaving the remaining hydrophobic modes unsmoothed and available for further analyses as secondary eigenfunctions. In these receptor eigenfunctions, we find a set of statistical wavelength matches between peptide ligands and their G-protein and tyrosine kinase coupled receptors, ranging across examples from 13.10 amino acids in acid fibroblast growth factor to 2.18 residues in corticotropin releasing factor. We find that the wavelet-located receptor modes in the extracellular loops are compatible with studies of receptor chimeric exchanges and point mutations. A nonbinding corticotropin-releasing factor receptor mutant is shown to have lost the signatory mode common to the normal receptor and its ligand. Hydrophobic free energy eigenfunctions and their transformations offer new quantitative physical homologies in database searches for peptide-receptor matches.

A spectroscopy study of nearby late-type stars, possible members of stellar kinematic groups

Context. Nearby late-type stars are excellent targets for seeking young objects in stellar associations and moving groups. The origin of these structures is still misunderstood, and lists of moving group members often change with time and also from author to author. Most members of these groups have been identified by means of kinematic criteria, leading to an important contamination of previous lists by old field stars. Aims. We attempt to identify unambiguous moving group members among a sample of nearby-late type stars by studying their kinematics, lithium abundance, chromospheric activity, and other age-related properties. Methods. High-resolution echelle spectra (R ~ 57 000) of a sample of nearby late-type stars are used to derive accurate radial velocities that are combined with the precise Hipparcos parallaxes and proper motions to compute galactic-spatial velocity components. Stars are classified as possible members of the classical moving groups according to their kinematics. The spectra are also used to study several age-related properties for young late-type stars, i.e., the equivalent width of the lithium Li i 6707.8 Å line or the R'_HK index. Additional information like X-ray fluxes from the ROSAT All-Sky Survey or the presence of debris discs is also taken into account. The different age estimators are compared and the moving group membership of the kinematically selected candidates are discussed. Results. From a total list of 405 nearby stars, 102 have been classified as moving group candidates according to their kinematics. i.e., only ~25.2% of the sample. The number reduces when age estimates are considered, and only 26 moving group candidates (25.5% of the 102 candidates) have ages in agreement with the star having the same age as an MG member.

Estimation Models for Nonuniformly Sampled Signals–Application to Multiple Delay Estimation

This letter presents a method to model propagation channels for estimation, in which the sampling scheme can be arbitrary. Additionally, the method yields accurate models, with a size that converges to the channel duration, measured in Nyquist periods. It can be viewed as an improvement on the usual discretization based on regular sampling at the Nyquist rate. The method is introduced in the context of multiple delay estimation using the MUSIC estimator, and is assessed through a numerical example.

Parametrizable Architecture for Function Recursive Evaluation

Paper submitted to the XVIII Conference on Design of Circuits and Integrated Systems (DCIS), Ciudad Real, España, 2003.

Parametrized Architecture for Hough Transform Recursive Evaluation

Paper submitted to International Workshop on Spectral Methods and Multirate Signal Processing (SMMSP), Barcelona, España, 2003.

Hough Transform recursive evaluation using Distributed Arithmetic

Paper submitted to the IFIP International Conference on Very Large Scale Integration (VLSI-SOC), Darmstadt, Germany, 2003.

FFT Interpolation From Nonuniform Samples Lying in a Regular Grid

This paper presents a method to interpolate a periodic band-limited signal from its samples lying at nonuniform positions in a regular grid, which is based on the FFT and has the same complexity order as this last algorithm. This kind of interpolation is usually termed “the missing samples problem” in the literature, and there exists a wide variety of iterative and direct methods for its solution. The one presented in this paper is a direct method that exploits the properties of the so-called erasure polynomial and provides a significant improvement on the most efficient method in the literature, which seems to be the burst error recovery (BER) technique of Marvasti’s The paper includes numerical assessments of the method’s stability and complexity.

Calculus, with analytic geometry.

Includes index.

Practical analytic geometry with applications to aircraft /

"Answers": p. 273-277.

Rank test of location optimal for hyperbolic secant distribution

There are at least two reasons for a symmetric, unimodal, diffuse tailed hyperbolic secant distribution to be interesting in real-life applications. It displays one of the common types of non normality in natural data and is closely related to the logistic and Cauchy distributions that often arise in practice. To test the difference in location between two hyperbolic secant distributions, we develop a simple linear rank test with trigonometric scores. We investigate the small-sample and asymptotic properties of the test statistic and provide tables of the exact null distribution for small sample sizes. We compare the test to the Wilcoxon two-sample test and show that, although the asymptotic powers of the tests are comparable, the present test has certain practical advantages over the Wilcoxon test.

Central elements of the elliptic Zn monodromy matrix algebra at roots of unity

The central elements of the algebra of monodromy matrices associated with the Z(n) R-matrix are studied. When the crossing parameter w takes a special rational value w = n/N, where N and n are positive coprime integers, the center is substantially larger than that in the generic case for which the quantum determinant provides the center. In the trigonometric limit, the situation corresponds to the quantum group at roots of unity. This is a higher rank generalization of the recent results by Belavin and Jimbo. (c) 2004 Elsevier B.V. All rights reserved.

Mechanical vibration characteristics of bell-type pump maintings

This thesis describes an analytical and experimental study to determine the mechanical characteristics of the pump mounting, bell housing type. For numerical purposes, the mount was modelled as a thin circular cylindrical shell with cutouts, stiffened with rings and stringers; the boundary conditions were considered to be either clamped-free or clamped-supporting rigid heavy mass. The theoretical study was concerned with both the static response and the free vibration characteristics of the mount. The approach was based on the Rayleigh-Ritz approximation technique using beam characteristic (axial) and trigonometric (Circumferential) functions in the displacement series, in association with the Love - Timoshenko thin shell theory. Studies were carried out to determine the effect of the supported heavy mass on the static response, frequencies and mode shapes; in addition, the effects of stringers, rings and cutouts on vibration characteristics were investigated. The static and dynamic formulations were both implemented on the Hewlett Packard 9845 computer. The experimental study was conducted to evaluate the results of the natural frequencies and mode shapes, predicted numerically. In the experimental part, a digital computer was used as an experiment controller, which allowed accurate and quick results. The following observations were made: 1. Good agreements were obtained with the results of other investigators. 2. Satisfactory agreement was achieved between the theoretical and experimental results. 3. Rings coupled the axial modal functions of the plain cylinder and tended to increase frequencies, except for the torsion modes where frequencies were reduced. Stringers coupled the circumferential modal functions and tended to decrease frequencies. The effect of rings was stronger than that of stringers. 4. Cutouts tended to reduce frequencies; in general, but this depends on the location of the cutouts; if they are near the free edge then an increase in frequencies is obtained. Cutouts coupled both axial and circumferential modal functions. 5. The supported heavy mass had similar effects to those of the rings, but in an exaggerated manner, particularly in the reduction of torsion frequencies. 6. The method of analysis was found to be a convenient analytical tool for estimating the overall behaviour of the shell with cutouts.

Finite element analysis of the statics of and vibrations in axisymmetric shells

The finite element process is now used almost routinely as a tool of engineering analysis. From early days, a significant effort has been devoted to developing simple, cost effective elements which adequately fulfill accuracy requirements. In this thesis we describe the development and application of one of the simplest elements available for the statics and dynamics of axisymmetric shells . A semi analytic truncated cone stiffness element has been formulated and implemented in a computer code: it has two nodes with five degrees of freedom at each node, circumferential variations in displacement field are described in terms of trigonometric series, transverse shear is accommodated by means of a penalty function and rotary inertia is allowed for. The element has been tested in a variety of applications in the statics and dynamics of axisymmetric shells subjected to a variety of boundary conditions. Good results have been obtained for thin and thick shell cases .

On the numerical solution of a Cauchy problem for the Laplace equation via a direct integral equation approach

We investigate the problem of determining the stationary temperature field on an inclusion from given Cauchy data on an accessible exterior boundary. On this accessible part the temperature (or the heat flux) is known, and, additionally, on a portion of this exterior boundary the heat flux (or temperature) is also given. We propose a direct boundary integral approach in combination with Tikhonov regularization for the stable determination of the temperature and flux on the inclusion. To determine these quantities on the inclusion, boundary integral equations are derived using Green’s functions, and properties of these equations are shown in an L2-setting. An effective way of discretizing these boundary integral equations based on the Nystr¨om method and trigonometric approximations, is outlined. Numerical examples are included, both with exact and noisy data, showing that accurate approximations can be obtained with small computational effort, and the accuracy is increasing with the length of the portion of the boundary where the additionally data is given.

An integral equation method for a mixed initial boundary value problem for unsteady Stokes system in a doubly-connected domain

We present a novel numerical method for a mixed initial boundary value problem for the unsteady Stokes system in a planar doubly-connected domain. Using a Laguerre transformation the unsteady problem is reduced to a system of boundary value problems for the Stokes resolvent equations. Employing a modied potential approach we obtain a system of boundary integral equations with various singularities and we use a trigonometric quadrature method for their numerical solution. Numerical examples are presented showing that accurate approximations can be obtained with low computational cost.