Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

Polarisation diversity of conformal arrays based on geometric algebra via convex optimisation

A simple and general design procedure is presented for the polarisation diversity of arbitrary conformal arrays; this procedure is based on the mathematical framework of geometric algebra and can be solved optimally using convex optimisation. Aside from being simpler and more direct than other derivations in the literature, this derivation is also entirely general in that it expresses the transformations in terms of rotors in geometric algebra which can easily be formulated for any arbitrary conformal array geometry. Convex optimisation has a number of advantages; solvers are widespread and freely available, the process generally requires a small number of iterations and a wide variety of constraints can be readily incorporated. The study outlines a two-step approach for addressing polarisation diversity in arbitrary conformal arrays: first, the authors obtain the array polarisation patterns using geometric algebra and secondly use a convex optimisation approach to find the optimal weights for the polarisation diversity problem. The versatility of this approach is illustrated via simulations of a 7×10 cylindrical conformal array. © 2012 The Institution of Engineering and Technology.

THE SENSITIVITY OF 2D COMPRESSOR INCIDENCE RANGE TO IN-SERVICE GEOMETRIC VARIATION

The loss mechanisms which control 2D incidence range are discussed with an emphasis on determining which real in-service geometric variations will have the largest impact. For the majority of engine compressor blades (Minlet>0.55) both the negative and positive incidence limits are controlled by supersonic patches. It is shown that these patches are highly sensitive to the geometric variations close to, and around the leading edge. The variations used in this study were measured from newly manufactured as well as ex-service blades. Over most the high pressure compressor considered, it was shown that manufacture variations dominated. The first part of the paper shows that, despite large geometric variations (~10% of leading edge thickness), the incidence range responded in a linear way. The result of this is that the geometric variations have little effect on the mean incidence range of a row of blades. In the second part of the paper a region of the design space is identified where non-linear behavior can result in a 10% reduction in positive incidence range. The mechanism for this is reported and design guidelines for its avoidance offered. In the final part of the paper, the linear behavior at negative incidence and the transonic nature of the flow is exploited to design a robust asymmetric leading edge with a 5% increase in incidence range.

Rank-preserving geometric means of positive semi-definite matrices

The generalization of the geometric mean of positive scalars to positive definite matrices has attracted considerable attention since the seminal work of Ando. The paper generalizes this framework of matrix means by proposing the definition of a rank-preserving mean for two or an arbitrary number of positive semi-definite matrices of fixed rank. The proposed mean is shown to be geometric in that it satisfies all the expected properties of a rank-preserving geometric mean. The work is motivated by operations on low-rank approximations of positive definite matrices in high-dimensional spaces.© 2012 Elsevier Inc. All rights reserved.

Riemannian metric and geometric mean for positive semidefinite matrices of fixed rank

This paper introduces a new metric and mean on the set of positive semidefinite matrices of fixed-rank. The proposed metric is derived from a well-chosen Riemannian quotient geometry that generalizes the reductive geometry of the positive cone and the associated natural metric. The resulting Riemannian space has strong geometrical properties: it is geodesically complete, and the metric is invariant with respect to all transformations that preserve angles (orthogonal transformations, scalings, and pseudoinversion). A meaningful approximation of the associated Riemannian distance is proposed, that can be efficiently numerically computed via a simple algorithm based on SVD. The induced mean preserves the rank, possesses the most desirable characteristics of a geometric mean, and is easy to compute. © 2009 Society for Industrial and Applied Mathematics.

Geometric optimization methods for independent component analysis applied on gene expression data

DNA microarrays provide a huge amount of data and require therefore dimensionality reduction methods to extract meaningful biological information. Independent Component Analysis (ICA) was proposed by several authors as an interesting means. Unfortunately, experimental data are usually of poor quality- because of noise, outliers and lack of samples. Robustness to these hurdles will thus be a key feature for an ICA algorithm. This paper identifies a robust contrast function and proposes a new ICA algorithm. © 2007 IEEE.

Geometric perspectives on MDO and MDO architectures

Two main perspectives have been developed within the Multidisciplinary Design Optimization (MDO) literature for classifying and comparing MDO architectures: a numerical point of view and a formulation/data flow point of view. Although significant work has been done here, these perspectives have not provided much in the way of a priori information or predictive power about architecture performance. In this report, we outline a new perspective, called the geometric perspective, which we believe will be able to provide such predictive power. Using tools from differential geometry, we take several prominent architectures and describe mathematically how each constructs the space through which it moves. We then consider how the architecture moves through the space which it has constructed. Taken together, these investigations show how each architecture relates to the original feasible design manifold, how the architectures relate to each other, and how each architecture deals with the design coupling inherent to the original system. This in turn lays the groundwork for further theoretical comparisons between and analyses of MDO architectures and their behaviour using tools and techniques derived from differential geometry. © 2012 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

Geometric phase of a bipartite system with Dzyaloshinski-Moriya interaction

The Berry phase of a bipartite system described by a Heisenberg XXZ model driven by a one-site magnetic field is investigated. The effect of the Dzyaloshinski-Moriya (DM) anisotropic interaction on the Berry phase is discussed. It is found that the DM interaction affects the Berry phase monotonously. and can also cause sudden change of the Berry phase for some weak magnetic field cases. (c) 2008 Elsevier B.V. All rights reserved.

Ultrafast geometric manipulation of electron spin and detection of the geometric phase via Faraday rotation spectroscopy

Time-resolved Faraday rotation spectroscopy is currently exploited as a powerful technique to probe spin dynamics in semiconductors. We propose here an all-optical approach to geometrically manipulate electron spin and to detect the geometric phase by this type of extremely sensitive experiment. The global nature of the geometric phase can make the quantum manipulation more stable, which may find interesting applications in quantum devices.

Nonadiabatic geometric quantum computation with trapped ions

We propose a nonadiabatic scheme for geometric quantum computation with trapped ions. By making use of the Aharonov-Anandan phase, the proposed scheme not only preserves the globally geometric nature in quantum computation, but also provides the advantage of nonadiabaticity that overcomes the problem of slow evolution in the existing adiabatic schemes. Moreover, the present scheme requires only two atomic levels in each ion, making it an appealing candidate for quantum computation.

A Novel Geometric Algorithm for Blind Image Restoration Based on High-Dimensional Space

A novel geometric algorithm for blind image restoration is proposed in this paper, based on High-Dimensional Space Geometrical Informatics (HDSGI) theory. In this algorithm every image is considered as a point, and the location relationship of the points in high-dimensional space, i.e. the intrinsic relationship of images is analyzed. Then geometric technique of "blurring-blurring-deblurring" is adopted to get the deblurring images. Comparing with other existing algorithms like Wiener filter, super resolution image restoration etc., the experimental results show that the proposed algorithm could not only obtain better details of images but also reduces the computational complexity with less computing time. The novel algorithm probably shows a new direction for blind image restoration with promising perspective of applications.