Novel algorithm for phylogenetic analysis of proteins: application to analysis of the evolution of H5N1 influenza viruses

The highly pathogenic avian influenza virus (HPAIV) A subtype H5N1 is causing threat to human health over the years. Phylogenetic analysis is an important tool for analyzing the evolution of influenza. A novel phylogenetic algorithm based on a new protein distance measure derived from the informational spectrum method (ISM) has been presented. The new phylogenetic approach allows assessment of functional evolution of protein sequences. The new ISM-based phylogenetic approach has been found to overcome some drawbacks of other phylogenetic approaches, particularly concerning sensitivity to a single mutation, deletion and the position of the mutation. The ISM-based approach applied to hemagglutinin subunit 1 protein (HA1) of HPAIV A subtype H5N1 viruses in Egypt between 2006 and 2011, revealed clear clustering in two groups, with one growing group of H5N1 viruses after 2009 with increased number of human infections with H5N1. Four group-specific mutations are identified which are important for increased human tropism and the pandemic potential.     

Wavespeed analysis: Approximating Arrhenius kinetics with step-function kinetics

The accuracy of using step-function approximations to the Arrhenius exponential in computing the wavespeed in combustion wave propagation is investigated. Gaseous and gasless combustion, and first- and second-order reactions are included in the study. The theoretical analysis is based on Melnikov theory from dynamical systems. The error is shown to be small in most instances. The analytical results are supported with numerical simulations.     

Sten Andersson is 80

There is a special collection of contribution in the August 2012 issue of Structural Chemistry honoring the Swedish crystallographer Sten Andersson. This Encomium emphasizes the exemplary characteristics of his oeuvre.     

Enumeration of polycarborane isomers: especially dicarboranes

Various sorts of isomer enumeration problems are addressed in the context of polycarboranes, with special illustrative focus on the case of dicarboranes, for which then various numerical results are given. A systematic and general Pólya-theoretic methodology is used to make the computations, including some new techniques being applicable to a wide range of nano-structures built from a framework of like local subunits.     

First-order transitions in spherical models: Finite-size scaling

Finite-size behavior near the first-order phase boundary of ferromagnetic spherical models is investigated for block- and cylinder-shaped systems ind dimensions. The bulk thermodynamic singularities are rounded and, asymptotically for large size, obey appropriate scaling laws. Both short-range interactions and long-range couplings, decaying like 1/r^d+ with >0, are analyzed: the short-range results agree precisely with a recently developed scaling theory forO(n) symmetric systems in the limitn. More generally, the scaling functions are universal, depending only on . Explicit aspects of the shape and interactions enter only in the spin wave or Goldstone mode contributions which appear, technically, as corrections to scaling. An appendix analyzes the truncation error in the approximation, by many-fold sums, of multivariate integrals with integrands diverging like [_ja_{j j} ² ]^- as 0.     

Pionic decay of hypernuclei

The mass number dependence of the total pionic decay rate of hypernuclei is evaluated under the closure approximation by using DDHF single-particle wave functions and taking into account the pion distortion and absorption. The effect ofNN andN correlations are then incorporated and found to give a drastic enhancement especially in heavy hypernuclei. More detailed features are discussed for partial and total decay rates of typical light hypernuclei.Presented at the symposium Mesons and Light Nuclei, Bechyn, Czechoslovakia, May 27–June 1, 1985.     

Metal nanoslit lenses with polarization-selective design

We present comprehensive studies on thin diffraction lenses made of arrays of subwavelength, parallel nanoslits in a gold film. Such a nanoslit lens can operate either as a conventional convex or concave lens. The lenses can be designed to focus linearly polarized light with polarization either perpendicular (TM-lens) or parallel to the slits (TE-lens), while the orthogonal polarization diverges when passing through the lens. The designs of each lens are initially built on the dispersion relations for wave propagation through a parallel-plate waveguide. Both TM- and TE-lenses were realized experimentally, and full-wave numerical simulations fully support the experimental results.     

On the coherent inelastic processes in collisions of elementary particles with nuclei at ultrarelativistic energies

The coherent inelastic processes of the type a → b, which may take place in the interaction of hadrons and γ quanta with nuclei at very high energies (the nucleus remains the same), are theoretically investigated. Analytical formulas for the effective cross-section σ_coh(a→b) are obtained.     

Morphology-dependent photonic circuit elements

We theoretically propose and experimentally demonstrate the design of a novel one-dimensional ringlike macroscopic optical circuit element. The similarity between morphologies of an optical planar waveguide and a whispering-gallery axially symmetric solid-state resonator is used.     

A simple method to measure 13CH2 heteronuclear dipolar cross-correlation spectral densities

Here, we report a method to simultaneously determine CH2 cross-correlation spectral densities and T1 relaxation times in the laboratory and rotating frames. To accomplish this, we have employed an indirect approach that is based on measurement of differences in relaxation rates acquired with and without cross-correlation terms. The new method, which can be employed using multidimensional NMR and standard relaxation pulse sequences, is validated experimentally by investigation of a selectively 13C-enriched hexadecapeptide and the uniformly 13C-enriched immunoglobulin-binding domain of streptococcal protein G (GB1). Use of this approach makes determination of CH2 cross-correlation spectral densities in uniformly 13C-enriched proteins now routine and provides novel information concerning their internal motions.