Parametric multiple sequence alignment and phylogeny construction

Bounds are given on the size of the parameter-space decomposition induced by multiple sequence alignment problems where phylogenetic information may be given or inferred. It is shown that many of the usual formulations of these problems fall within the same integer parametric framework, implying that the number of distinct optima obtained as the parameters are varied across their ranges is polynomially bounded in the length and number of sequences.     

Optimized prefactored compact schemes

The numerical simulation of aeroacoustic phenomena requires high-order accurate numerical schemes with low dispersion and dissipation errors. In this paper we describe a strategy for developing high-order accurate prefactored compact schemes, requiring very small stencil support. These schemes require fewer boundary stencils and offer simpler boundary condition implementation than existing compact schemes. The prefactorization strategy splits the central implicit schemes into forward and backward biased operators. Using Fourier analysis, we show it is possible to select the coefficients of the biased operators such that their dispersion characteristics match those of the original central compact scheme and their numerical wavenumbers have equal and opposite imaginary components. This ensures that when the forward and backward stencils are added, the original central compact scheme is recovered. To extend the resolution characteristic of the schemes, an optimization strategy is employed in which formal order of accuracy is sacrificed in preference to enhanced resolution characteristics across the range of wavenumbers realizable on a given mesh. The resulting optimized schemes yield improved dispersion characteristics compared to the standard sixth- and eighth-order compact schemes making them more suitable for high-resolution numerical simulations in gas dynamics and computational aeroacoustics. The efficiency, accuracy and convergence characteristics of the new optimized prefactored compact schemes are demonstrated by their application to several test problems.     

Packing two disks into a polygonal environment

We consider the following problem. Given a polygon P, possibly with holes, and having n vertices, compute a pair of equal radius disks that do not intersect each other, are contained in P, and whose radius is maximized. Our main result is a simple randomized algorithm whose expected running time, on any input, is O(nlogn). This is optimal in the algebraic decision tree model of computation.     

An Efficient Method for the Synthesis of 3-Cyano-6-hydroxy-2(1H)-pyridinones under Microwave Irradiation and Solvent-free Conditions

Summary. Three component condensation of alkylacetoacetates, primary amines, and alkyl cyanoacetates catalyzed by solid supports under microwave irradiation gave N-alkyl 3-cyano-6-hydroxy-2(1H)-pyridinones with high yields. Upon carrying out the reaction under the same condition on acidic alumina, zeolite HY, silica gel, and montmorillonite K-10, the best yields were achieved by silica gel. Corresponding author. E-mail: balalaie@yahoo.com Received August 28, 2002; accepted September 3, 2002     

Computational analysis of native and modified oligofructosides

This paper presents a quantum chemical calculation of native (2–7 fructoside residues) and chemically modified (2–4 fructoside residues) levan molecule models. A levan modification was carried out by oxidation and the following reduction or hyrdazonation of the fructoside rings. The conformational particularity and reaction ability was studied for the native and for the modified levan molecules.     

Reactivities of tetraalkyltin complexes toward Pt/HY zeolite

Tetraalkyltin complexes, SnR₄ (R = Me, Et, Pr, Bu) could react with Pt/HY at 193, 243, 273 and 333 K, respectively. The reactions occurred on the surface of the zeolite and the organotin grafted zeolites were characterized in detail. The framework and the microporous structure of the grafted Pt/HY zeolites were retained. However, the modified zeolites showed better size selectivity in the absorption of hydrocarbons.     

Study of a vibrating plate: comparison between experimental (ESPI) and analytical results

Real-time electronic speckle pattern interferometry (ESPI) was used for tuning and visualization of natural frequencies of a trapezoidal plate. The plate was excited to resonant vibration by a sinusoidal acoustical source, which provided a continuous range of audio frequencies. Fringe patterns produced during the time-average recording of the vibrating plate—corresponding to several resonant frequencies—were registered. From these interferograms, calculations of vibrational amplitudes by means of zero-order Bessel functions were performed in some particular cases. The system was also studied analytically. The analytical approach developed is based on the Rayleigh–Ritz method and on the use of non-orthogonal right triangular co-ordinates. The deflection of the plate is approximated by a set of beam characteristic orthogonal polynomials generated by using the Gram–Schmidt procedure. A high degree of correlation between computational analysis and experimental results was observed.     

Homogenization of two-phase flow: high contrast of phase permeabilityHomogénéisation d'écoulement diphasique : grand contraste de perméabilité d'une phase

The steady-state two-phase flow non-linear equation is considered in the case when one of phases has low effective permeability in some periodic set, while on the complementary set it is high; the second phase has no contrast of permeabilities in different zones. A homogenization procedure gives the homogenized model with macroscopic effective permeability of the second phase depending on the gradient and on the second order derivatives of the macroscopic pressure of the first phase. This effect cannot be obtained by classical (one small parameter) homogenization. To cite this article: G.P. Panasenko, G. Virnovsky, C. R. Mecanique 331 (2003).     

Future pathways for combinatorial chemistry

Summary Investment in combinatorial chemistry (combichem) in the pharmaceutical industry is being driven by the need for increased efficiency. Results from pioneers in the field have demonstrated where mixture or discrete compound synthesis is useful, and what mixture sizes and compound concentrations are appropriate. To make the techniques of combichem of general utility in drug discovery, a broad range of advances is still required. Conversion of organic chemistry to solid phase conditions is key, as are developments in linkers and resins. Library design methodology requires further development. Combinatorial biosynthesis of focused libraries of natural products holds great promise for capitalising on hardwon natural product leads. Miniaturisation of screens is required to reduce the cost of screening combinatorial libraries. Developments in the processes preceding and following synthesis are required to enable the flow of increased numbers of compounds without new bottlenecks developing. The impact of combinatorial chemistry will be greatly enhanced by synergy with ongoing parallel developments in genetic technologies, screening technologies and bioinformatics.