FIRST ORDER QUASILINEAR EQUATIONS IN SEVERAL INDEPENDENT VARIABLES WITH SINGULAR INITIAL DATA L~p（P＜∞）

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Cofolga: a genetic algorithm for finding the common folding of two RNAs

In order to predict non-coding RNA genes and functions on the basis of genome sequences, accurate secondary structure prediction is useful. Although single-sequence folding programs such as mfold have been successful, it is of great importance to develop a novel approach for further improvement of the prediction performance. In the present paper, a secondary structure prediction method based on genetic algorithm, Cofolga, is proposed. The program developed performs folding and alignment of two homologous RNAs simultaneously. Cofolga was tested with a dataset composed of 13 tRNAs, seven 5S rRNAs, five RNase P RNAs, and five SRP RNAs; as a result, it turned out that the average prediction accuracies for the tRNAs, 5S rRNAs, RNase P RNAs, and SRP RNAs obtained by Cofolga with an optimal weight factor and default parameters were 83.6, 81.8, 73.5, and 67.7%, respectively. These results were superior to those obtained by a single-sequence folding based on free-energy minimization in which corresponding average prediction accuracies were 52.4, 47.4, 57.7, and 52.3%, respectively. Cofolga has a post-processing in which a single-sequence folding is performed after fixation of a predicted common structure; this post-processing enables Cofolga to predict a structure that is present in one of two RNAs alone. The executable files of Cofolga (for Windows/Unix/Mac) can be obtained by an e-mail request.     

Parallel Calculation of Accurate Path Lines in Virtual Environments through Exploitation of Multi-Block CFD Data Set Topology

The use of Virtual Reality (VR) techniques for the investigation of complex flow phenomena offers distinct advantages in comparison to conventional visualization techniques. Especially for unsteady flows, VR methodology provides an intuitive approach for the exploration of simulated fluid flows. However, the visualization of Computational Fluid Dynamics (CFD) data is often too time-consuming to be carried out in real-time, and thus violates essential constraints concerning real-time interaction and visualization. To overcome this obstacle, we make use of the fact that typically a multi-block approach is employed for domain decomposition, and we use the corresponding data structures for the computation of path lines and for parallelization. In this paper, we present the synthesis of fragmented multi-block data sets and our implementation of an accurate path line integration scheme in order to speed up path line computations. We report on the results of our efforts and describe a combination of this algorithm with a highly efficient visualization approach of large amounts of particle traces, thus considerably improving interactivity when exploring large scale CFD data sets.Mathematics Subject Classifications (2000) 76Mxx, 76M27, 76M28, 65M55, 65L05, 65L06, 65D05, 65Y05, 68U05.     

Linear low-rank approximation and nonlinear dimensionality reduction

We present our recent work on both linear and nonlinear data reduction methods and algorithms: for the linear case we discuss results on structure analysis of SVD of column-partitioned matrices and sparse low-rank approximation; for the nonlinear case we investigate methods for nonlinear dimensionality reduction and manifold learning. The problems we address have attracted great deal of interest in data mining and machine learning.     

Magnetic alignment in nominally non-magnetic hexagonal metal hydrides: NMR

Powders of three hexagonal metal-hydrides or -deuterides are found to align in 4.4–8.3 T magnetic fields used for NMR. The field-alignment is unexpected, since all three systems have very small susceptibilities, as demonstrated by sharp NMR lines. The extent of alignment runs from nearly complete to barely detectable in ZrBe₂(H,D)_x, LuD₃, and YD₃, respectively. The preferred alignment direction in ZrBe₂(H,D)_x is with the crystallites’ c-axis perpendicular to B, while the c-axis and B tend to be parallel in LuD₃ and YD₃. The susceptibilities χ_|| and χ are determined from bulk magnetization measurements in aligned ZrBe₂H_1.4 powder. The alignment must be considered for proper analysis of NMR spectra in these and related materials.     

Structure and polarity of 8CB films evaporated onto solid substrates

Brewster-angle reflection ellipsometry and surface optical second harmonic generation were used to study the growth of 4'-n-octyl-4-cyanobiphenyl (8CB) films evaporated in air onto polymeric and quartz glass substrates. The layer-by-layer growth of the films terminates after formation of two distinctive interfacial layers. Both of these two layers are polar and tilted. In the first layer the molecules lie nearly flat on the surface, while in the second layer they point on average about 50° toward the surface normal. The dipole moment of the second layer has a lower magnitude and an opposite direction with respect to the dipole moment of the first layer.     

On initial conditions for a boundary stabilized hybrid Euler-Bernoulli beam

We consider here small flexural vibrations of an Euler-Bernoulli beam with a lumped mass at one end subject to viscous damping force while the other end is free and the system is set to motion with initial displacementy ⁰(x) and initial velocityy ¹ (x). By investigating the evolution of the motion by Laplace transform, it is proved (in dimensionless units of length and time) that

Convex polytopes all of whose reverse lexicographic initial ideals are squarefree

A compressed polytope is an integral convex polytope any of whose reverse lexicographic initial ideals is squarefree. A sufficient condition for a -polytope to be compressed will be presented. One of its immediate consequences is that the class of compressed -polytopes includes (i) hypersimplices, (ii) order polytopes of finite partially ordered sets, and (iii) stable polytopes of perfect graphs.

     

Adsorption of hydrophobic polyelectrolytes onto oppositely charged surfaces

We present a scaling theory for the adsorption of a weakly charged polyelectrolyte chain in a poor solvent onto an oppositely charged surface. Depending on the fraction of charged monomers and on the solvent quality for uncharged monomers, the globule in the bulk of the solution has either a spherical conformation or a necklace structure. At sufficiently high surface charge density, a chain in the globular conformation adsorbs in a flat pancake conformation due to the Coulombic attraction to the oppositely charged surface. Different adsorption regimes are predicted depending on two screening lengths (the Debye screening length monitored by the salt concentration and the Gouy-Chapman length monitored by the surface charge density), on the degree of ionization of the polymer and on the solvent strength. At low bulk ionic strength, an increase in the surface charge density may induce a transition from an adsorbed necklace structure to a uniform pancake due to the enhanced screening of the intra-chain Coulombic repulsion by the counterions localized near the surface. Received 12 April 2001     

Computational methods for the structural alignment of molecules

In drug design, often enough, no structural information on a particular receptor protein is available. However, frequently a considerable number of different ligands is known together with their measured binding affinities towards a receptor under consideration. In such a situation, a set of plausible relative superpositions of different ligands, hopefully approximating their putative binding geometry, is usually the method of choice for preparing data for the subsequent application of 3D methods that analyze the similarity or diversity of the ligands. Examples are 3D-QSAR studies, pharmacophore elucidation, and receptor modeling. An aggravating fact is that ligands are usually quite flexible and a rigorous analysis has to incorporate molecular flexibility. We review the past six years of scientific publishing on molecular superposition. Our focus lies on automatic procedures to be performed on arbitrary molecular structures. Methodical aspects are our main concern here. Accordingly, plain application studies with few methodical elements are omitted in this presentation. While this review cannot mention every contribution to this actively developing field, we intend to provide pointers to the recent literature providing important contributions to computational methods for the structural alignment of molecules. Finally we provide a perspective on how superposition methods can effectively be used for the purpose of virtual database screening. In our opinion it is the ultimate goal to detect analogues in structure databases of nontrivial size in order to narrow down the search space for subsequent experiments.