Frank-Condon principle and adjustment of optical waveguides with nonhomogeneous refractive indices

The adjustment of two different selfocs is considered using both exact formulas for the mode-connection coefficients expressed in terms of Hermite polynomials of several variables and a qualitative approach based on the Frank-Condon principle. Several examples of the refractive-index dependence are studied and illustrative plots for these examples are presented. The connection with the tomographic approach to quantum states of a two-dimensional oscillator and the Frank-Condon factors is established.Comment: 8 pages, 4 figures, published version (layout of figures changed, typos corrected, references added

Stochastic Chemical Kinetics with Energy Parameters

International audienceAbstact: We introduce new models of energy redistribution in stochastic chemical kinetics with several molecule types and energy parameters. The main results concern the situations when there are product form measures. Using a probabilistic interpretation of the related Boltzmann equation, we find some invariant measures explicitly and prove convergence to them.Résumé : Nous introduisons de nouveaux modèles de réseaus de cinétique chimique, avec plusieurs types de molécules et de redistribution d'énergie. Les principaux résultats concernent les cas où les mesures invariantes ont une forme produit. Grâce à une interprétation probabiliste, certaines de ces mesures sont calculées explicitement et on montre qu'elles sont effectivement atteintes par convergence

CORRIE: enzyme sequence annotation with confidence estimates

Using a previously developed automated method for enzyme annotation, we report the re-annotation of the ENZYME database and the analysis of local error rates per class. In control experiments, we demonstrate that the method is able to correctly re-annotate 91% of all Enzyme Classification (EC) classes with high coverage (755 out of 827). Only 44 enzyme classes are found to contain false positives, while the remaining 28 enzyme classes are not represented. We also show cases where the re-annotation procedure results in partial overlaps for those few enzyme classes where a certain inconsistency might appear between homologous proteins, mostly due to function specificity. Our results allow the interactive exploration of the EC hierarchy for known enzyme families as well as putative enzyme sequences that may need to be classified within the EC hierarchy. These aspects of our framework have been incorporated into a web-server, called CORRIE, which stands for Correspondence Indicator Estimation and allows the interactive prediction of a functional class for putative enzymes from sequence alone, supported by probabilistic measures in the context of the pre-calculated Correspondence Indicators of known enzymes with the functional classes of the EC hierarchy. The CORRIE server is available at:

Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors

Today, annotated amino acid sequences of more and more transcription factors (TFs) are readily available. Quantitative information about their DNA-binding specificities, however, are hard to obtain. Position frequency matrices (PFMs), the most widely used models to represent binding specificities, are experimentally characterized only for a small fraction of all TFs. Even for some of the most intensively studied eukaryotic organisms (i.e., human, rat and mouse), roughly one-sixth of all proteins with annotated DNA-binding domain have been characterized experimentally. Here, we present a new method based on support vector regression for predicting quantitative DNA-binding specificities of TFs in different eukaryotic species. This approach estimates a quantitative measure for the PFM similarity of two proteins, based on various features derived from their protein sequences. The method is trained and tested on a dataset containing 1 239 TFs with known DNA-binding specificity, and used to predict specific DNA target motifs for 645 TFs with high accuracy

Reflection and refraction from a vertical layer of surface SH-waves radiated from a point source on a free from tensions boundary

With the help of the asymptotic boundary layer method, the transformation of an elastic SH-polarized surface wave of whispering gallery type (the so-called Love wave) is analyzed in the case where this wave passes many times through a vertical layer between two half-planes

Boundary layer method in the problem of far propagation of surface SV-waves

The SV polarized wave field is investigated in an elastic gradient layer of constant width. A point source is situated on the boundary of the layer. Rigid contact conditions are assumed to be valid on the boundary between the layer and an elastic half-space. It is shown that the interference field in the principal approximation far from the source does not depend on the relation between the phase velocity and the transversal and longitudinal velocities in the half-space