Computing topological invariants with one and two-matrix models

A generalization of the Kontsevich Airy-model allows one to compute the intersection numbers of the moduli space of p-spin curves. These models are deduced from averages of characteristic polynomials over Gaussian ensembles of random matrices in an external matrix source. After use of a duality, and of an appropriate tuning of the source, we obtain in a double scaling limit these intersection numbers as polynomials in p. One can then take the limit p to -1 which yields a matrix model for orbifold Euler characteristics. The generalization to a time-dependent matrix model, which is equivalent to a two-matrix model, may be treated along the same lines ; it also yields a logarithmic potential with additional vertices for general p.Comment: 30 pages, added references, changed conten

Using orthologous and paralogous proteins to identify specificity determining residues

Background: Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which determine specificity of protein-DNA and protein-ligand recognition. Finding such residues is crucial for understanding mechanisms of molecular recognition and for rational protein and drug design. Results: Assuming conservation of specificity among orthologs and different specificity of paralogs, we identify residues which correlate with this grouping by specificity. The method is taking advantage of complete genomes to find multiple orthologs and paralogs. The central part of this method is a procedure to compute statistical significance of the predictions. The procedure is based on a simple statistical model of protein evolution. When applied to a large family of bacterial transcription factors, our method identified 12 residues that are presumed to determine the protein-DNA and protein-ligand recognition specificity. Structural analysis of the proteins and available experimental results strongly support our predictions. Our results suggest new experiments aimed at rational re-design of specificity in bacterial transcription factors by a minimal number of mutations. Conclusions: While sets of orthologous and paralogous proteins can be easily derived from complete genomic sequences, our method can identify putative specificity determinants in such proteins

On the algebraic structures connected with the linear Poisson brackets of hydrodynamics type

The generalized form of the Kac formula for Verma modules associated with linear brackets of hydrodynamics type is proposed. Second cohomology groups of the generalized Virasoro algebras are calculated. Connection of the central extensions with the problem of quntization of hydrodynamics brackets is demonstrated

Dynamical Structure Factors for Dimerized Spin Systems

We discuss the transition strength between the disordered ground state and the basic low-lying triplet excitation for interacting dimer materials by presenting theoretical calculations and series expansions as well as inelastic neutron scattering results for the material KCuCl_3. We describe in detail the features resulting from the presence of two differently oriented dimers per unit cell and show how energies and spectral weights of the resulting two modes are related to each other. We present results from the perturbation expansion in the interdimer interaction strength and thus demonstrate that the wave vector dependence of the simple dimer approximation is modified in higher orders. Explicit results are given in 10th order for dimers coupled in 1D, and in 2nd order for dimers coupled in 3D with application to KCuCl_3 and TlCuCl_3.Comment: 17 pages, 6 figures, part 2 is based on cond-mat/021133

On a class of integrable systems connected with GL(N,\RR)

In this paper we define a new class of the quantum integrable systems associated with the quantization of the cotangent bundle $T^*(GL(N))$ to the Lie algebra $\frak{gl}_N$. The construction is based on the Gelfand-Zetlin maximal commuting subalgebra in $U(\frak{gl}_N)$. We discuss the connection with the other known integrable systems based on $T^*GL(N)$. The construction of the spectral tower associated with the proposed integrable theory is given. This spectral tower appears as a generalization of the standard spectral curve for integrable system.Comment: LaTeX, 13 page

Fermi Detection of the Pulsar Wind Nebula HESS J1640-465

We present observations of HESS J1640-465 with the Fermi-LAT. The source is detected with high confidence as an emitter of high-energy gamma-rays. The spectrum lacks any evidence for the characteristic cutoff associated with emission from pulsars, indicating that the emission arises primarily from the pulsar wind nebula. Broadband modeling implies an evolved nebula with a low magnetic field resulting in a high gamma-ray to X-ray flux ratio. The Fermi emission exceeds predictions of the broadband model, and has a steeper spectrum, possibly resulting from a distinct excess of low energy electrons similar to what is inferred for both the Vela X and Crab pulsar wind nebulae.Comment: 6 pages, 5 figures, accepted for publication in Ap

Discrete integrable systems, positivity, and continued fraction rearrangements

In this review article, we present a unified approach to solving discrete, integrable, possibly non-commutative, dynamical systems, including the $Q$- and $T$-systems based on $A_r$. The initial data of the systems are seen as cluster variables in a suitable cluster algebra, and may evolve by local mutations. We show that the solutions are always expressed as Laurent polynomials of the initial data with non-negative integer coefficients. This is done by reformulating the mutations of initial data as local rearrangements of continued fractions generating some particular solutions, that preserve manifest positivity. We also show how these techniques apply as well to non-commutative settings.Comment: 24 pages, 2 figure

Comparative Genomic Analysis of the Regulation of Aromatic Metabolism in Betaproteobacteria

Aromatic compounds are a common carbon and energy source for many microorganisms, some of which can even degrade toxic chloroaromatic xenobiotics. This comparative study of aromatic metabolism in 32 Betaproteobacteria species describes the links between several transcription factors (TFs) that control benzoate (BenR, BenM, BoxR, BzdR), catechol (CatR, CatM, BenM), chlorocatechol (ClcR), methylcatechol (MmlR), 2,4-dichlorophenoxyacetate (TfdR, TfdS), phenol (AphS, AphR, AphT), biphenyl (BphS), and toluene (TbuT) metabolism. We characterize the complexity and variability in the organization of aromatic metabolism operons and the structure of regulatory networks that may differ even between closely related species. Generally, the upper parts of pathways, rare pathway variants, and degradative pathways of exotic and complex, in particular, xenobiotic compounds are often controlled by a single TF, while the regulation of more common and/or central parts of the aromatic metabolism may vary widely and often involves several TFs with shared and/or dual, or cascade regulation. The most frequent and at the same time variable connections exist between AphS, AphR, AphT, and BenR. We have identified a novel LysR-family TF that regulates the metabolism of catechol (or some catechol derivative) and either substitutes CatR(M)/BenM, or shares functions with it. We have also predicted several new members of aromatic metabolism regulons, in particular, some COGs regulated by several different TFs