4,345 research outputs found
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
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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 to the
Lie algebra . The construction is based on the Gelfand-Zetlin
maximal commuting subalgebra in . We discuss the connection
with the other known integrable systems based on . 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 - and
-systems based on . 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
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