Trends of the major porin gene (ompF) evolution

OmpF is one of the major general porins of Enterobacteriaceae that belongs to the first line of bacterial defense and interactions with the biotic as well as abiotic environments. Porins are surface exposed and their structures strongly reflect the history of multiple interactions with the environmental challenges. Unfortunately, little is known on diversity of porin genes of Enterobacteriaceae and the genus Yersinia especially. We analyzed the sequences of the ompF gene from 73 Yersinia strains covering 14 known species. The phylogenetic analysis placed most of the Yersinia strains in the same line assigned by 16S rDNA-gyrB tree. Very high congruence in the tree topologies was observed for Y. enterocolitica, Y. kristensenii, Y. ruckeri, indicating that intragenic recombination in these species had no effect on the ompF gene. A significant level of intra- and interspecies recombination was found for Y. aleksiciae, Y. intermedia and Y. mollaretii. Our analysis shows that the ompF gene of Yersinia has evolved with nonrandom mutational rate under purifying selection. However, several surface loops in the OmpF porin contain positively selected sites, which very likely reflect adaptive diversification Yersinia to their ecological niches. To our knowledge, this is a first investigation of diversity of the porin gene covering the whole genus of the family Enterobacteriaceae. This study demonstrates that recombination and positive selection both contribute to evolution of ompF, but the relative contribution of these evolutionary forces are different among Yersinia species

Semiclassical measures and the Schroedinger flow on Riemannian manifolds

In this article we study limits of Wigner distributions (the so-called semiclassical measures) corresponding to sequences of solutions to the semiclassical Schroedinger equation at times scales $\alpha_{h}$ tending to infinity as the semiclassical parameter $h$ tends to zero (when $\alpha _{h}=1/h$ this is equivalent to consider solutions to the non-semiclassical Schreodinger equation). Some general results are presented, among which a weak version of Egorov's theorem that holds in this setting. A complete characterization is given for the Euclidean space and Zoll manifolds (that is, manifolds with periodic geodesic flow) via averaging formulae relating the semiclassical measures corresponding to the evolution to those of the initial states. The case of the flat torus is also addressed; it is shown that non-classical behavior may occur when energy concentrates on resonant frequencies. Moreover, we present an example showing that the semiclassical measures associated to a sequence of states no longer determines those of their evolutions. Finally, some results concerning the equation with a potential are presented.Comment: 18 pages; Theorems 1,2 extendend to deal with arbitrary time-scales; references adde

Quantum Graphs II: Some spectral properties of quantum and combinatorial graphs

The paper deals with some spectral properties of (mostly infinite) quantum and combinatorial graphs. Quantum graphs have been intensively studied lately due to their numerous applications to mesoscopic physics, nanotechnology, optics, and other areas. A Schnol type theorem is proven that allows one to detect that a point belongs to the spectrum when a generalized eigenfunction with an subexponential growth integral estimate is available. A theorem on spectral gap opening for ``decorated'' quantum graphs is established (its analog is known for the combinatorial case). It is also shown that if a periodic combinatorial or quantum graph has a point spectrum, it is generated by compactly supported eigenfunctions (``scars'').Comment: 4 eps figures, LATEX file, 21 pages Revised form: a cut-and-paste blooper fixe

Hydrodynamic limit for weakly asymmetric simple exclusion processes in crystal lattices

We investigate the hydrodynamic limit for weakly asymmetric simple exclusion processes in crystal lattices. We construct a suitable scaling limit by using a discrete harmonic map. As we shall observe, the quasi-linear parabolic equation in the limit is defined on a flat torus and depends on both the local structure of the crystal lattice and the discrete harmonic map. We formulate the local ergodic theorem on the crystal lattice by introducing the notion of local function bundle, which is a family of local functions on the configuration space. The ideas and methods are taken from the discrete geometric analysis to these problems. Results we obtain are extensions of ones by Kipnis, Olla and Varadhan to crystal lattices.Comment: 41 pages, 7 figure

Analytic and Reidemeister torsion for representations in finite type Hilbert modules

For a closed Riemannian manifold we extend the definition of analytic and Reidemeister torsion associated to an orthogonal representation of fundamental group on a Hilbert module of finite type over a finite von Neumann algebra. If the representation is of determinant class we prove, generalizing the Cheeger-M\"uller theorem, that the analytic and Reidemeister torsion are equal. In particular, this proves the conjecture that for closed Riemannian manifolds with positive Novikov-Shubin invariants, the L2 analytic and Reidemeister torsions are equal.Comment: 78 pages, AMSTe

Quantization of the Riemann Zeta-Function and Cosmology

Quantization of the Riemann zeta-function is proposed. We treat the Riemann zeta-function as a symbol of a pseudodifferential operator and study the corresponding classical and quantum field theories. This approach is motivated by the theory of p-adic strings and by recent works on stringy cosmological models. We show that the Lagrangian for the zeta-function field is equivalent to the sum of the Klein-Gordon Lagrangians with masses defined by the zeros of the Riemann zeta-function. Quantization of the mathematics of Fermat-Wiles and the Langlands program is indicated. The Beilinson conjectures on the values of L-functions of motives are interpreted as dealing with the cosmological constant problem. Possible cosmological applications of the zeta-function field theory are discussed.Comment: 14 pages, corrected typos, references and comments adde

Elliptic operators on manifolds with singularities and K-homology

It is well known that elliptic operators on a smooth compact manifold are classified by K-homology. We prove that a similar classification is also valid for manifolds with simplest singularities: isolated conical points and fibered boundary. The main ingredients of the proof of these results are: an analog of the Atiyah-Singer difference construction in the noncommutative case and an analog of Poincare isomorphism in K-theory for our singular manifolds. As applications we give a formula in topological terms for the obstruction to Fredholm problems on manifolds with singularities and a formula for K-groups of algebras of pseudodifferential operators.Comment: revised version; 25 pages; section with applications expande

Band spectra of rectangular graph superlattices

We consider rectangular graph superlattices of sides l1, l2 with the wavefunction coupling at the junctions either of the delta type, when they are continuous and the sum of their derivatives is proportional to the common value at the junction with a coupling constant alpha, or the "delta-prime-S" type with the roles of functions and derivatives reversed; the latter corresponds to the situations where the junctions are realized by complicated geometric scatterers. We show that the band spectra have a hidden fractal structure with respect to the ratio theta := l1/l2. If the latter is an irrational badly approximable by rationals, delta lattices have no gaps in the weak-coupling case. We show that there is a quantization for the asymptotic critical values of alpha at which new gap series open, and explain it in terms of number-theoretic properties of theta. We also show how the irregularity is manifested in terms of Fermi-surface dependence on energy, and possible localization properties under influence of an external electric field. KEYWORDS: Schroedinger operators, graphs, band spectra, fractals, quasiperiodic systems, number-theoretic properties, contact interactions, delta coupling, delta-prime coupling.Comment: 16 pages, LaTe

Essential self-adjointness of magnetic Schr\"odinger operators on locally finite graphs

We give sufficient conditions for essential self-adjointness of magnetic Schr\"odinger operators on locally finite graphs. Two of the main theorems of the present paper generalize recent results of Torki-Hamza.Comment: 14 pages; The present version differs from the original version as follows: the ordering of presentation has been modified in several places, more details have been provided in several places, some notations have been changed, two examples have been added, and several new references have been inserted. The final version of this preprint will appear in Integral Equations and Operator Theor