Probabilistic sequence alignments: realistic models with efficient algorithms

Alignment algorithms usually rely on simplified models of gaps for computational efficiency. Based on an isomorphism between alignments and physical helix-coil models, we show in statistical mechanics that alignments with realistic laws for gaps can be computed with fast algorithms. Improved performances of probabilistic alignments with realistic models of gaps are illustrated. Probabilistic and optimization formulations are compared, with potential implications in many fields and perspectives for computationally efficient extensions to Markov models with realistic long-range interactions

Numerical results for extremal problem for eigenvalues of the Laplacian

info:eu-repo/semantics/publishedVersio

Smooth-filamental transition of active tracer fields stirred by chaotic advection

The spatial distribution of interacting chemical fields is investigated in the non-diffusive limit. The evolution of fluid parcels is described by independent dynamical systems driven by chaotic advection. The distribution can be filamental or smooth depending on the relative strength of the dispersion due to chaotic advection and the stability of the chemical dynamics. We give the condition for the smooth-filamental transition and relate the H\"older exponent of the filamental structure to the Lyapunov exponents. Theoretical findings are illustrated by numerical experiments.Comment: 4 pages, 3 figure

The internal magnetic field in superconducting ferromagnets

We have measured the nonlinear response to the ac magnetic field in the superconducting weak ferromagnet Ru-1222, at different regimes of sample cooling which provides unambiguous evidence of the interplay of the domain structure and the vorticity in the superconducting state. This is {\em direct} proof of coexistence of ferromagnetic and superconductive order parameters in high-$T_c$ ruthenocuprates.Comment: 9 pages, 6 figure

Exploring Halo Substructure with Giant Stars. XV. Discovery of a Connection between the Monoceros Ring and the Triangulum-Andromeda Overdensity?

Thanks to modern sky surveys, over twenty stellar streams and overdensity structures have been discovered in the halo of the Milky Way. In this paper, we present an analysis of spectroscopic observations of individual stars from one such structure, "A13", first identified as an overdensity using the M giant catalog from the Two Micron All-Sky Survey. Our spectroscopic observations show that stars identified with A13 have a velocity dispersion of $\lesssim$ 40 $\mathrm{km~s^{-1}}$, implying that it is a genuine coherent structure rather than a chance super-position of random halo stars. From its position on the sky, distance ($\sim$15~kpc heliocentric), and kinematical properties, A13 is likely to be an extension of another low Galactic latitude substructure -- the Galactic Anticenter Stellar Structure (also known as the Monoceros Ring) -- towards smaller Galactic longitude and farther distance. Furthermore, the kinematics of A13 also connect it with another structure in the southern Galactic hemisphere -- the Triangulum-Andromeda overdensity. We discuss these three connected structures within the context of a previously proposed scenario that one or all of these features originate from the disk of the Milky Way.Comment: 12 pages, 9 figures. Accepted for publication in Ap

Reactive dynamics of inertial particles in nonhyperbolic chaotic flows

Anomalous kinetics of infective (e.g., autocatalytic) reactions in open, nonhyperbolic chaotic flows are important for many applications in biological, chemical, and environmental sciences. We present a scaling theory for the singular enhancement of the production caused by the universal, underlying fractal patterns. The key dynamical invariant quantities are the effective fractal dimension and effective escape rate, which are primarily determined by the hyperbolic components of the underlying dynamical invariant sets. The theory is general as it includes all previously studied hyperbolic reactive dynamics as a special case. We introduce a class of dissipative embedding maps for numerical verification.Comment: Revtex, 5 pages, 2 gif figure

Epidemiological determinants and PCR results in Central African inhabitants with a new and frequent HTLV indeterminate Western Blot pattern exhibiting mostly p28, p32, p36, and a shifted GD21

International audiencen.

Underestimated Passive Volcanic Sulfur Degassing Implies Overestimated Anthropogenic Aerosol Forcing

The Arctic is warming at almost four times the global rate. An estimated sixty percent of greenhouse-gas-induced Arctic warming has been offset by anthropogenic aerosols, but the contribution of aerosols to radiative forcing (RF) represents the largest uncertainty in estimating total RF, largely due to unknown preindustrial aerosol abundance. Here, sulfur isotope measurements in a Greenland ice core show that passive volcanic degassing contributes up to 66 ± 10% of preindustrial ice core sulfate in years without major eruptions. A state-of-the-art model indicates passive volcanic sulfur emissions influencing the Arctic are underestimated by up to a factor of three, possibly because many volcanic inventories do not include hydrogen sulfide emissions. Higher preindustrial volcanic sulfur emissions reduce modeled anthropogenic Arctic aerosol cooling by up to a factor of two (+0.11 to +0.29 W m−2), suggesting that underestimating passive volcanic sulfur emissions has significant implications for anthropogenic-induced Arctic climate change

Effect of Hund coupling in the one-dimensional SU(4) Hubbard model

The one-dimensional SU(4) Hubbard model perturbed by Hund coupling is studied, away from half-filling, by means of renormalization group and bosonization methods. A spectral gap is always present in the spin-orbital sector irrespective of the magnitude of the Coulomb repulsion. We further distinguish between two qualitatively different regimes. At small Hund coupling, we find that the symmetry of the system is dynamically enlarged to SU(4) at low energy with the result of {\it coherent} spin-orbital excitations. When the charge sector is not gapped, a superconducting instability is shown to exist. At large Hund coupling, the symmetry is no longer enlarged to SU(4) and the excitations in the spin sector become {\it incoherent}. Furthermore, the superconductivity can be suppressed in favor of the conventional charge density wave state.Comment: 10 pages, 1 figur

Exploiting Coordination Effects for the Regioselective Zincation of Diazines Using TMPZnX⋅LiX (X=Cl, Br)

A new method for regioselective zincations of challenging N-heterocyclic substrates such as pyrimidines and pyridazine was reported using bimetallic bases TMPZnX⋅LiX (TMP=2,2,6,6-tetramethylpiperidyl; X=Cl, Br). Reactions occurred under mild conditions (25-70 °C, using 1.75 equivalents of base without additives), furnishing 2-zincated pyrimidines and 3-zincated pyridazine, which were then trapped with a variety of electrophiles. Contrasting with other s-block metalating systems, which lack selectivity in their reactions even when operating at low temperatures, these mixed Li/Zn bases enabled unprecedented regioselectivities that cannot be replicated by either LiTMP nor Zn(TMP)2 on their own. Spectroscopic and structural interrogations of organometallic intermediates involved in these reactions have shed light on the complex constitution of reaction mixtures and the origins of their special reactivities