The crystal structure of the three-iron ferredoxin II from Desulfovibrio gigas

AbstractThe crystal structure of oxidized ferredoxin II from the sulfate-reducing bacterium Desulfovibrio gigas has been determined and refined at 1.7 Å resolution. The folding of the polypeptide chain is similar to that of the 2[4Fe-4S] ferredoxin in Peptococcus aerogenes, except for an extended helical segment near the C-terminus. The single [3Fe-4S] cluster in D. gigas is similar to a [4Fe-4S] cluster, but lacks one Fe atom and is coordinated to Cys-8, -14 and -50. The side chain of Cys-11 is not bound to the cluster, but is rotated toward the solvent and modified by some, as yet undetermined, chemical group. Cys-18 and Cys-42 form a disulfide bridge. A previously undetected extra amino acid is found after residue 55

An adaptive finite element method for the infinity Laplacian

We construct a finite element method (FEM) for the infinity Laplacian. Solutions of this problem are well known to be singular in nature so we have taken the opportunity to conduct an a posteriori analysis of the method deriving residual based estimators to drive an adaptive algorithm. It is numerically shown that optimal convergence rates are regained using the adaptive procedure

Small and Large Diameter, Water-Table Observation Wells Compared

SHALLOW ground-water investigations usually involve the use of various sizes of perforated observation wells and/or sometimes batteries of piezometer tubes. Such equipment is used to determine the position of the water table, defined as the upper surface of the saturation zone and also the surface of atmospheric pressure (3, 4) 0 . The zone of saturation, however, often extends above the surface of atmospheric pressure a distance dependent primarily on the soil texture

Some flows in shape optimization

Geometric flows related to shape optimization problems of Bernoulli type are investigated. The evolution law is the sum of a curvature term and a nonlocal term of Hele-Shaw type. We introduce generalized set solutions, the definition of which is widely inspired by viscosity solutions. The main result is an inclusion preservation principle for generalized solutions. As a consequence, we obtain existence, uniqueness and stability of solutions. Asymptotic behavior for the flow is discussed: we prove that the solutions converge to a generalized Bernoulli exterior free boundary problem

Experiences with Modelling Issues in Building Probabilistic Networks

Abstract. Building a probabilistic network for a real-life application is a difficult and time-consuming task. Methodologies for building such a network, however, are still lacking. Also, literature on network-specific modelling issues is quite scarce. As we have developed a large proba-bilistic network for a complex medical domain, we have encountered and resolved numerous non-trivial modelling issues. Since many of these is-sues pertain not only to our application but are likely to emerge for other applications as well, we feel that sharing them will contribute to engineering probabilistic networks in general.

Three efficient numerical models to analyse the step problem in shallow water

In this paper, the problem of acoustic wave propagation in a waveguide of infinite extent is modelled, taking into account constant depth in each section of the sea. Efficient numerical strategies in the frequency domain are addressed to investigate two-dimensional acoustic wave propagation in a shallow water configuration, considering a step in the rigid bottom and a flat free surface. The time domain responses are obtained by means of an inverse Fast Fourier Transform (FFT) of results computed in the frequency domain. The numerical approaches used here are based on the Boundary Element Method (BEM) and the Method of Fundamental Solutions (MFS). In the numerical models only the inclined or vertical interface between the sub-regions of different depth are discretized, as Green׳s functions that take into account the presence of free and rigid surfaces are used. These Green׳s functions are obtained either by eigenfunction expansion or by Ewald׳s method. A detailed discussion on the performance of these formulations is carried out, with the aim of finding an efficient numerical formulation to solve the step problem in shallow water

Dynamics of tournaments: the soccer case

A random walk-like model is considered to discuss statistical aspects of tournaments. The model is applied to soccer leagues with emphasis on the scores. This competitive system was computationally simulated and the results are compared with empirical data from the English, the German and the Spanish leagues and showed a good agreement with them. The present approach enabled us to characterize a diffusion where the scores are not normally distributed, having a short and asymmetric tail extending towards more positive values. We argue that this non-Gaussian behavior is related with the difference between the teams and with the asymmetry of the scores system. In addition, we compared two tournament systems: the all-play-all and the elimination tournaments.Comment: To appear in EPJ

Radiative corrections to the excitonic molecule state in GaAs microcavities

The optical properties of excitonic molecules (XXs) in GaAs-based quantum well microcavities (MCs) are studied, both theoretically and experimentally. We show that the radiative corrections to the XX state, the Lamb shift $\Delta^{\rm MC}_{\rm XX}$ and radiative width $\Gamma^{\rm MC}_{\rm XX}$, are large, about $10-30$ of the molecule binding energy $\epsilon_{\rm XX}$, and definitely cannot be neglected. The optics of excitonic molecules is dominated by the in-plane resonant dissociation of the molecules into outgoing 1$\lambda$-mode and 0$\lambda$-mode cavity polaritons. The later decay channel, ``excitonic molecule $\to$ 0$\lambda$-mode polariton + 0$\lambda$-mode polariton'', deals with the short-wavelength MC polaritons invisible in standard optical experiments, i.e., refers to ``hidden'' optics of microcavities. By using transient four-wave mixing and pump-probe spectroscopies, we infer that the radiative width, associated with excitonic molecules of the binding energy $\epsilon_{\rm XX} \simeq 0.9-1.1$ meV, is $\Gamma^{\rm MC}_{\rm XX} \simeq 0.2-0.3$ meV in the microcavities and $\Gamma^{\rm QW}_{\rm XX} \simeq 0.1$ meV in a reference GaAs single quantum well (QW). We show that for our high-quality quasi-two-dimensional nanostructures the $T_2 = 2 T_1$ limit, relevant to the XX states, holds at temperatures below 10 K, and that the bipolariton model of excitonic molecules explains quantitatively and self-consistently the measured XX radiative widths. We also find and characterize two critical points in the dependence of the radiative corrections against the microcavity detuning, and propose to use the critical points for high-precision measurements of the molecule bindingenergy and microcavity Rabi splitting.Comment: 16 pages, 11 figures, accepted for publication in Phys. Rev.

Dynamic Scaling and Two-Dimensional High-Tc Superconductors

There has been ongoing debate over the critical behavior of two-dimensional superconductors; in particular for high Tc superconductors. The conventional view is that a Kosterlitz-Thouless-Berezinskii transition occurs as long as finite size effects do not obscure the transition. However, there have been recent suggestions that a different transition actually occurs which incorporates aspects of both the dynamic scaling theory of Fisher, Fisher, and Huse and the Kosterlitz-Thouless-Berezinskii transition. Of general interest is that this modified transition apparently has a universal dynamic critical exponent. Some have countered that this apparent universal behavior is rooted in a newly proposed finite-size scaling theory; one that also incorporates scaling and conventional two-dimensional theory. To investigate these issues we study DC voltage versus current data of a 12 angstrom thick YBCO film. We find that the newly proposed scaling theories have intrinsic flexibility that is relevant to the analysis of the experiments. In particular, the data scale according to the modified transition for arbitrarily defined critical temperatures between 0 K and 19.5 K, and the temperature range of a successful scaling collapse is related directly to the sensitivity of the measurement. This implies that the apparent universal exponent is due to the intrinsic flexibility rather than some real physical property. To address this intrinsic flexibility, we propose a criterion which would give conclusive evidence for phase transitions in two-dimensional superconductors. We conclude by reviewing results to see if our criterion is satisfied.Comment: 14 page

The Planetary Nebula Luminosity Function at the Dawn of Gaia

The [O III] 5007 Planetary Nebula Luminosity Function (PNLF) is an excellent extragalactic standard candle. In theory, the PNLF method should not work at all, since the luminosities of the brightest planetary nebulae (PNe) should be highly sensitive to the age of their host stellar population. Yet the method appears robust, as it consistently produces < 10% distances to galaxies of all Hubble types, from the earliest ellipticals to the latest-type spirals and irregulars. It is therefore uniquely suited for cross-checking the results of other techniques and finding small offsets between the Population I and Population II distance ladders. We review the calibration of the method and show that the zero points provided by Cepheids and the Tip of the Red Giant Branch are in excellent agreement. We then compare the results of the PNLF with those from Surface Brightness Fluctuation measurements, and show that, although both techniques agree in a relative sense, the latter method yields distances that are ~15% larger than those from the PNLF. We trace this discrepancy back to the calibration galaxies and argue that, due to a small systematic error associated with internal reddening, the true distance scale likely falls between the extremes of the two methods. We also demonstrate how PNLF measurements in the early-type galaxies that have hosted Type Ia supernovae can help calibrate the SN Ia maximum magnitude-rate of decline relation. Finally, we discuss how the results from space missions such as Kepler and Gaia can help our understanding of the PNLF phenomenon and improve our knowledge of the physics of local planetary nebulae.Comment: 12 pages, invited review at the conference "The Fundamental Cosmic Distance Scale: State of the Art and Gaia Perspective", to appear in Astrophysics and Space Scienc