Spanning avalanches in the three-dimensional Gaussian random-field Ising model with metastable dynamics: Field dependence and geometrical properties

Spanning avalanches in the 3D Gaussian Random Field Ising Model (3D-GRFIM) with metastable dynamics at T=0 have been studied. Statistical analysis of the field values for which avalanches occur has enabled a Finite-Size Scaling (FSS) study of the avalanche density to be performed. Furthermore, a direct measurement of the geometrical properties of the avalanches has confirmed an earlier hypothesis that several types of spanning avalanches with two different fractal dimensions coexist at the critical point. We finally compare the phase diagram of the 3D-GRFIM with metastable dynamics with the same model in equilibrium at T=0.

Identification of GPx8 as a novel cellular substrate of the hepatitis C virus NS3-4A protease

Background: The hepatitis C virus (HCV) NS3-4A protease is not only an essential component of the viral replication complex and a prime target for antiviral intervention but also a key player in the persistence and pathogenesis of HCV. It cleaves and thereby inactivates two crucial adaptor proteins in viral RNA sensing and innate immunity (MAVS and TRIF) as well as a phosphatase involved in growth factor signaling (TC-PTP). The aim of this study was to identify novel cellular substrates of the NS3-4A protease and to investigate their role in the life cycle and pathogenesis of HCV. Methods: Cell lines inducibly expressing the NS3-4A protease were analyzed in basal as well as interferon- α -stimulated states by stable isotopic labeling using amino acids in cell culture (SILAC) coupled with protein separation and mass spectrometry. Candidates fulfilling strin- gent criteria for potential substrates or products of the NS3-4A protease were further investigated in different experimental sys- tems as well as in liver biopsies from patients with chronic hep- atitis C. Results: SILAC coupled with protein separation and mass spectrometry yielded > 5000 proteins of which 21 can- didates were selected for further analyses. These allowed us to identify GPx8, a membrane-associated peroxidase involved in disulfide bond formation in the endoplasmic reticulum, as a novel cellular substrate of the HCV NS3-4A protease. Cleavage occurs at cysteine in position 11, removing the cytosolic tip of GPx8, and was observed in different experimental systems as well as in liver biopsies from patients with chronic hepatitis C. Further functional studies, involving overexpression and RNA silencing, revealed that GPx8 is a proviral factor involved in viral particle production but not in HCV entry or RNA replica- tion. Conclusions: GPx8 is a proviral host factor cleaved by the HCV NS3-4A protease. Studies investigating the consequences of cleavage for GPx8 function are underway. The identification of novel cellular substrates of the HCV NS3-4A protease should yield new insights into the HCV life cycle and the pathogenesis of hepatitis C and may reveal novel angles for therapeutic inter- vention.

Diluted three-dimensional random field Ising model at zero temperature with metastable dynamics.

The influence of vacancy concentration on the behavior of the three-dimensional random field Ising model with metastable dynamics is studied. We have focused our analysis on the number of spanning avalanches which allows us a clear determination of the critical line where the hysteresis loops change from continuous to discontinuous. By a detailed finite-size scaling analysis we determine the phase diagram and numerically estimate the critical exponents along the whole critical line. Finally, we discuss the origin of the curvature of the critical line at high vacancy concentration.

Optical response of two-dimensional few-electron concentric double quantum rings: A local-spin-density-functional theory study

We have investigated the dipole charge- and spin-density response of few-electron two-dimensional concentric nanorings as a function of the intensity of a erpendicularly applied magnetic field. We show that the dipole response displays signatures associated with the localization of electron states in the inner and outer ring favored by the perpendicularly applied magnetic field. Electron localization produces a more fragmented spectrum due to the appearance of additional edge excitations in the inner and outer ring.

Dimensional reduction and gauge group reduction in Bianchi-type cosmology

In this paper we examine in detail the implementation, with its associated difficulties, of the Killing conditions and gauge fixing into the variational principle formulation of Bianchi-type cosmologies. We address problems raised in the literature concerning the Lagrangian and the Hamiltonian formulations: We prove their equivalence, make clear the role of the homogeneity preserving diffeomorphisms in the phase space approach, and show that the number of physical degrees of freedom is the same in the Hamiltonian and Lagrangian formulations. Residual gauge transformations play an important role in our approach, and we suggest that Poincaré transformations for special relativistic systems can be understood as residual gauge transformations. In the Appendixes, we give the general computation of the equations of motion and the Lagrangian for any Bianchi-type vacuum metric and for spatially homogeneous Maxwell fields in a nondynamical background (with zero currents). We also illustrate our counting of degrees of freedom in an appendix.

MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.

A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcription start site profiles, the mapping of transcription factor binding sites based on ChIP-chip data and the identification of quantitative trait loci (QTL) from whole genome SNP profiles. Input to such an analysis is a set of genome coordinates associated with counts or intensities. The output consists of a discrete number of peaks with respective volumes, extensions and center positions. We have developed for this purpose a flexible one-dimensional clustering tool, called MADAP, which we make available as a web server and as standalone program. A set of parameters enables the user to customize the procedure to a specific problem. The web server, which returns results in textual and graphical form, is useful for small to medium-scale applications, as well as for evaluation and parameter tuning in view of large-scale applications, requiring a local installation. The program written in C++ can be freely downloaded from ftp://ftp.epd.unil.ch/pub/software/unix/madap. The MADAP web server can be accessed at http://www.isrec.isb-sib.ch/madap/.

Pairing in two-dimensional boson-fermion mixtures

The possibilities of pairing in two-dimensional boson-fermion mixtures are carefully analyzed. It is shown that the boson-induced attraction between two identical fermions dominates the p wave pairing at low density. For a given fermion density, the pairing gap becomes maximal at a certain optimal boson concentration. The conditions for observing pairing in current experiments are discussed.

Role of the GNOM gene in Arabidopsis apical-basal patterning--From mutant phenotype to cellular mechanism of protein action.

How the apical-basal axis of polarity is established in embryogenesis is still a mystery in plant development. This axis appeared specifically compromised by mutations in the Arabidopsis GNOM gene. Surprisingly, GNOM encodes an ARF guanine-nucleotide exchange factor (ARF-GEF) that regulates the formation of vesicles in membrane trafficking. In-depth functional analysis of GNOM and its closest relative, GNOM-LIKE 1 (GNL1), has provided a mechanistic explanation for the development-specific role of a seemingly mundane trafficking regulator. The current model proposes that GNOM is specifically involved in the endosomal recycling of the auxin-efflux carrier PIN1 to the basal plasma membrane in provascular cells, which in turn is required for the accumulation of the plant hormone auxin at the future root pole through polar auxin transport. Thus, the analysis of GNOM highlights the importance of cell-biological processes for a mechanistic understanding of development.

Semiclassical coupled wave theory and its application to TE waves in one dimensional crystals

A semiclassical coupled-wave theory is developed for TE waves in one-dimensional periodic structures. The theory is used to calculate the bandwidths and reflection/transmission characteristics of such structures, as functions of the incident wave frequency. The results are in good agreement with exact numerical simulations for an arbitrary angle of incidence and for any achievable refractive index contrast on a period of the structure.

Dynamics of the two-dimensional gonihedric spin model

In this paper, we study dynamical aspects of the two-dimensional (2D) gonihedric spin model using both numerical and analytical methods. This spin model has vanishing microscopic surface tension and it actually describes an ensemble of loops living on a 2D surface. The self-avoidance of loops is parametrized by a parameter ¿. The ¿=0 model can be mapped to one of the six-vertex models discussed by Baxter, and it does not have critical behavior. We have found that allowing for ¿¿0 does not lead to critical behavior either. Finite-size effects are rather severe, and in order to understand these effects, a finite-volume calculation for non-self-avoiding loops is presented. This model, like his 3D counterpart, exhibits very slow dynamics, but a careful analysis of dynamical observables reveals nonglassy evolution (unlike its 3D counterpart). We find, also in this ¿=0 case, the law that governs the long-time, low-temperature evolution of the system, through a dual description in terms of defects. A power, rather than logarithmic, law for the approach to equilibrium has been found.

Studying Avalanches in the ground-state of the two-dimensional random field Ising model driven by an external field

We study the exact ground state of the two-dimensional random-field Ising model as a function of both the external applied field B and the standard deviation ¿ of the Gaussian random-field distribution. The equilibrium evolution of the magnetization consists in a sequence of discrete jumps. These are very similar to the avalanche behavior found in the out-of-equilibrium version of the same model with local relaxation dynamics. We compare the statistical distributions of magnetization jumps and find that both exhibit power-law behavior for the same value of ¿. The corresponding exponents are compared.

Side-branch growth in two-dimensional dendrits. Part II: Phase-field model

The development of side-branching in solidifying dendrites in a regime of large values of the Peclet number is studied by means of a phase-field model. We have compared our numerical results with experiments of the preceding paper and we obtain good qualitative agreement. The growth rate of each side branch shows a power-law behavior from the early stages of its life. From their birth, branches which finally succeed in the competition process of side-branching development have a greater growth exponent than branches which are stopped. Coarsening of branches is entirely defined by their geometrical position relative to their dominant neighbors. The winner branches escape from the diffusive field of the main dendrite and become independent dendrites.