A coupled Temperley-Lieb algebra for the superintegrable chiral Potts chain

The hamiltonian of the $N$-state superintegrable chiral Potts (SICP) model is written in terms of a coupled algebra defined by $N-1$ types of Temperley-Lieb generators. This generalises a previous result for $N=3$ obtained by J. F. Fjelstad and T. M\r{a}nsson [J. Phys. A {\bf 45} (2012) 155208]. A pictorial representation of a related coupled algebra is given for the $N=3$ case which involves a generalisation of the pictorial presentation of the Temperley-Lieb algebra to include a pole around which loops can become entangled. For the two known representations of this algebra, the $N=3$ SICP chain and the staggered spin-1/2 XX chain, closed (contractible) loops have weight $\sqrt{3}$ and weight $2$, respectively. For both representations closed (non-contractible) loops around the pole have weight zero. The pictorial representation provides a graphical interpretation of the algebraic relations. A key ingredient in the resolution of diagrams is a crossing relation for loops encircling a pole which involves the parameter $\rho= e^{ 2\pi \mathrm{i}/3}$ for the SICP chain and $\rho=1$ for the staggered XX chain. These $\rho$ values are derived assuming the Kauffman bracket skein relation.Comment: 10 pages, 4 figures, further cubic relations adde

Quantification of reachable attractors in asynchronous discrete dynamics

Motivation: Models of discrete concurrent systems often lead to huge and complex state transition graphs that represent their dynamics. This makes difficult to analyse dynamical properties. In particular, for logical models of biological regulatory networks, it is of real interest to study attractors and their reachability from specific initial conditions, i.e. to assess the potential asymptotical behaviours of the system. Beyond the identification of the reachable attractors, we propose to quantify this reachability. Results: Relying on the structure of the state transition graph, we estimate the probability of each attractor reachable from a given initial condition or from a portion of the state space. First, we present a quasi-exact solution with an original algorithm called Firefront, based on the exhaustive exploration of the reachable state space. Then, we introduce an adapted version of Monte Carlo simulation algorithm, termed Avatar, better suited to larger models. Firefront and Avatar methods are validated and compared to other related approaches, using as test cases logical models of synthetic and biological networks. Availability: Both algorithms are implemented as Perl scripts that can be freely downloaded from http://compbio.igc.gulbenkian.pt/nmd/node/59 along with Supplementary Material.Comment: 19 pages, 2 figures, 2 algorithms and 2 table

Variable Selection and Model Averaging in Semiparametric Overdispersed Generalized Linear Models

We express the mean and variance terms in a double exponential regression model as additive functions of the predictors and use Bayesian variable selection to determine which predictors enter the model, and whether they enter linearly or flexibly. When the variance term is null we obtain a generalized additive model, which becomes a generalized linear model if the predictors enter the mean linearly. The model is estimated using Markov chain Monte Carlo simulation and the methodology is illustrated using real and simulated data sets.Comment: 8 graphs 35 page

Fragmentation Instability of Molecular Clouds: Numerical Simulations

We simulate fragmentation and gravitational collapse of cold, magnetized molecular clouds. We explore the nonlinear development of an instability mediated by ambipolar diffusion, in which the collapse rate is intermediate to fast gravitational collapse and slow quasistatic collapse. Initially uniform stable clouds fragment into elongated clumps with masses largely determined by the cloud temperature, but substantially larger than the thermal Jeans mass. The clumps are asymmetric, with significant rotation and vorticity, and lose magnetic flux as they collapse. The clump shapes, intermediate collapse rates, and infall profiles may help explain observations not easily fit by contemporary slow or rapid collapse models.Comment: 25pp, 20 small eps figures, in press ApJ, April 1, 200

Assessing Tolerance to Heavy-Metal Stress in Arabidopsis thaliana Seedlings

The deposited book chapter is a post-print version and has been submitted to peer review.The deposited book chapter version contains attached the supplementary materials within the pdf.This publication hasn't any creative commons license associated.The deposited book chapter is part of the book series: "Environmental Responses in Plants: Methods and Protocols" (pp.197-208) published by Springer.Heavy-metal soil contamination is one of the major abiotic stress factors that, by negatively affecting plant growth and development, severely limit agricultural productivity worldwide. Plants have evolved various tolerance and detoxification strategies in order to cope with heavy-metal toxicity while ensuring adequate supply of essential micronutrients at the whole-plant as well as cellular levels. Genetic studies in the model plant Arabidopsis thaliana have been instrumental in elucidating such mechanisms. The root assay constitutes a very powerful and simple method to assess heavy-metal stress tolerance in Arabidopsis seedlings. It allows the simultaneous determination of all the standard growth parameters affected by heavy-metal stress (primary root elongation, lateral root development, shoot biomass, and chlorophyll content) in a single experiment. Additionally, this protocol emphasizes the tips and tricks that become particularly useful when quantifying subtle alterations in tolerance to a given heavy-metal stress, when simultaneously pursuing a large number of plant lines, or when testing sensitivity to a wide range of heavy metals for a single line.Fundação para a Ciência e a Tecnologia grants: (EXPL/AGR-PRO/1013/2013, SFRH/BPD/44640/2008); GREEN-it "Bioresources for Sustainability": (UID/Multi/04551/2013).info:eu-repo/semantics/publishedVersio

Possible explanations for different surface quality in laser cutting with 1 micron and 10 microns beams

In laser　cutting　of　thick　steel　sheets,　quality　difference　is　observed　between　cut　surfaces　obtained　with 1 micron and 10 micron laser beams. This paper investigates physical mechanisms for this interesting and important problem of the wavelength dependence. First, striation generation process is described, based on a 3D structure of melt flow on a kerf front, which was revealed for the first time by our recent experimental observations. Two fundamental processes are suggested to explain the difference in the cut surface quality: destabilization of the melt flow in the central part of the kerf front and downward displacement of discrete melt accumulations along the side parts of the front. Then each of the processes is analyzed using a simplified analytical model. The results show that in both processes, different angular dependence of the absorptivity of the laser beam can result in the quality difference. Finally we propose use of radial polarization to improve the quality with the 1 micron wavelength

Infrared point source variability between the Spitzer and MSX surveys of the Galactic mid-plane

We present a list of 552 sources with suspected variability, based on a comparison of mid-infrared photometry from the GLIMPSE I and MSX surveys, which were carried out nearly a decade apart. We were careful to address issues such as the difference in resolution and sensitivity between the two surveys, as well as the differences in the spectral responses of the instruments. We selected only sources where the IRAC 8.0 and MSX 8.28 micron fluxes differ by more than a factor of two, in order to minimize contamination from sources where the difference in fluxes at 8 micron is due to a strong 10 micron silicate feature. We present a subset of 40 sources for which additional evidence suggests variability, using 2MASS and MIPSGAL data. Based on a comparison with the variability flags in the IRAS and MSX Point-Source Catalogs we estimate that at least a quarter of the 552 sources, and at least half of the 40 sources are truly variable. In addition, we tentatively confirm the variability of one source using multi-epoch IRAS LRS spectra. We suggest that most of the sources in our list are likely to be Asymptotic Giant Branch stars.Comment: 47 pages, 12 Figures, 3 Tables, accepted for publication in A

Structural and magnetic properties of E-Fe_{1-x}Co_xSi thin films deposited via pulsed laser deposition

We report pulsed laser deposition synthesis and characterization of polycrystalline Fe1-xCox Si thin films on Si (111). X-ray diffraction, transmission electron, and atomic force microscopies reveal films to be dense, very smooth, and single phase with a cubic B20 crystal structure. Ferromagnetism with significant magnetic hysteresis is found for all films including nominally pure FeSi films in contrast to the very weak paramagnetism of bulk FeSi. For Fe1-xCoxSi this signifies a change from helimagnetism in bulk, to ferromagnetism in thin films. These ferromagnetic thin films are promising as a magnetic-silicide/silicon system for polarized current production, manipulation, and detection.Comment: 12 pages, 4 figures accepted in the Applied Physics Letter

The Major Facilitator Superfamily Transporter ZIFL2 Modulates Cesium and Potassium Homeostasis in Arabidopsis

Potassium (K(+)) is an essential mineral nutrient for plant growth and development, with numerous membrane transporters and channels having been implicated in the maintenance and regulation of its homeostasis. The cation cesium (Cs(+)) is toxic for plants but shares similar chemical properties to the K(+) ion and hence competes with its transport. Here, we report that K(+) and Cs(+) homeostasis in Arabidopsis thaliana also requires the action of ZIFL2 (Zinc-Induced Facilitator-Like 2), a member of the Major Facilitator Superfamily (MFS) of membrane transporters. We show that the Arabidopsis ZIFL2 is a functional transporter able to mediate K(+) and Cs(+) influx when heterologously expressed in yeast. Promoter-reporter, reverse transcription-PCR and fluorescent protein fusion experiments indicate that the predominant ZIFL2.1 isoform is targeted to the plasma membrane of endodermal and pericyle root cells. ZIFL2 loss of function and overexpression exacerbate and alleviate plant sensitivity, respectively, upon Cs(+) and excess K(+) supply, also influencing Cs(+) whole-plant partitioning. We propose that the activity of this Arabidopsis MFS carrier promotes cellular K(+) efflux in the root, thereby restricting Cs(+)/K(+) xylem loading and subsequent root to shoot translocation under conditions of Cs(+) or high K(+) external supply.FCT fellowships: (SFRH/BPD/44640/2008, SFRH/BPD/81221/2011)