The effect of the range of interaction on the phase diagram of a globular protein

Thermodynamic perturbation theory is applied to the model of globular proteins studied by ten Wolde and Frenkel (Science 277, pg. 1976) using computer simulation. It is found that the reported phase diagrams are accurately reproduced. The calculations show how the phase diagram can be tuned as a function of the lengthscale of the potential.Comment: 20 pages, 5 figure

Dilaton constraints and LHC prospects

The Standard Model Higgs searches using the first 1-2 fb-1 of LHC data can be used to put interesting constraints on new scalar particles other than the Higgs. We investigate one such scenario in which electroweak symmetry is broken via strongly coupled conformal dynamics. This scenario contains a neutral scalar dilaton---the Goldstone boson associated with spontaneously broken scale invariance---with a mass below the conformal symmetry breaking scale and couplings to Standard Model particles similar (but not identical) to those of the Standard Model Higgs boson. We translate the LEP and LHC Higgs limits to constrain the dilaton mass and conformal breaking scale. The conformal breaking scale f is constrained to be above 1 TeV for dilaton masses between 145 and 600 GeV, though it can be as low as 400 GeV for dilaton masses below 110 GeV. We also show that (i) a dilaton chi with mass below 110 GeV and consistent with the LEP constraints can appear in gg --> chi --> gamma gamma with a rate up to ~10 times the corresponding Standard Model Higgs rate, and (ii) a dilaton with mass of several hundred GeV is much narrower than the corresponding Standard Model Higgs, leading to improved search sensitivity in chi --> ZZ --> 4l.Comment: 15 pages, 12 figures, References added, Figure 10 modified, Figure 11 adde

Onset of collective and cohesive motion

We study the onset of collective motion, with and without cohesion, of groups of noisy self-propelled particles interacting locally. We find that this phase transition, in two space dimensions, is always discontinuous, including for the minimal model of Vicsek et al. [Phys. Rev. Lett. {\bf 75},1226 (1995)] for which a non-trivial critical point was previously advocated. We also show that cohesion is always lost near onset, as a result of the interplay of density, velocity, and shape fluctuations.Comment: accepted for publication in Phys. Rev. Let

Permutation-invariant distance between atomic configurations

We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables to directly compare different atomic environments with an arbitrary number of particles, without going through a space of reduced dimensionality (i.e. fingerprints) as an intermediate step. Moreover, this distance is naturally invariant through permutations of atoms, avoiding the time consuming associated minimization required by other common criteria (like the Root Mean Square Distance). Finally, the invariance through global rotations is accounted for by a minimization procedure in the space of rotations solved by Monte Carlo simulated annealing. A formal framework is also introduced, showing that the distance we propose verifies the property of a metric on the space of atomic configurations. Two examples of applications are proposed. The first one consists in evaluating faithfulness of some fingerprints (or descriptors), i.e. their capacity to represent the structural information of a configuration. The second application concerns structural analysis, where our distance proves to be efficient in discriminating different local structures and even classifying their degree of similarity

Coordination of Foliar and Wood Anatomical Traits Contributes to Tropical Tree Distributions and Productivity along the Malay-Thai Peninsula

Drought is a critical factor in plant species distributions. Much research points to its relevance even in moist tropical regions. Recent studies have begun to elucidate mechanisms underlying the distributions of tropical tree species with respect to drought; however, how such desiccation tolerance mechanisms correspond with the coordination of hydraulic and photosynthetic traits in determining species distributions with respect to rainfall seasonality deserves attention. In the present study, we used a common garden approach to quantify inherent differences in wood anatomical and foliar physiological traits in 21 tropical tree species with either widespread (occupying both seasonal and aseasonal climates) or southern (restricted to aseasonal forests) distributions with respect to rainfall seasonality. Use of congeneric species pairs and phylogenetically independent contrast analyses allowed examination of this question in a phylogenetic framework. Widespread species opted for wood traits that provide biomechanical support and prevent xylem cavitation and showed associated reductions in canopy productivity and consequently growth rates compared with southern species. These data support the hypothesis that species having broader distributions with respect to climatic variability will be characterized by traits conducive to abiotic stress tolerance. This study highlights the importance of the well-established performance vs. stress tolerance trade-off as a contributor to species distributions at larger scales

Criterion for purely elastic Taylor-Couette instability in the flows of shear-banding fluids

In the past twenty years, shear-banding flows have been probed by various techniques, such as rheometry, velocimetry and flow birefringence. In micellar solutions, many of the data collected exhibit unexplained spatio-temporal fluctuations. Recently, it has been suggested that those fluctuations originate from a purely elastic instability of the flow. In cylindrical Couette geometry, the instability is reminiscent of the Taylor-like instability observed in viscoelastic polymer solutions. In this letter, we describe how the criterion for purely elastic Taylor-Couette instability should be adapted to shear-banding flows. We derive three categories of shear-banding flows with curved streamlines, depending on their stability.Comment: 6 pages, 3 figure

Potential "ways of thinking" about the shear-banding phenomenon

Shear-banding is a curious but ubiquitous phenomenon occurring in soft matter. The phenomenological similarities between the shear-banding transition and phase transitions has pushed some researchers to adopt a 'thermodynamical' approach, in opposition to the more classical 'mechanical' approach to fluid flows. In this heuristic review, we describe why the apparent dichotomy between those approaches has slowly faded away over the years. To support our discussion, we give an overview of different interpretations of a single equation, the diffusive Johnson-Segalman (dJS) equation, in the context of shear-banding. We restrict ourselves to dJS, but we show that the equation can be written in various equivalent forms usually associated with opposite approaches. We first review briefly the origin of the dJS model and its initial rheological interpretation in the context of shear-banding. Then we describe the analogy between dJS and reaction-diffusion equations. In the case of anisotropic diffusion, we show how the dJS governing equations for steady shear flow are analogous to the equations of the dynamics of a particle in a quartic potential. Going beyond the existing literature, we then draw on the Lagrangian formalism to describe how the boundary conditions can have a key impact on the banding state. Finally, we reinterpret the dJS equation again and we show that a rigorous effective free energy can be constructed, in the spirit of early thermodynamic interpretations or in terms of more recent approaches exploiting the language of irreversible thermodynamics.Comment: 14 pages, 6 figures, tutorial revie

Modeling the nitrogen fluxes in the Black Sea using a 3D coupledhydrodynamical-biogeochemical model: transport versus biogeochemicalprocesses, exchanges across the shelf break and comparison of the shelf anddeep sea ecodynamics

A 6-compartment biogeochemical model of nitrogen cycling and plankton productivity has been coupled with a 3D general circulation model in an enclosed environment (the Black Sea) so as to quantify and compare, on a seasonal and annual scale, the typical internal biogeochemical functioning of the shelf and of the deep sea as well as to estimate the nitrogen and water exchanges at the shelf break. Model results indicate that the annual nitrogen net export to the deep sea roughly corresponds to the annual load of nitrogen discharged by the rivers on the shelf. The model estimated vertically integrated gross annual primary production is 130gCm-2yr-1 for the whole basin, 220gCm-2yr-1 for the shelf and 40gCm-2yr-1 for the central basin. In agreement with sediment trap observations, model results indicate a rapid and efficient recycling of particulate organic matter in the sub-oxic portion of the water column (60-80m) of the open sea. More than 95% of the PON produced in the euphotic layer is recycled in the upper 100m of the water column, 87% in the upper 80 m and 67% in the euphotic layer. The model estimates the annual export of POC towards the anoxic layer to 4 1010molyr-1. This POC is definitely lost for the system and represents 2% of the annual primary production of the open sea

On the Irreducible BRST Quantization of Spin-5/2 Gauge Fields

Spin-5/2 gauge fields are quantized in an irreducible way within both the BRST and BRST-anti-BRST manners. To this end, we transform the reducible generating set into an irreducible one, such that the physical observables corresponding to these two formulations coincide. The gauge-fixing procedure emphasizes on the one hand the differences among our procedure and the results obtained in the literature, and on the other hand the equivalence between our BRST and BRST-anti-BRST approaches.Comment: 12 pages, latex 2.09, no figure

Elastic turbulence in shear banding wormlike micelles

We study the dynamics of the Taylor-Couette flow of shear banding wormlike micelles. We focus on the high shear rate branch of the flow curve and show that for sufficiently high Weissenberg numbers, this branch becomes unstable. This instability is strongly sub-critical and is associated with a shear stress jump. We find that this increase of the flow resistance is related to the nucleation of turbulence. The flow pattern shows similarities with the elastic turbulence, so far only observed for polymer solutions. The unstable character of this branch led us to propose a scenario that could account for the recent observations of Taylor-like vortices during the shear banding flow of wormlike micelles