Spin Resolution of the Electron-Gas Correlation Energy: Positive same-spin contribution

The negative correlation energy per particle of a uniform electron gas of density parameter $r_s$ and spin polarization $\zeta$ is well known, but its spin resolution into up-down, up-up, and down-down contributions is not. Widely-used estimates are incorrect, and hamper the development of reliable density functionals and pair distribution functions. For the spin resolution, we present interpolations between high- and low-density limits that agree with available Quantum Monte Carlo data. In the low-density limit for $\zeta = 0$, we find that the same-spin correlation energy is unexpectedly positive, and we explain why. We also estimate the up and down contributions to the kinetic energy of correlation.Comment: new version, to appear in PRB Rapid Communicatio

Clustering Genes of Common Evolutionary History.

Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent-due to events such as incomplete lineage sorting or horizontal gene transfer-it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modeling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such "process-agnostic" approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance and clustering methods; their comparative performance in the context of tree incongruence is largely unknown. Furthermore, because standard model selection criteria such as AIC cannot be applied to problems with a variable number of topologies, the issue of inferring the optimal number of clusters is poorly understood. Here, we perform a large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history. We observe that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward's method. We also introduce two statistical tests to infer the optimal number of clusters and show that they strongly outperform the silhouette criterion, a general-purpose heuristic. We illustrate the usefulness of the approach by 1) identifying errors in a previous phylogenetic analysis of yeast species and 2) identifying topological incongruence among newly sequenced loci of the globeflower fly genus Chiastocheta We release treeCl, a new program to cluster genes of common evolutionary history (http://git.io/treeCl)

On the lower bound on the exchange-correlation energy in two dimensions

We study the properties of the lower bound on the exchange-correlation energy in two dimensions. First we review the derivation of the bound and show how it can be written in a simple density-functional form. This form allows an explicit determination of the prefactor of the bound and testing its tightness. Next we focus on finite two-dimensional systems and examine how their distance from the bound depends on the system geometry. The results for the high-density limit suggest that a finite system that comes as close as possible to the ultimate bound on the exchange-correlation energy has circular geometry and a weak confining potential with a negative curvature

Patterns of Flavour Violation in a Warped Extra Dimensional Model with Custodial Protection

We present a particular warped extra dimensional model, where the flavour diagonal and flavour non-diagonal Z boson couplings to left-handed down quarks are protected by the custodial symmetry P_LR. After a brief introduction of the model and of its main theoretical motivations, we present a complete study of rare K and B meson decays, including K+ --> pi+ nu anti-nu, K_L --> pi0 nu anti-nu, B_{s,d} --> mu+ mu- and B_{s,d} --> X_{s,d} nu anti-nu. In particular we restrict the parameter space of the model to the subspace which fits all quark masses, CKM mixing parameters and all the measured Delta F=2 observables, keeping the Kaluza-Klein scale in the reach of LHC (~(2-3)TeV). There we show that, in addition to the one loop contribution of the Standard Model (SM), the dominating new physics contribution to the rare decays of K and B_{s,d} mesons is the tree level exchange of the Z boson of the SM governed by right-handed couplings to down-type quarks. In order to reduce the parameter dependence, we study correlations between various branching ratios of B and K mesons and between Delta F=1 and Delta F=2 observables. The patterns that we find allow to distinguish this new physics scenario from the SM and can offer an opportunity to future experiments to confirm or rule out the model.Comment: 10 pages, 8 figures, To appear in the proceedings of DISCRETE '08, 11-16 December 2008, Valencia, Spai

Extracellular DNA provides structural integrity to a Micrococcus luteus biofilm

Force spectroscopy was used to show that extracellular DNA (eDNA) has a pre-eminent structural role in a biofilm. The adhesive behavior of extracellular polymeric substances to poly(ethylene terephthalate), a model hydrophobic surface, was measured in response to their degradation by hydrolytic enzymes known for their biofilm dispersion potential: DNaseI, protease, cellulase, and mannanase. Only treatment with DNaseI significantly decreased the adhesive force of the model bacterium Micrococcus luteus with the surface, and furthermore this treatment almost completely eliminated any components of the biofilm maintaining the adhesion, establishing a key structural role for eDNA

A Taxonomy of Causality-Based Biological Properties

We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a theoretical point of view, biochemical reactions are abstractly represented as causal implications and the produced metabolites as causal consequences of the implication representing the corresponding reaction. The fact that a reactant is produced is represented by means of the chain of reactions that have made it exist. Such representation abstracts away from quantities, stoichiometric and thermodynamic parameters and constitutes the basis for the characterization of our properties. Moreover, we propose an effective method for verifying our properties based on an abstract model of system dynamics. This consists of a new abstract semantics for the system seen as a concurrent network and expressed using the Chemical Ground Form calculus. We illustrate an application of this framework to a portion of a real metabolic pathway

Rare K and B Decays in a Warped Extra Dimension with Custodial Protection

We present a complete study of rare K and B meson decays in a warped extra dimensional model with a custodial protection of (both diagonal and non-diagonal) Z d_L^i \bar d_L^j couplings, including K^+ -> pi^+ nu anti-nu, K_L -> pi^0 nu anti-nu, K_L -> pi^0 l^+ l^-, K_L -> mu^+ mu^-, B_{s,d} -> mu^+ mu^-, B -> K nu anti-nu, B -> K^* nu anti-nu and B -> X_{s,d} nu anti-nu. In this model in addition to Standard Model one loop contributions these processes receive tree level contributions from the Z boson and the new heavy electroweak gauge bosons. We analyse all these contributions that turn out to be dominated by tree level Z boson exchanges governed by right-handed couplings to down-type quarks. Imposing all existing constraints from Delta F=2 transitions analysed by us recently and fitting all quark masses and CKM mixing parameters we find that a number of branching ratios for rare K decays can differ significantly from the SM predictions, while the corresponding effects in rare B decays are modest, dominantly due to the custodial protection being more effective in B decays than in K decays. In order to reduce the parameter dependence we study correlations between various observables within the K system, within the B system and in particular between K and B systems, and also between Delta F=2 and Delta F=1 observables. These correlations allow for a clear distinction between this new physics scenario and models with minimal flavour violation or the Littlest Higgs Model with T-parity, and could give an opportunity to future experiments to confirm or rule out the model. We show how our results would change if the custodial protection of Z d_L^i bar d^j_L couplings was absent. In the case of rare B decays the modifications are spectacular.Comment: 50 pages, 17 figures. v2: minor clarifying comments and references added. v3: few clarifying comments added, matches published versio