One-Flavour Hybrid Monte Carlo with Wilson Fermions

The Wilson fermion determinant can be written as product of the determinants of two hermitian positive definite matrices. This formulation allows to simulate non-degenerate quark flavors by means of the hybrid Monte Carlo algorithm. A major numerical difficulty is the occurrence of nested inversions. We construct a Uzawa iteration scheme which treats the nested system within one iterative process.Comment: 11 pages, to appear in proceedings of the workshop "Numerical Challenges in Lattice QCD", Springer Verla

Implementing Green Infrastructure for the Spatial Planning of Peri-Urban Areas in Geneva, Switzerland

The concept of green infrastructure (GI) seeks to identify and prioritize areas of high ecological value for wildlife and people, to improve the integration of natural values in landscape planning decisions. In 2018, the canton of Geneva, Switzerland, established a roadmap for biodiversity conservation, which includes the operationalization of GI covering 30% of the territory by 2030. In this paper, we demonstrate a GI mapping framework in the canton of Geneva. Our approach is based on the combined assessment of three 'pillars', namely species' distribution, landscape structure and connectivity, and ecosystem services, to optimize the allocation of conservation actions using the spatial prioritization software, Zonation. The identified priority conservation areas closely overlap existing natural reserves. Including the three pillars in the landscape prioritization should also improve adhesion to the GI idea, without undermining the protection of threatened species. With regards to land use planning, public and private land parcels with high values for GI may require specific incentives to maintain their desirable characteristics, as they are more likely to be degraded than areas with more building restrictions. Visualizing priority conservation areas in a spatially explicit manner will support decision-makers in Geneva to optimally allocate limited resources for ecosystem preservation.Peer reviewe

KELT-6b: A P~7.9 d Hot Saturn Transiting a Metal-Poor Star with a Long-Period Companion

We report the discovery of KELT-6b, a mildly-inflated Saturn-mass planet transiting a metal-poor host. The initial transit signal was identified in KELT-North survey data, and the planetary nature of the occulter was established using a combination of follow-up photometry, high-resolution imaging, high-resolution spectroscopy, and precise radial velocity measurements. The fiducial model from a global analysis including constraints from isochrones indicates that the V=10.38 host star (BD+31 2447) is a mildly evolved, late-F star with T_eff=6102 \pm 43 K, log(g_*)=4.07_{-0.07}^{+0.04} and [Fe/H]=-0.28 \pm 0.04, with an inferred mass M_*=1.09 \pm 0.04 M_sun and radius R_star=1.58_{-0.09}^{+0.16} R_sun. The planetary companion has mass M_P=0.43 \pm 0.05 M_J, radius R_P=1.19_{-0.08}^{+0.13} R_J, surface gravity log(g_P)=2.86_{-0.08}^{+0.06}, and density rho_P=0.31_{-0.08}^{+0.07} g~cm^{-3}. The planet is on an orbit with semimajor axis a=0.079 \pm 0.001 AU and eccentricity e=0.22_{-0.10}^{+0.12}, which is roughly consistent with circular, and has ephemeris of T_c(BJD_TDB)=2456347.79679 \pm 0.00036 and P=7.845631 \pm 0.000046 d. Equally plausible fits that employ empirical constraints on the host star parameters rather than isochrones yield a larger planet mass and radius by ~4-7%. KELT-6b has surface gravity and incident flux similar to HD209458b, but orbits a host that is more metal poor than HD209458 by ~0.3 dex. Thus, the KELT-6 system offers an opportunity to perform a comparative measurement of two similar planets in similar environments around stars of very different metallicities. The precise radial velocity data also reveal an acceleration indicative of a longer-period third body in the system, although the companion is not detected in Keck adaptive optics images.Comment: Published in AJ, 17 pages, 15 figures, 6 table

Recent progress in first-principles studies of magnetoelectric multiferroics

Materials that combine magnetic and ferroelectric properties have generated increasing interest over the last few years, due to both their diverse properties and their potential utility in new types of magnetoelectric device applications. In this review we discuss recent progress in the study of such magnetoelectric multiferroics which has been achieved using computational first-principles methods based on density functional theory. In particular, we show how first-principles methods have been successfully used to explain various properties of multiferroic materials and to predict novel effects and new systems that exhibit multiferroic properties.Comment: 25 pages, 4 figures, to appear in a special issue of "Current Opinion in Solid State and Materials science" on "Theory and Modeling of Ferroelectric Materials

Polarization state of the optical near-field

The polarization state of the optical electromagnetic field lying several nanometers above complex dielectric structures reveals the intricate light-matter interaction that occurs in this near-field zone. This information can only be extracted from an analysis of the polarization state of the detected light in the near-field. These polarization states can be calculated by different numerical methods well-suited to near--field optics. In this paper, we apply two different techniques (Localized Green Function Method and Differential Theory of Gratings) to separate each polarisation component associated with both electric and magnetic optical near-fields produced by nanometer sized objects. The analysis is carried out in two stages: in the first stage, we use a simple dipolar model to achieve insight into the physical origin of the near-field polarization state. In the second stage, we calculate accurate numerical field maps, simulating experimental near-field light detection, to supplement the data produced by analytical models. We conclude this study by demonstrating the role played by the near-field polarization in the formation of the local density of states.Comment: 9 pages, 11 figures, accepted for publication in Phys. Rev.

Deficiency of the Adhesive Protein Complex Lymphocyte Function Antigen 1, Complement Receptor Type 3, Glycoprotein p150,95 in a Girl with Recurrent Bacterial Infections Effects on Phagocytic Cells and Lymphocyte Functions

Abstract A patient presenting delayed umbilical cord detachment, severe recurrent bacterial infections, and inability to form pus exhibited a profound defect in the expression of a-and 8-chains of the receptor for the C3bi fragment of C3 (CR3), lymphocyte function antigen I (LFA-1) molecule, and the p150,95 molecule found on neutrophils, monocytes, and lymphocyte membranes. This was shown by immunofluorescence studies using specific monoclonal antibodies, rosette formation with C3bi-coated erythrocytes, and immunoprecipitation for the LFA-1 complex. These membrane defects were responsible for abnormal phagocytic cell functions including adherence to nylon wool, cell movement, phagocytosis, and opsonized particle-induced oxidative response and for defective natural killer cell activity. In addition, lymphocyte function deficiencies previously unobserved in this disease were found. Cytolytic T lymphocyte activity was profoundly reduced; a-and y-interferon production were impaired. Finally, there was no antibody production to vaccinal antigens whereas the antibody responses to polysaccharides and to cytomegalovirus were found to be normal. The cytotoxic T cell deficiency could be expected from previous blocking experiments of this function with monoclonal antibodies to LFA-1 and is probably related to an extremely severe deficiency in LFA-1 expression in this patient. Anomalies in interferon and in antibody production suggest additional role(s) of the LFA-1 complex in monocyte/T lymphocyte/B lymphocyte cell interactions that have not yet been envisaged

Tailoring r-index for Document Listing Towards Metagenomics Applications

A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of a set of species with each species represented by its highly similar strains. It has been recently shown that accurate read assignment can be achieved with k-mer hashing-based pseudoalignment: a read is assigned to species A if each of its k-mer hits to a reference collection is located only on strains of A. We study the underlying primitives required in pseudoalignment and related tasks. We propose three space-efficient solutions building upon the document listing with frequencies problem. All the solutions use an r-index (Gagie et al., SODA 2018) as an underlying index structure for the text obtained as concatenation of the set of species, as well as for each species. Given t species whose concatenation length is n, and whose Burrows-Wheeler transform contains r runs, our first solution, based on a grammar-compressed document array with precomputed queries at non terminal symbols, reports the frequencies for the distinct documents in which the pattern of length m occurs in time. Our second solution is also based on a grammar-compressed document array, but enhanced with bitvectors and reports the frequencies in time, over a machine with wordsize w. Our third solution, based on the interleaved LCP array, answers the same query in time. We implemented our solutions and tested them on real-world and synthetic datasets. The results show that all the solutions are fast on highly-repetitive data, and the size overhead introduced by the indexes are comparable with the size of the r-index.Peer reviewe

The Homeodomain Derived Peptide Penetratin Induces Curvature of Fluid Membrane Domains

BACKGROUND:Protein membrane transduction domains that are able to cross the plasma membrane are present in several transcription factors, such as the homeodomain proteins and the viral proteins such as Tat of HIV-1. Their discovery resulted in both new concepts on the cell communication during development, and the conception of cell penetrating peptide vectors for internalisation of active molecules into cells. A promising cell penetrating peptide is Penetratin, which crosses the cell membranes by a receptor and metabolic energy-independent mechanism. Recent works have claimed that Penetratin and similar peptides are internalized by endocytosis, but other endocytosis-independent mechanisms have been proposed. Endosomes or plasma membranes crossing mechanisms are not well understood. Previously, we have shown that basic peptides induce membrane invaginations suggesting a new mechanism for uptake, "physical endocytosis". METHODOLOGY/PRINCIPAL FINDINGS:Herein, we investigate the role of membrane lipid phases on Penetratin induced membrane deformations (liquid ordered such as in "raft" microdomains versus disordered fluid "non-raft" domains) in membrane models. Experimental data show that zwitterionic lipid headgroups take part in the interaction with Penetratin suggesting that the external leaflet lipids of cells plasma membrane are competent for peptide interaction in the absence of net negative charges. NMR and X-ray diffraction data show that the membrane perturbations (tubulation and vesiculation) are associated with an increase in membrane negative curvature. These effects on curvature were observed in the liquid disordered but not in the liquid ordered (raft-like) membrane domains. CONCLUSIONS/SIGNIFICANCE:The better understanding of the internalisation mechanisms of protein transduction domains will help both the understanding of the mechanisms of cell communication and the development of potential therapeutic molecular vectors. Here we showed that the membrane targets for these molecules are preferentially the fluid membrane domains and that the mechanism involves the induction of membrane negative curvature. Consequences on cellular uptake are discussed

Localization of preformed Cooper pairs in disordered superconductors

International audienceThe most profound effect of disorder on electronic systems is the localization of the electrons transforming an otherwise metallic system into an insulator. If the metal is also a superconductor then, at low temperatures, disorder can induce a pronounced transition from a superconducting into an insulating state. An outstanding question is whether the route to insulating behaviour proceeds through the direct localization of Cooper pairs or, alternatively, by a two-step process in which the Cooper pairing is first destroyed followed by the standard localization of single electrons. Here we address this question by studying the local superconducting gap of a highly disordered amorphous superconductor by means of scanning tunnelling spectroscopy. Our measurements reveal that, in the vicinity of the superconductor-insulator transition, the coherence peaks in the one-particle density of states disappear whereas the superconducting gap remains intact, indicating the presence of localized Cooper pairs. Our results provide the first direct evidence that the superconductor-insulator transition in some homogeneously disordered materials is driven by Cooper-pair localization