Evaluating kernels on Xeon Phi to accelerate Gysela application

This work describes the challenges presented by porting parts ofthe Gysela code to the Intel Xeon Phi coprocessor, as well as techniques used for optimization, vectorization and tuning that can be applied to other applications. We evaluate the performance of somegeneric micro-benchmark on Phi versus Intel Sandy Bridge. Several interpolation kernels useful for the Gysela application are analyzed and the performance are shown. Some memory-bound and compute-bound kernels are accelerated by a factor 2 on the Phi device compared to Sandy architecture. Nevertheless, it is hard, if not impossible, to reach a large fraction of the peek performance on the Phi device,especially for real-life applications as Gysela. A collateral benefit of this optimization and tuning work is that the execution time of Gysela (using 4D advections) has decreased on a standard architecture such as Intel Sandy Bridge.Comment: submitted to ESAIM proceedings for CEMRACS 2014 summer school version reviewe

Contribution of the screened self-energy to the Lamb shift of quasidegenerate states

Expressions for the effective Quantum Electrodynamics (QED) Hamiltonian due to self-energy screening (self-energy correction to the electron-electron interaction) are presented. We use the method of the two-time Green's function, which handles quasidegenerate atomic states. From these expression one can evaluate energy corrections to, e.g., 1s2p 3P1 and 1s2p 1P1 in helium and two-electron ions, to all orders in Z\alph

Ancestral genome estimation reveals the history of ecological diversification in Agrobacterium

Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres

Size-Dependent Surface Plasmon Dynamics in Metal Nanoparticles

We study the effect of Coulomb correlations on the ultrafast optical dynamics of small metal particles. We demonstrate that a surface-induced dynamical screening of the electron-electron interactions leads to quasiparticle scattering with collective surface excitations. In noble-metal nanoparticles, it results in an interband resonant scattering of d-holes with surface plasmons. We show that this size-dependent many-body effect manifests itself in the differential absorption dynamics for frequencies close to the surface plasmon resonance. In particular, our self-consistent calculations reveal a strong frequency dependence of the relaxation, in agreement with recent femtosecond pump-probe experiments.Comment: 8 pages + 4 figures, final version accepted to PR

Relativistic and Radiative Energy Shifts for Rydberg States

We investigate relativistic and quantum electrodynamic effects for highly-excited bound states in hydrogenlike systems (Rydberg states). In particular, hydrogenic one-loop Bethe logarithms are calculated for all circular states (l = n-1) in the range 20 <= n <= 60 and successfully compared to an existing asymptotic expansion for large principal quantum number n. We provide accurate expansions of the Bethe logarithm for large values of n, for S, P and circular Rydberg states. These three expansions are expected to give any Bethe logarithms for principal quantum number n > 20 to an accuracy of five to seven decimal digits, within the specified manifolds of atomic states. Within the numerical accuracy, the results constitute unified, general formulas for quantum electrodynamic corrections whose validity is not restricted to a single atomic state. The results are relevant for accurate predictions of radiative shifts of Rydberg states and for the description of the recently investigated laser-dressed Lamb shift, which is observable in a strong coherent-wave light field.Comment: 8 pages; RevTeX

The first evidence for multiple pulsation axes: a new roAp star in the Kepler field, KIC 10195926

We have discovered a new rapidly oscillating Ap star among the Kepler Mission target stars, KIC 10195926. This star shows two pulsation modes with periods that are amongst the longest known for roAp stars at 17.1 min and 18.1 min, indicating that the star is near the terminal age main sequence. The principal pulsation mode is an oblique dipole mode that shows a rotationally split frequency septuplet that provides information on the geometry of the mode. The secondary mode also appears to be a dipole mode with a rotationally split triplet, but we are able to show within the improved oblique pulsator model that these two modes cannot have the same axis of pulsation. This is the first time for any pulsating star that evidence has been found for separate pulsation axes for different modes. The two modes are separated in frequency by 55 microHz, which we model as the large separation. The star is an alpha^2 CVn spotted magnetic variable that shows a complex rotational light variation with a period of Prot = 5.68459 d. For the first time for any spotted magnetic star of the upper main sequence, we find clear evidence of light variation with a period of twice the rotation period; i.e. a subharmonic frequency of $\nu_{\rm rot}/2$. We propose that this and other subharmonics are the first observed manifestation of torsional modes in an roAp star. From high resolution spectra we determine Teff = 7400 K, log g = 3.6 and v sin i = 21 km/s. We have found a magnetic pulsation model with fundamental parameters close to these values that reproduces the rotational variations of the two obliquely pulsating modes with different pulsation axes. The star shows overabundances of the rare earth elements, but these are not as extreme as most other roAp stars. The spectrum is variable with rotation, indicating surface abundance patches.Comment: 17 pages; 16 figures; MNRA

Line shape analysis of the Kβ\beta transition in muonic hydrogen

The K$\beta$ transition in muonic hydrogen was measured with a high-resolution crystal spectrometer. The spectrum is shown to be sensitive to the ground-state hyperfine splitting, the corresponding triplet-to-singlet ratio, and the kinetic energy distribution in the $3p$ state. The hyperfine splitting and triplet-to-singlet ratio are found to be consistent with the values expected from theoretical and experimental investigations and, therefore, were fixed accordingly in order to reduce the uncertainties in the further reconstruction of the kinetic energy distribution. The presence of high-energetic components was established and quantified in both a phenomenological, i.e. cascade-model-free fit, and in a direct deconvolution of the Doppler broadening based on the Bayesian approach.Comment: 22 pages, 21 figure