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

Perturbation Approach to the Self Energy of non-S Hydrogenic States

We present results on the self-energy correction to the energy levels of hydrogen and hydrogenlike ions. The self energy represents the largest QED correction to the relativistic (Dirac-Coulomb) energy of a bound electron. We focus on the perturbation expansion of the self energy of non-S states, and provide estimates of the so-called A60 perturbative coefficient, which can be considered as a relativistic Bethe logarithm. Precise values of A60 are given for many P, D, F and G states, while estimates are given for other electronic states. These results can be used in high-precision spectroscopy experiments in hydrogen and hydrogenlike ions. They yield the best available estimate of the self-energy correction of many atomic states.Comment: 18 pages (in 2-column format), 21 figures. Version 2 (June 20, 2003) includes minor modification

Adaptive Covariance Estimation with model selection

We provide in this paper a fully adaptive penalized procedure to select a covariance among a collection of models observing i.i.d replications of the process at fixed observation points. For this we generalize previous results of Bigot and al. and propose to use a data driven penalty to obtain an oracle inequality for the estimator. We prove that this method is an extension to the matricial regression model of the work by Baraud

DNA chirality-dependent stimulation of topoisomerase IV activity by the C-terminal AAA+ domain of FtsK

We have studied the stimulation of topoisomerase IV (Topo IV) by the C-terminal AAA+ domain of FtsK. These two proteins combine to assure proper chromosome segregation in the cell. Stimulation of Topo IV activity was dependent on the chirality of the DNA substrate: FtsK stimulated decatenation of catenated DNA and relaxation of positively supercoiled [(+)ve sc] DNA, but inhibited relaxation of negatively supercoiled [(−)ve sc] DNA. The DNA translocation activity of FtsK was not required for stimulation, but was required for inhibition. DNA chirality did not affect any of the activities of FtsK, suggesting that FtsK possesses an inherent Topo IV stimulatory activity that is presumably mediated by protein–protein interactions, the stability of Topo IV on the DNA substrate dictated the effect observed. Inhibition occurs because FtsK can strip distributively acting topoisomerase off (−)ve scDNA, but not from either (+)ve scDNA or catenated DNA where the enzyme acts processively. Our analyses suggest that FtsK increases the efficiency of trapping of the transfer segment of DNA during the catalytic cycle of the topoisomerase

Toward high-precision values of the self energy of non-S states in hydrogen and hydrogen-like ions

The method and status of a study to provide numerical, high-precision values of the self-energy level shift in hydrogen and hydrogen-like ions is described. Graphs of the self energy in hydrogen-like ions with nuclear charge number between 20 and 110 are given for a large number of states. The self-energy is the largest contribution of Quantum Electrodynamics (QED) to the energy levels of these atomic systems. These results greatly expand the number of levels for which the self energy is known with a controlled and high precision. Applications include the adjustment of the Rydberg constant and atomic calculations that take into account QED effects.Comment: Minor changes since previous versio