Polymorphix: a sequence polymorphism database

Within-species sequence variation data are of special interest since they contain information about recent population/species history, and the molecular evolutionary forces currently in action in natural populations. These data, however, are presently dispersed within generalist databases, and are difficult to access. To solve this problem, we have developed Polymorphix, a database dedicated to sequence polymorphism. It contains within-species homologous sequence families built using EMBL/GenBank under suitable similarity and bibliographic criteria. Polymorphix is an ACNUC structured database allowing both simple and complex queries for population genomic studies. Alignments within families as well as phylogenetic trees can be download. When available, outgroups are included in the alignment. Polymorphix contains sequences from the nuclear, mitochondrial and chloroplastic genomes of every eukaryote species represented in EMBL. It can be accessed by a web interface (http://pbil.univ-lyon1.fr/polymorphix/query.php)

Modeling the Radiative Signatures of Turbulent Heating in Coronal Loops

The statistical properties of the radiative signature of a coronal loop subject to turbulent heating obtained from a three-dimensional (3D) magnetohydrodynamics (MHD) model are studied. The heating and cooling of a multistrand loop is modeled and synthetic spectra for Fe XII 195.12, Fe XV 284.163, and Fe XIX 1118.06 ? are calculated, covering a wide temperature range. The results show that the statistical properties of the thermal and radiative energies partially reflect those of the heating function in that power-law distributions are transmitted, but with very significant changes in the power-law indices. There is a strong dependence on the subloop geometry. Only high-temperature radiation (?107 K) preserves reasonably precise information on the heating function

Interference effects and Stark broadening in XUV intrashell transitions in aluminum under conditions of intense XUV free-electron-laser irradiation

International audienceQuantum mechanical interference effects in the line broadening of intrashell transitions are investigated for dense plasma conditions. Simulations that involved LS J -split level structure and intermediate coupling discovered unexpected strong line narrowing for intrashell transitions L-L while M-L transitions remained practically unaffected by interference effects. This behavior allows a robust study of line narrowing in dense plasmas. Simulations are carried out for XUV transitions of aluminum that have recently been observed in experiments with the FLASH free-electron laser in Hamburg irradiating solid aluminum samples with intensities greater than 10^16 W/cm^2 . We explore the advantageous case of Al that allows, first, simultaneous observation of M-L transitions and L-L intrashell transitions with high-resolution grating spectrometers and, second, has a convenient threshold to study interference effects at densities much below solid. Finally, we present simulations at near solid density where the line emission transforms into a quasi-continuum

Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics

BACKGROUND: A large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input/ouput methods, data storage requirements and data analysis algorithms. Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications. RESULTS: We present Bio++, a set of Object Oriented libraries written in C++. Available components include classes for data storage and handling (nucleotide/amino-acid/codon sequences, trees, distance matrices, population genetics datasets), various input/output formats, basic sequence manipulation (concatenation, transcription, translation, etc.), phylogenetic analysis (maximum parsimony, markov models, distance methods, likelihood computation and maximization), population genetics/genomics (diversity statistics, neutrality tests, various multi-locus analyses) and various algorithms for numerical calculus. CONCLUSION: Implementation of methods aims at being both efficient and user-friendly. A special concern was given to the library design to enable easy extension and new methods development. We defined a general hierarchy of classes that allow the developer to implement its own algorithms while remaining compatible with the rest of the libraries. Bio++ source code is distributed free of charge under the CeCILL general public licence from its website

Bent crystal spectrometer for both frequency and wavenumber resolved x-ray scattering at a seeded free-electron laser

We present a cylindrically curved GaAs x-ray spectrometer with energy resolution $\Delta E/E = 1.1\cdot 10^{-4}$ and wave-number resolution of $\Delta k/k = 3\cdot 10^{-3}$, allowing plasmon scattering at the resolution limits of the Linac Coherent Light Source (LCLS) x-ray free-electron laser. It spans scattering wavenumbers of 3.6 to $5.2/$\AA\ in 100 separate bins, with only 0.34\% wavenumber blurring. The dispersion of 0.418~eV/$13.5\,\mu$m agrees with predictions within 1.3\%. The reflection homogeneity over the entire wavenumber range was measured and used to normalize the amplitude of scattering spectra. The proposed spectrometer is superior to a mosaic HAPG spectrometer when the energy resolution needs to be comparable to the LCLS seeded bandwidth of 1~eV and a significant range of wavenumbers must be covered in one exposure

The Phase-Contrast Imaging Instrument at the Matter in Extreme Conditions Endstation at LCLS

We describe the Phase-Contrast Imaging instrument at the Matter in Extreme Conditions (MEC) endstation of the Linac Coherent Light Source. The instrument can image phenomena with a spatial resolution of a few hundreds of nanometers and at the same time reveal the atomic structure through X-ray diffraction, with a temporal resolution better than 100 femtosecond. It was specifically designed for studies relevant to High-Energy-Density Science and can monitor, e.g., shock fronts, phase transitions, or void collapses. This versatile instrument was commissioned last year and is now available to the MEC user community

Imaging Shock Waves in Diamond with Both High Temporal and Spatial Resolution at an XFEL

The advent of hard x-ray free-electron lasers (XFELs) has opened up a variety of scientific opportunities in areas as diverse as atomic physics, plasma physics, nonlinear optics in the x-ray range and protein crystallography. In this article, we access a new field of science by measuring quantitatively the local bulk properties and dynamics of matter under extreme conditions, in this case by using the short XFEL pulse to image an elastic compression wave in diamond. The elastic wave was initiated by an intense optical laser pulse and was imaged at different delay times after the optical pump pulse using magnified x-ray phase-contrast imaging. The temporal evolution of the shock wave can be monitored, yielding detailed information on shock dynamics, such as the shock velocity, the shock front width and the local compression of the material. The method provides a quantitative perspective on the state of matter in extreme conditions

Recovery of Metastable Dense Bi Synthesized by Shock Compression

X-ray free electron laser (XFEL) sources have revolutionized our capability to study ultrafast material behavior. Using an XFEL, we revisit the structural dynamics of shock compressed bismuth, resolving the transition sequence on shock release in unprecedented details. Unlike previous studies that found the phase-transition sequence on shock release to largely adhere to the equilibrium phase diagram (i.e., Bi-V → Bi-III → Bi-II → Bi-I), our results clearly reveal previously unseen, non-equilibrium behavior at these conditions. On pressure release from the Bi-V phase at 5 GPa, the Bi-III phase is not formed but rather a new metastable form of Bi. This new phase transforms into the Bi-II phase which in turn transforms into a phase of Bi which is not observed on compression. We determine this phase to be isostructural with β-Sn and recover it to ambient pressure where it exists for 20 ns before transforming back to the Bi-I phase. The structural relationship between the tetragonal β-Sn phase and the Bi-II phase (from which it forms) is discussed. Our results show the effect that rapid compression rates can have on the phase selection in a transforming material and show great promise for recovering high-pressure polymorphs with novel material properties in the future

Observation of ultrafast solid-density plasma dynamics using femtosecond X-ray pulses from a free-electron laser

The complex physics of the interaction between short pulse high intensity lasers and solids is so far hardly accessible by experiments. As a result of missing experimental capabilities to probe the complex electron dynamics and competing instabilities, this impedes the development of compact laser-based next generation secondary radiation sources, e.g. for tumor therapy [Bulanov2002,ledingham2007], laboratory-astrophysics [Remington1999,Bulanov2015], and fusion [Tabak2014]. At present, the fundamental plasma dynamics that occur at the nanometer and femtosecond scales during the laser-solid interaction can only be elucidated by simulations. Here we show experimentally that small angle X-ray scattering of femtosecond X-ray free-electron laser pulses facilitates new capabilities for direct in-situ characterization of intense short-pulse laser plasma interaction at solid density that allows simultaneous nanometer spatial and femtosecond temporal resolution, directly verifying numerical simulations of the electron density dynamics during the short pulse high intensity laser irradiation of a solid density target. For laser-driven grating targets, we measure the solid density plasma expansion and observe the generation of a transient grating structure in front of the pre-inscribed grating, due to plasma expansion, which is an hitherto unknown effect. We expect that our results will pave the way for novel time-resolved studies, guiding the development of future laser-driven particle and photon sources from solid targets

Observation of Ultrafast Solid-Density Plasma Dynamics Using Femtosecond X-Ray Pulses from a Free-Electron Laser

The complex physics of the interaction between short-pulse ultrahigh-intensity lasers and solids is so far difficult to access experimentally, and the development of compact laser-based next-generation secondary radiation sources, e.g., for tumor therapy, laboratory astrophysics, and fusion, is hindered by the lack of diagnostic capabilities to probe the complex electron dynamics and competing instabilities. At present, the fundamental plasma dynamics that occur at the nanometer and femtosecond scales during the laser-solid interaction can only be elucidated by simulations. Here we show experimentally that small-angle x-ray scattering of femtosecond x-ray free-electron laser pulses facilitates new capabilities for direct in situ characterization of intense short-pulse laser-plasma interactions at solid density that allows simultaneous nanometer spatial and femtosecond temporal resolution, directly verifying numerical simulations of the electron density dynamics during the short-pulse high-intensity laser irradiation of a solid density target. For laser-driven grating targets, we measure the solid density plasma expansion and observe the generation of a transient grating structure in front of the preinscribed grating, due to plasma expansion. The density maxima are interleaved, forming a double frequency grating in x-ray free-electron laser projection for a short time, which is a hitherto unknown effect. We expect that our results will pave the way for novel time-resolved studies, guiding the development of future laser-driven particle and photon sources from solid targets