Absolute value preconditioning for symmetric indefinite linear systems

We introduce a novel strategy for constructing symmetric positive definite (SPD) preconditioners for linear systems with symmetric indefinite matrices. The strategy, called absolute value preconditioning, is motivated by the observation that the preconditioned minimal residual method with the inverse of the absolute value of the matrix as a preconditioner converges to the exact solution of the system in at most two steps. Neither the exact absolute value of the matrix nor its exact inverse are computationally feasible to construct in general. However, we provide a practical example of an SPD preconditioner that is based on the suggested approach. In this example we consider a model problem with a shifted discrete negative Laplacian, and suggest a geometric multigrid (MG) preconditioner, where the inverse of the matrix absolute value appears only on the coarse grid, while operations on finer grids are based on the Laplacian. Our numerical tests demonstrate practical effectiveness of the new MG preconditioner, which leads to a robust iterative scheme with minimalist memory requirements

Exploration of a Unique Uranium Mediated Carbon-Carbon Radical Coupling Reaction

Designing an efficient nuclear fuel cycle has motivated decades of research on aqueous phase uranium chemistry. As such, studies are often limited by the formation of unreactive uranium oxides and/or solubility issues. Carrying out reactions in non-aqueous solvents addresses said problems and enables explorations into previously unattainable reactivity and fundamental properties of uranium. One such feat is the syntheses of uranium alkyls, as they permit research into bond interactions between uranium and carbon. Considering uranium’s oxophilicity, we investigated the relatively understudied uranium(III) alkyls—both their reactivity and reaction mechanism—towards oxygen-containing reagents. In an inert atmosphere, various uranium alkyl complexes were treated with substituted phosphine oxides, which provide electronic and steric modularity. Products were characterized via nuclear magnetic resonance (NMR), electronic absorption, and infrared spectroscopies. X-ray crystallographic data were obtained whenever possible. We observed the formation of a new carbon-carbon bond between the alkyl unit and phosphine oxide in a one-electron mechanism, while maintaining the U(III) oxidation state. This radical coupling was favored by electron-poor phosphine oxide and impeded by electron-rich analogs. The ability for the alkyl to form stable radicals drives the reaction forward. All attempts to capture the radical were unsuccessful, as the formation of the new uranium complexes appears to occur in concert with the homolytic cleavage of the U—C bond. To the best of our knowledge, such reactivity with phosphine oxides is unprecedented in the field of coordination chemistry

Observations of radio pulses from CU Virginis

The magnetic chemically peculiar star CU Virginis is a unique astrophysical laboratory for stellar magnetospheres and coherent emission processes. It is the only known main sequence star to emit a radio pulse every rotation period. Here we report on new observations of the CU Virginis pulse profile in the 13 and 20\,cm radio bands. The profile is known to be characterised by two peaks of 100$\%$ circularly polarised emission that are thought to arise in an electron-cyclotron maser mechanism. We find that the trailing peak is stable at both 13 and 20\,cm, whereas the leading peak is intermittent at 13\,cm. Our measured pulse arrival times confirm the discrepancy previously reported between the putative stellar rotation rates measured with optical data and with radio observations. We suggest that this period discrepancy might be caused by an unknown companion or by instabilities in the emission region. Regular long-term pulse timing and simultaneous multi-wavelength observations are essential to clarify the behaviour of this emerging class of transient radio source.Comment: Accepted by MNRAS Letters; 5 pages, 2 figures, 3 table

Radiative hydrodynamics simulations of red supergiant stars: II. simulations of convection on Betelgeuse match interferometric observations

Context. The red supergiant (RSG) Betelgeuse is an irregular variable star. Convection may play an important role in understanding this variability. Interferometric observations can be interpreted using sophisticated simulations of stellar convection. Aims. We compare the visibility curves and closure phases obtained from our 3D simulation of RSG convection with CO5BOLD to various interferometric observations of Betelgeuse from the optical to the H band in order to characterize and measure the convection pattern on this star. Methods. We use 3D radiative-hydrodynamics (RHD) simulation to compute intensity maps in different filters and we thus derive interferometric observables using the post-processing radiative transfer code OPTIM3D. The synthetic visibility curves and closure phases are compared to observations. Results. We provide a robust detection of the granulation pattern on the surface of Betelgeuse in the optical and in the H band based on excellent fits to the observed visibility points and closure phases. Moreover, we determine that the Betelgeuse surface in the H band is covered by small to medium scale (5-15 mas) convection-related surface structures and a large (30 mas) convective cell. In this spectral region, H2O molecules are the main absorbers and contribute to the small structures and to the position of the first null of the visibility curve (i.e. the apparent stellar radius).Comment: 11 pages, Accepted for publication on A&

The close circumstellar environment of Betelgeuse - Adaptive optics spectro-imaging in the near-IR with VLT/NACO

Context: Betelgeuse is one the largest stars in the sky in terms of angular diameter. Structures on the stellar photosphere have been detected in the visible and near-infrared as well as a compact molecular environment called the MOLsphere. Mid-infrared observations have revealed the nature of some of the molecules in the MOLsphere, some being the precursor of dust. Aims: Betelgeuse is an excellent candidate to understand the process of mass loss in red supergiants. Using diffraction-limited adaptive optics (AO) in the near-infrared, we probe the photosphere and close environment of Betelgeuse to study the wavelength dependence of its extension, and to search for asymmetries. Methods: We obtained AO images with the VLT/NACO instrument, taking advantage of the "cube" mode of the CONICA camera to record separately a large number of short-exposure frames. This allowed us to adopt a "lucky imaging" approach for the data reduction, and obtain diffraction-limited images over the spectral range 1.04-2.17 $\mu$m in 10 narrow-band filters. Results: In all filters, the photosphere of Betelgeuse appears partly resolved. We identify an asymmetric envelope around the star, with in particular a relatively bright "plume" extending in the southwestern quadrant up to a radius of approximately six times the photosphere. The CN molecule provides an excellent match to the 1.09 mic bandhead in absorption in front of the stellar photosphere, but the emission spectrum of the plume is more difficult to interpret. Conclusions: Our AO images show that the envelope surrounding Betelgeuse has a complex and irregular structure. We propose that the southwestern plume is linked either to the presence of a convective hot spot on the photosphere, or to the rotation of the star.Comment: 12 pages. Astronomy and Astrophysics (2009) in pres

The molecular and dusty composition of Betelgeuse's inner circumstellar environment

The study of the atmosphere of red supergiant stars in general and of Betelgeuse (alpha Orionis) in particular is of prime importance to understand dust formation and how mass is lost to the interstellar medium in evolved massive stars. A molecular shell, the MOLsphere (Tsuji, 2000a), in the atmosphere of Betelgeuse has been proposed to account for the near- and mid-infrared spectroscopic observations of Betelgeuse. The goal is to further test this hypothesis and to identify some of the molecules in this MOLsphere. We report on measurements taken with the mid-infrared two-telescope beam combiner of the VLTI, MIDI, operated between 7.5 and 13.5 $\mu$m. The data are compared to a simple geometric model of a photosphere surrounded by a warm absorbing and emitting shell. Physical characteristics of the shell are derived: size, temperature and optical depth. The chemical constituents are determined with an analysis consistent with available infrared spectra and interferometric data. We are able to account for the measured optical depth of the shell in the N band, the ISO-SWS spectrum and K and L band interferometric data with a shell whose inner and outer radii are given by the above range and with the following species: H2O, SiO and Al2O3. These results confirm the MOLsphere model. We bring evidence for more constituents and for the presence of species participating in the formation of dust grains in the atmosphere of the star, i.e. well below the distance at which the dust shell is detected. We believe these results bring key elements to the understanding of mass loss in Betelgeuse and red supergiants in general and bring support to the dust-driven scenario.Comment: 11 pages, 10 figures, accepted for publication in A&

The Arctic Predictability and Prediction on Seasonal-to-Interannual TimEscales (APPOSITE) data set version 1

Abstract. Recent decades have seen significant developments in climate prediction capabilities at seasonal-to-interannual timescales. However, until recently the potential of such systems to predict Arctic climate had rarely been assessed. This paper describes a multi-model predictability experiment which was run as part of the Arctic Predictability and Prediction On Seasonal to Interannual Timescales (APPOSITE) project. The main goal of APPOSITE was to quantify the timescales on which Arctic climate is predictable. In order to achieve this, a coordinated set of idealised initial-value predictability experiments, with seven general circulation models, was conducted. This was the first model intercomparison project designed to quantify the predictability of Arctic climate on seasonal to interannual timescales. Here we present a description of the archived data set (which is available at the British Atmospheric Data Centre), an assessment of Arctic sea ice extent and volume predictability estimates in these models, and an investigation into to what extent predictability is dependent on the initial state. The inclusion of additional models expands the range of sea ice volume and extent predictability estimates, demonstrating that there is model diversity in the potential to make seasonal-to-interannual timescale predictions. We also investigate whether sea ice forecasts started from extreme high and low sea ice initial states exhibit higher levels of potential predictability than forecasts started from close to the models' mean state, and find that the result depends on the metric. Although designed to address Arctic predictability, we describe the archived data here so that others can use this data set to assess the predictability of other regions and modes of climate variability on these timescales, such as the El Niño–Southern Oscillation

Parameter identification problems in the modelling of cell motility

We present a novel parameter identification algorithm for the estimation of parameters in models of cell motility using imaging data of migrating cells. Two alternative formulations of the objective functional that measures the difference between the computed and observed data are proposed and the parameter identification problem is formulated as a minimisation problem of nonlinear least squares type. A Levenberg–Marquardt based optimisation method is applied to the solution of the minimisation problem and the details of the implementation are discussed. A number of numerical experiments are presented which illustrate the robustness of the algorithm to parameter identification in the presence of large deformations and noisy data and parameter identification in three dimensional models of cell motility. An application to experimental data is also presented in which we seek to identify parameters in a model for the monopolar growth of fission yeast cells using experimental imaging data. Our numerical tests allow us to compare the method with the two different formulations of the objective functional and we conclude that the results with both objective functionals seem to agree

De Novo Growth Zone Formation from Fission Yeast Spheroplasts

Eukaryotic cells often form polarized growth zones in response to internal or external cues. To understand the establishment of growth zones with specific dimensions we used fission yeast, which grows as a rod-shaped cell of near-constant width from growth zones located at the cell tips. Removing the cell wall creates a round spheroplast with a disorganized cytoskeleton and depolarized growth proteins. As spheroplasts recover, new growth zones form that resemble normal growing cell tips in shape and width, and polarized growth resumes. Regulators of the GTPase Cdc42, which control width in exponentially growing cells, also control spheroplast growth zone width. During recovery the Cdc42 scaffold Scd2 forms a polarized patch in the rounded spheroplast, demonstrating that a growth zone protein can organize independent of cell shape. Rga4, a Cdc42 GTPase activating protein (GAP) that is excluded from cell tips, is initially distributed throughout the spheroplast membrane, but is excluded from the growth zone after a stable patch of Scd2 forms. These results provide evidence that growth zones with normal width and protein localization can form de novo through sequential organization of cellular domains, and that the size of these growth zones is genetically controlled, independent of preexisting cell shape

Building Hierarchical Grid Storage Using the Gfarm Global File System and the JuxMem Grid Data-Sharing Service

International audienceAs more and more large-scale applications need to generate and process very large volumes of data, the need for adequate storage facilities is growing. It becomes crucial to efficiently and reliably store and retrieve large sets of data that may be shared at the global scale. Based on previous systems for global data sharing (global file systems, grid data-sharing services), this paper proposes a hierarchical approach for grid storage, which combines the access efficiency of RAM storage with the scalability and persistence of the global file system approach. Our proposal has been validated through a prototype that couples the Gfarm file system with the JuxMem data-sharing service. Experiments on the Grid'5000 testbed confirm the advantages of our approach