Spectropolarimetry with CRISP at the Swedish 1-m Solar Telescope

CRISP (Crisp Imaging Spectro-polarimeter), the new spectropolarimeter at the Swedish 1-m Solar Telescope, opens a new perspective in solar polarimetry. With better spatial resolution (0.13") than Hinode in the Fe I 6302 A line and similar polarimetric sensitivity reached through postprocessing, CRISP complements the SP spectropolarimeter onboard Hinode. We present some of the data which we obtained in our June 2008 campaign and preliminary results from LTE inversions of a pore containing umbral dots.Comment: To appear in "Magnetic Coupling between the Interior and the Atmosphere of the Sun", eds. S.S. Hasan and R.J. Rutten, Astrophysics and Space Science Proceedings, Springer-Verlag, Heidelberg, Berlin, 200

Cosmological Adaptive Mesh Refinement

We describe a grid-based numerical method for 3D hydrodynamic cosmological simulations which is adaptive in space and time and combines the best features of higher order--accurate Godunov schemes for Eulerian hydrodynamics with adaptive particle--mesh methods for collisionless particles. The basis for our method is the structured adaptive mesh refinement (AMR) algorithm of Berger & Collela (1989), which we have extended to cosmological hydro + N-body simulations. The resulting multiscale hybrid method is a powerful alternative to particle-based methods in current use. The choices we have made in constructing this algorithm are discussed, and its performance on the Zeldovich pancake test problem is given. We present a sample application of our method to the problem of first structure formation. We have achieved a spatial dynamic range $L_{box}/\Delta x > 250,000$ in a 3D multispecies gas + dark matter calculation, which is sufficient to resolve the formation of primordial protostellar cloud cores starting from linear matter fluctuations in an expanding FRW universe.Comment: 14 pages, 3 figures (incl. one large color PS) to appear in "Numerical Astrophysics 1998", eds. S. Miyama & K. Tomisaka, Tokyo, March 10-13, 199

On the benefits of tasking with OpenMP

Tasking promises a model to program parallel applications that provides intuitive semantics. In the case of tasks with dependences, it also promises better load balancing by removing global synchronizations (barriers), and potential for improved locality. Still, the adoption of tasking in production HPC codes has been slow. Despite OpenMP supporting tasks, most codes rely on worksharing-loop constructs alongside MPI primitives. This paper provides insights on the benefits of tasking over the worksharing-loop model by reporting on the experience of taskifying an adaptive mesh refinement proxy application: miniAMR. The performance evaluation shows the taskified implementation being 15–30% faster than the loop-parallel one for certain thread counts across four systems, three architectures and four compilers thanks to better load balancing and system utilization. Dynamic scheduling of loops narrows the gap but still falls short of tasking due to serial sections between loops. Locality improvements are incidental due to the lack of locality-aware scheduling. Overall, the introduction of asynchrony with tasking lives up to its promises, provided that programmers parallelize beyond individual loops and across application phases.Peer ReviewedPostprint (author's final draft

An open and parallel multiresolution framework using block-based adaptive grids

A numerical approach for solving evolutionary partial differential equations in two and three space dimensions on block-based adaptive grids is presented. The numerical discretization is based on high-order, central finite-differences and explicit time integration. Grid refinement and coarsening are triggered by multiresolution analysis, i.e. thresholding of wavelet coefficients, which allow controlling the precision of the adaptive approximation of the solution with respect to uniform grid computations. The implementation of the scheme is fully parallel using MPI with a hybrid data structure. Load balancing relies on space filling curves techniques. Validation tests for 2D advection equations allow to assess the precision and performance of the developed code. Computations of the compressible Navier-Stokes equations for a temporally developing 2D mixing layer illustrate the properties of the code for nonlinear multi-scale problems. The code is open source

Put a tiger in your tank: the polyclad flatworm Maritigrella crozieri as a proposed model for evo-devo

Polyclad flatworms are an early branching clade within the rhabditophoran Platyhelminthes. They provide an interesting system with which to explore the evolution of development within Platyhelminthes and amongst Spiralia (Lophotrochozoa). Unlike most other flatworms, polyclads undergo spiral cleavage (similar to that seen in some other spiralian taxa), they are the only free-living flatworms where development via a larval stage occurs, and they are the only flatworms in which embryos can be reared outside of their protective egg case, enabling embryonic manipulations. Past work has focused on comparing early cleavage patterns and larval anatomy between polyclads and other spiralians. We have selected Maritigrella crozieri, the tiger flatworm, as a suitable polyclad species for developmental studies, because it is abundant and large in size compared to other species. These characteristics have facilitated the generation of a transcriptome from embryonic and larval material and are enabling us to develop methods for gene expression analysis and immunofluorescence techniques. Here we give an overview of M. crozieri and its development, we highlight the advantages and current limitations of this animal as a potential evo-devo model and discuss current lines of research

Gravitational Collapse and Fragmentation in Molecular Clouds with Adaptive Mesh Refinement

We describe a powerful methodology for numerical solution of 3-D self-gravitational hydrodynamics problems with extremely high resolution. Our method utilizes the technique of local adaptive mesh refinement (AMR), employing multiple grids at multiple levels of resolution. These grids are automatically and dynamically added and removed as necessary to maintain adequate resolution. This technology allows for the solution of problems in a manner that is both more efficient and more versatile than other fixed and variable resolution methods. The application of AMR to simulate the collapse and fragmentation of a molecular cloud, a key step in star formation, is discussed. Such simulations involve many orders of magnitude of variation in length scale as fragments form. In this paper we briefly describe the methodology and present an illustrative application for nonisothermal cloud collapse. We describe the numerical Jeans condition, a criterion for stability of self-gravitational hydrodynamics problems. We show the first well-resolved nonisothermal evolutionary sequence beginning with a perturbed dense molecular cloud core that leads to the formation of a binary system consisting of protostellar cores surrounded by distinct protostellar disks. The scale of the disks, of order 100 AU, is consistent with observations of gaseous disks surrounding single T-Tauri stars and debris disks surrounding systems such as $\beta$ Pictoris.Comment: 10 pages, 6 figures (color postscript). To appear in the proceedings of Numerical Astrophysics 1998, Tokyo, March 10-13, 199

Helicity at Photospheric and Chromospheric Heights

In the solar atmosphere the twist parameter $\alpha$ has the same sign as magnetic helicity. It has been observed using photospheric vector magnetograms that negative/positive helicity is dominant in the northern/southern hemisphere of the Sun. Chromospheric features show dextral/sinistral dominance in the northern/southern hemisphere and sigmoids observed in X-rays also have a dominant sense of reverse-S/forward-S in the northern/southern hemisphere. It is of interest whether individual features have one-to-one correspondence in terms of helicity at different atmospheric heights. We use UBF \Halpha images from the Dunn Solar Telescope (DST) and other \Halpha data from Udaipur Solar Observatory and Big Bear Solar Observatory. Near-simultaneous vector magnetograms from the DST are used to establish one-to-one correspondence of helicity at photospheric and chromospheric heights. We plan to extend this investigation with more data including coronal intensities.Comment: 5 pages, 1 figure, 1 table To appear in "Magnetic Coupling between the Interior and the Atmosphere of the Sun", eds. S.S. Hasan and R.J. Rutten, Astrophysics and Space Science Proceedings, Springer-Verlag, Heidelberg, Berlin, 200

Multiple-length-scale elastic instability mimics parametric resonance of nonlinear oscillators

Spatially confined rigid membranes reorganize their morphology in response to the imposed constraints. A crumpled elastic sheet presents a complex pattern of random folds focusing the deformation energy while compressing a membrane resting on a soft foundation creates a regular pattern of sinusoidal wrinkles with a broad distribution of energy. Here, we study the energy distribution for highly confined membranes and show the emergence of a new morphological instability triggered by a period-doubling bifurcation. A periodic self-organized focalization of the deformation energy is observed provided an up-down symmetry breaking, induced by the intrinsic nonlinearity of the elasticity equations, occurs. The physical model, exhibiting an analogy with parametric resonance in nonlinear oscillator, is a new theoretical toolkit to understand the morphology of various confined systems, such as coated materials or living tissues, e.g., wrinkled skin, internal structure of lungs, internal elastica of an artery, brain convolutions or formation of fingerprints. Moreover, it opens the way to new kind of microfabrication design of multiperiodic or chaotic (aperiodic) surface topography via self-organization.Comment: Submitted for publicatio

Penile metastasis from primary transitional cell carcinoma of the renal pelvis: first manifestation of systemic spread

BACKGROUND: Almost one-third of all penile metastases are detected at the same time as a primary tumor, whereas the remaining two-thirds are detected a mean of 18 months after the discovery of the primary tumor. Cutaneous metastasis of transitional cell carcinoma (TCC) is extremely rare and generally accepted as the late manifestation of a systemic spread. CASE PRESENTATION: We report the first case of simultaneous penile and lung metastases from a primary TCC of the renal pelvis in a 76-year-old man, that occurred 8 years after a left nephroureterectomy. CONCLUSIONS: This case report underscores the importance of physical examinations of the skin of patients who undergo surgical procedures for TCC from bladder as well as from the upper urinary tract, including those seemingly without metastatic disease, because of the possibility of skin and penile metastatic spread

The course of mental health problems in children presenting with abdominal pain in general practice

Objective. To investigate the course of mental health problems in children presenting to general practice with abdominal pain and to evaluate the extent to which abdominal pain characteristics during follow-up predict the presence of mental health problems at 12 months' follow-up. Design. A prospective cohort study with one-year follow-up. Setting. 53 general practices in the Netherlands, between May 2004 and March 2006. Subjects. 281 children aged 4-17 years. Main outcome measures. The presence of a depressive problem, an anxiety problem, and multiple non-specific somatic symptoms at follow-up and odds ratios of duration, frequency, and severity of abdominal pain with these mental health problems at follow-up. Results. A depressive problem persisted in 24/74 children (32.9%; 95% CI 22.3-44.9%), an anxiety problem in 13/43 (30.2%; 95% CI 17.2-46.1%) and the presence of multiple non-specific somatic symptoms in 75/170 children (44.1%; 95% CI 36.7-51.6%). None of the abdominal pain characteristics predicted a depressive or an anxiety problem at 12 months' follow-up. More moments of moderate to severe abdominal pain predicted the presence of multiple nonspecific somatic symptoms at follow-up. Conclusions. In one-third of the children presenting to general practice for abdominal pain, anxiety and depressive problems persist during one year of follow-up. Characteristics of the abdominal pain during the follow-up period do not predict anxiety or depressive problems after one-year follow-up. We recommend following over time children seen in primary care with abdominal pain