Inter-network regions of the Sun at millimetre wavelengths

The continuum intensity at wavelengths around 1 mm provides an excellent way to probe the solar chromosphere. Future high-resolution millimetre arrays, such as the Atacama Large Millimeter Array (ALMA), will thus produce valuable input for the ongoing controversy on the thermal structure and the dynamics of this layer. Synthetic brightness temperature maps are calculated on basis of three-dimensional radiation (magneto-)hydrodynamic (MHD) simulations. While the millimetre continuum at 0.3mm originates mainly from the upper photosphere, the longer wavelengths considered here map the low and middle chromosphere. The effective formation height increases generally with wavelength and also from disk-centre towards the solar limb. The average intensity contribution functions are usually rather broad and in some cases they are even double-peaked as there are contributions from hot shock waves and cool post-shock regions in the model chromosphere. Taking into account the deviations from ionisation equilibrium for hydrogen gives a less strong variation of the electron density and with it of the optical depth. The result is a narrower formation height range. The average brightness temperature increases with wavelength and towards the limb. The relative contrast depends on wavelength in the same way as the average intensity but decreases towards the limb. The dependence of the brightness temperature distribution on wavelength and disk-position can be explained with the differences in formation height and the variation of temperature fluctuations with height in the model atmospheres.Comment: 15 pages, 10 figures, accepted for publication in A&A (15.05.07

On The Evolution of Magnetic White Dwarfs

We present the first radiation magnetohydrodynamics simulations of the atmosphere of white dwarf stars. We demonstrate that convective energy transfer is seriously impeded by magnetic fields when the plasma-beta parameter, the thermal to magnetic pressure ratio, becomes smaller than unity. The critical field strength that inhibits convection in the photosphere of white dwarfs is in the range B = 1-50 kG, which is much smaller than the typical 1-1000 MG field strengths observed in magnetic white dwarfs, implying that these objects have radiative atmospheres. We have then employed evolutionary models to study the cooling process of high-field magnetic white dwarfs, where convection is entirely suppressed during the full evolution (B > 10 MG). We find that the inhibition of convection has no effect on cooling rates until the effective temperature (Teff) reaches a value of around 5500 K. In this regime, the standard convective sequences start to deviate from the ones without convection owing to the convective coupling between the outer layers and the degenerate reservoir of thermal energy. Since no magnetic white dwarfs are currently known at the low temperatures where this coupling significantly changes the evolution, effects of magnetism on cooling rates are not expected to be observed. This result contrasts with a recent suggestion that magnetic white dwarfs with Teff < 10,000 K cool significantly slower than non-magnetic degenerates.Comment: 11 pages, 12 figures, accepted for publication in the Astrophysical Journa

Entwicklung eines situationsbezogenen Konzeptes zur Regulation des Erbsenwicklers in Gemüse- und Körnererbsen

Das Ziel des Projektes war es, ein Konzept zur Risikobewertung des Erbsenwicklerbefalls in Anbauregionen von Gemüseerbsen zu entwickeln, in dem präventive Maßnahmen und eine bedarfsgerechte Option zur Direktbekämpfung integriert sind. Die Datenerfassung zur Beurteilung von Risikolagen erfolgte in Erbsenanbaugebieten in Hessen und Sachsen, beide mit Schwerpunkt auf ökologischen Landbau. Die Risikobewertung umfasste die Abschätzung der Schlaggefährdung durch den Erbsenwickler innerhalb der Anbaugebiete mittels zeitlich-räumlicher Analysen und die Berücksichtigung phänologischer Daten zum Erscheinen, Flugaktivität und Entwicklung des Erbsenwicklers in Abhängigkeit von Temperatur und Photoperiode. Basierend auf der Risikobewertung sollten Entscheidungen zum Einsatz ökologischer Regulierungsverfahren getroffen werden können, die in einem zweiten Projektteil bearbeitet wurden. Die Regulierung des Erbsenwicklers wurde in einem Parzellenversuch über die präventiven Maßnahmen Sortenwahl und Aussaatzeitpunkt und eine bedarfsgerechte Direktbekämpfung untersucht. Als Ergebnis konnten die wesentlichen Faktoren, die für eine Risikobewertung zum Erbsenwicklerbefall notwendig sind, definiert werden: a) ein zeitlich-räumlicher Zusammenhang zwischen den vorjährigen Erbsenflächen und dem Erbsenwicklerauftreten im Folgejahr b) ein Einfluss von Photoperiode und Temperatur auf die Entwicklung der Überwinterungsstadien von C. nigricana, sowie Erscheinen und Flugaktivität der adulten Erbsenwickler c) eine Steuerung der zeitlichen Koinzidenzvermeidung von empfindlichen Entwicklungsstadien der Erbsenpflanze und dem Erbsenwicklerauftreten durch Sortenwahl und Aussaatzeitpunkt. Der Einsatz einer Pyrethrin-Rapsöl Formulierung hat eine variable Wirkung in der Regulierung des Erbsenwicklers gezeigt. Der Befall konnte nur bei geringem Befallsdruck unterhalb der sehr niedrigen Schadtoleranzgrenze von 0,5% geschädigter Ernteerbsen gehalten werden; bei einer starken Schädlingsdichte konnte keine ausreichende Befallsreduktion erreicht werden

High-order aberration compensation with Multi-frame Blind Deconvolution and Phase Diversity image restoration techniques

Context. For accurately measuring intensities and determining magnetic field strengths of small-scale solar (magnetic) structure, knowledge of and compensation for the point spread function is crucial. For images recorded with the Swedish 1-meter Solar Telescope, restoration with Multi-Frame Blind Deconvolution and Joint Phase Diverse Speckle methods lead to remarkable improvements in image quality but granulation contrasts that are too low, indicating additional stray light. Aims. We propose a method to compensate for stray light from high-order atmospheric aberrations not included in MFBD and JPDS processing. Methods. To compensate for uncorrected aberrations, a reformulation of the image restoration process is proposed that allows the average effect of hundreds of high-order modes to be compensated for by relying on Kolmogorov statistics for these modes. The applicability of the method requires simultaneous measurements of Fried's parameter r0. The method is tested with simulations as well as real data and extended to include compensation for conventional stray light. Results. We find that only part of the reduction of granulation contrast in SST images is due to uncompensated high-order aberrations. The remainder is still unaccounted for and attributed to stray light from the atmosphere, the telescope with its re-imaging system and to various high-altitude seeing effects. Conclusions. We conclude that statistical compensation of high-order modes is a viable method to reduce the loss of contrast occurring when a limited number of aberrations is explicitly compensated for with MFBD and JPDS processing. We show that good such compensation is possible with only 10 recorded frames. The main limitation of the method is that already MFBD and JPDS processing introduces high-order compensation that, if not taken into account, can lead to over-compensation.Comment: in press in Astronomy & Astrophysic

An improved filtering algorithm for big read datasets and its application to single-cell assembly

Background: For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots of redundant data. A filtering of this data prior to assembly is advisable. Brown et al. (2012) presented the algorithm Diginorm for this purpose, which filters reads based on the abundance of their k-mers. Methods: We present Bignorm, a faster and quality-conscious read filtering algorithm. An important new algorithmic feature is the use of phred quality scores together with a detailed analysis of the k-mer counts to decide which reads to keep. Results: We qualify and recommend parameters for our new read filtering algorithm. Guided by these parameters, we remove in terms of median 97.15% of the reads while keeping the mean phred score of the filtered dataset high. Using the SDAdes assembler, we produce assemblies of high quality from these filtered datasets in a fraction of the time needed for an assembly from the datasets filtered with Diginorm. Conclusions: We conclude that read filtering is a practical and efficient method for reducing read data and for speeding up the assembly process. This applies not only for single cell assembly, as shown in this paper, but also to other projects with high mean coverage datasets like metagenomic sequencing projects. Our Bignorm algorithm allows assemblies of competitive quality in comparison to Diginorm, while being much faster. Bignorm is available for download at https://git.informatik.uni-kiel.de/axw/Bignorm

First high-resolution look at the quiet Sun with ALMA at 3 mm

We present an overview of high resolution quiet Sun observations, from disk center to the limb, obtained with the Atacama Large mm and sub-mm Array (ALMA) at 3 mm. Seven quiet Sun regions were observed with resolution of up to 2.5" by 4.5". We produced both average and snapshot images by self-calibrating the ALMA visibilities and combining the interferometric images with full disk solar images. The images show well the chromospheric network, which, based on the unique segregation method we used, is brighter than the average over the fields of view of the observed regions by $\sim 305$ K while the intranetwork is less bright by $\sim 280$ K, with a slight decrease of the network/intranetwork contrast toward the limb. At 3 mm the network is very similar to the 1600 \AA\ images, with somewhat larger size. We detected for the first time spicular structures, rising up to 15" above the limb with a width down to the image resolution and brightness temperature of $\sim$ 1800 K above the local background. No trace of spicules, either in emission or absorption, was found on the disk. Our results highlight ALMA's potential for the study of the quiet chromosphere.Comment: Astronomy and Astrophysics (Letters), in pres

An improved filtering algorithm for big read datasets and its application to single-cell assembly

Background: For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots of redundant data. A filtering of this data prior to assembly is advisable. Brown et al. (2012) presented the algorithm Diginorm for this purpose, which filters reads based on the abundance of their k-mers. Methods: We present Bignorm, a faster and quality-conscious read filtering algorithm. An important new algorithmic feature is the use of phred quality scores together with a detailed analysis of the k-mer counts to decide which reads to keep. Results: We qualify and recommend parameters for our new read filtering algorithm. Guided by these parameters, we remove in terms of median 97.15% of the reads while keeping the mean phred score of the filtered dataset high. Using the SDAdes assembler, we produce assemblies of high quality from these filtered datasets in a fraction of the time needed for an assembly from the datasets filtered with Diginorm. Conclusions: We conclude that read filtering is a practical and efficient method for reducing read data and for speeding up the assembly process. This applies not only for single cell assembly, as shown in this paper, but also to other projects with high mean coverage datasets like metagenomic sequencing projects. Our Bignorm algorithm allows assemblies of competitive quality in comparison to Diginorm, while being much faster. Bignorm is available for download at https://git.informatik.uni-kiel.de/axw/Bignorm

First analysis of solar structures in 1.21 mm full-disc ALMA image of the Sun

Various solar features can be seen on maps of the Sun in the mm and sub-mm wavelength range. The recently installed Atacama Large Millimeter/submillimeter Array (ALMA) is capable of observing the Sun in that wavelength range with an unprecedented spatial, temporal and spectral resolution. To interpret solar observations with ALMA the first important step is to compare ALMA maps with simultaneous images of the Sun recorded in other spectral ranges. First we identify different structures in the solar atmosphere seen in the optical, IR and EUV parts of the spectrum (quiet Sun (QS), active regions (AR), prominences on the disc, magnetic inversion lines (IL), coronal holes (CH) and coronal bright points (CBPs)) in a full disc solar ALMA image. The second aim is to measure the intensities (brightness temperatures) of those structures and compare them with the corresponding QS level. A full disc solar image at 1.21 mm obtained on December 18, 2015 during a CSV-EOC campaign with ALMA is calibrated and compared with full disc solar images from the same day in H\alpha, in He I 1083 nm core, and with SDO images (AIA at 170 nm, 30.4 nm, 21.1 nm, 19.3 nm, and 17.1 nm and HMI magnetogram). The brightness temperatures of various structures are determined by averaging over corresponding regions of interest in the ALMA image. Positions of the QS, ARs, prominences on the disc, ILs, CHs and CBPs are identified in the ALMA image. At 1.21 mm ARs appear as bright areas (but sunspots are dark), while prominences on the disc and CHs are not discernible from the QS background, although having slightly less intensity than surrounding QS regions. ILs appear as large, elongated dark structures and CBPs correspond to ALMA bright points. These results are in general agreement with sparse earlier measurements at similar wavelengths. The identification of CBPs represents the most important new result.Comment: 9 pages, 3 figure

Carbon monoxide in the solar atmosphere I. Numerical method and two-dimensional models

The radiation hydrodynamic code CO5BOLD has been supplemented with the time-dependent treatment of chemical reaction networks. Advection of particle densities due to the hydrodynamic flow field is also included. The radiative transfer is treated frequency-independently, i.e. grey, so far. The upgraded code has been applied to two-dimensional simulations of carbon monoxide (CO) in the non-magnetic solar photosphere and low chromosphere. For this purpose a reaction network has been constructed, taking into account the reactions which are most important for the formation and dissociation of CO under the physical conditions of the solar atmosphere. The network has been strongly reduced to 27 reactions, involving the chemical species H, H2, C, O, CO, CH, OH, and a representative metal. The resulting CO number density is highest in the cool regions of the reversed granulation pattern at mid-photospheric heights and decreases strongly above. There, the CO abundance stays close to a value of 8.3 on the usual logarithmic abundance scale with [H]=12 but is reduced in hot shock waves which are a ubiquitous phenomenon of the model atmosphere. For comparison, the corresponding equilibrium densities have been calculated, based on the reaction network but also under assumption of instantaneous chemical equilibrium by applying the Rybicki & Hummer (RH) code by Uitenbroek (2001). Owing to the short chemical timescales, the assumption holds for a large fraction of the atmosphere, in particular the photosphere. In contrast, the CO number density deviates strongly from the corresponding equilibrium value in the vicinity of chromospheric shock waves. Simulations with altered reaction network clearly show that the formation channel via hydroxide (OH) is the most important one under the conditions of the solar atmosphere.Comment: 15 pages, 6 figures, final version will contain online materia