On the nature of the circumstellar medium of the remarkable Type Ia/IIn supernova SN 2002ic

We present results from the first high-resolution, high signal-to-noise ratio spectrum of SN 2002ic. The resolved Ha line has a P Cygni-type profile, clearly demonstrating the presence of a dense, slow-moving (~100 km s-1) outflow. We have additionally found a huge near-infrared excess, hitherto unseen in Type Ia supernovae. We argue that this is due to an infrared light-echo arising from the pre-existing dusty circumstellar medium. We deduce a circumstellar medium mass probably exceeding 0.3 Msolar produced by a mass-loss rate greater than several times 10-4 Msolar yr-1. For the progenitor, we favour a single-degenerate system where the companion is a post-asymptotic giant branch star. As a by-product of our optical data, we are able to provide a firm identification of the host galaxy of SN 2002ic.

Rapid identification of precursor cDNAs encoding five structural classes of antimicrobial peptides from pickerel frog (Rana palustris) skin secretion by single step “shotgun” cloning.

The skin secretion of the North American pickerel frog (Rana palustris) has long been known to have pronounced noxious/toxic properties and to be highly effective in defence against predators and against other sympatric amphibians. As it consists largely of a complex mixture of peptides, it has been subjected to systematic peptidomic study but there has been little focus on molecular cloning of peptide-encoding cDNAs and by deduction, the biosynthetic precursors that they encode. Here, we demonstrate that the cDNAs encoding the five major structural families of antimicrobial peptides can be elucidated by a single step “shotgun” cloning approach using a cDNA library constructed from the source material of the peptidomic studies—the defensive skin secretion itself. Using a degenerate primer pool designed to a highly conserved nucleic acid sequence 5' to the initiation codon of known antimicrobial peptide precursor transcripts, we amplified cDNA sequences representing five major classes of antimicrobial peptides, such as esculentins, brevinins, ranatuerins, palustrins and temporins. Bioinformatic comparisons of precursor open-reading frames and nucleic acid sequences revealed high degrees of structural similarities between analogous peptides of R. palustris and the Chinese bamboo odorous frog, Rana versabilis. This approach thus constitutes a robust technique that can be used either alone or ideally, in parallel with peptidomic analysis of skin secretion, to rapidly extract primary structural information on amphibian skin secretion peptides and their biosynthetic precursors.

Effective collision strengths for allowed transitions among the n

Aims.In this paper we report on calculations of collision strengths and effective collision strengths for allowed transitions among the $n \le$ 5 degenerate levels of Al XIII.
Methods.The Dirac atomic R-matrix code (DARC) has been adopted for these calculations.
Results.Collision strengths are reported over a wide energy range below 300 Ryd, and effective collision strengths are provided for electron temperatures of 4.4 $\le$ log $T_{\rm e} \le$ 6.8 K.

Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters

Phosphonates are organic compounds that contain a C-P bond and are a poorly characterized component of the marine phosphorus cycle. They may represent a potential source of bioavailable phosphorus, particularly in oligotrophic conditions. This study has investigated the distribution of the phnA gene which encodes phosphonoacetate hydrolase, the enzyme that mineralizes phosphonoacetate. Using newly designed degenerate primers targeting the phnA gene we analysed the potential for phosphonoacetate utilization in DNA and cDNA libraries constructed from a phytoplankton bloom in the Western English Channel during July 2006. Total RNA was isolated and reverse transcribed and phosphonoacetate hydrolase (phnA) transcripts were PCR amplified from the cDNA with the degenerate primers, cloned and sequenced. Phylogenetic analysis demonstrated considerable diversity with 14 sequence types yielding five unique phnA protein groups. We also identified 28 phnA homologues in a 454-pyrosequencing metagenomic and metatranscriptomic study from a coastal marine mesocosm, indicating that > 3% of marine bacteria in this study contained phnA. phnA homologues were also present in a metagenomic fosmid library from this experiment. Finally, cultures of four isolates of potential coral pathogens belonging to the Vibrionaceae contained the phnA gene. In the laboratory, these isolates were able to grow with phosphonoacetate as sole P and C source. The fact that the capacity to utilize phosphonoacetate was evident in each of the three coastal environments suggests the potential for widespread utilization of this bioavailable P source.

Evidence for phosphonate usage in the coral holobiont

Phosphonates are characterized by a stable carbon-phosphorus bond and commonly occur as lipid conjugates in invertebrate cell membranes. Phosphonoacetate hydrolase encoded by the phnA gene, catalyses the cleavage of phosphonoacetate to acetate and phosphate. In this study, we demonstrate the unusually high phnA diversity in coral-associated bacteria. The holobiont of eight coral species tested positive when screened for phnA using degenerate primers. In two soft coral species, Sinularia and Discosoma, sequencing of the phnA gene showed 13 distinct groups on the basis of 90% sequence identity across 100% of the sequence. A total of 16 bacterial taxa capable of using phosphonoacetate as the sole carbon and phosphorus source were isolated; 8 of which had a phnA+ genotype. This study enhances our understanding of the wide taxonomic and environmental distribution of phnA, and highlights the importance of phosphonates in marine ecosystems. The ISME Journal (2010) 4, 45-461; doi:10.1038/ismej.2009.129; published online 3 December 2009

Electroconvection in a homeotropic bent-rod nematic liquid crystal beyond the dielectric inversion frequency

We characterize the structural transitions in an initially homeotropic bent-rod nematic liquid crystal excited by ac fields of frequency f well above the dielectric inversion point f(i). From the measured principal dielectric constants and electrical conductivities of the compound, the Carr-Helfrich conduction regime is anticipated to extend into the sub-megahertz region. Periodic patterned states occur through secondary bifurcations from the Freedericksz distorted state. An anchoring transition between the bend Freedericksz (1317) and degenerate planar (DP) states is detected. The BF state is metastable well above the Freedericksz threshold and gives way to the DP state, which persists in the field-off condition for several hours. Numerous +1 and -1 umbilics form at the onset of BF distortion, the former being largely of the chiral type. They survive in the DP configuration as linear defects, nonsingular in the core. In the BF regime, not far from fi, periodic Williams-like domains form around the umbilics; they drift along the director easy axis right from their onset. With increasing f, the wave vector of the periodic domains switches from parallel to normal disposition with respect to the c vector. Well above fi, a broadband instability is found.

Stability and dynamical behavior in a lake-model and implications for regime shifts in real lakes

A modified abstract version of the Comprehensive Aquatic Simulation Model (CASM) is found to exhibit three types of folded bifurcations due to nutrient loading. The resulting bifurcation diagrams account for nonlinear dynamics such as regime shifts and cyclic changes between clear-water state and turbid state that have actually been observed in real lakes. In particular, pulse-perturbation simulations based on the model presented suggest that temporal behaviors of real lakes after biomanipulations can be explained by pulse-dynamics in complex ecosystems, and that not only the amplitude (manipulated abundance of organisms) but also the phase (timing) is important for restoring lakes by biomanipulation. Ecosystem management in terms of possible irreversible changes in ecosystems induced by regime shifts is also discussed. (c) 2007 Elsevier B.V All rights reserved.

On the limits of spectral methods for frequency estimation

An algorithm is presented which generates pairs of oscillatory random time series which have identical periodograms but differ in the number of oscillations. This result indicates the intrinsic limitations of spectral methods when it comes to the task of measuring frequencies. Other examples, one from medicine and one from bifurcation theory, are given, which also exhibit these limitations of spectral methods. For two methods of spectral estimation it is verified that the particular way end points are treated, which is specific to each method, is, for long enough time series, not relevant for the main result.

Pattern formation of chevrons in the conduction regime in homeotropically aligned liquid crystals

We report on chevrons (herringbonelike patterns) observed in homeotropically aligned liquid crystals with high electric conductivity. We focus our attention on two types of chevrons observed in the conduction regime. The threshold voltage and the characteristic double periodicity of chevrons (i.e., the short wavelength lambda(1) of the striated rolls and the long wavelength lambda(2) Of the chevron bands) have been measured as functions of the applied electric frequency f. With the aid of a crossed polarizer set, we have, in addition, determined the director field which shows a periodic in-plane rotation for our chevrons (with a wavelength lambda(2)) We arrived at the types of chevrons after qualitatively different bifurcation sequences with increasing voltage. The frequency dependence of lambda(2) also shows a qualitatively different behavior with respect to the two types of chevrons. The experimental results are discussed in terms of recent theoretical investigations.

Nonlinear excitations in strongly-coupled plasma lattices: envelope solitons, kinks and intrinsic localized modes

Ensembles of charged particles (plasmas) are a highly complex form of matter, most often modeled as a many-body system characterized by weak inter-particle interactions (electrostatic coupling). However, strongly-coupled plasma configurations have recently been produced in laboratory, either by creating ultra-cold plasmas confined in a trap or by manipulating dusty plasmas in discharge experiments. In this paper, the nonlinear aspects involved in the motion of charged dust grains in a one-dimensional plasma monolayer (crystal) are discussed. Different types of collective excitations are reviewed, and characteristics and conditions for their occurrence in dusty plasma crystals are discussed, in a quasi-continuum approximation. Dust crystals are shown to support nonlinear kink-shaped supersonic solitary longitudinal excitations, as well as modulated envelope localized modes associated with longitudinal and transverse vibrations. Furthermore, the possibility for intrinsic localized modes (ILMs) — Discrete Breathers (DBs) — to occur is investigated, from first principles. The effect of mode-coupling is also briefly considered. The relation to previous results on atomic chains, and also to experimental results on strongly-coupled dust layers in gas discharge plasmas, is briefly discussed.

Creation of persistent, straight, 2 mm long laser driven channels in underdense plasmas

The experimental study of the behavior of deuterium plasma with densities between 2 X 1018 and 2 x 10(20) cm(-3), subjected to a 6 TW, 30 ps, 3 X 10(18) W cm(-2) laser pulse, is presented Conclusive experimental proof that a single straight channel is generated when the laser pulse interacts with the lowest densities is provided This channel shows no small-scale longitudinal density modulations, extends up to 2 mm in length and persists for up to 150 ps after the peak of the interaction Bifurcation of the channel after 1 mm propagation distance is observed for the first time For higher density interactions, above the relativistic self-focusing threshold, bubblelike structures are observed to form at late times These observations have implications for both laser wakefield accelerators and fast ignition inertial fusion studies (C) 2010 American Institute of Physics [doi 10 1063/1 3505305]

Phonons, Instabilities and Origin of Polarization in KDP Crystals

The -phonons of KH2PO4 (KDP) and its deuterated analog DKDP are studied via first-principles linear response calculations. The paraelectric phase shows two instabilities. One for a z-polarized mode, which leads to the spontaneous polarization Ps of the ferroelectric phase. The other corresponds to a two-fold degenerate xy-polarized mode. Other phonons are analyzed, which couple to the ferroelectric one at large amplitudes and are relevant for the ferroelectric transition. We show that Ps is mainly of electronic nature, since it arises mostly from an off-diagonal component of the Born effective charge tensor of H, with minor contribution from P atoms displacements.

Collective decoherence of cold atoms coupled to a Bose-Einstein condensate

We examine the time evolution of cold atoms (impurities) interacting with an environment consisting of a degenerate bosonic quantum gas. The impurity atoms differ from the environment atoms, being of a different species. This allows one to superimpose two independent trapping potentials, each being effective only on one atomic kind, while transparent to the other. When the environment is homogeneous and the impurities are confined in a potential consisting of a set of double wells, the system can be described in terms of an effective spin-boson model, where the occupation of the left or right well of each site represents the two (pseudo)-spin states. The irreversible dynamics of such system is here studied exactly, i.e. not in terms of a Markovian master equation. The dynamics of one and two impurities is remarkably different in respect of the standard decoherence of the spin-boson system. In particular, we show: (i) the appearance of coherence oscillations, (ii) the presence of super and subdecoherent states that differ from the standard ones of the spin-boson model, and (iii) the persistence of coherence in the system at long times. We show that this behaviour is due to the fact that the pseudospins have an internal spatial structure. We argue that collective decoherence also prompts information about the correlation length of the environment. In a one-dimensional (1D) configuration, one can change even more strongly the qualitative behaviour of the dephasing just by tuning the interaction of the bath.

High-velocity features: A ubiquitous property of Type Ia supernovae

Evidence of high-velocity features (HVFs) such as those seen in the near-maximum spectra of some Type Ia supernovae (SNe Ia; e. g., SN 2000cx) has been searched for in the available SN Ia spectra observed earlier than 1 week before B maximum. Recent observational efforts have doubled the number of SNe Ia with very early spectra. Remarkably, all SNe Ia with early data ( seven in our Research Training Network sample and 10 from other programs) show signs of such features, to a greater or lesser degree, in Ca II IR and some also in the Si II lambda 6355 line. HVFs may be interpreted as abundance or density enhancements. Abundance enhancements would imply an outer region dominated by Si and Ca. Density enhancements may result from the sweeping up of circumstellar material (CSM) by the highest velocity SN ejecta. In this scenario, the high incidence of HVFs suggests that a thick disk and/or a high-density companion wind surrounds the exploding white dwarf, as may be the case in single degenerate systems. Large-scale angular fluctuations in the radial density and abundance distribution may also be responsible: this could originate in the explosion and would suggest a deflagration as the more likely explosion mechanism. CSM interaction and surface fluctuations may coexist, possibly leaving different signatures on the spectrum. In some SNe, the HVFs are narrowly confined in velocity, suggesting the ejection of blobs of burned material.