High-resolution crystal structure of the intramolecular d(TpA) thymine-adenine photoadduct and its mechanistic implications.

A high-resolution crystal structure is reported for d(TpA)*, the intramolecular thymine–adenine photoadduct that is produced by direct ultraviolet excitation of the dinucleoside monophosphate d(TpA). It confirms the presence of a central 1,3-diazacyclooctatriene ring linking the remnants of the T and A bases, as previously deduced from heteronuclear NMR measurements by Zhao et al. (The structure of d(TpA)*, the major photoproduct of thymidylyl-(3'-5')-deoxyadenosine. Nucleic Acids Res., 1996, 24, 1554–1560). Within the crystal, the d(TpA)* molecules exist as zwitterions with a protonated amidine fragment of the eight-membered ring neutralizing the charge of the internucleotide phosphate monoanion. The absolute configuration at the original thymine C5 and C6 atoms is determined as 5S,6R. This is consistent with d(TpA)* arising by valence isomerization of a precursor cyclobutane photoproduct with cis–syn stereochemistry that is generated by [2 + 2] photoaddition of the thymine 5,6-double bond across the C6 and C5 positions of adenine. This mode of photoaddition should be favoured by the stacked conformation of adjacent T and A bases in B-form DNA. It is probable that the primary photoreaction is mechanistically analogous to pyrimidine dimerization despite having a much lower quantum yield.

Excited ions in intense femtosecond laser pulses: Laser-induced recombination

Electron-ion recombination in a laser-induced electron recollision is of fundamental importance as the underlying mechanism responsible for the generation of high harmonic radiation, and hence for the production of attosecond pulse trains in the extreme ultraviolet and soft X-ray spectral regions. By using an ion beam target, remotely prepared to be partially in long-lived excited states, the recombination process has for the first time been directly observed and studied.

Deposition of Uranium Precipitates in Dolomitic Gravel Fill

Uranium-containing precipitates have been observed in a dolomitic gravel fill near the Department of Energy (DOE) S-3 Ponds former waste disposal site as a result of exposure to acidic (pH 3.4) groundwater contaminated with U (33 mg L-1), Al3+ (900 mg L-1), and NO3- (14?000 mg L-1). The U containing precipitates fluoresce a bright green under ultraviolet (UV) short-wave light which identify U-rich coatings on the gravel. Scanning electron microscopy (SEM) microprobe analysis show U concentration ranges from 1.6-19.8% (average of 7%) within the coatings with higher concentrations at the interface of the dolomite fragments. X-ray absorption near edge structure spectroscopy (XANES) indicate that the U is hexavalent and extended X-ray absorption fine structure spectroscopy (EXAFS) shows that the uranyl is coordinated by carbonate. The exact nature of the uranyl carbonates are difficult to determine, but some are best described by a split K+-like shell similar to grimselite [K4Na(UO2)(CO3)3·H2O] and other regions are better described by a single Ca2+-like shell similar to liebigite [Ca2(UO2)(CO3)3·11(H2O)] or andersonite [Na2CaUO2(CO3)3 · 6H2O]. The U precipitates are found in the form of white to light yellow cracked-formations as coatings on the dolomite gravel and as detached individual precipitates, and are associated with amorphous basalumnite [Al4(SO4)(OH)10·4H2O].

Characterization of stationary and pulsed inductively coupled RF discharges for plasma sterilization

Sterilization of bio-medical materials using radio frequency (RF) excited inductively coupled plasmas (ICPs) has been investigated. A double ICP has been developed and studied for homogenous treatment of three-dimensional objects. Sterilization is achieved through a combination of ultraviolet light, ion bombardment and radical treatment. For temperature sensitive materials, the process temperature is a crucial parameter. Pulsing of the plasma reduces the time average heat strain and also provides additional control of the various sterilization mechanisms. Certain aspects of pulsed plasmas are, however, not yet fully understood. Phase resolved optical emission spectroscopy and time resolved ion energy analysis illustrate that a pulsed ICP ignites capacitively before reaching a stable inductive mode. Time resolved investigations of the post-discharge, after switching off the RF power, show that the plasma boundary sheath in front of a substrate does not fully collapse for the case of hydrogen discharges. This is explained by electron heating through super-elastic collisions with vibrationally excited hydrogen molecules.

Iron abundances of B-type post-asymptotic giant branch stars in globular clusters: Barnard29 in M13 and ROA5701 in ωCen

High-resolution optical and ultraviolet (UV) spectra of two B-type post-asymptotic giant branch (post-AGB) stars in globular clusters, Barnard29 in M13 and ROA5701 in ?Cen, have been analysed using model atmosphere techniques. The optical spectra have been obtained with FEROS on the ESO 2.2-m telescope and the 2d-Coudé spectrograph on the 2.7-m McDonald telescope, while the UV observations are from the Goddard high-resolution spectrograph on the Hubble Space Telescope (HST). Abundances of light elements (C, N, O, Mg, Al and S) plus Fe have been determined from the optical spectra, while the UV data provide additional Fe abundance estimates from FeIII absorption lines in the 1875-1900 Å wavelength region. A general metal underabundance relative to young B-type stars is found for both Barnard29 and ROA5701. These results are consistent with the metallicities of the respective clusters, as well as with previous studies of the objects. The derived abundance patterns suggest that the stars have not undergone a gas-dust separation, contrary to previous suggestions, although they may have evolved from the AGB before the onset of the third dredge-up. However, the Fe abundances derived from the HST spectra are lower than those expected from the metallicities of the respective clusters, by 0.5 dex for Barnard29 and 0.8 dex for ROA5701. A similar systematic underabundance is also found for other B-type stars in environments of known metallicity, such as the Magellanic Clouds. These results indicate that the FeIII UV lines may yield abundance values which are systematically too low by typically 0.6 dex and hence such estimates should be treated with caution.

Iron abundances from optical FeIII absorption lines in B-type stellar spectra

The role of optical FeIII absorption lines in B-type stars as iron abundance diagnostics is considered. To date, ultraviolet Fe lines have been widely used in B-type stars, although line blending can severely hinder their diagnostic power. Using optical spectra, covering a wavelength range ~3560-9200Å, a sample of Galactic B-type main-sequence and supergiant stars of spectral types B0.5 to B7 are investigated. A comparison of the observed FeIII spectra of supergiants, and those predicted from the model atmosphere codes TLUSTY [plane-parallel, non-local thermodynamic equilibrium (LTE)], with spectra generated using SYNSPEC (LTE), and CMFGEN (spherical, non-LTE), reveal that non-LTE effects appear small. In addition, a sample of main-sequence and supergiant objects, observed with the Fiber-fed Extended Range Optical Spectrograph (FEROS), reveal LTE abundance estimates consistent with the Galactic environment and previous optical studies. Based on the present study, we list a number of FeIII transitions which we recommend for estimating the iron abundance from early B-type stellar spectra.

The iron abundance of the Magellanic Bridge

High-resolution Hubble Space Telescope ultraviolet spectra for five B-type stars in the Magellanic Bridge and in the Large (LMC) and Small (SMC) Magellanic Clouds have been analysed to estimate their iron abundances. Those for the Clouds are lower than estimates obtained from late-type stars or the optical lines in B-type stars by approximately 0.5 dex. This may be due to systematic errors possibly arising from non-local thermodynamic equilibrium (non-LTE) effects or from errors in the atomic data, as similar low Fe abundances have previously been reported from the analysis of the ultraviolet spectra of Galactic early-type stars. The iron abundance estimates for all three Bridge targets appear to be significantly lower than those found for the SMC and LMC by approximately -0.5 and -0.8 dex, respectively, and these differential results should not be affected by any systematic errors present in the absolute abundance estimates. These differential iron abundance estimates are consistent with the underabundances for C, N, O, Mg and Si of approximately -1.1 dex relative to our Galaxy previously found in our Bridge targets. The implications of these very low metal abundances for the Magellanic Bridge are discussed in terms of metal deficient material being stripped from the SMC.

Transition region velocity oscillations observed by EUNIS-06

Spectroscopic measurements of NOAA AR 10871, obtained with the Extreme Ultraviolet Normal Incidence Spectrograph (EUNIS) sounding rocket instrument on 2006 April 12, reveal velocity oscillations in the He II 303.8 angstrom emission line formed at T approximate to 5; 10(4) K. The oscillations appear to arise in a bright active region loop arcade about 25 '' wide which crosses the EUNIS slit. The period of these transition region oscillations is 26 +/- 4 s, coupled with a velocity amplitude of +/- 10 km s(-1), detected over four complete cycles. Similar oscillations are observed in lines formed at temperatures up to T approximate to 4; 10(5) K, but we find no evidence for the coupling of these velocity oscillations with corresponding phenomena in the corona. We interpret the detected oscillations as originating from an almost purely adiabatic plasma, and infer that they are generated by the resonant transmission of MHD waves through the lower active region atmospheres. Through the use of seismological techniques, we establish that the observed velocity oscillations display wave properties most characteristic of fast body global sausage modes.

Spatially resolved diagnostics on a micro atmospheric pressure plasma jet

Despite enormous potential for technological applications, fundamentals of stable non-equilibrium micro-plasmas at ambient pressure are still only partly understood. Micro-plasma jets are one sub-group of these plasma sources. For an understanding it is particularly important to analyse transport phenomena of energy and particles within and between the core and effluent of the discharge. The complexity of the problem requires the combination and correlation of various highly sophisticated diagnostics yielding different information with an extremely high temporal and spatial resolution. A specially designed rf microscale atmospheric pressure plasma jet (µ-APPJ) provides excellent access for optical diagnostics to the discharge volume and the effluent region. This allows detailed investigations of the discharge dynamics and energy transport mechanisms from the discharge to the effluent. Here we present examples for diagnostics applicable to different regions and combine the results. The diagnostics applied are optical emission spectroscopy (OES) in the visible and ultraviolet and two-photon absorption laser-induced fluorescence spectroscopy. By the latter spatially resolved absolutely calibrated density maps of atomic oxygen have been determined for the effluent. OES yields an insight into energy transport mechanisms from the core into the effluent. The first results of spatially and phase-resolved OES measurements of the discharge dynamics of the core are presented.

Stress resistance and disease resistance in seaweeds: The role of reactive oxygen metabolism

It has become clear over the last 15-20 years that the immediate effect of a wide range of environmental stresses, and of infection, on vascular plants is to increase the formation of reactive oxygen species (ROS) and to impose oxidative stress on the cells. Since 1994, sufficient examples of similar responses in a broad range of marine macroalgae have been described to show that reactive oxygen metabolism also underlies the mechanisms by which seaweeds respond (and become resistant) to stress and infection. Desiccation, freezing, low temperatures, high light, ultraviolet radiation, and heavy metals all tend to result in a gradual and continued buildup of ROS because photosynthesis is inhibited and excess energy results in the formation of singlet oxygen. The response to other stresses (infection or oligosaccharides which signal that infection is occurring, mechanical stress, hyperosmotic shock) is quite different-a more rapid and intense, but short-lived production of ROS, described as an

Quantitative studies of the optical and UV spectra of Galactic early B supergiants - I. Fundamental parameters

Aims. We undertake an optical and ultraviolet spectroscopic analysis of a sample of 20 Galactic B0-B5 supergiants of luminosity classes Ia, Ib, Iab, and II. Fundamental stellar parameters are obtained from optical diagnostics and a critical comparison of the model predictions to observed UV spectral features is made.

Observations towards early-type stars in the ESO-POP Survey - II. Searches for intermediate- and high-velocity clouds

We present Ca it K and Ti it optical spectra of early-type stars taken mainly from the ultraviolet and visual echelle spectrograph (LIVES) Paranal Observatory Project, plus H 1 21-cm spectra, from the Vila-Elisa and Leiden-Dwingeloo Surveys, which are employed to obtain distances to intermediate- and high-velocity clouds (IHVCs). H I emission at a velocity of -117 km s(-1) towards the sightline HD 30677 (l, b = 190 degrees.2, -22 degrees.2) with column density -1.7 x 10(19) cm(-2) has no corresponding Ca Pi K absorption in the LIVES spectrum, which has a signal-to-noise ratio (S/N) of 610 per resolution element. The star has a spectroscopically determined distance of 2.7 kpc, and hence sets this as a firm lower distance limit towards Anti-Centre cloud ACII. Towards another sightline (HD 46185 with 1, b = 222 0, -10 degrees.1), H1 at a velocity of +122 km s(-1) and column density of 1.2 x 10(19) cm(-2) is seen. The corresponding Ca Pi K spectrum has a S/N of 780, although no absorption is observed at the cloud velocity. This similarly places a firm lower distance limit of 2.9 kpc towards this parcel of gas that may be an intermediate-velocity (IV) cloud. The lack of IV Ca it absorption towards HD 196426 (1, b = 45 degrees.8, -23 degrees.3) at a S/N of 500 reinforces a lower distance limit of -700 pc towards this part of complex gp, where the H I column density is 1.1 x 1019 cm(-2) and velocity is +78 km s(-1). Additionally, no IV Cart is seen in absorption in the spectrum of HD 19445, which is strong in H I with a column density of 8 x 10(19) cm(-2) at a velocity of - -42 km s(-1), placing a firm although uninteresting lower distance limit of 39 pc to this part of IV South. Finally, no high-velocity Call K absorption is seen towards HD 115363 (l, b = 306.0,-1.0) at a S/N of 410, placing a lower distance of -3.2 kpc towards the HVC gas at velocity of - +224 km s(-1) and WE column density of 5.2 x 10(19) cm(-2). This gas is in the same region of the sky as complex WE (Wakker 2001), but at higher velocities. The non-detection of Ca it K absorption sets a lower distance of -3.2 kpc towards the HVC, which is unsurprising if this feature is indeed related to the Magellanic System.

Plasma diagnostics of active-region evolution and implications for coronal heating

A detailed study is presented of the decaying solar-active region NOAA 10103 observed with the Coronal Diagnostic Spectrometer (CDS), the Michelson Doppler Imager (MDI) and the Extreme-ultraviolet Imaging Telescope (EIT) onboard the Solar and Heliospheric Observatory (SOHO). Electron-density maps formed using Si x (356.03 angstrom/347.41 angstrom) show that the density varies from similar to 10(10) cm(-3) in the active-region core to similar to 7 x 108 cm-3 at the region boundaries. Over the 5 d of observations, the average electron density fell by similar to 30 per cent. Temperature maps formed using Fe XVI (335.41 angstrom)/Fe XIV (334.18 angstrom) show electron temperatures of similar to 2.34 x 10(6) K in the active-region core and similar to 2.10 x 10(6) K at the region boundaries. Similarly to the electron density, there was a small decrease in the average electron temperature over the 5-d period. The radiative, conductive and mass-flow losses were calculated and used to determine the resultant heating rate (P-H). Radiative losses were found to dominate the active-region cooling process. As the region decayed, the heating rate decreased by almost a factor of 5 between the first and last day of observations. The heating rate was then compared to the total unsigned magnetic flux (Phi(tot) = integral dA vertical bar B-z vertical bar), yielding a power law of the form P-H similar to Phi(0.81 +/- 0.32)(tot) This result suggests that waves rather than nanoflares may be the dominant heating mechanism in this active region.

Spectroscopy of astrophysical plasmas in the laboratory

Most of the matter in the universe is in the few form of a plasma. Over the past years physicists have produced laboratory plasmas that can mimic those observed in astrophysics. The best known is probably the tokamak, which has similar physical conditions and plasma processes to those found in collisionally dominated solar and stellar transition regions and coronae. Spectroscopy of such laboratory plasmas, in, particular at, ultraviolet and X-ray wavelengths, has greatly aided our understanding of their astrophysical counterparts. More recently, experiments have been performed on the Z Machine at the Sandia National Laboratory in the USA with the aim of creating, for the first time, steady-state photoionization-dominated plasmas that recreate the conditions found in some accretion-powered X-ray sources, such as X-ray binaries. In the future, experiments are envisaged with laser-produced plasmas at AWE Aldermaston that may be able to mimic the steady-state conditions found in high-energy accretion-powered sources, including the central regions of active galaxies.

Generation of Atomic Oxygen in the Effluent of an Atmospheric Pressure Plasma Jet

The planar 13.56MHz RF-excited low temperature atmospheric pressure plasma jet (APPJ) investigated in this study is operated with helium feed gas and a small molecular oxygen admixture. The effluent leaving the discharge through the jet’s nozzle contains very few charged particles and a high reactive oxygen species’ density. As its main reactive radical, essential for numerous applications, the ground state atomic oxygen density in the APPJ’s effluent is measured spatially resolved with two-photon absorption laser induced fluorescence spectroscopy. The atomic oxygen density at the nozzle reaches a value of ~1016 cm-3. Even at several centimetres distance still 1% of this initial atomic oxygen density can be detected. Optical emission spectroscopy (OES) reveals the presence of short living excited oxygen atoms up to 10 cm distance from the jet’s nozzle. The measured high ground state atomic oxygen density and the unaccounted for presence of excited atomic oxygen require further investigations on a possible energy transfer from the APPJ’s discharge region into the effluent: energetic vacuum ultraviolet radiation, measured by OES down to 110 nm, reaches far into the effluent where it is presumed to be responsible for the generation of atomic oxygen.