The geometry and ionization structure of the wind in the eclipsing nova-like variables RW Tri and UX UMa

The UV spectra of nova-like variables are dominated by emission from the accretion disk, modified by scattering in a wind emanating from the disk. Here, we model the spectra of RW Tri and UX UMa, the only two eclipsing nova-like variables which have been observed with the Hubble Space Telescope in the far-ultraviolet, in an attempt to constrain the geometry and the ionization structure of their winds. Using our Monte Carlo radiative transfer code, we computed spectra for simply parameterized axisymmetric biconical outflow models and were able to find plausible models for both systems. These reproduce the primary UV resonance lines-N v, Si iv, and C iv-in the observed spectra in and out of eclipse. The distribution of these ions in the wind models is similar in both cases as is the extent of the primary scattering regions in which these lines are formed. The inferred mass-loss rates are 6%-8% of the mass accretion rates for the systems. We discuss the implication of our point models for our understanding of accretion disk winds in cataclysmic variables. © 2010. The American Astronomical Society. All rights reserved.

Antiproton induced DNA damage: proton like in flight, carbon-ion like near rest

Biological validation of new radiotherapy modalities is essential to understand their therapeutic potential. Antiprotons have been proposed for cancer therapy due to enhanced dose deposition provided by antiproton-nucleon annihilation. We assessed cellular DNA damage and relative biological effectiveness (RBE) of a clinically relevant antiproton beam. Despite a modest LET (,19 keV/mm), antiproton spread out Bragg peak (SOBP) irradiation caused significant residual c-H2AX foci compared to X-ray, proton and antiproton plateau irradiation. RBE of ,1.48 in the SOBP and ,1 in the plateau were measured and used for a qualitative effective dose curve comparison with proton and carbon-ions. Foci in the antiproton SOBP were larger and more structured compared to X-rays, protons and carbon-ions. This is likely due to overlapping particle tracks near the annihilation vertex, creating spatially correlated DNA lesions. No biological effects were observed at 28–42 mm away from the primary beam suggesting minimal risk from long-range secondary particles.

Modification of the formation of high-Mach number electrostatic shock-like structures by the ion acoustic instability

The formation of unmagnetized electrostatic shock-like structures with a high Mach number is examined with one- and two-dimensional particle-in-cell (PIC) simulations. The structures are generated through the collision of two identical plasma clouds, which consist of equally hot electrons and ions with a mass ratio of 250. The Mach number of the collision speed with respect to the initial ion acoustic speed of the plasma is set to 4.6. This high Mach number delays the formation of such structures by tens of inverse ion plasma frequencies. A pair of stable shock-like structures is observed after this time in the 1D simulation, which gradually evolve into electrostatic shocks. The ion acoustic instability, which can develop in the 2D simulation but not in the 1D one, competes with the nonlinear process that gives rise to these structures. The oblique ion acoustic waves fragment their electric field. The transition layer, across which the bulk of the ions change their speed, widens and their speed change is reduced. Double layer-shock hybrid structures develop.

Beam profiles of proton and carbon ions in the relativistic transparency regime

Ion acceleration from relativistic laser solid interactions has been of particular interest over the last decade. While beam profiles have been studied for target normal sheath acceleration (TNSA), such profiles have yet to be described for other mechanisms. Here, experimental data is presented, investigating ion beam profiles from acceleration governed by relativistic transparent laser plasma interaction. The beam shape of carbon C6+ ions and protons has been measured simultaneously with a wide angle spectrometer. It was found that ion beams deviate from the typical Gaussian-like shape found with TNSA and that the profile is governed by electron dynamics in the volumetric laser-plasma interaction with a relativistically transparent plasma; due to the ponderomotive force electrons are depleted from the center of the laser axis and form lobes affecting the ion beam structure. The results are in good agreement with high resolution three-dimensional-VPIC simulations and can be used as a new tool to experimentally distinguish between different acceleration mechanisms.

A Coordination and Ligand Replacement Based Three-Input Colorimetric Logic Gate Sensing Platform for Melamine, Mercury Ions, and Cysteine

Discrimination of different species in various target scopes within a single sensing platform can provide many advantages such as simplicity, rapidness, and cost effectiveness. Here we design a three-input colorimetric logic gate based on the aggregation and anti-aggregation of gold nanoparticles (Au NPs) for the sensing of melamine, cysteine, and Hg2+. The concept takes advantages of the highly specific coordination and ligand replacement reactions between melamine, cysteine, Hg2+, and Au NPs. Different outputs are obtained with the combinational inputs in the logic gates, which can serve as a reference to discriminate different analytes within a single sensing platform. Furthermore, besides the intrinsic sensitivity and selectivity of Au NPs to melamine-like compounds, the “INH” gates of melamine/cysteine and melamine/Hg2+ in this logic system can be employed for sensitive and selective detections of cysteine and Hg2+, respectively.

Energy levels, radiative rates and electron impact excitation rates for transitions in He-like Fe XXV, Co XXVI, Ni XXVII, Cu XXVIII and Zn XXIX

We report calculations of energy levels, radiative rates and electron impact excitation cross sections and rates for transitions in He-like Fe XXV, Co XXVI, Ni XXVII, Cu XXVIII and Zn XXIX. The grasp (general-purpose relativistic atomic structure package) is adopted for calculating energy levels and radiative rates. For determining the collision strengths and subsequently the excitation rates, the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 49 levels of each ion. Additionally, theoretical lifetimes are listed for all 49 levels of the above five ions. Collision strengths are averaged over a Maxwellian velocity distribution and the effective collision strengths obtained listed over a wide temperature range up to 10 ^7.7 K. Comparisons are made with similar data obtained using the flexible atomic code (fac) to highlight the importance of resonances, included in calculations with darc, in the determination of effective collision strengths. Discrepancies between the collision strengths from darc and fac, for some transitions, are also discussed. Finally, discrepancies between the present results of effective collision strengths with the darc code and earlier semi-relativistic R-matrix data are noted over a wide range of electron temperatures for many transitions in all ions. 

Energy levels, radiative rates and electron impact excitation rates for transitions in He-like Ga XXX, Ge XXXI, As XXXII, Se XXXIII and Br XXXIV

We report calculations of energy levels, radiative rates and electron impact excitation cross sections and rates for transitions in He-like Ga XXX, Ge XXXI, As XXXII, Se XXXIII and Br XXXIV. The grasp (general-purpose relativistic atomic structure package) is adopted for calculating energy levels and radiative rates. For determining the collision strengths, and subsequently the excitation rates, the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 49 levels of each ion. Additionally, theoretical lifetimes are provided for all 49 levels of the above five ions. Collision strengths are averaged over a Maxwellian velocity distribution and the effective collision strengths obtained listed over a wide temperature range up to 10⁸ K. Comparisons are made with similar data obtained using the flexible atomic code (fac) to highlight the importance of resonances, included in calculations with darc, in the determination of effective collision strengths. Discrepancies between the collision strengths from darc and fac, particularly for some forbidden transitions, are also discussed. Finally, discrepancies between the present results for effective collision strengths with the darc code and earlier semi-relativistic R-matrix data are noted over a wide range of electron temperatures for many transitions in all ions. © 2013 The Royal Swedish Academy of Sciences.

Energy levels, radiative rates and electron impact excitation rates for transitions in He-like Ti XXI, v XXII, Cr XXIII and Mn XXIV

We report calculations of energy levels, radiative rates and electron impact excitation cross sections and rates for transitions in He-like Ti XXI, V XXII, Cr XXIII and Mn XXIV. grasp (general-purpose relativistic atomic structure package) is adopted for calculating energy levels and radiative rates. For determining the collision strengths and subsequently the excitation rates, the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 49 levels of each ion. Additionally, theoretical lifetimes are listed for all the 49 levels of the above four ions. Collision strengths are averaged over a Maxwellian velocity distribution and the effective collision strengths obtained listed over a wide temperature range up to 10 ^7.5K. Comparisons are made with similar data obtained using the flexible atomic code (fac) to highlight the importance of resonances, included in calculations with darc, in the determination of effective collision strengths. Discrepancies between the collision strengths from darc and fac, in particular for forbidden transitions, are also discussed. Finally, discrepancies between the present results for effective collision strengths with the darc code and earlier semi-relativistic R-matrix data are noted over a wide range of electron temperatures for many transitions in all ions. 

Beamed neutron emission driven by laser accelerated light ions

Highly anisotropic, beam-like neutron emission with peak flux of the order of 10^9 n/sr was obtained from light nuclei reactions in a pitcher–catcher scenario, by employing MeV ions driven by subpetawatt laser. The spatial profile of the neutron beam, fully captured for the first time by employing a CR39 nuclear track detector, shows a FWHMdivergence angle of ~70 deg, with a peak flux nearly an order of magnitude higher than the isotropic component elsewhere. The observed beamed flux of neutrons is highly favourable for a wide range of applications, and indeed for further transport and moderation to thermal energies. A systematic study employing various combinations of pitcher–catcher materials indicates the dominant reactions being d(p, n+p)1Hand d(d,n)3He. Albeit insufficient cross-section data are available for modelling, the observed anisotropy in the neutrons’ spatial and spectral profiles are most likely related to the directionality and high energy of the projectile ions.

Single-photon single ionization of W+ ions: experiment and theory

Experimental and theoretical results are reported for photoionization of Ta-like (W+) tungsten ions. Absolute cross sections were measured in the energy range 16–245 eV employing the photon–ion merged-beam setup at the advanced light source in Berkeley. Detailed photon-energy scans at 100 meV bandwidth were performed in the 16–108 eV range. In addition, the cross section was scanned at 50 meV resolution in regions where fine resonance structures could be observed. Theoretical results were obtained from a Dirac–Coulomb R-matrix approach. Photoionization cross section calculations were performed for singly ionized atomic tungsten ions in their 5s²5p⁶5d⁴(⁵D)6s ⁶Dj.  J = 1/2, ground level and the associated excited metastable levels with J = 3/2, 5/2, 7/2 and 9/2. Since the ion beams used in the experiments must be expected to contain long-lived excited states also from excited configurations, additional cross-section calculations were performed for the second-lowest term, 5d⁵⁶Sj, J = 5/2, and for the 4F term, 5d³6s^{2 4}Fj, with J = 3/2, 5/2, 7/2 and 9/2. Given the complexity of the electronic structure of W+ the calculations reproduce the main features of the experimental cross section quite well.

Valence-shell photoionization of chlorinelike Ar+ ions

Absolute cross-section measurements for valence-shell photoionization of Ar + ions are reported for photon energies ranging from 27.4 eV to 60.0 eV. The data, taken by merging beams of ions and synchrotron radiation at a photon energy resolution of 10 meV, indicate that the primary ion beam was a statistically weighted mixture of the 2P o3/2 ground state and the 2P o1/2 metastable state of Ar +. Photoionization of this Cell-like ion is characterized by multiple Rydberg series of autoionizing resonances superimposed on a direct photoionization continuum. Observed resonance lineshapes indicate interference between indirect and direct photoionization channels. Resonance features are spectroscopically assigned and their energies and quantum defects are tabulated. The measurements are satisfactorily reproduced by theoretical calculations based on an intermediate coupling semi-relativistic Breit-Pauli approximation.

Metal ions and protein folding: conformational and functional interplay

Dissertation presented to obtain a PhD degree in Biochemistry at Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Synthesis, structural analysis, and magnetic behaviour of three fumarate bridged coordination polymers: five-fold interpenetrated diamond-like net of Ni-II, sheets of Ni-II and Co-II

The hydrothermal reactions of Ni(NO3)(2).6H(2)O, disodium fumarate (fum) and 1,2-bis(4-pyridyl)ethane (bpe)/1,3-bis(4-pyridyl) propane (bpp) in aqueous-methanol medium yield one 3-D and one 2-D metal-organic hybrid material, [Ni(fum)(bpe)] (1) and [Ni(fum)(bpp)(H2O)] (2), respectively. Complex 1 possesses a novel unprecedented structure, the first example of an "unusual mode" of a five-fold distorted interpenetrated network with metal-ligand linkages where the four six-membered windows in each adamantane-type cage are different. The structural characterization of complex 2 evidences a buckled sheet where nickel ions are in a distorted octahedral geometry, with two carboxylic groups, one acting as a bis-chelate, the other as a bis-monodentate ligand. The metal ion completes the coordination sphere through one water molecule and two bpp nitrogens in cis position. Variable-temperature magnetic measurements of complexes 1 and 2 reveal the existence of very weak antiferromagnetic intramolecular interactions and/or the presence of single-ion zero field splitting (D) of isolated Ni-II ions in both the compounds. Experimentally, both the J parameters are close, comparable and very small. Considering zero-field splitting of Ni-II, the calculated D values are in agreement with values reported in the literature for Ni-II ions. Complex 3, [{Co(phen)}(2)(fum)(2)] (phen=1,10-phenanthroline) is obtained by diffusing methanolic solution of 1,10-phenanthroline on an aqueous layer of disodium fumarate and Co(NO3)(2).6H(2)O. It consists of dimeric Co-II(phen) units, doubly bridged by carboxylate groups in a distorted syn-syn fashion. These fumarate anions act as bis-chelates to form corrugated sheets. The 2D layer has a (4,4) topology, with the nodes represented by the centres of the dimers. The magnetic data were fitted ignoring the very weak coupling through the fumarate pathway and using a dimer model.

Guanine specific binding at a DNA junction formed by d[CG(5-BrU)ACG]2 with a topoisomerase poison in the presence of Co2+Ions†,‡

The structure of the duplex d[CG(5-BrU)ACG]2 bound to 9-bromophenazine-4-carboxamide has been solved through MAD phasing at 2.0 Å resolution. It shows an unexpected and previously unreported intercalation cavity stabilized by the drug and novel binding modes of Co2+ ions at certain guanine N7 sites. For the intercalation cavity the terminal cytosine is rotated to pair with the guanine of a symmetry-related duplex to create a pseudo-Holliday junction geometry, with two such cavities linked through the minor groove interactions of the N2/N3 guanine sites at an angle of 40°, creating a quadruplex-like structure. The mode of binding of the drug is shown to be disordered, with the major conformations showing the side chain bound to the N7 position of adjacent guanines. The other end of the duplex exhibits a terminal base fraying in the presence of Co2+ ions linking symmetry-related guanines, causing the helices to intertwine through the minor groove. The stabilization of the structure by the intercalating drug shows that this class of compound may bind to DNA junctions as well as duplex DNA or to strand-nicked DNA (‘hemi-intercalated'), as in the cleavable complex. This suggests a structural basis for the dual poisoning of topoisomerase I and II enzymes by this family of drugs.

Tuning chelation by the surfactant-like peptide A6H using predetermined pH values

We examine the self-assembly of a peptide A6H comprising a hexa-alanine sequence A6 with a histidine (H) “head group”, which chelates Zn2+ cations. We study the self assembly of A6H and binding of Zn2+ ions in ZnCl2 solutions, under acidic and neutral conditions. A6H self-assembles into nanotapes held together by a β-sheet structure in acidic aqueous solutions. By dissolving A6H in acidic ZnCl2 solutions, the carbonyl oxygen atoms in A6H chelate the Zn2+ ions and allow for β-sheet formation at lower concentrations, consequently reducing the onset concentration for nanotape formation. A6H mixed with water or ZnCl2 solutions under neutral conditions produces short sheets or pseudocrystalline tapes, respectively. The imidazole ring of A6H chelates Zn2+ ions in neutral solutions. The internal structure of nanosheets and pseudocrystalline sheets in neutral solutions is similar to the internal structure of A6H nanotapes in acidic solutions. Our results show that it is possible to induce dramatic changes in the self-assembly and chelation sites of A6H by changing the pH of the solution. However, it is likely that the amphiphilic nature of A6H determines the internal structure of the self-assembled aggregates independent from changes in chelation.