Thermal denaturation of fluctuating finite DNA chains: the role of bending rigidity in bubble nucleation

Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of broken bonds, or bubble, compared to the double stranded state, the inclusion of the molecular conformational degrees of freedom in a more general mesoscopic model is needed. In this paper we do so by presenting a 1D Ising model, which describes the internal base pair states, coupled to a discrete worm like chain model describing the chain configurations [J. Palmeri, M. Manghi, and N. Destainville, Phys. Rev. Lett. 99, 088103 (2007)]. This coupled model is exactly solved using a transfer matrix technique that presents an analogy with the path integral treatment of a quantum two-state diatomic molecule. When the chain fluctuations are integrated out, the denaturation transition temperature and width emerge naturally as an explicit function of the model parameters of a well defined Hamiltonian, revealing that the transition is driven by the difference in bending (entropy dominated) free energy between bubble and double-stranded segments. The calculated melting curve (fraction of open base pairs) is in good agreement with the experimental melting profile of polydA-polydT. The predicted variation of the mean-square-radius as a function of temperature leads to a coherent novel explanation for the experimentally observed thermal viscosity transition. Finally, the influence of the DNA strand length is studied in detail, underlining the importance of finite size effects, even for DNA made of several thousand base pairs.Comment: Latex, 28 pages pdf, 9 figure

Radiative transition rates and collision strengths for Si II

Aims. This work reports radiative transition rates and electron impact excitation collision strengths for levels of the 3s23p, 3s3p2, 3s24s, and 3s23d configurations of Siii. Methods. The radiative data were computed using the Thomas-Fermi-Dirac-Amaldi central potential, but with the modifications introduced by Bautista (2008) that account for the effects of electron-electron interactions. We also introduce new schemes for the optimization of the variational parameters of the potential. Additional calculations were carried out with the Relativistic Hartree-Fock and the multiconfiguration Dirac-Fock methods. Collision strengths in LS-coupling were calculated in the close coupling approximation with the R-matrix method. Then, fine structure collision strengths were obtained by means of the intermediate-coupling frame transformation (ICFT) method which accounts for spin-orbit coupling effects. Results. We present extensive comparisons between the results of different approximations and with the most recent calculations and experiment available in the literature. From these comparisons we derive a recommended set of gf- values and radiative transition rates with their corresponding estimated uncertainties. We also study the effects of different approximations in the representation of the target ion on the electron-impact collision strengths. Our most accurate set of collision strengths were integrated over a Maxwellian distribution of electron energies and the resulting effective collision strengths are given for a wide range of temperatures. Our results present significant differences from recent calculations with the B-spline non-orthogonal R-matrix method. We discuss the sources of the differences.Comment: 6 figures, 5 tables within text, 2 electronic table

Nitrogen K-shell photoabsorption

Reliable atomic data have been computed for the spectral modeling of the nitrogen K lines, which may lead to useful astrophysical diagnostics. Data sets comprise valence and K-vacancy level energies, wavelengths, Einstein $A$-coefficients, radiative and Auger widths and K-edge photoionization cross sections. An important issue is the lack of measurements which are usually employed to fine-tune calculations so as to attain spectroscopic accuracy. In order to estimate data quality, several atomic structure codes are used and extensive comparisons with previous theoretical data have been carried out. In the calculation of K photoabsorption with the Breit--Pauli $R$-matrix method, both radiation and Auger damping, which cause the smearing of the K edge, are taken into account. This work is part of a wider project to compute atomic data in the X-ray regime to be included in the database of the popular {\sc xstar} modeling code

Mere Exposure Alters Category Learning of Novel Objects

We investigated how mere exposure to complex objects with correlated or uncorrelated object features affects later category learning of new objects not seen during exposure. Correlations among pre-exposed object dimensions influenced later category learning. Unlike other published studies, the collection of pre-exposed objects provided no information regarding the categories to be learned, ruling out unsupervised or incidental category learning during pre-exposure. Instead, results are interpreted with respect to statistical learning mechanisms, providing one of the first demonstrations of how statistical learning can influence visual object learning

A Quantitative Comparison of Opacities Calculated Using the Distorted- Wave and R\boldsymbol{R}-Matrix Methods

The present debate on the reliability of astrophysical opacities has reached a new climax with the recent measurements of Fe opacities on the Z-machine at the Sandia National Laboratory \citep{Bailey2015}. To understand the differences between theoretical results, on the one hand, and experiments on the other, as well as the differences among the various theoretical results, detailed comparisons are needed. Many ingredients are involved in the calculation of opacities; deconstructing the whole process and comparing the differences at each step are necessary to quantify their importance and impact on the final results. We present here such a comparison using the two main approaches to calculate the required atomic data, the $R$-Matrix and distorted-wave methods, as well as sets of configurations and coupling schemes to quantify the effects on the opacities for the $Fe\ XVII$ and $Ni\ XIV$ ions.Comment: 10 pages, 2 figure

Use of nanofiltration membrane technology for ceramic industry wastewater treatment

A study has been undertaken of an advanced wastewater treatment approach using polymer nanofiltration membranes, in an attempt to obtain water of sufficient quality to allow it to be reused in the same production process or, alternatively, to be discharged without any problems. The study has initially focused on the removal of organic matter (reduction of COD) and the most representative ions present in the wastewater, such as Na+ , Mg2+, Cl- , and SO4 2- . In a first part of the study, with a view to optimising the experimental phase, a simulation has been performed of the nanofiltration process using the NanoFlux software. Among other things, the simulation allows the most suitable membranes to be selected as a function of the permeate flow rate and desired level of retention in the substances to be removed. The subsequent experimentation was carried out in a laboratory tangential filtration system that works with flat membranes. It was found that retention values of about 90% were obtained for the studied substances, with a good permeate flow rate, using low operating pressures. These results demonstrate the feasibility of the studied technology and its potential as a treatment for improving ceramic industry wastewater qualit

Decay Properties of K-Vacancy States in Fe X-Fe XVII

We report extensive calculations of the decay properties of fine-structure K-vacancy levels in Fe X-Fe XVII. A large set of level energies, wavelengths, radiative and Auger rates, and fluorescence yields has been computed using three different standard atomic codes, namely Cowan's HFR, AUTOSTRUCTURE and the Breit-Pauli R-matrix package. This multi-code approach is used to the study the effects of core relaxation, configuration interaction and the Breit interaction, and enables the estimate of statistical accuracy ratings. The K-alpha and KLL Auger widths have been found to be nearly independent of both the outer-electron configuration and electron occupancy keeping a constant ratio of 1.53+/-0.06. By comparing with previous theoretical and measured wavelengths, the accuracy of the present set is determined to be within 2 mA. Also, the good agreement found between the different radiative and Auger data sets that have been computed allow us to propose with confidence an accuracy rating of 20% for the line fluorescence yields greater than 0.01. Emission and absorption spectral features are predicted finding good correlation with measurements in both laboratory and astrophysical plasmas.Comment: 13 pages, 4 figures. Submitted to A&A. Electronic Table 3-4 available at http://lheawww.gsfc.nasa.gov/users/palmeri/patrick.htm

Atomic data for the K-vacancy states of Fe XXIV

As part of a project to compute improved atomic data for the spectral modeling of iron K lines, we report extensive calculations and comparisons of atomic data for K-vacancy states in Fe XXIV. The data sets include: (i) energy levels, line wavelengths, radiative and Auger rates; (ii) inner-shell electron impact excitation rates and (iii) fine structure inner-shell photoionization cross sections. The calculations of energy levels and radiative and Auger rates have involved a detailed study of orbital representations, core relaxation, configuration interaction, relativistic corrections, cancellation effects and semi-empirical corrections. It is shown that a formal treatment of the Breit interaction is essential to render the important magnetic correlations that take part in the decay pathways of this ion. As a result, the accuracy of the present A-values is firmly ranked at better than 10% while that of the Auger rates at only 15%. The calculations of collisional excitation and photoionization cross sections take into account the effects of radiation and spectator Auger dampings. In the former, these effects cause significant attenuation of resonances leading to a good agreement with a simpler method where resonances are excluded. In the latter, resonances converging to the K threshold display symmetric profiles of constant width that causes edge smearing.Comment: 18 pages, 8 figures, submitted to Astronomy & Astrophysics 200

HD 65949: Rosetta Stone or Red Herring

HD 65949 is a late B star with exceptionally strong Hg II at 3984[A], but it is not a typical HgMn star. The Re II spectrum is of extraordinary strength. Abundances, or upper limits are derived here for 58 elements based on a model with Teff = 13100K, and log(g) = 4.0. Even-Z elements through nickel show minor deviations from solar abundances. Anomalies among the odd-Z elements through copper are mostly small. Beyond the iron peak, a huge scatter is found. The abundance pattern of the heaviest elements resembles the N=126 r-process peak of solar material, though not in detail. We find a significant correlation of the abundance excesses with second ionization potentials for elements with Z > 30. This indicates the relevance of photospheric or near-photospheric processes. We explore a model with mass accretion of exotic material followed by the more commonly accepted differentiation by diffusion. That model leads to a number of predictions which challenge future work. Likely primary and secondary masses are near 3.3 and 1.6 M(solar), with a separation of ca. 0.25 AU. New atomic structure calculations are presented in two appendices.Comment: Accepted by MNRAS: 16 pages, 5 figure

Radiative and Auger decay data for modelling nickel K lines

Radiative and Auger decay data have been calculated for modelling the K lines in ions of the nickel isonuclear sequence, from Ni$^+$ up to Ni$^{27+}$. Level energies, transition wavelengths, radiative transition probabilities, and radiative and Auger widths have been determined using Cowan's Hartree--Fock with Relativistic corrections (HFR) method. Auger widths for the third-row ions (Ni$^+$--Ni$^{10+}$) have been computed using single-configuration average (SCA) compact formulae. Results are compared with data sets computed with the AUTOSTRUCTURE and MCDF atomic structure codes and with available experimental and theoretical values, mainly in highly ionized ions and in the solid state.Comment: submitted to ApJS. 42 pages. 12 figure