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

Evaluation of the burden of HPV-related hospitalizations as a useful tool to increase awareness: 2007–2017 data from the sicilian hospital discharge records

In light of the implementation of human papillomavirus (HPV) prevention strategies, epidemiological studies in different geographical areas are required in order to assess the impact of HPV-related diseases. The purpose of the present study was to describe the burden of HPV-related hospitalizations in Sicily. A retrospective observational study estimated 43,531 hospitalizations attributable to HPV from 2007 to 2017. During the observed period, there was a decrease for all HPV-related conditions with a higher reduction, among neoplasms, for cervical cancer (annual percent change (APC) = −9.9%, p < 0.001). The median age for cervical cancer was 45 years old, with an increasing value from 43 to 47 years (p < 0.001). The age classes with greater decreases in hospital admissions for invasive cancers were women aged 35 years or more (APC range from −5.5 to −9.86) and 25–34 years old (APC = −11.87, p < 0.001) for women with cervical carcinoma in situ. After ten years for vaccine introduction and sixteen years for cervical cancer screening availability, a relatively large decrease in hospital admissions for cervical cancer and other HPV-related diseases in Sicily was observed. Some clinical characteristics of hospitalization, such as increasing age, are suggestive clues for the impact of preventive strategies, but further research is needed to confirm this relationship

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

Dissipation of the 3^He A-B Transition

A rigorous hydrodynamic theory of the A-B transition is presented. All dissipative processes are considered. At low interface velocities, those occurring on hydrodynamic length scales, not considered hitherto, are most probably the dominant ones.Comment: 13 pages, REVTeX, 2 figures, ITP-UH 13/9

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

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