Denaturation transition of stretched DNA

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent $c$ for which we find the new value $c=4\nu-1/2$ such that the transition is second order with $c=1.85<2$ in $d=3$. We show that a finite stretching force $F$ destabilizes DNA, corresponding to a lower melting temperature $T(F)$, in agreement with single-molecule DNA stretching experiments.Comment: 5 pages, 3 figure

Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation

The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrization of the PBD model, and critically discussed. The statistics of extended open bubbles and bound clusters is formulated and results are presented for selected examples.Comment: to appear in a special issue of the Journal of Nonlinear Mathematical Physics (ed. G. Gaeta

A multi-satellite study of accelerated ionospheric ion beams above the polar cap

This paper presents a study of nearly field-aligned outflowing ion beams observed on the Cluster satellites over the polar cap. Data are taken at geocentric radial distances of the order of 5&amp;ndash;9 &lt;i&gt;R&lt;sub&gt;E&lt;/sub&gt;&lt;/i&gt;. The distinction is made between ion beams originating from the polar cusp/cleft and beams accelerated almost along the magnetic field line passing by the spacecraft. Polar cusp beams are characterized by nearly field-aligned proton and oxygen ions with an energy ratio E&lt;sub&gt;O+&lt;/sub&gt; / E&lt;sub&gt;H+&lt;/sub&gt;, of the order of 3 to 4, due to the ion energy repartition inside the source and to the latitudinal extension of the source. Rapid variations in the outflowing ion energy are linked with pulses/modifications of the convection electric field. Cluster data allow one to show that these perturbations of the convection velocity and the associated ion structures propagate at the convection velocity. &lt;P style=&quot;line-height: 20px;&quot;&gt; In contrast, polar cap local ion beams are characterized by field-aligned proton and oxygen ions with similar energies. These beams show the typical inverted V structures usually observed in the auroral zone and are associated with a quasi-static converging electric field indicative of a field-aligned electric field. The field-aligned potential drop fits well the ion energy profile. The simultaneous observation of precipitating electrons and upflowing ions of similar energies at the Cluster orbit indicates that the spacecraft are crossing the mid-altitude part of the acceleration region. In the polar cap, the parallel electric field can thus extend to altitudes higher than 5&amp;nbsp;Earth radii. A detailed analysis of the distribution functions shows that the ions are heated during their parallel acceleration and that energy is exchanged between H&lt;sup&gt;+&lt;/sup&gt; and O&lt;sup&gt;+&lt;/sup&gt;. Furthermore, intense electrostatic waves are observed simultaneously. These observations could be due to an ion-ion two-stream instability

MeV magnetosheath ions energized at the bow shock

A causal relationship between midlatitude magnetosheath energetic ions and bow shock magnetic geometry was previously established for ion energy up to 200 keV e−1 for the May 4, 1998, storm event. This study demonstrates that magnetosheath ions with energies above 200 keV up to 1 MeV simply extend the ion spectrum to form a power law tail. Results of cross-correlation analysis suggest that these ions also come directly from the quasi-parallel bow shock, not the magnetosphere. This is confirmed by a comparison of energetic ion fluxes simultaneously measured in the magnetosheath and at the quasi-parallel bow shock when both regions are likely connected by the magnetic field lines. We suggest that ions are accelerated at the quasi-parallel bow shock to energies as high as 1 MeV and subsequently transported into the magnetosheath during this event

Photon- and meson-induced reactions on the nucleon

In an unitary effective Lagrangian model we develop a unified description of both meson scattering and photon-induced reactions on the nucleon. Adding the photon to an already existing model for meson-nucleon scattering yields both Compton and meson photoproduction amplitudes. In a simultaneous fit to all available data involving the final states $\gamma N$, $\pi N$, $\pi\pi N$, $\eta N$ and $K \Lambda$ the parameters of the nucleon resonances are extracted.Comment: 57 pages, 14 figures, LaTex (uses Revtex and graphicx). Submitted to Phys. Rev. C. References updated, Fig. 14 change

Circulating markers of arterial thrombosis and late-stage age-related macular degeneration: a case-control study.

PURPOSE: The aim of this study was to examine the relation of late-stage age-related macular degeneration (AMD) with markers of systemic atherothrombosis. METHODS: A hospital-based case-control study of AMD was undertaken in London, UK. Cases of AMD (n=81) and controls (n=77) were group matched for age and sex. Standard protocols were used for colour fundus photography and to classify AMD; physical examination included height, weight, history of or treatment for vascular-related diseases and smoking status. Blood samples were taken for measurement of fibrinogen, factor VIIc (FVIIc), factor VIIIc, prothrombin fragment F1.2 (F1.2), tissue plasminogen activator, and von Willebrand factor. Odds ratios from logistic regression analyses of each atherothrombotic marker with AMD were adjusted for age, sex, and established cardiovascular disease risk factors, including smoking, blood pressure, body mass index, and total cholesterol. RESULTS: After adjustment FVIIc and possibly F1.2 were inversely associated with the risk of AMD; per 1 standard deviation increase in these markers the odds ratio were, respectively, 0.62 (95% confidence interval 0.40, 0.95) and 0.71 (0.46, 1.09). None of the other atherothrombotic risk factors appeared to be related to AMD status. There was weak evidence that aspirin is associated with a lower risk of AMD. CONCLUSIONS: This study does not provide strong evidence of associations between AMD and systematic markers of arterial thrombosis, but the potential effects of FVIIc, and F1.2 are worthy of further investigation

Evidence for Factorization in Three-body B --> D(*) K- K0 Decays

Motivated by recent experimental results, we use a factorization approach to study the three-body B --> D(*) K- K0 decay modes. Two mechanisms are proposed for kaon pair production: current-produced (from vacuum) and transition (from B meson). The Bbar0 --> D(*)+ K- K0 decay is governed solely by the current-produced mechanism. As the kaon pair can be produced only by the vector current, the matrix element can be extracted from e+ e- --> K Kbar processes via isospin relations. The decay rates obtained this way are in good agreement with experiment. Both current-produced and transition processes contribute to B- --> D(*)0 K- K0 decays. By using QCD counting rules and the measured B- --> D(*)0 K- K0 decay rates, the measured decay spectra can be understood.Comment: 17 pages, 6 figure

Pion and Kaon Vector Form Factors

We develop a unitarity approach to consider the final state interaction corrections to the tree level graphs calculated from Chiral Perturbation Theory ($\chi PT$) allowing the inclusion of explicit resonance fields. The method is discussed considering the coupled channel pion and kaon vector form factors. These form factors are then matched with the one loop $\chi PT$ results. A very good description of experimental data is accomplished for the vector form factors and for the $\pi\pi$ P-wave phase shifts up to $\sqrt{s}\lesssim 1.2$ GeV, beyond which multiparticle states play a non negligible role. In particular the low and resonance energy regions are discussed in detail and for the former a comparison with one and two loop $\chi PT$ is made showing a remarkable coincidence with the two loop $\chi PT$ results.Comment: 20 pages, 7 figs, to appear in Phys. Rev.

Photo- and Electroproduction of Eta Mesons

Eta photo- and electroproduction off the nucleon is investigated in an effective lagrangian approach that contains Born terms and both vector meson and nucleon resonance contributions. In particular, we review and develop the formalism for coincidence experiments with polarization degrees of freedom. The different response functions appearing in single and double polarization experiments have been studied. We will present calculations for structure functions and kinematical conditions that are most sensitive to details of the lagrangian, in particular with regard to contributions of nucleon resonances beyond the dominant $S_{11}$(1535) resonance.Comment: 24 pages RevTeX/LaTeX2.09, NFSS1, 13 figures (in separate file (tar,gzip and uue)), accepted for publication in Z. Phys.

Effective Lagrangian Approach to the Theory of Eta Photoproduction in the N∗(1535)N^{*}(1535) Region

We investigate eta photoproduction in the $N^{*}(1535)$ resonance region within the effective Lagrangian approach (ELA), wherein leading contributions to the amplitude at the tree level are taken into account. These include the nucleon Born terms and the leading $t$-channel vector meson exchanges as the non-resonant pieces. In addition, we consider five resonance contributions in the $s$- and $u$- channel; besides the dominant $N^{*}(1535)$, these are: $N^{*}(1440),N^{*}(1520),N^{*}(1650)$ and $N^{*}(1710)$. The amplitudes for the $\pi^\circ$ and the $\eta$ photoproduction near threshold have significant differences, even as they share common contributions, such as those of the nucleon Born terms. Among these differences, the contribution to the $\eta$ photoproduction of the $s$-channel excitation of the $N^{*}(1535)$ is the most significant. We find the off-shell properties of the spin-3/2 resonances to be important in determining the background contributions. Fitting our effective amplitude to the available data base allows us to extract the quantity $\sqrt{\chi \Gamma_\eta} A_{1/2}/\Gamma_T$, characteristic of the photoexcitation of the $N^{*}(1535)$ resonance and its decay into the $\eta$-nucleon channel, of interest to precise tests of hadron models. At the photon point, we determine it to be $(2.2\pm 0.2)\times 10^{-1} GeV^{-1}$ from the old data base, and $(2.2\pm 0.1) \times 10^{-1} GeV^{-1}$ from a combination of old data base and new Bates data. We obtain the helicity amplitude for $N^{*}(1535)\rightarrow \gamma p$ to be $A_{1/2}=(97\pm 7)\times 10^{-3} GeV^{-1/2}$ from the old data base, and $A_{1/2}=(97\pm 6)\times 10^{-3} GeV^{-1/2}$ from the combination of the old data base and new Bates data, compared with the results of the analysis of pion photoproduction yielding $74\pm 11$, in the same units.Comment: 43 pages, RevTeX, 9 figures available upon request, to appear in Phys. Rev.