Coarse-grained modelling of supercoiled RNA

We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.Comment: 8 pages + 5 pages Supplementary Materia

Structure of 13^{13}Be probed via secondary beam reactions

The low-lying level structure of the unbound neutron-rich nucleus $^{13}$Be has been investigated via breakup on a carbon target of secondary beams of $^{14,15}$B at 35 MeV/nucleon. The coincident detection of the beam velocity $^{12}$Be fragments and neutrons permitted the invariant mass of the $^{12}$Be+$n$ and $^{12}$Be+$n$+$n$ systems to be reconstructed. In the case of the breakup of $^{15}$B, a very narrow structure at threshold was observed in the $^{12}$Be+$n$ channel. Contrary to earlier stable beam fragmentation studies which identified this as a strongly interacting $s$-wave virtual state in $^{13}$Be, analysis here of the $^{12}$Be+$n$+$n$ events demonstrated that this was an artifact resulting from the sequential-decay of the $^{14}$Be(2$^+$) state. Single-proton removal from $^{14}$B was found to populate a broad low-lying structure some 0.70 MeV above the neutron-decay threshold in addition to a less prominent feature at around 2.4 MeV. Based on the selectivity of the reaction and a comparison with (0-3)$\hbar\omega$ shell-model calculations, the low-lying structure is concluded to most probably arise from closely spaced J$^\pi$=1/2$^+$ and 5/2$^+$ resonances (E$_r$=0.40$\pm$0.03 and 0.85$^{+0.15}_{-0.11}$ MeV), whilst the broad higher-lying feature is a second 5/2$^+$ level (E$_r$=2.35$\pm$0.14 MeV). Taken in conjunction with earlier studies, it would appear that the lowest 1/2$^+$ and 1/2$^-$ levels lie relatively close together below 1 MeV.Comment: 14 pages, 13 figures, 2 tables. Accepted for publication in Physical Review

Measuring total reaction cross-sections at energies near the coulomb barrier by the active target method

An experimental technique is described that is able to measure reaction cross-sections at energies around the Coulomb barrier by using low intensity beams and a Si detector as an active target. Set-up optimization was carefully investigated in terms of collimation, detector efficiency and pile-up rejection. The method has been tested by measuring the total reaction cross-section sigma(R)(E) for the (7)Li + (28)Si system in the energy range of E(lab) = 12-16 MeV. The deduced excitation function sigma(R)(E) agrees with the data obtained in a previous experiment. The presented technique can also be applied in order to determine total reaction cross-sections for low intensity radioactive beams at energies around the Coulomb barrier. (C) 2009 Elsevier B.V. All rights reserved. Nuclear Instruments & Methods in Physics Research Section a-Accelerators Spectrometers Detectors and Associated Equipmen

Heavy residue excitation functions for the collisions 6, 7Li + 64Zn near the Coulomb barrier

Excitation functions for the production of heavy residues have been measured for the collisions 6, 7Li+64Zn at energies around and below the Coulomb barrier. The cross sections for heavy residue production have been measured using an activation technique, detecting off-line the characteristic atomic x-rays emitted in the electron capture decay of the reaction products. The experimental relative yields of the residues have been compared with statistical model calculations performed by using the code cascade. Such a comparison suggests that heavy residue production is dominated by complete fusion at above-barrier energies, whereas different processes like incomplete fusion and/or transfer become dominant in the sub-barrier energy region. The heavy residue excitation function ratio between the 6Li- and 7Li-induced collisions shows an increasing trend as the energy decreases below the barrier

Elastic scattering and heavy residue production in the collisions 6,7Li+64 Zn around the Coulomb barrier

Elastic scattering angular distributions and heavy residue production cross sections have been measured at different energies around the Coulomb barrier for the systems 6,7 Li+ 64 Zn. Optical model fits of the elastic angular distributions were performed using a renormalized double folding potential and absence of usual threshold anomaly in the optical potential was found. Excitation functions for heavy residue production have been measured using an activation technique. Comparison of the data with the results of different calculations show that complete fusion is the dominant reaction mechanism above the barrier, whereas the heavy residue yield below the barrier is mainly due to incomplete fusion and transfer

Experimental study of the collision 11Be + 64Zn around the Coulomb barrier

In this paper details of the experimental procedure and data analysis of the collision of 11Be+64Zn around the Coulomb barrier are described and discussed in the framework of different theoretical approaches. In a previous work [ A. Di Pietro et al. Phys. Rev. Lett. 105 022701 (2010)], the elastic scattering angular distribution of the collisions 9, 10Be+64Zn as well as the angular distribution for the quasielastic scattering and transfer/breakup cross sections for the 11Be+64Zn reaction were briefly reported. The suppression of the quasielastic angular distribution in the Coulomb-nuclear interference angular region observed in the collision of the 11Be halo nucleus with respect to the other two beryllium isotopes was interpreted as being caused by a long-range absorption owing to the long decay length of the 11Be wave function. In this paper, new continuum-discretized coupled-channel calculations of the 11Be+64Zn reaction are reported in the attempt to interpret the effect of coupling with the breakup channels on the measured cross sections. The calculations show that the observed suppression of the Coulomb-nuclear interference peak is caused by a combined effect of Coulomb and nuclear couplings to the breakup channels

Evidence of strong effects of the 11Be halo structure on reaction processes at energies around the Coulomb barrier

The collision induced by the three Beryllium isotopes, 9, 10, 11Be, on 64Zn target were investigated at Ec.m. ≈ 1.4 the Coulomb barrier. Elastic scattering angular distributions were measured for the 9, 10Be collisions whereas, in the 11Be case the quasielastic scattering angular distribution was obtained. A strong damping of the quasielastic cross-section was observed in the 11Be case, especially in the angular range around the Coulomb-nuclear interference peak. In this latter case a large total-reaction cross-section is found, more than a factor of two larger than the ones extracted in the reactions induced by the non-halo Beryllium isotopes. A large contribution to the total-reaction cross-section in the 11Be case could be attributed to transfer and/or break-up events

Elastic Scattering and Reaction Mechanisms of the Halo Nucleus 11Be around the Coulomb Barrier

Collisions induced by 9, 10, 11Be on a 64Zn target at the same c.m. energy were studied. For the first time, strong effects of the 11Be halo structure on elastic-scattering and reaction mechanisms at energies near the Coulomb barrier are evidenced experimentally. The elastic-scattering cross section of the 11Be halo nucleus shows unusual behavior in the Coulomb-nuclear interference peak angular region. The extracted total-reaction cross section for the 11Be collision is more than double the ones measured in the collisions induced by 9, 10Be. It is shown that such a strong enhancement of the total-reaction cross section with 11Be is due to transfer and breakup processes

Projectile structure effects in the collisions 6,7Li+64Zn around the Coulomb barrier.

We measured elastic scattering angular distributions and cross sections for heavy residue production for the systems 6,7 Li+ 64 Zn at different energies around the Coulomb barrier. The elastic scattering angular distributions have been reproduced by optical model fits using a renormalized double folding potential for the real and imaginary parts. Absence of usual threshold anomaly in the optical potential was found. The excitation functions for heavy residue production were measured using an activation technique. Comparison with different calculations suggest that complete fusion is the dominant reaction mechanism above the barrier whereas, below the Coulomb barrier, incomplete fusion and transfer dominate

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na +] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA