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The amount and type of self-entanglement of DNA filaments is significantly affected by spatial confinement, which is ubiquitous in biological systems. Motivated by recent advancements in single DNA molecule experiments based on nanofluidic devices, and by the introduction of algorithms capable of detecting knots in open chains, we investigate numerically the entanglement of linear, open DNA chains confined inside nano-slits. The results regard the abundance, type and length of occurring knots and are compared with recent findings for DNA inside nano-channels. In both cases, the width of the confining region, D, spans the 30nm- 1\mu m range and the confined DNA chains are 1 to 4\mu m long. It is found that the knotting probability is maximum for slit widths in the 70-100nm range. However, over the considered DNA contour lengths, the maximum incidence of knots remains below 20%, while for channel confinement it tops 50%. Further differences of the entanglement are seen for the average contour length of the knotted region which drops significantly below D ~100nm for channel-confinement, while it stays approximately constant for slit-like confinement. These properties ought to reverberate in different kinetic properties of linear DNA depending on confinement and could be detectable experimentally or exploitable in nano-technological applications., Comment: 7 pages, 5 figures

Between the launch of the \textit{GGS Wind} spacecraft in 1994 November and the end of 2010, the Konus-\textit{Wind} experiment detected 296 short-duration gamma-ray bursts (including 23 bursts which can be classified as short bursts with extended emission). During this period, the IPN consisted of up to eleven spacecraft, and using triangulation, the localizations of 271 bursts were obtained. We present the most comprehensive IPN localization data on these events. The short burst detection rate, $\sim$18 per year, exceeds that of many individual experiments., Comment: Published version

The Schroedinger equation is solved for an A-nucleon system using an expansion of the wave function in nonsymmetrized hyperspherical harmonics. Our approach is both an extension and a modification of the formalism developed by Gattobigio et al.. The extension consists in the inclusion of spin and isospin degrees of freedom such that a calculation with more realistic NN potential models becomes possible, whereas the modification allows a much simpler determination of the fermionic ground state. The approach is applied to four- and six-body nuclei (4He, 6Li) with various NN potential models. It is shown that the results for ground-state energy and radius agree well with those from the literature., Comment: 15 pages

In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA. The confining geometry and DNA elasticity are key parameters: we find that facilitated diffusion is most efficient inside an isotropic volume, and on a flexible polymer. By considering the typical copy numbers of proteins in vivo, we show that the speedup due to sliding becomes insensitive to fine tuning of parameters, rendering facilitated diffusion a robust mechanism to speed up intracellular diffusion-limited reactions. The parameter range we focus on is relevant for in vitro systems and for facilitated diffusion on yeast chromatin.

We report results of an extensive analysis of the X-ray nova XTE J1859+226 observed with BeppoSAX and RXTE during its 1999 outburst. We modelled the source spectrum with a multicolour blackbody-like feature plus the generic Comptonization model BMC which has the advantage of providing spectral description of the emitted-radiation properties without assumptions on the underlying physical process. The multicolour component is attributed to the geometrically thin accretion disk, while the Comptonization spectrum is claimed to originate in the innermost sub-Keplerian region of the system (transition layer). We find that XTE J1859+226 covers all the spectral states typical of black-hole sources during its evolution across the outburst, however during the very high state, when the disk contribution to the total luminosity is more than 70% and the root mean square variability > 5%, the high-energy photon index is closer to a hard state value (Gamma ~ 1.8). The BMC normalization and photon index Gamma well correlate with the radio emission, and we also observed a possible saturation effect of Gamma at the brightest radio emission levels. A strong positive correlation was found between the fraction of Comptonized seed photons and the observed integrated root mean square variability, which strengthens the idea that most of the fast variability in these systems is provided by the innermost Compton cloud, which may be also identified as a jet., Comment: 12 pages, 8 figures, accepted for publication in MNRAS

We present an ab-initio study of the isoscalar monopole excitations of 4He using different realistic nuclear interactions, including modern effective field theory potentials. In particular we concentrate on the transition form factor $F_{\cal M}$ to the narrow $0^+$ resonance close to threshold. F_M exhibits a strong potential model dependence, and can serve as a kind of prism to distinguish among different nuclear force models. Comparing to the measurements obtained from inelastic electron scattering off 4He, one finds that the state-of-the-art theoretical transition form factors are at variance with experimental data, especially in the case of effective field theory potentials. We discuss some possible reasons for such discrepancy, which still remains a puzzle., Comment: 5 pages, 3 figures, minor changes

An ab-initio method for determining the dynamical structure function of an interacting many--body quantum system has been devised by combining a generalized integral transform method with Quantum Monte Carlo methods. As a first application, the coherent and, separately, the incoherent excitation spectrum of bulk atomic 4He has been computed, both in the low and intermediate momentum range. The peculiar form of the kernel in the integral transform of the dynamical structure function allows to predict, without using any model, both position and width of the collective excitations in the maxon--roton region, as well as the second collective peak. A prediction of the dispersion of the single--particle modes described by the incoherent part is also presented., Comment: 11 pages, 3 figures

By performing Monte Carlo sampling of $N$-steps self-avoiding polygons embedded on different Bravais lattices we explore the robustness of universality in the entropic, metric and geometrical properties of knotted polymer rings. In particular, by simulating polygons with $N$ up to $10^5$ we furnish a sharp estimate of the asymptotic values of the knot probability ratios and show their independence on the lattice type. This universal feature was previously suggested although with different estimates of the asymptotic values. In addition we show that the scaling behavior of the mean squared radius of gyration of polygons depends on their knot type only through its correction to scaling. Finally, as a measure of the geometrical self-entanglement of the SAPs we consider the standard deviation of the writhe distribution and estimate its power-law behavior in the large $N$ limit. The estimates of the power exponent do depend neither on the lattice nor on the knot type, strongly supporting an extension of the universality property to some features of the geometrical entanglement., Comment: submitted to Phys.Rev.E

The LOFT mission concept is one of four candidates selected by ESA for the M3 launch opportunity as Medium Size missions of the Cosmic Vision programme. The launch window is currently planned for between 2022 and 2024. LOFT is designed to exploit the diagnostics of rapid X-ray flux and spectral variability that directly probe the motion of matter down to distances very close to black holes and neutron stars, as well as the physical state of ultra-dense matter. These primary science goals will be addressed by a payload composed of a Large Area Detector (LAD) and a Wide Field Monitor (WFM). The LAD is a collimated (<1 degree field of view) experiment operating in the energy range 2-50 keV, with a 10 m^2 peak effective area and an energy resolution of 260 eV at 6 keV. The WFM will operate in the same energy range as the LAD, enabling simultaneous monitoring of a few-steradian wide field of view, with an angular resolution of <5 arcmin. The LAD and WFM experiments will allow us to investigate variability from submillisecond QPO's to year-long transient outbursts. In this paper we report the current status of the project., Comment: Proceedings of SPIE, Vol. 8443, Paper No. 8443-85, 2012

The Large Observatory for X-ray Timing (LOFT) is one of the four candidate ESA M3 missions considered for launch in the 2022 time-frame. It is specifically designed to perform fast X-ray timing and probe the status of the matter near black holes and neutron stars. The LOFT scientific payload is composed of a Large Area Detector (LAD) and a Wide Field Monitor (WFM). The LAD is a 10 m2-class pointed instrument with 20 times the collecting area of the best past timing missions (such as RXTE) over the 2-30 keV range, which holds the capability to revolutionize studies of X-ray variability down to the millisecond time scales. Its ground-breaking characteristic is a low mass per unit surface, enabling an effective area of ~10 m^2 (@10 keV) at a reasonable weight. The development of such large but light experiment, with low mass and power per unit area, is now made possible by the recent advancements in the field of large-area silicon detectors - able to time tag an X-ray photon with an accuracy <10 {\mu}s and an energy resolution of ~260 eV at 6 keV - and capillary-plate X-ray collimators. In this paper, we will summarize the characteristics of the LAD instrument and give an overview of its capabilities., Comment: Proceedings of SPIE, Vo. 8443, Paper No. 8443-87

We present an overview of the evolution of ab initio methods for few-nucleon systems with A \ge 4, tracing the progress made that today allows precision calculations for these systems. First a succinct description of the diverse approaches is given. In order to identify analogies and differences the methods are grouped according to different formulations of the quantum mechanical many-body problem. Various significant applications from the past and present are described. We discuss the results with emphasis on the developments following the original implementations of the approaches. In particular we highlight benchmark results which represent important milestones towards setting an ever growing standard for theoretical calculations. This is relevant for meaningful comparisons with experimental data. Such comparisons may reveal whether a specific force model is appropriate for the description of nuclear dynamics., Comment: extension of the previous version from 70 to 78 pages, 24 figures, 17 tables, in press: Progress in Particle and Nuclear Physics

Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m range and slits widths spanning continuously the 50--1250nm range. The metric scaling predicted by de Gennes' blob model is shown to hold for both linear and circularised DNA up to the strongest levels of confinement. More notably, the topological properties of the circularised DNA molecules have two major differences compared to three-dimensional confinement. First, the overall knotting probability is non-monotonic for increasing confinement and can be largely enhanced or suppressed compared to the bulk case by simply varying the slit width. Secondly, the knot population consists of knots that are far simpler than for three-dimensional confinement. The results suggest that nano-slits could be used in nano-fluidic setups to produce DNA rings having simple topologies (including the unknot) or to separate heterogeneous ensembles of DNA rings by knot type., Comment: 12 pages, 10 figures

We calculate the average power density spectra (PDS) of 244 long gamma-ray bursts detected with the Swift Burst Alert Telescope in the 15-150 keV band from January 2005 to August 2011. For the first time we derived the average PDS in the source rest frame of 97 GRBs with known redshift. For 49 of them an average PDS was also obtained in a common source-frame energy band to account for the dependence of time profiles on energy. Previous results obtained on BATSE GRBs with unknown redshift showed that the average spectrum in the 25-2000 keV band could be modelled with a power-law with a 5/3 index over nearly two decades of frequency with a break at ~1 Hz. Depending on the normalisation and on the subset of GRBs considered, our results show analogous to steeper slopes (between 1.7 and 2.0) of the power-law. However, no clear evidence for the break at ~1 Hz was found, although the softer energy band of BAT compared with BATSE might account for that. We instead find a break at lower frequency corresponding to a typical source rest frame characteristic time of a few seconds. We furthermore find no significant differences between observer and source rest frames. Notably, no distinctive PDS features are found for GRBs with different intrinsic properties of the prompt emission either. Finally, the average PDS of GRBs at higher redshifts shows possibly shallower power-law indices than that of low-z GRBs. It is not clear whether this is due to an evolution with z of the average PDS., Comment: 20 pages, 13 figures, accepted to MNRAS

The effects of entanglement in solutions and melts of unknotted ring polymers have been addressed by several theoretical and numerical studies. The system properties have been typically profiled as a function of ring contour length at fixed solution density. Here, we use a different approach to investigate numerically the equilibrium and kinetic properties of solutions of model ring polymers. Specifically, the ring contour length is maintained fixed, while the interplay of inter- and intra-chain entanglement is modulated by varying both solution density (from infinite dilution up to \approx 40 % volume occupancy) and ring topology (by considering unknotted and trefoil-knotted chains). The equilibrium metric properties of rings with either topology are found to be only weakly affected by the increase of solution density. Even at the highest density, the average ring size, shape anisotropy and length of the knotted region differ at most by 40% from those of isolated rings. Conversely, kinetics are strongly affected by the degree of inter-chain entanglement: for both unknots and trefoils the characteristic times of ring size relaxation, reorientation and diffusion change by one order of magnitude across the considered range of concentrations. Yet, significant topology-dependent differences in kinetics are observed only for very dilute solutions (much below the ring overlap threshold). For knotted rings, the slowest kinetic process is found to correspond to the diffusion of the knotted region along the ring backbone., Comment: 17 pages, 11 figures

Blue phases (BPs) are liquid crystals made up by networks of defects, or disclination lines. While existing phase diagrams show a striking variety of competing metastable topologies for these networks, very little is known as to how to kinetically reach a target structure, or how to switch from one to the other, which is of paramount importance for devices. We theoretically identify two confined blue phase I systems in which by applying an appropriate series of electric field it is possible to select one of two bistable defect patterns. Our results may be used to realise new generation and fast switching energy-saving bistable devices in ultrathin surface treated BPI wafers., Comment: 4 pages, 3 figures. Accepted for publication in Phys. Rev. Lett

The 3He transverse electron scattering response function R_T(q,omega) is calculated in the quasi-elastic peak region and beyond for momentum transfers q = 500, 600 and 700 MeV/c. Distinct from our previous work for these kinematics where we included meson exchange currents and relativistic corrections we now additionally include Delta isobar currents (Delta-IC). The Delta-IC contribution increases the quasi-elastic peak height by about 5% and leads to an excellent agreement with experimental data in the whole peak region. In addition it is shown that effects due to the three-nucleon force largely cancel those due to the Delta-IC in the peak region. Finally, we have found that Delta-IC are important for three-body break-up reactions in the so-called dip region. This could explain why in a previous study of such a reaction, where Delta degrees of freedom were not included, no agreement between experimental and theoretical results could be obtained., Comment: 6 pages, 4 figures

We report the results from an archival XMM-Newton observation of the Supergiant Fast X-ray Transient (SFXT) IGR J18483-0311 during its apastron passage. The measured 0.5--10 keV luminosity state (1.3$\times10^{33}$ erg s$^{-1}$) is the lowest ever reported in the literature, it is best fitted by an absorbed black body model yielding parameters consistent with previous measurements. In addition, we find evidence of an emission line feature at $\sim$3.3 keV in the 0.5--10 keV EPIC-pn source spectrum. We show that its physical explanation in terms of atomic emission line appears unlikely and conversely we attempt to ascribe it to an electron cyclotron emission line which would implies a neutron star magnetic field of the order of $\sim3\times10^{11}$ G. A possible hint of the first harmonic is also found. If firmly confirmed by future longer X-ray observations, this would be the first detection ever of a cyclotron feature in the X-ray spectrum of a SFXT, with important implications on theoretical models., Comment: Contributed talk to appear in the proceedings of the "8th INTEGRAL Workshop - The Restless Gamma-ray Universe", held in Dublin on 27-30 September 2010; PoS(INTEGRAL 2010)049

The interplay of geometrical and topological entanglement in semiflexible knotted polymer rings confined inside a spherical cavity is investigated using advanced numerical methods. By using stringent and robust algorithms for locating knots, we characterize how the knot length lk depends on the ring contour length, Lc and the radius of the confining sphere, Rc . In the no- and strong- confinement cases we observe weak knot localization and complete knot delocalization, respectively. We show that the complex interplay of lk, Lc and Rc that seamlessly bridges these two limits can be encompassed by a simple scaling argument based on deflection theory. The same argument is used to rationalize the multiscale character of the entanglement that emerges with increasing confinement., Comment: 9 pages 9 figures

We introduce a combined Restrained MD/Parallel Tempering approach to study the difference in free energy as a function of a set of collective variables between two states in presence of unknown slow degrees of freedom. We applied this method to study the relative stability of the amorphous vs crystalline nanoparticles of size ranging between 0.8 and 1.8 nm as a function of the temperature. We found that, at variance with bulk systems, at low T small nanoparticles are amorphous and undergo an amorphous-to-crystalline phase transition at higher T. On the contrary, large nanoparticles recover the bulk-like behavior: crystalline at low $T$ and amorphous at high T.

Blue phases are networks of disclination lines, which occur in cholesteric liquid crystals near the transition to the isotropic phase. They have recently been used for the new generation of fast switching liquid crystal displays. Here we study numerically the steady states and switching hydrodynamics of blue phase I (BPI) and blue phase II (BPII) cells subjected to an electric field. When the field is on, there are three regimes: for very weak fields (and strong anchoring at the boundaries) the blue phases are almost unaffected, for intermediate fields the disclinations twist (for BPI) and unzip (for BPII), whereas for very large voltages the network dissolves in the bulk of the cell. Interestingly, we find that a BPII cell can recover its original structure when the field is switched off, whereas a BPI cell is found to be trapped more easily into metastable configurations. The kinetic pathways followed during switching on and off entails dramatic reorganisation of the disclination networks. We also discuss the effect of changing the director field anchoring at the boundary planes and of varying the direction of the applied field., Comment: 17 pages, 11 figures

In this review we provide an organized summary of the theoretical and computational results which are available for polymers subject to spatial or topological constraints. Because of the interdisciplinary character of the topic, we provide an accessible, non-specialist introduction to the main topological concepts, polymer models, and theoretical/computational methods used to investigate dense and entangled polymer systems. The main body of our review deals with: (i) the effect that spatial confinement has on the equilibrium topological entanglement of one or more polymer chains and (ii) the metric and entropic properties of polymer chains with fixed topological state. These problems have important technological applications and implications for the life-sciences. Both aspects, especially the latter, are amply covered. A number of selected open problems are finally highlighted., Comment: 117 pages, 46 figures; minor corrections (typos and references)

Simulations in which a globular ring polymer with delocalized knots is separated in two interacting loops by a slipping link, or in two non-interacting globuli by a wall with a hole, show how the minimal crossing number of the knots controls the equilibrium statistics. With slipping link the ring length is divided between the loops according to a simple law, but with unexpectedly large fluctuations. These are suppressed only for unknotted loops, whose length distribution shows always a fast power law decay. We also discover and explain a topological effect interfering with that of surface tension in the globule translocation through a membrane nanopore., Comment: 4 pages, 5 figures

The Supermodel provides an accurate description of the thermal contribution by the hot intracluster plasma which is crucial for the analysis of the hard excess. In this paper the thermal emissivity in the Coma cluster is derived starting from the intracluster gas temperature and density profiles obtained by the Supermodel analysis of X-ray observables: the XMM-Newton temperature profile and the Rosat brightness distribution. The Supermodel analysis of the BeppoSAX/PDS hard X-ray spectrum confirms our previous results, namely an excess at the c.l. of ~4.8sigma and a nonthermal flux of 1.30+-0.40x 10^-11 erg cm^-2 s^-1 in the energy range 20-80 keV. A recent joint XMM-Newton/Suzaku analysis reports an upper limit of ~6x10^-12 erg cm^-2 s^-1 in the energy range 20-80 keV for the nonthermal flux with an average gas temperature of 8.45+-0.06 keV, and an excess of nonthermal radiation at a confidence level above 4sigma, without including systematic effects, for an average XMM-Newton temperature of 8.2 keV in the Suzaku/HXD-PIN FOV, in agreement with our earlier PDS analysis. Here we present a further evidence of the compatibility between the Suzaku and BeppoSAX spectra, obtained by our Supermodel analysis of the PDS data, when the smaller size of the HXD-PIN FOV and the two different average temperatures derived by XMM-Newton and by the joint XMM-Newton/Suzaku analysis are taken into account. The consistency of the PDS and HXD-PIN spectra reaffirms the presence of a nonthermal component in the hard X-ray spectrum of the Coma cluster. The Supermodel analysis of the PDS data reports an excess at c.l. above 4sigma also for the higher average temperature of 8.45 keV thanks to the PDS FOV considerably greater than the HXD-PIN FOV., Comment: 18 pages, 7 figures, accepted for publication in ApJ