Chaperone-assisted translocation of flexible polymers in three dimensions

Polymer translocation through a nanometer-scale pore assisted by chaperones binding to the polymer is a process encountered in vivo for proteins. Studying the relevant models by computer simulations is computationally demanding. Accordingly, previous studies are either for stiff polymers in three dimensions or flexible polymers in two dimensions. Here, we study chaperone-assisted translocation of flexible polymers in three dimensions using Langevin dynamics. We show that differences in binding mechanisms, more specifically, whether a chaperone can bind to a single or multiple sites on the polymer, lead to substantial differences in translocation dynamics in three dimensions. We show that the single-binding mode leads to dynamics that is very much like that in the constant-force driven translocation and accordingly mainly determined by tension propagation on the cis side. We obtain $\beta \approx 1.26$ for the exponent for the scaling of the translocation time with polymer length. This fairly low value can be explained by the additional friction due to binding particles. The multiple-site binding leads to translocation whose dynamics is mainly determined by the trans side. For this process we obtain $\beta \approx 1.36$. This value can be explained by our derivation of $\beta = 4/3$ for constant-bias translocation, where translocated polymer segments form a globule on the trans side. Our results pave the way for understanding and utilizing chaperone-assisted translocation where variations in microscopic details lead to rich variations in the emerging dynamics.Comment: 10 pages, 12 figure

Dynamics of polymer ejection from capsid

Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes place within the drift-dominated region there is a very high probability for the ejection process not to be completed. Introducing a small aligning force at the pore entrance enhances ejection dramatically. Such a pore asymmetry is a candidate for a mechanism by which a viral ejection is completed. By detailed high-resolution simulations we show that such capsid ejection is an out-of-equilibrium process that shares many common features with the much studied driven polymer translocation through a pore in a wall or a membrane. We find that the escape times scale with polymer length, $\tau \sim N^\alpha$. We show that for the pore without the asymmetry the previous predictions corroborated by Monte Carlo simulations do not hold. For the pore with the asymmetry the scaling exponent varies with the initial monomer density (monomers per capsid volume) $\rho$ inside the capsid. For very low densities $\rho \le 0.002$ the polymer is only weakly confined by the capsid, and we measure $\alpha = 1.33$, which is close to $\alpha = 1.4$ obtained for polymer translocation. At intermediate densities the scaling exponents $\alpha = 1.25$ and $1.21$ for $\rho = 0.01$ and $0.02$, respectively. These scalings are in accord with a crude derivation for the lower limit $\alpha = 1.2$. For the asymmetrical pore precise scaling breaks down, when the density exceeds the value for complete confinement by the capsid, $\rho \gtrapprox 0.25$. The high-resolution data show that the capsid ejection for both pores, analogously to polymer translocation, can be characterized as a multiplicative stochastic process that is dominated by small-scale transitions.Comment: 10 pages, 6 figure

Magnetic excitations in nuclei with neutron excess

The excitation of the $1^+$, $2^-$ and $3^+$ modes in $^{16}$O, $^{22}$O, $^{24}$O, $^{28}$O, $^{40}$Ca, $^{48}$Ca, $^{52}$Ca and $^{60}$Ca nuclei is studied with self-consistent random phase approximation calculations. Finite-range interactions of Gogny type, containing also tensor-isospin terms, are used. We analyze the evolution of the magnetic resonances with the increasing number of neutrons, the relevance of collective effects, the need of a correct treatment of the continuum and the role of the tensor force.Comment: 18 pages, 12 figures, 2 tables, accepted for publication in Physical Review

Collectivity-induced quenching of signatures for shell closures

Mass differences are an often used as signature and measure for shell closure. Using the angular-momentum projected Generator Coordinate Method and the Skyrme interaction SLy4, we analyze the modification of mass differences due to static deformation and dynamic fluctuations around the mean-field ground state.Comment: 7 pages, 4 figure

Overconstrained estimates of neutrinoless double beta decay within the QRPA

Estimates of nuclear matrix elements for neutrinoless double beta decay (0nu2beta) based on the quasiparticle random phase approximations (QRPA) are affected by theoretical uncertainties, which can be substantially reduced by fixing the unknown strength parameter g_pp of the residual particle-particle interaction through one experimental constraint - most notably through the two-neutrino double beta decay (2nu2beta) lifetime. However, it has been noted that the g_pp adjustment via 2\nu2\beta data may bring QRPA models in disagreement with independent data on electron capture (EC) and single beta decay (beta^-) lifetimes. Actually, in two nuclei of interest for 0nu2beta decay (Mo-100 and Cd-116), for which all such data are available, we show that the disagreement vanishes, provided that the axial vector coupling g_A is treated as a free parameter, with allowance for g_A<1 (``strong quenching''). Three independent lifetime data (2nu2beta, EC, \beta^-) are then accurately reproduced by means of two free parameters (g_pp, g_A), resulting in an overconstrained parameter space. In addition, the sign of the 2nu2beta matrix element M^2nu is unambiguously selected (M^2nu>0) by the combination of all data. We discuss quantitatively, in each of the two nuclei, these phenomenological constraints and their consequences for QRPA estimates of the 0nu2beta matrix elements and of their uncertainties.Comment: Revised version (27 pages, including 10 figures), focussed on Mo-100 and Cd-116. To appear in J. Phys. G: Nucl. Phys. (2008

Search for 2\beta\ decays of 96Ru and 104Ru by ultra-low background HPGe gamma spectrometry at LNGS: final results

An experiment to search for double beta decay processes in 96Ru and 104Ru, which are accompanied by gamma rays, has been realized in the underground Gran Sasso National Laboratories of the I.N.F.N. (Italy). Ruthenium samples with masses of about (0.5-0.7) kg were measured with the help of ultra-low background high purity Ge gamma ray spectrometry. After 2162 h of data taking the samples were deeply purified to reduce the internal contamination of 40K. The last part of the data has been accumulated over 5479 h. New improved half life limits on 2\beta+/\epsilon \beta+/2\epsilon\ processes in 96Ru have been established on the level of 10^{20} yr, in particular for decays to the ground state of 96Mo: T1/2(2\nu 2\beta+) > 1.4 10^{20} yr, T1/2(2\nu \epsilon\beta+) > 8.0 10^{19} yr and T1/2(0\nu 2K) > 1.0 10^{21} yr (all limits are at 90% C.L.). The resonant neutrinoless double electron captures to the 2700.2 keV and 2712.7 keV excited states of 96Mo are restricted as: T1/2(0\nu KL) > 2.0 10^{20} yr and T1/2(0\nu 2L) > 3.6 10^{20} yr, respectively. Various two neutrino and neutrinoless 2\beta\ half lives of 96Ru have been estimated in the framework of the QRPA approach. In addition, the T1/2 limit for 0\nu 2\beta- transitions of 104Ru to the first excited state of 104Pd has been set as > 6.5 10^{20} yr.Comment: 14 pages, 5 figures, 2 tables; version accepted for publication on Phys. Rev.

Extension of random-phase approximation preserving energy weighted sum rules: an application to a 3-level Lipkin model

A limitation common to all extensions of random-phase approximation including only particle-hole configurations is that they violate to some extent the energy weighted sum rules. Considering one such extension, the improved RPA (IRPA), already used to study the electronic properties of metallic clusters, we show how it can be generalized in order to eliminate this drawback. This is achieved by enlarging the configuration space, including also elementary excitations corresponding to the annihilation of a particle (hole) and the creation of another particle (hole) on the correlated ground state. The approach is tested within a solvable 3-level model.Comment: 2 figure