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

Two neutrino positron double beta decay of 106^{106}Cd for 0+→0+0^+ \to 0^+ transition

The two neutrino positron double beta decay of $^{106}$Cd for 0$^{+} \to$ 0$^{+}$ transition has been studied in the Hartree-Fock-Bogoliubov model in conjunction with the summation method. In the first step, the reliability of the intrinsic wave functions of $^{106}$Cd and $^{106}$Pd nuclei has been tested by comparing the theoretically calculated results for yrast spectra, reduced $B(E2$:$0^{+}\to 2^{+})$ transition probabilities, quadrupole moments $Q(2^{+})$ and gyromagnetic factors $g(2^{+})$ with the available experimental data. In the second step, the nuclear transition matrix element $M_{2\nu}$ and the half-life $T_{1/2}^{2\nu}$ for 0$^{+}\to$ 0$^{+}$ transition have been calculated with these wave functions. Moreover, we have studied the effect of deformation on nuclear transition matrix element M$_{2\nu}.$Comment: 20 page

Ground state particle-particle correlations and double beta decay

A self-consistent formalism for the double beta decay of Fermi type is provided. The particle-particle channel of the two-body interaction is considered first in the mean field equations and then in the QRPA. The resulting approach is called the QRPA with a self-consistent mean field (QRPASMF). The mode provided by QRPASMF, does not collapse for any strength of the particle-particle interaction. The transition amplitude for double beta decay is almost insensitive to the variation of the particle-particle interaction. Comparing it with the result of the standard pnQRPA, it is smaller by a factor 6. The prediction for transition amplitude agrees quite well with the exact result. The present approach is the only one which produces a strong decrease of the amplitude and at the same time does not alter the stability of the ground state.Comment: 23 pages, 7 figure

Predicting poor compliance with follow-up and intrauterine contraception services after medical termination of pregnancy

Background Attendance at post-abortion follow-up visits is poor, but little is known about factors affecting it. Objective To assess the factors associated with non-compliance with post-abortion services and to evaluate differences in rates of attendance and intrauterine device (IUD) insertion according to the type of service provision. Methods 605 women undergoing a first trimester medical termination of pregnancy (MTOP) and planning to use intrauterine contraception were randomised into two groups. Women in the intervention group (n=306) were booked to have IUD insertion 1-4 weeks after the MTOP at the hospital providing the abortion, while women in the control group (n=299) were advised to contact their primary healthcare (PHC) centre for follow-up and IUD insertion. Results In the intervention group, 21 (6.9%) women failed to attend the fol low-up visit, whereas in the control group 67 (22.4%) women did not contact the PHC to schedule a follow-up (p Conclusions Factors predicting low compliance with post-MTOP fol low-up are few. Comprehensive provision of abortion care and post-abortion services seems beneficial for minimising the loss to fol low-up and delay in initiation of effective contraception.Peer reviewe

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