A dedicated haem lyase is required for the maturation of a novel bacterial cytochrome c with unconventional covalent haem binding

In bacterial c-type cytochromes, the haem cofactor is covalently attached via two cysteine residues organized in a haem c-binding motif. Here, a novel octa-haem c protein, MccA, is described that contains only seven conventional haem c-binding motifs (CXXCH), in addition to several single cysteine residues and a conserved CH signature. Mass spectrometric analysis of purified MccA from Wolinella succinogenes suggests that two of the single cysteine residues are actually part of an unprecedented CX15CH sequence involved in haem c binding. Spectroscopic characterization of MccA identified an unusual high-potential haem c with a red-shifted absorption maximum, not unlike that of certain eukaryotic cytochromes c that exceptionally bind haem via only one thioether bridge. A haem lyase gene was found to be specifically required for the maturation of MccA in W. succinogenes. Equivalent haem lyase-encoding genes belonging to either the bacterial cytochrome c biogenesis system I or II are present in the vicinity of every known mccA gene suggesting a dedicated cytochrome c maturation pathway. The results necessitate reconsideration of computer-based prediction of putative haem c-binding motifs in bacterial proteomes

Scaling property and peculiar velocity of global monopoles

We investigate the scaling property of global monopoles in the expanding universe. By directly solving the equations of motion for scalar fields, we follow the time development of the number density of global monopoles in the radiation dominated (RD) universe and the matter dominated (MD) universe. It is confirmed that the global monopole network relaxes into the scaling regime and the number per hubble volume is a constant irrespective of the cosmic time. The number density $n(t)$ of global monopoles is given by $n(t) \simeq (0.43\pm0.07) / t^{3}$ during the RD era and $n(t) \simeq (0.25\pm0.05) / t^{3}$ during the MD era. We also examine the peculiar velocity $v$ of global monopoles. For this purpose, we establish a method to measure the peculiar velocity by use of only the local quantities of the scalar fields. It is found that $v \sim (1.0 \pm 0.3)$ during the RD era and $v \sim (0.8 \pm 0.3)$ during the MD era. By use of it, a more accurate analytic estimate for the number density of global monopoles is obtained.Comment: 17 pages, 8 figures, to appear in Phys. Rev.

Lattice-switch Monte Carlo

We present a Monte Carlo method for the direct evaluation of the difference between the free energies of two crystal structures. The method is built on a lattice-switch transformation that maps a configuration of one structure onto a candidate configuration of the other by `switching' one set of lattice vectors for the other, while keeping the displacements with respect to the lattice sites constant. The sampling of the displacement configurations is biased, multicanonically, to favor paths leading to `gateway' arrangements for which the Monte Carlo switch to the candidate configuration will be accepted. The configurations of both structures can then be efficiently sampled in a single process, and the difference between their free energies evaluated from their measured probabilities. We explore and exploit the method in the context of extensive studies of systems of hard spheres. We show that the efficiency of the method is controlled by the extent to which the switch conserves correlated microstructure. We also show how, microscopically, the procedure works: the system finds gateway arrangements which fulfill the sampling bias intelligently. We establish, with high precision, the differences between the free energies of the two close packed structures (fcc and hcp) in both the constant density and the constant pressure ensembles.Comment: 34 pages, 9 figures, RevTeX. To appear in Phys. Rev.

Cosmological Evolution of Global Monopoles

We investigate the cosmological evolution of global monopoles in the radiation dominated (RD) and matter dominated (MD) universes by numerically solving field equations of scalar fields. It is shown that the global monopole network relaxes into the scaling regime, unlike the gauge monopole network. The number density of global monopoles is given by $n(t) \simeq (0.43\pm0.07) / t^{3}$ during the RD era and $n(t) \simeq (0.25\pm0.05) / t^{3}$ during the MD era. Thus, we have confirmed that density fluctuations produced by global monopoles become scale invariant and are given by $\delta \rho \sim 7.2(5.0) \sigma^{2} / t^{2}$ during the RD (MD) era, where $\sigma$ is the breaking scale of the symmetry.Comment: 6 pages, 2 figures, to appear in Phys. Rev. D (R

Dynamics of ions in the selectivity filter of the KcsA channel

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications

Orbital Wave and its Observation in Orbital Ordered Titanates and Vanadates

We present a theory of the collective orbital excitation termed orbital wave in perovskite titanates and vanadates with the triply degenerate $t_{2g}$ orbitals. The dispersion relations of the orbital waves for the orbital ordered LaVO$_3$, YVO$_3$ and YTiO$_3$ are examined in the effective spin-orbital coupled Hamiltonians associated with the Jahn-Teller type couplings. We propose possible scattering processes for the Raman and inelastic neutron scatterings from the orbital wave and calculate the scattering spectra for titanates and vanadates. It is found that both the excitation spectra and the observation methods of the orbital wave are distinct qualitatively from those for the $e_g$ orbital ordered systems.Comment: 9 pages, 7 figure

Doping-dependent study of the periodic Anderson model in three dimensions

We study a simple model for $f$-electron systems, the three-dimensional periodic Anderson model, in which localized $f$ states hybridize with neighboring $d$ states. The $f$ states have a strong on-site repulsion which suppresses the double occupancy and can lead to the formation of a Mott-Hubbard insulator. When the hybridization between the $f$ and $d$ states increases, the effects of these strong electron correlations gradually diminish, giving rise to interesting phenomena on the way. We use the exact quantum Monte-Carlo, approximate diagrammatic fluctuation-exchange approximation, and mean-field Hartree-Fock methods to calculate the local moment, entropy, antiferromagnetic structure factor, singlet-correlator, and internal energy as a function of the $f-d$ hybridization for various dopings. Finally, we discuss the relevance of this work to the volume-collapse phenomenon experimentally observed in f-electron systems.Comment: 12 pages, 8 figure

Pseudogap formation of four-layer BaRuO3_3 and its electrodynamic response changes

We investiaged the optical properties of four-layer BaRuO$_{3}$, which shows a fermi-liquid-like behavior at low temperature. Its optical conductivity spectra clearly displayed the formation of a pseudogap and the development of a coherent peak with decreasing temperature. Temperature-dependences of the density $n$ and the scattering rate $1/\tau$ of the coherent component were also derived. As the temperature decreases, both $n$ and $1/\tau$ decrease for four-layer BaRuO$_{3}$. These electrodynamic responses were compared with those of nine-layer BaRuO$_{3}$, which also shows a pseudogap formation but has an insulator-like state at low temperature. It was found that the relative rates of change of both $n$ and $1/\tau$ determine either metallic or insulator-like responses in the ruthenates. The optical properties of the four-layer ruthenate were also compared with those of other pseudogap systems, such as high $T_{c}$ cuprates and heavy electron systems.Comment: 7 figures. submitted to Phys. Rev.

RQM description of the charge form factor of the pion and its asymptotic behavior

The pion charge and scalar form factors, $F_1(Q^2)$ and $F_0(Q^2)$, are first calculated in different forms of relativistic quantum mechanics. This is done using the solution of a mass operator that contains both confinement and one-gluon-exchange interactions. Results of calculations, based on a one-body current, are compared to experiment for the first one. As it could be expected, those point-form, and instant and front-form ones in a parallel momentum configuration fail to reproduce experiment. The other results corresponding to a perpendicular momentum configuration (instant form in the Breit frame and front form with $q^+=0$) do much better. The comparison of charge and scalar form factors shows that the spin-1/2 nature of the constituents plays an important role. Taking into account that only the last set of results represents a reasonable basis for improving the description of the charge form factor, this one is then discussed with regard to the asymptotic QCD-power-law behavior $Q^{-2}$. The contribution of two-body currents in achieving the right power law is considered while the scalar form factor, $F_0(Q^2)$, is shown to have the right power-law behavior in any case. The low-$Q^2$ behavior of the charge form factor and the pion-decay constant are also discussed.}Comment: 30 pages, 10 figure

The politics of a South African catholic student movement

No abstract available