Structure of a rare non-standard sequence k-turn bound by L7Ae protein

Kt-23 from Thelohania solenopsae is a rare RNA kink turn (k-turn) where an adenine replaces the normal guanine at the 2n position. L7Ae is a member of a strongly conserved family of proteins that bind a range of k-turn structures in the ribosome, box C/D and H/ACA small nucleolar RNAs and U4 small nuclear RNA. We have solved the crystal structure of T. solenopsae Kt-23 RNA bound to Archeoglobus fulgidus L7Ae protein at a resolution of 2.95 Å. The protein binds in the major groove displayed on the outer face of the k-turn, in a manner similar to complexes with standard k-turn structures. The k-turn adopts a standard N3 class conformation, with a single hydrogen bond from A2b N6 to A2n N3. This contrasts with the structure of the same sequence located in the SAM-I riboswitch, where it adopts an N1 structure, showing the inherent plasticity of k-turn structure. This potentially can affect any tertiary interactions in which the RNA participates

P-band in a rotating optical lattice

We investigate the effects of rotation on the excited bands of a tight binding lattice, focusing particulary on the first excited (p-) band. Both the on-site energies and the hopping between lattice sites are modified by the effective magnetic field created by rotation, causing a non-trivial splitting and magnetic fine structure of the p-band. We show that Peierls substitution can be modified to describe p-band under rotation, and use this method to derive an effective Hamiltonian. We compare the spectrum of the effective Hamiltonian with a first principles calculation of the magnetic band structure and find excellent agreement, confirming the validity of our approach. We also discuss the on-site interaction terms for bosons and argue that many-particle phenomena in a rotating p-band can be investigated starting from this effective Hamiltonian.Comment: 7 pages, 4 figures, new discussion of effective Hamiltonian, references adde

Tunneling and delocalization in hydrogen bonded systems: a study in position and momentum space

Novel experimental and computational studies have uncovered the proton momentum distribution in hydrogen bonded systems. In this work, we utilize recently developed open path integral Car-Parrinello molecular dynamics methodology in order to study the momentum distribution in phases of high pressure ice. Some of these phases exhibit symmetric hydrogen bonds and quantum tunneling. We find that the symmetric hydrogen bonded phase possesses a narrowed momentum distribution as compared with a covalently bonded phase, in agreement with recent experimental findings. The signatures of tunneling that we observe are a narrowed distribution in the low-to-intermediate momentum region, with a tail that extends to match the result of the covalently bonded state. The transition to tunneling behavior shows similarity to features observed in recent experiments performed on confined water. We corroborate our ice simulations with a study of a particle in a model one-dimensional double well potential that mimics some of the effects observed in bulk simulations. The temperature dependence of the momentum distribution in the one-dimensional model allows for the differentiation between ground state and mixed state tunneling effects.Comment: 14 pages, 13 figure

Lifshitz Transition in Underdoped Cuprates

Recent studies show that quantum oscillations thought to be associated with a density wave reconstructed Fermi surface disappear at a critical value of the doping for YBa2Cu3O6+y, and the cyclotron mass diverges as the critical value is approached from the high doping side. We argue that the phenomenon is due to a Lifshitz transition where the pockets giving rise to the quantum oscillations connect to form an open (quasi-1d) Fermi surface. The estimated critical doping is close to that found by experiment, and the theory predicts a logarithmic divergence of the cyclotron mass with a coefficient comparable to that observed in experiment.Comment: 4 pages, 4 figure

Octet Baryon Charge Radii, Chiral Symmetry and Decuplet Intermediate States

We compute the octet baryon charge radii to O(1/Heavy^3) in heavy baryon chiral perturbation theory. We examine the effect of including the decuplet of spin-3/2 baryons explicitly. We find that it does no t improve the level of agreement between the HBchiPT and experimental values for the Sigma^- charge radius.Comment: 9 pages, 2 figures. Uses axodraw.sty, include

Phonons in aluminum at high temperatures studied by inelastic neutron scattering

Inelastic neutron scattering measurements on aluminum metal were performed at temperatures of 10, 150, 300, 525, and 775 K using direct-geometry Fermi chopper spectrometers. The temperature dependent phonon density of states (DOS) was determined from the scattering, and was used to fit Born–von Kármán models of lattice dynamics. The shifts in the phonon frequencies with increasing temperature were largely explained by the softening of the longitudinal force constants out to third nearest neighbors. A significant broadening of the phonon spectra at high temperatures was also measured. The phonon DOS was used to determine the vibrational contributions to the entropy of aluminum as a function of temperature. All other contributions to the entropy of aluminum were calculated or assessed, and the total entropy was in excellent agreement with the NIST-JANAF compilation [M. W. Chase, J. Phys. Chem. Ref. Data Monogr. 9, 59 (1998)]. Anharmonic effects were attributed to phonon-phonon interactions. The quasiharmonic approximation was generally successful, but its weaknesses are discussed

Drag of two-dimensional small-amplitude symmetric and asymmetric wavy walls in turbulent boundary layers

Included are results of an experimental investigation of low-speed turbulent flow over multiple two-dimensional transverse rigid wavy surfaces having a wavelength on the order of the boundary-layer thickness. Data include surface pressure and total drag measurements on symmetric and asymmetric wall waves under a low-speed turbulent boundary-layer flow. Several asymmetric wave configurations exhibited drag levels below the equivalent symmetric (sine) wave. The experimental results compare favorably with numerical predictions from a Reynolds-averaged Navier-Stokes spectral code. The reported results are of particular interest for the estimation of drag, the minimization of fabrication waviness effects, and the study of wind-wave interactions

Variational cluster approach to correlated electron systems in low dimensions

A self-energy-functional approach is applied to construct cluster approximations for correlated lattice models. It turns out that the cluster-perturbation theory (Senechal et al, PRL 84, 522 (2000)) and the cellular dynamical mean-field theory (Kotliar et al, PRL 87, 186401 (2001)) are limiting cases of a more general cluster method. Results for the one-dimensional Hubbard model are discussed with regard to boundary conditions, bath degrees of freedom and cluster size.Comment: 4 pages, final version with minor change