Energy gaps and roton structure above the nu=1/2 Laughlin state of a rotating dilute Bose-Einstein condensate

Exact diagonalization study of a rotating dilute Bose-Einstein condensate reveals that as the first vortex enters the system the degeneracy of the low-energy yrast spectrum is lifted and a large energy gap emerges. As more vortices enter with faster rotation, the energy gap decreases towards zero, but eventually the spectrum exhibits a rotonlike structure above the nu=1/2 Laughlin state without having a phonon branch despite the short-range nature of the interaction.Comment: 4 pages, 4 figures, 1 tabl

Bacillus subtilis Cw1Q (previous YjbJ) is a bifunctional enzyme exhibiting muramidase and soluble-lytic transglycosylase activities

CwIQ (previous YjbJ) is one of the putative cell wall hydrolases in Bacillus subtilis. Its domain has an amino acid sequence similar to the soluble-lytic transglycosylase (SLT) of Escherichia coli Slt70 and also goose lysozyme (muramidase). To characterize the enzyme, the domain of CwIQ was cloned and expressed in E. coil. The purified CwIQ protein exhibited cell wall hydrolytic activity. Surprisingly, RP-HPLC, mass spectrometry (MS), and MS/MS analyses showed that CwIQ produces two products, 1,6-anhydro-N-acetylmuramic acid and N-acetylmuramic acid, thus indicating that CwIQ is a bifunctional enzyme. The site-directed mutagenesis revealed that glutamic acid 85 (Glu-85) is an amino acid residue essential to both activities. (C) 2010 Elsevier Inc. All rights reserved.ArticleBIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 398(3):606-612 (2010)journal articl

Collimated Jet or Expanding Outflow: Possible Origins of GRBs and X-Ray Flashes

We investigate the dynamics of an injected outflow propagating in a progenitor in the context of the collapsar model for gamma-ray bursts (GRBs) through two dimensional axisymmetric relativistic hydrodynamic simulations. Initially, we locally inject an outflow near the center of a progenitor. We calculate 25 models, in total, by fixing its total input energy to be 10^{51} ergs s^{-1} and radius of the injected outflow to be $7\times 10^7$ cm while varying its bulk Lorentz factor, $\Gamma_{0} = 1.05\sim 5$, and its specific internal energy, $\epsilon_0/c^2 = 0.1\sim 30$. The injected outflow propagates in the progenitor and drives a large-scale outflow or jet. We find a smooth but dramatic transition from a collimated jet to an expanding outflow among calculated models. The maximum Lorentz factor is, on the other hand, sensitive to both of $\Gamma_0$ and $\epsilon_0$; roughly $\Gamma_{\rm max} \sim \Gamma_0 (1+\epsilon_0/c^2)$. Our finding will explain a smooth transition between the GRBs, X-ray rich GRBs (XRRs) and X-ray Flashes (XRFs) by the same model but with different $\epsilon_0$ values.Comment: Comments 51 pages, 21 figures. accepted for publication in ApJ high resolution version is available at http://www.mpa-garching.mpg.de/~mizuta/COLLAPSAR/collapsar.htm

Low-Lying Excitations from the Yrast Line of Weakly Interacting Trapped Bosons

Through an extensive numerical study, we find that the low-lying, quasi-degenerate eigenenergies of weakly-interacting trapped N bosons with total angular momentum L are given in case of small L/N and sufficiently small L by E = L hbar omega + g[N(N-L/2-1)+1.59 n(n-1)/2], where omega is the frequency of the trapping potential and g is the strength of the repulsive contact interaction; the last term arises from the pairwise repulsive interaction among n octupole excitations and describes the lowest-lying excitation spectra from the Yrast line. In this case, the quadrupole modes do not interact with themselves and, together with the octupole modes, exhaust the low-lying spectra which are separated from others by N-linear energy gaps.Comment: 5 pages, RevTeX, 2 figures, revised version, submitted to PR

Tunneling and rattling in clathrate crystal

We present tunneling and rattling motions of an off-center guest atom in cage referring to a clathrate crystal La_3Pd_{20}Ge_6. The elastic constant C_{44} of La_3Pd_{20}Ge_6 shows a Debye-type dispersion around 20 K obeying a relaxation time tau = tau_0exp(E/k_{B}T) with an attempt time tau_0 = 2.0*10^{-12} sec and an activation energy E = 197 K. At low temperatures below 3 K down to 20 mK, the C_{44} shows a softening of C_{44} = C_{44}^0(T-T_C^0)/(T-Theta) with T_C^0 = -337.970 mK and Theta = -338.044 mK. These facts are attributed to two different types of the off-center motions with Gamma_5 symmetry in 4a-site cage of La_3Pd_{20}Ge_6, a thermally activated rattling motion over the potential hill and a tunneling motion through the potential hill at low temperatures.Comment: 5 pages, 4 figures, to be published Phys. Rev.

Identification and Characterization of a Novel Polysaccharide Deacetylase C (PdaC) from Bacillus subtilis

Cell wall metabolism and cell wall modification are very important processes that bacteria use to adjust to various environmental conditions. One of the main modifications is deacetylation of peptidoglycan. The polysaccharide deacetylase homologue, Bacillus subtilis YjeA (renamed PdaC), was characterized and found to be a unique deacetylase. The pdaC deletion mutant was sensitive to lysozyme treatment, indicating that PdaC acts as a deacetylase. The purified recombinant and truncated PdaC from Escherichia coli deacetylated B. subtilis peptidoglycan and its polymer, (-GlcNAc-MurNAc[-L-Ala-D-Glu]-)(n). Surprisingly, RP-HPLC and ESI-MS/MS analyses showed that the enzyme deacetylates N-acetylmuramic acid (MurNAc) not GlcNAc from the polymer. Contrary to Streptococcus pneumoniae PgdA, which shows high amino acid sequence similarity with PdaC and is a zinc-dependent GlcNAc deacetylase toward peptidoglycan, there was less dependence on zinc ion for deacetylation of peptidoglycan by PdaC than other metal ions (Mn2+, Mg2+, Ca2+). The kinetic values of the activity toward B. subtilis peptidoglycan were K-m = 4.8 mM and k(cat) = 0.32 s(-1). PdaC also deacetylated N-acetylglucosamine (GlcNAc) oligomers with a K-m = 12.3 mM and k(cat) = 0.24 s(-1) toward GlcNAc(4). Therefore, PdaC has GlcNAc deacetylase activity toward GlcNAc oligomers and MurNAc deacetylase activity toward B. subtilis peptidoglycan.ArticleJOURNAL OF BIOLOGICAL CHEMISTRY. 287(13):9765-9776 (2012)journal articl

Analysis of optical magnetoelectric effect in GaFeO_3

We study the optical absorption spectra in a polar ferrimagnet GaFeO_3. We consider the E1, E2 and M1 processes on Fe atoms. It is shown that the magnetoelectric effect on the absorption spectra arises from the E1-M1 interference process through the hybridization between the 4p and 3d states in the noncentrosymmetry environment of Fe atoms. We perform a microscopic calculation of the spectra on a cluster model of FeO_6 consisting of an octahedron of O atoms and an Fe atom displaced from the center with reasonable values for Coulomb interaction and hybridization. We obtain the magnetoelectric spectra, which depend on the direction of magnetization, as a function of photon energy in the optical region 1.0-2.5 eV, in agreement with the experiment.Comment: 18 pages, 5 figure

Mechanistic dissection of premature translation termination induced by acidic residues-enriched nascent peptide

Ribosomes polymerize nascent peptides through repeated inter-subunit rearrangements between the classic and hybrid states. The peptidyl-tRNA, the intermediate species during translation elongation, stabi-lizes the translating ribosome to ensure robust continuity of elongation. However, the translation of acidic residue-rich sequences destabilizes the ribosome, leading to a stochastic premature translation cessation termed intrinsic ribosome destabilization (IRD), which is still ill-defined. Here, we dissect the molecular mechanisms underlying IRD in Escherichia coli. Reconstitution of the IRD event reveals that (1) the prolonged ribosome stalling enhances IRD-mediated translation discontinuation, (2) IRD depends on temperature, (3) the destabilized 70S ribosome complex is not necessarily split, and (4) the destabilized ribosome is subjected to peptidyl-tRNA hydrolase-mediated hydrolysis of the peptidyl-tRNA without subunit splitting or recycling factors-mediated subunit splitting. Collectively, our data indicate that the translation of acidic-rich sequences alters the conformation of the 70S ribosome to an aberrant state that allows the noncanonical pre-mature termination

Estimating the risk of species interaction loss in mutualistic communities

Funder: Royal Commission for the Exhibition of 1851 (GB)Funder: Cambridge TrustFunder: Cambridge Depatment of ZoologyFunder: Grantham Foundation for the Protection of the Environment; funder-id: http://dx.doi.org/10.13039/100008118Funder: Kenneth Miller TrustFunder: ArcadiaInteractions between species generate the functions on which ecosystems and humans depend. However, we lack an understanding of the risk that interaction loss poses to ecological communities. Here, we quantify the risk of interaction loss for 4,330 species interactions from 41 empirical pollination and seed dispersal networks across 6 continents. We estimate risk as a function of interaction vulnerability to extinction (likelihood of loss) and contribution to network feasibility, a measure of how much an interaction helps a community tolerate environmental perturbations. Remarkably, we find that more vulnerable interactions have higher contributions to network feasibility. Furthermore, interactions tend to have more similar vulnerability and contribution to feasibility across networks than expected by chance, suggesting that vulnerability and feasibility contribution may be intrinsic properties of interactions, rather than only a function of ecological context. These results may provide a starting point for prioritising interactions for conservation in species interaction networks in the future