Pick-up ions and associated wave energy transport at Comet P/Halley: A case study

During the flyby of the spacecraft Giotto at comet p/Halley Poynting vectors and Elsässer variables have been determined to study wave propagation directions. The observed wave properties are compared with the theoretically predicted RH −, LH + and LH − wave modes. Between 10:36 and 19:11 SCET on March 13, 1986 the predicted dominating energy propagation direction mostly corresponds with the observed one. Only between 12:11 and 13:44 SCET there is no agreement. In this region the excitation of waves is dominated by pick‐up ions which are not locally implanted ions in the solar wind but have been picked‐up outside the plasma regime studied, and whose free energy is not already used up

Coherent η\eta-photoproduction on 4^4He and 12^{12}C in the near-threshold region

Coherent $\eta$ meson photoproduction on $^4$He and $^{12}$C is considered in the near-threshold region. The elementary $\eta$ photoproduction operator includes contributions from the $S_{11}(1535)$ and $D_{13}(1520)$ resonances as well as $t$-channel vector meson exchange and the nucleon pole terms. Due to the suppression of the dominant $S_{11}(1535)$ resonance for spin and isospin saturated nuclei, the reaction is mainly governed by $\omega$ exchange. Furthermore, the influence of Fermi motion and of different prescriptions for the choice of the invariant reaction energy $W_{\gamma N}$ in the elementary amplitude is studied.Comment: 27 pages revtex including 9 postscript figure

Excitation-assisted inelastic processes in trapped Bose-Einstein condensates

We find that inelastic collisional processes in Bose-Einstein condensates induce local variations of the mean-field interparticle interaction and are accompanied by the creation/annihilation of elementary excitation. The physical picture is demonstrated for the case of three body recombination in a trapped condensate. For a high trap barrier the production of high energy trapped single particle excitations results in a strong increase of the loss rate of atoms from the condensate.Comment: 4 pages, no figure

Optimized production of a cesium Bose-Einstein condensate

We report on the optimized production of a Bose-Einstein condensate of cesium atoms using an optical trapping approach. Based on an improved trap loading and evaporation scheme we obtain more than $10^5$ atoms in the condensed phase. To test the tunability of the interaction in the condensate we study the expansion of the condensate as a function of scattering length. We further excite strong oscillations of the trapped condensate by rapidly varying the interaction strength.Comment: 9 pages, 7 figures, submitted to Appl. Phys.

Stabilization of the number of Bose-Einstein condensed atoms in evaporative cooling via three-body recombination loss

The dynamics of evaporative cooling of magnetically trapped $^{87}$Rb atoms is studied on the basis of the quantum kinetic theory of a Bose gas. We carried out the quantitative calculations of the time evolution of conventional evaporative cooling where the frequency of the radio-frequency magnetic field is swept exponentially. This "exponential-sweep cooling" is known to become inefficient at the final stage of the cooling process due to a serious three-body recombination loss. We precisely examine how the growth of a Bose-Einstein condensate depends on the experimental parameters of evaporative cooling, such as the initial number of trapped atoms, the initial temperature, and the bias field of a magnetic trap. It is shown that three-body recombination drastically depletes the trapped $^{87}$Rb atoms as the system approaches the quantum degenerate region and the number of condensed atoms finally becomes insensitive to these experimental parameters. This result indicates that the final number of condensed atoms is well stabilized by a large nonlinear three-body loss against the fluctuations of experimental conditions in evaporative cooling.Comment: 7 pages, REVTeX4, 8 eps figures, Phys. Rev A in pres

HH-suite3 for fast remote homology detection and deep protein annotation.

BACKGROUND: HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins. RESULTS: We developed a single-instruction multiple-data (SIMD) vectorized implementation of the Viterbi algorithm for profile HMM alignment and introduced various other speed-ups. These accelerated the search methods HHsearch by a factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is ∼10× faster than PSI-BLAST and ∼20× faster than HMMER3. Jobs to perform HHsearch and HHblits searches with many query profile HMMs can be parallelized over cores and over cluster servers using OpenMP and message passing interface (MPI). The free, open-source, GPLv3-licensed software is available at https://github.com/soedinglab/hh-suite . CONCLUSION: The added functionalities and increased speed of HHsearch and HHblits should facilitate their use in large-scale protein structure and function prediction, e.g. in metagenomics and genomics projects

Limit on suppression of ionization in metastable neon traps due to long-range anisotropy

This paper investigates the possibility of suppressing the ionization rate in a magnetostatic trap of metastable neon atoms by spin-polarizing the atoms. Suppression of the ionization is critical for the possibility of reaching Bose-Einstein condensation with such atoms. We estimate the relevant long-range interactions for the system, consisting of electric quadrupole-quadrupole and dipole-induced dipole terms, and develop short-range potentials based on the Na_2 singlet and triplet potentials. The auto-ionization widths of the system are also calculated. With these ingredients we calculate the ionization rate for spin-polarized and for spin-isotropic samples, caused by anisotropy of the long-range interactions. We find that spin-polarization may allow for four orders of magnitude suppression of the ionization rate for Ne. The results depend sensitively on a precise knowledge of the interaction potentials, however, pointing out the need for experimental input. The same model gives a suppression ratio close to unity for metastable xenon in accordance with experimental results, due to a much increased anisotropy in this case.Comment: 15 pages including figures, LaTex/RevTex, uses epsfig.st

Phase-fluctuating 3D condensates in elongated traps

We find that in very elongated 3D trapped Bose gases, even at temperatures far below the BEC transition temperature Tc, the equilibrium state will be a 3D condensate with fluctuating phase (quasicondensate). At sufficiently low temperatures the phase fluctuations are suppressed and the quasicondensate turns into a true condensate. The presence of the phase fluctuations allows for extending thermometry of Bose-condensed gases well below those established in current experiments.Comment: 5 pages REVTeX, 3 figures, misprints correcte

Vector meson dominance and the rho meson

We discuss the properties of vector mesons, in particular the rho^0, in the context of the Hidden Local Symmetry (HLS) model. This provides a unified framework to study several aspects of the low energy QCD sector. Firstly, we show that in the HLS model the physical photon is massless, without requiring off field diagonalization. We then demonstrate the equivalence of HLS and the two existing representations of vector meson dominance, VMD1 and VMD2, at both tree level and one loop order. Finally the S matrix pole position is shown to provide a model and process independent means of specifying the rho mass and width, in contrast to the real axis prescription currently used in the Particle Data Group tables.Comment: 18 pages, REVTE

Cln5 represents a new type of cysteine-basedS-depalmitoylase linked to neurodegeneration

Genetic CLN5 variants are associated with childhood neurodegeneration and Alzheimer’s disease; however, the molecular function of ceroid lipofuscinosis neuronal protein 5 (Cln5) is unknown. We solved the Cln5 crystal structure and identified a region homologous to the catalytic domain of members of the N1pC/P60 superfamily of papain-like enzymes. However, we observed no protease activity for Cln5; and instead, we discovered that Cln5 and structurally related PPPDE1 and PPPDE2 have efficient cysteine palmitoyl thioesterase (S-depalmitoylation) activity using fluorescent substrates. Mutational analysis revealed that the predicted catalytic residues histidine-166 and cysteine-280 are critical for Cln5 thioesterase activity, uncovering a new cysteine-based catalytic mechanism for S-depalmitoylation enzymes. Last, we found that Cln5-deficient neuronal progenitor cells showed reduced thioesterase activity, confirming live cell function of Cln5 in setting S-depalmitoylation levels. Our results provide new insight into the function of Cln5, emphasize the importance of S-depalmitoylation in neuronal homeostasis, and disclose a new, unexpected enzymatic function for the N1pC/P60 superfamily of proteins