Supplanting crystallography or supplementing microscopy? A combined approach to the study of an enveloped virus

The recent advances in the resolution obtained by single-particle reconstructions from cryo-electron microscopy (cryo-EM) have led to an increase in studies that combine X-ray crystallographic results with those of electron microscopy (EM). Here, such a combination is described in the determination of the structure of an enveloped animal virus, Semliki Forest virus, at 9 Å resolution. The issues of model bias in determination of the structure, the definition of resolution in a single-particle reconstruction, the effect of the correction of the contrast-transfer function on the structure determined and the use of a high-resolution structure of a subunit in the interpretation of the structure of the complex are addressed

Advanced vehicle separation apparatus

A method of obtaining test data from two independent models or bodies in a conventional wind tunnel is described. The system makes efficient use of wind tunnel test time with computer control performing complex coordinate transformations necessary for model positioning. The apparatus is designed to be used in any of the three Unitary Wind Tunnels at NASA-Ames Research Center. Mechanical design details and a brief description of the control system for the separation apparatus are presented

Bosonic sector of the two-dimensional Hubbard model studied within a two-pole approximation

The charge and spin dynamics of the two-dimensional Hubbard model in the paramagnetic phase is first studied by means of the two-pole approximation within the framework of the Composite Operator Method. The fully self-consistent scheme requires: no decoupling, the fulfillment of both Pauli principle and hydrodynamics constraints, the simultaneous solution of fermionic and bosonic sectors and a very rich momentum dependence of the response functions. The temperature and momentum dependencies, as well as the dependency on the Coulomb repulsion strength and the filling, of the calculated charge and spin susceptibilities and correlation functions are in very good agreement with the numerical calculations present in the literature

Quantum State Reconstruction of a Bose-Einstein Condensate

We propose a tomographic scheme to reconstruct the quantum state of a Bose-Einstein condensate, exploiting the radiation field as a probe and considering the atomic internal degrees of freedom. The density matrix in the number state basis can be directly retrieved from the atom counting probabilities.Comment: 11 pages, LaTeX file, no figures, to appear in Europhysics Letter

A Study of the Antiferromagnetic Phase in the Hubbard Model by means of the Composite Operator Method

We have investigated the antiferromagnetic phase of the 2D, the 3D and the extended Hubbard models on a bipartite cubic lattice by means of the Composite Operator Method within a two-pole approximation. This approach yields a fully self-consistent treatment of the antiferromagnetic state that respects the symmetry properties of both the model and the algebra. The complete phase diagram, as regards the antiferromagnetic and the paramagnetic phases, has been drawn. We firstly reported, within a pole approximation, three kinds of transitions at half-filling: Mott-Hubbard, Mott-Heisenberg and Heisenberg. We have also found a metal-insulator transition, driven by doping, within the antiferromagnetic phase. This latter is restricted to a very small region near half filling and has, in contrast to what has been found by similar approaches, a finite critical Coulomb interaction as lower bound at half filling. Finally, it is worth noting that our antiferromagnetic gap has two independent components: one due to the antiferromagnetic correlations and another coming from the Mott-Hubbard mechanism.Comment: 20 pages, 37 figures, RevTeX, submitted to Phys. Rev.

RNA packaging motor: From structure to quantum mechanical modelling and sequential-stochastic mechanism

The bacteriophages of the Cystoviridae family package their single stranded RNA genomic precursors into empty capsid (procapsids) using a hexameric packaging ATPase motor (P4). This molecular motor shares sequence and structural similarity with RecA-like hexameric helicases. A concerted structural, mutational and kinetic analysis helped to define the mechanical reaction coordinate, i.e. the conformational changes associated with RNA translocation. The results also allowed us to propose a possible scheme of coupling between ATP hydrolysis and translocation which requires the cooperative action of three consecutive subunits. Here, we first test this model by preparing hexamers with defined proportions of wild type and mutant subunits and measuring their activity. Then, we develop a stochastic kinetic model which accounts for the catalytic cooperativity of the P4 hexamer. Finally, we use the available structural information to construct a quantum-chemical model of the chemical reaction coordinate and obtain a detailed description of the electron density changes during ATP hydrolysis. The model explains the results of the mutational analyses and yields new insights into the role of several conserved residues within the ATP binding pocket. These hypotheses will guide future experimental work

Overcoming the false-minima problem in direct methods: Structure determination of the packaging enzyme P4 from bacteriophage φ13

The problems encountered during the phasing and structure determination of the packaging enzyme P4 from bacteriophage φ13 using the anomalous signal from selenium in a single-wavelength anomalous dispersion experiment (SAD) are described. The oligomeric state of P4 in the virus is a hexamer (with sixfold rotational symmetry) and it crystallizes in space group C2, with four hexamers in the crystallographic asymmetric unit. Current state-of-the-art ab initio phasing software yielded solutions consisting of 96 atoms arranged as sixfold symmetric clusters of Se atoms. However, although these solutions showed high correlation coefficients indicative that the substructure had been solved, the resulting phases produced uninterpretable electron-density maps. Only after further analysis were correct solutions found (also of 96 atoms), leading to the eventual identification of the positions of 120 Se atoms. Here, it is demonstrated how the difficulties in finding a correct phase solution arise from an intricate false-minima problem. © 2005 International Union of Crystallography - all rights reserved

The Pauli Equation for Probability Distributions

The "marginal" distributions for measurable coordinate and spin projection is introduced. Then, the analog of the Pauli equation for spin-1/2 particle is obtained for such probability distributions instead of the usual wave functions. That allows a classical-like approach to quantum mechanics. Some illuminating examples are presented.Comment: 14 pages, ReVTe

Permutation symmetry for the tomographic probability distribution of a system of identical particles

The symmetry properties under permutation of tomograms representing the states of a system of identical particles are studied. Starting from the action of the permutation group on the density matrix we define its action on the tomographic probability distribution. Explicit calculations are performed in the case of the two-dimensional harmonic oscillator.Comment: 13 pages, latex, no figure