1,339 research outputs found
Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli.
The translational GTPase BipA regulates the expression of virulence and pathogenicity factors in several eubacteria. BipA-dependent expression of virulence factors occurs under starvation conditions, such as encountered during infection of a host. Under these conditions, BipA associates with the small ribosomal subunit. BipA also has a second function to promote the efficiency of late steps in biogenesis of large ribosomal subunits at low temperatures, presumably while bound to the ribosome. During starvation, the cellular concentration of stress alarmone guanosine-3', 5'-bis pyrophosphate (ppGpp) is increased. This increase allows ppGpp to bind to BipA and switch its binding specificity from ribosomes to small ribosomal subunits. A conformational change of BipA upon ppGpp binding could explain the ppGpp regulation of the binding specificity of BipA. Here, we present the structures of the full-length BipA from Escherichia coli in apo, GDP-, and ppGpp-bound forms. The crystal structure and small-angle x-ray scattering data of the protein with bound nucleotides, together with a thermodynamic analysis of the binding of GDP and of ppGpp to BipA, indicate that the ppGpp-bound form of BipA adopts the structure of the GDP form. This suggests furthermore, that the switch in binding preference only occurs when both ppGpp and the small ribosomal subunit are present. This molecular mechanism would allow BipA to interact with both the ribosome and the small ribosomal subunit during stress response
Fully electromagnetic nonlinear gyrokinetic equations for tokamak edge turbulence
An energy conserving set of the fully electromagnetic nonlinear gyrokinetic Vlasov equation and Maxwell's equations, which is applicable to both L-mode turbulence with large amplitude and H-mode turbulence in the presence of high E Χ B shear has been derived. The phase-space action variational Lie perturbation method ensures the preservation of the conservation laws of the underlying Vlasov-Maxwell system. Our generalized ordering takes ρ[sub ]i [\sub]<< ρϑ¡ ~ LE ~ Lp << R (here ρ[sub ]i [\sub] is the thermal ion Larmor radius and ρϑ¡ = [B over Bϑ] ρ[sub ]i [\sub]), as typically observed in the tokamak H-mode edge, with LE and Lp being the radial electric field and pressure gradient lengths. We take κ[sub ] perpendicular to[/sub] ρ[sub ]i [\sub] ~ 1 for generality, and keep the relative fluctuation amplitudes eδφ ⁄ Τ[sub ]i [\sub]~ δΒ ⁄ Β up to the second order. Extending the electrostatic theory in the presence of high E Χ B shear [Hahm, Phys. Plasmas 3, 4658 (1996)], contributions of electromagnetic fluctuations to the particle charge density and current are explicitly evaluated via pull-back transformation from the gyrocenter distribution function in the gyrokinetic Maxwell's equation
Electronic structure of crystalline binary and ternary Cd-Te-O compounds
The electronic structure of crystalline CdTe, CdO, -TeO,
CdTeO and CdTeO is studied by means of first principles
calculations. The band structure, total and partial density of states, and
charge densities are presented. For -TeO and CdTeO, Density
Functional Theory within the Local Density Approximation (LDA) correctly
describes the insulating character of these compounds. In the first four
compounds, LDA underestimates the optical bandgap by roughly 1 eV. Based on
this trend, we predict an optical bandgap of 1.7 eV for CdTeO. This
material shows an isolated conduction band with a low effective mass, thus
explaining its semiconducting character observed recently. In all these oxides,
the top valence bands are formed mainly from the O 2p electrons. On the other
hand, the binding energy of the Cd 4d band, relative to the valence band
maximum, in the ternary compounds is smaller than in CdTe and CdO.Comment: 13 pages, 15 figures, 2 tables. Accepted in Phys Rev
ELM triggering conditions for the integrated modeling of H-mode plasmas
Recent advances in the integrated modeling of ELMy H-mode plasmas are
presented. A model for the H-mode pedestal and for the triggering of ELMs
predicts the height, width, and shape of the H-mode pedestal and the frequency
and width of ELMs. Formation of the pedestal and the L-H transition is the
direct result of ExB flow shear suppression of anomalous transport. The
periodic ELM crashes are triggered by either the ballooning or peeling MHD
instabilities. The BALOO, DCON, and ELITE ideal MHD stability codes are used to
derive a new parametric expression for the peeling-ballooning threshold. The
new dependence for the peeling-ballooning threshold is implemented in the ASTRA
transport code. Results of integrated modeling of DIII-D like discharges are
presented and compared with experimental observations. The results from the
ideal MHD stability codes are compared with results from the resistive MHD
stability code NIMROD.Comment: 12th International Congress on Plasma Physics, 25-29 October 2004,
Nice (France
GaN and InN nanowires grown by MBE: a comparison
Morphological, optical and transport properties of GaN and InN nanowires
grown by molecular beam epitaxy (MBE) have been studied. The differences
between the two materials in respect to growth parameters and optimization
procedure was stressed. The nanowires crystalline quality has been investigated
by means of their optical properties. A comparison of the transport
characteristics was given. For each material a band schema was shown, which
takes into account transport and optical features and is based on Fermi level
pinning at the surface.Comment: 5 pages, 5 figure
Composite Skyrme Model with Vector Mesons
We study the composite Skyrme model, proposed by Cheung and G\"{u}rsey,
introducing vector mesons in a chiral Lagrangian. We calculate the static
properties of baryons and compare with results obtained from models without
vector mesons.Comment: LaTeX, 9 pages, 3 figures, to be published in Phys. Rev.
Two-dimensional turbulence in magnetised plasmas
In an inhomogeneous magnetised plasma the transport of energy and particles
perpendicular to the magnetic field is in general mainly caused by quasi
two-dimensional turbulent fluid mixing. The physics of turbulence and structure
formation is of ubiquitous importance to every magnetically confined laboratory
plasma for experimental or industrial application. Specifically, high
temperature plasmas for fusion energy research are also dominated by the
properties of this turbulent transport. Self-organisation of turbulent vortices
to mesoscopic structures like zonal flows is related to the formation of
transport barriers that can significantly enhance the confinement of a fusion
plasma. This subject of great importance in research is rarely touched on in
introductory plasma physics or continuum dynamics courses. Here a brief
tutorial on 2D fluid and plasma turbulence is presented as an introduction to
the field, appropriate for inclusion in undergraduate and graduate courses.Comment: This is an author-created, un-copyedited version of an article
published in European Journal of Physics. IOP Publishing Ltd is not
responsible for any errors or omissions in this version of the manuscript or
any version derived from it. The definitive publisher authenticated version
is available online at doi: 10.1088/0143-0807/29/5/00
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