bluuebunny/crossref_metadata_2025 huggingface dataset:
An analytic solution of high-beta equilibrium in a large aspect ratio tokamak
Authors: Cowley S. C. , Kaw P. K. , Kelly R. S. , Kulsrud R. M.
Published: July 2002

An analytic solution of the high-beta (εβ̄p∼βq2/ε≫1) equilibrium of a large aspect ratio tokamak is presented. Two arbitrary flux functions, the pressure profile p(ψ) and the safety factor profile q(ψ), specify the equilibrium. The solution splits into two asymptotic regions: the core region where ψ is a function of the major radius alone and a narrow boundary layer region adjoining the conducting wall. The solutions in the two regions are asymptotically matched to each other. For monotonic pressure profiles, the Shafranov shift is equal to the minor radius. For beta much bigger than 1, the solution contains a region (in place of the magnetic axis) of zero magnetic field and constant pressure. At high beta the quantity βI, which is essentially proportional to the pressure over the total current squared, is largely independent of pressure. The important ramifications of limited βI for high-beta reactors are discussed. Generalizations to shaped cross sections and hollow pressure profiles are outlined. The problem of equilibrium reconstruction in the high-beta regime is also considered.
Resistive toroidal stability of internal kink modes in circular and shaped tokamaks
Authors: Bondeson A. , Vlad G. , Lütjens H.
Published: July 2002

The linear resistive magnetohydrodynamical stability of the n=1 internal kink mode in tokamaks is studied numerically. The stabilizing influence of small aspect ratio [Holmes et al., Phys. Fluids B 1, 788 (1989)] is confirmed, but it is found that shaping of the cross section influences the internal kink mode significantly. For finite pressure and small resistivity, curvature effects at the q=1 surface make the stability sensitively dependent on shape, and ellipticity is destabilizing. Only a very restricted set of finite pressure equilibria is completely stable for q0 < 1. A typical result is that the resistive kink mode is slowed down by toroidal effects to a weak resistive tearing/interchange mode. It is suggested that weak resistive instabilities are stabilized during the ramp phase of the sawteeth by effects not included in linear resistive magnetohydrodynamics. Possible mechanisms for triggering a sawtooth crash are discussed.
Electromagnetic wave scattering from magnetic fluctuations in tokamaks
Authors: Vahala Linda , Vahala George , Bretz N.
Published: July 2002

Cross sections are calculated for electromagnetic wave scattering and mode transformation from magnetic and density fluctuations in a homogeneous plasma. For the special case of scattering perpendicular to the magnetic field, density fluctuations scatter ordinary to ordinary and extraordinary to extraordinary modes—but cannot transform these modes. On the other hand, magnetic fluctuations perpendicular to the field can transform modes but cannot scatter on a single branch. For incident frequencies on the order of the electron plasma frequency or gyrofrequency, the cross sections for scattering and transformation due to field and density fluctuations have a similar value. Estimates are given for scattering in a tokamak plasma with special emphasis on the question of how to detect and localize magnetic field fluctuations. Ray tracing calculations, estimates of practical limitations on polarization technique, and lower bound estimates on density and magnetic fluctuation levels show that magnetic fluctuations can be detected and localized by this method.
Planar laser-driven ablation: Effect of inhibited electron thermal conduction
Authors: Fabbro Rémy , Max Claire , Fabre Edouard
Published: July 2002

A model for planar laser-driven ablation is presented, including the effects of inhibited electron thermal conduction. Localized deposition of laser energy at the critical-density surface is assumed. A steady-state solution in the conduction zone is joined to a rarefaction wave in the underdense corona. The global flow structure is calculated, as well as the ablation pressure, ablation rate, and hydrodynamic efficiency. Criteria are developed for the importance of the inertial force caused by the acceleration of the slab. The results agree well with time-dependent computer simulations using a Lagrangian hydrodynamics code.
Temperature fluctuations and heat transport in the edge regions of a tokamak
Authors: Liewer P. C. , McChesney J. M. , Zweben S. J. , Gould R. W.
Published: July 2002

Electron temperature fluctuations have been investigated in the edge region of the Caltech research tokamak [S. J. Zweben and R. W. Gould, Nucl. Fusion 25, 171 (1985)], and an upper limit to this fluctuation level was found at T̃e/Te ≲15%. This measurement, together with previous measurements of density and electric and magnetic field fluctuations, allows a unique comparison of the heat transport resulting from three basic turbulent mechanisms: (1) heat flux from the particle flux resulting from microscopic density and electric field fluctuations; (2) thermal conduction resulting from microscopic temperature and electric field fluctuations; and (3) thermal conduction resulting from microscopic magnetic field fluctuations. The measurements indicate that, in the edge regions, the electron heat transport caused by the measured turbulence-induced particle flux is comparable to or greater than that caused by the thermal conduction associated with the electron temperature and electric field fluctuations, and is significantly greater than that resulting from the measured magnetic fluctuations. This electron heat loss caused by the plasma turbulence is found to be an important electron energy loss mechanism in the edge regions.
Ion transport in toroidally rotating tokamak plasmas
Authors: Catto Peter J. , Bernstein Ira B. , Tessarotto Massimo
Published: July 2002

An efficient and systematic treatment of classical and neoclassical transport in all regimes of collisionality is formulated that permits toroidal rotation speeds on the order of the ion thermal speed for arbitrary aspect ratio, cross section, and poloidal magnetic field strength. A more convenient, but somewhat unconventional, form of the reduced kinetic equation is derived that is shown to extend the previous form by properly retaining electric field modifications. The generalized kinetic description is exploited to evaluate explicitly the radial fluxes of toroidal angular momentum and energy in a pure plasma via a variational formulation. The specific results obtained in the Pfirsch–Schlüter regime are substantially more general than previous evaluations; also, significant improvements are made in the banana regime.
Three-dimensional equilibrium and stability of ionospheric plasma clouds
Authors: Drake J. F. , Mulbrandon M. , Huba J. D.
Published: July 2002

The equilibrium and stability of three-dimensional (3-D) ionospheric plasma clouds is investigated. The equilibrium density profile is assumed to be a 3-D water bag with a circular cross section transverse to B, and an ellipsoidal cross section parallel to B. The equilibrium potential consists of two parts: a polarization potential driven by a uniform neutral wind, and an ambipolar potential driven by parallel electron pressure. The latter potential is shown to cause sheared azimuthal plasma flows perpendicular to B. A stability analysis of this equilibrium is carried out. It is found that the E×B instability, which causes the structuring of ionospheric plasma clouds, can be stabilized by the shear in the azimuthal flow. A marginal stability criterion is derived. On the basis of this stability criteria, striations of barium clouds in the ionospheric F region should be stable to further bifurcation, as is observed
Defining a universal and continuous Strouhal–Reynolds number relationship for the laminar vortex shedding of a circular cylinder
Authors: Williamson C. H. K.
Published: July 2002

The existence of a discontinuity in the Strouhal–Reynolds number relationship for the laminar vortex shedding of a cylinder is found to be caused by a change in the mode of oblique shedding. By ‘‘inducing’’ parallel shedding (from manipulating end conditions) the resulting Strouhal curve becomes completely continuous and agrees very well with the oblique-shedding data, if it is transformed by S0=Sθ/cos θ (where Sθ is the Strouhal number corresponding with the oblique-shedding angle θ). The curve also agrees with data from a completely different facility. This provides evidence that this Strouhal curve (S0) is universal (for a circular cylinder).
Transient growth in two- and three-dimensional boundary layers
Authors: Breuer Kenneth S. , Kuraishi Takeo
Published: July 2002

The evolution of localized three-dimensional disturbance in two- and three-dimensional laminar boundary layers is examined. The linearized Navier–Stokes equations for three-dimensional disturbances in a three-dimensional parallel shear flow are solved numerically using Fourier transform Chebyshev collocation techniques. Modal analysis shows that substantial short-term energy growth can be obtained even when all instability waves are damped. This transient growth can increase the initial disturbance energy by two or three orders of magnitude, at which stage nonlinear interactions might lead to a breakdown to turbulent flow, bypassing the traditional Tollmien–Schlichting instability mechanism. The dependence of the transient growth on wave number, Reynolds number, sweep angle and Hartree parameter is determined and a method for predicting the maximum transient growth is proposed and found to be reasonably accurate over a wide parameter range. Localized disturbances are also examined and it is found that the bypass growth mechanism can enhance the formation of cross-flow vortices in a three-dimensional flow. Some implications are discussed, particularly with respect to the observed effects of roughness on transition location.
Spreading of drops on solid surfaces in a quasi-static regime
Authors: Shikhmurzaev Yulii D.
Published: July 2002

The problem of interaction of a drop with a solid boundary is formulated in the framework of a recently developed theory of the three-phase contact line motion and analyzed in the case of finite Bond and small capillary and Weber numbers. Evolution of the free-surface shape in a quasi-static regime of the drop spreading under gravity on a horizontal plane and on the surface of a rotating disk is investigated. In the considered regime, the free-surface shape deformation in time is independent of the initial conditions of the drop deposition onto the solid surface, while the three-phase contact-line motion is described by the same equations as in a general case. This feature makes the quasi-static regime informative and desirable from the point of view of investigation of the wetting phenomenon. Accuracy of the so-called “spherical cap approximation’’ often used in experimental studies of wetting is discussed. The theory describes both the “spontaneous” and “forced” regimes of the drop spreading and the transition between them. The results are compared with experimental data.
Transitional regimes of low-Prandtl thermal convection in a cylindrical cell
Authors: Verzicco R. , Camussi R.
Published: July 2002

The transitions from the onset of convection to fully developed turbulence of a Rayleigh–Bénard flow, in a low-aspect-ratio cell and in mercury, are studied through three-dimensional numerical simulation of the Navier–Stokes equations. The calculation of the growth rate of the azimuthal energy modes permitted the accurate determination of the critical Rayleigh number for the establishment of the convective regime (Rac=3750) which is in good agreement with analytical and other numerical results. Increasing the Rayleigh number, the flow remained steady up to Ra≃2.11×104 when an oscillatory instability was observed. Further increases in the Rayleigh produced a chaotic state through the period doubling mechanism and finally the turbulent state was achieved. It is shown that for Ra⩾Rac the mean flow consists of a large-scale convective cell which persists in the whole range of studied Rayleigh numbers (Ra⩽106). The dependence of the Nusselt number over the Rayleigh number is also analyzed and, for Ra⩾3.75×104, when the turbulent state is reached, a power law in quantitative agreement with previous results at higher Ra is observed.
A comparative numerical study of the Richtmyer-Meshkov instability with nonlinear analysis in two and three dimensions
Authors: Li X. L. , Zhang Q.
Published: July 2002

A shock driven inter-facial instability, known as the Richtmyer-Meshkov instability, is studied numerically in two and three dimensions and in the nonlinear regime. The numerical solution is tested for convergence under computational mesh refinement and is compared with the predictions of a recently developed nonlinear theory based on the Padé approximation and asymptotic matching. Good agreement has been found between numerical solutions and predictions of the nonlinear theory in both two and three dimensions and for both the reflected shock and the reflected rarefaction wave cases. The numerical study is extended to the re-shock experiment in which the fluid interface interacts initially with the incident shock. Later, as the transmitted shock bounces back from the wall, the fluid interface is re-shocked.
Flow visualization in porous media via Positron Emission Tomography
Authors: Khalili A. , Basu A. J. , Pietrzyk U.
Published: July 2002

We demonstrate here the use of a non-invasive technique based on Positron Emission Tomography (PET) in visualizing and in making quantitative measurements of scalar transport through natural opaque permeable sediments. Along with various other possibilities, this technique has the potential to help improve the understanding of processes that take place at the seabeds between the porewater and the overlying water, which result in exchange of nutrients, toxins and solute. Unlike many other methods, PET is able to produce full three-dimensional pictures of the percolation of fluid through not only “constructed” but also natural porous media.
Large eddy simulation of a nonpremixed reacting jet: Application and assessment of subgrid-scale combustion models
Authors: DesJardin Paul E. , Frankel Steven H.
Published: July 2002

Results from large eddy simulations (LES) and direct numerical simulations (DNS) of a two-dimensional, spatially developing, compressible planar free jet undergoing an idealized, exothermic, chemical reaction of the type F+rOx→(1+r)P are presented in order to assess several subgrid-scale (SGS) combustion models. Both a priori and a posteriori assessments are conducted. The SGS turbulence model used is the dynamic Smagorinsky model (DSM). Two classes of SGS combustion models are employed in this study. These include the conserved scalar approach and the direct closure approach. Specifically, the SGS combustion models involve several forms of direct filtered reaction rate closures, including a scale similarity filtered reaction rate model (SSFRRM), and a mixing controlled strained laminar flamelet model (SLFM) in the form of thermochemical state relationships, obtained from the DNS, and two assumed forms for the subgrid mixture fraction filtered density function (FDF). In general, LES results are in reasonable agreement with DNS results and highlight the performance of the various SGS combustion models. In particular, in the context of the present study, it is found that: (1) the SLFM cases overpredict product formation due to their inability to capture finite-rate chemistry effects; (2) due to the relatively low values of the SGS mixture fraction variance in the flow under study, the SLFM results are not sensitive to the form of the assumed FDF; and (3) in comparison to the other models investigated, the SSFRRM combustion model provides the best agreement with the DNS for product formation.
Roughness-induced receptivity to crossflow vortices on a swept wing
Authors: Ng L. L. , Crouch J. D.
Published: July 2002

The generation of stationary crossflow vortices on the 45 degree swept NLF (2)-0415 airfoil at the Arizona State University Unsteady Wind Tunnel (AIAA Paper No. 96-0184, 1996; Ph.D. thesis, Arizona State University, 1996) is analyzed using a finite Reynolds-number linear receptivity theory. The receptivity theory is based on the locally-parallel flow approximation and also neglects surface curvature. The vortices are excited by a spanwise periodic array of circular roughness elements located near the attachment line. The amplitudes of the crossflow vortices at the source location are computed and compared with the experimental results. In general, the agreement is remarkably good. This suggests that the combined effect of nonparallel flow and surface curvature on the receptivity is not significant for the range of conditions considered. The linear analysis captures the receptivity variations with Reynolds number, roughness geometry, and roughness location. When the roughness height is small, the initial amplitudes of the roughness-generated crossflow vortices are well predicted using the finite Reynolds-number receptivity theory. Nonlinear effects appeared to become significant only when the roughness height exceeds about 10% of the local boundary layer displacement thickness.
Nonlinear interactions of chemical reactions and viscous fingering in porous media
Authors: De Wit A. , Homsy G. M.
Published: July 2002

Nonlinear interactions of chemical reactions and viscous fingering are studied in porous media by direct numerical simulations of Darcy’s law coupled to the evolution equation for the concentration of a chemically reacting solute controlling the viscosity of miscible solutions. Chemical kinetics introduce important topological changes in the fingering pattern: new robust pattern formation mechanisms such as droplet formation and enhanced tip splitting are evidenced and analyzed.
Momentum-energy transport from turbulence driven by parallel flow shear
Authors: Dong J. Q. , Horton W. , Bengtson Roger D. , Li G. X.
Published: July 2002

The low-frequency E×B turbulence driven by the shear in the mass flow velocity parallel to the magnetic field is studied using the fluid theory in a slab configuration with magnetic shear. Ion temperature gradient effects are taken into account. The eigenfunctions of the linear instability are asymmetric about the mode rational surfaces. Quasilinear Reynolds stress induced by such asymmetric fluctuations produces momentum and energy transport across the magnetic field. Analytic formulas for the parallel and perpendicular Reynolds stress, viscosity, and energy transport coefficients are given. Experimental observations of the parallel and poloidal plasma flows on the Texas Experimental Tokamak Upgrade (TEXT-U) are presented and compared with the theoretical models.
Systematic comparison of a theory-based transport model with a multi-tokamak profile database
Authors: Kinsey Jon , Singer Clifford , Djemil Toufik , Cox Dennis , Bateman Glenn
Published: July 2002

A theoretical model of flux-surface-averaged radial transport in tokamaks has been tested and re-calibrated against a well-documented set of temperature and density profiles from a pre-defined set of discharges from six tokamaks. The transport theory includes neoclassical, drift/ηi, circulating electron mode, kinetic ballooning, neoclassical magnetohydrodynamic (MHD), and resistive ballooning effects. Allowing for no explicitly adjustable free parameters and no a posteriori exclusion of data subsets, the nominal theory reproduced observed temperatures and electron densities with relative error about two orders of magnitude smaller than the range over which machine parameters and resulting plasma parameters varied in the reference discharges examined. An important feature of this study is a well-defined procedure for setting boundary conditions at an appropriate location just inside the inner-most ‘‘closed’’ magnetic flux surface.
Propagation of ultraintense laser pulses through overdense plasma layers
Authors: Guérin S. , Mora P. , Adam J. C. , Héron A. , Laval G.
Published: July 2002

Due to relativistic effects, a large amplitude electromagnetic wave can propagate in a classically overdense plasma with ω2p≳ω2≳ω2p/γ, where ωp is the plasma frequency, ω the laser frequency, and γ the relativistic factor of an electron in the laser field. Particle-in-cell simulations are used to study the interaction of an ultrahigh intensity laser pulse in normal incidence on a one-dimensional preformed plasma layer. Both electrons and ions dynamics are included. The width of the layer is 10 to 30 μm and the plasma is characterized by (ωp/ω)2=1.5. During the penetration of the electromagnetic wave a large longitudinal electric field is generated. It results in a strong longitudinal heating of electrons which reach relativistic temperatures. This heating further lowers the effective plasma frequency ωp/γ so the layer becomes almost transparent after the plasma crossing by the wave front. Velocity of the wave front, reflection and transmission rates are studied as functions of the incident energy flux, the plasma thickness, and the pulse duration.
Three-dimensional simulations of Nova high growth factor capsule implosion experiments
Authors: Marinak M. M. , Tipton R. E. , Landen O. L. , Murphy T. J. , Amendt P. , Haan S. W. , Hatchett S. P. , Keane C. J. , McEachern R. , Wallace R.
Published: July 2002

Capsule implosion experiments carried out on the Nova laser [E. M. Campbell et al., Rev. Sci. Instrum. 57, 2101 (1986)] are simulated with the three-dimensional HYDRA radiation hydrodynamics code [NTIS Document No. DE-96004569 (M. M. Marinak et al. in UCRL-LR-105821-95-3)]. Simulations of ordered, near single mode perturbations indicate that structures which evolve into round spikes can penetrate farthest into the hot spot. Bubble-shaped perturbations can burn through the capsule shell fastest, in which case they cause even more damage. A simulation of a capsule with a multimode perturbation of moderate amplitude shows spike amplitudes evolving in good agreement with a saturation model during the deceleration phase. The presence of sizable low mode asymmetry, caused either by drive asymmetry or perturbations in the capsule shell, can dramatically affect the manner in which spikes approach the center of the hot spot. Three-dimensional coupling between the low mode shell perturbations intrinsic to Nova capsules and the drive asymmetry is found to be important, bringing the simulated neutron yields into closer agreement with the experimental values.
Transport properties of energetic particles in a turbulent electrostatic field
Authors: Manfredi G. , Dendy R. O.
Published: July 2002

The diffusion of test particles in a turbulent electrostatic field is investigated numerically. The field is obtained by solving the Hasegawa–Mima model for two-dimensional drift turbulence. It is shown that nonlinear coupling significantly reduces the level of transport compared to the linear regime, and the physical mechanisms leading to this effect are analyzed in detail. Finite Larmor radius effects, relevant to alpha-particle transport in tokamaks, also reduce the diffusion rate. The scaling of the diffusion coefficient with Larmor radius is derived from a closure theory, and the predictions are compared to results from computer experiments. It is suggested that measured diffusion rates of particles with different Larmor radii can be used to obtain information about the turbulence.
Solitary wave structures in presence of nonisothermal ions in a dusty plasma
Authors: Kakati M. , Goswami K. S.
Published: July 2002

The nonlinear properties of solitary wave structures in the presence of non-isothermal ions, electrons, and charged dust grains are reported. The modification in the amplitude and the width of the solitary wave structures due to the inclusion of the effects of reflected ions and charged dust grains are investigated.
Comment on “Effects of wiggler and axial guide fields on wave propagation in a free-electron laser” [Phys. Plasmas 5, 4079 (1998)]
Authors: Stenflo L. , Shukla P. K.
Published: July 2002

The nonlinear dispersion relation of Mehdian et al. [Phys. Plasmas 5, 4079 (1998)] has been compared with that of previous authors. The physics of free electron lasers (FEL) of circularly polarized electromagnetic waves in a multicomponent magnetoplasma, as well as a suggestion for a FEL in a strongly magnetized electron–positron plasma, is discussed.
Direct observations of the structural phases of crystallized ion plasmas
Authors: Mitchell T. B. , Bollinger J. J. , Huang X.-P. , Itano W. M. , Dubin D. H. E.
Published: July 2002

Laser-cooled Be+9 ions confined in a Penning trap were directly observed, and the images were used to characterize the structural phases of the ions. With the ions in two-dimensionally extended lattice planes, five different stable crystalline phases were observed, and the energetically favored structure could be sensitively tuned by changing the areal density of the confined ions. Qualitatively similar structural phase transitions occur or are predicted to occur in other planar single-component systems with a variety of interparticle interactions. Closed-shell structures were observed with small ion clouds that were spherical or prolate, and crystals with long-range order were observed in the centers of clouds with large numbers of ions. These experimental results are in good agreement with theoretical predictions for the strongly coupled one-component plasma.
Autoresonant (nonstationary) excitation of a collective nonlinear mode
Authors: Fajans J. , Gilson E. , Friedland L.
Published: July 2002

The autoresonant (nonlinear phase locking) manipulation of the diocotron mode in a non-neutral plasma is investigated. Autoresonance is a very general phenomenon in driven nonlinear oscillator and wave systems. By sweeping or chirping the drive frequency, autoresonance allows the amplitude of a nonlinear wave to be controlled without the use of feedback. The experimental results, including a novel scaling relation, are in excellent agreement with a simple theoretical model. These are the first controlled laboratory studies of autoresonance in a collective plasma system.
Interelectrode plasma parameters and plasma deposition in a hot refractory anode vacuum arc
Authors: Beilis I. I. , Keidar M. , Boxman R. L. , Goldsmith S.
Published: July 2002

The new mode of Vacuum arc-Hot Refractory Anode Vacuum Arc-was studied experimentally using a Langmuir probe, two types of thermal probes, and film collection substrates. The plasma density, electron temperature, plasma energy flux, cathode erosion, mass deposition rate on a substrate, and macroparticle contamination in the deposited films were measured. The arc initially operated as a usual vacuum arc sustained by cathode spots, i.e., and the vapor and plasma source located at the cathode spot. At a later stage the anode heated up and metal vapor originating at the cathode was re-evaporated from the nonconsumable hot graphite anode. Initially, plasma density was about (3–4)⋅1020 m−3 but it increased with time, reaching about 2⋅1021 m−3 after 60 s in a 340 A arc. The electron temperature initially was about 1.6 eV and decreased with time to a steady-state value of about 1.1 eV after 20 s. The radial plasma energy flux generated by 175 and 340 A arcs was about 1 and 2 MW/m2, respectively, at 1.6 cm from the electrode axis. The deposition rate on substrates placed 110–120 mm from the electrode axis reached about 2 μm/min. The density of macroparticles found on substrates exposed during the first 60 s of arcing was ∼103 macroparticles per mm2, however, this density was reduced to about 1 macroparticle per mm2 on substrates exposed to only the second 30 s period.
Coherent beam addition of GaAlAs lasers by binary phase gratings
Authors: Leger James R. , Swanson Gary J. , Veldkamp Wilfrid B.
Published: July 2002

A general technique for combining laser beams coherently using binary gratings has been developed. Experiments were performed with lasers from a monolithic linear GaAlAs array. The grating transmittance profile was designed to convert the light beams from the array into a single beam with high efficiency. Optical feedback through the grating locked the lasers together in proper relative phase. The far-field diffraction pattern of the sum was practically identical in shape to that of a single laser. Coupling efficiencies greater than 80% appear to be feasible with this technique. The method is applicable to a variety of laser systems (gas, solid state, etc.) and is readily extendable to a two-dimensional array of lasers.
Effect of surface losses on soliton propagation in Josephson junctions
Authors: Davidson A. , Pedersen N. F. , Pagano S.
Published: July 2002

We have explored numerically the effects on soliton propagation of a third order damping term in the modified sine-Gordon equation. In Josephson tunnel junctions such a term corresponds physically to quasiparticle losses within the metal electrodes of the junction. We find that this loss term plays the dominant role in determining the shape and stability of the soliton at high velocity.
Synthesis of diamond by laser-induced chemical vapor deposition
Authors: Kitahama Katsuki , Hirata Kazuhiko , Nakamatsu Hirohide , Kawai Shichio , Fujimori Naoji , Imai Takahiro , Yoshino Hiroshi , Doi Akira
Published: July 2002

Diamond has been obtained by ArF excimer laser-induced chemical vapor deposition. The reaction was carried out by use of C2H2 diluted with H2 as a source gas and at the pressure range of 8–75 Torr. The products were characterized by scanning electron microscopy and reflection electron diffraction. Deposits prepared in the temperature range of 40–800 °C, which were measured by the thermocouple attached to the substrate, show several lines of diamond in the reflection electron diffraction photographs. The fact that the laser beam must be concentrated for the diamond formation to occur strongly suggests that the reaction proceeds through a multiple photon process.
Lateral photoeffect in thin amorphous superlattice films of Si and Ti grown on a Si substrate
Authors: Levine B. F. , Willens R. H. , Bethea C. G. , Brasen D.
Published: July 2002

The lateral photoeffect in a new type of amorphous superlattice film, consisting of 6 Å of Ti and 13 Å of Si grown on a Si substrate, is discussed. The photovoltage varies extremely linearly with light spot position and can thus be used in accurate position sensitive detectors.
High efficiency indium oxide/cadmium telluride solar cells
Authors: Nakazawa T. , Takamizawa K. , Ito K.
Published: July 2002

Solar cells have been fabricated by reactive deposition of thin-film n-In2O3 onto single-crystal p-CdTe. The cell has a total area solar power conversion efficiency of 13.4% which corresponds to an active area efficiency of 14.4% at air mass 1.5 without antireflection coatings. The cell consists of a buried homojunction structure with low dark saturation current density.
Surface-emitting distributed feedback semiconductor laser
Authors: Macomber S. H. , Mott J. S. , Noll R. J. , Gallatin G. M. , Gratrix E. J. , O’Dwyer S. L. , Lambert S. A.
Published: July 2002

Electrically pumped, surface-emitting distributed feedback lasers were for the first time demonstrated without any facet reflections. The devices contained second-order gratings etched into a thin p-AlGaAs cladding layer surface. A gold ohmic contact deposited directly onto the p-AlGaAs grating surface provided strong coupling to the waveguide mode. Single spatial mode devices with low divergence output beams and single frequency spectra were obtained at room temperature.
Elimination of birefringence in garnet films for magneto-optic waveguide devices
Authors: Wolfe R. , Fratello V. J. , McGlashan-Powell M.
Published: July 2002

The linear birefringence of magneto-optic garnet thin films, which interferes with the Faraday rotation in waveguide devices, can be reduced to small values by growing multilayer films to minimize the shape effect, annealing at high temperatures to reduce the growth-induced effect, and growing the films in compression to control the photoelastic effect. The remaining birefringence can be reduced to zero by chemically etching the film until the effects exactly cancel each other at a particular wavelength. This etch-tuning procedure is demonstrated on a two-layer bismuth-yttrium iron garnet (Bi-YIG) film at wavelengths of 1.51 and 1.32 μm. Extinction ratios of 100 to 1 have been achieved at 45° and 90° Faraday rotations at both wavelengths.
Preparation and characterization of some AIBIICV type semiconductors
Authors: Bacewicz R. , Ciszek T. F.
Published: July 2002

Crystals of LiZnP, LiCdP, and LiZnAs are prepared by direct fusion of constituent elements. All three materials are found to be p-type semiconductors. Absorption edge and photoconductivity spectra are measured. Band gaps are estimated to be 1.25 eV for LiZnAs, 1.3 eV for LiCdP, and 2.1 eV for LiZnP.
A structural basis for integrin activation by the cytoplasmic tail of the α
IIb
-subunit
Authors: Vinogradova Olga , Haas Tom , Plow Edward F. , Qin Jun
Published: July 2002

A key step in the activation of heterodimeric integrin adhesion receptors is the transmission of an agonist-induced cellular signal from the short α- and/or β-cytoplasmic tails to the extracellular domains of the receptor. The structural details of how the cytoplasmic tails mediate such an inside-out signaling process remain unclear. We report herein the NMR structures of a membrane-anchored cytoplasmic tail of the α
IIb
-subunit and of a mutant α
IIb
-cytoplasmic tail that renders platelet integrin α
IIb
β
3
constitutively active. The structure of the wild-type α
IIb
-cytoplasmic tail reveals a “closed” conformation where the highly conserved N-terminal membrane-proximal region forms an α-helix followed by a turn, and the acidic C-terminal loop interacts with the N-terminal helix. The structure of the active mutant is significantly different, having an “open” conformation where the interactions between the N-terminal helix and C-terminal region are abolished. Consistent with these structural differences, the two peptides differ in function: the wild-type peptide suppressed α
IIb
β
3
activation, whereas the mutant peptide did not. These results provide an atomic explanation for extensive biochemical/mutational data and support a conformation-based “on/off switch” model for integrin activation.
Motility initiation in herring sperm is regulated by reverse sodium-calcium exchange
Authors: Vines Carol A. , Yoshida Kaoru , Griffin Frederick J. , Pillai Murali C. , Morisawa Masaaki , Yanagimachi Ryuzo , Cherr Gary N.
Published: July 2002

Sperm of the Pacific herring,
Clupea pallasi
, are unique in that they are immotile upon spawning in the environment. Herring sperm have evolved to remain motionless for up to several days after spawning, yet are still capable of fertilizing eggs. An egg chorion ligand termed “sperm motility initiation factor” (SMIF) induces motility in herring sperm and is required for fertilization. In this study, we show that SMIF induces calcium influx, sodium efflux, and a membrane depolarization in herring sperm. Sperm motility initiation by SMIF depended on decreased extracellular sodium (<350 mM) and could be induced in the absence of SMIF in very low sodium seawater. Motility initiation depended on ≥ 1 mM extracellular calcium. Calcium influx caused by SMIF involved both the opening of voltage-gated calcium channels and reverse sodium–calcium (Na
+
/Ca
2+
) exchange. Membrane depolarization was slightly inhibited by a calcium channel blocker and markedly inhibited by a Na
+
/Ca
2+
exchange inhibitor. Sodium efflux caused by SMIF-initiated motility was observed when using both extracellular and intracellular sodium probes. A Na
+
/Ca
2+
exchange antigen was shown to be present on the surface of the sperm, primarily over the midpiece, by using an antibody to the canine Na
+
/Ca
2+
exchanger. This antibody recognized a 120-kDa protein that comigrated with the canine myocyte Na
+
/Ca
2+
exchanger. Sperm of Pacific herring are now shown to use reverse Na
+
/Ca
2+
exchange in motility initiation. This mechanism of regulation of motility initiation may have evolved for both maintenance of immotility after spawning as well as ligand-induced motility initiation.
Extreme genome reduction in
Buchnera
spp.: Toward the minimal genome needed for symbiotic life
Authors: Gil Rosario , Sabater-Muñoz Beatriz , Latorre Amparo , Silva Francisco J. , Moya Andrés
Published: July 2002

Buchnera
is a mutualistic intracellular symbiont of aphids. Their association began about 200 million years ago, with host and symbiont lineages evolving in parallel since that time. During this coevolutionary process,
Buchnera
has experienced a dramatic decrease of genome size, retaining only essential genes for its specialized lifestyle. Previous studies reported that genome size in
Buchnera
spp. is very uniform, suggesting that genome shrinkage occurred early in evolution, and that modern lineages retain the genome size of a common ancestor. Our physical mapping of
Buchnera
genomes obtained from five aphid lineages shows that the genome size is not conserved among them, but has been reduced down to 450 kb in some species. Here we show evidence of six species with a genome size smaller than
Mycoplasma genitalium
, the smallest bacterial genome reported thus far (580 kb). Our findings strongly suggest that the
Buchnera
genome is still experiencing a reductive process toward a minimum set of genes necessary for its symbiotic lifestyle.
The Dun1 checkpoint kinase phosphorylates and regulates the ribonucleotide reductase inhibitor Sml1
Authors: Zhao Xiaolan , Rothstein Rodney
Published: July 2002

Cell cycle checkpoints are evolutionarily conserved surveillance systems that protect genomic stability and prevent oncogenesis in mammals. One important target of checkpoint control is ribonucleotide reductase (RNR), which catalyzes the rate-limiting step in dNTP and DNA synthesis. In both yeast and humans, RNR is transcriptionally induced after DNA damage via Mec1/Rad53 (yeast) and ATM/CHK2 (human) checkpoint pathways. In addition, yeast checkpoint proteins Mec1 and Rad53 also regulate the RNR inhibitor Sml1. After DNA damage or at S phase, Mec1 and Rad53 control the phosphorylation and concomitant degradation of Sml1 protein. This new layer of control contributes to the increased dNTP production likely necessary for DNA repair and replication; however, the molecular mechanism is unclear. Here we show that Dun1, a downstream kinase of Mec1/Rad53, genetically and physically interacts with Sml1
in vivo
. The absence of Dun1 activity leads to the accumulation of Sml1 protein at S phase and after DNA damage. As a result,
dun1
Δ strains need more time to finish DNA replication, are defective in mitochondrial DNA propagation, and are sensitive to DNA-damaging agents. Moreover, phospho-Sml1 is absent or dramatically reduced in
dun1
Δ cells. Finally, Dun1 can phosphorylate Sml1
in vitro
. These results suggest that Dun1 kinase function is the last step required in the Mec1/Rad53 cascade to remove Sml1 during S phase and after DNA damage.
Bean α-amylase inhibitor 1 in transgenic peas (
Pisum sativum
) provides complete protection from pea weevil (
Bruchus pisorum
) under field conditions
Authors: Morton Roger L. , Schroeder Hart E. , Bateman Kaye S. , Chrispeels Maarten J. , Armstrong Eric , Higgins Thomas J. V.
Published: July 2002

Two α-amylase inhibitors, called αAI-1 and αAI-2, that share 78% amino acid sequence identity and have a differential specificity toward mammalian and insect α-amylases are present in different accessions of the common bean (
Phaseolus vulgaris
). Using greenhouse-grown transgenic peas (
Pisum sativum
), we have shown previously that expression of αAI-1 in pea seeds can provide complete protection against the pea weevil (
Bruchus pisorum
). Here, we report that αAI-1 also protects peas from the weevil under field conditions. The high degree of protection is explained by our finding that αAI-1 inhibits pea bruchid α-amylase by 80% over a broad pH range (pH 4.5–6.5). αAI-2, on the other hand, is a much less effective inhibitor of pea bruchid α-amylase, inhibiting the enzyme by only 40%, and only in the pH 4.0–4.5 range. Nevertheless, this inhibitor was still partially effective in protecting field-grown transgenic peas against pea weevils. The primary effect of αAI-2 appeared to be a delay in the maturation of the larvae. This contrasts with the effect of αAI-1, which results in larval mortality at the first or second instar. These results are discussed in relationship to the use of amylase inhibitors with different specificities to bring about protection of crops from their insect pests or to decrease insect pest populations below the economic injury level.
The Arf GTPase-activating protein ASAP1 regulates the actin cytoskeleton
Authors: Randazzo Paul A. , Andrade Josefa , Miura Koichi , Brown Megan T. , Long Ya-Qiu , Stauffer Stacey , Roller Peter , Cooper Jonathan A.
Published: July 2002

Arf family GTP-binding proteins are best characterized as regulators of membrane traffic, but recent studies indicate an additional role in cytoskeletal organization. An Arf GTPase-activating protein of the centaurin β family, ASAP1 (also known as centaurin β4), binds Arf and two other known regulators of the actin cytoskeleton, the tyrosine kinase Src and phosphatidylinositol 4,5-bisphosphate. In this paper, we show that ASAP1 localizes to focal adhesions and cycles with focal adhesion proteins when cells are stimulated to move. Overexpression of ASAP1 altered the morphology of focal adhesions and blocked both cell spreading and formation of dorsal ruffles induced by platelet-derived growth factor (PDGF). On the other hand, ASAP1, with a mutation that disrupted GTPase-activating protein activity, had a reduced effect on cell spreading and increased the number of cells forming dorsal ruffles in response to PDGF. These data support a role for an Arf GTPase-activating protein, ASAP1, as a regulator of cytoskeletal remodeling and raise the possibility that the Arf pathway is a target for PDGF signaling.
Supramolecular self-assembled fullerene nanostructures
Authors: Georgakilas Vasilios , Pellarini Federica , Prato Maurizio , Guldi Dirk M. , Melle-Franco Manuel , Zerbetto Francesco
Published: July 2002

Four ionic fullerene derivatives, which are relatively soluble in polar solvents, are shown to organize into morphologically different nanoscale structures. Spheres, nanorods, and nanotubules form in water depending on the side chain appendage of the fullerene spheroid. Images at different nanoscale structures were obtained via transmission electron microscopy. Also, computer simulations were used for investigating the relative spatial arrangements. The efficient method to fabricate almost perfect and uniformly shaped nanotubular crystals, which order spontaneously by self-assembly, opens the way to the possibility of exploiting the fullerene properties at the nanometer scale.
Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR
Authors: Lee Sang-Won , Berger Scott J. , Martinović Suzana , Paša-Tolić Ljiljana , Anderson Gordon A. , Shen Yufeng , Zhao Rui , Smith Richard D.
Published: July 2002

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry coupled with capillary reverse-phase liquid chromatography was used to characterize intact proteins from the large subunit of the yeast ribosome. High mass measurement accuracy, achieved by “mass locking” with an internal standard from a dual electrospray ionization source, allowed identification of ribosomal proteins. Analyses of the intact proteins revealed information on cotranslational and posttranslational modifications of the ribosomal proteins that included loss of the initiating methionine, acetylation, methylation, and proteolytic maturation. High-resolution separations permitted differentiation of protein isoforms having high structural similarity as well as proteins from their modified forms, facilitating unequivocal assignments. The study identified 42 of the 43 core large ribosomal subunit proteins and 58 (of 64 possible) core large subunit protein isoforms having unique masses in a single analysis. These results demonstrate the basis for the high-throughput analyses of complex mixtures of intact proteins, which we believe will be an important complement to other approaches for defining protein modifications and their changes resulting from physiological processes or environmental perturbations.
Molecular and genealogical evidence for a founder effect in Fanconi anemia families of the Afrikaner population of South Africa
Authors: Tipping A. J. , Pearson T. , Morgan N. V. , Gibson R. A. , Kuyt L. P. , Havenga C. , Gluckman E. , Joenje H. , de Ravel T. , Jansen S. , Mathew C. G.
Published: July 2002

Fanconi anemia (FA) is a rare, genetically heterogeneous autosomal
recessive disorder associated with progressive aplastic anemia,
congenital abnormalities, and cancer. FA has a very high incidence in
the Afrikaner population of South Africa, possibly due to a founder
effect. Previously we observed allelic association between polymorphic
markers flanking the FA group A gene (
FANCA
) and disease
chromosomes in Afrikaners. We genotyped 26 FA families with
microsatellite and single nucleotide polymorphic markers and detected
five
FANCA
haplotypes. Mutation scanning of the
FANCA
gene revealed association of these haplotypes with
four different mutations. The most common was an intragenic deletion of
exons 12–31, accounting for 60% of FA chromosomes in 46 unrelated
Afrikaner FA patients, while two other mutations accounted for an
additional 20%. Screening for these mutations in the European
populations ancestral to the Afrikaners detected one patient from the
Western Ruhr region of Germany who was heterozygous for the major
deletion. The mutation was associated with the same unique
FANCA
haplotype as in Afrikaner patients. Genealogical
investigation of 12 Afrikaner families with FA revealed that all were
descended from a French Huguenot couple who arrived at the Cape on June
5, 1688, whereas mutation analysis showed that the carriers of the
major mutation were descendants of this same couple. The molecular and
genealogical evidence is consistent with transmission of the major
mutation to Western Germany and the Cape near the end of the 17th
century, confirming the existence of a founder effect for FA in South
Africa.
Characterization of the 1918 “Spanish” influenza virus neuraminidase gene
Authors: Reid Ann H. , Fanning Thomas G. , Janczewski Thomas A. , Taubenberger Jeffery K.
Published: July 2002

The “Spanish” influenza pandemic of 1918 was characterized by exceptionally high mortality, especially among young adults. The surface proteins of influenza viruses, hemagglutinin and neuraminidase, play important roles in virulence, host specificity, and the human immune response. The complete coding sequence of hemagglutinin was reported last year. This laboratory has now determined the complete coding sequence of the neuraminidase gene of the 1918 virus. Influenza RNA fragments were isolated from lung tissue of three victims of the 1918 flu; complete sequence was generated from A/Brevig Mission/1/18, with confirmatory sequencing carried out on A/South Carolina/1/18 and A/New York/1/18. The 1918 neuraminidase gene sequence was compared with other N1 subtype neuraminidase genes, including 9 N1 strains newly sequenced for this study. The 1918 neuraminidase shares many sequence and structural characteristics with avian strains, including the conserved active site, wild-type stalk length, glycosylation sites, and antigenic sites. Phylogenetically, the 1918 neuraminidase gene appears to be intermediate between mammals and birds, suggesting that it was introduced into mammals just before the 1918 pandemic.