bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of the Orszag–Tang vortex system in a compressible medium. II. Supersonic flow
Authors: Picone J. Michael , Dahlburg Russell B.
Published: July 2002

The numerical investigation of Orszag–Tang vortex system in compressible magnetofluids continues, this time using initial conditions with embedded supersonic regions. The simulations have initial average Mach numbers M=1.0 and 1.5 and β=10/3 with Lundquist numbers S=50, 100, or 200. Depending on the particular set of parameters, the numerical grid contains 2562 or 5122 collocation points. The behavior of the system differs significantly from that found previously for the incompressible and subsonic analogs. Shocks form at the downstream boundaries of the embedded supersonic regions outside the central magnetic X point and produce strong local current sheets that dissipate appreciable magnetic energy. Reconnection at the central X point, which dominates the incompressible and subsonic systems, peaks later and has a smaller impact as M increases from 0.6 to 1.5. Reconnection becomes significant only after shocks reach the central region, compressing the weak current sheet there. Similarly, the correlation between the momentum and magnetic field begins significant growth later than in subsonic and incompressible flows. The shocks bound large compression regions, which dominate the wave-number spectra of autocorrelations in mass density, velocity, and magnetic field. The normalized spectral amplitude of the cross helicity is almost zero over the middle and upper portions of the wave-number domain, unlike the incompressible and subsonic flows. The thermal and magnetic pressures are anticorrelated over a wide wave-number range during the earlier portion of the calculations, consistent with the presence of quasistationary structures bounded by shocks.
Stability of ion-temperature-gradient-driven modes in the presence of sheared poloidal flows
Authors: Wang X.-H. , Diamond P. H. , Rosenbluth M. N.
Published: July 2002

The linear theory of the sonic ion-temperature-gradient-driven mode in the presence of sheared poloidal rotation is discussed in the context of a hydrodynamic model. Analytical and numerical calculations show that the growth rate increases for weak shear, but then decreases when the shearing frequency exceeds the mode frequency. This trend is a consequence of the coupling of radial eigenmodes induced by the asymmetric effective potential and the absorption and damping due to resonance between the wave frequency and shearing frequency. The former dominates at weak shear, resulting in destabilization, while the latter dominates for strong shear, resulting in stabilization. Mixing length estimates of the turbulent diffusivity are given, and a novel bifurcation scenario for the L→H transition is discussed.
Self-similar solutions for trapping and diffusion of magnetic flux during formation of field-reversed configuration
Authors: Bud’ko A. B. , Karlson E. T. , Liberman M. A.
Published: July 2002

Self-similar solutions are given that represent an analytical theory of implosion and extension stages of a Θ pinch before the magnetic field lines reconnection in course of formation of field-reversed configuration. Effects of Ohmic dissipation, thermal conductivity, and plasma turbulence are included. The self-similar solutions, obtained in an explicit analytical form, demonstrate that magnetic flux is trapped during the implosion and expansion stages for a classical plasma, and that losses of magnetic flux are possible for a turbulent plasma during the expansion stage. The rate of flux trapping and diffusion is expressed in terms of experimental parameters.
A fully nonlinear characteristic method for gyrokinetic simulation
Authors: Parker S. E. , Lee W. W.
Published: July 2002

A new scheme that evolves the perturbed part of the distribution function along a set of characteristics that solves the fully nonlinear gyrokinetic equations is presented. This low-noise nonlinear characteristic method for particle simulation is an extension of the partially linear weighting scheme, and may be considered an improvement over existing δf methods. Some of the features of this new method include the ability to keep all nonlinearities, particularly those associated with the velocity space, the use of conventional particle loading techniques, and also the retention of the conservation properties of the original gyrokinetic system in the numerically converged limit. The new method is used to study a one-dimensional drift wave model that isolates the parallel velocity nonlinearity. A mode coupling calculation for the saturation amplitude is given, which is in good agreement with the simulation results. Finally, the method is extended to the electromagnetic gyrokinetic equations in general geometry.
Limits on the magnetic field strength for critical ionization velocity interaction
Authors: Brenning N.
Published: July 2002

A theoretical lower limit to the magnetic field strength required for critical ionization velocity (vc) interaction is found to correspond to the requirement v<vA(1+βe)1/2, which can also be expressed as ωpe/ωce<(c/v)[(1+βe) ×me/mi]1/2. This limit is found to agree, within the experimental uncertainties, with the results from all the vc experiments in the impact configuration. The different experiments have very different physical characteristics, and cover large ranges in plasma densities, stream velocities, and magnetic field strengths. A theoretical upper limit to the magnetic field strength is also found, corresponding to the requirement ωpe/ωce ≫(me/mn)1/2.
Coulomb solid of small particles in plasmas
Authors: Ikezi H.
Published: July 2002

Small particles in plasmas can form a coulomb lattice. The conditions for solidification in a laboratory plasma are discussed.
Measurements and implications of Zeff profiles on the DIII-D tokamak
Authors: Schissel D. P. , Stockdale R. E. , St. John H. , Tang W. M.
Published: July 2002

Here Zeff profiles have been obtained across the entire minor radius of the DIII-D [Fusion Technol. 8, 441 (1985); Plasma Physics and Controlled Nuclear Fusion Research, 1986 (IAEA, Vienna, 1987), Vol. 1, p. 159] tokamak from measurements of visible bremsstrahlung continuum radiation. The Zeff profiles are presented for Ohmic divertor and limiter plasmas as well as for neutral beam heated H-mode and L-mode plasmas. The measured Zeff profiles are found to have small gradients over the entire plasma cross section. This implies that resistivity gradient driven electrostatic modes are unlikely to influence the confinement properties in the edge region of these discharges. The H-mode plasma has a centrally peaked Zeff profile and a relatively flat electron density profile that suggests the existence of a negative value for the parameter ηi.
Near-field pressure radiation and flow characteristics in low supersonic circular and elliptic jets
Authors: Gutmark E. , Schadow K. C. , Wilson K. J. , Bicker C. J.
Published: July 2002

The near-field pressure fluctuations of circular and elliptic underexpanded supersonic jets were studied experimentally. Unlike the case of low subsonic jets, the pressure fluctuation characteristics at the minor axis plane of the elliptic jet were very different from those of the major axis plane. The amplitude of the pressure fluctuations at the minor axis was more than an order of magnitude higher than at the other plane. This section of the jet was also characterized by a larger spreading rate and higher amplification rate of the velocity fluctuations. The circular jet was similar to the major axis plane of the elliptic jet. The spectra of the near-field pressure fluctuations of both jets exhibited the highest peak at a frequency corresponding to the jets’ preferred mode frequency. The spectral peak related to the screech tone was much stronger at the minor axis plane and had the same frequency as at the other plane. The amplitude of the dominant pressure fluctuation frequencies was mapped in the entire near field, and each one was found to be dominant in a different region.
Energy transfer in numerically simulated wall-bounded turbulent flows
Authors: Domaradzki J. Andrzej , Liu Wei , Härtel Carlos , Kleiser Leonhard
Published: July 2002

Using velocity fields obtained in direct numerical simulations of turbulent convection and of turbulent channel flow, the energy transfer process among lateral scales of motion in these low Reynolds number flows is analyzed. In all cases the energy is transferred most effectively between scales of similar size. As a result, the subgrid-scale energy transfer is caused almost exclusively by interactions between resolved scales and subgrid scales characterized by wave numbers not greater than twice the cutoff wave number. The scale dependence of forward and inverse energy transfers contributing to the total subgrid-scale eddy viscosity is discussed. The local energy transfer between small scales is strongly affected by the nonlocal interactions characterized by a scale separation greater than a factor of 2 in wave number. However, the direct energy transfer between scales satisfying this condition is one order of magnitude less than the local energy transfer between scales of similar size.
Asymmetric instability of a viscid capillary jet in an inviscid media
Authors: Avital E.
Published: July 2002

The instability of asymmetric disturbances in a full circular viscid jet is investigated. It is found that asymmetric disturbances can be dominant for moderate modes and intermediate axial wave numbers for a low Weber number (≊10−5). But no asymmetric disturbance with maximum wave growth higher than the axisymmetric one was found.
The curvature of material lines in chaotic cavity flows
Authors: Liu M. , Muzzio F. J.
Published: July 2002

Material line folding is studied in two-dimensional chaotic cavity flows. Line folding is measured by the local curvature k=l×l′/‖l‖3, where l(q) is an infinitesimal vector in the tangential direction of the line, q is a coordinate along the line, and l′ is the derivative of l with respect to q. It is shown both analytically and numerically that folding is always accompanied by compression. The vector l′ plays a crucial role as a driving force for the stretching and folding processes. A material line is stretched when l′ is tangential to the line and it is folded when l′ is normal to the line. The spatial structure of the curvature field is computed numerically. The short-time structure of the curvature field is similar to the structure of unstable manifolds of periodic hyperbolic points, and closely resembles patterns observed in tracer mixing experiments and in stretching field computations. The long time structure of the field asymptotically approaches an entirely different time-independent structure. Probability density functions of curvature are independent of both time and initial conditions.
Numerical study of nonlinear shallow water waves produced by a submerged moving disturbance in viscous flow
Authors: Zhang Daohua , Chwang Allen T.
Published: July 2002

Two-dimensional solitary waves generated by a submerged body moving near the critical speed in a shallow water channel are studied numerically. The incompressible Navier–Stokes equations in a curvilinear free-surface-fitted coordinate system are solved by the finite difference method. The present numerical results are compared with the existing experimental data, and with the numerical solutions of two inviscid-flow models, i.e. the general Boussinesq equation and the forced Korteweg-de Vries equation. It is found that the viscous effect in the boundary layer around the body and on the bottom of the channel plays an important role in the generation of solitary waves on the free surface. Hence the Navier–Stokes solutions have a better agreement with the experimental data than those obtained from two inviscid-flow models. The effect of the submergence depth of the body on the waves generated is also investigated. It reveals that waves are insensitive to the submergence depth of the body, except for a small region quite close to the bottom of the water channel.
Subgrid-scale energy transfer and near-wall turbulence structure
Authors: Piomelli Ugo , Yu Yunfang , Adrian Ronald J.
Published: July 2002

Conditional averages of the velocity field, subgrid-scale (SGS) stresses and SGS dissipation are calculated using the velocity fields obtained from the DNS of plane channel flow. The detection criteria isolate the coherent turbulent structures that contribute most strongly to the energy transfer between the large, resolved scales and the subgrid, unresolved, ones. Separate averages are computed for forward and backward scatter. The interscale energy transfer is found to be strongly correlated with the presence of the turbulent structures typical of wall-bounded flows: quasi-streamwise and hairpin vortices, sweeps and ejections. In the buffer layer, strong SGS dissipation is observed near lifted shear layers; the forward scatter is associated with ejections, the backscatter with sweeps. Both backward and forward scatter occur in close proximity to longitudinal vortices that form a very shallow angle to the wall. Further away from the solid boundary, in the logarithmic region and beyond, both forward and backward energy transfer are associated prevalently with ejections. Eddy viscosity models do not predict the three-dimensional structure of these events adequately, while scale-similar models reproduce the correlation between the large-scale coherent structures and the SGS events more accurately.
Energy balance for turbulent flow around a surface mounted cube placed in a channel
Authors: Hussein H. J. , Martinuzzi R. J.
Published: July 2002

Results of an experimental investigation of the inhomogeneous, three-dimensional flow around a surface mounted cube in a channel are presented. LDA measurements of single-point velocity correlations are used to determine the production, convection and transport of the turbulence kinetic energy, k, in the obstacle wake. The turbulence dissipation rate is obtained as a closing term to the balance of the k-transport equation. The results provide some insight to the evolution of the turbulence dissipation rate from the near field recirculation zone to the asymptotic wake. Also presented is a comparison between measured and modeled transport terms.
Large eddy simulation of particle-laden turbulent channel flow
Authors: Wang Qunzhen , Squires Kyle D.
Published: July 2002

Particle transport in fully-developed turbulent channel flow has been investigated using large eddy simulation (LES) of the incompressible Navier–Stokes equations. Calculations were performed at channel flow Reynolds numbers, Reτ, of 180 and 644 (based on friction velocity and channel half width); subgrid-scale stresses were parametrized using the Lagrangian dynamic eddy viscosity model. Particle motion was governed by both drag and gravitational forces and the volume fraction of the dispersed phase was small enough such that particle collisions were negligible and properties of the carrier flow were not modified. Material properties of the particles used in the simulations were identical to those in the DNS calculations of Rouson and Eaton [Proceedings of the 7th Workshop on Two-Phase Flow Predictions (1994)] and experimental measurements of Kulick et al. [J. Fluid Mech. 277, 109 (1994)]. Statistical properties of the dispersed phase in the channel flow at Reτ=180 are in good agreement with the DNS; reasonable agreement is obtained between the LES at Reτ=644 and experimental measurements. It is shown that the LES correctly predicts the greater streamwise particle fluctuation level relative to the fluid and increasing anisotropy of velocity fluctuations in the dispersed phase with increasing values of the particle time constant. Analysis of particle fluctuation levels demonstrates the importance of production by mean gradients in the particle velocity as well as the fluid-particle velocity correlation. Preferential concentration of particles by turbulence is also investigated. Visualizations of the particle number density field near the wall and along the channel centerline are similar to those observed in DNS and the experiments of Fessler et al. [Phys. Fluids 6, 3742 (1994)]. Quantitative measures of preferential concentration are also in good agreement with Fessler et al. [Phys. Fluids 6, 3742 (1994)].
A vortex-based subgrid stress model for large-eddy simulation
Authors: Misra Ashish , Pullin D. I.
Published: July 2002

A class of subgrid stress (SGS) models for large-eddy simulation (LES) is presented based on the idea of structure-based Reynolds-stress closure. The subgrid structure of the turbulence is assumed to consist of stretched vortices whose orientations are determined by the resolved velocity field. An equation which relates the subgrid stress to the structure orientation and the subgrid kinetic energy, together with an assumed Kolmogorov energy spectrum for the subgrid vortices, gives a closed coupling of the SGS model dynamics to the filtered Navier–Stokes equations for the resolved flow quantities. The subgrid energy is calculated directly by use of a local balance between the total dissipation and the sum of the resolved-scale dissipation and production by the resolved scales. Simple one- and two-vortex models are proposed and tested in which the subgrid vortex orientations are either fixed by the local resolved velocity gradients, or rotate in response to the evolution of the gradient field. These models are not of the eddy viscosity type. LES calculations with the present models are described for 323 decaying turbulence and also for forced 323 box turbulence at Taylor Reynolds numbers Rλ in the range Rλ≃30 (fully resolved) to Rλ=∞. The models give good agreement with experiment for decaying turbulence and produce negligible SGS dissipation for forced turbulence in the limit of fully resolved flow.
Flowfield characteristics of an aerodynamic acoustic levitator
Authors: Yarin A. L. , Brenn G. , Keller J. , Pfaffenlehner M. , Ryssel E. , Tropea C.
Published: July 2002

A droplet held in a single-axis ultrasonic levitator will principally sustain a certain external blowing along the levitation axis, which introduces the possibility of investigating heat and/or mass transfer from the droplet under conditions which are not too remote from those in spray systems. The focus of the present work is on the influence of the acoustic field on the external flow. More specifically, an axisymmetric submerged gas jet in an axial standing acoustic wave is examined, both in the absence and presence of a liquid droplet. Flow visualization is first presented to illustrate the global flow effects and the operating windows of jet velocities and acoustic powers which are suitable for further study. An analytic and numeric solution, based on the parabolic boundary layer equations are then given for the case of no levitated droplet, providing quantitative estimates of the acoustic field/flow interaction. Detailed velocity measurements using a laser Doppler anemometer verify the analytic results and extend these to the case of a levitated droplet. Some unresolved discrepancy remains in predicting the maximum velocity attainable before the droplet is blown out of the levitator. Two methods are developed to estimate the sound pressure level in the levitator by comparing flowfield patterns with analytic results. These results and observations are used to estimate to what extent acoustic aerodynamic levitators can be used in the future for investigating transport properties of individual droplets.
Mixing enhancement via nozzle trailing edge modifications in a high speed rectangular jet
Authors: Kim J.-H. , Samimy M.
Published: July 2002

An aspect ratio 3 rectangular nozzle with design Mach number 2 was used to investigate the effects of trailing edge modifications on mixing enhancement and to explore the sources of streamwise vorticity at the fully expanded jet Mach numbers 1.75, 2.0, and 2.5. The trailing edge modifications are simple cut-outs in the plane of the nozzle at the nozzle exit. The investigation of mixing and interaction between mixing layers and vortices was performed by the laser sheet illumination technique. Through surface flow visualizations and wall pressure measurements, the investigation of the major source of streamwise vorticity was carried out. In addition, the variation of thrust generated by the nozzle with modified trailing edges was investigated. In the underexpanded flow condition, the major source of streamwise vorticity was determined to be the spanwise surface pressure gradient on the modification. Substantial mixing enhancement was achieved in this flow regime. On the other hand, in the overexpanded flow regime, the role of streamwise vortices in mixing and the source of streamwise vorticity were unclear, and mixing enhancement was not substantial. No measurable thrust loss or gain was obtained for nozzles with trailing edge modifications, regardless of the type of modification.
Vortex dynamics investigation using an acoustic technique
Authors: Manneville S. , Robres J. H. , Maurel A. , Petitjeans P. , Fink M.
Published: July 2002

A new acoustic technique using the double time-reversal mirrors system and based on geometrical acoustics, is used to study a vortical flow. The interaction between the sound and a vortex is described in details. This technique has been applied to the study of a stretched vortex. This vortex is generated by stretching the vorticity of a boundary layer in a low velocity water channel. It is shown that the velocity field can be reconstructed from the phase distortion of an ultrasonic wave. The technique gives access to a complete characterization of the vortex dynamics, such as the temporal evolution of its size, its circulation and its position.
Rotation shear induced fluctuation decorrelation in a toroidal plasma
Authors: Hahm T. S.
Published: July 2002

The enhanced decorrelation of fluctuations by the combined effects of the E×B flow (VE) shear, the parallel flow (V∥) shear, and the magnetic shear is studied in toroidal geometry. A two-point nonlinear analysis previously utilized in a cylindrical model [Phys. Fluids B 2, 1 (1990)] shows that the reduction of the radial correlation length below its ambient turbulence value (Δr0) is characterized by the ratio between the shearing rate ωs and the ambient turbulence scattering rate ΔωT. The derived shearing rate is given by ω2s= (Δr0)2[(1/Δφ2){(∂/∂r)(qVE/r)}2 +(1/Δη2){(∂/∂r)(V∥/qR)}2], where Δφ and Δη are the correlation angles of the ambient turbulence along the toroidal and parallel directions. This result deviates significantly from the cylindrical result for high magnetic shear or for ballooning-like fluctuations. For suppression of flute-like fluctuations, only the radial shear of qVE/r contributes, and the radial shear of V∥/qR is irrelevant regardless of the plasma rotation direction.
Electrostatic sheath at the boundary of a dusty plasma
Authors: Ma Jin-Xiu , Yu M. Y.
Published: July 2002

The effect of massive charged dust grains on plasma–wall interaction is investigated using the electrostatic probe model for the dust charging process. It is shown that the dust grains can have a substantial effect on the behavior of the electrostatic potential and particle densities near the wall.
Nonlinear mean field electrodynamics of turbulent dynamos
Authors: Gruzinov A. V. , Diamond P. H.
Published: July 2002

Mean field electrodynamics of turbulent dynamos taking into account Lorentz forces of the generated magnetic fields is derived and studied. Small-scale magnetic fields that are much stronger than the mean field B0 modify the fluid turbulence in such a way as to suppress the α effect: α=α0(1+R)−1, where α0 is the kinematic value, and the reduction factor is proportional to the magnetic Reynolds number Rm, R=RmB20/(4πρv2), and v is the characteristic turbulent velocity. In two dimensions the analog is turbulent magnetic diffusivity suppression. Suppression becomes noticeable at very low values of the mean magnetic field, B20∼ρv2/Rm. The modification of turbulence by the small-scale magnetic fields is discussed.
Effects of E×B velocity shear and magnetic shear on turbulence and transport in magnetic confinement devices
Authors: Burrell K. H.
Published: July 2002

One of the scientific success stories of fusion research over the past decade is the development of the E×B shear stabilization model to explain the formation of transport barriers in magnetic confinement devices. This model was originally developed to explain the transport barrier formed at the plasma edge in tokamaks after the L (low) to H (high) transition. This concept has the universality needed to explain the edge transport barriers seen in limiter and divertor tokamaks, stellarators, and mirror machines. More recently, this model has been applied to explain the further confinement improvement from H (high) mode to VH (very high) mode seen in some tokamaks, where the edge transport barrier becomes wider. Most recently, this paradigm has been applied to the core transport barriers formed in plasmas with negative or low magnetic shear in the plasma core. These examples of confinement improvement are of considerable physical interest; it is not often that a system self-organizes to a higher energy state with reduced turbulence and transport when an additional source of free energy is applied to it. The transport decrease that is associated with E×B velocity shear effects also has significant practical consequences for fusion research. The fundamental physics involved in transport reduction is the effect of E×B shear on the growth, radial extent, and phase correlation of turbulent eddies in the plasma. The same fundamental transport reduction process can be operational in various portions of the plasma because there are a number of ways to change the radial electric field Er. An important theme in this area is the synergistic effect of E×B velocity shear and magnetic shear. Although the E×B velocity shear appears to have an effect on broader classes of microturbulence, magnetic shear can mitigate some potentially harmful effects of E×B velocity shear and facilitate turbulence stabilization. Considerable experimental work has been done to test this picture of E×B velocity shear effects on turbulence; the experimental results are generally consistent with the basic theoretical models.
Complex magnetohydrodynamic bow shock topology in field-aligned low-β flow around a perfectly conducting cylinder
Authors: De Sterck H. , Low B. C. , Poedts S.
Published: July 2002

Two-dimensional ideal magnetohydrodynamic (MHD) simulations are presented that demonstrate several novel phenomena in MHD shock formation. The stationary symmetrical flow of a uniform, planar, field-aligned, low-β and superfast magnetized plasma around a perfectly conducting cylinder is calculated. The velocity of the incoming flow is chosen such that the formation of fast switch-on shocks is possible. Using a time marching procedure, a stationary bow shock is obtained, composed of two consecutive interacting shock fronts. The leading shock front has a dimpled shape and is composed of fast, intermediate and hydrodynamic shock parts. A second shock front follows the leading front. Additional intermediate shocks and tangential discontinuities are present in the downstream part of the flow. The intermediate shocks are of the 1–3, 1–4, 2–4 and 1=2–3=4 types. This is a confirmation in two dimensions of recent results on the admissibility of these types of shocks. Recently it has also been shown that the 1=2–3=4 shock, embedded in a double compound wave, is present in the analytical solution of some planar one-dimensional MHD Riemann problems. This MHD flow with interacting shocks may have applications for some observed features of fast solar Coronal Mass Ejections and other phenomena in low-β space plasmas.
Evidence for intermittency in Earth’s plasma sheet and implications for self-organized criticality
Authors: Angelopoulos V. , Mukai T. , Kokubun S.
Published: July 2002

It has been proposed recently that a description of the magnetosphere as a system in a state of self-organized criticality would be fruitful for understanding (and predicting) the global response to solar wind input. In this paper it is shown that the proposed description fits the characteristics of magnetotail plasma flows and their variability. According to observations, the magnetotail is in a bi-modal state: nearly stagnant, except when driven turbulent by transport-efficient fast flows. The distributions of flows are in agreement with sporadic (intermittent) variability in the magnetotail. The variability may resemble hydrodynamic turbulence around a jet. The presence of turbulence alters the conductivity and the mass/momentum diffusion properties across the plasma sheet and may permit cross-scale coupling of localized jets into a global perturbation. Bursty-flow-driven turbulence is a physical process that may have an important role to play in the establishment of a state of self-organized criticality.
Electron density measurements of electron beam pumped XeCl laser mixtures
Authors: Kimura W. D. , Guyer Dean R. , Moody S. E. , Seamans J. F. , Ford D. H.
Published: July 2002

Time-dependent electron density measurements of electron beam pumped XeCl laser mixtures (nonlasing) are performed using a CO2 (10.6 μm) quadrature interferometer. The electron beam pulse length is ≊500 ns (full width at half-maximum) and delivers ≳10 A/cm2 at the foil. Electron densities are measured as a function of the halogen (HCl) and xenon concentration. For a 99.3% Ne/1.5% Xe/0.16% HCl mixture at 3000 Torr, the electron density peaks near the beginning of the pulse at ≊7×1014 cm−3, decreases to 3×1014 cm−3, then gradually increases to ≊6×1014 cm−3 at the end of the pulse. As the initial halogen concentration is reduced, the electron density increases, rising dramatically near the end of the pulse. This increase in the electron density later in the pulse is accompanied by a decrease of the XeCl* sidelight fluorescence.
Interface traps and P
b centers in oxidized (100) silicon wafers
Authors: Gerardi Gary J. , Poindexter Edward H. , Caplan Philip J. , Johnson Noble M.
Published: July 2002

The band-gap energy distribution of Pb centers on oxidized (100) Si wafers has been determined and compared with interface electrical trap density Dit. Two different Pb centers are observed on (100) Si: Pb0, which has the structure ⋅Si≡Si3, and is essentially identical to the sole Pb center observed on (111) Si; and Pb1, of presently uncertain identity, but clearly different in nature from Pb0. By electric field-controlled electron paramagnetic resonance (EPR) and capacitance-voltage (C-V) measurements, it is found that Pb0 has its (0↔1) electron transition at Ev+0.3 eV and its (1↔2) transition at Ev+0.85 eV. Similarly, Pb1 has its (0↔1) transition at Ev+0.45 eV and its (1↔2) transition at Ev+0.8 eV. The Pb band-gap density correlates qualitatively and quantitatively with the electrical trap density Dit from C-V analysis; nonbonded Pb orbitals are found to be the source of about 50% of the characteristic traps in dry-oxidized, unannealed (100) Si wafers.
New type cryogenic thermometer using sputtered Zr-N films
Authors: Yotsuya Tsutom , Yoshitake Masaaki , Yamamoto Junya
Published: July 2002

A new type thin-film thermometer using sputtered Zr-N films especially for cryogenic temperature range has been developed. Zr-N thermometers have high sensitivity in a wide temperature region from 300 to 2 K or even lower, and have a response quick enough to detect the second sound in superfluid helium. It is found that the developed thermometers are insensitive to magnetic field. Temperature error induced by application of magnetic field up to 6 T is only less than 4.5 mK at 4.2 K.
Experimental determination of the nanocrystalline volume fraction in silicon thin films from Raman spectroscopy
Authors: Bustarret E. , Hachicha M. A. , Brunel M.
Published: July 2002

The effect of crystallite sizes L smaller than 100 nm on the integrated Raman cross section Σc of the transverse optical (TO) mode of fcc silicon was studied experimentally in fully nanocrystallized thin films. The Σc/Σa (amorphous) ratio of this mode is shown to be 1 up to L=30 Å, and to decay exponentially down to 0.1 at larger L. A systematic procedure taking into account both this effect and the experimental optical absorption coefficient αexp at the excitation wavelength is then proposed for the determination of the crystalline volume fraction in mixed phase (amorphous/nanocrystalline) silicon systems by Raman measurements.
Regulation of starvation- and virus-induced autophagy by the eIF2α kinase signaling pathway
Authors: Tallóczy Zsolt , Jiang Wenxia , Virgin Herbert W. , Leib David A. , Scheuner Donalyn , Kaufman Randal J. , Eskelinen Eeva-Liisa , Levine Beth
Published: July 2002

The eIF2α kinases are a family of evolutionarily conserved
serine/threonine kinases that regulate stress-induced translational
arrest. Here, we demonstrate that the yeast eIF2α kinase,
GCN2
, the target phosphorylation site of Gcn2p, Ser-51
of eIF2α, and the eIF2α-regulated transcriptional transactivator,
GCN4
, are essential for another fundamental stress
response, starvation-induced autophagy. The mammalian
IFN-inducible eIF2α kinase, PKR, rescues starvation-induced
autophagy in
GCN2
-disrupted yeast, and
pkr
null and Ser-51 nonphosphorylatable mutant eIF2α
murine embryonic fibroblasts are defective in autophagy triggered by
herpes simplex virus infection. Furthermore, PKR and eIF2α
Ser-51-dependent autophagy is antagonized by the herpes simplex virus
neurovirulence protein, ICP34.5. Thus, autophagy is a novel
evolutionarily conserved function of the eIF2α kinase pathway that is
targeted by viral virulence gene products.
Nitrogen availability alters the expression of carnivory in the northern pitcher plant,
Sarracenia
purpurea
Authors: Ellison Aaron M. , Gotelli Nicholas J.
Published: July 2002

Atmospheric transport and deposition of nutrients, especially nitrogen, is a global environmental problem with well-documented consequences for ecosystem dynamics. However, monitoring nitrogen deposition is relatively expensive, monitoring stations are widely spaced, and estimates and predicted impacts of nitrogen deposition are currently derived from spatial modeling and interpolation of limited data. Ombrotrophic (“rain-fed”) bogs are nutrient-poor ecosystems that are especially sensitive to increasing nutrient input, and carnivorous plants, which are characteristic of these widespread ecosystem types, may be especially sensitive indicators of N deposition. Botanical carnivory is thought to have evolved in nutrient-poor and well-lit habitats such as bogs because the marginal benefits accruing from carnivory exceed the marginal photosynthetic costs associated with the maintenance of carnivorous organs. However, the production of carnivorous organs can be a phenotypically plastic trait. The northern pitcher plant,
Sarracenia purpurea,
produces leaves specialized for prey capture and nutrient uptake (pitchers) and leaves that are more efficient at photosynthesis (phyllodia). We hypothesized that relative allocation to these two types of leaves reflects ambient nitrogen availability. We manipulated nutrient availability to plants with leaf enrichment and whole-plot fertilization experiments. Increased nitrogen, but not phosphorus, reduced production of pitchers relative to phyllodia; this result provided empirical support for the cost–benefit model of the evolution of botanical carnivory. Because this phenotypic shift in leaf production occurs in ecological time, our results suggest that
S. purpurea
could be a reliable and inexpensive biological indicator of nitrogen deposition rates. This suggestion is supported by field observations across a geographic gradient of nitrogen deposition.
mda-5: An interferon-inducible putative RNA helicase with double-stranded RNA-dependent ATPase activity and melanoma growth-suppressive properties
Authors: Kang Dong-chul , Gopalkrishnan Rahul V. , Wu Qingping , Jankowsky Eckhard , Pyle Anna Marie , Fisher Paul B.
Published: July 2002

Human melanoma cells can be reprogrammed to terminally differentiate and irreversibly lose proliferative capacity by appropriate pharmacological manipulation. Subtraction hybridization identified melanoma differentiation-associated gene-5 (mda-5) as a gene induced during differentiation, cancer reversion, and programmed cell death (apoptosis). This gene contains both a caspase recruitment domain and putative DExH group RNA helicase domains. Atypical helicase motifs of MDA-5 deviate from consensus sequences but are well conserved in a potentially new group of cloned and hypothetical proteins.mda-5is an early response gene inducible by IFN and tumor necrosis factor-α, responding predominantly to IFN-β. Protein kinase C activation by mezerein further augments mda-5 expression induced by IFN-β. Expression ofmda-5is controlled transcriptionally by IFN-β, and the MDA-5 protein localizes in the cytoplasm.mda-5displays RNA-dependent ATPase activity, and ectopic expression ofmda-5in human melanoma cells inhibits colony formation. In these contexts,mda-5may function as a mediator of IFN-induced growth inhibition and/or apoptosis. MDA-5 is a double-stranded RNA-dependent ATPase that contains both a caspase recruitment domain and RNA helicase motifs, with a confirmed association with growth and differentiation in human melanoma cells.
Arsenite-induced Cdc25C degradation is through the KEN-box and ubiquitin–proteasome pathway
Authors: Chen Fei , Zhang Zhuo , Bower Jacquelyn , Lu Yongju , Leonard Stephen S. , Ding Min , Castranova Vince , Piwnica-Worms Helen , Shi Xianglin
Published: July 2002

Arsenite is a known human carcinogen that induces tumorigenesis through either a genotoxic or an epigenetic mechanism. In this study, the effect of arsenite on cell cycle regulation and the mechanisms that contribute to this effect were investigated. Treatment of the cells with arsenite suppressed cell proliferation and reduced cell viability in a dose- or time-dependent manner. Analysis of cell cycle profile and cell cycle regulatory proteins indicated that arsenite arrested the cell cycle at G
2
/M phase, partially through induction of cell division cycle 25 (Cdc25) isoform C (Cdc25C) degradation via ubiquitin–proteasome pathways. Mutation of the putative KEN box within the region 151 to 157 of human Cdc25C or treatment of the cells with a peptide competitor encompassing the KEN box partially inhibited arsenite-induced ubiquitination of Cdc25C. Thus, these results indicate that the regulated ubiquitination of Cdc25C may be involved in the arsenite-induced proteolytic down-regulation of Cdc25C activity in the G
2
/M phase of the cell cycle and suggest a link between cell cycle and the carcinogenic effects of arsenite.
Isotope-labeled immunoassays without radiation waste
Authors: Shan Guomin , Huang Wei , Gee Shirley J. , Buchholz Bruce A. , Vogel John S. , Hammock Bruce D.
Published: July 2002

The practice of immunoassay has experienced a widespread transition
from radioisotopic labeling to nonisotopic labeling over the last two
decades. Radioisotope labels have drawbacks that hamper their
applications: (
i
) perceived radiation hazards of
reagents, (
ii
) regulatory requirements and disposal
problems of working with radioactive materials, and
(
iii
) short shelf-life of the labeled
reagents. The advantage of isotopic labeling is the incorporation into
analytes without altering structure or reactivity, as is often the case
with ELISA or fluorescent detection systems. We developed a format for
isotope label immunoassay with the long-life isotope
14
C as
the label and accelerator mass spectrometer (AMS) as the detection
system. AMS quantifies attomole levels of several isotopes, including
14
C. With this exquisite sensitivity, the sensitivity of an
immunoassay is limited by the
K
d
of the
antibody and not the detection system. The detection limit of the
assays for atrazine and
2,3,7,8-tetrachlorodibenzo-
p
-dioxin was 2.0 ×
10
−10
M and 2.0 × 10
−11
M,
respectively, approximately an order of magnitude below the standard
enzyme immunoassay. Notably, <1 dpm (0.45 pCi) of
14
C-labeled compound was used in each assay, which is well
below the limit of disposal (50 nCi per g) as nonradioactive waste.
Thus, endogenous reporter ligands quantified by AMS provide
the advantages of an RIA without the associated problems of radioactive
waste.
Predominant role of endothelial nitric oxide synthase in vascular endothelial growth factor-induced angiogenesis and vascular permeability
Authors: Fukumura Dai , Gohongi Takeshi , Kadambi Ananth , Izumi Yotaro , Ang Jennifer , Yun Chae-Ok , Buerk Donald G. , Huang Paul L. , Jain Rakesh K.
Published: July 2002

Nitric oxide (NO) plays a critical role in vascular endothelial
growth factor (VEGF)-induced angiogenesis and vascular
hyperpermeability. However, the relative contribution of different NO
synthase (NOS) isoforms to these processes is not known. Here, we
evaluated the relative contributions of endothelial and inducible NOS
(eNOS and iNOS, respectively) to angiogenesis and permeability of
VEGF-induced angiogenic vessels. The contribution of eNOS was assessed
by using an
eNOS-
deficient mouse, and iNOS contribution
was assessed by using a selective inhibitor
[
l
-
N
6
-(1-iminoethyl) lysine,
l
-NIL] and an
iNOS-
deficient mouse.
Angiogenesis was induced by VEGF in type I collagen gels placed in the
mouse cranial window. Angiogenesis, vessel diameter, blood flow rate,
and vascular permeability were proportional to NO levels measured with
microelectrodes: Wild-type (WT) ≥ WT with
l
-NIL or
iNOS
−/−
>
eNOS
−/−
≥
eNOS
−/−
with
l
-NIL. The role
of NOS in VEGF-induced acute vascular permeability increase in
quiescent vessels also was determined by using
eNOS-
and
iNOS-
deficient mice. VEGF superfusion significantly
increased permeability in both WT and
iNOS
−/−
mice but not in
eNOS
−/−
mice. These findings suggest that
eNOS plays a predominant role in VEGF-induced angiogenesis and vascular
permeability. Thus, selective modulation of eNOS activity is a
promising strategy for altering angiogenesis and vascular permeability
in vivo
.
IL-4 inhibits osteoclast formation through a direct action on osteoclast precursors via peroxisome proliferator-activated receptor γ1
Authors: Bendixen Amy C. , Shevde Nirupama K. , Dienger Krista M. , Willson Timothy M. , Funk Colin D. , Pike J. Wesley
Published: July 2002

IL-4 is a pleiotropic immune cytokine secreted by activated TH2 cells that inhibits bone resorption bothin vitroandin vivo. The cellular targets of IL-4 action as well as its intracellular mechanism of action remain to be determined. We show here that IL-4 inhibits receptor activator of NF-κB ligand-induced osteoclast differentiation through an action on osteoclast precursors that is independent of stromal cells. Interestingly, this inhibitory effect can be mimicked by both natural as well as synthetic peroxisome proliferator-activated receptor γ1 (PPARγ1) ligands and can be blocked by the irreversible PPARγ antagonist GW 9662. These findings suggest that the actions of IL-4 on osteoclast differentiation are mediated by PPARγ1, an interpretation strengthened by the observation that IL-4 can activate a PPARγ1-sensitive luciferase reporter gene in RAW264.7 cells. We also show that inhibitors of enzymes such as 12/15-lipoxygenase and the cyclooxygenases that produce known PPARγ1 ligands do not abrogate the IL-4 effect. These findings, together with the observation that bone marrow cells from 12/15-lipoxygenase-deficient mice retain sensitivity to IL-4, suggest that the cytokine may induce novel PPARγ1 ligands. Our results reveal that PPARγ1 plays an important role in the suppression of osteoclast formation by IL-4 and may explain the beneficial effects of the thiazolidinedione class of PPARγ1 ligands on bone loss in diabetic patients.
Programmed cell death mediated by
ced-3
and
ced-4
protects
Caenorhabditis elegans
from
Salmonella typhimurium
-mediated killing
Authors: Aballay Alejandro , Ausubel Frederick M.
Published: July 2002

Programmed cell death (PCD) in mammals has been implicated in
several disease states including cancer, autoimmune disease, and
neurodegenerative disease. In
Caenorhabditis
elegans
, PCD is a normal component of development. We find that
Salmonella typhimurium
colonization of the
C.
elegans
intestine leads to an increased level of cell death in
the worm gonad.
S. typhimurium
-mediated germ-line cell
death is not observed in
C. elegans ced-3
and
ced-4
mutants in which developmentally regulated cell
death is blocked, and
ced-3
and
ced-4
mutants are hypersensitive to
S. typhimurium
-mediated
killing. These results suggest that PCD may be involved in the
C. elegans
defense response to pathogen attack.
An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated β-sheet structure for amyloid
Authors: Balbirnie Melinda , Grothe Robert , Eisenberg David S.
Published: July 2002

X-ray diffraction and other biophysical tools reveal features of
the atomic structure of an amyloid-like crystal. Sup35, a prion-like
protein in yeast, forms fibrillar amyloid assemblies intrinsic to its
prion function. We have identified a polar peptide from the N-terminal
prion-determining domain of Sup35 that exhibits the amyloid properties
of full-length Sup35, including cooperative kinetics of aggregation,
fibril formation, binding of the dye Congo red, and the characteristic
cross-β x-ray diffraction pattern. Microcrystals of this peptide also
share the principal properties of the fibrillar amyloid, including a
highly stable, β-sheet-rich structure and the binding of Congo red.
The x-ray powder pattern of the microcrystals, extending to 0.9-Å
resolution, yields the unit cell dimensions of the well-ordered
structure. These dimensions restrict possible atomic models of this
amyloid-like structure and demonstrate that it forms packed,
parallel-stranded β-sheets. The unusually high density of the
crystals shows that the packed β-sheets are dehydrated, despite the
polar character of the side chains. These results suggest that amyloid
is a highly intermolecularly bonded, dehydrated array of densely packed
β-sheets. This dry β-sheet could form as Sup35 partially unfolds to
expose the peptide, permitting it to hydrogen-bond to the same peptide
of other Sup35 molecules. The implication is that amyloid-forming units
may be short segments of proteins, exposed for interactions by partial
unfolding.
Targeting protein inactivation through an oligomerization chain reaction
Authors: Contegno Francesco , Cioce Mario , Pelicci Pier Giuseppe , Minucci Saverio
Published: July 2002

A general strategy for inactivation of target proteins is presented, which we have termed “oligomerization chain reaction.” This technique is based on the fusion of the self-associating coiled-coil (CC) domain of the nuclear factor promyelocytic leukemia (PML) to target proteins that are able to self-associate naturally. Oligomerization through the CC region of promyelocytic leukemia, and through the natural self-associating domain, triggers the oligomerization chain reaction, leading to formation of large molecular weight complexes and functional inactivation of the target. As a test case, we have chosen the oncosuppressor p53, naturally occurring as a tetramer. Fusion of the CC to p53 leads to formation of stable high molecular weight complexes—as shown by size exclusion chromatography—to which wild-type p53 is recruited with high efficiency. CC-p53 chimeras delocalize wild-type p53 to the cytoplasm and inhibit its transcriptional regulatory properties, resulting in a loss of p53 function. We propose that this strategy may be of general application to self-associating factors and represent a complementary approach to currently used functional inactivation-based strategies.