bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear bound on unstable field energy in relativistic electron beams and plasmas
Authors: Davidson Ronald C. , Yoon Peter H.
Published: July 2002

This paper makes use of Fowler’s method [J. Math Phys. 4, 559 (1963)] to determine the nonlinear thermodynamic bound on field energy in unstable plasmas or electron beams in which the electrons are relativistic. Treating the electrons as the only active plasma component, the nonlinear Vlasov–Maxwell equations and the associated global conservation constraints are used to calculate the lowest upper bound on the field energy [ΔℰF]max that can evolve for the general initial electron distribution function fb 0≡fb(x,p,0). The results are applied to three choices of the initial distribution function  fb 0. Two of the distribution functions have an inverted population in momentum p⊥ perpendicular to the magnetic field B0êz, and the third distribution function reduces to a bi-Maxwellian in the nonrelativistic limit. The lowest upper bound on the efficiency of radiation generation, ηmax=[ΔℰF]max/[V−1∫d3x∫ d3p(γ−1)mc2fb 0], is calculated numerically over a wide range of system parameters for varying degrees of initial anisotropy.
Toroidal studies of sawtooth oscillations in tokamaks
Authors: Aydemir A. Y. , Wiley J. C. , Ross D. W.
Published: July 2002

Tokamak sawtooth oscillations are studied with a nonreduced, fully toroidal, resistive magnetohydrodynamic (MHD) model that includes Ohmic heating, and parallel and perpendicular thermal conductions. Effects of perpendicular transport in producing different types of sawteeth, varying from simple, periodic oscillations to giant sawteeth with temperature modulations of order unity, and compound sawteeth with multiple relaxations, are demonstrated. Some of the recent experimental observations from large tokamaks, such as the fast crash times and a presumed topological anomaly in the x-ray tomography pictures, thought to be inconsistent with the Kadomtsev reconnection model, are examined and possible explanations are offered.
Magnetohydrodynamic modes driven by anomalous electron viscosity and their role in fast sawtooth crashes
Authors: Aydemir A. Y.
Published: July 2002

Dispersion relations are derived for both small- and large-Δ′ modes (m≥2 and m=1 modes, respectively) driven by anomalous electron viscosity. Under the assumption that the anomalous kinematic electron viscosity is comparable to the anomalous electron thermal diffusivity, it is found that the viscous mode typically has a higher growth rate than the corresponding resistive mode. Computational results in cylindrical and toroidal geometries are compared with theory and some nonlinear results for viscous m=1 modes in both circular and D-shaped boundaries are presented and their possible role in fast sawtooth crashes is discussed.
Relativistic effects on microwave reflectometry
Authors: Mazzucato E.
Published: July 2002

A simple formula for tracking the cutoffs of waves in the electron cyclotron range of frequencies is presented for plasmas with electron temperatures similar to those of existing large tokamaks (∼10 keV) and conditions of negligible wave absorption.
A Korteweg–de Vries equation modified by viscosity for waves in a channel of uniform but arbitrary cross section
Authors: Das K. P.
Published: July 2002

A KdV equation modified by viscosity is derived for weakly nonlinear long waves propagating in a channel of uniform but arbitrary cross section. The case of high Reynolds number is considered, and the method of matched asymptotic expansion is employed. The equation derived here is found to be similar to the corresponding equation for a two-dimensional layer of liquid derived by previous authors. The only difference is that the dispersive, nonlinear, and viscous terms are multiplied by constants dependent on the cross section geometry of the channel.
Nernst effect in laser-produced plasmas
Authors: Nishiguchi A. , Yabe T. , Haines M. G.
Published: July 2002

A transverse magnetic field B is found to be convected by the electron heat flux qe because of the Nernst effect, i.e., with a velocity VT(∼2qe/3neTe). The mechanism is clarified by the two-electron-fluid model. In laser-driven ablation the convection is toward the overdense region and B can be amplified by 10–100 times because ∇ ⋅ VT<0, making B/ni almost constant for λmfp>c/ωpe.
Transport of sedimenting Brownian particles in a rotating Poiseuille flow
Authors: Nadim A. , Cox R. G. , Brenner H.
Published: July 2002

Generalized Taylor dispersion theory is used to analyze the convective and diffusive transport of sedimenting colloidal particles occurring within a Poiseuille flow in a horizontal circular pipe that is being rotated slowly about its symmetry axis. Such rigid-body rotation serves to keep the particles permanently in suspension despite their non-neutral buoyancy, thereby preventing deposition of the particles on the cylinder bottom. In the ‘‘large’’ particle limit, where transverse diffusion is small compared with sedimentation, expressions are derived for the mean axial velocity and Taylor dispersivity of the colloidal particles. A novel flow field fractionation (FFF) scheme based thereon is proposed for continuously separating particles of different sizes and/or densities.
Velocity diffusion in two-frequency electron cyclotron resonance heating
Authors: Lichtenberg A. J. , Lieberman M. A. , Howard J. E. , Cohen R. H.
Published: July 2002

Two-frequency electron cyclotron resonance heating (ECRH) is modeled by a four-dimensional mapping derived from the nonrelativistic single particle equations of motion. The model includes changes in parallel energy due to the spatially separate resonance zones. The intrinsic diffusion in parallel energy leads to axial losses in a magnetic trap which can rival those induced by collisions. An analytical model for this process gives a loss rate in good agreement with a numerical simulation. The quasilinear diffusion rate into the loss cone and the rate of Arnold diffusion through the adiabatic barrier are calculated for practical ECRH experiments, and compared with similar effects arising from interparticle collisions.
The Korteweg–de Vries equation modified by viscosity for waves in a two-layer fluid in a channel of arbitrary cross section
Authors: Das K. P. , Chakrabarti J.
Published: July 2002

Using a two-layer fluid model, Korteweg–de Vries (KdV) equations modified by viscosity are derived that describe weakly nonlinear long waves propagating along a channel of uniform but arbitrary cross section. Equations are deduced for both surface waves and internal waves. The case of high Reynolds number is considered, and the method of matched asymptotic expansion is employed. The coefficients of the KdV equation, which depend on the geometry of the channel cross section, are determined exactly for a rectangular cross section. Some particular cases including the Boussinesq limit are considered.
Two-dimensional features of virtual cathode and microwave emission
Authors: Woo Wee-yong
Published: July 2002

A two-dimensional model for the electron flow in the presence of a virtual cathode is presented. The model allows for electron reflexing and velocity distribution spread. Solutions with substantial radial flow agree closely with high-power microwave emission observed in experiments. The radial motion is the result of the self-magnetic field of the beam, which bends some of the electrons from propagating to side walls to reflex between real and virtual cathodes. The resulting plasma frequency solution agrees with the measured microwave frequency, which scales linearly with the diode current instead of the square-root scaling for a one-dimensional flow. Scaling laws are derived and agree with experimental measurements.
An analytic theory and formulation of a local magnetohydrodynamic lattice gas model
Authors: Chen H. , Matthaeus W. H. , Klein L. W.
Published: July 2002

A theoretical description of the newly developed magnetohydrodynamic lattice gas model [Phys. Rev. Lett. 58, 1845 (1987)] is presented. The model is a direct extension of the lattice gas model for incompressible Navier–Stokes fluids. [Phys. Rev. Lett. 56, 1506 (1986)]. In the present model the magnetic force and the magnetic induction effects are formulated with local microscopic dynamical rules only, using a bidirectional random walk process. The development of the theory strongly emphasizes the symmetries connecting the microscopic and macroscopic physics. A preliminary numerical test is described.
Nonlinear unstable viscous fingers in Hele–Shaw flows. I. Experiments
Authors: Kopf-Sill Anne R. , Homsy G. M.
Published: July 2002

Post-instability viscous fingering in rectilinear flow in a Hele–Shaw cell has been studied experimentally. Of particular interest was the characterization of the range of length scales associated with tip splitting, over a reasonably wide range of parameters. A digital imaging system was used to record the patterns as a function of time, which allowed properties such as the tip velocity, finger width, perimeter, and area to be studied as functions of time and capillary number. The tip velocity was observed to be approximately constant regardless of the occurrence of splitting events, and the average finger width decreased as the degree of supercriticality increased. Quantitative measures of the fact that there is a limit to the complexity of viscous fingers are provided, and that over the range of parameters studied, no evidence for fractal fingering exists. A discussion of the dynamics of tip splitting explains why this is so.
Plasmoid propagation in a transverse magnetic field and in a magnetized plasma
Authors: Wessel F. J. , Hong R. , Song J. , Fisher A. , Rostoker N. , Ron A. , Li R. , Fan R. Y.
Published: July 2002

The propagation of plasmoids (neutralized ion beams) in a vacuum transverse-magnetic field has been studied in the University of California, Irvine laboratory for several years [Phys. Fluids 24, 739 (1981); 25, 730, 2353 (1982); 26, 2276 (1983); J. Appl. Phys. 64, 73 (1988)]. These experiments have confirmed that the plasmoid propagates by the E×B drift in a low beta and high beta plasmoid beam (0.01<β<300), where β is the ratio of beam kinetic energy to magnetic field energy. The polarization electric field E arises from the opposite deflection of the plasmoid ions and electrons, because of the Lorentz force, and allows the plasmoid to propagate undeflected at essentially the initial plasmoid velocity. In these experiments, plasmoids (150 keV, 5 kA, 50–100 A/cm2, 1 μ sec) were injected into transverse fields of Bt=0–400 G. Anomalously fast penetration of the transverse magnetic field has been observed as in the ‘‘Porcupine’’ experiments [J. Geophys. Res. 91, 10,183 (1987)]. The most recent experiments are aimed at studying the plasmoid propagation dynamics and losses in the presence of a background, magnetized plasma which is intended to short the induced polarization electric field and stop the beam. Background plasma was generated by TiH4 plasma guns fired along Bt to produce a plasma density, np =1012 −1014 cm−3 . Preliminary results indicate that the beam propagation losses increase with the background plasma density; compared to vacuum propagation, roughly a 50% reduction in ion current density was noted 70 cm downstream from the anode for np∼1013 cm−3 . Principal diagnostics include magnetically insulated Faraday cups, floating potential probes, calorimeters, microwave interferometer, and thermal-witness paper.
Thermal nonequilibrium modeling using the direct simulation Monte Carlo method: Application to rotational energy
Authors: Choquet Isabelle
Published: July 2002

Individual probabilities of energy exchange, appearing in the Boltzmann equation, are proposed. They are developed, for a continuous internal energy, to reproduce, on average, the expected relaxation times. The problem consists in linking the required individual probability to the relaxation time to be reproduced. It is stated, for a given collisional model, from the Boltzmann equation collisional kernel. The underlying assumptions are put forward. A new and systematic resolution method, based on the Laplace transformation, is then presented in detail. Illustrations are proposed, within the frame of the direct simulation Monte Carlo method of Bird, investigating two collisional models. The first one is the widely used variable hard sphere model. Next, an original application to the generalized hard sphere model is also performed. Examples of resolutions are carried out studying rotational relaxation. The rotational models previously developed are included in the results obtained. A new hypothesis used to state the problem is discussed in the light of numerical calculations and of a recent mathematical study.
Stability of the lower cusped solitary waves
Authors: Shen Samuel S. , Manohar Ram P. , Gong Lianger
Published: July 2002

In this paper we provide a numerical verification of Malomed’s conjecture [Physica D 32, 393 (1988)]. Among the two cusped solitary waves of a locally forced Korteweg-de Vries equation, the lower one is stable.
A generalization for Parker rotational relaxation model based on variable soft sphere collision model
Authors: Koura Katsuhisa
Published: July 2002

A generalization for the Parker rotational relaxation model is made on the basis of the variable soft sphere collision model. The statistical inelastic cross section model for the Monte Carlo direct simulation of rotational relaxation is modified to reproduce Parker’s rotational collision number for the variable soft sphere model.
The nature of particle contacts in sedimentation
Authors: Zeng Shulin , Kerns Edward T. , Davis Robert H.
Published: July 2002

An experimental study of the contact of a falling sphere with a neutrally buoyant sphere in a viscous fluid is described. The experiments used a mixture of polyalklene glycol and tetrabromoethane as the Newtonian fluid, together with a pair of equal-sized Teflon■ and nylon spheres of 6.355 mm diameter. The spheres have microscopic surface roughness, which allows them to make physical contact when in close approach. This contact breaks the symmetry of the relative trajectory of the two spheres and affects the rate at which the heavy sphere moves past the neutrally buoyant one. The experimental observations verify the roll/slip model of Davis [Phys. Fluids A 4, 2607 (1992)] for the interaction of the two spheres in contact. This model assumes that contact prevents the nominal surfaces from approaching closer than a minimum separation equal to the effective roughness height, and that the tangential component of the contact force is described by solid friction theory. A friction coefficient of 0.28±0.02 provides the best agreement between theory and experiment, with some variation observed when the experiments were repeated for the same and different pairs of spheres.
Retarded motion of bubbles in Hele–Shaw cells
Authors: Maruvada S. R. K. , Park C.-W.
Published: July 2002

The motion of bubbles in a Hele–Shaw cell driven by a surrounding fluid or by gravity has been studied. Assuming that the surrounding fluid wets the solid wall and that the bubble surface is rigid due to the surfactant influence, the translational velocity of an elliptic bubble is estimated. The result indicates that the bubble velocity can decrease by an order of magnitude compared to the prediction of Taylor and Saffman [Q. J. Mech. Appl. Math. 12, 265 (1959)] due to the surfactant influence. The retarded bubble velocity is apparently in reasonable agreement with the experimental observations of Kopf-Sill and Homsy [Phys. Fluids 31, 18 (1988)], suggesting that the puzzling observations by them are likely to be due to the surface active contaminants.
Vibrational favoring effect in DSMC dissociation models
Authors: Wadsworth Dean C. , Wysong Ingrid J.
Published: July 2002

Several common models for dissociation reactions in direct simulation Monte Carlo calculations are analyzed quantitatively under general equilibrium and nonequilibrium conditions. The models differ in the degree to which the internal energy of the colliding particles contributes to the probability of dissociation. Test calculations in an equilibrium bath show that the temperature dependence of the predicted equilibrium rate constant, a commonly used measure of accuracy, is dominated by the collision selection algorithm, rather than the details of the dissociation model, and is thus a poor measure of physical validity or accuracy. The distribution of internal energy states of molecules selected for dissociation under the bath conditions, as used for analysis here, is a preferred means to assess accuracy, and is available qualitatively from existing theory. Recent state-specific quasi-classical trajectory calculations allow for quantitative assessment for certain molecules. Certain singularities present in a recent threshold dissociation model [Phys. Fluids 8, 1293 (1996)] are mediated by recourse to the full threshold equations. Sensitivity studies are performed to show the effect of the details of the numerical implementation. A simple generalization of a Weak Vibrational Bias model [Phys. Fluids 6, 3473 (1994)] is suggested to include rotational favoring. The present analysis provides a means to generate quantitatively a two-temperature rate constant, commonly applied in continuum models, for arbitrary conditions. Calibrated simulations which differ only in the dissociation model are performed for the hypersonic stagnation streamline problem to confirm the order of magnitude decrease in dissociation relative to a standard nonfavored model under conditions of large nonequilibrium.
Large eddy simulation of turbulent front propagation with dynamic subgrid models
Authors: Im Hong G. , Lund Thomas S. , Ferziger Joel H.
Published: July 2002

Dynamic models for large eddy simulation of the G-equation of turbulent premixed combustion are proposed and tested in forced homogeneous isotropic turbulence. The basic idea is to represent the “filtered propagation term” as “propagation of the filtered front at higher speed,” where the enhanced filtered-front speed is modeled. The validity of the linear relation between the turbulent flame speed and turbulence intensity is examined through the use of filtered direct numerical simulation (DNS) data. These tests show a range of scalings from linear to cubic depending on the ratio of the turbulence intensity to flame speed as well as the filter type. Filtered DNS data are also used to evaluate the proposed dynamic model for the turbulent flame speed. It is found that the model is very sensitive to the manner in which the subgrid-scale kinetic energy is estimated. It is also found that accurate predictions of the turbulent flame speed can be obtained provided a good estimate of the subgrid-scale kinetic energy is used. Simulations are also run using the new dynamic model and the results are shown to compare well with DNS results.
Short-wavelength instabilities of waves in rotating stratified fluids
Authors: Miyazaki Takeshi , Adachi Kei
Published: July 2002

Standing and propagating plane waves in a rigidly rotating stably stratified fluid are considered. Based on a WKB analysis, it is shown numerically that almost all of them are unstable with respect to three-dimensional short-wavelength perturbations. The waves whose wavenumber vector is parallel to the axis of rotation and stratification are stabilized as the Brunt-Väisälä frequency N (normalized by the angular velocity of rigid rotation) increases, whereas the inclined waves are unstable at any N. These instabilities are caused by parametric resonances of low order (first and second) and the instability growth rate is determined theoretically, when the wave amplitude is small.
Near-grid-scale energy transfer and coherent structures in the convective planetary boundary layer
Authors: Lin Ching-Long
Published: July 2002

Coherent structures associated with forward- and backward-scatter energy transfer in the convective planetary boundary layer are studied using large-eddy simulation. A box filter is adopted for calculation of the resolved near-grid-scale stress tensor (Lij), strain-rate tensor (Sij) and dissipation rate (LijSij). Results of conditional sampling at two different heights are presented. The conditional events are resolved dissipation rate and vertical velocity fluctuation. The latter is to distinguish the forward and backward scatter associated with upward and downward motions, respectively. Near the surface, the forward-scatter event with positive vertical velocity fluctuation is physically associated with large-scale elongated updrafts. Therefore, the contribution of spanwise component L22S22 to the resolved dissipation rate is most significant. In the outer layer, the forward-scatter event with positive vertical velocity fluctuation occurs at the top of rising updrafts, consistent with negative S33 and the dominance of L33S33. In like manner, the forward scatter with negative vertical velocity fluctuation is found ahead of downdraft motions where S33 is negative and L33S33 dominates. Near the surface, the off-diagonal component L13S13 becomes dominant as the result of downdraft motions to the surface. For the backward scatter, the vertical diagonal component L33S33 is strongest except near the surface in regions of downward motions where L13S13 tends to be most intense. The strong L33S33 event is embedded within updrafts and is characterized by minimum pressure. Flow visualization suggests that the backward scatter occurs on the upwash side of the vortex where updrafts pass through. It is argued that the diameters of vortices can be effectively increased by nearby updrafts, representing energy transfer from small- to large-scale structures. The backward scatter associated with downward motions near the surface appears to generate small-scale counter-rotating motions, resembling sweeps.
Theory of relativistic backward wave oscillators operating near cutoff
Authors: Miller S. M. , Antonsen T. M. , Levush B. , Bromborsky A. , Abe D. K. , Carmel Y.
Published: July 2002

A numerical model for analyzing backward-wave oscillators (BWOs) operating near the upper edge of the transmission band is presented. The model is used to calculate starting currents for two finite length devices, an X-band BWO (f=8.4 GHz) and a J-band BWO (f=5.5 GHz). The operating frequency and efficiency predicted by the nonlinear numerical simulations are compared with experimental data for each device.
Poloidal asymmetry and gradient drive in core electron density and temperature fluctuations on the Texas Experimental Tokamak-Upgrade
Authors: Watts Christopher , Gandy R. F. , Cima G. , Bravenec R. V. , Ross D. W. , Wootton A. J. , Ouroua A. , Heard J. W. , Crowley T. P. , Schoch P. M. , Brower D. L. , Jiang Y. , Deng B. , Domier C. W. , Luhmann N. C.
Published: July 2002

Electron temperature and density fluctuations are measured in the core of the Texas Experimental Tokamak-Upgrade (TEXT-U) [P. H. Edmonds, E. R. Solano, and A. J. Wootton, in Proceedings of the 15th Symposium on Fusion Technology, Utrecht (Elsevier Science, Amsterdam, 1989), Vol. 1, p. 342] plasma across the poloidal cross section. The high spatial resolution of the heavy-ion beam probe (HIBP) and correlation radiometry of electron cyclotron emission (CRECE) reveal that both the density and temperature fluctuations are strongly poloidally asymmetric. Temperature fluctuation measurements indicate a broadband drift wave feature localized near the plasma equatorial plane on both the high- and low-field sides, which is consistent with density fluctuation measurements by far infrared (FIR) scattering. In contrast, the HIBP observes this feature localized only to the low-field side. Excellent spatial resolution allows us to investigate whether changes in the gradient affect the fluctuation amplitudes. We find that indeed, the temperature fluctuations increase with the electron temperature gradient. Results also link density fluctuations to changes in the density gradient.
Effect of the zero spatial harmonic in a slow electromagnetic wave on operation of relativistic backward-wave oscillators
Authors: Vlasov A. N. , Nusinovich G. S. , Levush B.
Published: July 2002

A linear theory of resonant backward-wave oscillators (BWOs) that takes into account the zero spatial harmonic is developed. It is shown that, depending on the phase shift, this harmonic can either increase or decrease the starting current of the device. The nonlinear theory shows the same effect of the phase shift on the maximum efficiency of the BWO. The numerical analysis of nonstationary processes has also demonstrated the effect of the phase shift on the range of beam current values in which the BWO operates in a steady-state single-frequency regime. The effect of boundary conditions at the cathode end of the slow-wave structure on the phase shift between harmonics is also analyzed.
Pulsed currents carried by whistlers. IX. In situ measurements of currents disrupted by plasma erosion
Authors: Urrutia J. M. , Stenzel R. L.
Published: July 2002

In a magnetized laboratory plasma described in the companion paper [Stenzel and Urrutia, Phys. Plasmas 4, 26 (1997)], a large positive voltage step (V≫kTe/e) is applied to electrodes. The current front propagates in the whistler mode in the parameter regime of electron magnetohydrodynamics. The topology of the current density is that of nested helices. Large transient currents in excess of the electron saturation current can be drawn. A transient radial electric field associated with the current rise, excites a compressional, large amplitude, radially outgoing sound wave, which leaves the current channel depleted of plasma. The current collapses due to the density erosion. Electric field reversal excites a rarefaction wave which leads to a partial density and current recovery. Periodic plasma inflow and outflow cause the current to undergo strong relaxation oscillations at a frequency determined by the electrode diameter and the sound speed. In addition, a broad spectrum of microinstabilities is observed in regions of high current density. For drift velocities approaching the thermal speed, the spectrum extends beyond the ion plasma frequency (ωpi) up to the electron plasma frequency (ωpe). Correlation measurements above ωpi reveal modes propagating along the electron drift at speeds above the sound speed but well below the electron drift speed.
Nonlinear magnetosonic waves in a multi-ion-species plasma
Authors: Boldyrev S.
Published: July 2002

Magnetosonic waves are intensively studied due to their importance in space plasmas and also in fusion plasmas where they are used in particle acceleration and heating experiments. In the present paper, the magnetosonic waves propagating in a multi-ion-species plasma perpendicular to an external magnetic field are investigated. Due to the presence of several ion species, this mode splits into two branches: high- and low-frequency modes. This opens a new channel of nonlinear interactions (between these two modes), and qualitatively changes the picture of turbulence in the long-wave region. Considering the limit of a cold collisionless plasma, a general system describing the propagation of nonlinearly coupled high- and low-frequency waves is derived. This system includes the Korteweg–de Vries (KdV), Boussinesq, and Zakharov equations as limiting cases. Solitary solutions of the system of coupled equations are obtained.
Mode structure of turbulent electron temperature fluctuations in the Texas Experimental Tokamak Upgrade
Authors: Deng B. H. , Brower D. L. , Cima G. , Domier C. W. , Luhmann N. C. , Watts C.
Published: July 2002

High spatial resolution electron cyclotron emission imaging (ECEI) has been employed on TEXT-U [Texas Experimental Tokamak Upgrade, G. Cima et al., Phys. Plasmas 2, 720 (1995)] to measure turbulent electron temperature fluctuations using an intensity interferometric technique. With the first dispersion relation measurements in the plasma confinement region, a broadband spectral feature is identified at poloidal wave numbers consistent with expectations for electron drift waves.
Irradiation uniformity for high-compression laser-fusion experiments
Authors: Skupsky S. , Craxton R. S.
Published: July 2002

High-compression direct-drive laser-fusion experiments require the rms laser-irradiation nonuniformity to be below the 1%–2% level. The combination of two-dimensional smoothing by spectral dispersion (SSD), phase plates, polarization smoothing, and beam overlap are shown to be sufficient to reach this goal. Here is presented a discussion of the mathematical formalism of two-dimensional SSD with numerical calculations illustrating the factors that affect irradiation uniformity. The levels of uniformity that can be achieved on the OMEGA laser [T. R. Boehly et al., Opt. Commun. 133, 495 (1997)] at the University of Rochester and at the National Ignition Facility (NIF) [Paisner et al., Laser Focus World 30, 75 (1994)] being built at the Lawrence Livermore National Laboratory are examined.
Noninductive current profile broadening by electric and magnetic fluctuations
Authors: Rax J. M. , Robiche J. , Kostyukov I.
Published: July 2002

The relativistic stochastic kinetic equations describing noninductive current generation in the presence of generic low frequency electric and magnetic turbulent fields is analyzed. The limitations of previous phenomenological models based on local diffusion are discussed. The difference between electric and magnetic current profile broadening is analyzed. The width of the noninductive current channel is calculated as a function of the electric and magnetic fields autocorrelations functions.
Quantum kinetic equations for nonideal plasmas: Bound states and ionization kinetics
Authors: Kremp D. , Bornath Th. , Bonitz M. , Kraeft W. D. , Schlanges M.
Published: July 2002

In this paper, nonequilibrium properties of strongly coupled plasmas are considered. Usually, such problems are dealt with using Boltzmann– or Lenard–Balescu-type equations. However, for the application to strongly coupled plasmas, these equations exhibit several shortcomings. So, it is not possible (i), to describe the short time kinetics, (ii), to recover the correct (energy) conservation laws and thermodynamics, and, (iii), to account for the formation or destruction of bound states. Therefore, the kinetics of strongly coupled plasmas is considered starting from the Kadanoff–Baym equations, which are known to overcome the above limitations. This is demonstrated by a numerical solution of the two-time Kadanoff–Baym equations in second Born approximation. To be able to discuss approximations which are physically more interesting, it is advantageous to proceed to the time diagonal Kadanoff–Baym equations. In first order gradient expansion, generalizations of the Boltzmann and of the Lenard–Balescu kinetic equations are derived accounting for the bound state problem, too. Thus, the shortcomings (i)–(iii) mentioned above are overcome. Finally, the kinetic equations are applied to the problem of ionization kinetics.
Alignment of thin films by glancing angle ion bombardment during deposition
Authors: Yu Lock See , Harper James M. E. , Cuomo Jerome J. , Smith David A.
Published: July 2002

Glancing angle ion bombardment during thin-film deposition is shown to have a pronounced alignment effect on crystallographic orientation. Restricted fiber texture is achieved in Nb films deposited at room temperature onto amorphous silica substrates by Ar ion beam sputtering, with simultaneous bombardment by 200 eV Ar+ ions at 20° from glancing angle. The alignment direction corresponds to a channeling direction for the incident ions between (110) planes, for which a low sputtering yield is expected. The degree of alignment is measured as a function of ion/atom arrival rate ratio up to 1.3 Ar+ ions per Nb film atom, and is shown to increase monotonically with the fraction resputtered.
Structure of nonrectangular HgCdTe superlattices grown by laser molecular beam epitaxy
Authors: Cheung J. T. , Cirlin E.-H. , Otsuka N.
Published: July 2002

Laser molecular beam epitaxy offers instantaneous and accurate composition and thickness control that was used successfully to grow HgCdTe-based superlattice structures with rectangular, trapezoidal, triangular, and sawtooth-shaped quantum wells. Their structures were characterized with cross-sectional transmission electron microscopy and low-temperature Auger depth profiling.
Structure determination of micelle-like intermediates in amyloid β-protein fibril assembly by using small angle neutron scattering
Authors: Yong Winnie , Lomakin Aleksey , Kirkitadze Marina D. , Teplow David B. , Chen Sow-Hsin , Benedek George B.
Published: July 2002

Increasing evidence supports the hypothesis that amyloid
β-protein (Aβ) assembly is a key pathogenic feature of Alzheimer's
disease. Thus, understanding the assembly process offers opportunities
for the development of strategies for treating this devastating
disease. In prior studies, Aβ was found to form micelle-like
aggregates under acidic conditions. These structures exhibited an
average observed hydrodynamic radius of 7 nm. They were found to be in
rapid equilibrium with Aβ monomers or low molecular weight oligomers,
and were centers of fibril nucleation. Here the technique of small
angle neutron scattering has been used to determine the structure of
these Aβ micelles. The data reveal that the micellar assemblies
comprise 30–50 Aβ monomers and have elongated geometries. The best
fit of the data to a uniform spherocylinder yields a radius ≈2.4 nm
and cylinder length ≈11 nm. These structure parameters remain
constant over more than a decade in concentration range. The
concentration independence of the length of the cylindrical aggregate
indicates the presence of an internal nonrepetitive structure that
spans the entire length of the Aβ assembly.
Directed molecular evolution of ADP-glucose pyrophosphorylase
Authors: Salamone Peter R. , Kavakli I. Halil , Slattery Casey J. , Okita Thomas W.
Published: July 2002

ADP-glucose pyrophosphorylase catalyzes a rate-limiting reaction in prokaryotic glycogen and plant starch biosynthesis. Despite sharing similar molecular size and catalytic and allosteric regulatory properties, the prokaryotic and higher plant enzymes differ in higher-order protein structure. The bacterial enzyme is encoded by a single gene whose product of
ca
. 50,000 Da assembles into a homotetrameric structure. Although the higher plant enzyme has a similar molecular size, it is made up of a pair of large subunits and a pair of small subunits, encoded by different genes. To identify the basis for the evolution of AGPase function and quaternary structure, a potato small subunit homotetrameric mutant, TG-15, was subjected to iterations of DNA shuffling and screened for enzyme variants with up-regulated catalytic and/or regulatory properties. A glycogen selection/screening regimen of buoyant density gradient centrifugation and iodine vapor colony staining on glucose-containing media was used to increase the stringency of selection. This approach led to the isolation of a population of AGPase small subunit homotetramer enzymes with enhanced affinity toward ATP and increased sensitivity to activator and/or greater resistance to inhibition than TG-15. Several enzymes displayed a shift in effector preference from 3-phosphoglycerate to fructose-6 phosphate or fructose-1,6-bis-phosphate, effectors used by specific bacterial AGPases. Our results suggest that evolution of AGPase, with regard to quaternary structure, allosteric effector selectivity, and effector sensitivity, can occur through the introduction of a few point mutations alone with low-level recombination hastening the process.
clag9
: A cytoadherence gene in
Plasmodium falciparum
essential for binding of parasitized erythrocytes to CD36
Authors: Trenholme Katharine R. , Gardiner Donald L. , Holt Deborah C. , Thomas Elizabeth A. , Cowman Alan F. , Kemp David J.
Published: July 2002

The propensity of isolates of the malaria parasite
Plasmodium falciparum
to delete a segment of chromosome 9 has provided positional information that has allowed us to identify a gene necessary for cytoadherence. It has been termed the cytoadherence-linked asexual gene (
clag9
).
clag9
encodes at least nine exons and is expressed in blood stages. The hydrophobicity profile of the predicted CLAG9 protein identifies up to four transmembrane domains. We show here that targeted gene disruption of
clag
9 ablated cytoadherence to C32 melanoma cells and purified CD36. DNA-induced antibodies to the
clag9
gene product reacted with a polypeptide of 220 kDa in the parental malaria clone but not in clones with a disrupted
clag9
gene.
Altered ubiquitination and stability of aquaporin-1 in hypertonic stress
Authors: Leitch Virginia , Agre Peter , King Landon S.
Published: July 2002

Aquaporin-1 (AQP1) water channel protein expression is increased by
hypertonic stress. The contribution of changes in protein stability to
hypertonic induction of AQP1 have not been described. Incubation of
BALB/c fibroblasts spontaneously expressing AQP1 with proteasome
inhibitors increased AQP1 expression, suggesting basal
proteasome-dependent degradation of the protein. Degradation by the
proteasome is thought to be triggered by polyubiquitination of a target
protein. To determine whether AQP1 is ubiquitinated,
immunoprecipitation with anti-AQP1 antibodies was performed, and the
resultant samples were probed by protein immunoblot for the presence of
ubiquitin. Immunoblots demonstrated ubiquitination of AQP1 under
control conditions that increased after treatment with proteasome
inhibitors (MG132, lactacystin). Exposure of cells to hypertonic medium
for as little as 4 h decreased ubiquitination of AQP1, an effect
that persisted through 24 h in hypertonic medium. Using metabolic
labeling with [
35
S]methionine, the half-life of AQP1
protein under isotonic conditions was found to be <4 h. AQP1 protein
half-life was markedly increased by exposure of cells to hypertonic
medium. These observations provide evidence that aquaporins are a
target for ubiquitination and proteasome-dependent degradation.
Additionally, these studies demonstrate that reduced protein
ubiquitination and increased protein stability lead to increased levels
of AQP1 expression during hypertonic stress.
Mantle cell lymphoma is characterized by inactivation of the
ATM
gene
Authors: Schaffner Claudia , Idler Irina , Stilgenbauer Stephan , Döhner Hartmut , Lichter Peter
Published: July 2002

In mantle cell lymphoma (MCL), the translocation t(11;14) is
considered the cytogenetic hallmark of the disease. Recently, however,
deletion of the chromosomal region 11q22-q23 has been identified as a
frequent event in this type of cancer, indicating the existence of a
pathogenically relevant tumor suppressor gene in this region. The
deleted segment contains the
ATM
(ataxia telangiectasia
mutated) gene.
ATM
is an interesting candidate as a
tumor suppressor gene because constitutive inactivation of the gene
predisposes ataxia telangiectasia patients to lymphoid malignancies. To
assess the potential involvement of the gene in MCL lymphomagenesis, we
performed mutation analysis of
ATM
in 12 sporadic cases
of MCL, 7 of them with a deletion of one
ATM
gene copy,
by using single-strand conformation polymorphism analysis of reverse
transcription–PCR-amplified mRNA and subsequent DNA sequencing. In all
seven cases containing a deletion of one
ATM
allele, a
point mutation in the remaining allele was detected, which resulted in
aberrant transcript splicing, truncation, or alteration of the protein.
In addition, biallelic
ATM
mutations were identified in
two MCLs that did not contain 11q deletions. Interestingly, in three
cases analyzed, the
ATM
mutations detected in the tumor
cells were not present in nonmalignant cells, demonstrating their
somatic rather than germ-line origin. The inactivation of both alleles
of the
ATM
gene by deletion and deleterious point mutation
in the majority of cases analyzed indicates that
ATM
plays a role in the initiation and/or progression of MCL.
Proton shuttle in green fluorescent protein studied by dynamic simulations
Authors: Lill Markus A. , Helms Volkhard
Published: July 2002

As a direct simulation of a multistep proton transfer reaction involving protein residues, the proton relay shuttle between A and I forms of green fluorescent protein (GFP) is simulated in atomic detail by using a special molecular dynamics simulation technique. Electronic excitation of neutral chromophore in wild-type GFP is generally followed by excited-state proton transfer to a nearby glutamic acid residue via a water molecule and a serine residue. Here we show that the second and third transfer steps occur ultrafast on time scales of several tens of femtoseconds. Proton back-shuttle in the ground state is slower and occurs in a different sequence of events. The simulations provide atomic models of various intermediates and yield realistic rate constants for proton transfer events. In particular, we argue that the I form observed spectroscopically under equilibrium conditions may differ from the I form observed as a fast intermediate by an
anti
to
syn
rotation of the carboxyl proton of neutral Glu-222.
Using RNA interference to identify genes required for RNA interference
Authors: Dudley Nathaniel R. , Labbé Jean-Claude , Goldstein Bob
Published: July 2002

RNA interference (RNAi) is a phenomenon in which double-stranded RNA (dsRNA) silences endogenous gene expression. By injecting pools of dsRNAs into
Caenorhabditis elegans
, we identified a dsRNA that acts as a potent suppressor of the RNAi mechanism. We have used coinjection of dsRNAs to identify four additional candidates for genes involved in the RNAi mechanism in
C. elegans
. Three of the genes are
C. elegans mes
genes, some of which encode homologs of the
Drosophila
chromatin-binding Polycomb-group proteins. We have used loss-of-function mutants to confirm a role for
mes-3
,
-4
, and
-6
in RNAi. Interestingly, introducing very low levels of dsRNA can bypass a requirement for these genes in RNAi. The finding that genes predicted to encode proteins that associate with chromatin are involved in RNAi in
C. elegans
raises the possibility that chromatin may play a role in RNAi in animals, as it does in plants.
A signature of the T → R transition in human hemoglobin
Authors: Mihailescu Mihaela-Rita , Russu Irina M.
Published: July 2002

Allosteric effects in hemoglobin arise from the equilibrium between
at least two energetic states of the molecule: a tense state, T, and a
relaxed state, R. The two states differ from each other in the number
and energy of the interactions between hemoglobin subunits. In the T
state, constraints between subunits oppose the structural changes
resulting from ligand binding. In the R state, these constraints are
released, thus enhancing ligand-binding affinity. In the present work,
we report the presence of four sites in hemoglobin that are
structurally stabilized in the R relative to the T state. These sites
are Hisα103(G10) and Hisα122(H5) in each α subunit of hemoglobin.
They are located at the α
1
β
1
and
α
2
β
2
interfaces of the hemoglobin tetramer,
where the histidine side chains form hydrogen bonds with specific
residues from the β chains. We have measured the solvent exchange
rates of side chain protons of Hisα103(G10) and Hisα122(H5) in both
deoxygenated and ligated hemoglobin by NMR spectroscopy. The exchange
rates were found to be higher in the deoxygenated-T than in ligated-R
state. Analysis of exchange rates in terms of the local unfolding model
revealed that the structural stabilization free energy at each of these
two histidines is larger by ≈1.5 kcal/(mol tetramer) in the R
relative to the T state. The location of these histidines at the
intradimeric α
1
β
1
and
α
2
β
2
interfaces also suggests a role for
these interfaces in the allosteric equilibrium of hemoglobin.
Transcription-coupled and DNA damage-dependent ubiquitination of RNA polymerase II
in vitro
Authors: Lee Keng-Boon , Wang Dong , Lippard Stephen J. , Sharp Phillip A.
Published: July 2002

Transcription-coupled repair (TCR) is essential for the rapid, preferential removal of DNA damage in active genes. The large subunit of RNA polymerase (Pol) II is ubiquitinated in cells after UV-irradiation or cisplatin treatment, which induces DNA damage preferentially repaired by TCR. Several human mutations, such as Cockayne syndrome complementation groups A and B, are defective in TCR and incapable of Pol II ubiquitination upon DNA damage. Here we demonstrate a correlation between ubiquitination of RNA Pol II and arrest of transcription
in vitro
. Ubiquitination of Pol II is significantly induced by α-amanitin, an amatoxin that blocks Pol II elongation and causes its degradation in cells. Pol II undergoes similar ubiquitination on DNA containing cisplatin adducts that arrest transcription. Stimulation of ubiquitination requires the addition of template DNA and does not occur in the presence of an antibody to the general transcription factor TFIIB, indicating the transcription dependence of the reaction. We propose that components of the reaction recognize elongating Pol II–DNA complexes arrested by α-amanitin or cisplatin lesions, triggering ubiquitination.
Mice lacking DNA topoisomerase IIIβ develop to maturity but show a reduced mean lifespan
Authors: Kwan Kelvin Y. , Wang James C.
Published: July 2002

Targeted gene disruption in the murine
TOP3β
gene-encoding DNA topoisomerase IIIβ was carried out. In contrast to
the embryonic lethality of mutant mice lacking DNA topoisomerase
IIIα,
top3β
−/−
nulls are viable and
grow to maturity with no apparent defects. Mice lacking DNA
topoisomerase IIIβ have a shorter life expectancy than their
wild-type littermates, however. The mean lifespan of the
top3β
−/−
mice is about 15 months,
whereas that of their wild-type littermates is longer than 2 years.
Mortality of the
top3β
−/−
nulls
appears to correlate with lesions in multiple organs, including
hypertrophy of the spleen and submandibular lymph nodes,
glomerulonephritis, and perivascular infiltrates in various organs.
Because the DNA topoisomerase III isozymes are likely to interact with
helicases of the RecQ family, enzymes that include the determinants of
human Bloom, Werner, and Rothmund–Thomson syndromes, the shortened
lifespan of
top3β
−/−
mice points to
the possibility that the DNA topoisomerase III isozymes might be
involved in the pathogenesis of progeroid syndromes caused by defective
RecQ helicases.
Constitutive activation ofStat5aby retrovirus integration in early pre-B lymphomas of SL/Kh strain mice
Authors: Tsuruyama Tatsuaki , Nakamura Takuro , Jin Guang , Ozeki Munetaka , Yamada Yoshihiro , Hiai Hiroshi
Published: July 2002

We found that the second intron ofStat5awas one of the common integration sites of the endogenous ecotropic murine leukemia virus, i.e.,SL/Kh virus integration-1(Svi1), in early pre-B lymphomas in SL/Kh mice. The high expression of STAT5A induced bySvi1integration and activation accelerated the transcription of its target genes such asc-Myc. Transfection of the constitutively activeStat5amutant cDNA, but not of the wild-type cDNA, to the bone marrow cells induced colony formation of pre-B cells in a methylcellulose medium and escaped from dependence on IL-7. Such growth depended on a genetic factor in the SL/Kh strain. Consitutively high expression of Stat5a either by retrovirus integration or transfection of active mutant cDNA can be lymphomagenic to early pre-B cells in collaboration with a certain genetic background factor of mice.