bluuebunny/crossref_metadata_2025 huggingface dataset:
The observation of singularities in the boundary of patches of constant vorticity
Authors: Buttke Thomas F.
Published: July 2002

The equations of motion describing inviscid fluid flow are solved numerically in two dimensions for the case where the flow can be described by patches of constant vorticity. The case where the vorticity is described initially by two circular patches is studied in detail. The numerical evidence indicates that when the minimum distance between the two patches is initially less than the radius of the patches a singularity forms in finite time on the boundary curves of the patches. The singularity appears to be a jump discontinuity in the tangent vector of the boundary curve.
The control of transient disturbances in a flat plate boundary layer through active wall motion
Authors: Breuer Kenneth S. , Haritonidis Joseph H. , Landahl Marten T.
Published: July 2002

Experimental results are presented demonstrating the evolution and control of a large amplitude and highly three-dimensional disturbance in a laminar boundary layer. A localized disturbance was introduced into a laminar boundary layer at Reδ* =1095 by means of a flexible membrane mounted on a flat plate. For low amplitudes, the disturbance initially decayed, leaving a slowly growing wave packet comprised of linearly unstable Orr–Sommerfeld modes. At higher amplitudes, the disturbance grew rapidly, leading to a turbulent spot. The high-amplitude disturbance was acted upon by an active wall counterdisturbance consisting of a traveling bump at the wall. The counterdisturbance was generated by an array of eight small flexible membranes mounted next to one another, flush with the wall and activated in rapid succession. The breakdown of the disturbance to a turbulent spot is shown to be delayed by the active wall motion by approximately 50δ*. The active wall motion is shown to inhibit the development of the initial disturbance and to decrease the amplification rate of spanwise vorticity by reducing the level of cross-stream stretching ∂w/∂z.
A family of analytical solutions of the motions of double-branched spiral vortex sheets
Authors: Kaneda Yukio
Published: July 2002

A family of analytical solutions is given for the motions of double-branched exponential spiral vortex sheets. The flow field induced by the vortex sheet is unsteady and preserves a self-similar flow pattern; the flow field can be parametrized by two amplitudes and two phases. The family includes as a special case Alexander’s solutions [Phys. Fluids 14, 231 (1971)] for double-branched vortex sheets possessing a certain central symmetry. Two special solutions of the family give exact expressions for time-dependent gravity-free free-surface flows.
Taylor dispersion in the presence of time-periodic convection phenomena. Part II. Transport of transversely oscillating Brownian particles in a plane Poiseuille flow
Authors: Shapiro M. , Brenner H.
Published: July 2002

The general theory of Taylor dispersion phenomena in time-periodic flows, developed in Part I [Phys. Fluids A 2, 1731 (1990)], is used to analyze convective–diffusive transport processes for noninteracting neutrally buoyant Brownian particles suspended in a plane Poiseuille flow within a duct bounded laterally by two parallel plates, and subject to the influence of transverse oscillating forces acting upon the suspended particles. The mean axial particle velocity and Taylor–Aris dispersivity are calculated in the large transverse Peclet number limit (‘‘large particle’’ limit), corresponding to circumstances for which particle transport is dominated by convection over diffusion. Effects arising from the externally imposed oscillatory frequency and amplitude are described in terms of a single dimensionless parameter, one whose magnitude may be manipulated to control the axial solute flux. Increasing the dimensionless oscillation period T̄ significantly decreases the axial dispersivity, whereas the functional dependence of the mean axial particle velocity upon T̄ exhibits a maximum. Physicochemical phenomena arising from the oscillatory force thereby furnish a novel field-flow fractionation (FFF) scheme for separating Brownian particles of different sizes.
Transition from steady to periodic liquid-metal magnetohydrodynamic flow in a sliding electrical contact
Authors: Talmage Gita , Walker John S. , Brown Samuel H. , Sondergaard Neal A.
Published: July 2002

In homopolar motors and generators, large dc electric currents pass through the sliding electrical contacts between rotating copper disks (rotors) and static copper surfaces shrouding the rotor tips (stators). A liquid metal in the small radial gap between the rotor tip and concentric stator surface can provide a low-resistance, low-drag electrical contact. Since there is a strong magnetic field in the region of the electrical contacts, there are large electromagnetic body forces on the liquid metal. The primary, azimuthal motion consists of simple Couette flow, plus an electromagnetically driven flow with large extremes of the azimuthal velocity near the rotor corners. The secondary flow involves the radial and axial velocity components, is driven by the centrifugal force associated with the primary flow, and is opposed by the electromagnetic body force, so that the circulation varies inversely as the square of the magnetic-field strength. Three flow regimes are identified as the angular velocity Ω of the rotor is increased. For small Ω, the primary flow is decoupled from the secondary flow. As Ω increases, the secondary flow begins to convect the azimuthal-velocity peaks radially outward, which in turn changes the centrifugal force driving the secondary flow. At some critical value of Ω, the flow becomes periodic through the coupling of the primary and secondary flows. The azimuthal-velocity peaks begin to move radially in and out with an accompanying oscillation in the secondary-flow strength.
Stability of a Z pinch at the Pease–Braginskii current
Authors: Cochran F. L. , Robson A. E.
Published: July 2002

The stability of a Z pinch carrying the Pease–Braginskii current is examined using a two-dimensional compressible magnetohydrodynamic (MHD) code that includes resistivity and bremsstrahlung. It is found that the growth rate of m=0 perturbations depends upon the Lundquist number S and that the pinch is stable when S is less than about 6 for ka= (1)/(3) and less than about 1 for ka=1, where k is the wave number and a is the pinch radius.
Interaction of impurity ions with a weakly non-Maxwellian simple hydrogenic plasma
Authors: Terry William K.
Published: July 2002

The average acceleration of an ensemble of ‘‘test particles’’ in a plasma is called the ‘‘dynamical friction’’; the average rate at which their velocity vectors spread out in velocity space is expressed in a velocity-space diffusion-rate tensor. These quantities have been derived for impurity ions interacting with a weakly non-Maxwellian simple hydrogenic plasma. The derivation is sketched briefly in this Brief Communication; for details, the reader is referred to a supplementary report (see NTIS Document No. DE88017137).
Electron distribution function in a Lorentz plasma with a time-varying electric field
Authors: Abdel-Gawad H. I.
Published: July 2002

In this paper, the effect of a harmonically varying electric field on the runaway electrons in a Lorentz plasma is studied. It will be shown that runaway electrons are inhibited even for a moderate value of the frequency of the applied electric field, compared with the collision frequency, provided that the magnitude of the field is much smaller than the Dreicer field.
Ballooning transformation
Authors: Newcomb William A.
Published: July 2002

A study is made of the stability against localized perturbations of an idealized toroidal magnetostatic equilibrium. The principal new result is a corrected version of the so-called ‘‘ballooning transformation’’ whereby periodic perturbations of the toroidal system are mapped onto aperiodic perturbations of the corresponding unbounded system.
Simple method for calculating island widths
Authors: Cary John R. , Hanson James D.
Published: July 2002

A simple method for calculating magnetic island widths has been developed. This method uses only that information obtained from integrating along the closed field line at the island center. Thus, this method is computationally less intensive than the usual method of producing surfaces of section of sufficient detail to locate and resolve the island separatrix. This method has been implemented numerically and used to analyze the buss work islands of ATF [Fusion Technol. 10, 179 (1986)]. In this case the method proves to be accurate to at least within 20% even though the islands are within a factor of 2 of overlapping.
Stimulated Brillouin sidescattering from line-focus laser-produced plasmas
Authors: Villeneuve D. M.
Published: July 2002

Stimulated Brillouin sidescattering in line-focus-geometry laser-produced plasmas was investigated with a 532 nm wavelength pump laser at intensities up to 3 × 1013 W/cm2. While sidescattered light was observed, it was less intense than the specularly scattered pump laser light, and less intense than the backscattered Brillouin light. It was not enhanced when using foil targets which became underdense during the pump pulse, nor was it affected by changes in the pump laser polarization.
Generation of electromagnetic radiation from a rotating electron ring in a rippled magnetic field
Authors: Yin Y. Z. , Bekefi G.
Published: July 2002

Calculations show that modes resembling the free-electron laser (FEL) instability are excited when electrons move in quasicircular orbits under the combined action of a uniform axial magnetic field and an azimuthally periodic wiggler magnetic field. In the model, a thin annular ring of rotating electrons is confined in a hollow cylindrical waveguide, or between concentric cylinders comprising a coaxial waveguide, and the dispersion equations for the transverse magnetic (TMlm ) modes are derived and analyzed. Coherent radiation occurs near frequencies ω corresponding to the crossing points of the electromagnetic modes ω=ωc(l,m) and the beam modes ω=(l+N)Ω∥, where ωc and Ω∥ are the waveguide cutoff frequency and the electron cyclotron frequency, respectively, and N is the number of wiggler periods.
A passive scalar field convected by turbulence
Authors: Qian J.
Published: July 2002

Classical statistical mechanics is applied to the study of a passive scalar field convected by isotropic turbulence. A complete set of independent real parameters and dynamic equations are worked out to describe the dynamic state of the passive scalar field. The corresponding Liouville equation is solved by a perturbation method based upon a Langevin–Fokker–Planck model. The closure problem is treated by a variational approach reported in earlier papers. Two integral equations are obtained for two unknown functions: the scalar variance spectrum F(k) and the effective damping coefficient Ω(k). The appearance of the energy spectrum of the velocity field in the two integral equations represents the coupling of the scalar field with the velocity field. As an application of the theory, the two integral equations are solved to derive the inertial-convective-range spectrum, obtaining F(k)=0.61 χε−1/3 k−5/3. Here χ is the dissipation rate of the scalar variance and ε is the dissipation rate of the energy of the velocity field. This theoretical value of the scalar Kolmogorov constant, 0.61, is in good agreement with experiments.
Flute vortices in nonuniform magnetic fields
Authors: Yu M. Y. , Shukla P. K. , Varma R. K.
Published: July 2002

Localized double vortices associated with the flute modes are shown to exist. Special emphasis is given to the effect of the convective variation of the fluid magnetic moment. It is shown that the latter effect considerably modifies the existence regions of the vortices.
A nonlocal analysis of drift and drift-cyclotron waves in cylindrical geometry
Authors: Ferraro R. D. , Sanuki H. , Littlejohn Robert G. , Fried B. D.
Published: July 2002

An analysis of electron drift waves and drift-cyclotron waves has been carried out in cylindrical geometry using a k-space integral equation. The model assumes a low-β electrostatic plasma in a straight magnetic field with a Gaussian density profile. Above the threshold for the drift-cyclotron instability, a complicated spectrum of modes is found, with the fundamental radial eigenmode not necessarily the most unstable. In solving the integral equation, improved computational efficiency is obtained by decomposing the eigenfunctions on an associated Laguerre polynomial basis, a method which works best for low-azimuthal (m<25) and low-radial (n<10) mode numbers.
Kink stability of long ion layers
Authors: Ishida Akio
Published: July 2002

By means of the two-fluid model, the kink stability of a long thin field-reversed ion layer immersed in a dense low-temperature background plasma is studied theoretically. The two-fluid variational quadratic form with the assumption of rigid displacements in the radial direction yields a new kink stability condition that includes the effect of the nonzero real frequency of the modes, which results from the inertia of the ion layer. Although it was neglected in previous analyses, this effect is essential to explain the numerical results of Harned [Phys. Fluids 25, 1915 (1982)]. As the ratio of the density of the background plasma to that of the ion layer increases, this new kink stability condition reduces to the conventional condition. The physical mechanism for the kink instability is discussed by means of an analogy with the electrostatic two-stream instability.
Structure functions in a rotationally dominated turbulent flow
Authors: Mory M. , Hopfinger E. J.
Published: July 2002

Structure functions are presented for the rotationally dominated flow first studied by Hopfinger, Browand, and Gagne [J. Fluid Mech. 125, 505 (1982)]. These were obtained from an image analysis of the streaks traced by neutrally buoyant particles in the fluid. In the first part of the paper the validity of the technique, first proposed by Griffiths and Hopfinger [Deep Sea Res. 31, 245 (1984)], is demonstrated. Results presented in the second part indicate a spectral distribution of energy varying like E1(k)∝k−5/2, where k is the wavenumber. The tendency toward two-dimensionality of the flow and the consequent effect on the energy dissipation rate are confirmed. The discrepancy between the measured spectral distribution and the predicted k−3 law for two-dimensional turbulence is interpreted as a result of the low Reynolds numbers achieved in the experiments.
Transport and modulation of relativistic electron beams by periodic ion channels
Authors: Miller J. D. , Gilgenbach R. M.
Published: July 2002

A theoretical investigation of an intense relativistic electron beam propagating in a periodic ion channel is presented. Analytic expressions for the electric field are found for the case of a cosine modulation of the channel ion density. Two different types of channels are considered: (i) periodic beam-induced ionization channels, and (ii) periodic channels created by an external source. Analytical conditions are derived for the matched radius of the beam and for approximate envelope motion using the ‘‘smooth’’ approximation. Numerical solutions to the envelope equation show that by changing the period or the space-charge neutralization fraction of the channel the beam can be made to focus and diverge or to undergo stable, modulated transport. It is shown that the results are qualitatively similar to previous work concerning periodic magnetic and electrostatic focusing.
Free boundary skin current magnetohydrodynamic equilibria
Authors: Reusch Michael F.
Published: July 2002

Function theoretic methods in the complex plane are used to develop simple parametric hodograph formulas that generate sharp boundary equilibria of arbitrary shape. The related method of Gorenflo [Z. Angew. Math. Phys. 16, 279 (1965)] and Merkel (Ph.D. thesis, University of Munich, 1965) is discussed. A numerical technique for the construction of solutions, based on one of the methods, is presented. A study is made of the bifurcations of an equilibrium of general form.
Cascade model of turbulence
Authors: Qian J.
Published: July 2002

A simple low-order dynamic system is proposed to simulate the energy cascade process of a fully developed hydrodynamic turbulence, and a series of numerical experiments is conducted. The main structural properties of this dynamic system are the same as those of the normalized Navier–Stokes equation. A quick estimation of its first Lyapunov exponent λ1 is made by calculating the chaos index at sampling points on trajectories. The large positive values (20–22) of λ1 indicate that the system is highly chaotic and that it has a strange attractor. After the transient period the dynamic system moves along its strange attractor, and a very wide inertial range is observed, in which the energy flux across the wavenumbers is a constant and equal to the energy dissipation rate. Moreover, the Kolmogorov − (5)/(3) spectrum is obtained as a statistical property of chaotic trajectories along the strange attractor.
A cascade-transport model for turbulent shear flows
Authors: Lewalle Jacques , Tavlarides Lawrence L.
Published: July 2002

A simple model for local spectral resolution in turbulent shear flows is developed. The original cascade model of Desnyanski and Novikov contains time derivatives, spectral transfer, and viscous dissipation terms for shell-averaged turbulent energy. The model is adapted for shear flows by the addition of a convective derivative, a turbulence production term, and a turbulent transport term. Both production and transport are based on a spectral distribution of the eddy viscosity. When integrated over all scales, the model reduces to the κ equation of κ-ε models, whereas in uniform mean flows it reduces to the original cascade model. Calibration of the model constants is achieved based on experimental results for homogeneous shear flow.
Drop-formed vortex rings—The generation of vorticity
Authors: Cresswell R. W. , Morton B. R.
Published: July 2002

Vortex rings are seen to form when dyed water drops strike a water surface and their formation and structure depend on height of fall and surface tension. The assumption that a vortex sheet envelopes the penetrating drop, frequently stated without explanation in the literature, does not explain these factors and this paper shows why it is incorrect. Alternative mechanisms have been proposed in the literature but none explains adequately the vorticity generation or the restriction of vortex ring formation to low Weber numbers. This paper proposes a mechanism based on the generation of vorticity on relaxation of surface stresses at coalescence. The condition that the surface viscous stress be continuous across the water-air interface leads to a boundary condition on vorticity and the total amount of vorticity generated depends on the quantity which can be diffused into the fluid interior from the boundary during coalescence. At low values of Weber number this condition appears to be sufficient to generate enough vorticity to allow flow separation at the surface, such separation being a necessary condition for vortex sheet roll-up and ring production. The existence of a critical Weber number above which vortex rings do not form is the result of a balance between the rate at which the ring of contact moves outward associated with on the one hand, the action of surface tension forces and, on the other, the rate of surface destruction due to the coming together of surfaces. If surface destruction dominates then the fluid elements to which the surface viscous stress boundary condition applies will become part of the fluid interior before diffusion has carried significant vorticity away from the surface.
Large eddy simulation of the proximal region of a spatially developing circular jet
Authors: Olsson M. , Fuchs L.
Published: July 2002

Large eddy simulations (LES) of spatially developing circular jets were carried out. The subgrid scale (SGS) model was of a dynamic type and was based on an assumed asymptotic behaviour of the SGS-stress. This assumption is valid only for adequate spatial and temporal resolutions. The effects of the SGS-model were studied by comparing simulations with and without SGS-model. LES with different spatial resolutions were performed to study the effects of the spatial resolution on the numerical solution. The numerical results were compared with experimental data. Simulations were performed for the Reynolds numbers 1⋅104, 5⋅104 and 50⋅104 to study the Reynolds numbers effects in the proximal region of the jet. The turbulent intensity increases from a low initial level, given by a low amplitude white noise disturbance in the inlet, to a high level in the studied proximal region of the jet. For the lower Reynolds numbers certain amplified frequencies were found, at Strouhal numbers about 0.3 and the corresponding first two harmonics, which agree well with experimental observations. The spatial resolution was found to be adequate to support the longitudinal and transversal Taylor length scales. A new bound for the dynamic model parameter is proposed and it is studied a priori using the computed flow fields. This bound is based on the non-negativity of the total dissipation, i.e. an entropy condition for the sum of viscous-, SGS- and numerical- dissipation, in the discrete transport equation of the resolved scale-energy.
The kinematics of the vortex ring structure generated by a bursting bubble
Authors: Buchholz James H. J. , Sigurdson Lorenz W.
Published: July 2002

The vortex structure created by a bursting bubble has been photographically studied. A vortex model has been constructed, which describes the evolution of the structure, and the phenomenon has been simulated numerically using two two-dimensional vortex blob models. The bubble is situated on a shallow pool of fluid that is on the top face of a vertical cylinder. Two upward-moving vortex rings with colinear axes are formed within 15 ms after bubble rupture. The two rings leapfrog to form a structure consisting of a vortex ring that sheds lobes of fluid that are sometimes similar in appearance to hairpin vortex loops. This evolution occurs within 100 ms of the initiation of bubble rupture, when the ring Reynolds number is approximately 170. The computational model produced images with a close resemblance to the physical structure, and was used to support the theory that the trailing lobes are rotational and consist of the vortex ring that was initially leading.
Non-self-similar behavior of the von Neumann reflection
Authors: Kobayashi S. , Adachi T. , Suzuki T.
Published: July 2002

The purpose of the present paper is to consider the von Neumann reflection (vNR) which takes place for a small incident shock Mach number and a small wedge angle. A series of experiments has been performed with ordinary smooth straight wedges and step-like wedges that simulate the former. The reflection configuration over the step-like wedge has suggested unsteady characteristics of the vNR. Contrary to the established notion of shock reflection phenomena over straight wedges, while the triple point trajectory was approximately a straight line through the apex of the wedge, the vNR showed unsteadiness in the relation between angles of incidence and reflection (ωi,ωr), and thus the flow-field proved to be non-self-similar near the triple point. Based on the measured values, the incident angle for the reflected wave and the Mach number of the flow ahead of the reflected wave were estimated. These values show that the reflected wave is not a Mach wave, but it moves on the (ωi,ωr)-plane almost along a trivial solution. In particular, the flow Mach number ahead of the reflected wave approaches unity, which leads to analytical formulas for angles of incidence and reflection as functions of the incident shock Mach number only. The reflected wave degenerates to a normal Mach wave as the incident shock proceeds. In the case of the vNR, the von Neumann paradox takes place only at an early stage of reflection, and the paradox is resolved later, since the flow properties such as angles of incidence and reflection are given by the trivial solution which is a particular solution for the three-shock theory.
Comment on ‘‘Stability of coupled tearing and twisting modes in tokamaks’’ [Phys. Plasmas 1, 3308 (1994)]
Authors: Li Ding
Published: July 2002

Recently an incorrect dispersion relation (Ref. 2 and 3) was used in a publication by Connor et al. (Ref. 1) for toroidally coupled tearing and twisting modes. The aim of this comment is to pointout how this incorrect assumption affects the derivation of the coupled modes. (AIP)
Response to ‘‘Comment on ‘Stability of coupled tearing and twisting modes in tokamaks’’’ [Phys. Plasmas 1, 3308 (1994)]
Authors: Connor J. W. , Hastie R. J. , Taylor J. B.
Published: July 2002

The authors contend that incorrect inferences are drawn by Ding Li regarding the sources of error and of the basis function method used in the calculations of toroidally coupled tearing modes. (AIP)
A new solution method for the gyrokinetic Fokker-Planck equation
Authors: Tessarotto M. , Gregoratto D. , Zheng L.-J.
Published: July 2002

A new non-perturbative and non-variational solution method is proposed for the gyrokinetic equation, based on a suitable approximation for the linearized Fokker-Planck collision operator. The approach, which allows, in principle, the accurate evaluation of arbitrary moments of the distribution function for a weakly collisional magnetoplasma with toroidal equilibria of arbitrary aspect-ratio, is susceptible of numerous significant applications, both for transport calculations, i.e., in particular, leading to the evaluation of neoclassical fluxes, as well for the investigation of linear stability analyses of dissipative perturbations.
Three-dimensional closed field line magnetohydrodynamic equilibria without symmetries
Authors: Salat A. , Kaiser R.
Published: July 2002

Exact three-dimensional volume current solutions of the magnetohydrodynamic (MHD) equations are presented. The configurations are infinitely extended along a straight axis and have neither cylindrical nor helical nor mirror symmetry. All field lines lie in planes orthogonal to the axis and are closed around it. The surfaces of constant pressure have elliptical cross sections, whose ellipticity and orientation are arbitrary functions along the axis.
Influence of profile shape on the diocotron instability in a non-neutral plasma column
Authors: Davidson Ronald C. , Felice Gian Marco
Published: July 2002

In this paper we examine theoretically the influence of density profile shape on the diocotron instability in a cylindrical, low-density (ωpe2≪ωce2) non-neutral electron plasma column confined radially by a uniform axial magnetic field B0êz. The analysis assumes electrostatic flute perturbations (∂/∂z=0) about an axisymmetric equilibrium density profile ne0(r), where r=(x2+y2)1/2 is the radial distance from the column axis. Two classes of density profiles with inverted population in radius r are considered. These are the following: (a) a step-function density profile with uniform density n̂e⋅Δ in the column interior 0⩽r<rb−, and uniform density n̂e in an outer annular region rb−<r<rb+; and (b) a continuously-varying density profile of the form ne0(r)=n̂e(Δ+r2/rb2)(1−r2/rb2)2 over the interval 0⩽r<rb. Here, n̂e, rb−, rb+ and rb are positive constants, and the dimensionless parameter Δ measures the degree of “hollowness” of the equilibrium density profile ne0(r). Detailed linear stability properties are calculated for a wide range of system parameters, including values of the “filling factor” Δ, radial location rw of the cylindrical conducting wall, azimuthal mode number l, etc. As a general remark, in both cases, it is found that small increases in Δ from the value Δ=0 (corresponding to the strongest diocotron instability) can have a large effect on the growth rate and detailed properties of the instability. In addition, for the step-function density profile, the instability tends to be algebraic in nature and have a large growth rate in the unstable region of parameter space, whereas for the continuously-varying density profile, the instability is typically much weaker and involves a narrow class of resonant particles at radius r=rs satisfying the resonance condition ωr−lωE(rs)=0. Here, ωr=Re ω is the real oscillation frequency, and ωE(r)=−cEr0(r)/rB0 is the equilibrium E0×B0êz rotation velocity of the plasma column.
Kinetic longitudinal eigenmodes for an inhomogeneous plasma diode with resolved sheaths using a Landau analogy
Authors: Löfgren T.
Published: July 2002

Electrostatic waves in strongly inhomogeneous systems are analyzed using initial value formulations of the kinetic equations. The method resolves the gradual reflection in a trapped electron population, the successive acceleration of a kinetic beam, and it includes the outer circuit. The regularity of the electric field in the sheaths turns out to be crucial. At the turning points for closed trajectories, representing particles with a circulation time that is an integer number of inverse wave frequencies, it is shown that weak oscillating double charge layers can form. This phenomenon does not exist for homogeneous systems, since the structures rest on particle reflection. The final equations are solved numerically to illustrate the technique. Resonant damping and the singular space charge structures in the sheaths are the main differences compared with inhomogeneous fluid theory.
(100) and (111) oriented CdTe grown on (100) oriented GaAs by molecular beam epitaxy
Authors: Ballingall J. M. , Wroge M. L. , Leopold D. J.
Published: July 2002

Techniques are described for growing (100) and (111) oriented CdTe on (100) oriented GaAs by molecular beam epitaxy. Structural characterization reveals that there are substantial differences in crystalline quality between the two orientations, (111) being superior. Single-crystalline (100) oriented films can be grown on oxidized GaAs surfaces, but the crystalline quality is improved if the oxide is desorbed prior to growth.
Faceting on
3
He crystals
Authors: Alles H. , Babkin A. , Jochemsen R. , Parshin A. Ya. , Todoshchenko I. A. , Tsepelin V.
Published: July 2002

It has been predicted by Landau that, ideally at low temperatures, crystals should show many different types of facets, i.e., flat smooth faces on their surface, but this so-called “devil's staircase” phenomenon has been difficult to observe experimentally. In this paper we describe our recent experiments, in which altogether 11 different types of facets have been identified on growing
3
He crystals at the temperature of 0.55 mK by using a unique low-temperature Fabry–Pérot interferometer. Previously only 3 types of facets had been seen in this system. We have also measured the growth velocities of different facets, and our interpretation of the obtained results yields the conclusion that
3
He has much stronger coupling of the liquid–solid interface to the crystal lattice than has been expected. After an introduction we present a short theoretical background about the equilibrium crystal shape and the roughening transitions, which is followed by the description of our experimental results and discussion.
On the direct determination of three-dimensional crystallographic phases at low resolution: Crambin at 6 Å
Authors: Dorset Douglas L.
Published: July 2002

Using a pseudo-atom approach, the three-dimensional crystallographic phases for the protein crambin (
a
= 40.76,
b
= 18.49,
c
= 22.33 Å, β = 90.61°, space group P2
1
) were determined to 6 Å by direct methods. First, the centrosymmetric
h
0ℓ set was assigned phases by symbolic addition, and the initial solution was then refined by Fourier methods. Phase values of strong reflections were then permuted, and the decision to change the phase value for two of these was made by consulting a cross-correlation of the experimental density histogram to the theoretical or known histogram for the protein. The two-dimensional basis was then extended by the Sayre equation into three dimensions by assigning a phase to a third allowed hkℓ origin-defining reflection and an algebraic value to another axial reflection. The correct solution was again identified by the histogram correlation, yielding a solution in which the mean phase error for all 98 reflections was 61.5° or 23.1° for the 21 most intense reflections. A parallel study with another protein indicates this method may have general utility.
Position-specific trapping of topoisomerase I–DNA cleavage complexes by intercalated benzo[
a
]- pyrene diol epoxide adducts at the 6-amino group of adenine
Authors: Pommier Yves , Laco Gary S. , Kohlhagen Glenda , Sayer Jane M. , Kroth Heiko , Jerina Donald M.
Published: July 2002

DNA topoisomerase I (top1) is the target of potent anticancer
agents, including camptothecins and DNA intercalators, which reversibly
stabilize (trap) top1 catalytic intermediates (cleavage complexes). The
aim of the present study was to define the structural relationship
between the site(s) of covalently bound intercalating agents, whose
solution conformations in DNA are known, and the site(s) of top1
cleavage. Two diastereomeric pairs of oligonucleotide 22-mers, derived
from a sequence used to determine the crystal structure of top1–DNA
complexes, were synthesized. One pair contained either a
trans
-opened 10
R
- or
10
S
-benzo[
a
]pyrene 7,8-diol
9,10-epoxide adduct at the
N
6
-amino group of
a central 2′-deoxyadenosine residue in the scissile strand, and the
other pair contained the same two adducts in the nonscissile strand.
These adducts were derived from the
(+)-(7
R
,8
S
,9
S
,10
R
)-
and
(−)-(7
S
,8
R
,9
R
,10
S
)-7,8-diol
9,10-epoxides in which the benzylic 7-hydroxyl group and the epoxide
oxygen are
trans
. On the basis of analogy with known
solution conformations of duplex oligonucleotides containing these
adducts, we conclude that top1 cleavage complexes are trapped when the
hydrocarbon adduct is intercalated between the base pairs flanking a
preexisting top1 cleavage site, or between the base pairs immediately
downstream (3′ relative to the scissile strand) from this site. We
propose a model with the +1 base rotated out of the duplex, and in
which the intercalated adduct prevents religation of the corresponding
nucleotide at the 5′ end of the cleaved DNA. These results suggest
mechanisms whereby intercalating agents interfere with the normal
function of human top1.
Chemical defense: Aquatic beetle (
Dineutes hornii
) vs. fish (
Micropterus salmoides
)
Authors: Eisner Thomas , Aneshansley Daniel J.
Published: July 2002

Captive largemouth bass (
Micropterus salmoides
)
reject the gyrinid beetle,
Dineutes hornii.
They also
reject edible items (mealworms) treated by topical addition of the
norsesquiterpene gyrinidal, the principal component of the defensive
secretion of the beetle. The bass' oral tolerance of gyrinidal varies
broadly as a function of the gyrinidal dosage and the state of
satiation of the fish. When taking a
D. hornii
or a
gyrinidal-treated mealworm in the mouth, the fish subjects the item to
an intensive oral flushing behavior, seemingly intended to rid the item
of gyrinidal. The duration of oral flushing is itself a function of the
gyrinidal dosage and the state of satiation of the bass. To counter
oral flushing,
D. hornii
emits its secretion as a slow
trickle. Duration of emission is slightly longer (1.5 min) than the
time (1.3 min) invested by the bass in flushing a
D.
hornii
before rejecting the beetle. We postulate that flush
resistance may be a general feature of defensive chemical delivery
systems in aquatic prey, given that oral flushing may be a common
strategy of fish.
Nonatomic games on Loeb spaces
Authors: Khan M. Ali , Sun Yeneng
Published: July 2002

In the setting of noncooperative game theory, strategic
negligibility of individual agents, or diffuseness of information, has
been modeled as a nonatomic measure space, typically the unit interval
endowed with Lebesgue measure. However, recent work has shown that with
uncountable action sets, for example the unit interval, there do not
exist pure-strategy Nash equilibria in such nonatomic games. In this
brief announcement, we show that there is a perfectly satisfactory
existence theory for nonatomic games provided this nonatomicity is
formulated on the basis of a particular class of measure spaces,
hyperfinite Loeb spaces. We also emphasize other desirable properties
of games on hyperfinite Loeb spaces, and present a synthetic treatment,
embracing both large games as well as those with incomplete
information.
Neurocytopathic effects of beta-amyloid-stimulated monocytes: a potential mechanism for central nervous system damage in Alzheimer disease.
Authors: London J A , Biegel D , Pachter J S
Published: July 2002

Growing evidence indicates that cells of the mononuclear phagocyte lineage, which includes peripheral blood monocytes (PBM) and tissue macrophages, participate in a variety of neurodestructive events and may play a pivotal role in neurodegenerative conditions such as Alzheimer disease. The present study sought to determine whether exposure of PBM to beta-amyloid peptide (A beta), the major protein of the amyloid fibrils that accumulate in the brain in Alzheimer disease, could induce cytopathic activity in these cells upon their subsequent incubation with neural tissue. PBM were incubated with A beta for 3 days, centrifuged and washed to remove traces of cell-free A beta, and then applied to organotypic cultures of rat brain for varying periods of time. By using a cell-viability assay to quantitate neurocytopathic effect, an increase in the ratio of dead to live cells was detected in cultures containing A beta-stimulated PBM versus control PBM (stimulated with either bovine serum albumin or reverse A beta peptide) as early as 3 days after coculture. The ratio of dead to live cells increased further by 10 days of coculture. By 30 days of coculture, the dead to live cell ratio remained elevated, and the intensity of neurocytopathic effect was such that large areas of brain mass dissociated from the cultures. These results indicate that stimulation of PBM with A beta significantly heightens their neurocytopathic activity and highlight the possibility that inflammatory reactions in the brain play a role in the neurodegeneration that accompanies Alzheimer disease.
Distinct mechanisms of splicing regulation
in vivo
by the
Drosophila
protein Sex-lethal
Authors: Granadino Begoña , Penalva Luiz O. F. , Green Michael R. , Valcárcel Juán , Sánchez Lucas
Published: July 2002

The protein Sex-lethal (SXL) controls pre-mRNA splicing of two genes involved in
Drosophila
sex determination: transformer (
tra
) and the
Sxl
gene itself. Previous
in vitro
results indicated that SXL antagonizes the general splicing factor U2AF
65
to regulate splicing of
tra
. In this report, we have used transgenic flies expressing chimeric proteins between SXL and the effector domain of U2AF
65
to study the mechanisms of splicing regulation by SXL
in vivo
. Conferring U2AF activity to SXL relieves its inhibitory activity on
tra
splicing but not on
Sxl
splicing. Therefore, antagonizing U2AF
65
can explain
tra
splicing regulation both
in vitro
and
in vivo
, but this mechanism cannot explain splicing regulation of
Sxl
pre-mRNA. These results are a direct proof that
Sxl
, the master regulatory gene in sex determination, has multiple and separable activities in the regulation of pre-mRNA splicing.
Selective packaging of cargo molecules into endoplasmic reticulum-derived COPII vesicles
Authors: Campbell Joseph L. , Schekman Randy
Published: July 2002

Coated vesicles transport proteins from the endoplasmic reticulum (ER) to the Golgi apparatus. The formation of transport vesicles
in vitro
requires the incubation of an ER-membrane fraction with three protein fractions collectively known as
co
at
p
rotein II (COPII; Sar1p, Sec23p/Sec24p, and Sec13p/Sec31p). We used this assay to investigate how targeting [v-SNARE,
v
esicle-
s
oluble
N
SF (
N
-ethylmaleimide-
s
ensitive
f
actor)
a
ttachment protein
re
ceptor], putative adapter (e.g., Emp24p), and cargo molecules are captured into ER-derived COPII vesicles. Analysis of fusion proteins strongly suggests that the cytoplasmic domain of the v-SNARE protein Sec22p is required for its packaging into ER-derived COPII vesicles. We examined the packaging requirements for various molecules by individually titrating each of the COPII components. More Sar1p (the GTP-binding protein that initiates vesicles budding) is needed to package the membrane-associated v-SNAREs and Emp24p than is needed to package the soluble secretory protein glycosylated pro-α-factor (gpαF). Microsomes prepared from a strain overproducing Sec12p (the nucleotide exchange protein that recruits Sar1p to the ER) produce vesicles containing gpαF without the addition of exogenous Sar1p, whereas the v-SNAREs and Emp24p are not efficiently packaged under these conditions. Addition of Sar1p to these microsomes leads to increased packaging of v-SNAREs and Emp24p with no increase in the packaging of gpαF. Finally, we show that membranes prepared from strains with mutations in the
SEC16
gene are more defective for the packaging of v-SNARE molecules and Emp24p than they are for the packaging of gpαF. These results point to the possibility that diverse signals or adapters participate in the capture of secretory and membrane cargo molecules into COPII transport vesicles.
Targeted oncogenesis of hormone-negative pancreatic islet progenitor cells
Authors: Jetton Thomas L. , Moates J. Michael , Lindner Jill , Wright Christopher V. E. , Magnuson Mark A.
Published: July 2002

Transgenic mice containing an upstream glucokinase (βGK) promoter– simian virus 40 T antigen (Tag) fusion gene develop neuroendocrine tumors primarily in the pancreas, gut, and pituitary. Pancreatic tumors from a line with delayed tumorigenesis were of two different types: insulinomas and noninsulinomas. The noninsulinomas are often periductal in location, express none of the four major islet peptide hormones, Glut-2, Pdx1, tyrosine hydroxylase, Pax4, Pax6, or Nkx6.1, but do express glucokinase, Sur1, Isl1, Hnf3β, Hnf6, Beta2/NeuroD, and Nkx2.2. Cells from two different noninsulinoma tumors, when adapted to culture, began to express either insulin, glucagon, or somatostatin. Given the partial gene expression repertoire of the noninsulinoma tumors, their apparent periductal origin, and the ability of these cells to partially cytodifferentiate in culture, we suggest that these tumors are derived from islet progenitor cells. Thus, βGK–Tag transgenic mice provide a new model system for studying the events that occur during both islet cell neogenesis and normal embryonic development.
Recent developments in superstring theory
Authors: Schwarz John H.
Published: July 2002

There have been many remarkable developments in our understanding of superstring theory in the past few years, a period that has been described as “the second superstring revolution.” In particular, what once appeared to be five distinct theories are now recognized to be different manifestations of a single (unique) underlying theory. Some of the evidence for this, based on dualities and the appearance of an eleventh dimension, is presented. Also, a specific proposal for the underlying theory, called “Matrix Theory,” is described. The presentation is intended primarily for the benefit of nonexperts.
Implications of a primordial origin for the dispersion in D/H in quasar absorption systems
Authors: Copi Craig J. , Olive Keith A. , Schramm David N.
Published: July 2002

We explore the difficulties with a primordial origin of variations of D/H in quasar absorption systems. In particular we examine options such as a very large-scale inhomogeneity in the baryon content of the universe. We show that very large-scale (much larger than 1 Mpc) isocurvature perturbations are excluded by current cosmic microwave background observations. Smaller-scale
ad hoc
perturbations (∼1 Mpc) still may lead to a large dispersion in primordial abundances but are subject to other constraints.
mRNAs coding for neurotransmitter receptors and voltage-gated sodium channels in the adult rabbit visual cortex after monocular deafferentiation
Authors: Nguyen Quoc-Thang , Matute Carlos , Miledi Ricardo
Published: July 2002

It has been postulated that, in the adult visual cortex, visual inputs modulate levels of mRNAs coding for neurotransmitter receptors in an activity-dependent manner. To investigate this possibility, we performed a monocular enucleation in adult rabbits and, 15 days later, collected their left and right visual cortices. Levels of mRNAs coding for voltage-activated sodium channels, and for receptors for kainate/α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA),
N
-methyl-
d
-aspartate (NMDA), γ-aminobutyric acid (GABA), and glycine were semiquantitatively estimated in the visual cortices ipsilateral and contralateral to the lesion by the
Xenopus
oocyte/voltage-clamp expression system. This technique also allowed us to study some of the pharmacological and physiological properties of the channels and receptors expressed in the oocytes. In cells injected with mRNA from left or right cortices of monocularly enucleated and control animals, the amplitudes of currents elicited by kainate or AMPA, which reflect the abundance of mRNAs coding for kainate and AMPA receptors, were similar. There was no difference in the sensitivity to kainate and in the voltage dependence of the kainate response. Responses mediated by NMDA, GABA, and glycine were unaffected by monocular enucleation. Sodium channel peak currents, activation, steady-state inactivation, and sensitivity to tetrodotoxin also remained unchanged after the enucleation. Our data show that mRNAs for major neurotransmitter receptors and ion channels in the adult rabbit visual cortex are not obviously modified by monocular deafferentiation. Thus, our results do not support the idea of a widespread dynamic modulation of mRNAs coding for receptors and ion channels by visual activity in the rabbit visual system.
Derivation of the relationship between neutral mutation and fixation solely from the definition of selective neutrality
Authors: Tomizawa Jun-ichi
Published: July 2002

A mutation whose fixation is independent of natural selection is termed a neutral mutation. Therefore selective neutrality of a mutation can be defined by independence of its fixation from natural selection. By the population genetic approach, Kimura [Kimura, M. (1962)
Genetics
47, 713–719] predicted that the probability of fixation of a neutral mutation (
u
) is equal to the frequency of the new allele at the start (
p
). The approach traced the temporal sequence of the fixation process, and the prediction was obtained by assuming the selective equality of neutral mutant and wild-type alleles during the fixation process. The prediction, however, has not been verified by observation. In the present study, I search for the mathematical equation that represents the definition of selective neutrality. Because the definition concerns only mutation and fixation, an ideal approach should deal only with these and not with the intervening process of fixation. The approach begins by analysis of the state of fixation of a neutral mutation, and its relation with the initial state is deduced logically from the definition. The approach shows that the equality of the alleles during the fixation process is equivalent to the equality of probability of their ultimate fixation in a steady state. Both are manifestations of the definition of selective neutrality. Then, solely from this dual nature of the definition, the equality between
u
and
p
is derived directly. Therefore, the definition of selective neutrality can be represented by the equation
u
=
p
.