bluuebunny/crossref_metadata_2025 huggingface dataset:
Conditional methods in application for Lagrangian modeling
Authors: Klimenko A. Y.
Published: July 2002

The exact unclosed equation for the phase-space density function (or corresponding Lagrangian pdf) in turbulent flows is obtained using conditional techniques. The equation has direct implications for stochastic Lagrangian models based on the assumption of similarity with a Markov process. The problem of random particle sources is examined and the appropriate correcting term is suggested.
Nonlinear Poiseuille flow in a gas
Authors: Tij Mohamed , Sabbane Mohamed , Santos Andrés
Published: July 2002

The nonlinear Boltzmann equation for the steady planar Poiseuille flow generated by an external field g is exactly solved through order g2. It is shown that the pressure and temperature profiles, as well as the momentum and heat fluxes, are in qualitative disagreement with the Navier–Stokes predictions. For instance, the temperature has a local minimum at the middle layer instead of a maximum. Also, a longitudinal component of the heat flux exists in the absence of gradients along that direction and normal stress differences appear although the flow is incompressible. To account for these g2-order effects, which are relevant when the hydrodynamic quantities change over a characteristic length of the order of the mean free path, it is shown that the Chapman–Enskog expansion should be carried out three steps beyond the Navier–Stokes level.
A numerical study of Richtmyer–Meshkov instability driven by cylindrical shocks
Authors: Zhang Qiang , Graham Mary Jane
Published: July 2002

As an incident shock wave hits a material interface between two fluids of different densities, the interface becomes unstable. Small disturbances at the interface start to grow. This interfacial instability is known as a Richtmyer–Meshkov (RM) instability. It plays an important role in the studies of inertial confinement fusion and supernova. The majority of studies of the RM instability were in plane geometry—namely, plane shocks in Cartesian coordinates. We present a systematic numerical study of the RM instability driven by cylindrical shocks for both the imploding and exploding cases. The imploding (exploding) case refers to a cylindrical shock colliding with the material interface from the outside in (inside out). The phenomenon of reshock caused by the waves reflected from the origin is also studied. A qualitative understanding of this system has been achieved. Detailed studies of the growth rate of the fingers at the unstable interface are presented.
Silo hiccups: Dynamic effects of dilatancy in granular flow
Authors: Le Pennec Thierry , Jo/rgen Målo/y Knut , Flekko/y Eirik G. , Messager Jean Claude , Ammi Madani
Published: July 2002

The granular flow through an open silo is investigated experimentally. A mechanism based both on the dilation of the granular medium and an interaction with the interstitial gas causes the flow to stop at regular intervals. The experiments are carried out at different surrounding pressures P0, and it is found that the intermittent flow becomes continuous at sufficiently low P0, showing that the intermittency is linked to the interaction the gas. The scaling of the average flow rate with particle size further supports our view of the gas-grain interaction.
Nonlinear propagation of small-amplitude modified electron acoustic solitary waves and double layer in semirelativistic plasmas
Authors: Sah O. P. , Goswami K. S.
Published: July 2002

Considering an unmagnetized plasma consisting of relativistic drifting electrons and nondrifting thermal ions and by using reductive perturbation method, a usual Korteweg–de Vries (KdV) equation and a generalized form of KdV equation are derived. It is found that while the former governs the dynamics of a small-amplitude rarefactive modified electron acoustic (MEA) soliton, the latter governs the dynamics of a weak compressive modified electron acoustic double layer. The influences of relativistic effect on the propagation of such a soliton and double layer are examined. The relevance of this investigation to space plasma is pointed out.
The ergodic limit of multipass absorption for fast wave current drive in tokamaks
Authors: Kupfer K. , Forest C. B. , Petty C. C. , Pinsker R. I.
Published: July 2002

In many parameter regimes of interest for fast wave current drive (FWCD) in tokamaks, direct absorption of the fast wave by resonant electrons is a weak process and multipass absorption is an important issue. Although both full wave codes and ray tracing codes have been developed to model FWCD, in the multipass regime these tools are computationally intensive, and yield little insight into the nature of the solutions. In this work, an alternative approach is considered. Based on the wave kinetic equation, a natural limit emerges for the multipass regime, where wave energy density, convected along stochastic ray trajectories, uniformly fills the entire accessible phase space. In this ergodic, weak damping limit, the absorbed power density and corresponding wave-driven current density are readily obtained by calculating the appropriate set of one-dimensional k-space integrals at every point in configuration space. The method is used here to model FWCD on the DIII-D tokamak [R. I. Pinsker and the DIII-D Team, Plasma Physics and Controlled Nuclear Fusion Research 1992 (International Atomic Energy Agency, Vienna, 1993), Vol. 1, p. 683]. An example for reactor-grade plasma parameters is also considered.
Self-similarity of stochastic magnetic field lines near the X-point
Authors: Abdullaev S. S. , Zaslavsky G. M.
Published: July 2002

The properties of magnetic field line trajectories near a separatrix are studied and the renormalization invariance of the Hamiltonian of the system near the X-point is considered in relation to the perturbation amplitude. To describe the footprint of intersections of the trajectories with an arbitrarily positioned plane, the shifted separatrix map is derived and applied to the analysis of the magnetic field lines dynamics in the stochastic layer and to the magnetic footprint. The numerical simulations confirm the renormalization invariance of the field line equations, surface of section of the field line trajectories, and magnetic footprint obtained by the shifted separatrix map for a simple Hamiltonian system, which is topologically equivalent to the single null poloidal divertor of a tokamak.
Nonlinear evolution of the alpha-particle-driven toroidicity-induced Alfvén eigenmode
Authors: Wu Yanlin , White Roscoe B. , Chen Yang , Rosenbluth M. N.
Published: July 2002

A fast and efficient numerical algorithm using energy conservation is developed to study the interaction of high-energy particles with a toroidicity-induced Alfvén eigenmode (TAE). A Hamiltonian guiding center code is used to simulate the alpha particle motion and a nonlinear δf scheme is employed to calculate the wave-particle energy exchange. The code is benchmarked using the bump-on-tail problem and simulation results agree with analytical estimates. For a single TAE mode, the particle radial excursion is much less than the spacing between the resonances produced by the poloidal harmonics for International Thermonuclear Experimental Reactor parameters. Resonant particles that lose their energy to the wave can become trapped poloidally, but transfer to a loss orbit through this mechanism does not occur. Modification of the particle distribution leading to mode saturation is observed.
Nonlinear ideal magnetohydrodynamics with surface currents
Authors: Pfirsch D.
Published: July 2002

A formulation of nonlinear magnetohydrodynamics with surface currents and plasma flow on the basis of a Hamilton principle is presented. In particular, transition conditions containing contributions from the plasma flow are obtained for the first time. The formulation is also applied to the linearized theory around static equilibria. It yields the well-known energy principle.
The effects of Coulomb collisions on the propagation of cold-plasma waves
Authors: Brambilla Marco
Published: July 2002

Explicit expressions for the corrections δε to the cold-plasma dielectric tensor due to Coulomb collisions have been obtained. These expressions, derived from the Fokker–Planck operator in the Landau form, are ‘‘exact’’ to first order in νcoll/ω, and can be used to evaluate the dissipation due to collisions between particles of arbitrary charge-to-mass ratios. Collisions between particles of the same species do not contribute to dissipation, as expected. In the high-frequency domain, when the ion mobility is negligible, electron–ion collisions can be accounted for by adding to the frequency an appropriate imaginary part, which coincides with νe/i up to a numerical factor close to unity. In the general case, collisional dissipation is proportional to the difference of the mobility of the two colliding species, again as expected from elementary considerations. The results obtained for arbitrary charge-to-mass ratios can be of practical relevance in the ion cyclotron and magnetohydrodynamic frequency ranges, where the perpendicular mobilities of ions and electrons are comparable, and in the case of collisions between hydrogen isotopes and impurities.
Transform-limited coherent synchrotron radiation wavepackets in a chirped pulse free-electron laser
Authors: Hartemann F. V. , Le Sage G. P. , Troha A. L. , Luhmann N. C. , Fochs S. N.
Published: July 2002

A novel source of transform-limited pulses of coherent electromagnetic radiation relying on the synchrotron radiation process in a fast wave guiding structure is investigated theoretically. An ultrashort electron bunch transversally accelerated by a periodic external field is considered. At grazing, where the bunch and group velocities are matched, the duration of the resulting ultrawideband chirped pulse is governed by group velocity dispersion instead of slippage. Because of the intimate connection between the rate of chirping and the bandwidth, the corresponding pulse duration is shown to be very close to the Fourier transform limit. In addition, the propagation of such chirped pulses through a guiding structure with negative group velocity dispersion is investigated both theoretically and computationally. The spectral and temporal characteristics of the chirped and compressed pulses are derived analytically. Detailed computer calculations complement this theoretical analysis.
Instability of the Lembège–Pellat equilibrium under ideal magnetohydrodynamics
Authors: Hurricane O. A. , Pellat R. , Coroniti F. V.
Published: July 2002

The magnetotail-like equilibrium model of Lembège and Pellat [Phys. Fluids, 25, 1995 (1982)] has been used in a number of stability calculations over the past 13 years. Most of these computations examine collisionless tearing—a mode of tail instability first suggested by Coppi et al. [Phys. Rev. Lett. 16, 1207 (1966)]—or other kinetic modes and involve both analytical and computer analysis. In this Communication it is shown, analytically, that the equilibrium model of Lembège and Pellat is unstable according to ideal magnetohydrodynamics (MHD). More precisely, for the ideal MHD stability theory of Bernstein et al. [Proc. R. Soc. London Ser. A 244, 17 (1958)] it is proven that Λ=p′+Γp (v″/v′)<0.
Electromagnetic instability in nonuniform resistive electron magnetohydrodynamics
Authors: Mirza Arshad M. , Murtaza G. , Shukla P. K.
Published: July 2002

A local dispersion relation for electromagnetic modes in a nonuniform collisional magnetized electron plasma with fixed ion background is derived, taking into account equilibrium magnetic field and pressure gradients, as well as impurity radiation losses. The dispersion relation is then analyzed both analytically as well as numerically. It is found that for a low-β plasma, the principal source for the generation of unstable modes is the impurity radiation loss; whereas for a high-β plasma, the various effects such as the electron streaming, the electron–ion collisions, finite electron thermal conductivity, and impurity radiation losses are shown to be responsible for unstable perturbations. The results should be useful in the interpretation of nonthermal electromagnetic fluctuations in nonuniform collision-dominated magnetoplasmas with impurities.
Stability of force-free Taylor states in a new version of magnetic flux-averaged magnetohydrodynamics
Authors: Pfirsch D. , Sudan R. N.
Published: July 2002

It is observed that the recently developed magnetic flux-averaged magnetohydrodynamics (AMHD) [Phys. Plasmas 1, 2488 (1994)] is incompatible with Taylor’s theorem, which states that the lowest-energy state of force-free equilibria based on the conservation of the helicity integral is absolutely stable for vanishingly small resistivity. By a modification of the Lagrangian from which AMHD is derived, a modified version of AMHD that is compatible with Taylor’s theorem is obtained. It also provides an energy principle for examining the linear instability of resistive equilibria, which has a great advantage over resistive MHD.
Theoretical modeling of a weak correlation effect in a nonideal plasma
Authors: Dwivedi C. B. , Bannur V. M.
Published: July 2002

Weak correlation effect in a nonideal plasma system has been modeled within a fluid description by an average classical Coulomb interaction potential in dynamic momentum equation of the electrons. This is the lowest order correction and models the small deviation from the ideal gas behavior of the plasma. Numerical solution of the Poisson equation shows a reasonably good agreement with the earlier calculation based on the statistical formulation of the particle correlation in plasmas. Effects of the particle correlation may be displayed through the modification in the dispersion characteristics of the plasma waves/sheath potential at a surface in contact with the nonideal plasma.
Lower-hybrid-like wave in a dusty plasma with charge fluctuation
Authors: Mahanta L. , Goswami K. S. , Bujarbarua S.
Published: July 2002

The dispersion relation for the case of a lower-hybrid-like wave in a dusty plasma is obtained taking into account the charge fluctuation. It is found that charge fluctuation terms lead to a novel dissipation of the lower-hybrid-like modes in a dusty plasma.
On the fast rotational equilibrium of a non-neutral plasma column
Authors: Bhattacharyya S. N.
Published: July 2002

The equation governing the stability of a single species non-neutral plasma column to small amplitude electrostatic perturbations is shown to remain unchanged under a certain transformation. This transformation can be used to predict the stability of the fast rotational equilibrium using the results for the slow rotational equilibrium. For the fast rotational equilibrium the zero frequency modes, which can give rise to field error driven transport, are identified.
Finite Larmor radius magnetohydrodynamics of the Rayleigh–Taylor instability
Authors: Huba J. D.
Published: July 2002

The evolution of the Rayleigh–Taylor instability is studied using finite Larmor radius (FLR) magnetohydrodynamic (MHD) theory. Finite Larmor radius effects are introduced in the momentum equation through an anisotropic ion stress tensor. Roberts and Taylor [Phys. Rev. Lett. 3, 197 (1962)], using fluid theory, demonstrated that FLR effects can stabilize the Rayleigh–Taylor instability in the short-wavelength limit (kLn≫1, where k is the wave number and Ln is the density gradient scale length). In this paper a linear mode equation is derived that is valid for arbitrary kLn. Analytic solutions are presented in both the short-wavelength (kLn≫1) and long-wavelength (kLn≪1) regimes, and numerical solutions are presented for the intermediate regime (kLn∼1). The long-wavelength modes are shown to be the most difficult to stabilize. More important, the nonlinear evolution of the Rayleigh–Taylor instability is studied using a newly developed two-dimensional (2-D) FLR MHD code. The FLR effects are shown to be a stabilizing influence on the Rayleigh–Taylor instability; the short-wavelength modes are the easiest to stabilize, consistent with linear theory. In the nonlinear regime, the FLR effects cause the ‘‘bubbles and spikes’’ that develop because of the Rayleigh–Taylor instability to convect along the density gradient and to tilt. Applications of this model to space and laboratory plasma phenomena are discussed.
Active optical guiding and gain guiding in a free electron laser
Authors: Seo Y.
Published: July 2002

Relative significance of a gain guiding and an active optical guiding due to a nonlinear frequency shift is investigated by comparing the properties of radiation modes of a high gain Compton and a Raman free electron laser. A significant role of the active guiding has been identified from the comparison.
Nonlinear theory of resonant slow waves in dissipative layers
Authors: Ruderman M. S. , Hollweg J. V. , Goossens M.
Published: July 2002

Linear dissipative magnetohydrodynamics (MHD) shows that driven MHD waves in magnetic plasmas with high Reynolds number exhibit a near resonant behaviour if the frequency of the wave becomes equal to the local Alfvén or slow frequency of a magnetic surface. This near resonant behaviour is confined to a thin dissipative layer which embraces the resonant magnetic surface. Although the driven MHD waves have small amplitudes far away from the resonant magnetic surface, this near-resonant behaviour in the dissipative layer may cause a breakdown of linear theory. In the present paper we deal with the nonlinear behaviour of driven MHD waves in the slow wave dissipative layer. The method of matched asymptotic expansions is used to obtain the nonlinear equation for wave variables inside the dissipative layer. The concept of connection formulae introduced into the theory of linear resonant MHD waves by Sakurai, Goossens, and Hollweg [Sol. Phys. 133, 227 (1991)] is extended to include nonlinear effects in the dissipative layer for slow resonant waves. The absorption of the slow resonant wave in the dissipative layer generates a shear flow parallel to the magnetic surfaces with a characteristic velocity of the order of ε1/2, where ε is the dimensionless amplitude of perturbations far away from the dissipative layer.
Local test of parallel electrical resistivity in the Tokamak Fusion Test Reactor
Authors: Batha S. H. , Levinton F. M. , Ramsey A. T. , Schmidt G. L. , Zarnstorff M. C.
Published: July 2002

Local, time-resolved measurements have been made of the response of the internal magnetic-field distribution to large changes in the total plasma current. Measurements were made by the motional Stark effect (MSE) polarimeter on the Tokamak Fusion Test Reactor (TFTR). [R. J. Hawryluk et al., Proceedings of the 11th International Conference on Plasma Physics and Controlled Nuclear Fusion (International Atomic Energy Agency, Vienna, 1987) Vol. I, p. 51.] A direct test of the classical and neoclassical resistivity models was made by comparing the predicted field evolution using either model to that measured. It was found that the neoclassical resistivity model was a better predictor of the local magnetic-field temporal evolution than was the classical model.
Instabilities driven by electron velocity and temperature gradients in tokamak scrape-off layers with non-uniform parallel currents
Authors: Farengo Ricardo
Published: July 2002

A study of instabilities driven by gradients in the parallel electron velocity and electron temperature in magnetized plasmas bounded by a conducting surface is presented. The parameters and general conditions considered are relevant for the scrape-off layer of magnetically confined plasmas. The inclusion, for the first time, of a finite current and a current gradient results in unstable modes which are quite different from the modes driven solely by the electron temperature gradient. In the parameter regime corresponding to high power discharges with attached plasmas, where the typical scale length of the velocity gradient is much shorter than that of the temperature gradient, the velocity gradient is the dominant effect. The anomalous thermal diffusivity, from mixing length theory, obtained including the velocity gradient is larger than that obtained including only the temperature gradient.
Integrable parameter regimes and stationary states of nonlinearly coupled electromagnetic and ion-acoustic waves
Authors: Rao N. N.
Published: July 2002

A systematic analysis of the stationary propagation of nonlinearly coupled electromagnetic and ion-acoustic waves in an unmagnetized plasma via the ponderomotive force is carried out. For small but finite amplitudes, the governing equations have a Hamiltonian structure, but with a kinetic energy term that is not positive definite. The Hamiltonian is similar to the well-known Hénon–Heiles Hamiltonian of nonlinear dynamics, and is completely integrable in three regimes of the allowed parameter space. The corresponding second invariants of motion are also explicitly obtained. The integrable parameter regimes correspond to supersonic values of the Mach number, which characterizes the propagation speed of the coupled waves. On the other hand, in the sub- as well as near-sonic regimes, the coupled mode equations admit different types of exact analytical solutions, which represent nonlinear localized eigenstates of the electromagnetic field trapped in the density cavity due to the ponderomotive potential. While the density cavity has always a single-dip structure, for larger amplitudes it can support higher-order modes having a larger number of nodes in the electromagnetic field. In particular, we show the existence of a new type of localized electromagnetic wave whose field intensity has a triple-hump structure. For typical parameter values, the triple-hump solitons propagate with larger Mach numbers that are closer to the sonic limit than the single- as well as the double-hump solitons, but carry a lesser amount of the electromagnetic field energy. A comparison between the different types of solutions is carried out. The possibility of the existence of trapped electromagnetic modes having a larger number of humps is also discussed.
Drift-ballooning modes in the presence of charged dust impurities in a nonuniform rotating magnetoplasma
Authors: Shukla P. K. , Mirza Arshad M. , Murtaza G. , Faria R. T.
Published: July 2002

The linear and nonlinear properties of drift-ballooning modes in the presence of an equilibrium electric field and stationary charged dust grains are examined. It is found that the presence of these two contribute to the stability of the ballooning mode. Furthermore, the nonlinear coupling between finite amplitude drift-ballooning modes gives rise to different types of coherent vortex structures, which can affect the transport properties of an inhomogeneous magnetized plasma. The relevance of the investigation to laboratory and astrophysical plasmas is discussed.
Structure of driven Alfvén waves with oblique magnetic field and dissipation
Authors: Ruderman M. S. , Wright A. N.
Published: July 2002

The quasi-resonant behavior of linear Alfvén waves in one-dimensional magnetized weakly resistive plasmas with the slightly inclined equilibrium magnetic field is studied. The analysis concentrates on the behavior of the y-component of the velocity, v, which is the component perpendicular both to the inhomogeneity direction and to the equilibrium magnetic field, and the z-component of the velocity, w, which is the component along the inhomogeneity direction. It is shown that the behavior of v and w is described by the functions F(σ;Λ) and G(σ;Λ), where σ is the dimensionless distance along the inhomogeneity direction and the parameter Λ characterizes the relative importance of resistivity and the magnetic field inclination near the quasi-resonant position. The functions F(σ;Λ) and G(σ;Λ) are generalizations of the F and G functions introduced by Goossens, Ruderman, and Hollweg [Sol. Phys. 157, 75 (1995)] and coincide with them for Λ=0. The behavior of F(σ;Λ) and G(σ;Λ) is studied numerically for different values of Λ. It changes from monotonic to oscillatory when Λ is increased. It is shown that the connection formulas giving the jumps of w and the perturbation of the total pressure across the quasi-resonant layer and the rate of energy dissipation in the quasi-resonant layer are independent of the inclination angle.
Dipole and octapole field reversals in a rotating spherical shell: Magnetohydrodynamic dynamo simulation
Authors: Ochi Márcia M. , Kageyama Akira , Sato Tetsuya
Published: July 2002

Computer simulation results of a compressible magnetohydrodynamic (MHD) dynamo in a rotating spherical shell are presented. The reversal of either the dipole or the octapole field polarity is observed accompanying flip–flop magnetic energy transitions. Three energy transitions are observed. The dipole reversal occurs in the first transition. In the initial stage of the dipole reversal, the magnetic energy is about five times larger than the kinetic energy, and the convection pattern consists essentially of six straight cyclonic and anticyclonic vortex column pairs aligned to the rotation axis. In the intermediate stage, the magnetic energy decreases and the field is observed to change direction in some regions. This is accompanied by reorganization of the vortex columns and a transition to a new energy level. In the final stage, the field is completely reversed, the number of convection columns is increased and the magnetic energy is lower than in the second stage. In the other two magnetic energy transitions, the octapole component reverses polarity.
Fluctuation level bursts in a model of internal transport barrier formation
Authors: López-Bruna D. , Newman D. E. , Carreras B. A. , Diamond P. H.
Published: July 2002

A model of internal transport barriers (ITB) is developed that, in addition to the typical features of ITB models (the phase transition character with a power threshold, barrier front propagation, etc.), exhibits an oscillatory/bursty behavior close to the transition. This behavior comes from the competition between the driving and suppression mechanisms for the turbulence. The onset of the oscillations has a power threshold, Posc, below the power threshold for the transition to the enhanced confinement regime, Pth. In the calculations, Posc∼0.5Pth. This suggests that the oscillations avoid an early transition at Pth=Posc, so any mechanism that eliminates the oscillations may lower the transition power.
Nonlinear hydromagnetic waves in a plasma filled cylindrical wave guide
Authors: Hamabata Hiromitsu
Published: July 2002

An exact axisymmetric wave solution of the nonlinear magnetohydrodynamic equations for a highly conducting incompressible fluid within a perfectly conducting cylindrical wave guide is obtained. The solution represents a cylindrical wave guide mode propagating in the axial direction with constant velocity under the influence of the helical magnetic field.
Detailed dynamics of electron beams self-trapped and accelerated in a self-modulated laser wakefield
Authors: Chen S.-Y. , Krishnan M. , Maksimchuk A. , Wagner R. , Umstadter D.
Published: July 2002

The electron beam generated in a self-modulated laser-wakefield accelerator is characterized in detail. A transverse normalized emittance of 0.06 π mm mrad, the lowest ever for an electron injector, was measured for 2 MeV electrons. The electron beam was observed to have a multicomponent beam profile and energy distribution. The latter also undergoes discrete transitions as the laser power or plasma density is varied. In addition, dark spots that form regular modes were observed in the electron beam profile. These features are explained by analysis and test particle simulations of electron dynamics during acceleration in a three-dimensional plasma wakefield.
Intermixing of AlxGa1−xAs/GaAs superlattices by pulsed laser irradiation
Authors: Ralston J. , Moretti A. L. , Jain R. K. , Chambers F. A.
Published: July 2002

Intermixing of AlxGa1−xAs/GaAs superlattices is demonstrated utilizing laser pulses of a few nanosecond duration. Raman spectroscopy and sputter Auger profiling have been used to assess the degree of intermixing and residual damage in the laser irradiated samples. The results indicate that irradiating with the spatially uniform beam of the excimer laser generates a completely intermixed alloy with no detected residual damage. A thermal melting model is used to qualitatively describe the results.
Isotopic enrichment in a plasma centrifuge
Authors: Del Bosco E. , Dallaqua R. S. , Ludwig G. O. , Bittencourt J. A.
Published: July 2002

High rotational velocity and centrifugal isotopic separation of carbon in a vacuum-arc plasma centrifuge are presented. Enrichments of up to 390% for 13C are measured at 6 cm radius with angular rotation frequencies in excess of 1.0×105 rad/s in an axial magnetic field of 0.12 T.
Quantum-confined Stark effect in InGaAs/InP quantum wells grown by organometallic vapor phase epitaxy
Authors: Bar-Joseph I. , Klingshirn C. , Miller D. A. B. , Chemla D. S. , Koren U. , Miller B. I.
Published: July 2002

We report the first observation of the quantum-confined Stark effect in InGaAs/InP multiple quantum wells grown by organometallic vapor phase epitaxy. The effect is observed both in transmission and photoconductivity measurements. The observed spectral shift agrees with the theory.
Fast P-doped silicon bolometer for detecting heat pulses
Authors: Boragno C. , Valbusa U. , Pignatel G.
Published: July 2002

A new detector of ballistic phonons is presented. It is a P-doped Si bolometer realized on top of a (100)Si crystal by ion implantation. The open circuit responsivity of the bolometer is 8000 V/W and the response time less than 50 ns. Time-resolved spectra of ballistic phonons propagating in the same Si crystal along the 〈100〉 direction are reported.
Benzene chemisorption on amorphous silicon
Authors: Tache N. , Chang Y. , Kelly M. K. , Margaritondo G. , Quaresima C. , Capozi M. , Perfetti P. , Piancastelli M. N.
Published: July 2002

A stable chemisorption state was discovered for benzene on amorphous silicon at room temperature. Its establishment implies high reactivity and a catalytic role of the substrate in breaking C–H bonds. This suggests that amorphous silicon, similar to cleaved silicon, can catalyze interesting surface chemical reactions involving aromatic molecules.
Light-induced defects in hydrogenated amorphous silicon alloys
Authors: Skumanich Andrew , Amer Nabil M.
Published: July 2002

The effect of light illumination on gap state absorption of hydrogenated amorphous silicon (a-Si:H) alloys has been investigated using photothermal deflection spectroscopy. The alloys studied were the large gap materials a-SiC:H and a-SiO:H and the narrow gap a-SiGe:H and a-Ge:H. The results indicate a direct relationship between the gap energy and defect formation. As the gap opens, the number of metastable defects increases; whereas for the narrow gap materials, significantly fewer defects are observed. This behavior is consistent with the interpretation of defect formation by electron-hole recombination.
Kinetics, energetics, and origins of defects in amorphous Si:H
Authors: Redfield David
Published: July 2002

A unified explanation is derived relating ‘‘stable’’ and metastable deep-level defects in amorphous Si:H, the existence of a universal saturated density of metastable defects, the temperature dependence of that saturation density, the increases with doping of both the density of ‘‘stable’’ defects and sensitivity to light, and the slow relaxation of dark properties. This follows from the defect energetics, and a completed analysis of the kinetics of formation and anneal of defects that is fully symmetric. It is concluded that the dominant defects are extrinsic in origin, probably involving a complex with a dopant atom.
Selective growth condition in disilane gas source silicon molecular beam epitaxy
Authors: Hirayama Hiroyuki , Tatsumi Toru , Aizaki Naoaki
Published: July 2002

Selective epitaxial growth condition in the disilane gas source silicon molecular beam epitaxy was studied as functions of the substrate temperature and the growth rate. At lower substrate temperature or at lower silicon growth rate, perfect selectivity was attained. The selectivity dependence on the temperature and that on the growth rate indicate that the control of the disilane molecule’s dissociation on the SiO2 surface is important for selective growth.
Plasma x-ray source for lithography generated by a ≊30 J, 30 ns KrF laser
Authors: Davis G. M. , Gower M. C. , O’Neill F. , Turcu I. C. E.
Published: July 2002

A plasma x-ray source for lithography is generated by focusing ≊30 J, 30 ns KrF laser pulses onto Cu targets at irradiances up to 2×1014 W/cm2. Energy conversion efficiency from 249 nm laser light to x rays at 1.0 keV≤hν≤1.4 keV is measured as a function of target irradiance and the maximum efficiency is ≊2.5%. The full width half-maximum duration of the plasma x-ray pulse is ≊5 ns which corresponds to a peak power x-ray conversion efficiency ≊7.5%.
Lipid mediator-induced expression of bactericidal/ permeability-increasing protein (BPI) in human mucosal epithelia
Authors: Canny Geraldine , Levy Ofer , Furuta Glenn T. , Narravula-Alipati Sailaja , Sisson Richard B. , Serhan Charles N. , Colgan Sean P.
Published: July 2002

Epithelial cells which line mucosal surfaces are the first line of defense against bacterial invasion and infection. Recent studies have also indicated that epithelial cells contribute significantly to the orchestration of ongoing inflammatory processes. Here, we demonstrate that human epithelial cells express bactericidal/permeability-increasing protein (BPI), an antibacterial and endotoxin-neutralizing molecule previously associated with neutrophils. Moreover, we demonstrate that such BPI expression is transcriptionally regulated by analogs of endogenously occurring anti-inflammatory eicosanoids (aspirin-triggered lipoxins, ATLa). Initial studies to verify microarray analysis revealed that epithelial cells of wide origin (oral, pulmonary, and gastrointestinal mucosa) express BPI and each is similarly regulated by aspirin-triggered lipoxins. Studies aimed at localization of BPI revealed that such expression occurs on the cell surface of cultured epithelial cell lines and dominantly localizes to epithelia in human mucosal tissue. Functional studies employing a BPI-neutralizing anti-serum revealed that surface BPI blocks endotoxin-mediated signaling in epithelia and killsSalmonellatyphimurium. These studies identify a previously unappreciated “molecular shield” for protection of mucosal surfaces against Gram-negative bacteria and their endotoxin.
β-Catenin, a novel prognostic marker for breast cancer: Its roles in cyclin D1 expression and cancer progression
Authors: Lin Shiaw-Yih , Xia Weiya , Wang Jo C. , Kwong Ka Yin , Spohn Bill , Wen Yong , Pestell Richard G. , Hung Mien-Chie
Published: July 2002

β-Catenin can function as an oncogene when it is translocated to the nucleus, binds to T cell factor or lymphoid enhancer factor family members, and transactivates its target genes. In this study, we demonstrate that cyclin D1 is one of the targets of β-catenin in breast cancer cells. Transactivation of β-catenin correlated significantly with cyclin D1 expression both in eight breast cell lines
in vitro
and in 123 patient samples. More importantly, we found that high β-catenin activity significantly correlated with poor prognosis of the patients and was a strong and independent prognostic factor in breast cancer. Our studies, therefore, indicated that β-catenin can be involved in breast cancer formation and/or progression and may serve as a target for breast cancer therapy.
Involvement of multiple intracellular release channels in calcium sparks of skeletal muscle
Authors: González A. , Kirsch W. G. , Shirokova N. , Pizarro G. , Brum G. , Pessah I. N. , Stern M. D. , Cheng H. , Ríos E.
Published: July 2002

In many types of muscle, intracellular Ca
2+
release for contraction consists of brief Ca
2+
sparks. Whether these result from the opening of one or many channels in the sarcoplasmic reticulum is not known. Examining massive numbers of sparks from frog skeletal muscle and evaluating their Ca
2+
release current, we provide evidence that they are generated by multiple channels. A mode is demonstrated in the distribution of spark rise times in the presence of the channel activator caffeine. This finding contradicts expectations for single channels evolving reversibly, but not for channels in a group, which collectively could give rise to a stereotyped spark. The release channel agonists imperatoxin A, ryanodine, and bastadin 10 elicit fluorescence events that start with a spark, then decay to steady levels roughly proportional to the unitary conductances of 35%, 50%, and 100% that the agonists, respectively, promote in bilayer experiments. This correspondence indicates that the steady phase is produced by one open channel. Calculated Ca
2+
release current decays 10- to 20-fold from spark to steady phase, which requires that six or more channels be open during the spark.
HDA2 and HDA3 are related proteins that interact with and are essential for the activity of the yeast histone deacetylase HDA1
Authors: Wu Jiansheng , Carmen Andrew A. , Kobayashi Ryuji , Suka Noriyuki , Grunstein Michael
Published: July 2002

Histone deacetylase HDA1, the prototype for the class II mammalian
deacetylases, is likely the catalytic subunit of the HDA1-containing
complex that is involved in TUP1-specific repression and global
deacetylation in yeast. Although the class I RPD3-like enzymatic
complexes have been well characterized, little is known about the
identity and interactions of the factors that associate to form the
HDA1 complex. In this paper, we identify related HDA2 and HDA3 proteins
that are found in the HDA1 complex and show that HDA1 interacts with
itself and with the HDA2-HDA3 subcomplex to form a likely tetramer.
These interactions are necessary for catalytic activity because
mutations in any of the three components disrupt activity both
in vitro
and
in vivo
. In this respect the
HDA1 complex differs from yeast RPD3, which has components such as SIN3
that are not essential for activity
in vitro
, and yeast
HOS3, which has intrinsic
in vitro
activity as a
homodimer in the absence of other subunits.
Expanding the biosynthetic repertoire of plant type III polyketide synthases by altering starter molecule specificity
Authors: Jez Joseph M. , Bowman Marianne E. , Noel Joseph P.
Published: July 2002

Type III polyketide synthases (PKS) generate an array of natural products by condensing multiple acetyl units derived from malonyl-CoA to thioester-linked starter molecules covalently bound in the PKS active site. One strategy adopted by Nature for increasing the functional diversity of these biosynthetic enzymes involves modifying polyketide assembly by altering the preference for starter molecules. Chalcone synthase (CHS) is a ubiquitous plant PKS and the first type III PKS described functionally and structurally. Guided by the three-dimensional structure of CHS, Phe-215 and Phe-265, which are situated at the active site entrance, were targeted for site-directed mutagenesis to diversify CHS activity. The resulting mutants were screened against a panel of aliphatic and aromatic CoA-linked starter molecules to evaluate the degree of starter molecule specificity in CHS. Although wild-type CHS accepts a number of natural CoA thioesters, it does not use
N
-methylanthraniloyl-CoA as a substrate. Substitution of Phe-215 by serine yields a CHS mutant that preferentially accepts this CoA-thioester substrate to generate a novel alkaloid, namely
N
-methylanthraniloyltriacetic acid lactone. These results demonstrate that a point mutation in CHS dramatically shifts the molecular selectivity of this enzyme. This structure-based approach to metabolic redesign represents an initial step toward tailoring the biosynthetic activity of plant type III PKS.
Diketo acid inhibitor mechanism and HIV-1 integrase: Implications for metal binding in the active site of phosphotransferase enzymes
Authors: Grobler Jay A. , Stillmock Kara , Hu Binghua , Witmer Marc , Felock Peter , Espeseth Amy S. , Wolfe Abigail , Egbertson Melissa , Bourgeois Michele , Melamed Jeffrey , Wai John S. , Young Steve , Vacca Joseph , Hazuda Daria J.
Published: July 2002

The process of integrating the reverse-transcribed HIV-1 DNA into the host chromosomal DNA is catalyzed by the virally encoded enzyme integrase (IN). Integration requires two metal-dependent reactions, 3′ end processing and strand transfer. Compounds that contain a diketo acid moiety have been shown to selectively inhibit the strand transfer reaction of IN
in vitro
and in infected cells and are effective as inhibitors of HIV-1 replication. To characterize the molecular basis of inhibition, we used functional assays and binding assays to evaluate a series of structurally related analogs. These studies focused on investigating the role of the conserved carboxylate and metal binding. We demonstrate that an acidic moiety such as a carboxylate or isosteric heterocycle is not required for binding to the enzyme complex but is essential for inhibition and confers distinct metal-dependent properties on the inhibitor. Binding requires divalent metal and resistance is metal dependent with active site mutants displaying resistance only when the enzymes are evaluated in the context of Mg
2+
. The mechanism of action of these inhibitors is therefore likely a consequence of the interaction between the acid moiety and metal ion(s) in the IN active site, resulting in a functional sequestration of the critical metal cofactor(s). These studies thus have implications for modeling active site inhibitors of IN, designing and evaluating analogs with improved efficacy, and identifying inhibitors of other metal-dependent phosphotransferases.
Gene expression analysis reveals matrilysin as a key regulator of pulmonary fibrosis in mice and humans
Authors: Zuo Fengrong , Kaminski Naftali , Eugui Elsie , Allard John , Yakhini Zohar , Ben-Dor Amir , Lollini Lance , Morris David , Kim Yong , DeLustro Barbara , Sheppard Dean , Pardo Annie , Selman Moises , Heller Renu A.
Published: July 2002

Pulmonary fibrosis is a progressive and largely untreatable group of disorders that affects up to 100,000 people on any given day in the United States. To elucidate the molecular mechanisms that lead to end-stage human pulmonary fibrosis we analyzed samples from patients with histologically proven pulmonary fibrosis (usual interstitial pneumonia) by using oligonucleotide microarrays. Gene expression patterns clearly distinguished normal from fibrotic lungs. Many of the genes that were significantly increased in fibrotic lungs encoded proteins associated with extracellular matrix formation and degradation and proteins expressed in smooth muscle. Using a combined set of scoring systems we determined that matrilysin (matrix metalloproteinase 7), a metalloprotease not previously associated with pulmonary fibrosis, was the most informative increased gene in our data set. Immunohistochemisry demonstrated increased expression of matrilysin protein in fibrotic lungs. Furthermore, matrilysin knockout mice were dramatically protected from pulmonary fibrosis in response to intratracheal bleomycin. Our results identify matrilysin as a mediator of pulmonary fibrosis and a potential therapeutic target. They also illustrate the power of global gene expression analysis of human tissue samples to identify molecular pathways involved in clinical disease.
Reaction coordinates of biomolecular isomerization
Authors: Bolhuis Peter G. , Dellago Christoph , Chandler David
Published: July 2002

Transition path sampling has been applied to the molecular dynamics of the alanine dipeptide in vacuum and in aqueous solution. The analysis shows that more degrees of freedom than the traditional dihedral angles, φ and ψ, are necessary to describe the reaction coordinates for isomerization of this molecule. In vacuum, an additional dihedral angle is identified as significant. In solution, solvent variables are shown to play a significant role, and this role appears to be more specific than can be captured by friction models. Implications for larger molecules are discussed.
Oncolytic herpes simplex virus vector with enhanced MHC class I presentation and tumor cell killing
Authors: Todo Tomoki , Martuza Robert L. , Rabkin Samuel D. , Johnson Paul A.
Published: July 2002

Oncolytic herpes simplex virus type 1 (HSV-1) vectors are promising therapeutic agents for cancer. Their efficacy depends on the extent of both intratumoral viral replication and induction of a host antitumor immune response. To enhance these properties while employing ample safeguards, two conditionally replicating HSV-1 vectors, termed G47Δ and R47Δ, have been constructed by deleting theα47gene and the promoter region ofUS11fromγ34.5-deficient HSV-1 vectors, G207 and R3616, respectively. Because theα47gene product is responsible for inhibiting the transporter associated with antigen presentation (TAP), its absence led to increased MHC class I expression in infected human cells. Moreover, some G47Δ-infected human melanoma cells exhibited enhanced stimulation of matched antitumor T cell activity. The deletion also places the lateUS11gene under control of the immediate-earlyα47promoter, which suppresses the reduced growth properties ofγ34.5-deficient mutants. G47Δ and R47Δ showed enhanced viral growth in a variety of cell lines, leading to higher virus yields and enhanced cytopathic effect in tumor cells. G47Δ was significantly more efficaciousin vivothan its parent G207 at inhibiting tumor growth in both immune-competent and immune-deficient animal models. Yet, when inoculated into the brains of HSV-1-sensitive A/J mice at 2 × 106plaque forming units, G47Δ was as safe as G207. These results suggest that G47Δ may have enhanced antitumor activity in humans.
Position-effect protection and enhancer blocking by the chicken β-globin insulator are separable activities
Authors: Recillas-Targa Félix , Pikaart Michael J. , Burgess-Beusse Bonnie , Bell Adam C. , Litt Michael D. , West Adam G. , Gaszner Miklos , Felsenfeld Gary
Published: July 2002

The 1.2-kb DNA sequence element (5′HS4) at the 5′ end of the chicken β-globin locus has the two defining properties of an insulator: it prevents an “external” enhancer from acting on a promoter when placed between them (“enhancer blocking”) and acts as a barrier to chromosomal position effect (CPE) when it surrounds a stably integrated reporter. We previously reported that a single CTCF-binding site in 5′HS4 is necessary and sufficient for enhancer blocking. We show here that a 250-bp “core” element from within 5′HS4 is sufficient to confer protection against silencing of transgenes caused by CPE. Further dissection of the core reveals that 5′HS4 is a compound element in which it is possible to separate enhancer blocking and barrier activities. We demonstrate that full protection against CPE is conferred by mutant 5′HS4 sequences from which the CTCF-binding site has been deleted. In contrast, mutations of four other protein binding sites within 5′HS4 result in varying reductions in the ability to protect against CPE. We find that binding sites for CTCF are neither necessary nor sufficient for protection against CPE. Comparison of the properties of 5′HS4 with those of other CTCF-binding enhancer-blocking elements suggests that CPE protection is associated with maintenance of a high level of histone acetylation near the insulator, conferred by insulator binding-proteins other than CTCF.