bluuebunny/crossref_metadata_2025 huggingface dataset:
Light-emitting diodes and laser diodes based on a Ga1−xInxAs/GaAs1−ySby type II superlattice on InP substrate
Authors: Peter M. , Kiefer R. , Fuchs F. , Herres N. , Winkler K. , Bachem K.-H. , Wagner J.
Published: July 2002

We report on the fabrication and characterization of light-emitting diodes (LEDs) and laser diodes with a staggered type II Ga1−xInxAs/GaAs1−ySby superlattice (SL) as the active region. SLs were grown strain compensated on the InP substrate using metalorganic chemical vapor deposition. The LEDs show room-temperature electroluminescence up to 2.14 μm, the index-guided diode lasers displayed cw laser emission at 1.71 μm up to 300 K. The spontaneous emission spectrum was found to show a significant blueshift with increasing injection current density, resulting in shorter laser emission wavelengths for the diode laser than for the LED.
Structures of the linear silicon carbides SiC4 and SiC6: Isotopic substitution and Ab Initio theory
Authors: Gordon V. D. , Nathan E. S. , Apponi A. J. , McCarthy M. C. , Thaddeus P. , Botschwina P.
Published: July 2002

The structures of two linear silicon carbides, SiC4 and SiC6, have been determined by a combination of isotopic substitution and large-scale coupled-cluster ab initio calculations, following detection of all of the singly substituted isotopic species in a supersonic molecular beam with a Fourier transform microwave spectrometer. Rotational constants obtained by least-squares fitting transition frequencies were used to derive experimental structures; except for those nearest the center of mass, individual bond lengths for both chains have an error of less than 0.008 Å. Accurate equilibrium structures were derived by converting the experimental rotational constants to equilibrium constants using the vibration–rotation coupling constants from coupled-cluster calculations, including connected triple substitutions. Equilibrium dipole moments and harmonic vibrational frequencies were also calculated for both chains. On the basis of the calculated vibration–rotation and l-type doubling constants, weak rotational satellites from a low-lying vibrational state of SiC4 were assigned to v6, a bending mode calculated to lie about 205 cm−1 above the ground state. A recommended ab initio equilibrium structure for SiC8 has also been established.
Vibrational relaxation of vibrationally and rotationally excited CO molecules by He atoms
Authors: Krems Roman V.
Published: July 2002

This work presents a detailed quantum mechanical study of rovibrationally inelastic He+CO collisions in a wide range of translational and internal energies of the collision partners. Fully converged coupled states calculations of rate constants for vibrational relaxation of CO(v=1) by He are found to be in excellent agreement with experimental measurements at temperatures between 35 and 1500 K. The role of rotational energy for vibrational relaxation of CO is investigated and it is illustrated that the CO molecules in the first excited vibrational state can exhibit near-resonant vibrational relaxation when they are initially in high rotational excitation and the collision energy is small. A reduced channel coupled states approach neglecting low vibrational states in the basis set is implemented for calculations of rate constants for vibrational and rotational energy transfer in collisions of vibrationally excited CO molecules with He atoms. It is shown that initial vibrational excitation significantly increases rate constants for vibrationally inelastic collisions but does not affect purely rotational energy transfer.
Stabilizing the Richardson eigenvector algorithm by controlling chaos
Authors: He Song
Published: July 2002

By viewing the operations of the Richardson purification algorithm as a discrete time dynamical process, we propose a method to overcome the instability of this eigenvector algorithm by controlling chaos. We present theoretical analysis and numerical results on the behavior and performance of the stabilized algorithm.  © 1997 American Institute of Physics.
AuO+ and AuO+2 gaseous ions formed during the sputter deposition of Au films in Ar-O2 discharges
Authors: Aita Carolyn Rubin
Published: July 2002

AuO+ and AuO+2 gaseous ions formed during the sputtering of an Au target in 1.0×10−2 Torr, rf-excited Ar-O2 discharges were studied by glow-discharge mass spectrometry. These ions are created from neutral species in the negative glow and are incident on the substrate during a sputter deposition. The relative flux of AuO+2 /Au+, AuO+/Au+, and AuO+2 /AuO+ was determined for gas compositions from 100% Ar to 100% O2. The results show that the arrival of Au-oxide species at the substrate, in addition to Au atoms, must be taken into account when modeling the growth of Au films sputter deposited in O2-bearing discharges.
Optical oscillator strengths for isoelectronic ions of sodium
Authors: Ganas P. S.
Published: July 2002

An analytic atomic independent-particle model potential adjusted to experimental energy levels is used to generate wave functions for the valence and excited states of isoelectronic ions of sodium from Z=12–22. Using the Born approximation and LS coupling, we calculate optical oscillator strengths for excitations of the valence electron from the 1s22s22p23s(2S1/2) ground state. The results are compared to experiment and other calculations.
Scanning tunneling microscopy bit making on highly oriented pyrolytic graphite: Initial results
Authors: Miller Jimmie A. , Hocken Robert J.
Published: July 2002

A scanning tunneling microscope was used to modify the surface structure of highly oriented pyrolytic graphite in air. By superimposing 0.1-μs pulses on the substrate bias, we consistently manufactured hole-hill combinations (‘‘bits’’) of 2–3 nm. A 40-nm L-shaped structure was created. We describe the experiments and relevant results.
Morphology and growth process of thermally induced oxide precipitates in Czochralski silicon
Authors: Sueoka K. , Ikeda N. , Yamamoto T. , Kobayashi S.
Published: July 2002

The morphology and growth process of oxide precipitates in Czochralski silicon have been studied with prolonged thermal treatments up to 700 h at intermediate temperatures (700–900 °C). It was found with transmission electron microscopy observation that (i) the morphology of precipitates changes from platelet to aggregation of polyhedra at both 800 and 900 °C during isothermal heat treatment, and (ii) the growth of platelet precipitates follows a t1/2 law.
Anisotropic etching of polymers in SO2/O2 plasmas: Hypotheses on surface mechanisms
Authors: Pons Michel , Pelletier Jacques , Joubert Olivier
Published: July 2002

A study of the anisotropy of the etching of resists in SO2-based plasmas is performed in a distributed electron-cyclotron-resonance plasma excited at 2.45 GHz with independent radio frequency biasing at 13.56 MHz. Emphasis is put on the comparison of the profiles and etch rates obtained in pure oxygen and SO2-containing plasmas as a function of substrate temperature and ion bombardment energy. For a constant ion bombardment intensity, a significant decrease in the etch rate obtained using pure SO2 plasmas is observed as compared to pure O2 plasmas. The evolution of the etch rate with ion energy also shows quite different behavior. In contrast to pure oxygen plasmas, perfect anisotropic profiles can be obtained on cooled substrates with SO2-containing gas mixtures. A likely explanation for these results is to assume that sulfur acts as a passivating layer at temperatures close to or below room temperature. The surface mechanisms involved in this sulfur passivation and the conditions required to obtain an effective sidewall passivation are discussed. Based on similar mechanisms, the operating conditions required to obtain perfect anisotropic profiles in pure oxygen plasmas are deduced and compared to the experimental data.
Optical spectra and crystal field analysis of Dy3+ in Cs2NaDyCl6 and Cs2NaYCl6: Dy3+(5 mol %)
Authors: Foster David R. , Richardson F. S.
Published: July 2002

Optical absorption and emission measurements are reported for the Cs2NaDyCl6 and Cs2NaYCl6: Dy3+(5 mol %) systems under variable-temperature (10–298 K) conditions. For both systems, the data are compatible with the retention of octahedral (Oh) site symmetry at the Dy3+ ions over the entire 298 to 10 K temperature range. The only differentiation between the systems is the much greater quantum efficiency of 4F9/2 emission in the doped system vs that in the neat system. Forty-five crystal-field levels spanning 18 multiplets of the Dy3+ 4f9 electronic configuration are located and assigned, and an additional 12 crystal-field levels associated with six other multiplet manifolds are located, but left unassigned. These energy level results are analyzed on the basis of a nine-parameter 4f-electron Hamiltonian operating within a complete Russell–Saunders (SLJ) basis set for the 4f9 configuration of Dy3+. The most intense electric-dipole vibronic lines observed in the optical spectra are assigned to one-phonon vibronic transitions associated with the three odd-parity ‘‘moiety’’ modes of the DyCl3−6 octahedral clusters: ν3(t1u), ν4(t1u), and ν6(t2u). Intensity calculations are reported for both the no-phonon magnetic-dipole (origin) transitions and the one-phonon (ν3, ν4, and ν6) electric-dipole vibronic transitions.
Binary nucleation in acid–water systems. II. Sulfuric acid–water and a comparison with methanesulfonic acid–water
Authors: Wyslouzil B. E. , Seinfeld J. H. , Flagan R. C. , Okuyama K.
Published: July 2002

This work presents a systematic investigation of binary nucleation rates for sulfuric acid and water and the effect of temperature on these rates at isothermal, subsaturated conditions. The results from nucleation rate measurements for the sulfuric acid (H2SO4) –water system are discussed and compared to those previously presented for methanesulfonic acid (MSA)–water [B. E. Wyslouzil, J. H. Seinfeld, R. C. Flagan, and K. Okuyama, J. Chem. Phys. (submitted)]. Experiments were conducted at relative humidities (Rh) ranging from 0.006<Rh<0.65, relative acidities (Ra) in the range of 0.04<Ra<0.46, and at three temperatures, T=20, 25, and 30 °C, in the continuous flow mixing-type apparatus described in Paper I. Particles were formed by binary nucleation and grew by condensation as the mixed stream flowed through an isothermal glass tube. Number concentrations observed at the exit of the nucleation and growth tube as a function of Rh and Ra are extremely sensitive to the binary nucleation rate, and from these data the nucleation rate was estimated as a function of saturation level and temperature. Particle size distributions were also measured using a specially constructed differential mobility analyzer. As anticipated, the H2SO4 particles formed by nucleation and growth are much smaller than those formed in the MSA–water experiments, but particle size distribution measurements confirm that most of the particles formed are being observed. The ratio of experimental to theoretical nucleation rates, Jexpt/Jtheor, was found to be a strong function of the predicted number of acid molecules in the critical nucleus for both the H2SO4 –water and MSA–water systems.
Local-field effects in the second-harmonic generation from Langmuir–Blodgett monolayers
Authors: Ui H. , Tomioka A. , Nishiwaki T. , Miyano K.
Published: July 2002

The validity of the local-field approximation (LFA) has been tested in hemicyanine dye Langmuir–Blodgett monolayers. Resonant structures of absorption and the second-harmonic generation revealed that LFA is adequate to describe the second-harmonic generation in the monolayers even when the intermolecular interaction is very strong (H aggregate). A simple calculation procedure is also presented which enables one to treat monolayers as a macroscopic object in a consistent manner with the microscopic structure.
Coupling of electrons to intermolecular phonons in molecular charge transfer dimers: A resonance Raman study
Authors: Pedron D. , Speghini A. , Mulloni V. , Bozio R.
Published: July 2002

We report resonance Raman scattering (RRS) spectra and Raman excitation profiles (REP) of a system containing π dimers of identical molecular radical ions measured with laser excitation in resonance with the charge transfer (CT) transition. A Peierls–Hubbard (PH) Hamiltonian has been used to model the investigated system and to calculate its optical and RRS properties. Results are reported for two polyoxometallate salts of tetrathiafulvalene (TTF), namely (TTF)2(W6O19) and (TTF)2(Mo6O19) whose structures contain almost isolated (TTF+)2 dimers. The RRS spectra of (TTF)2(W6O19), measured in resonance with the CT absorption band centered at 832 nm, show three phonon modes located at 55, 90, and 116 cm−1 which are strongly resonance enhanced. These modes have been associated to the out-of-phase combinations of the translational motions of the two molecules composing the dimer. Such modes are effective in modulating the intradimer transfer integral, thus providing an efficient mechanism for coupling with the electronic system and for enhancement of the scattering intensity at resonance with the CT transition. The REP for the three strongly coupled modes of (TTF)2(W6O19) have been measured with laser excitation wavelengths ranging from 740 to 930 nm. Quantitative analysis of the REP data has been performed based on a perturbative solution of the PH model to second order in the electron-molecular-vibration (EMV) and electron-intermolecular-phonon (EIP) interactions. The CT absorption profile and the REP’s have been calculated using a time correlator technique and the model parameters have been optimized in order to fit the experimental REP data. Infrared vibronic absorptions of (TTF)2(W6O19), originated by the EMV coupling, have been measured and independent information on the electronic parameters of the PH model have been derived. This has made the choice of the fitting parameters used for the REP calculations rather unambiguous and has allowed us to obtain, for the first time, reliable experimental estimates of the EIP coupling constants.
Electron binding energy and long-range electronic coupling: A theoretical study
Authors: Sengupta B. , Curtiss L. A. , Miller J. R.
Published: July 2002

Electronic couplings in long-range electron transfer have been calculated using ab initio molecular orbital theory to investigate the effect of the binding energy of the electron on the decay of through-space and through-bond couplings. Through-space and through-bond couplings for anions and cations of the CF3 dimer and of CnH2n and CnF2n chains were calculated by ab initio molecular orbital theory. The anions and cations provide systems for which the electron binding energies, Be, differ by about a factor of 10. Through-space couplings decay exponentially, exp(−βR), with increasing distance, R, between the donor/acceptor carbon atoms. The decay coefficient β varies approximately as B1/2e. In contrast, the decay coefficients for through-bond coupling in CnF2n and CnH2n chains are not affected significantly by the binding energy of the electron.
Integrable discretizations of the Bogoyavlensky lattices
Authors: Suris Yuri B.
Published: July 2002

Discretizations of the Bogoyavlensky lattices are introduced, belonging to the same hierarchies as the continuous-time systems. The construction exemplifies the general scheme for integrable discretization of systems on Lie algebras with r-matrix Poisson brackets. An initial value problem for the difference equations is solved in terms of a factorization problem in a group. Interpolating Hamiltonian flows are found.
On the essential spectrum of transport operators on L1-spaces
Authors: Latrach Khalid , Jeribi Aref
Published: July 2002

In a recent article by the first author [J. Math. Phys. 35, 6199–6212 (1994)] the essential spectrum of transport operator was analyzed in Lp-spaces for p∈(1,+∞). The purpose of the present work is to extend this analysis to the case of L1-spaces. After establishing preliminary results we define the notion of the weak spectrum which we characterize by means of Fredholm operators. We show, in particular, that in L1-spaces the weak spectrum is nothing else but the essential spectrum. Using the same techniques as in the above-mentioned work, we prove the stability of the essential spectrum of a one-dimensional transport operator with general boundary conditions where an abstract boundary operator relates the incoming and the outgoing fluxes. Sufficient conditions are given in terms of boundary and collision operators, assuring the stability of the essential spectrum. We show also that our results remain valid for neutron transport operators in arbitrary dimension.
Time-resolved luminescent spectra of J-aggregates with exciton traps
Authors: Malyukin Yu. V.
Published: July 2002

The possibility of coexistence of free and self-trapped excitons in one-dimensional molecular chains (J-aggregates) has been proved on the basis of experimental study of time-resolved low-temperature luminescence spectra.
The aerodynamic admittance of a square plate in a flow with a fully coherent fluctuation
Authors: Drabble M. J. , Grant I. , Armstrong B. J. , Barnes F. H.
Published: July 2002

Measurements are presented of the aerodynamic admittance of a square plate in a flow with a fully coherent fluctuation in the free-stream velocity. The admittance relates the fluctuating force acting on the plate in the flow direction to the fluctuation in the flow velocity. It is found that, as the fluctuation frequency increases, the admittance increases from unity (its value by definition at zero frequency) in contrast to the decrease found in a turbulent flow. Furthermore, if it is assumed that the fluctuating force has two components, one involving a drag coefficient and the other a virtual mass coefficient, then the measurements show that the two coefficients are frequency dependent. Their variation with frequency is presented.
Rotating, nonlinearly stratified flow past an isolated obstacle
Authors: Foster M. R. , Davies P. A. , Spence G. S. M.
Published: July 2002

The effects of density profile nonlinearities upon topographic steering in rapidly rotating, stratified flows are considered. The vorticity equation describing the topographic interaction is derived for a stable density profile of arbitrary form, and numerical solutions, valid under the condition Ε≫E1/2, are obtained for shallow obstacles of parabolic shape, over a range of values of the (parabolic) density profile curvature, the bulk stratification, and the obstacle height, taken here to be O(Ε). (Here, Ε and E are the Rossby and Ekman numbers, respectively, of the flow.) The results (i) demonstrate that for linear and nonlinear density profiles there are vertical attenuations of the streamline deflections above the obstacle, and (ii) confirm the dependence of this attenuation upon the bulk stratification S in the fluid. It is found that near the top of the obstacle the streamline curvature increases as the value of S increases. Furthermore, it is shown that for a given value of S, the vertical extent of the topographically induced disturbance field is reduced as the degree of nonlinearity in the density profile is increased. The decay of vorticity with height above the obstacle is also shown to be very sensitive to the degree of nonlinearity, with nonlinear density gradients exhibiting much larger values of surface vorticity than linear gradient counterparts, under otherwise identical conditions. Good qualitative agreement is found with results of previous laboratory experiments by Davies and Rahm [Phys. Fluids 25, 1931 (1982)]. The consequences of neglecting Ekman suction effects in the analysis are discussed with regard to the boundary layer structures on the solid surfaces; inclusion of Ekman suction is shown to result in the occurrence of a wake in the nonlinear problem.
Fluid mixing during melting
Authors: Woods Andrew W.
Published: July 2002

The different modes of convection that can arise when a solid of one pure phase melts into a binary fluid are described. These depend upon the relative density of the molten solid and the binary fluid and upon whether the solid lies above or beneath the liquid. The case in which compositionally buoyant melt rises and mixes into an overlying denser liquid is studied. A global model describing the conservation of mass, concentration and enthalpy during the melting is presented. This is successfully compared with a number of new laboratory experiments. The model is extended to include the formation of crystals in the liquid as it cools. This suggests a simple estimate of the maximum amount of crustal melt produced when a hot, molten magma intrudes and melts the floor of a magma chamber in the continental crust.
Nonsymmetric Saffman–Taylor fingers
Authors: Brener Efim , Levine Herbert , Tu Yuhai
Published: July 2002

The Saffman–Taylor family of viscous fingering patterns is generalized to the case of nonsymmetric forcing; this type of forcing would occur if the Hele–Shaw cells were rotated (about the flow axis) in the presence of a gravitational field. At small surface energy, the selected pattern is determined analytically, which, not surprisingly, lacks reflection symmetry about the middle of the cell. The connection of this problem to that of nonsymmetric dendritic crystal growth is briefly discussed.
Pressure field, feedback, and global instabilities of subsonic spatially developing mixing layers
Authors: Grinstein F. F. , Oran E. S. , Boris J. P.
Published: July 2002

Two-dimensional numerical simulations of compressible, subsonic, planar shear flows, are used to investigate the role of feedback in the reinitiation of vortex roll-up. The study deals with unforced, spatially evolving mixing layers for which the propagation of acoustic disturbances can be resolved and boundary effects are ensured to be negligible. The calculated pattern of coherent structures shows global self-sustaining instabilities in which new vortex roll-ups are triggered in the initial shear layer by pressure disturbances originating in the fluid accelerations downstream. This reinitiation mechanism, absent in the linear treatments of stability, is demonstrated conclusively here and examined as a function of Mach number and free-stream velocity ratio. The global instability becomes less efficient in reinitiating vortex roll-up in the initial shear layer when the acoustic propagation velocities on the sides of the mixing layer approach each other, i.e., as the incompressible regime is approached, and as the free-stream velocity ratios approach unity.
Quasilinear diffusion rates of cometary ions
Authors: Yoon Peter H. , Ziebell L. F.
Published: July 2002

The freshly created ions in the upstream region of the cometary bow shock usually form a ring-beam velocity distribution in the solar wind frame of reference. These newborn ions subsequently excite a variety of instabilities which in turn cause the ions to diffuse in pitch angle space to form a quasispherical shell velocity distribution. Such a process can be described by quasilinear kinetic theory. In the present paper, the detailed properties of the initial diffusion rates associated with the cometary newborn ions are studied for various physical parameters including the so-called injection angle α (that is, the average initial pitch angle associated with the ions) ranging from 0° (pure beam distribution) to 90° (pure ring distribution). It is shown that initial diffusion rates are strongly dependent upon the angle α, such that for 0°≤α≤60° (quasiparallel regime) the pitch angle diffusion rate remains relatively small, while for 60°≤α≤90° (quasiperpendicular regime) the diffusion rate increases substantially.
Strong plasma wave excitation by a ‘‘chirped’’ laser beat wave
Authors: Deutsch M. , Meerson B. , Golub J. E.
Published: July 2002

A modification of the plasma beat-wave excitation scheme is proposed, aimed at a significant increase of the resulting plasma wave amplitude. The modification employs two laser beams with a down-chirped beat frequency that follows, on the average, the amplitude-dependent frequency of the intense plasma wave. Numerical and analytical calculations that support the proposed scheme are presented. Also, new analytical solutions for the constant beat-frequency case are obtained. Finally, a plausible experimental setup is suggested, where one of two CO2 laser beams attains the necessary frequency chirp by passing through a diffraction grating pair.
Nonstationary stimulated Brillouin backscattering
Authors: Hüller S. , Mulser P. , Rubenchik A. M.
Published: July 2002

Stimulated Brillouin scattering (SBS) is investigated one dimensionally under conditions when the typical growth rate is comparable with the ion acoustic frequency. The equations for the three-wave interaction are modified according to strong coupling. Studies of SBS in homogeneous plasma slabs exhibit the onset of steady-state solutions. A reflecting rear boundary can cause the backscattering to show nonstationary behavior. In addition, inhomogeneous plasma profiles that include the critical density are studied using the electromagnetic wave equation together with a hydrodynamic approach for the ion fluid.
Steady-state solution of a two-dimensional Fokker–Planck equation with strong quasilinear diffusion for lower-hybrid current drive
Authors: Krapchev V. B. , Hewett D. W. , Bers A.
Published: July 2002

The two-dimensional Fokker–Planck equation with strong quasilinear diffusion on the tail of the electron distribution function is solved analytically and numerically. The quasilinear diffusion is taken to be parallel to the confining magnetic field of the plasma, as is appropriate for lower-hybrid current drive. The radio frequency fields that produce this quasilinear diffusion are assumed to be imposed by external sources. It is found that an appreciable broadening of the resonant plateau in the direction perpendicular to the toroidal magnetic field leads to more particles carrying the current. As a result both the current (J) and the power dissipated (Pd) are substantially enhanced, compared with the predictions of one-dimensional theory. The figure of merit J/Pd is three times larger than the one found from the one-dimensional theory.
Oscillation center theory and ponderomotive stabilization of low-frequency plasma modes
Authors: Similon Philippe L. , Kaufman Allan N. , Holm Darryl D.
Published: July 2002

Nonlinear, nondissipative ponderomotive theory is developed in relation to recent experimental results showing that externally imposed rf fields can stabilize an axisymmetric mirror plasma. First, the ponderomotive force problem is reexamined, with emphasis on self-consistency of the interaction between the plasma and high-frequency field. The averaged action principle for the antenna–plasma system yields self-consistent plasma and electromagnetic field dynamics on the oscillation-center time scale. The plasma equilibrium condition is expressed as a balance among plasma and magnetic pressure forces, including interchange, ponderomotive, and magnetization forces. Next, the spectral stability of such static equilibria is studied in the low-frequency magnetohydrodynamic (MHD) approximation, with a ΔW principle that incorporates the various ponderomotive contributions: particle effects, magnetization effects, and self-consistent adjustment of the rf field resulting from displacements of the plasma away from equilibrium. The ponderomotive potential energy functional is related to the antenna inductance and antenna current amplitude. Finally, the noncanonical Hamiltonian formulation for the system’s dynamics is given, in terms of Eulerian fields. It allows the construction of nonlinearly conserved functionals, which yield criteria for linearized Lyapunov stability, for both multifluid and MHD models. The Lyapunov stability conditions are related to the modified ΔW variational principle.
Electromagnetic filamentation instability of a whistler wave
Authors: Sharma O. P. , Patel V. L.
Published: July 2002

A high amplitude whistler wave propagating along the magnetic field lines (k0∥Bs) in a plasma is unstable to a transverse electromagnetic perturbation (k⊥k0), having a perturbed magnetic field B∥Bs∥ẑ, where Bs is the static magnetic field. The instability grows on an Alfvén time scale and is relevant when vo/vA≳ω0/ωc, where vo is the oscillatory velocity of electrons caused by the pump and vA is the Alfvén speed, ω0 is the frequency of the whistler pump, and ωc is the electron cyclotron frequency.
A quadratic-form analysis of the collisionless tearing mode
Authors: Chen J. , Lee Y. C.
Published: July 2002

In this paper a method is described to study the collisionless tearing mode properties in cases where complicated orbit integrals must be evaluated. The method is based on a quadratic form of a self-adjoint integrodifferential operator. No approximations are made for equilibrium orbits and perturbed fields in evaluating the necessary orbit integrals. The objective of the paper is to provide a rigorous theoretical basis for the method. Application to physical systems is demonstrated for the collisionless tearing mode in a non-Maxwellian neutral sheet. This method may be applied to other Vlasov instabilities and is particularly suited for problems where the numerical evaluation of orbit integrals is time consuming. In such cases, the present method can yield stability criteria with minimal computation.
Nonlinear wave interactions and evolution of a ring-beam distribution of energetic electrons
Authors: Kainer S. , Gaffey J. D. , Price C. P. , Hu X. W. , Zhou G. C.
Published: July 2002

A ring-beam distribution function of moderately relativistic electrons is unstable to electromagnetic and electrostatic waves. The results obtained in numerical simulations show that electromagnetic radiation corresponding to the normal modes of the background plasma is observed to grow even in the presence of a strong electrostatic instability and becomes very strong when the growth of the electrostatic Langmuir waves is minimized, and that the instability process is best described as a beam cyclotron resonance. Another strong radiation generated by the ring beam is the Z mode which is coupled to the electrostatic Langmuir wave. Under certain circumstances, these mechanisms may be significant in astrophysical situations.
Partial molar volume, surface area, and hydration changes for equilibrium unfolding and formation of aggregation transition state: High-pressure and cosolute studies on recombinant human IFN-γ
Authors: Webb Jonathan N. , Webb Serena D. , Cleland Jeffrey L. , Carpenter John F. , Randolph Theodore W.
Published: July 2002

The equilibrium dissociation of recombinant human IFN-γ was monitored as a function of pressure and sucrose concentration. The partial molar volume change for dissociation was −209 ± 13 ml/mol of dimer. The specific molar surface area change for dissociation was 12.7 ± 1.6 nm
2
/molecule of dimer. The first-order aggregation rate of recombinant human IFN-γ in 0.45 M guanidine hydrochloride was studied as a function of sucrose concentration and pressure. Aggregation proceeded through a transition-state species, N*. Sucrose reduced aggregation rate by shifting the equilibrium between native state (N) and N* toward the more compact N. Pressure increased aggregation rate through increased solvation of the protein, which exposes more surface area, thus shifting the equilibrium away from N toward N*. The changes in partial molar volume and specific molar surface area between the N* and N were −41 ± 9 ml/mol of dimer and 3.5 ± 0.2 nm
2
/molecule, respectively. Thus, the structural change required for the formation of the transition state for aggregation is small relative to the difference between N and the dissociated state. Changes in waters of hydration were estimated from both specific molar surface area and partial molar volume data. From partial molar volume data, estimates were 25 and 128 mol H
2
O/mol dimer for formation of the aggregation transition state and for dissociation, respectively. From surface area data, estimates were 27 and 98 mol H
2
O/mol dimer. Osmotic stress theory yielded values ≈4-fold larger for both transitions.
Inhibition of Plasmodium falciparum malaria using antisense oligodeoxynucleotides.
Authors: Barker R H , Metelev V , Rapaport E , Zamecnik P
Published: July 2002

We studied inhibition of growth of the malaria parasite Plasmodium falciparum in in vitro culture using antisense (AS) oligodeoxynucleotides (ODNs) against different target genes. W2 and W2mef strains of drug-resistant parasites were exposed to AS ODNs over 48 hr, and growth was determined by microscopic examination and [3H]hypoxanthine incorporation. At ODN concentrations of 1 microM, phosphorothioate (PS) ODNs inhibited growth in a target-independent manner. However, between 0.5 and 0.005 microM, ODNs against dihydrofolate reductase, dihydropteroate synthetase, ribonucleotide reductase, the schizont multigene family, and erythrocyte binding antigen EBA175 significantly inhibited growth compared with a PS AS ODN against human immunodeficiency virus, two AS ODNs containing eight mismatches, or the sense strand controls (P < 0.0001). The IC50 was approximately 0.05 microM, whereas that for non-sequence-specific controls was 15-fold higher. PS AS ODNs against DNA polymerase alpha showed less activity than that for other targets, whereas a single AS ODN against triose-phosphate isomerase did not differ significantly from controls. We conclude that at concentrations below 0.5 microM, PS AS ODNs targeted against several malarial genes significantly inhibit growth of drug-resistant parasites in a nucleotide sequence-dependent manner. This technology represents an alternative method for identifying malarial genes as potential drug targets.
Microsatellite instability in childhood rhabdomyosarcoma is locus specific and correlates with fractional allelic loss.
Authors: Visser M , Bras J , Sijmons C , Devilee P , Wijnaendts L C , van der Linden J C , Voûte P A , Baas F
Published: July 2002

Replication errors (RERs) were initially identified in hereditary nonpolyposis colon cancer and other tumors of Lynch syndrome II. Mutations in genes involved in mismatch repair give rise to a mutator phenotype, resulting in RERs. The mutator phenotype is thought to predispose to malignant transformation. Here we show that in the embryonal form of childhood rhabdomyosarcoma, RERs also occur, but in contrast to hereditary nonpolyposis colon cancer, only a subset of the microsatellite loci analyzed show RERs. The occurrence of RERs is strongly correlated with increased fractional allelic loss (P < 0.001), suggesting that the occurrence of RERs is a secondary phenomenon in rhabdomyosarcoma. Coincidental loss of genes involved in mismatch repair, possibly due to their proximity to tumor suppressor genes involved in tumor progression of embryonal form of childhood rhabdomyosarcoma, could explain the observed phenomenon.
Evolution of alcohol dehydrogenase genes in the palm and grass families.
Authors: Morton B R , Gaut B S , Clegg M T
Published: July 2002

The alcohol dehydrogenase (Adh; alcohol:NAD+ oxidoreductase, EC 1.1.1.1) gene family has two or three loci in a broad array of angiosperm species. The relative stability in the number of Adh loci led Gottlieb [Gottlieb, L. D. (1982) Science 216, 373-380] to propose that the Adh gene family arose from an ancient gene duplication. In this study, the isolation of three loci from the California fan palm (Washingtonia robusta) is reported. The three loci from palm are highly diverged. One palm Adh gene, referred to here as adhB, has been completely sequenced, including 950 nucleotides of the upstream regulatory region. For the second locus, adhA, 81% of the exon sequence is complete. Both show the same basic structure as grass Adh genes in terms of intron number and intron location. The third locus, adhC, for which only a small amount of sequence is available (12% of exon sequence) appears to be more highly diverged. Comparison of the Adh gene families from palms and grasses shows that the adh1 and adh2 genes of grasses, and the adhA and adhB genes of palms, arose by duplication following the divergence of the two families. This finding suggests that the multiple Adh loci in different monocot lineages are not the result of a single ancestral duplication but, rather, of multiple duplication events.
Induction of cellular immunity in chimpanzees to human tumor-associated antigen mucin by vaccination with MUC-1 cDNA-transfected Epstein-Barr virus-immortalized autologous B cells.
Authors: Pecher G , Finn O J
Published: July 2002

Aberrant glycosylation of the mucin molecule (encoded by the gene MUC-1) on human epithelial cell tumors leads to the exposure of tumor-associated epitopes recognized by patients' antibodies and cytotoxic T cells. Consequently, these epitopes could be considered targets for immunotherapy. We designed a cellular vaccine, employing, instead of tumor cells, autologous Epstein-Barr virus (EBV)-immortalized B cells as carriers of tumor-associated mucin, to take advantage of their costimulatory molecules for T-cell activation. The vaccine was tested in chimpanzees because of the identity of the human and chimpanzee MUC-1 tandem repeat sequence. EBV-immortalized B cells derived from two chimpanzees were transfected with MUC-1 cDNA, treated with glycosylation inhibitor phenyl-N-acetyl-alpha-D-galactosaminide to expose tumor-associated epitopes, irradiated, and injected subcutaneously four times at 3-week intervals. One vaccine preparation also contained cells transduced with the interleukin 2 (IL-2) cDNA and producing low levels of IL-2. Already after the first injection we found in the peripheral blood measurable frequency of cytotoxic T-cell precursors specific for underglycosylated mucin. The highest frequency observed was after the last boost, in the lymph node draining the vaccination site. Delayed-type hypersensitivity reaction to the injected immunogens was also induced, whereas no appearance of mucin-specific antibodies was seen. Long-term observation of the animals yielded no signs of adverse effects of this immunization. Autologous antigen-presenting cells, like EBV-immortalized B cells, expressing tumor-associated antigens are potentially useful immunogens for induction of cellular anti-tumor responses in vivo.
Intradimerically tethered DNA topoisomerase II is catalytically active in DNA transport.
Authors: Lindsley J E
Published: July 2002

A covalently cross-linked dimer of yeast DNA topoisomerase II was created by fusing the enzyme with the GCN4 leucine zipper followed by two glycines and a cysteine. Upon oxidation of the chimeric protein, a disulfide bond forms between the two carboxyl termini, covalently and intradimerically cross-linking the two protomers. In addition, all nine of the cysteines naturally occurring in topoisomerase II have been changed to alanines in this construct. This cross-linked, cysteine-less topoisomerase II is catalytically active in DNA duplex passage as indicated by ATP-dependent DNA supercoil relaxation and kinetoplast DNA decatenation assays. However, these experiments do not directly distinguish between a "one-gate" and a "two-gate" mechanism for the enzyme.
A yeast artificial chromosome-based map of the region of chromosome 20 containing the diabetes-susceptibility gene, MODY1, and a myeloid leukemia related gene.
Authors: Stoffel M , Le Beau M M , Espinosa R , Bohlander S F , Le Paslier D , Cohen D , Xiang K S , Cox N J , Fajans S S , Bell C I
Published: July 2002

We have generated a physical map of human chromosome bands 20q11.2-20q13.1, a region containing a gene involved in the development of one form of early-onset, non-insulin-dependent diabetes mellitus, MODY1, as well as a putative myeloid tumor suppressor gene. The yeast artificial chromosome contig consists of 71 clones onto which 71 markers, including 20 genes, 5 expressed sequence tags, 32 simple tandem repeat DNA polymorphisms, and 14 sequence-tagged sites have been ordered. This region spans about 18 Mb, which represents about 40% of the physical length of 20q. Using this physical map, we have refined the location of MODY1 to a 13-centimorgan interval (approximately equal to 7 Mb) between D20S169 and D20S176. The myeloid tumor suppressor gene was localized to an 18-centimorgan interval (approximately equal to 13 Mb) between RPN2 and D20S17. This physical map will facilitate the isolation of MODY1 and the myeloid tumor suppressor gene.
BCL8
, a novel gene involved in translocations affecting band 15q11–13 in diffuse large-cell lymphoma
Authors: Dyomin Vadim G. , Rao Pulivarthi H. , Dalla-Favera Riccardo , Chaganti R. S. K.
Published: July 2002

Translocations affecting the chromosomal region 15q11–13 and various other partners are recurrent in diffuse large-cell lymphomas (DLCL). To identify the putative gene, here named
BCL8
, involved in these translocations we have cloned the breakpoint region from a DLCL patient with t(14;15)(q32;q11–13) and the corresponding germ-line region from chromosome 15. The genomic locus on chromosome 15 is clonally rearranged in about 4% of DLCL in agreement with the frequency of 15q11–13 translocations. A probe derived from the
BCL8
locus on chromosome 15 detected a transcript in human testis and prostate, whereas no expression was found in spleen, thymus, and blood leukocytes. Analysis of the
BCL8
cDNA clones isolated from human testis cDNA library showed that the
BCL8
gene generates a major transcript of 2.6 kb and a less prominent 4.5-kb species due to differential polyadenylylation. By reverse transcription–PCR analysis of RNA extracted from frozen DLCL samples and lymphoma cell lines,
BCL8
expression was detected in all patients carrying 15q11–13 abnormalities and in a fraction of randomly selected DLCL patients. These results suggest that the
BCL8
gene is not normally expressed in lymphoid tissues, but its expression can be activated by chromosomal translocation or by other mechanisms in DLCL. Ectopic expression of
BCL8
in a significant proportion of DLCL suggests an important role for this gene in the molecular pathogenesis of B cell lymphoma.
A ribozyme-mediated, gene “knockdown” strategy for the identification of gene function in zebrafish
Authors: Xie Yuefeng , Chen Xiaozhuo , Wagner Thomas E.
Published: July 2002

The zebrafish system offers many unique opportunities for the study of molecular biology. To date, only random mutagenesis, and not directed gene knockouts, have been demonstrated in this system. To more fully develop the potential of the zebrafish system, an approach to effectively inhibit the expression of any targeted gene in the developing zebrafish embryo has been developed. This approach uses a transient, cytoplasmic, T7 expression system, injected into the fertilized zebrafish egg to rapidly produce high levels of a ribozyme directed against the mRNA encoded by the targeted gene to inhibit its expression. In a demonstration of this strategy, expression of the recessive dominant zebrafish
no tail
gene was effectively inhibited by using this strategy to yield a phenotype identical to that resulting from a known defective mutation in this same gene. This, ribozyme-mediated, message deletion strategy may have use in determining the function of genetic coding sequences of unknown function.
p53CP, a putative p53 competing protein that specifically binds to the consensus p53 DNA binding sites: A third member of the p53 family?
Authors: Bian Junhui , Sun Yi
Published: July 2002

p53 tumor suppressor protein negatively regulates cell growth, mainly through the transactivation of its downstream target genes. As a sequence-specific DNA binding transcription factor, p53 specifically binds to a 20-bp consensus motif 5′-PuPuPuC(A/T) (T/A)GPyPyPyPuPuPuC(A/T)(T/A)GPyPyPy-3′. We have now identified, partially purified, and characterized an additional ≈40-kDa nuclear protein, p53CP (p53 competing protein), that specifically binds to the consensus p53 binding sites found in several p53 downstream target genes, including
Waf-1
,
Gadd45
,
Mdm2
,
Bax
, and
RGC
. The minimal sequence requirement for binding is a 14-bp motif, 5′-CTTGCTTGAACAGG-3′ [5′-C(A/T)(T/A)GPyPyPyPuPuPuC(A/T)(T/A)G-3′], which includes the central nucleotides of the typical p53 binding site with one mismatch. p53CP and p53 (complexed with antibody) showed a similar binding specificity to
Waf-1
site but differences in
Gadd45
and
T3SF
binding. Like p53, p53CP also binds both double- and single-stranded DNA oligonucleotides. Important to note, cell cycle blockers and DNA damaging reagents, which induce p53 binding activity, were found to inhibit p53CP binding in p53-positive, but not in p53-negative, cells. This finding suggested a p53-dependent coordinate regulation of p53 and p53CP in response to external stimuli. p53CP therefore could be a third member of the p53 family, in addition to p53 and p73, a newly identified p53 homolog. p53CP, if sequestering p53 from its DNA binding sites through competitive binding, may provide a novel mechanism of p53 inactivation. Alternatively, p53CP may have p53-like functions by binding and transactivating p53 downstream target genes. Cloning of the p53CP gene ultimately will resolve this issue.
Characterization of the ATF/CREB site and its complex with GCN4
Authors: Hockings Susan C. , Kahn Jason D. , Crothers Donald M.
Published: July 2002

We have studied DNA minicircles containing the ATF/CREB binding site for GCN4 by using a combination of cyclization kinetics experiments and Monte Carlo simulations. Cyclization rates were determined with and without GCN4 for DNA constructs containing the ATF/CREB site separated from a phased A-tract multimer bend by a variable length phasing adaptor. The cyclization results show that GCN4 binding does not significantly change the conformation of the ATF/CREB site, which is intrinsically slightly bent toward the major groove. Monte Carlo simulations quantitate the ATF/CREB site structure as an 8° bend toward the major groove in a coordinate frame near the center of the site. The ATF/CREB site is underwound by 53° relative to the related AP-1 site DNA. The effect of GCN4 binding can be modeled either as a decrease in the local flexibility, corresponding to an estimated 60% increase in the persistence length for the 10-bp binding site, or possibly as a small decrease (1°) in intrinsic bend angle. Our results agree with recent electrophoretic and crystallographic studies and demonstrate that cyclization and simulation can characterize subtle changes in DNA structure and flexibility.
Computational learning reveals coiled coil-like motifs in histidine kinase linker domains
Authors: Singh Mona , Berger Bonnie , Kim Peter S. , Berger James M. , Cochran Andrea G.
Published: July 2002

The recent rapid growth of protein sequence databases is outpacing the capacity of researchers to biochemically and structurally characterize new proteins. Accordingly, new methods for recognition of motifs and homologies in protein primary sequences may be useful in determining how these proteins might function. We have applied such a method, an iterative learning algorithm, to analyze possible coiled coil domains in histidine kinase receptors. The potential coiled coils have not yet been structurally characterized in any histidine kinase, and they appear outside previously noted kinase homology regions. The learning algorithm uses a combination of established sequence patterns in known coiled coil proteins and histidine kinase sequence data to learn to recognize efficiently this coiled coil-like motif in the histidine kinases. The common appearance of the structural motif in a functionally important part of the receptors suggests hypotheses for kinase regulation and signal transduction.