bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical implementation of a mixed quantum classical rate theory
Authors: Liao Jie-Lou , Pollak Eli
Published: July 2002

The recently formulated mixed quantum classical rate theory (MQCLT) is implemented for a model system with two degrees of freedom. In MQCLT, one must compute the Wigner representation of the symmetrized thermal flux operator. This phase space flux distribution is then multiplied by the classical reaction probability to obtain the rate. The major computational difficulty is the multidimensional Fourier transform necessary for obtaining the Wigner distribution. The Fourier transform reintroduces a sign problem when attempting to estimate the MQCLT rate using Monte Carlo methods. Two different methods for overcoming the sign problem are explored in this paper. Numerical results are presented for a model problem of an Eckart barrier coupled bilinearly to a slow oscillator and compared with numerically exact results.
Photodissociation of water. II. Wave packet calculations for the photofragmentation of H2O and D2O in the B̃ band
Authors: van Harrevelt Rob , van Hemert Marc C.
Published: July 2002

A complete three-dimensional quantum mechanical description of the photodissociation of water in the B̃ band, starting from its rotational ground state, is presented. In order to include B̃-X̃ vibronic coupling and the B̃-Ã Renner–Teller coupling, diabatic electronic states have been constructed from adiabatic electronic states and matrix elements of the electronic angular momentum operators, following the procedure developed by A. J. Dobbyn and P. J. Knowles [Mol. Phys. 91, 1107 (1997)], using the ab initio results discussed in the preceding paper. The dynamics is studied using wave packet methods, and the evolution of the time-dependent wave function is discussed in detail. Results for the H2O and D2O absorption spectra, OH(A)/OH(X) and OD(A)/OD(X) branching ratios, and rovibrational distributions of the OH and OD fragments are presented and compared with available experimental data. The present theoretical results agree at least qualitatively with the experiments. The calculations show that the absorption spectrum and the product state distributions are strongly influenced by long-lived resonances on the adiabatic B̃ state. It is also shown that molecular rotation plays an important role in the photofragmentation process, due to both the Renner–Teller B̃-X̃ mixing, and the strong effect of out-of-plane molecular rotations (K>0) on the dynamics at near linear HOH and HHO geometries.
Vibrational spectroscopy of phosphaethyne (HCP). I. Potential energy surface, variational calculations, and comparison with experimental data
Authors: Beck C. , Schinke R. , Koput J.
Published: July 2002

A new potential energy surface for the electronic ground state of HCP (phosphaethyne) is presented. The ab initio calculations are based on the internally contracted multireference configuration interaction method using atomic basis functions of quintuple-zeta quality. The ca. 1 000 calculated energy points are fitted to a complex analytical function, which is employed in the subsequent quantum-mechanical variational calculations for total angular momentum J=0–2. The majority of the first 850 vibrational states is assigned in terms of three quantum numbers. The calculated energies are compared to various sets of experimental data—obtained from high-resolution Fourier-transform infrared spectra, dispersed fluorescence spectra, and stimulated-emission pumping spectra. The energy regime, which is covered, extends up to about 25 000 cm−1 above the ground vibrational state. The agreement is excellent; every experimentally assigned level is uniquely related to a calculated vibrational state. Some experimental misassignments at the lower ends of the high-energy polyads are corrected. The progression of “isomerization” (i.e., large-amplitude bending) states, which was experimentally observed by Ishikawa et al. [J. Chem. Phys. 106, 2980 (1997)], is quantitatively confirmed.
Generic Bell correlation between arbitrary local algebras in quantum field theory
Authors: Halvorson Hans , Clifton Rob
Published: July 2002

We prove that for any two commuting von Neumann algebras of infinite type, the open set of Bell correlated states for the two algebras is norm dense. We then apply this result to algebraic quantum field theory—where all local algebras are of infinite type—in order to show that for any two spacelike separated regions, there is an open dense set of field states that dictate Bell correlations between the regions. We also show that any vector state cyclic for one of a pair of commuting non-Abelian von Neumann algebras is entangled (i.e., nonseparable) across the algebras—from which it follows that every field state with bounded energy is entangled across any two spacelike separated regions.
Description of ordering, temperature dependence of susceptibility, and magnetostriction of a one-sublattice spin system with S=1 and strong biquadratic exchange
Authors: Kalita V. M. , Lozenko A. F.
Published: July 2002

The magnetic ordering model is considered for a single-lattice spin subsystem with S=1 and a large biquadratic exchange whose energy has the same order of magnitude as the bilinear exchange interaction energy. The expression for free energy is obtained in the microscopic approximation, and the phase states are defined and analyzed. The Landau potential is represented as a power expansion in the model microscopic free energy. This expression is used to describe the peculiarities of the temperature dependences of the magnetic susceptibility and magnetoelastic deformation.
Numerical analysis of steady flows of a gas condensing on or evaporating from its plane condensed phase on the basis of kinetic theory: Effect of gas motion along the condensed phase
Authors: Aoki Kazuo , Nishino Kenji , Sone Yoshio , Sugimoto Hiroshi
Published: July 2002

A semi-infinite expanse of a gas in contact with its plane condensed phase is considered. The steady gas flow condensing on or evaporating from the condensed phase is investigated numerically on the basis of the Boltzmann–Krook–Welander equation in the case where there is a gas motion along the condensed phase. First, it is shown by a time-dependent analysis that the steady evaporating flow is possible only when there is no gas motion along the condensed phase. Then, with the aid of time-dependent and time-independent analyses, the effect of gas motion along the condensed phase on the steady condensing flow is clarified. That is, the relation of the parameters at infinity and of the condensed phase that allows a steady flow, together with the accurate profiles of the steady solutions, is established. The present results of the half-space problem complete the boundary condition of the compressible Euler equation required in describing steady gas flows around the condensed phase of a smooth shape in the continuum flow limit.
Mixed convection flow in a curved annulus: Effect of radius ratio
Authors: Park S. O. , Choi H. K.
Published: July 2002

Fully developed mixed convection flow in a loosely curved annulus is examined. Analytic solutions in power series form, where the radius ratio is properly taken into account, are derived. It is found that the power series solution is in good agreement with the numerical solution. It is also illustrated that the dimensionless numbers based on hydraulic radius are adequate to characterize the inclination of the secondary flow cells.
Steady, three-dimensional, internally heated convection
Authors: Schubert G. , Glatzmaier G. A. , Travis B.
Published: July 2002

Numerical calculations have been carried out of steady, symmetric, three-dimensional modes of convection in internally heated, infinite Prandtl number, Boussinesq fluids at a Rayleigh number of 1.4×104 in a spherical shell with inner/outer radius of 0.55 and in a 3×3×1 rectangular box. Multiple patterns of convection occur in both geometries. In the Cartesian geometry the patterns are dominated by cylindrical cold downflows and a broad hot upwelling. In the spherical geometry the patterns consist of cylindrical cold downwellings centered either at the vertices of a tetrahedron or the centers of the faces of a cube. The cold downflow cylinders are immersed in a background of upwelling within which there are cylindrical hot concentrations (plumes) and hot halos around the downflows. The forced hot upflow return plumes of internally heated spherical convection are fundamentally different from the buoyancy-driven plumes of heated from below convection.
Anomalous transport in strongly inhomogeneous systems. II. The generalized hydrodynamics of a two-component plasma
Authors: Belyi V. V. , Dewulf D. , Paiva-Veretennicoff I.
Published: July 2002

Generalized hydrodynamical equations are derived for a nonequilibrium plasma characterized by different temperatures and velocities for the electrons and ions. Their conductivities and viscosities appear to be inhibited by supplementary dissipation mechanisms caused by the inhomogeneities of the system. These modifications have profound implications for the properties of propagation and damping of ion-acoustic waves in the system.
Wave-particle power transfer in a steady-state driven system
Authors: Berk H. L. , Breizman B. N. , Hamaguchi S.
Published: July 2002

The general expression of the power transfer from a high-energy ion beam to a background electrostatic plasma wave is obtained for arbitrary wave amplitude. It is verified that phase space gradients produced by a finite amplitude wave enhance the power transfer significantly.
Effect of ion streaming on the onset of the modulational instability
Authors: Salahuddin M. , Durrani I. R. , Saleem H.
Published: July 2002

The effect of ion streaming on the modulational instability (MI) of ion-acoustic waves in a collisionless unmagnetized plasma is studied. The nonlinear Schrödinger equation is derived by using the Krylov–Bogoliubov–Mitropolsky (KBM) perturbation technique. It is found that the value of the critical wavenumber kc is highly dependent upon the ion streaming velocity V0 and the system breaks into a number of stable and unstable regions. In the weak relativistic limit of V0, instability sets in for kc <1.47. It is reconfirmed that in the absence of ion streaming the modulational instability of ion-acoustic waves sets in at a critical wavenumber kc =1.47. UFaipxr
Beta limit of resistive plasma in a heliotron
Authors: Itoh K. , Ichiguchi K. , Itoh S.-I.
Published: July 2002

Stability against the interchange mode in heliotron devices is investigated, taking into account the effects of the resistivity, current diffusivity, ion viscosity, and thermal diffusivity. Critical beta for the low-mode-number stability is found at the finite beta value. For the range of plasma parameters of the present experiments, the resistive mode and current diffusive mode set comparable critical beta values, which are consistent with experimental observations. In future high-temperature plasmas, the current-diffusive mode could be important in determining the stability limit for the global mode.
Linear mode coupling of lower-hybrid waves in a tokamak
Authors: Mendonça J. T.
Published: July 2002

The linear coupling of electromagnetic modes propagating in a toroidal device is studied in detail, using a global or full wave approach. This study is directly linked to the spectral energy gap observed in lower-hybrid current drive experiments, but it is formulated in quite general terms and can eventually be applied to other kinds of waves. Exact solutions for the mode amplitudes and mode energies are derived, in two distinct regimes. The first is the degenerate regime corresponding to a single eigenfrequency and is equivalent to the fixed phase approximation used in the theory of nonlinear wave interaction. The second is the nondegenerate regime corresponding to different eigenfrequencies and is equivalent to the random phase approximation of the nonlinear theory. The stochastic or diffusive regimes studied in previous publications are also obtained when the quasiclassical or quasicontinuum limit of the nondegenerate regime is considered.
Electron cyclotron absorption in a loss cone distribution with temperature anisotropy
Authors: Sita Janaki M. , Dasgupta Brahmananda
Published: July 2002

The effects of temperature anisotropy in a weakly relativistic loss cone distribution on absorption of electron cyclotron waves propagating perpendicular to the magnetic field have been studied. The relevant dielectric tensor elements are calculated in terms of the generalized Dnestrovskii functions. The absorption coefficient is determined from the anti-Hermitian part of the dielectric tensor elements. The expression for absorption coefficient contains the effects of temperature anisotropy, contributions due to finite Larmor radius to all orders, and gyroharmonic overlaps to all orders. Variations in absorption as well as loss cone instability with respect to temperature anisotropy are found both for the ordinary mode around the fundamental harmonic and the extraordinary mode around the second harmonic of electron cyclotron frequency. It is found that with the increase of density and loss cone index, the effect of temperature anisotropy is pronounced.
Particle simulations of boundary-condition and hf-field effects on strong double layers in a collisionless bounded plasma
Authors: Bulanov S. V. , Kuhn S. , Sakharov A. S.
Published: July 2002

The evolution of electrostatic double layers (DL’s) in a collisionless plasma diode with injection of current-carrying plasma from both ends is systematically investigated by means of particle-in-cell simulations. These simulations have been performed with the one-dimensional electrostatic bounded-plasma codes PDW1 [J. Comput. Phys. 80, 253 (1989)] and PDP1 [J. Appl. Phys. 69, 2008 (1991)]. It is found that asymmetry in the injection conditions can shift the DL toward one of the boundaries and may either stabilize or destabilize it. If a given dc potential difference is applied between the electrodes and a time-independent DL exists, the latter is always found to be adjacent to the low-potential boundary of the diode. Application of a strong hf field, modeled by an ac bias, can lead to stabilization or destabilization of the DL, depending on the driving frequency. For boundary conditions corresponding to a given constant external-circuit current, the DL’s observed in the simulations are transient and decay on the time scale on which the diode fills with plasma. Of particular interest is the fact that in none of the simulations reported has a time-independent DL separating two extended regions of quasineutral plasma been obtained.
Ion sheet beams with parabolic density profiles
Authors: Abraham-Shrauner B. , Anderson O. A.
Published: July 2002

A model for a warm nonrelativistic ion sheet beam described by a reduced Vlasov–Maxwell approximation is extended to include parabolic beam densities. A single-humped ion distribution function is found analytically for a stationary beam, whose parabolic density at the beam edge is zero. For a special model of a rippled sheet beam with a nonlinear focusing force, the ion distribution function, the condition for a matched beam, and the emittance for the beam are determined.
Radiative losses and cooling rates in plasmas
Authors: Marchand R. , Bonnin X.
Published: July 2002

A precise definition is given of radiative losses and cooling rates; two rates commonly invoked when discussing impurity effects in plasmas. Radiative losses are directly measurable and they enter the total energy balance of the plasma. The electron cooling rate enters the electron thermal energy balance equation. The two rates are identical at steady ionization balance, in the absence of charge transfer. A simple approximate relation exists between them in a strongly ionizing regime, but they are not connected by a simple relation in a recombination regime.
Three-wave interactions in strong Langmuir turbulence
Authors: Li L. H. , Li X. Q.
Published: July 2002

Numerical simulations of three-wave interactions among Langmuir, ion-acoustic, and electromagnetic waves by means of an efficient algorithm developed here for solving full Zakharov equations show that total electric field collapses if the electrostatic field collapses when plasma temperature is much less than 0.5 MeV and thus relativistic effects can be neglected, and that the electromagnetic wave energy generated in the high-temperature Langmuir collapse comes to no less than one-tenth of the Langmuir wave energy even if the mean intensity of the collapsing wave packet increases by a factor of less than 5.
Requirements for three-dimensional resonant interaction of ion-acoustic solitons
Authors: Gabl Edward F.
Published: July 2002

A fluid analysis describing the growth of two interacting ion-acoustic solitons is adapted to the case of four ion-acoustic solitons interacting in three dimensions. The predicted amplitude of the newly created soliton agrees reasonably well with the amplitude measured in two previous experiments.
Effect of external magnetic field on the generation and transport of hot electrons in laser-target irradiation
Authors: Enright G. D. , Burnett N. H.
Published: July 2002

The effect of an externally applied magnetic field on the generation and transport of hot electrons in CO2 laser irradiation of cylindrical targets has been investigated. It is observed that an external magnetic field of 100 kG increases the energy coupled into the target by superhot (>100 keV) electrons by more than an order of magnitude. The transport of these electrons through a Mylar layer at solid density however is strongly inhibited by the presence of an imbedded magnetic field.
Oscillations of a viscous compound drop
Authors: Lyell M. J. , Wang T. G.
Published: July 2002

The effect of viscosity upon the normal modes of oscillation of a compound drop is studied. The general form of the dispersion relation is obtained. Typical numerical results are presented.
On the shore singularity of water waves. I. The local model
Authors: Meyer R. E.
Published: July 2002

The nonlinear equations governing inviscid water waves close to shore over beaches of small slope are discussed to elucidate their scope, limitations, and ramifications. Their decisive feature is a singularity of the differential equations themselves, and to open the way for analysis, an associated problem is formulated in terms of singular wave equations. The emphasis is on the identification of the questions of oceanographical relevance that can be asked and the ways in which they can be posed to construct the basis for a correct, mathematical analysis [R. E. Meyer, Adv. Appl. Math. (in press)] and for its application to shoaling predictions [R. E. Meyer, Phys. Fluids 29, XXX (1986)].
Effects of collisions on the trapped particle mode in a linear machine
Authors: Mathey O. , Sen A. K.
Published: July 2002

The effects of weak Coulomb and neutral collisions on the collisionless curvature driven trapped particle mode are studied in the Columbia Linear Machine [Phys. Rev. Lett. 57, 1729(1986)] by means of particle-conserving Krook and Fokker–Planck operators. Both types of collisionality are then combined, modeling neutral collisions with the conserving Krook and Coulomb collisions with a Lorentz model. The dispersion relation is then integrated over velocity space. Low Coulomb collisionality yields a small stabilizing correction to the magnetohydrodynamic collisionless mode, which scales as νe using the Krook model and ν1/2eC using a Lorentz pitch-angle operator. In higher collisionality regimes, both models tend to yield similar scalings.
Radiation effects on the ablation of mass in laser-produced plasmas
Authors: Marchand R. , Capjack C. E. , Lee Y. T.
Published: July 2002

The effect of x-ray radiation and transport on the ablated mass is considered in the computer simulation of laser-produced plasmas. Two regimes are identified. For times shorter than a critical time t0, the plasma is ‘‘classical,’’ in that the ablated mass computed when radiation effects are included is approximately the same as that when these effects are neglected. For longer times, however, the former is considerably larger than the latter. The dependence of t0 on the incident laser intensity and the influence of the laser wavelength and flux limiter used in the simulations are determined.
Structure of subcritical perpendicular shock waves
Authors: Ziegler Harald J. , Schindler Karl
Published: July 2002

The structure of quasineutral one-dimensional stationary perpendicular shock waves is investigated within a two fluid model. Dissipation is considered to occur by resistivity. The influence of the entropy increase on the shock structure and especially the evolution of Sagdeev’s potential for shocks of finite strength is discussed quantitatively. The global structure of shocks with small resistivity is treated analytically.
Linear theory of a sheet beam free electron laser
Authors: Antonsen T. M. , Latham P. E.
Published: July 2002

The linear theory of a free electron laser based on a sheet beam propagating in a narrow gap is developed. The three-dimensional structure of the radiation field is determined for an infinitely thin sheet beam. Included are the effects of diffraction and space charge. The possibility of diffractive suppression of unwanted modes is discussed.
A kinetic model for a reactive gas flow: Steady detonation and speeds of sound
Authors: Pandolfi Bianchi M. , Soares A. J.
Published: July 2002

Within discrete kinetic theory, steady detonation wave solutions are here characterized for a reacting hydrogen-oxygen system. Using a suitable kinetic model, the so-called velocity problem is first solved, finding the von Neumann and equilibrium final states, as well as the intermediate states of partial reaction. On the basis of the sonic properties of the flow at the equilibrium final state, the boundary problem is treated in order to characterize the following flow connecting the final state to the rear boundary. Some numerical results of the detonation problem are provided for the two-way autocatalytic reactions OH+M⇄H+O+M. The Hugoniot diagram of the model is carried out; the profile of the pressure is drawn and the detonation wave thickness is represented for different detonation wave velocities.
Surface equation of falling film flows with moderate Reynolds number and large but finite Weber number
Authors: Takeshi Ooshida
Published: July 2002

Waves on a thin liquid layer falling down a solid wall, either vertical or inclined, are studied by means of a reduced equation. This equation is developed by the regularized long-wave expansion method, which is a combination of the Padé approximation and the long-wave expansion. Its numerical solutions are compared with the calculations of the full Navier–Stokes equation, simplified Navier–Stokes equation (the “boundary-layer” equation), and the traditional long-wave equations, as well as with experimental measurements. When the Reynolds number R is as small as unity, the present equation agrees with the Navier–Stokes equation and also with the traditional long-wave equations. For larger values of R, the traditional long-wave equations lose their validity and make a false prediction, while the present equation agrees with the Navier–Stokes equation, as long as the rescaled Reynolds number δ*=R/W1/3 does not exceed unity in the case of vertical films. Unlike the “boundary-layer” equation developed by previous researchers and expected to be valid at moderate and large Reynolds number, the present equation governs the surface evolution alone without postulating to resolve the velocity field. The structure of the present equation, however, has a correspondence to the depth-averaged equations, which facilitates discussing the physical mechanism of the wave dynamics. In particular, the physical origin of the instability mechanism and the wave suppression mechanism are discussed in terms of Whitham’s wave hierarchy theory. The balance of several physical effects such as drag, gravity, and inertia are also discussed in this connection. The analysis of the tail structure of permanent solitary waves predicts that the R dependence of its tail length λ exhibits two distinct regimes in the λ-R diagram. The second regime, which is not predicted by the traditional long-wave equations, arises when the inertia effect becomes dominant.
Radiofrequency-heated enhanced confinement modes in the Alcator C-Mod tokamak
Authors: Takase Y. , Boivin R. L. , Bombarda F. , Bonoli P. T. , Christensen C. , Fiore C. , Garnier D. , Goetz J. A. , Golovato S. N. , Granetz R. , Greenwald M. , Horne S. F. , Hubbard A. , Hutchinson I. H. , Irby J. , LaBombard B. , Lipschultz B. , Marmar E. , May M. , Mazurenko A. , McCracken G. , O’Shea P. , Porkolab M. , Reardon J. , Rice J. , Rost C. , Schachter J. , Snipes J. A. , Stek P. , Terry J. , Watterson R. , Welch B. , Wolfe S.
Published: July 2002

Enhanced confinement modes up to a toroidal field of BT=8 T have been studied with up to 3.5 MW of radiofrequency (rf) heating power in the ion cyclotron range of frequencies (ICRF) at 80 MHz. H-mode is observed when the edge temperature exceeds a threshold value. The high confinement mode (H-mode) with higher confinement enhancement factors (H) and longer duration became possible after boronization by reducing the radiated power from the main plasma. A quasi-steady state with high confinement (H=2.0), high normalized beta (βN=1.5), low radiated power fraction (Pradmain/Ploss=0.3), and low effective charge (Zeff=1.5) has been obtained in Enhanced Dα H-mode. This type of H-mode has enhanced levels of continuous Dα emission and very little or no edge localized mode (ELM) activity, and reduced core particle confinement time relative to ELM-free H-mode. The pellet enhanced performance (PEP) mode is obtained by combining core fueling with pellet injection and core heating. A highly peaked pressure profile with a central value of 8 atmospheres was observed. The steep pressure gradient drives off-axis bootstrap current, resulting in a shear reversed safety factor (q) profile. Suppression of sawteeth appears to be important in maintaining the highly peaked pressure profile. Lithium pellets were found to be more effective than deuterium pellets in raising q0.
The influence of magnetization strength on the sheath: Implications for flush-mounted probes
Authors: Gunn J. P.
Published: July 2002

When the projected ion Larmor radius is larger than the Debye length, ion trajectories near a surface are unmagnetized and a magnetic presheath develops, whose electric field gradient serves to deflect the ion flow toward the surface normal so that it enters the sheath at the sound speed. When ions are very strongly magnetized, they remain tied to the field lines, even inside the sheath: there is no mechanism available to allow the existence of a magnetic presheath, and the Bohm criterion only applies to the parallel velocity, not the normal velocity. There are important consequences for flush-mounted probes because the shape of the ion branch of the I-V characteristic depends on the degree of sheath magnetization, a wide range of which has been investigated by means of one-dimensional particle-in-cell simulations. The results explain in a qualitative way the behavior of the ion current characteristics obtained using the Tokamak de Varennes (TdeV) [J. P. Gunn et al., Rev. Sci. Instrum. 66, 154 (1995)] flush-mounted probe system.
Characterization of enhanced Dα high-confinement modes in Alcator C-Mod
Authors: Greenwald M. , Boivin R. , Bonoli P. , Budny R. , Fiore C. , Goetz J. , Granetz R. , Hubbard A. , Hutchinson I. , Irby J. , LaBombard B. , Lin Y. , Lipschultz B. , Marmar E. , Mazurenko A. , Mossessian D. , Sunn Pedersen T. , Pitcher C. S. , Porkolab M. , Rice J. , Rowan W. , Snipes J. , Schilling G. , Takase Y. , Terry J. , Wolfe S. , Weaver J. , Welch B. , Wukitch S.
Published: July 2002

Regimes of high-confinement mode have been studied in the Alcator C-Mod tokamak [Hutchinson et al., Phys. Plasmas 1, 1511 (1994)]. Plasmas with no edge localized modes (ELM-free) have been compared in detail to a new regime, enhanced Dα (EDA). EDA discharges have only slightly lower energy confinement than comparable ELM-free ones, but show markedly reduced impurity confinement. Thus EDA discharges do not accumulate impurities and typically have a lower fraction of radiated power. The edge gradients in EDA seem to be relaxed by a continuous process rather than an intermittent one as is the case for standard ELMy discharges and thus do not present the first wall with large periodic heat loads. This process is probably related to fluctuations seen in the plasma edge. EDA plasmas are more likely at low plasma current (q>3.7), for moderate plasma shaping, (triangularity ∼0.35–0.55), and for high neutral pressures. As observed in soft x-ray emission, the pedestal width is found to scale with the same parameters that determine the EDA/ELM-free boundary.
Studies on the role of the hydrophobic domain of Ost4p in interactions with other subunits of yeast oligosaccharyl transferase
Authors: Kim Hyun , Park Hangil , Montalvo Lucy , Lennarz William J.
Published: July 2002

In the yeast,
Saccharomyces cerevisiae
, oligosaccharyl transferase (OT), which catalyzes the transfer of dolichol-linked oligosaccharide chains to nascent polypeptides in the endoplasmic reticulum, consists of nine nonidentical membrane protein subunits. Genetic and biochemical evidence indicated these nine proteins exist in three subcomplexes. Three of the OT subunits (Ost4p, Ost3p, and Stt3p) have been proposed to exist in one subcomplex. To investigate the interaction of these three membrane proteins, initially we carried out a mutational analysis of Ost4p, which is an extraordinarily small membrane protein containing only 36 amino acid residues. This analysis indicated that when single amino acid residues in a region close to the luminal face of the putative transmembrane domain of Ost4p were changed into an ionizable amino acid such as Lys or Asp, growth at 37°C and OT activity measured
in vitro
were impaired. In addition, using immunoprecipitation techniques and Western blot analysis, we found that with these mutations the interaction between Ost4p, Ost3p, and Stt3p was disrupted. Introduction of Lys or Asp residues at other positions in the putative transmembrane domain or at the N or C terminus of Ost4p had no effect on disrupting subunit interactions or impairing the activity of OT. These findings suggest that a localized region of the putative transmembrane domain of Ost4p mediates in stabilization of the interaction with the two other OT subunits (Ost3p and Stt3p) in a subcomplex in the endoplasmic reticulum membrane.
The structure of a stable intermediate in the A ↔ B DNA helix transition
Authors: Ng Ho-Leung , Kopka Mary L. , Dickerson Richard E.
Published: July 2002

The DNA dodecamer CATGGGCCCATG in a crystal structure of resolution 1.3 Å has a conformation intermediate between A and B DNA. This trapping of a stable intermediate suggests that the A and B DNA families are not discrete, as previously believed. The structure supports a base-centered rather than a backbone-centered mechanism for the A ↔ B transition mediated by guanine tracts. Interconversion between A and B DNA provides another means for regulating protein–DNA recognition.
Vitamin B12 and hepatitis C: Molecular biology and human pathology
Authors: Lott William B. , Takyar Seyedtaghi S. , Tuppen Joseph , Crawford Darrell H. G. , Harrison Michael , Sloots Theo P. , Gowans Eric J.
Published: July 2002

Cobalamins are stored in high concentrations in the human liver and
thus are available to participate in the regulation of hepatotropic
virus functions. We show that cyanocobalamin (vitamin B12) inhibited
the HCV internal ribosome entry site (IRES)-dependent translation of a
reporter gene
in vitro
in a dose-dependent manner
without significantly affecting the cap-dependent mechanism. Vitamin
B12 failed to inhibit translation by IRES elements from
encephalomyocarditis virus (EMCV) or classical swine fever virus
(CSFV). We also demonstrate a relationship between the total cobalamin
concentration in human sera and HCV viral load (a measure of viral
replication in the host). The mean viral load was two orders of
magnitude greater when the serum cobalamin concentration was above 200
pM (
P
< 0.003), suggesting that the total
cobalamin concentration in an HCV-infected liver is biologically
significant in HCV replication.
Selective inhibition of HIV replication in primary macrophages but not T lymphocytes by macrophage-derived chemokine
Authors: Cota Manuela , Mengozzi Manuela , Vicenzi Elisa , Panina-Bordignon Paola , Sinigaglia Francesco , Transidico Pietro , Sozzani Silvano , Mantovani Alberto , Poli Guido
Published: July 2002

Macrophage-derived chemokine (MDC) has been reported to inhibit different HIV-1 strains in activated peripheral blood mononuclear cells (T cell blasts), although other investigators have not confirmed these findings. Here we demonstrate that MDC inhibits the replication of CCR5-dependent (R5) HIV-1BaLin monocyte-derived macrophages (MDM), but not in T cell blasts, although with variable potency depending on donor variability. Analysis of HIV-1BaLproviral DNA synthesis in MDM indicated that the suppressive effect of MDC did not involve inhibition of early events such as entry or reverse transcription. Finally, an inverse correlation was observed between the levels of endogenous MDC secreted by uninfected MDM of different donors and the efficiency of different HIV strains, including two primary isolates with different coreceptor usage, to replicate in these cells. Thus, MDC represents an example of a chemokine inhibiting HIV replication in macrophages acting at one or more postentry levels in the virus life cycle.
Enhanced sensitivity of PTEN-deficient tumors to inhibition of FRAP/mTOR
Authors: Neshat Mehran S. , Mellinghoff Ingo K. , Tran Chris , Stiles Bangyan , Thomas George , Petersen Roseann , Frost Philip , Gibbons James J. , Wu Hong , Sawyers Charles L.
Published: July 2002

Recent evidence places the FRAP/mTOR kinase downstream of the phosphatidyl inositol 3-kinase/Akt-signaling pathway, which is up-regulated in multiple cancers because of loss of the PTEN tumor suppressor gene. We performed biological and biochemical studies to determine whether PTEN-deficient cancer cells are sensitive to pharmacologic inhibition of FRAP/mTOR by using the rapamycin derivative CCI-779.
In vitro
and
in vivo
studies of isogenic PTEN
+/+
and PTEN
−/−
mouse cells as well as human cancer cells with defined PTEN status showed that the growth of PTEN null cells was blocked preferentially by pharmacologic FRAP/mTOR inhibition. Enhanced tumor growth caused by constitutive activation of Akt in PTEN
+/+
cells also was reversed by CCI-779 treatment, indicating that FRAP/mTOR functions downstream of Akt in tumorigenesis. Loss of PTEN correlated with increased S6 kinase activity and phosphorylation of ribosomal S6 protein, providing evidence for activation of the FRAP/mTOR pathway in these cells. Differential sensitivity to CCI-779 was not explained by differences in biochemical blockade of the FRAP/mTOR pathway, because S6 phosphorylation was inhibited in sensitive and resistant cell lines. These results provide rationale for testing FRAP/mTOR inhibitors in PTEN null human cancers.
Characterization of an adapter subunit to a phosphatidylinositol (3)P 3-phosphatase: Identification of a myotubularin-related protein lacking catalytic activity
Authors: Nandurkar H. H. , Caldwell K. K. , Whisstock J. C. , Layton M. J. , Gaudet E. A. , Norris F. A. , Majerus P. W. , Mitchell C. A.
Published: July 2002

The D3-phosphoinositides act as second messengers by recruiting,
and thereby activating, diverse signaling proteins. We have previously
described the purification of a rat phosphatidylinositol 3-phosphate
[PtdIns(3)P] 3-phosphatase, comprising a heterodimer of a 78-kDa
adapter subunit in complex with a 65-kDa catalytic subunit. Here, we
have cloned and characterized the cDNA encoding the human 3-phosphatase
adapter subunit (3-PAP). Sequence alignment showed that 3-PAP shares
significant sequence similarity with the protein and lipid
3-phosphatase myotubularin, and with several other members of the
myotubularin gene family including SET-binding factor 1. However,
unlike myotubularin, 3-PAP does not contain a consensus
HCX
5
R catalytic motif. The 3-PAP sequence contains several
motifs that predict interaction with proteins containing Src homology-2
(SH2) domains, phosphotyrosine-binding (PTB) domains, members of the
14-3-3 family, as well as proteins with SET domains. Northern blot
analysis identified two transcripts (5.5 kb and 2.5 kb) with highest
abundance in human liver, kidney, lung, and placenta. 3-PAP
immunoprecipitates isolated from platelet cytosol hydrolyzed the
D3-phosphate from PtdIns(3)P and PtdIns 3,4-bisphosphate
[PtdIns(3,4)P
2
]. However, insect cell-expressed 3-PAP
recombinant protein was catalytically inactive, confirming our prior
prediction that this polypeptide represents an adapter subunit.
The semaphorin receptor plexin-B1 specifically interacts with active Rac in a ligand-dependent manner
Authors: Vikis Haris G. , Li Weiquan , He Zhigang , Guan Kun-Liang
Published: July 2002

Semaphorin molecules serve as axon guidance signals that regulate
the navigation of neuronal growth cones. Semaphorins have also been
implicated in other biological processes, including the immune
response. Plexins, acting either alone or in complex with neuropilins,
have recently been identified as functional semaphorin receptors.
However, the mechanisms of signal transduction by plexins remain
largely unknown. We have demonstrated a direct interaction between
plexin-B1 and activated Rac. Rac specifically interacts with the
cytosolic domain of plexin-B1, but not with that of plexin-A3 or -C1.
Neither RhoA nor Cdc42 interacts with plexin-B1, indicating that the
Rac/plexin-B1 interaction is highly specific. The binding of GTP and
the integrity of the Rac effector domain are required for the
interaction with plexin-B1. Furthermore, we have identified that a
Cdc42/Rac interactive binding (CRIB) motif in the cytosolic domain of
plexin-B1 is essential for its interaction with active Rac. We have
also observed that the semaphorin CD100, a ligand for plexin-B1,
stimulates the interaction between plexin-B1 and active Rac. Our
results support a model by which activated Rac plays a role in
mediating semaphorin signals, resulting in reorganization of actin
cytoskeletal structure.
The activation mechanism of rat vanilloid receptor 1 by capsaicin involves the pore domain and differs from the activation by either acid or heat
Authors: Welch J. M. , Simon S. A. , Reinhart P. H.
Published: July 2002

The recently cloned rat vanilloid receptor, VR1, can be activated
by capsaicin, acid, and heat. To determine the molecular mechanisms
facilitating channel opening in response to these stimuli, VR1 and six
channels containing charge neutralization point mutations surrounding
the putative channel pore domain were expressed and characterized in
Xenopus laevis
oocytes. Steady-state dose-response
relationships, current-voltage relationships, ionic selectivities, and
single-channel properties were recorded using voltage-clamp techniques.
Three of the mutant channels are significantly more sensitive to
capsaicin than is wild-type VR1, whereas none differed in their
activation by acidic pH or temperature. Furthermore, one of the mutants
has lost all positive cooperativity for capsaicin activation (Hill
coefficient ≅ 1, VR1 ≅ 2), is much more selective for
Ca
2+
, and exhibits a lower efficacy for acid than for
capsaicin activation. Single-channel recordings show that capsaicin-
and acid-activated channels have the same conductance, that the three
mutants with increased capsaicin sensitivity exhibit higher open
probabilities at submaximal capsaicin concentrations, and that the
gating properties of capsaicin activation differ from those of acid
activation. These data indicate that VR1 undergoes conformational
changes upon capsaicin binding that it does not undergo in response to
activation by protons or thermal stimuli. Furthermore, these structural
rearrangements include the putative pore domain and reveal the location
of an intracellular domain that contributes to the positive
cooperativity seen for capsaicin activation.
Crystal structure at 2.6-A resolution of human macrophage migration inhibitory factor.
Authors: Sun H W , Bernhagen J , Bucala R , Lolis E
Published: July 2002

Macrophage migration inhibitory factor (MIF) was the first cytokine to be described, but for 30 years its role in the immune response remained enigmatic. In recent studies, MIF has been found to be a novel pituitary hormone and the first protein identified to be released from immune cells on glucocorticoid stimulation. Once secreted, MIF counterregulates the immunosuppressive effects of steroids and thus acts as a critical component of the immune system to control both local and systemic immune responses. We report herein the x-ray crystal structure of human MIF to 2.6 angstrom resolution. The protein is a trimer of identical subunits. Each monomer contains two antiparallel alpha-helices that pack against a four-stranded beta-sheet. The monomer has an additional two beta-strands that interact with the beta-sheets of adjacent subunits to form the interface between monomers. The three beta-sheets are arranged to form a barrel containing a solvent-accessible channel that runs through the center of the protein along a molecular 3-fold axis. Electrostatic potential maps reveal that the channel has a positive potential, suggesting that it binds negatively charged molecules. The elucidated structure for MIF is unique among cytokines or hormonal mediators, and suggests that this counterregulator of glucocorticoid action participates in novel ligand-receptor interactions.
Serological analysis of Melan-A(MART-1), a melanocyte-specific protein homogeneously expressed in human melanomas.
Authors: Chen Y T , Stockert E , Jungbluth A , Tsang S , Coplan K A , Scanlan M J , Old L J
Published: July 2002

Recent progress in the structural identification of human melanoma antigens recognized by autologous cytotoxic T cells has led to the recognition of a new melanocyte differentiation antigen, Melan-A(MART-1). To determine the properties of the Melan-A gene product, Melan-A recombinant protein was produced in Escherichia coli and used to generate mouse monoclonal antibodies (mAbs). Two prototype mAbs, A103 and A355, were selected for detailed study. Immunoblotting results with A103 showed a 20-22-kDa doublet In Melan-A mRNA positive melanoma cell lines and no reactivity with Melan-A mRNA-negative cell lines. A355, in addition to the 20-22-kDa doublet, recognized several other protein species in Melan-A mRNA-positive cell lines. Immunocytochemical assays on cultured melanoma cells showed specific and uniform cytoplasmic staining in Melan-A mRNA-positive cell lines. Immunohistochemical analysis of normal human tissues with both mAbs showed staining of adult melanocytes and no reactivity with the other normal tissues tested. Analysis of 21 melanoma specimens showed homogenous staining of tumor cell cytoplasm in 16 of 17 Melan-A mRNA-positive cases and no reactivity with the three Melan-A mRNA-negative cases.
Evolutionary reconstruction of a hairpin deleted from the genome of an RNA virus.
Authors: Olsthoorn R C , van Duin J
Published: July 2002

The intercistronic region between the maturation and coat-protein genes of RNA phage MS2 contains important regulatory and structural information. The sequence participates in two adjacent stem-loop structures, one of which, the coat-initiator hairpin, controls coat-gene translation and is thus under strong selection pressure. We have removed 19 out of the 23 nucleotides constituting the intercistronic region, thereby destroying the capacity of the phage to build the two hairpins. The deletion lowered coat-protein yield more than 1000-fold, and the titer of the infectious clone carrying the deletion dropped 10 orders of magnitude as compared with the wild type. Two types of revertants were recovered. One had, in two steps, recruited 18 new nucleotides that served to rebuild the two hairpins and the lost Shine-Dalgarno sequence. The other type had deleted an additional six nucleotides, which allowed the reconstruction of the Shine-Dalgarno sequence and the initiator hairpin, albeit by sacrificing the remnants of the other stem-loop. The results visualize the immense genetic repertoire created by, what appears as, random RNA recombination. It would seem that in this genetic ensemble every possible new RNA combination is represented.
Three functional luciferase domains in a single polypeptide chain
Authors: Li Liming , Hong Robert , Hastings J. Woodland
Published: July 2002

We report a unique case of a gene containing three homologous and contiguous repeat sequences, each of which, after excision, cloning, and expression in
Escherichia coli
, is shown to code for a peptide catalyzing the same reaction as the native protein,
Gonyaulax polyedra
luciferase (
M
r
= 137). This enzyme, which catalyzes the light-emitting oxidation of a linear tetrapyrrole (dinoflagellate luciferin), exhibits no sequence similarities to other luciferases in databases. Sequence analysis also reveals an unusual evolutionary feature of this gene: synonymous substitutions are strongly constrained in the central regions of each of the repeated coding sequences.
An epidemic of tuberculosis with a high rate of tuberculin anergy among a population previously unexposed to tuberculosis, the Yanomami Indians of the Brazilian Amazon
Authors: Sousa Alexandra O. , Salem Julia I. , Lee Francis K. , Verçosa Maria C. , Cruaud Philippe , Bloom Barry R. , Lagrange Philippe H. , David Hugo L.
Published: July 2002

A survey of an emerging tuberculosis epidemic among the Yanomami Indians of the Amazonian rain forest provided a unique opportunity to study the impact of tuberculosis on a population isolated from contact with the tubercle bacillus for millennia until the mid-1960s. Within the Yanomami population, an extraordinary high prevalence of active tuberculosis (6.4% of 625 individuals clinically examined) was observed, indicating a high susceptibility to disease, even among bacille Calmette–Guérin-vaccinated individuals. Observational studies on cell-mediated and humoral immune responses of the Yanomami Indians compared with contemporary residents of the region suggest profound differences in immunological responsiveness to
Mycobacterium tuberculosis
infection. Among the Yanomami, a very high prevalence of tuberculin skin test anergy was found. Of patients with active tuberculosis, 46% had purified protein derivative of tuberculosis reactions <10 mm; similarly 58% of recent bacillus Calmette–Guérin vaccines exhibited skin test reactions <5 mm. The Yanomami also had higher titers of antibodies against
M. tuberculosis
glycolipid antigens (>70%) than the control subjects comprised of Brazilians of European descent (14%). The antibodies were mostly of the IgM isotype. Among the tuberculosis patients who also produced IgG antibodies, the titers of IgG4 were significantly higher among the Yanomami than in the control population. Although it was not possible to analyze T-cell responses or patterns of lymphokine production
in vitro
because of the remoteness of the villages from laboratory facilities, the results suggest that the first encounter of the Yanomami Indian population with tuberculosis engenders a diminished cell-mediated immune response and an increased production antibody responses, relative to other populations with extensive previous contact with the pathogen. These findings suggest that tuberculosis may represent a powerful selective pressure on human evolution that over centuries has shaped the nature of human immune responses to infection.