bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-photon ionization of alkali-halide clusters spectroscopy of excess-electron excited states
Authors: Labastie P. , L’Hermite J.-M. , Poncharal Ph. , Sence M.
Published: July 2002

NanFn−1 clusters are produced in a laser vaporization source. They are ionized by one-photon or resonant two-photon ionization, and detected in a high resolution time of flight mass spectrometer. By scanning the ionization wavelength, it is possible to obtain ionization potentials and absorption spectra of these clusters, for n ranging from 2 to 42. The results we obtain show many discrepancies with the cuboid model, which has proven valid for small sizes. The possible origin of these disagreements is discussed.
Diffusion-controlled electron transfer reactions: Subpicosecond fluorescence measurements of coumarin 1 quenched by aniline and N,N-dimethylaniline
Authors: Shannon Colman F. , Eads Daniel D.
Published: July 2002

The fluorescence quenching of a 7-aminocoumarin dye [coumarin 1 (C1)] by amine electron donors (aniline or N,N-dimethylaniline) in methanol was examined by picosecond time-resolved and steady-state fluorescence measurements. The quencher concentration dependence of the data was analyzed using the classic Smoluchowski model and the Collins and Kimball model of diffusion-controlled reactions. In addition, the Wilemski and Fixman model, which includes a distance-dependent sink term, was used to analyze the data. We have conclusively shown that the Smoluchowski model does not describe either the C1-aniline or the C1-dimethylaniline fluorescence quenching data. It was found that the Collins and Kimball model accurately described the C1-aniline data, but was inappropriate for the C1-dimethylaniline results. The addition of a simple position-dependent sink term to the Collins and Kimball model enabled both the C1-aniline and the C1-dimethylaniline time-resolved data to be accurately described. Analysis with a model incorporating a nonadiabatic electron transfer sink function revealed that both reactions have a strong distance dependence and that only the C1-aniline reaction can be classified as solely nonadiabatic electron transfer. Based on these analyses, we conclude that the C1-dimethylaniline reaction encompasses both the adiabatic and nonadiabatic limits of electron transfer. We also analyzed the temperature dependence of the reaction rate using Marcus nonadiabatic electron transfer theory to estimate the activation energy, the solvent reorganization energy, and the electronic coupling matrix element of the intrinsic electron transfer reaction. The average bimolecular reaction rate found was 8.77×109 M−1 s−1 for the C1-aniline reaction and 1.52×1010 M−1 s−1 for the C1-dimethylaniline reaction.
A potential distribution approach to fused heterochain molecules. I. Mixtures of hard dumbbells and spheres
Authors: Lee Lloyd L.
Published: July 2002

We apply the potential distribution theorems for the cavity distribution functions to the development of thermodynamic formulas for fused-sphere chain molecules. Alternative forms of the potential distribution theorems are derived: in terms of the cavity functions, and in terms of the singlet direct correlation functions. We point out the connections to integral equation theories. To determine the behavior of fused dispheres, we examine the successful Wertheim thermodynamic perturbation theory (TPT) at different bond lengths l in light of the cavity functions. For ternary mixtures of spheres S and B, and fused dispheres (SB), we discover a confluence point where all cavity functions at different mixture compositions converge. This takes place at the tangent disphere limit l=d (l being the bond length, and d, the hard sphere diameter). This point is also in common with the excess Helmholtz free energy from the TPT theory for tangent dumbbells. The cavity functions are obtained from the accurate equation of state of Boublík. To verify the chemical potentials calculated, we compare with new Monte Carlo simulations for mixtures of hard spheres and dumbbells. TPT does not hold for l<d. In order to have a quantitative expression for fused disphere properties, we propose an interpolation formula that performs well for both symmetric dispheres and asymmetric dispheres. This formula, though empirical, performs better than similar interpolative schemes proposed by Phan–Kierlik–Rosinberg. We have also derived purely thermodynamic formulas based on the TPT theory. These formulas can be exploited if one uses many of the existing thermodynamic properties correlations for mixtures.
Semiphenomenological theory of homogeneous vapor–liquid nucleation
Authors: Kalikmanov V. I. , van Dongen M. E. H.
Published: July 2002

A new semiphenomenological theory of homogeneous vapor–liquid nucleation is proposed. It is based on the Fisher droplet model applied at the saturation point within the framework of the kinetic approach. The microscopic surface tension of a droplet is supposed to have the Tolman form. The unknown Tolman length is naturally identified by equating a known empirical value of saturation pressure psat to the sum of the series over all droplet sizes for psat emerging from the Fisher model. The theory contains no adjustable parameters. Predictions of the new theory for various substances are compared with available experimental data and with the three other widely used theoretical models: classical nucleation theory, corrected Dillmann–Meier and Delale–Meier theory.
Ab initio predictions of structural and optical response properties of Na+n clusters: Interpretation of depletion spectra at low temperature
Authors: Bonačić-Koutecký V. , Pittner J. , Fuchs C. , Fantucci P. , Guest M. F. , Koutecký J.
Published: July 2002

We show that a comparison of the depletion spectra of Na+n (n=2–9,11,21) clusters recorded at low temperature and optically allowed transitions determined for the stable structures using ab initio methods accounting for electron correlation allows the assignment of the cluster geometry to the measured features. Due to the large mobility of atoms in alkali metal clusters, the influence of temperature on structural and electronic properties is significant. The lowering of temperature reveals new spectroscopic features which are structure dependent. Optical response properties of small cationic Na+n clusters are characterized by rich molecularlike spectroscopic patterns, also with increasing size, and differ substantially from those found for neutral clusters. It has been clearly demonstrated that not only the number of valence electrons but its mutual interplay with the geometric properties determine optical response features.
The quantum dynamics of an excess proton in water
Authors: Lobaugh J. , Voth Gregory A.
Published: July 2002

The quantum dynamics and energetics of an excess proton in water have been studied computationally. Comparison of a quantum mechanical treatment of the transferring proton and the water solvent is made with a classical treatment of the same system. The exchange of the proton between two water molecules is found to be an activationless quantum process. Analysis of the microscopic structure of the solvent around the proton transfer complex is also carried out, and the quantum infrared spectrum of the transferring proton is calculated and analyzed in terms of Zundel polarization. The Grötthus mechanism for proton migration in water is also examined within the context of the model. Grötthus behavior is suggested to depend critically on the dynamics of water molecules in the second solvation shell of the H5O+2 complex, as well as the inward fluctuations of the oxygen–oxygen distance of water molecules that hydrogen bond to the H5O+2 complex in the first solvation shell. The quantum effects on the nuclear dynamics are found to be significant.
Raman spectra of mass-selected nickel dimers in argon matrices
Authors: Wang Huaiming , Haouari Hanae , Craig Robert , Lombardi John R. , Lindsay D. M.
Published: July 2002

The absorption and Raman spectra for nickel dimers in an argon matrix prepared by the mass-selected ion deposition technique have been measured. A weak dimer absorption band is centered around 480 nm. Resonance Raman spectra obtained from exciting into the dimer 480 nm band show a vibrational progression for which ωe=259.2±3.0 cm−1 with ωexe=1.9±0.7 cm−1. The dinickel Raman spectra are discussed in terms of isotopic shifts, as well as the changeover from d–d bonding to s–s bonding along the series Fe2→Cu2.
Higher-order effects in the vibration–torsion–rotation spectra of a molecule with an internal rotor
Authors: Duan Yun-Bo , Zhang Hui-Min , Takagi Kojiro
Published: July 2002

The sequential contact transformation technique is applied to the vibrational–torsional–rotational Hamiltonian for molecules containing a threefold symmetric internal rotor, which makes it possible to analyze various higher-order vibration–torsion–rotation interactions and their effects in the vibration–torsion–rotation spectra of the molecule. The formalism for the calculation of Hamiltonian coefficients is developed in terms of the fundamental molecular parameters. The resulting formulas are applicable to analyze the molecular structure. The theory presented is applied to the calculation of the quartic and sixtic centrifugal distortion constants of the molecule.
Electronic structures of cobalt cluster cations: Photodissociation spectroscopy of Co+nAr (n=3–5) in the visible to near-infrared range
Authors: Minemoto Shinichirou , Terasaki Akira , Kondow Tamotsu
Published: July 2002

Photodissociation spectra of cobalt cluster ion–argon atom complexes, Co+nAr (n=3–5), were measured by detecting the product ions, Co+n and Con−1+, with a tunable laser pulse from an optical parametric oscillator in the photon-energy range from 0.7 to 2.8 eV. The photodissociation spectra thus obtained are equivalent to the optical absorption spectra of the underlying cobalt cluster ions, Co+n, because the argon atom is weakly bound to Co+n. The spectrum was analyzed by means of a spin-polarized DV-Xα calculation, and the electronic and the geometric structures of Co+3 and Co+4 were determined. The analysis shows that all the transitions in the entire energy range studied occur between occupied and unoccupied energy levels associated with 3d atomic orbitals (AOs) having the minority spin. The spin difference (difference in population per Co atom between the majority and the minority spins) was evaluated from the electronic structures thus obtained. The spin differences of 2.00 for Co+3 and 1.75 for Co+4 indicate ferromagnetic spin coupling in these cobalt cluster ions.
On the mechanism of C60 thin film laser-induced desorption
Authors: Winter B. , Mitzner R. , Kusch Ch. , Campbell E. E. B. , Hertel I. V.
Published: July 2002

The mechanism of thin film C60 laser desorption has been investigated using nanosecond and picosecond UV laser pulses. The desorption experiments were performed under ultrahigh-vacuum conditions using reflectron time-of-flight mass spectroscopy from which the velocity distributions of the desorbed ions and the dependence of the ion yield on the laser fluence were obtained. A strong nonlinear dependence of the desorption yield on laser fluence in the threshold region, indicative of a thermal mechanism, was found for both ns and ps pulses. Typically, the C+60 velocity distributions were bimodal and could be fitted by modified Maxwell–Boltzmann distributions. The fits to the slow contributions gave translational temperatures consistent with surface temperatures due to laser heating with ns pulses as estimated by solving the one-dimensional heat equation. In contrast, translational temperatures which are much too high to be consistent with purely thermal processes were obtained for the fast contributions. These fast contributions originate from different desorption mechanisms for the two different laser pulse lengths.
Phase space bottlenecks and rates of no-barrier fragmentation reactions into polyatomic molecules
Authors: Katō Toshiko
Published: July 2002

An expression of the microcanonical unimolecular rate for an arbitrary transition state surface in phase space is derived and applied to fragmentation reactions into polyatomic molecules without potential barrier. The transition state which has a ‘‘point of no return’’ property in unimolecular dissociation is defined as an interfragment bottleneck in phase space. The fragmentation rate based on the interfragment bottleneck in phase space is compared with the rate based on the transition state defined in configuration space. The rate derived from the flux which crosses the interfragment bottleneck by intermode energy transfer is found to be smaller than the rate derived from the Rice–Ramsperger–Kassel–Marcus or phase space theory by an approximate factor (s+r/2)|W̃|/E, where E is the total energy and |W̃| is the magnitude of the coupling energy between the reaction coordinate and the s-dimensional vibrational and r-dimensional rotational modes of the fragments. Phase space theory grossly overestimates the rate of fragmentation of small molecules with small |W̃| in the high energy range, because the theory does not take into account the slow process of intramolecular energy redistribution.
Spin-orbit induced radiationless transitions in organometallics: Quantum simulation of the intersystem crossing processes in the photodissociation of HCo(CO)4
Authors: Heitz Marie-Catherine , Ribbing Carl , Daniel Chantal
Published: July 2002

A theoretical description of the “fast” (<50 ps) intersystem crossing (ISC) processes occurring during the photodissociation of HCo(CO)4 is presented. The radiationless transitions are simulated by wave packet propagations on spin-orbit coupled two-dimensional potential energy surfaces (CASSCF/CCI) calculated along two reaction coordinates (qa=[Co–H] and qb=[Co–COax]). A mechanism of deactivation of the singlet excited state of HCo(CO)4 initially populated on UV excitation has been proposed. This mechanism differs slightly from the one deduced from a one-dimensional simulation performed separately, either along the Co–H bond or along the Co–COax bond: (i) in a very short time scale (<20 fs) 35% of the system dissociates toward the primary products H+Co(CO)4 (1E), whereas the 1E→3A1 and 1E→3E intersystem crossings occur within 50 ps; (ii) as soon as the lowest triplet states are populated, the system dissociates either to H+Co(CO)4 (3A1) or to H+Co(CO)4 (3E) on the corresponding potential energy surfaces; (iii) the indirect photodissociation mechanism through ISC may be described as a succession of elementary transitions followed by the homolysis of the metal–hydrogen bond.
Dissociation energies and heats of formation of NH and NH+
Authors: Tarroni Riccardo , Palmieri Paolo , Mitrushenkov Alexander , Tosi Paolo , Bassi Davide
Published: July 2002

Starting from the results of a recent ion–molecule reactive scattering experiment [Tosi et al., J. Chem. Phys. 100, 4300 (1994)], a precise estimate of the upper bound for the heat of formation of NH+ has been derived [ΔHf,0(NH+)⩽17.175±0.006 eV], and from this, upper and lower bounds for the heat of formation of NH and for the dissociation energies of NH+ (X 2Π and a 4Σ− states) and NH (X 3Σ−), respectively. In order to verify the degree of accuracy attainable on the theoretical counterpart for these systems, high level ab initio computations, using extended multireference configuration interaction expansion and recently developed core-valence correlation consistent basis sets [Woon et al., J. Chem. Phys. 103, 4572 (1995)], have been also performed, comparing the results with the corresponding values estimated from the experimental data and previous theoretical literature values.
Ferroelectric properties of pyridinium perrhenate
Authors: Wąsicki J. , Czarnecki P. , Pająk Z. , Nawrocik W. , Szczepański W.
Published: July 2002

Polycrystalline pyridinium perrhenate has been studied over a wide range of temperatures by differential thermal analysis, differential scanning calorimetry, proton NMR spectra and relaxation, and dielectric permittivity measurements. Two solid–solid phase transitions at 250 and 333 K have been revealed and the pyridinium cation reorientations characterized. The higher transition appears to be the Curie point of a new ferroelectric compound.
Nonlocality of the density functional for exchange and correlation: Physical origins and chemical consequences
Authors: Perdew John P. , Ernzerhof Matthias , Zupan Aleš , Burke Kieron
Published: July 2002

Gradient corrections to the local spin density approximation for the exchange-correlation energy Exc are increasingly useful in quantum chemistry and solid state physics. We present elementary physical arguments which explain the qualitative dependencies of the exchange and correlation energies upon the local density, local spin polarization, and reduced density gradient. The nearly local behavior of the generalized gradient approximation for Exc at valence-electron densities, due to strong cancellation between the nonlocalities of exchange and correlation, is shared by the exact linear response of the uniform electron gas. We further test and develop our rationale for the chemical and solid-state consequences of gradient corrections. We also partially explain the “conjointness” between the exchange energy and the noninteracting kinetic energy, whose generalized gradient approximation is tested here. An appendix presents the full expression for the gradient-corrected correlation potential.
Diffusion in binary liquid n-alkane and alkane-polyethylene blends
Authors: von Meerwall E. , Feick E. J. , Ozisik R. , Mattice W. L.
Published: July 2002

We have used the pulsed-gradient spin-echo proton nuclear magnetic resonance (NMR) method to measure two-component self-diffusion D in melts of two monodisperse polyethylenes, as well as in binary blends of n-dodecane and n-hexacontane, and of n-alkanes with the polyethylene (PE) specimens, over the full concentration range at various temperatures. In the n-alkane blends we observe ideal solution behavior at all concentrations, while in the alkane-PE blends the D ratio increases with rising PE content and molecular weight. This behavior is reproduced by standard free-volume theory including chain-end effects and measured variation of density with molecular weight and temperature. In PE melts and blends the theory must include the gradual transition from Rouse to reptative motion above an entanglement molecular weight which depends on PE concentration. Constraint release effects are included, and dilute solution behavior is modeled near infinite PE dilution. All free-volume parameters are taken from our earlier study of n-alkane melts; the extensions of that theory introduce only one additional adjustable parameter.
On classical theory of moments: Finite-set-of-moments approach. I. Non-negative distribution: Its even moments and Hankel transform
Authors: Kryachko Eugene S. , Koga Toshikatsu
Published: July 2002

For an unknown non-negative distribution Ω(z), the corresponding Hankel transform F(k) is introduced. It is proposed to partition F(k) in such a way that each component satisfies a linear differential relation whose solution gives an approximate Hankel transform in terms of a given finite set of even moments. As a result, for a known finite set of even moments, the non-negative distribution Ω(z) is obtained in the form of a finite sum of the definite differential and integral forms of the Gaussian distributions.
Casimir operators, duality, and the point groups
Authors: Sullivan J. J. , Siddall T. H.
Published: July 2002

In atomic or nuclear shell theory the quadratic Casimir operators can be used to evaluate the expectation values of two-body interactions among equivalent members of a shell. Racah has given closed expressions for these Casimir operators for all the groups in the Racah chain. In this paper an alternate derivation of these closed expressions based on duality with the symmetric group is given. The derivation allows extension of these expressions to situations in which equivalent spins are in an environment, such as a point group, for which the two-body interactions separate into distinct sets. Possible application to NMR systems with spin ≥1/2 are discussed.
The quartic oscillator
Authors: Lay Wolfgang
Published: July 2002

The quantum quartic oscillator is treated on the basis of a singularity-analytic approach to the central two-point connection problem of the triconfluent case of Heun’s differential equation. We split off the asymptotic factors by means of a specific linear transformation of the independent variable and represent the solution in terms of a Jaffé expansion. The result is a fourth-order linear difference equation of Poincaré–Perron type the asymptotic behavior of which is significant for the connection problem. This is investigated by means of the Birkhoff-set of the difference equation and leads to the exact eigenvalue-condition of the problem.
Subgrid-scale modeling with a variable length scale
Authors: Yoshizawa Akira
Published: July 2002

Length scale variation in subgrid-scale (SGS) modeling is studied using the results from a two-scale direct-interaction approximation. The length scale variation is generated by the advection of SGS eddies by grid-scale ones. This effect leads to the variation of a characteristic SGS length scale around the filter width in the Smagorinsky model. The present model shows that the usual Smagorinsky constant is not a universal constant in large eddy simulation of various types of turbulence.
Non-Gaussian statistics in isotropic turbulence
Authors: Chen Hudong , Herring Jackson R. , Kerr Robert M. , Kraichnan Robert H.
Published: July 2002

Several measures of non-Gaussian behavior in simulations of decaying isotropic turbulence are compared with predictions of the direct-interaction approximation (DIA) at an initial Rλ≈35. The quantities studied include the variances and wavenumber power spectra of (a) the total nonlinear term in the Navier–Stokes equation, (b) the time derivative of the velocity at a point, (c) pressure fluctuations, and (d) vorticity and dissipation fluctuations. The direct-interaction approximation gives a good quantitative prediction of the variance of the time derivative and the variance of total nonlinear term, and a fair qualitative prediction of the power spectrum associated with the latter. But DIA totally fails to capture the non-Gaussian statistics associated with pressure fluctuation and vorticity spottiness. Some discussion is given of demands that vorticity and dissipation statistics place upon theories of tubulence at moderate and high Reynolds numbers.
Motion of a sphere in a gas: Numerical solution of the linearized Boltzmann equation
Authors: Loyalka S. K.
Published: July 2002

An understanding of the motion (translation and rotation) of single particles in a gas is required in disciplines as diverse as environmental sciences, cloud physics, nanophase materials manufacturing, health and medical physics, astrophysics, and aeronautics. In this work an accurate description of a sphere’s motion based on the linearized Boltzmann equation is provided.
Edge waves on a longshore shear flow
Authors: Falqués A. , Iranzo V.
Published: July 2002

A theoretical analysis of the effect of a longshore mean shear flow on edge waves is performed in the framework of linear shallow water equations. A single equation describing edge waves as well as neutral shear waves is obtained. A numerical method of calculation is given for the dispersion relations and the wave pattern, accounting for any beach topography and any mean flow profile (remaining constant alongshore and with a straight shoreline). Numerical calculations are presented for a simple exponential flow profile and for a plane bottom. A Doppler shift in the frequencies and a variation in the offshore extension of the waves are found, depending on the maximum local Froude number of the current, F, defined as F = [V(x)/√gH(x)]max, where V(x) stands for the mean longshore current, H(x) for the depth, and g for the gravity. The maximum shift in frequency is for wave numbers of about Vx(0)2/gm and frequencies of about Vx(0), where Vx(0) is the shear at the shoreline and m is the beach slope. For instance, these maximum differences may reach about 40% for F=0.5. Waves of any wavelength can always propagate downstream, but they can propagate upstream only for F≤Fc∼0.7. For mean flows with F≥Fc only waves shorter or longer than some forbidden wavelengths can propagate against the current. An analytical dispersion relation of asymptotic general validity for short waves (corresponding to the gravity range in real beaches) is given. The numerical model as well as this analytical dispersion relation is tested by means of a nonplanar real topography.
Spectral behavior of capillary waves in gas–liquid flows
Authors: McCready Mark J.
Published: July 2002

An equation which expresses the behavior of the frequency spectrum for capillary waves occurring in horizontal gas–liquid flows is derived using a dynamic energy balance. This balance assumes that the energy source for these waves is nonlinear interactions between the dominant gravity–capillary waves and that, in the same manner as for single waves, the dissipation of energy is caused by viscosity. Experimental measurements for both water and a water–glycerin solution with a viscosity of 2 cP in an air flow are described well by the theory over a frequency range of 40–100 Hz.
Instabilities of a liquid film flowing down a slightly inclined plane
Authors: Floryan J. M. , Davis S. H. , Kelly R. E.
Published: July 2002

Falling films on inclined planes display surface and shear instability modes, the latter being important at small angles β of inclination of the plane. These modes are analyzed with particular attention paid to the effects of surface tension. The results show that the critical Reynolds number of the shear mode is nonmonotonic in either the angle β or the surface-tension parameter ζ but displays a local minimum at nonzero values of β and ζ. For large Reynolds number, an analysis shows that the shear mode is inviscidly stable, but that the surface mode is unstable.
Spectroscopic investigation of fast (ns) magnetic field penetration in a plasma
Authors: Sarfaty M. , Shpitalnik R. , Arad R. , Weingarten A. , Krasik Ya. E. , Fruchtman A. , Maron Y.
Published: July 2002

The time-dependent magnetic field spatial distribution in a coaxial positive-polarity plasma opening switch (POS) carrying a current ≂135 kA during ≂100 ns, was investigated by two methods. In the first, ionic line emission was observed simultaneously for two polarizations to yield the Doppler and Zeeman contributions to the line profiles. In the second method, the axial velocity distribution of ions was determined, giving the magnetic field through the ion equation of motion. This method requires knowledge of the electron density, here obtained from the observed particle ionization times. To this end, a lower bound for the electron kinetic energy was determined using various line intensities and time-dependent collisional-radiative calculations. An important necessity for POS studies is the locality of all measurements in r, z, and θ. This was achieved by using laser evaporation to seed the plasma nonperturbingly with the species desired for the various measurements. The Zeeman splitting and the ion motion showed magnetic field penetration through the 3.5 cm long plasma at a velocity ≂108 cm/s. The current density was found to be relatively high at the load-side edge of the switch plasma. It is suggested that this may cause plasma acceleration into the vacuum section toward the load, which is supported by charge-collector measurements. The fast magnetic field penetration agrees with estimates based on the Hall-field mechanism.
Wavelet analysis of ADITYA edge turbulence: Evidence of non-linear interaction
Authors: Jha R. , Saxena Y. C.
Published: July 2002

The edge turbulence in the ADITYA tokamak [Phys. Rev. Lett. 69, 1375 (1992)] is examined using wavelet analysis techniques. The wavelet filters are used to separate low and high frequency components. The filtered plasma density and floating potential fluctuations show leptokurtic non-Gaussianity (kurtosis, K≳3) at high frequencies, whereas, the low frequency components are nearly Gaussian. The recently developed wavelet bicoherence technique [Phys. Plasmas 2, 3017 (1995)] is extended to the Mexican hat wavelet. When the data are examined using wavelet bicoherence technique, it is found that the turbulent density and potential signals exhibit episodes of quadratic interaction in which low and high frequency components are coupled.
Zonal flow generation by parametric instability in magnetized plasmas and geostrophic fluids
Authors: Smolyakov A. I. , Diamond P. H. , Shevchenko V. I.
Published: July 2002

Two-dimensional magnetized plasmas and geostrophic fluids exhibit a common nonlinearity due to the advection of vorticity. It is shown here that due to this nonlinearity, the propagation of small scale wave packets is accompanied by instability of a low frequency, long wavelength component. This instability is the coherent hydrodynamic generalization of the resonant type mean flow instability identified recently [P. H. Diamond, M. N. Rosenbluth, F. L. Hinton, M. Malkov, J. Fleischer, and A. Smolyakov, 17th IAEA Fusion Energy Conference, IAEA-CN-69/TH3/1, Yokohama, 1998 (to be published, International Atomic Energy Agency, Vienna)]. The mechanism discussed here, along with the resonant type, constitutes the “hydrodynamic” and “kinetic” regimes of the same process, similar to the case of plasma-beam instabilities. It is suggested that this generic mechanism is responsible for the generation of mean flow in atmospheres of rotating planets and magnetized plasmas.
Catalytic efficiency and vitality of HIV-1 proteases from African viral subtypes
Authors: Velazquez-Campoy Adrian , Todd Matthew J. , Vega Sonia , Freire Ernesto
Published: July 2002

The vast majority of HIV-1 infections in Africa are caused by the A
and C viral subtypes rather than the B subtype prevalent in the United
States and Western Europe. Genomic differences between subtypes give
rise to sequence variations in the encoded proteins, including the
HIV-1 protease. Because some amino acid polymorphisms occur at sites
that have been associated with drug resistance in the B subtype, it is
important to assess the effectiveness of protease inhibitors that have
been developed against different subtypes. Here we report the enzymatic
characterization of HIV-1 proteases with sequences found in
drug-naïve Ugandan adults. The A protease used in these studies
differs in seven positions
(I13V/E35D/M36I/R41K/R57K/H69K/L89M) in relation to the
consensus B subtype protease. Another protease containing a subset of
these amino acid polymorphisms (M36I/R41K/H69K/L89M), which are
found in subtype C and other HIV subtypes, also was studied. Both
proteases were found to have similar catalytic constants,
k
cat
, as the B subtype. The C subtype
protease displayed lower
K
m
values against
two different substrates resulting in a higher (2.4-fold) catalytic
efficiency than the B subtype protease. Indinavir, ritonavir,
saquinavir, and nelfinavir inhibit the A and C subtype proteases with
2.5–7-fold and 2–4.5-fold weaker
K
i
s than
the B subtype. When all factors are taken into consideration it is
found that the C subtype protease has the highest vitality (4–11
higher than the B subtype) whereas the A subtype protease exhibits
values ranging between 1.5 and 5. These results point to a higher
biochemical fitness of the A and C proteases in the presence of
existing inhibitors.
Dominant/recessive behavior in the expression of molecular information: Self-assembly of inorganic macrocyclic architectures containing coordinatively unsaturated ligands
Authors: Funeriu Daniel P. , Rissanen Kari , Lehn Jean-Marie P.
Published: July 2002

The polytopic ligand 1 contains three different metal ion binding subunits forming two substructures that code for the self-assembly of two different coordination structures (helicate and grid type) under metal ion complexation. Reaction with Cu(II) and Zn(II) ions generates the coordinatively unsaturated architectures 8 and 9 resulting from the formation of two double helicate arrangements. Their crystal structure has been determined by x-ray diffraction. These results show that the double helical motif is expressed at the expense of the grid type one, indicating the dominant/recessive behavior of the system. Together with earlier studies on the linear combination and crossover processing schemes, the dominant/recessive generation of 8 and 9 completes the demonstration of principle of the modes of multiple expression of molecular information in a multicode programmed chemical system.
Does the granular matter?
Authors: Jaeger Heinrich M. , Shinbrot Troy , Umbanhowar Paul B.
Published: July 2002

Granular materials, such as sand, gravel, powders, and
pharmaceutical pills, are large aggregates of macroscopic, individually
solid particles, or “grains.” Far from being simple materials
with simple properties, they display an astounding range of complex
behavior that defies their categorization as solid, liquid, or gas.
Just consider how sand can stream through the orifice of an hourglass
yet support one's weight on the beach; how it can form patterns
strikingly similar to a liquid when vibrated, yet respond to stirring
by “unmixing” of large and small grains. Despite much effort,
there still is no comprehensive understanding of other forms of matter,
like ordinary fluids or solids. In what way, therefore, is granular
matter special, and what makes it so difficult to understand? An
emerging interdisciplinary approach to answering these questions
focuses directly on the material's discontinuous granular nature.
Kinetic and structural analysis of mutant CD4 receptors that are defective in HIV gp120 binding
Authors: Wu Hao , Myszka David G. , Tendian Susan W. , Brouillette Christie G. , Sweet Ray W. , Chaiken Irwin M. , Hendrickson Wayne A.
Published: July 2002

The T-cell antigen coreceptor CD4 also serves as the receptor for the envelope glycoprotein gp120 of HIV. Extensive mutational analysis of CD4 has implicated residues from a portion of the extracellular amino-terminal domain (D1) in gp120 binding. However, none of these proteins has been fully characterized biophysically, and thus the precise effects on molecular structure and binding interactions are unknown. In the present study, we produced soluble versions of three mutant CD4 molecules (F43V, G47S, and A55F) and characterized their structural properties, thermostability, and ability to bind gp120. Crystallographic and thermodynamic analysis showed minimal structural alterations in the F43V and G47S mutant proteins, which have solvent-exposed mutant side chains. In contrast, some degree of disorder appears to exist in the folded state of A55F, as a result of mutating a buried side chain. Real time kinetic measurements of the interaction of the mutant proteins with gp120 showed affinity decreases of 5-fold for G47S, 50-fold for A55F, and 200-fold for F43V. Although both rate constants for the binding reaction were affected by these mutations, the loss in affinity was mainly due to a decrease in on rates, with less drastic changes occurring in the off rates. These observations suggest the involvement of conformational adaptation in the CD4–gp120 interaction. Together, the structural and kinetic data confirm that F43V is a critical residue in gp120 recognition site, which may also include main chain interactions at residue Gly-47.
DNA damage and p53-mediated cell cycle arrest: A reevaluation
Authors: Pellegata Natalia S. , Antoniono Ronald J. , Redpath J. Leslie , Stanbridge Eric J.
Published: July 2002

Most mammalian cells exhibit transient delays in the G
1
and G
2
phases of the cell cycle after treatment with
radiation or radiomimetic compounds. p53 is required for the arrest in
G
1
, which provides time for DNA repair. Recently, a role of
p53 in the G
2
/M transition has also been suggested.
However, it has been reported that the presence of functional p53 does
not always correlate with the induction of these checkpoints. To
precisely assess the role of p53 in activating cell cycle checkpoints
and in cell survival after radiation, we studied the response of two
isogenic human fibrosarcoma cell lines differing in their p53 status
(wild type or mutant). We found that when irradiated cells undergo a
wild-type p53-dependent G
1
arrest, they do not subsequently
arrest in G
2
. Moreover, wild-type p53 cells irradiated past
the G
1
checkpoint arrest in G
2
but do not delay
in the subsequent G
1
phase. Furthermore, in these cell
lines, which do not undergo radiation-induced apoptosis, the
wild-type p53 cell line exhibited a greater radioresistance in terms of
clonogenic survival. These results suggest that the two checkpoints may
be interrelated, perhaps through a control system that determines,
depending on the extent of the damage, whether the cell needs to arrest
cell cycle progression at the subsequent checkpoint for further repair.
p53 could be a crucial component of this control system.
Assembly of a rod-shaped chimera of a trimeric GCN4 zipper and the HIV-1 gp41 ectodomain expressed in
Escherichia coli
Authors: Weissenhorn Winfried , Calder Lesley J. , Dessen Andréa , Laue Tom , Skehel John J. , Wiley Don C.
Published: July 2002

The HIV-1 envelope subunit gp41 plays a role in viral entry by initiating fusion of the viral and cellular membranes. A chimeric molecule was constructed centered on the ectodomain of gp41 without the fusion peptide, with a trimeric isoleucine zipper derived from GCN4 (pIIGCN4) on the N terminus and part of the trimeric coiled coil of the influenza virus hemagglutinin (HA) HA2 on the C terminus. The chimera pII-41-HA was overexpressed as inclusion bodies in bacteria and refolded to soluble aggregates that became monodisperse after treatment with protease. Either trypsin or proteinase K, used previously to define a protease-resistant core of recombinant gp41 [Lu, M., Blacklow, S. C. & Kim, P. S. (1995)
Nat. Struct. Biol.
2, 1075–1082], removed about 20–30 residues from the center of gp41 and all or most of the HA2 segment. Evidence is presented that the resulting soluble chimera, retaining the pIIGCN4 coiled coil at the N terminus, is an oligomeric highly α-helical rod about 130 Å long that crystallizes. The chimeric molecule is recognized by the Fab fragments of mAbs specific for folded gp41. A similar chimera was assembled from the two halves of the molecule expressed separately in different bacteria and refolded together. Crystals from the smallest chimera diffract x-rays to 2.6-Å resolution.
Making chemistry selectable by linking it to infectivity
Authors: Gao Changshou , Lin Chao-Hsiung , Lo Chih-Hung L. , Mao Shenlan , Wirsching Peter , Lerner Richard A. , Janda Kim D.
Published: July 2002

The link between recognition and replication is fundamental to the
operation of the immune system. In recent years, modeling this process
in a format of phage-display combinatorial libraries has afforded a
powerful tool for obtaining valuable antibodies. However, the ability
to readily select and isolate rare catalysts would expand the scope of
library technology. A technique in which phage infection controlled the
link between recognition and replication was applied to show that
chemistry is a selectable process. An antibody that operated by
covalent catalysis to form an acyl intermediate restored phage
infectivity and allowed selection from a library in which the catalyst
constituted 1 in 10
5
members. Three different selection
approaches were examined for their convenience and generality.
Incorporating these protocols together with well known affinity labels
and mechanism-based inactivators should allow the procurement of a wide
range of novel catalytic antibodies.
Assembly of an active enzyme by the linkage of two protein modules
Authors: Nixon A. E. , Warren M. S. , Benkovic S. J.
Published: July 2002

The feasibility of creating new enzyme activities from enzymes of known function has precedence in view of protein evolution based on the concepts of molecular recruitment and exon shuffling. The enzymes encoded by the
Escherichia coli
genes
pur
U and
pur
N, N
10
-formyltetrahydrofolate hydrolase and glycinamide ribonucleotide (GAR) transformylase, respectively, catalyze similiar yet distinct reactions. N
10
-formyltetrahydrofolate hydrolase uses water to cleave N
10
-formyltetrahydrofolate into tetrahydrofolate and formate, whereas GAR transformylase catalyses the transfer of formyl from N
10
-formyltetrahydrofolate to GAR to yield formyl-GAR and tetrahydrofolate. The two enzymes show significant homology (≈60%) in the carboxyl-terminal region which, from the GAR transformylase crystal structure and labeling studies, is known to be the site of N
10
-formyltetrahydrofolate binding. Hybrid proteins were created by joining varying length segments of the N-terminal region of the PurN gene (GAR binding region) and the C-terminal (N
10
-formyltetrahydrofolate binding) region of PurU. Active PurN/PurU hybrids were then selected for by their ability to complement an auxotrophic
E. coli
strain. Hybrids able to complement the auxotrophs were purified to homogeneity and assayed for activity. The specific activity of two hybrid proteins was within 100- to 1000-fold of the native
pur
N GAR transformylase validating the approach of constructing an enzyme active site from functional parts of others.
Aggregate community properties and the strength of species’ interactions
Authors: Hughes Jennifer B. , Roughgarden Joan
Published: July 2002

Although humanity depends on the continued, aggregate functioning
of natural ecosystems, few studies have explored the impact of
community structure on the stability of aggregate community properties.
Here we derive the stability of the aggregate property of community
biomass as a function of species’ competition coefficients for a
two-species model. The model predicts that the stability of community
biomass is relatively independent of the magnitude of the interaction
strengths. Instead, the degree of asymmetry of the interactions appears
to be key to community stability.
Prominence of the dopamine D2 short isoform in dopaminergic pathways
Authors: Khan Zafar U. , Mrzljak Ladislav , Gutierrez Antonia , de la Calle Adelaida , Goldman-Rakic Patricia S.
Published: July 2002

As a result of alternative splicing, the D2 gene of the dopamine receptor family exists in two isoforms. The D2 long is characterized by the insertion of 29 amino acids in the third cytoplasmic loop, which is absent in the short isoform. We have produced subtype-specific antibodies against both the D2 short and D2 long isoforms and found a unique compartmentalization between these two isoforms in the primate brain. The D2 short predominates in the cell bodies and projection axons of the dopaminergic cell groups of the mesencephalon and hypothalamus, whereas the D2 long is more strongly expressed by neurons in the striatum and nucleus accumbens, structures targeted by dopaminergic fibers. These results show that the splice variants of the dopamine D2 receptor are differentially distributed and possess distinct functions. The strategic localization of the D2 short isoform in dopaminergic cell bodies and axons strongly suggests that this isoform is the likely dopamine autoreceptor, whereas the D2 long isoform is primarily a postsynaptic receptor.
Lactone-ring-cleaving enzyme: Genetic analysis, novel RNA editing, and evolutionary implications
Authors: Kobayashi Michihiko , Shinohara Makoto , Sakoh Chigusa , Kataoka Michihiko , Shimizu Sakayu
Published: July 2002

A lactonohydrolase from
Fusarium oxysporum
AKU 3702 is an enzyme catalyzing the hydrolysis of aldonate lactones to the corresponding aldonic acids. The amino acid sequences of the NH
2
terminus and internal peptide fragments of the enzyme were determined to prepare synthetic oligonucleotides as primers for the PCR. An approximate 1,000-base genomic DNA fragment thus amplified was used as the probe to clone both genomic DNA and cDNA for the enzyme. The lactonohydrolase genomic gene consists of six exons separated by five short introns. A novel type of RNA editing, in which lactonohydrolase mRNA included the insertion of guanosine and cytidine residues, was observed. The predicted amino acid sequence of the cloned lactonohydrolase cDNA showed significant similarity to those of the gluconolactonase from
Zymomonas mobilis
, and paraoxonases from human and rabbit, forming a unique superfamily consisting of C-O cleaving enzymes and P-O cleaving enzymes. Lactonohydrolase was expressed under the control of the
lac
promoter in
Escherichia coli
.
Desoxyepothilone B is curative against human tumor xenografts that are refractory to paclitaxel
Authors: Chou Ting-Chao , Zhang Xiu-Guo , Harris Christina R. , Kuduk Scott D. , Balog Aaron , Savin Kenneth A. , Bertino Joseph R. , Danishefsky Samuel J.
Published: July 2002

The epothilones are naturally occurring, cytotoxic macrolides that function through a paclitaxel (Taxol)-like mechanism. Although structurally dissimilar, both classes of molecules lead to the arrest of cell division and eventual cell death by stabilizing cellular microtubule assemblies. The epothilones differ in their ability to retain activity against multidrug-resistant (MDR) cell lines and tumors where paclitaxel fails. In the current account, we focus on the relationship between epothilone and paclitaxel in the context of tumors with multiple drug resistance. The epothilone analogue
Z
-12,13-desoxyepothilone B (dEpoB) is >35,000-fold more potent than paclitaxel in inhibiting cell growth in the MDR DC-3F/ADX cell line. Various formulations, routes, and schedules of i.v. administration of dEpoB have been tested in nude mice. Slow infusion with a Cremophor-ethanol vehicle proved to be the most beneficial in increasing efficacy and decreasing toxicity. Although dEpoB performed similarly to paclitaxel in sensitive tumors xenografts (MX-1 human mammary and HT-29 colon tumor), its effects were clearly superior against MDR tumors. When dEpoB was administered to nude mice bearing our MDR human lymphoblastic T cell leukemia (CCRF-CEM/paclitaxel), dEpoB demonstrated a full curative effect. For human mammary adenocarcinoma MCF-7/Adr cells refractory to paclitaxel, dEpoB reduced the established tumors, markedly suppressed tumor growth, and surpassed other commonly used chemotherapy drugs such as adriamycin, vinblastine, and etoposide in beneficial effects.