bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular supercollisions: Evidence for large energy transfer in the collisional relaxation of highly vibrationally excited pyrazine by CO2
Authors: Mullin Amy S. , Michaels Chris A. , Flynn George W.
Published: July 2002

The temperature dependence of the collisional quenching of highly vibrationally excited pyrazine by CO2 molecules has been investigated for the temperature range 243–364 K using high resolution time resolved diode laser spectroscopy. Particular emphasis is placed on vibration to rotation-translation (V→R/T) energy transfer which leaves the CO2 vibrations unexcited and occurs predominantly through short-range repulsive forces. Vibrationally hot pyrazine is prepared by 248 nm excimer laser pumping, followed by rapid radiationless transitions to the ground electronic state. For the range of experimental cell temperatures used here, the nascent rotational population distributions of the 0000 ground state of CO2 resulting from collisions with hot pyrazine were probed at short times following excitation of pyrazine by the excimer laser pulse. The CO2 translational recoil velocity was also measured for individual rotational levels of the 0000 state. In addition, temperature dependent rate constants and probabilities were determined for energy transfer from the vibrationally hot pyrazine into individual rotational levels of the 0000 state of CO2. The rotational distributions, velocity recoils, and quenching rates exhibit a very weak temperature dependence for production of CO2 high J states, indicating that the CO2 molecules involved in these energy transfer events originate from rotational levels only slightly greater than the thermal mean J value. Based on these results, values for ΔE, the energy transfer from hot pyrazine to CO2 resulting in final CO2 0000 states J=58 through J=82, are estimated to range from 2550 to 7090 cm−1 in a single collision.
Computer simulation of a polymer electrolyte: Lithium iodide in amorphous poly(ethylene oxide)
Authors: Müller-Plathe Florian , van Gunsteren Wilfred F.
Published: July 2002

Systems of lithium iodide dissolved in poly(ethylene oxide), which are prototypes of polymer electrolytes used, for example, in batteries were studied by means of molecular dynamics simulations. Investigations were aimed at the molecular driving force behind the salt uptake, the mechanism of ion transport, participation of the polymer in ion transport, ion clustering, change of polymer properties by the presence of ions, and ionic conductivity. Particular attention has been given to the differences in behavior between (previously studied) neutral and ionic species dissolved in polymers.
A Monte Carlo study of titrating polyelectrolytes
Authors: Ullner Magnus , Jönsson Bo , Söderberg Bo , Peterson Carsten
Published: July 2002

Monte Carlo simulations have been used to study three different models for linear, titrating polyelectrolytes in a salt-free environment: (i) a rigid polymer with rigid bonds (rigid rod); (ii) a flexible polymer with rigid bonds; and (iii) a flexible polymer with flexible bonds. The use of a very efficient pivot algorithm has made it possible to simulate very long chains, with up to several thousand titrating groups. The results have been compared to a mean field approximation for a rigid rod and variational results emanating from a Flory type approach. It is found that the rigid rod mean field model gives a qualitatively correct description for the apparent dissociation constant for all three models. At room temperature, the energy contribution to the apparent dissociation constant often dominates over the entropic term, which partly explains the relative success of this approach. In the case of flexible bonds, both the conformational behavior and the behavior of the apparent dissociation constant are well described by a variational ansatz with a quadratic term, largely thanks to the harmonicity of the bonds themselves. The approach is less successful for rigid bonds, which becomes evident for highly charged chains where a harmonic entropy term is incorrect. This can be remedied by replacing it with an expression valid in the strong coupling regime. Empirical scaling expressions have also been found, primarily for the end-to-end distance.
Electronic excitation energies in copper selenide clusters
Authors: Schäfer Ansgar , Kollwitz Markus , Ahlrichs Reinhart
Published: July 2002

We report calculated singlet and triplet excitation energies in bare copper selenide clusters (Cu2Se)n up to n=18 and ligand-covered clusters (Cu2Se)n(PH3)m up to n=10 (m≤8). Various approaches for the calculation of excitation energies (including coupled cluster methods) are compared for small clusters which suggests the method of configuration interaction restricted to single substitutions (CIS) to give reasonable results with an error in the predicted energies of roughly +1 eV. The lowest CIS excitation energies show a steep increase with the cluster size up to about n=6 and a slow decrease for larger clusters, for which a rationalization is given. Even for the largest of the treated clusters the computed excitation energies are higher than 3.5 eV which suggests that these clusters are still far from showing β-Cu2Se bulk properties (energy gap 1 eV). The electronic excitations are found to be essentially of charge transfer character (Se→Cu).
Molecular theory of strain hardening of a polymer gel: Application to gelatin
Authors: Groot Robert D. , Bot Arjen , Agterof Wim G. M.
Published: July 2002

The elasticity of gelatin gels at large deformation has been measured for various experimental conditions. The general pattern is that stress increases with strain in a nonlinear way up to the point where the gel fails. To interpret this nonlinear stress increase, we studied a number of molecular models by Monte Carlo simulation and by mean-field methods. The effect of finite polymer length is studied via the FENE model (finite extensible nonlinear polymer connections) and via the exact statistics of Kramers’ model (chains of freely rotating stiff rods) for a small number of elements per chain. To investigate the effect of fractal connections, the end-point distribution that comes forward from scaling theory has been generalized to arbitrary fractal dimension. Finally we studied a heterogeneous network model: connections formed by rods and coils. We also discuss the consequence of microphase separation. Combining experiment and theory we conclude the following: (i) The elastically active network connections in gelatin are most certainly not Gaussian. (ii) Strain hardening in gelatin can be attributed to either: (a) finite polymer length (the chain length between connection points should be some 2.5 times the persistence length), or (b) a fractal structure of the polymer strands (the fractal dimension should be roughly df=1.3–1.5), or (c) the presence of both stiff rods and flexible coils (the length of the rods should be 1.4–4.4 times the radius of gyration of the coils). (iii) Models b and c describe the experimental data significantly better than model a. From a single parameter (the fractal dimension) the fractal model correctly describes (1) the nonlinearity of the stress–strain curve, (2) the scaling of Young’s modulus with polymer concentration, (3) the scaling of neutron scattering intensity with wave number, and (4) it predicts the scaling exponent of the linear dynamic modulus with frequency in the glassy transition zone (no experimental data available). The experimental parameters found for the rod+coils model suggest a Rouse diffusion controlled growth mechanism for the rods. Although the theory presented here is applied to gelatin, its formulation is quite general, and its implications are also relevant for other strain hardening polymer gels.
Binary nucleation kinetics. III. Transient behavior and time lags
Authors: Wyslouzil Barbara E. , Wilemski Gerald
Published: July 2002

Transient binary nucleation is more complex than unary because of the bidimensionality of the cluster formation kinetics. To investigate this problem qualitatively and quantitatively, we numerically solved the birth–death equations for vapor-to-liquid phase transitions. Our previous work [J. Chem. Phys 103, 1137 (1995)] showed that the customary saddle point and growth path approximations are almost always valid in steady state gas phase nucleation and only fail if the nucleated solution phase is significantly nonideal. The current work demonstrates that in its early transient stages, binary nucleation rarely, if ever, occurs via the saddle point. This affects not only the number of particles forming but their composition and may be important for nucleation in glasses and other condensed mixtures for which time scales are very long. Before reaching the state of saddle point nucleation, most binary systems pass through a temporary stage in which the region of maximum flux extends over a ridge on the free energy surface. When ridge crossing nucleation is the steady state solution, it thus arises quite naturally as an arrested intermediate state that normally occurs in the development of saddle point nucleation. While the time dependent and steady state distributions of the fluxes and concentrations for each binary system are strongly influenced by the gas composition and species impingement rates, the ratio of nonequilibrium to equilibrium concentrations has a quasiuniversal behavior that is determined primarily by the thermodynamic properties of the liquid mixture. To test our quantitive understanding of the transient behavior, we directly calculated the time lag for the saddle point flux and compared it with the available analytical predictions. Although the analytical results overestimate the time lag by factors of 1.2–5, they should be adequate for purposes of planning experiments. We also found that the behavior of the saddle point time lag can indicate when steady state ridge crossing nucleation will occur.
Resolution of anomalies in the geometry and vibrational frequencies of monobromosilylene (HSiBr) by pulsed discharge jet spectroscopy
Authors: Harjanto H. , Harper Warren W. , Clouthier Dennis J.
Published: July 2002

A detailed examination of the ground and first excited singlet electronic states of HSiBr has been carried out through analysis of the 500–400 nm band system, using pulsed discharge jet and laser-induced fluorescence techniques. HSiBr and DSiBr have been produced by an electric discharge through SiHBr3 and SiDBr3 vapor in argon. Rotational analysis of the 000 bands yielded the structural parameters r0″(SiH)=1.518(1) Å, r0″(SiBr)=2.237(1) Å, θ0″=93.4(3)°, r0′(SiH)=1.497(10) Å, r0′(SiBr)=2.208(2) Å, and θ0′=116.4(7)°. Previous anomalies in the geometric parameters and vibrational frequencies have been resolved and the ground state bond lengths and vibrational frequencies are found to be comparable to those of SiH and SiBr. Harmonic force fields have been determined for the ground and excited states and the radiative lifetime of HSiBr has been measured to be 598±18 ns.
Melting and evaporation of argon clusters
Authors: Rytkönen A. , Valkealahti S. , Manninen M.
Published: July 2002

Molecular dynamics simulation with a Nosé–Hoover thermostat was used to study melting and evaporation of free icosahedral argon clusters containing 13 to 1415 atoms. Clusters of 147 atoms or less were found to melt at temperatures clearly below the bulk melting temperature in agreement with previous results. Clusters containing 309 atoms or more were observed to desorb atoms at temperatures where the core of the cluster is solid. As a consequence of this a reliable determination of their melting temperatures using molecular dynamics was found to be complicated.
Pulsed discharge jet spectroscopy of DSiF and the equilibrium molecular structure of monofluorosilylene
Authors: Harper Warren W. , Hostutler David A. , Clouthier Dennis J.
Published: July 2002

The jet-cooled laser induced fluorescence excitation spectrum of the Ã 1A′′−X̃ 1A band system of DSiF has been observed using the pulsed discharge jet technique. Vibrational analysis of the spectrum yielded upper state harmonic vibrational frequencies of ω1=1322, ω2=444, and ω3=867 cm−1. Vibronic bands involving all of the upper state fundamentals of HSiF and DSiF have now been rotationally analyzed, allowing a determination of the excited state equilibrium structure as re′(SiH)=1.526±0.014 Å, re′(SiF)=1.597±0.003 Å, and θe′(HSiF)=115.0±0.6°. The harmonic frequencies and centrifugal distortion constants were used to obtain harmonic force fields and average (rz) structures for the ground and excited states. The ground state average structure was used to estimate the equilibrium structure of re″(SiH)=1.528±0.005 Å, re″(SiF)=1.603±0.003 Å, and θe″(HSiF)=96.9±0.5°.
Atomic Fukui function indices and local softness ab initio
Authors: Balawender Robert , Komorowski Ludwik
Published: July 2002

The complete and original calculation scheme beyond the finite difference approximation, for the atomic (and orbital) Fukui function (FF) indices is proposed. The method explores an expansion for derivatives of LCAO coefficients, ∂C/∂N=CU. The separation scheme for the U matrix has been elaborated at the ab initio level. Nucleophilic and electrophilic FF indices, as well as atomic softness, have been derived from the standard result of SCF HF ab initio calculations. The indices reproduce two effects; the change in orbital occupancy and the relaxation of the electronic system. The molecular hardness (softness) provided by this scheme explicitly includes these two effects.
The electronic spectrum of monoiodosilylene (HSiI) revisited
Authors: Clouthier Dennis J. , Harper Warren W. , Klusek Chad M. , Smith Tony C.
Published: July 2002

The Ã 1A″–X̃ 1A′ spectra of jet-cooled HSiI and DSiI have been studied using the pulsed discharge technique, using H3SiI and D3SiI as precursors. The excited state vibrational frequencies have been determined and the literature value of ν1′ substantially revised. Although a reliable excited state equilibrium structure was unattainable, the rotational constants of the 000 bands gave the structural parameters r0″(Si–I)=2.463(1) Å, r0″(Si–H)=1.534(1) Å, θ0″(HSiI)=92.4(1)°, r0′(Si–I)=2.436(1) Å, r0′(Si–H)=1.515(5) Å, and θ0′(HSiI)=114.9(2)°. The radiative lifetime of the 000 band has been measured to be 1230±30 ns. Trends in the structural parameters, vibrational frequencies, and their changes on electronic excitation for the monohalosilylenes have been discussed.
Semiempirical van der Waals/Cahn–Hilliard theory: Size dependence of the Tolman length
Authors: Gránásy László
Published: July 2002

The interfacial density profiles, pressure tensor, and Tolman-length δT are determined for the critical droplets of nonane in the framework of the semiempirical van der Waals/Cahn–Hilliard theory. It is shown that the Tolman’s length is strongly size dependent, and tends to a negative value for large drops; indicating that Tolman’s approximation for the curvature dependence of the interfacial free-energy γ≈γ∞/(1+2δT,eq/R) based on the equilibrium values δT,eq, and γ∞, is inaccurate for typical liquid nuclei.
Nuclear quadrupole coupling in Cl2C=CHCl and Cl2C=CH2: Evidence for systematic differences in orientations between internuclear and field gradient axes for terminal quadrupolar nuclei
Authors: Kisiel Z. , Białkowska-Jaworska E. , Pszczółkowski L.
Published: July 2002

The nuclear quadrupole hyperfine structure in rotational transitions of parent isotopomers of trichloroethylene, Cl235C=CH35Cl, and 1,1-dichloroethylene, Cl235C=CH2, was measured at sub-Doppler resolution with a pulsed supersonic beam, cavity Fourier transform microwave spectrometer. The complete inertial and principal nuclear quadrupole coupling tensors of all chlorine nuclei are determined. The three chlorine tensors for trichloroethylene have been assigned unambiguously to the structural positions of the chlorine nuclei on the basis of ab initio field gradient calculations. For both molecules the directions of the symmetry z axes of the field gradients at the chlorine nuclei show small, but significant, angular deviations δ from the directions of the respective CCl bonds. These differences are found to be well reproduced by ab initio calculations at the self-consistent field (SCF) level, with small sensitivity to the basis set. Similarly accurate reproduction of δ is demonstrated for various quadrupolar nuclei X=N, Cl, Br, and I terminal to CX bonds in several molecules. Consideration of contributions to the electric field gradient reveals that the small angular deviations δ reflect intermediate range molecular asymmetry about the bond axis to the measuring nucleus, at distances 1–4 Å away. In the case of two neighboring atoms bonded to the same intermediate atom as the probe nucleus the direction of the z axis at this nucleus will, in general, deviate towards the neighbor with greater Z, and therefore, with greater local electron density.
Regular and irregular vibrational states: Localized anharmonic modes in Ar3
Authors: Wright Nicholas J. , Hutson Jeremy M.
Published: July 2002

We present a method for calculating the energy levels and wave functions of floppy triatomic molecules such as the rare gas trimers. It is based upon a potential-optimized discrete variable representation and takes into account the wide-amplitude vibrations that occur in such systems. We have investigated the energy levels and wave functions for Ar3. The wave functions for the low-lying states show very regular behavior. Above the barrier to linearity, most of the wave functions are irregular but some have simple nodal patterns that suggest localization along periodic orbits. In addition to the “horseshoe” states previously described for H3+, we have identified localized features corresponding to symmetric and antisymmetric stretching vibrations around a linear configuration. The different localized modes can be combined to form more complex states in a manner analogous to normal modes.
Mixed quantum-classical dynamics
Authors: Kapral Raymond , Ciccotti Giovanni
Published: July 2002

Mixed quantum-classical equations of motion are derived for a quantum subsystem of light (mass m) particles coupled to a classical bath of massive (mass M) particles. The equation of motion follows from a partial Wigner transform over the bath degrees of freedom of the Liouville equation for the full quantum system, followed by an expansion in the small parameter μ=(m/M)1/2 in analogy with the theory of Brownian motion. The resulting mixed quantum-classical Liouville equation accounts for the coupled evolution of the subsystem and bath. The quantum subsystem is represented in an adiabatic (or other) basis and the series solution of the Liouville equation leads to a representation of the dynamics in an ensemble of surface-hopping trajectories. A generalized Pauli master equation for the evolution of the diagonal elements of the density matrix is derived by projection operator methods and its structure is analyzed in terms of surface-hopping trajectories.
The electronic spectrum of pyrrole
Authors: Christiansen Ove , Gauss Jürgen , Stanton John F. , Jo/rgensen Poul
Published: July 2002

The electronic spectrum of pyrrole has been investigated by performing calculations using a hierarchy of coupled-cluster models consisting of CCS, CC2, CCSD, and CC3. Basis-set effects have been investigated by carrying out calculations using correlation-consistent basis sets augmented with functions especially designed for the description of Rydberg states. Oscillator strengths, excited state dipole moments, and second moments of the electronic charge distributions have been used to characterize the electronic transitions and final states. Structures and vibrational frequencies have been calculated for a few selected states, and the importance of distinguishing between vertical and adiabatic transitions for accurate comparison with experiment has been emphasized. The experimental spectrum has been scrutinized in the relevant energy region, and the accuracy of recent calculations [CASPT2, MRMP, ADC(2)] has been critically reexamined.
From molecular clusters to bulk matter. II. Crossover from icosahedral to crystalline structures in CO2 clusters
Authors: Maillet Jean-Bernard , Boutin Anne , Fuchs Alain H.
Published: July 2002

The change in structure with size in (CO2)N clusters has been investigated in the crossover regime from icosahedral to cubic morphology (N=19 to 55) by molecular dynamics simulation. All the minima in the potential energy surface (PES) visited by the solid clusters at finite temperature have been characterized using a local structure analysis method. A simple picture of the change in free-energy minimum with size in CO2 solid clusters emerges from this work. It is based on the relative stability of two energy basins in the PES corresponding to the icosahedral and cubic-like structure, respectively. In addition, some evidence is provided for the existence of an icosahedral supercooled liquid in the size range near N∼50.
Competition between photochemistry and energy transfer in ultraviolet-excited diazabenzenes. II. Identifying the dominant energy donor for “supercollisions”
Authors: Sevy Eric T. , Michaels Chris A. , Tapalian H. Charles , Flynn George W.
Published: July 2002

CO 2 bath molecules scattered into J=72 of the 0000 vibrational state at short times after 248 or 266 nm UV excitation of pyrazine are probed using high resolution time resolved IR diode laser spectroscopy as a function of UV laser fluence from ∼3 to 80 mJ/cm2. The implications of pyrazine photodissociation for the interpretation of these collisional energy transfer experiments are considered. Specifically, the possibility that translationally hot HCN resulting from pyrazine dissociation may be the source of excitation for collisions that impart a large amount of rotational and translational energy to CO2 molecules is examined. Transient absorption measurements probing rotationally and translationally excited CO2 molecules produced following excitation of pyrazine are analyzed within the context of a kinetic scheme incorporating pyrazine photodissociation, as well as excitation of CO2 by both translationally hot HCN and vibrationally excited pyrazine. This analysis indicates that vibrationally hot pyrazine, which has sufficient energy to dissociate, is the source of excitation in collisions imparting large amounts of rotational and translational energy to CO2.
Infinitely many Lax pairs and symmetry constraints of the KP equation
Authors: Lou Sen-Yue , Hu Xing-Biao
Published: July 2002

Starting from a known Lax pair, one can get some infinitely many coupled Lax pairs, infinitely many nonlocal symmetries and infinitely many new integrable models in some different ways. In this paper, taking the well known Kadomtsev–Petviashvili (KP) equation as a special example, we show that infinitely many nonhomogeneous linear Lax pairs can be obtained by using infinitely many symmetries, differentiating the spectral functions with respect to the inner parameters. Using a known Lax pair and the Darboux transformations (DT), infinitely many nonhomogeneous nonlinear Lax pairs can also be obtained. By means of the infinitely many Lax pairs, DT and the conformal invariance of the Schwartz form of the KP equation, infinitely many new nonlocal symmetries can be obtained naturally. Infinitely many integrable models in (1+1)-dimensions, (2+1)-dimensions, (3+1)-dimensions and even in higher dimensions can be obtained by virtue of symmetry constraints of the KP equation related to the infinitely many Lax pairs.
Matrix elements for a generalized spiked harmonic oscillator
Authors: Hall Richard L. , Saad Nasser , von Keviczky Attila B.
Published: July 2002

Closed form expressions for the singular-potential integrals 〈m|x−α|n〉 are obtained with respect to the Gol’dman and Krivchenkov eigenfunctions for the singular potential Bx2+A/x2, B>0, A⩾0. The formulas obtained are generalizations of those found earlier by use of the odd solutions of the Schrödinger equation with the harmonic oscillator potential [Aguilera-Navarro et al., J. Math. Phys. 31, 99 (1990)].
Lie group classification of second-order ordinary difference equations
Authors: Dorodnitsyn Vladimir , Kozlov Roman , Winternitz Pavel
Published: July 2002

A group classification of invariant difference models, i.e., difference equations and meshes, is presented. In the continuous limit the results go over into Lie’s classification of second-order ordinary differential equations. The discrete model is a three point one and we show that it can be invariant under Lie groups of dimension 0⩽n⩽6.
Mixing characteristics of an inhomogeneous scalar in isotropic and homogeneous sheared turbulence
Authors: Nomura K. K. , Elghobashi S. E.
Published: July 2002

Turbulent mixing of an inhomogeneous passive scalar field is studied in the context of a nonpremixed reacting flow. Direct numerical simulations of an initial steplike scalar field subjected to homogeneous sheared turbulence have been performed and the results compared with those of the case of decaying isotropic turbulence. For both flow conditions, the gradient of the conserved scalar tends to align itself with the axis of the most compressive strain rate and orthogonal to the local vorticity. The magnitude of the scalar gradient is directly influenced by the local strain rate while its orientation is controlled by the local vorticity. Because of the directional features of sheared turbulence, the orientation of the scalar gradient is more ordered than in isotropic turbulence. In addition, the magnitude of vorticity indirectly affects that of the scalar gradient through strain-rate amplification by vortex stretching. In both flows, regions of high scalar-gradient magnitude or scalar dissipation (and therefore high reaction rates) tend to exist as sheets in the vicinity of sheetlike vortex structures of moderate to high vorticity. The probability density function (pdf) of the the scalar dissipation rate εF exhibits a nearly lognormal distribution with a slight negative skewness for both isotropic and sheared turbulence.
Linear and nonlinear evolution of double-humped ion distributions in strong unmagnetized shock structures
Authors: Abe Kanji , Sakaguchi Gyo
Published: July 2002

Ion distributions in shock structures are determined from the Fokker–Planck equation. If the shock Mack number is high, and the electron temperature Te in the shock structure is sufficiently higher than the ion temperature T1 far ahead of the shock wave, the ion distribution has a double-humped shape, and is unstable in the sense of a linear Landau analysis. Characteristic times in which the wave–ion interaction, the wave–wave interaction, and the ion trapping modify the ion distribution and/or the Landau-amplified electric field to a certain extent are estimated. If Te/T1 and the shock Mach number are sufficiently high, the wave–ion interaction has a strong influence on the evolution of the ion distribution, and competes with the ion–ion collisions in the shock structure.
Turbulence characteristics in cylindrical liquid jets
Authors: Mansour Adel , Chigier Norman
Published: July 2002

A study has been made of the flow patterns and turbulence characteristics in free liquid jets in order to determine the rate of decay of turbulence properties along the jet. Mean streamwise velocities and streamwise velocities and streamwise and cross-streamwise turbulence intensities were measured using laser Doppler velocimetry. The jet Reynolds number was varied between 1000 and 30 000, with the diameter of the liquid jet D=3.051 mm. Using a power law model for the time decay of turbulence kinetic energy, it was found that turbulence decays, on average with an exponent N=1, independent of the Reynolds number. A constant power for the decay implies Reynolds number similarity throughout this range. Substantial reductions in the degree of anisotropy occur downstream from the injector exit as the jet relaxes from a fully developed turbulent pipe flow profile to a flat profile. For the intermediate range of Reynolds numbers (10 000–20 000), the relaxation distance was 20D, almost independent of the Reynolds number. At high values of Reynolds number (20 000–30 000), the relaxation process was very fast, generally within three diameters from the injector exit.
Formation and temporal evolution of the Lamb-dipole
Authors: Nielsen A. H. , Rasmussen J. Juul
Published: July 2002

The formation and dynamics of dipolar vortex structures in two-dimensional flows are studied. Localized initial structures possessing a finite linear momentum are found to develop into dipoles by direct numerical solutions of the two-dimensional Navier-Stokes equations. The detailed structure of the evolving dipoles depend on the initial condition. However, the gross properties of their evolution are only weakly dependent on the detailed structure and can be well-described by the so-called Lamb-dipole solution. The viscous decay of the Lamb-dipole, leading to an expansion and a decreasing velocity, is well described by an adiabatic theory. During the expansion the dipole is found to trap fluid as it evolves.
Secondary breakup of axisymmetric liquid drops. I. Acceleration by a constant body force
Authors: Han Jaehoon , Tryggvason Grétar
Published: July 2002

The secondary breakup of liquid drops, accelerated by a constant body force, is examined for small density differences between the drops and the surrounding fluid. Two cases are examined in detail: a density ratio close to unity (ρd/ρo=1.15, where the Boussinesq approximation is valid) and a density ratio of ten. A finite difference/front tracking numerical technique is used to solve the unsteady Navier–Stokes equations for both the drops and the surrounding fluid. The breakup is controlled by the Eötvös number (Eo), the Ohnesorge number (Oh), and the viscosity and density ratios. If viscous effects are small (small Oh), the Eötvös number is the main controlling parameter. In the Boussinesq limit, as Eo increases the drops break up in a backward facing bag, transient breakup, and a forward facing bag mode. At a density ratio of ten, similar breakup modes are observed, with the exception that the forward facing bag mode is replaced by a shear breakup mode. Similar breakup modes have been seen experimentally for much larger density ratios. Although a backward facing bag is seen at low Oh, where viscous effects are small, comparisons with simulations of inviscid flows show that the bag breakup is a viscous phenomenon, due to boundary layer separation and the formation of a wake. At higher Oh, where viscous effects modify the evolution, the simulations show that the main effect of increasing Oh is to move the boundary between the different breakup modes to higher Eo. The results are summarized by “breakup maps” where the different breakup modes are shown in the Eo–Oh plane for different values of the viscosity and the density ratios.
On the Bernstein–Landau paradox
Authors: Sukhorukov A. I. , Stubbe P.
Published: July 2002

The essence of the Bernstein–Landau paradox is that in a stable unmagnetized plasma electrostatic waves exhibit collisionless Landau damping, while in a magnetized plasma the Bernstein modes, perpendicular to the magnetic field, are exactly undamped, independent of the strength of the magnetic field. This problem is the subject of the present study. An analytical solution of the initial value problem for perturbations perpendicular to the magnetic field is given, which is a generalization of the well-known Landau work to magnetized plasmas. By introducing, according to Plemelj’s prescription, plus- and minus-functions, having unique analytical properties, the character of the short-term and long-term plasma response is revealed, showing in the small magnetic field limit Landau damping in the first gyroperiod, followed by recurrence, and exhibiting irregular behavior with no damping at large times. The initial damping rate is seen to be close to the commonly used Landau damping rate for unmagnetized plasmas, however with a significant systematic deviation. A corrected expression for the Landau damping rate is found which yields a perfect description of the initial damping of oscillations perpendicular to a weak magnetic field. An alternative approach, expansion over Bernstein modes, is also employed. It is found that a zero-frequency (convective) mode, revealed earlier in particle simulations, is included in the complete linear treatment.
A comparison of three-dimensional multimode hydrodynamic instability growth on various National Ignition Facility capsule designs with HYDRA simulations
Authors: Marinak M. M. , Haan S. W. , Dittrich T. R. , Tipton R. E. , Zimmerman G. B.
Published: July 2002

Three similar cryogenic ignition capsule designs for the National Ignition Facility [J. Lindl, Phys. Plasmas 2, 3933 (1995)] are analyzed to determine surface roughness specifications required to mitigate the growth of hydrodynamic instabilities. These capsule utilize brominated plastic, polyimid and copper-doped beryllium ablator materials respectively. Direct three-dimensional numerical simulations with the HYDRA radiation hydrodynamic code [M. M. Marinak et al., Phys. Plasmas 3, 2070 (1996)] examine the growth of multimode perturbations seeded by roughness on the outer ablator and inner ice surfaces. The simulations, which showed weakly nonlinear behavior for optimized surfaces, were carried through ignition and burn. A three-dimensional multimode perturbation achieves somewhat larger amplitudes in the nonlinear regime than a corresponding two-dimensional simulation of the same rms amplitude. The beryllium and polyimid capsules exhibit enhanced tolerance of roughness on both the ice and ablator surfaces.
Polygon structure of plasma crystals
Authors: Ishihara Osamu
Published: July 2002

Stability and lattice oscillations are studied for polygon structures of plasma crystals under the forces of ion drags, gravitational fields, and sheath electric fields. Circular lattices of dust grains, trapped in the potential minimum of a wake potential produced in the presence of ion flow, are levitated horizontally under the balance of forces. Positive ions transfer momentum to a negatively charged dust particulate either by scattering due to Coulomb force or by direct capturing due to the finite size of the dust. Resulting drag force on the dust particulates makes a plasma an effective viscous medium and is found to be responsible for the stability condition of the structure. It is shown that the polygon structures of triangle, square, pentagon, or hexagon are stable against spatial perturbations and are accompanied by the oscillations with characteristic low frequency inversely proportional to the effective viscosity.
Reactions of thin-film titanium on silicon studied by Raman spectroscopy
Authors: Nemanich R. J. , Fulks R. T. , Stafford B. L. , Vander Plas H. A.
Published: July 2002

Thin Ti films have been deposited on Si 〈100〉 substrates and annealed to form silicide compounds. The annealings were performed in a vacuum rapid isothermal annealing system or in an UHV chamber. Raman spectra were obtained after various processing stages or in situ in the UHV system. The results indicate the simultaneous formation of crystalline Ti2O3 and a Ti silicide tentatively identified as TiSi. Higher temperature annealing to greater than 750 °C leads to the formation of TiSi2 and the disappearance of the Ti2O3 signal.
Capture and emission kinetics of individual Si:SiO2 interface states
Authors: Kirton M. J. , Uren M. J.
Published: July 2002

By studying the random telegraph signals in the drain current of small area metal-oxide-semiconductor field-effect transistors as a function of temperature, we show that carrier capture into individual interface states takes place via a multiphonon process. We demonstrate that the interface trap energy levels are temperature dependent as a result of entropy changes on trap ionization.
Point source terahertz optics
Authors: Fattinger Ch. , Grischkowsky D.
Published: July 2002

We demonstrate an ultrafast 10 μm sized, electric dipole source of terahertz radiation closely coupled to a 1 cm spherical mirror. This optical approach has the advantages of subpicosecond response times with essentially complete collection efficiency. Using this technique, we have generated and detected subpicosecond freely propagating electrical pulses.
Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR
Authors: Zheng Xiaofeng , Bevilacqua Philip C.
Published: July 2002

The human interferon-induced protein kinase, PKR, is an antiviral
agent that is activated by long stretches of double-stranded (ds)RNA.
PKR has an N-terminal dsRNA-binding domain that contains two tandem
copies of the dsRNA-binding motif and interacts with dsRNA in a
nonsequence-specific fashion. Surprisingly, PKR can be regulated by
certain viral and cellular RNAs containing non-Watson–Crick features.
We found that RNAs containing bulges in the middle of a helix can bind
to p20, a C-terminal truncated PKR containing the dsRNA-binding domain.
Bulges are known to change the global geometry of RNA by bending the
helical axis; therefore, we investigated the conformational changes of
bulged RNA caused by PKR binding. A 66-mer DNA-RNA(+/−
A
3
bulge)-DNA chimera was constructed and annealed to a
complementary RNA strand. This duplex forces the protein to bind in the
middle. A 66-mer duplex with a top strand composed of
DNA-DNA(+/−A
3
bulge)-RNA was used as a control. Gel
mobility-shift changes among the RNA-protein complexes are consistent
with straightening of bulged RNA on protein binding. In addition, a
van't Hoff analysis of p20 binding to bulged RNA reveals a favorable
ΔΔH° and an unfavorable ΔΔS° relative to binding to
straight dsRNA. These thermodynamic parameters are in good agreement
with predictions from a nearest-neighbor analysis for RNA straightening
and support a model in which the helical junction flanking the bulge
stacks on protein binding. The ability of dsRNA-binding motif proteins
to recognize and straighten bent RNA has implications for modulating
the topology of RNAs
in vivo
.
A human aminoacyl-tRNA synthetase as a regulator of angiogenesis
Authors: Wakasugi Keisuke , Slike Bonnie M. , Hood John , Otani Atsushi , Ewalt Karla L. , Friedlander Martin , Cheresh David A. , Schimmel Paul
Published: July 2002

Aminoacyl-tRNA synthetases catalyze the first step of protein synthesis. It was shown recently that human tyrosyl-tRNA synthetase (TyrRS) can be split into two fragments having distinct cytokine activities, thereby linking protein synthesis to cytokine signaling pathways. Tryptophanyl-tRNA synthetase (TrpRS) is a close homologue of TyrRS. A natural fragment, herein designated as mini TrpRS, was shown by others to be produced by alternative splicing. Production of this fragment is reported to be stimulated by IFN-γ, a cytokine that also stimulates production of angiostatic factors. Mini TrpRS is shown here to be angiostatic in a mammalian cell culture system, the chicken embryo, and two independent angiogenesis assays in the mouse. The full-length enzyme is inactive in the same assays. Thus, protein synthesis may be linked to the regulation of angiogenesis by a natural fragment of TrpRS.
Specificity and robustness in transcription control networks
Authors: Sengupta Anirvan M. , Djordjevic Marko , Shraiman Boris I.
Published: July 2002

Recognition by transcription factors of the regulatory DNA elements upstream of genes is the fundamental step in controlling gene expression. How does the necessity to provide stability with respect to mutation constrain the organization of transcription control networks? We examine the mutation load of a transcription factor interacting with a set of
n
regulatory response elements as a function of the factor/DNA binding specificity and conclude on theoretical grounds that the optimal specificity decreases with
n
. The predicted correlation between variability of binding sites (for a given transcription factor) and their number is supported by the genomic data for
Escherichia coli
. The analysis of
E. coli
genomic data was carried out using an algorithm suggested by the biophysical model of transcription factor/DNA binding. Complete results of the search for candidate transcription factor binding sites are available at
http://www.physics.rockefeller.edu/∼boris/public/search_ecoli
.
Cho, a second endonuclease involved in
Escherichia coli
nucleotide excision repair
Authors: Moolenaar Geri F. , van Rossum-Fikkert Sari , van Kesteren Marian , Goosen Nora
Published: July 2002

Nucleotide excision repair removes damages from the DNA by incising the damaged strand on the 3′ and 5′ sides of the lesion. In
Escherichia coli
, the two incisions are made by the UvrC protein, which consists of two functional halves. The N-terminal half contains the catalytic site for 3′ incision and the C-terminal half contains the residues involved in 5′ incision. The genome of
E. coli
contains an SOS-inducible gene (
ydjQ
) encoding a protein that is homologous to the N-terminal half of UvrC. In this paper we show that this protein, which we refer to as Cho (UvrC homologue), can incise the DNA at the 3′ side of a lesion during nucleotide excision repair. The incision site of Cho is located 4 nt further away from the damage compared with the 3′ incision site of UvrC. Cho and UvrC bind to different domains of UvrB, which is probably the reason of the shift in incision position. Some damaged substrates that are poorly incised by UvrC are very efficiently incised by Cho. We propose that
E. coli
uses Cho for repair of such damages
in vivo
. Initially, most of the lesions in the cell will be repaired by the action of UvrC alone. Remaining damages, that for structural reasons obstruct the 3′ incision by UvrC, will be repaired by the combined action of Cho (for 3′ incision) and UvrC (for 5′ incision).
Recurrent evolution of DNA-binding motifs in the
Drosophila
centromeric histone
Authors: Malik Harmit S. , Vermaak Danielle , Henikoff Steven
Published: July 2002

All eukaryotes contain centromere-specific histone H3 variants (CenH3s), which replace H3 in centromeric chromatin. We have previously documented the adaptive evolution of the
Drosophila
CenH3 (Cid) in comparisons of
Drosophila melanogaster
and
Drosophila simulans
, a divergence of ≈2.5 million years. We have proposed that rapidly changing centromeric DNA may be driving CenH3's altered DNA-binding specificity. Here, we compare Cid sequences from a phylogenetically broader group of
Drosophila
species to suggest that Cid has been evolving adaptively for at least 25 million years. Our analysis also reveals conserved blocks not only in the histone-fold domain but also in the N-terminal tail. In several lineages, the N-terminal tail of Cid is characterized by subgroup-specific oligopeptide expansions. These expansions resemble minor groove DNA binding motifs found in various histone tails. Remarkably, similar oligopeptides are also found in N-terminal tails of human and mouse CenH3 (Cenp-A). The recurrent evolution of these motifs in CenH3 suggests a packaging function for the N-terminal tail, which results in a unique chromatin organization at the primary constriction, the cytological marker of centromeres.
An artificial transcriptional activating region with unusual properties
Authors: Lu Xiangyang , Ansari Aseem Z. , Ptashne Mark
Published: July 2002

We describe a series of transcriptional activators generated by adding amino acids (eight in one case, six in another) to fragments of the yeast
Saccharomyces cerevisiae
activator Gal4 that dimerize and bind DNA. One of the novel activating regions identified by this procedure is unusual, compared with previously characterized yeast activating regions, in the following ways: it works more strongly than does Gal4's natural activating region as assayed in yeast; it is devoid of acidic residues; and several lines of evidence suggest that it sees targets in the yeast transcriptional machinery at least partially distinct from those seen by Gal4's activating region.
Delineating developmental and metabolic pathwaysin vivoby expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays
Authors: Miki Rika , Kadota Koji , Bono Hidemasa , Mizuno Yosuke , Tomaru Yasuhiro , Carninci Piero , Itoh Masayoshi , Shibata Kazuhiro , Kawai Jun , Konno Hideaki , Watanabe Sachihiko , Sato Kenjiro , Tokusumi Yumiko , Kikuchi Noriko , Ishii Yoshiyuki , Hamaguchi Yohei , Nishizuka Itaru , Goto Hitoshi , Nitanda Hiroyuki , Satomi Susumu , Yoshiki Atsushi , Kusakabe Moriaki , DeRisi Joseph L. , Eisen Michael B. , Iyer Vishwnath R. , Brown Patrick O. , Muramatsu Masami , Shimada Hiroshi , Okazaki Yasushi , Hayashizaki Yoshihide
Published: July 2002

We have systematically characterized gene expression patterns in 49 adult and embryonic mouse tissues by using cDNA microarrays with 18,816 mouse cDNAs. Cluster analysis defined sets of genes that were expressed ubiquitously or in similar groups of tissues such as digestive organs and muscle. Clustering of expression profiles was observed in embryonic brain, postnatal cerebellum, and adult olfactory bulb, reflecting similarities in neurogenesis and remodeling. Finally, clustering genes coding for known enzymes into 78 metabolic pathways revealed a surprising coordination of expression within each pathway among different tissues. On the other hand, a more detailed examination of glycolysis revealed tissue-specific differences in profiles of key regulatory enzymes. Thus, by surveying global gene expression by using microarrays with a large number of elements, we provide insights into the commonality and diversity of pathways responsible for the development and maintenance of the mammalian body plan.
Incision of DNA–protein crosslinks by UvrABC nuclease suggests a potential repair pathway involving nucleotide excision repair
Authors: Minko Irina G. , Zou Yue , Lloyd R. Stephen
Published: July 2002

DNA–protein crosslinks (DPCs) arise in biological systems as a result of exposure to a variety of chemical and physical agents, many of which are known or suspected carcinogens. The biochemical pathways for the recognition and repair of these lesions are not well understood in part because of methodological difficulties in creating site-specific DPCs. Here, a strategy for obtaining site-specific DPCs is presented, and
in vitro
interactions of the
Escherichia coli
nucleotide excision repair (NER) UvrABC nuclease at sites of DPCs are investigated. To create site-specific DPCs, the catalytic chemistry of the T4 pyrimidine dimer glycosylase/apurinic/apyrimidinic site lyase (T4-pdg) has been exploited, namely, its ability to be covalently trapped to apurinic/apyrimidinic sites within duplex DNA under reducing conditions. Incubation of the DPCs with UvrABC proteins resulted in DNA incision at the 8th phosphate 5′ and the 5th and 6th phosphates 3′ to the protein-adducted site, generating as a major product of the reaction a 12-mer DNA fragment crosslinked with the protein. The incision occurred only in the presence of all three protein subunits, and no incisions were observed in the nondamaged complementary strand. The UvrABC nuclease incises DPCs with a moderate efficiency. The proper assembly and catalytic function of the NER complex on DNA containing a covalently attached 16-kDa protein suggest that the NER pathway may be involved in DPC repair and that at least some subset of DPCs can be removed by this mechanism without prior proteolytic degradation.