bluuebunny/crossref_metadata_2025 huggingface dataset:
Domain catalyzed chemical reactions: A molecular dynamics simulation of isomerization kinetics
Authors: Toxvaerd S.
Published: March 2004

The model for domain catalyzed isomerization kinetics in condensed fluids [S. Toxvaerd, Phys. Rev. Lett. 85, 4747 (2000)] is applied for a diluted mixture of a chiral solute with a consolute temperature. The solution is quench to phase separation at temperatures below the consolute temperature. The droplet coalescence enhances the isomerization kinetics due to the substantial excess pressure inside the small droplets given by the Laplace equation. The domain catalyzed isomerization kinetics breaks the symmetry, and the droplets end with only one dominating species. We argue that D-Glyceraldehyde which is only moderately solvable in water and which has played a crucial role in the evolution is a candidate for the stereo specific ordering in bio-organic matter.
Theoretical studies on dynamics and thermochemistry of the reactions CF3CHCl2+Cl→CF3CCl2+HCl and CF3CHFCl+Cl→CF3CFCl+HCl
Authors: Li Bo , Liu Jing-yao , Li Ze-sheng , Wu Jia-yan , Sun Chia-chung
Published: March 2004

A dual-level direct dynamics study has been carried out for the two hydrogen abstraction reactions CF3CHCl2+Cl and CF3CHFCl+Cl. The geometries and frequencies of the stationary points are optimized at the BHLYP/6-311G(d,p), B3LYP/6-311G(d,p), and MP2/6-31G(d) levels, respectively, with single-point calculations for energy at the BHLYP/6-311++G(3df,2p), G3(MP2), and QCISD(T)/6-311G(d,p) levels. The enthalpies of formation for the species CF3CHCl2, CF3CHFCl, CF3CCl2, and CF3CFCl are evaluated at higher levels. With the information of the potential energy surface at BHLYP/6-311++G(3df,2p)//6-311G(d,p) level, we employ canonical variational transition-state theory with small-curvature tunneling correction to calculate the rate constants. The agreement between theoretical and experimental rate constants is good in the measured temperature range 276–382 K. The effect of fluorine substitution on reactivity of the C–H bond is discussed.
Ultraviolet spectroscopy of pyrene in a supersonic jet and in liquid helium droplets
Authors: Rouillé Gaël , Krasnokutski Serge , Huisken Friedrich , Henning Thomas , Sukhorukov Oleksandr , Staicu Angela
Published: March 2004

In a series of experiments devoted to the study of polycyclic aromatic hydrocarbons for astrophysical applications, the S2←S0 transition of jet-cooled pyrene (C16H10) at 321 nm has been studied by an absorption technique for the first time. The spectra observed by cavity ring-down spectroscopy closely resemble the excitation spectra obtained earlier by laser-induced fluorescence (LIF) and show the same band clusters arising from the vibronic interaction of S2 with S1. We have also investigated pyrene when it was incorporated into 380 mK cold helium droplets. These spectra which were recorded employing LIF and molecular beam depletion spectroscopy are broadened and redshifted by 0.94 nm but retain the essential features of the gas phase spectra.
Near threshold photoionization of the ground and first excited states of C2
Authors: Toffoli Daniele , Lucchese Robert R.
Published: March 2004

Calculations using the multichannel Schwinger configuration-interaction method are presented for the photoionization from the ground and the first excited states of the C2 molecule. Both single channel and multichannel calculations are presented in a photon energy range from the threshold to about 50 eV of photon energy. For the ground state, inclusion of both intrinsic and dynamical correlation effects is seen to strongly alter the picture of the photoionization process inferred from single-channel frozen-core Hartree–Fock calculations [N. T. Padial et al., Astrophys. J. 298, 369 (1985)]. Furthermore, the photoionization study of the first excited state of molecular carbon has revealed the presence of strong interchannel coupling between the 3σg→kσu channel and the photoionization channels leading to the A 4Πg and f 2Πg ionic states in the near threshold region.
Double photoionization of C60 and C70 in the valence region
Authors: Kou J. , Mori T. , Kumar S. V. K. , Haruyama Y. , Kubozono Y. , Mitsuke K.
Published: March 2004

Photoion yields from gaseous fullerenes, C60 and C70, for production of singly and doubly charged ions are measured by mass spectrometry combined with tunable synchrotron radiation at hν=25–150 eV. Since the signal of triply or highly charged ions is very weak, the total photoionization yield curve can be estimated from the sum of the yields of the singly and doubly charged ions. A distinct feature appears in the resultant curve of C60 which is absent in the calculated total photoabsorption cross section previously reported. This difference is attributed to C602+ ions chiefly produced by spectator Auger ionization of the shape resonance states followed by tunneling of the trapped electron or by cascade Auger ionization. Ratios between the yields of doubly and singly charged ions for C60 and C70 are larger than unity at hν>50 eV. These ratios are quite different from those reported in the experiments using electron impact ionization.
Novel torsion balance based on a spherical superconducting suspension
Authors: Hammond Giles D. , Pulido-Paton Antonio , Speake Clive C. , Trenkel Christian
Published: March 2004

We report on the progress that has been made on the development of a spherical superconducting torsion balance in which the traditional fiber is replaced with a Meissner effect suspension operating at 4.2 K. The instrument can levitate a mass of 18 g in persistent mode and currently operates in a helium exchange gas pressure of a few mTorr. A superconducting rotation detector incorporating a superconducting quantum interference device magnetometer has been developed to interrogate the angular position of the torsion balance and provide its natural period. The natural period can be programmed from 25 s to 150 s by varying the current stored in the detector. The detector also offers the possibility of applying external torques onto the torsion balance for the purpose of servocontrol, and a simple derivative control has been developed. The properties of the rotation detector can be predicted from measurements of the inductances of the circuit components. The total measured torque noise is 2×10−13 Nm/√Hz at around 0.02 Hz. This is two orders of magnitude higher than the intrinsic thermal noise and we are currently investigating possible sources of this excess noise. The highest quality factor that has been observed is 4×104 at a period of 40 s, and this corresponds to an ultimate sensitivity of 2×10−16 Nm/√Hz.
Highly stable atom-tracking scanning tunneling microscopy
Authors: Rerkkumsup Pongpun , Aketagawa Masato , Takada Koji , Togawa Yoichi , Thinh Nguyen Tien , Kozuma Yosuke
Published: March 2004

In this article, we propose a technique for highly stabilized atom-tracking control of a scanning tunneling microscope (STM) tip by referring to an atomic point on a regular crystalline surface. Our aim is to prevent jumping of the STM tip to neighboring atoms and to use it even in a noisy environment. Graphite crystal, whose lattice spacing is approximately 0.25 nm, was utilized as the reference. To improve the performance of the tracking controller against external disturbances, the influence of a disturbance on the STM under various environmental conditions was compared experimentally with the frequency response of the open-loop tracking system. The atom-tracking conditions required to avoid jumping of the STM tip are proposed and applied to the design of the tracking controller by referring to the results of the comparison. The new tracking controller consists of integrator, tracer, and limiter units. The integrator unit is designed to eliminate the steady-state error due to thermal drift. A phase-lag low-pass filter is utilized as the tracer unit to compensate for the dominant disturbance due to vibration/acoustic noise with a frequency lower than the cutoff frequency, fco, of the open-loop tracking system. To improve the phase margin condition of the controller at fco and to suppress the disturbance with a frequency higher than fco, the limiter is designed to include a phase-lead high-pass filter and a saturator whose output is less than one-half of the lattice spacing. The performance of the stabilizing technique, which is to combine the new tracking controller with enhanced STM stiffness, was evaluated using internal/external artificial disturbance generators. The experimental results show that the proposed method has a high capability for maintaining atom-tracking control without any jumping of the STM tip, even in a noisy environment.
Non-Newtonian behavior in simple fluids
Authors: Delhommelle Jerome , Petravic J. , Evans Denis J.
Published: March 2004

Using nonequilibrium molecular dynamics simulations, we study the non-Newtonian rheology of a microscopic sample of simple fluid. The calculations were performed using a configurational thermostat which unlike previous nonequilibrium molecular dynamics or nonequilibrium Brownian dynamics methods does not exert any additional constraint on the flow profile. Our findings are in agreement with experimental results on concentrated “hard sphere”-like colloidal suspensions. We observe: (i) a shear thickening regime under steady shear; (ii) a strain thickening regime under oscillatory shear at low frequencies; and (iii) shear-induced ordering under oscillatory shear at higher frequencies. These results significantly differ from previous simulation results which showed systematically a strong ordering for all frequencies. They also indicate that shear thickening can occur even in the absence of a solvent.
Dopant distribution in a Tm3+–Yb3+ codoped silica based glass ceramic: An infrared-laser induced upconversion study
Authors: Lahoz F. , Martı́n I. R. , Méndez-Ramos J. , Núñez P.
Published: March 2004

The optically active dopant distribution in a Tm3+–Yb3+ doped silica based glass ceramic sample has been investigated. A systematic analysis of the upconversion fluorescence of the Tm3+–Yb3+ codoped glass and glass ceramic has been performed at room temperature. Tm3+ and Yb3+ single doped glass and glass ceramics have also been included in the study. Upon infrared excitation at 790 nm into the H43 level of the Tm3+ ions a blue upconversion emission is observed, which is drastically increased in the Yb3+ codoped samples. A rate equation model confirmed the energy transfer upconversion mechanism. Based on these results, the temporal dynamic curves of the levels involved in the upconversion process, H43, F5/22, and G41 were interpreted in the glass ceramic samples. The contribution of the optically active Tm3+ and Yb3+ ions in the crystalline and in the vitreous phase of the glass ceramic was distinguished and the ratio of Tm3+ ions in the crystalline phase could be quantified for the 1 mol % Tm3+–2.5 mol % Yb3+ glass ceramic. A surprising result was obtained for that concentration: the main contribution to the upconversion emission of the glass ceramic is due to Tm3+–Yb3+ ions in the vitreous phase.
First-principle molecular dynamics with ultrasoft pseudopotentials: Parallel implementation and application to extended bioinorganic systems
Authors: Giannozzi P. , De Angelis F. , Car R.
Published: March 2004

We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for parallelization that includes special features to deal with the augmented charge in the contest of Vanderbilt’s ultrasoft pseudopotentials. We also discuss a simple approach to model molecular systems with a net charge and/or large dipole/quadrupole moments. We present test applications to manganese and iron porphyrins representative of a large class of biologically relevant metalorganic systems. Our results show that accurate density-functional theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.
Transport coefficients of aqueous dodecyltrimethylammonium bromide solutions: Comparison between experiments, analytical calculations and numerical simulations
Authors: Jardat M. , Durand-Vidal S. , Da Mota N. , Turq P.
Published: March 2004

We study dynamical properties of ionic species in aqueous solutions of dodecyltrimethylammonium bromide, for several concentrations below and above the critical micellar concentration (cmc). New experimental determinations of the electrical conductivity are given which are compared to results obtained from an analytical transport theory; transport coefficients of ions in these solutions above the cmc are also computed from Brownian dynamics simulations. Analytical calculations as well as the simulation treat the solution within the framework of the continuous solvent model. Above the cmc, three ionic species are considered: the monomer surfactant, the micelle and the counterion. The analytical transport theory describes the structural properties of the electrolyte solution within the mean spherical approximation and assumes that the dominant forces which determine the deviations of transport processes from the ideal behavior (i.e., without any interactions between ions) are hydrodynamic interactions and electrostatic relaxation forces. In the simulations, both direct interactions and hydrodynamic interactions between solutes are taken into account. The interaction potential is modeled by pairwise repulsive 1/r12 interactions and Coulomb interactions. The input parameters of the simulation (radii and self-diffusion coefficients of ions at infinite dilution) are partially obtained from the analytical transport theory which fits the experimental determinations of the electrical conductivity. Both the electrical conductivity of the solution and the self-diffusion coefficients of each species computed from Brownian dynamics are compared to available experimental data. In every case, the influence of hydrodynamic interactions (HIs) on the transport coefficients is investigated. It is shown that HIs are crucial to obtain agreement with experiments. In particular, the self-diffusion coefficient of the micelle, which is the largest and most charged species in the present system, is enhanced when HIs are included whereas the diffusion coefficients of the monomer and the counterion are roughly not influenced by HIs.
Acetone hydration in supercritical water: C-NMR13 spectroscopy and Monte Carlo simulation
Authors: Takebayashi Yoshihiro , Yoda Satoshi , Sugeta Tsutomu , Otake Katsuto , Sako Takeshi , Nakahara Masaru
Published: March 2004

The C-NMR13 chemical shift of acetone δ(13C=O) was measured in aqueous solution at high temperatures up to 400 °C and water densities of 0.10–0.60 g/cm3 for the study of hydration structure in the supercritical conditions. The average number NHB of hydrogen bonds (HBs) between an acetone and solvent waters and the energy change ΔE upon the HB formation were evaluated from the δ and its temperature dependence, respectively. At 400 °C, NHB is an increasing function of the water density, the increase being slower at higher water densities. The acetone–water HB formation is exothermic in supercritical water with larger negative ΔE at lower water densities (−3.3 kcal/mol at 0.10 g/cm3 and −0.3 kcal/mol at 0.60 g/cm3), in contrast to the positive ΔE in ambient water (+0.078 kcal/mol at 4 °C). The corresponding Monte Carlo simulations were performed to calculate the radial and orientational distribution functions of waters around the acetone molecule. The density dependence of NHB calculated at 400 °C is in a qualitative agreement with the experimental results. In the supercritical conditions, the HB angle in a neighboring acetone–water pair is weakly influenced by the water density, because of the absence of collective HB structure. This is in sharp contrast to the hydration structure in ambient water, where the acetone–water HB formation is orientationally disturbed by the tetrahedral HB network formation among the surrounding waters.
Triple point of Lennard-Jones fluid in slit nanopore: Solidification of critical condensate
Authors: Kanda Hideki , Miyahara Minoru , Higashitani Ko
Published: March 2004

We report the results of a molecular dynamics simulation that looked for the triple point of Lennard-Jones fluid in slit-shaped nanopores. The simulation method employed for this purpose is able to maintain vapor–liquid coexistence in a nanopore at a specific equilibrium bulk-phase pressure. The triple point is the freezing point of the critical condensate. The triple-point temperature could be higher or lower than the bulk triple point, depending on the pore size. This is thought to be due to two opposing factors: the elevating effect of the pore-wall potential energy, and the depressing effect of the capillary condensate’s tensile condition. Because of the cancellation, the deviation of the triple-point temperature from the bulk triple-point temperature was not considered significant. The pressure of the triple point, however, was significantly different from that of the bulk triple point. A simple model to describe the triple point is developed and shown to agree well with the results of the simulation. The importance of the two factors in nanoscale pores, which cannot be described by the classic Gibbs–Thomson equation, is emphasized.
Small-angle neutron scattering study of structural changes in temperature sensitive microgel colloids
Authors: Stieger Markus , Richtering Walter , Pedersen Jan Skov , Lindner Peter
Published: March 2004

The structure of temperature-sensitive poly(N-isopropylacrylamide) microgels in dilute suspension was investigated by means of small-angle neutron scattering. A direct modeling expression for the scattering intensity distribution was derived which describes very well the experimental data at all temperatures over an extensive q range. The overall particle form as well as the internal structure of the microgel network is described by the model. The influence of temperature, cross-linking density, and particle size on the structure was revealed by radial density profiles and clearly showed that the segment density in the swollen state is not homogeneous, but gradually decays at the surface. The density profile reveals a box profile only when the particles are collapsed at elevated temperatures. An increase of the cross-linking density resulted in both an increase of the polymer volume fraction in the inner region of the particle and a reduction of the smearing of the surface. The polymer volume fraction inside the colloid decreased with increasing particle size. The structural changes are in good agreement with the kinetics of the emulsion copolymerization used to prepare the microgel colloids.
Electron attachment to C2Cl4 and Trojan horse ionization
Authors: Chen Edward C. M. , Chen Edward S.
Published: March 2004

In a recent study of tetrachloroethylene, the anion yield curves were analyzed using three published negative-ion Morse potentials. Unexpected ions at zero electron energy were explained by the “Trojan horse” mechanism. This communication also attributes formation of Cl2(−) at higher energies to a Trojan horse mechanism. Six new Morse potentials are calculated to account for the observed anion states. These combine all extant electron impact and attachment data. The electron affinity of the C2Cl3 radical, 3.1(1) eV, and the C–Cl bond dissociation energy 4.0(1) eV are reported.
Spectral difference Lanczos method for efficient time propagation in quantum control theory
Authors: Farnum John D. , Mazziotti David A.
Published: March 2004

Spectral difference methods represent the real-space Hamiltonian of a quantum system as a banded matrix which possesses the accuracy of the discrete variable representation (DVR) and the efficiency of finite differences. When applied to time-dependent quantum mechanics, spectral differences enhance the efficiency of propagation methods for evolving the Schrödinger equation. We develop a spectral difference Lanczos method which is computationally more economical than the sinc-DVR Lanczos method, the split-operator technique, and even the fast-Fourier-Transform Lanczos method. Application of fast propagation is made to quantum control theory where chirped laser pulses are designed to dissociate both diatomic and polyatomic molecules. The specificity of the chirped laser fields is also tested as a possible method for molecular identification and discrimination.
Barrier-free intermolecular proton transfer induced by excess electron attachment to the complex of alanine with uracil
Authors: Dąbkowska Iwona , Rak Janusz , Gutowski Maciej , Nilles J. Michael , Stokes Sarah T. , Bowen Kit H.
Published: March 2004

The photoelectron spectrum of the uracil–alanine anionic complex (UA)− has been recorded with 2.540 eV photons. This spectrum reveals a broad feature with a maximum between 1.6 and 2.1 eV. The vertical electron detachment energy is too large to be attributed to an (UA)− anionic complex in which an intact uracil anion is solvated by alanine, or vice versa. The neutral and anionic complexes of uracil and alanine were studied at the B3LYP and second-order Møller–Plesset level of theory with 6-31++G** basis sets. The neutral complexes form cyclic hydrogen bonds and the three most stable neutral complexes are bound by 0.72, 0.61, and 0.57 eV. The electron hole in complexes of uracil with alanine is localized on uracil, but the formation of a complex with alanine strongly modulates the vertical ionization energy of uracil. The theoretical results indicate that the excess electron in (UA)− occupies a π* orbital localized on uracil. The excess electron attachment to the complex can induce a barrier-free proton transfer (BFPT) from the carboxylic group of alanine to the O8 atom of uracil. As a result, the four most stable structures of the uracil–alanine anionic complex can be characterized as a neutral radical of hydrogenated uracil solvated by a deprotonated alanine. Our current results for the anionic complex of uracil with alanine are similar to our previous results for the anion of uracil with glycine [Eur. Phys. J. D 20, 431 (2002)], and together they indicate that the BFPT process is not very sensitive to the nature of the amino acid’s hydrophobic residual group. The BFPT to the O8 atom of uracil may be relevant to the damage suffered by nucleic acid bases due to exposure to low energy electrons.
Thermal dependence of electrical characteristics of micromachined silica microchannel plates
Authors: Tremsin Anton S. , Vallerga John V. , Siegmund Oswald H. W. , Beetz Charles P. , Boerstler Robert W.
Published: March 2004

Micromachined silica microchannel plates (MCPs) under development have a number of advantages over standard glass MCPs and open completely new possibilities in detector technologies. In this article we present the results of our studies on the thermal properties of silica microchannel plates (sMCPs). Similar to standard glass microchanel plates the resistance of silica MCPs was measured to change exponentially with temperature with a negative thermal coefficient of −0.036 per °C, somewhat larger than that of standard glass MCPs. The resistance also decreases linearly with the applied voltage, with the voltage coefficient of −3.1×10−4 V−1. With the knowledge of these two coefficients, our thermal model allows the calculation of the maximum voltage, which can be applied to a given MCP without inducing a thermal runaway. A typical 25 mm diam, 240 μm thick sMCP with 6 μm pores has to have the resistance larger than ∼30 MΩ to operate safely at voltages up to 800 V. With this model we can also calculate the time required for a given silica MCP to reach the point of thermal equilibrium after a voltage increase. We hope that the ongoing efforts on a proper modification of the sMCP semiconducting layer will lead to the production of new MCPs with a small negative or even a positive thermal coefficient, reducing the possibility of thermal runaways of low-resistance MCPs required for high count rate applications.
Performance comparison and modeling of PZN, PMN, and PZT stacked actuators in a levered flexure mechanism
Authors: Woody Shane C. , Smith Stuart T.
Published: March 2004

This article presents a theoretical and experimental assessment of a translation stage design based on a piezoelectric actuator and levering mechanism. This mechanism incorporates stacked piezoelectric actuators of dimensions 5×5×5 mm3 with each stack made from ten plates of 0.5 mm thickness pushing against a symmetric lever design with an ideal amplification of 6.05:1. Three different stacks made from PZN, PMN, and PZT were tested in a nominally similar mechanism to produce displacements of 101, 104, and 33 μm, respectively. Because of their different elastic moduli, the fundamental resonances with each respective device were 670, 729, and 759 Hz. Lagrange analysis of a lumped model of the mechanism is used to estimate the fundamental mode natural frequency of the system while a model for “lost motion” is also presented. This system has been assembled and evaluated experimentally to assess the validity of the models. In general, these models are shown to provide a reasonable estimate of the mechanism performance in terms of lost motion while predicting higher values for the fundamental frequency. The deviations from the model are consistent with the uncertainties associated with rigid body assumptions and the unknown compliances of assembly interfaces and suggest directions for future research in the modeling of such systems.
In-plane deformation of cantilever plates with applications to lateral force microscopy
Authors: Sader John E. , Green Christopher P.
Published: March 2004

The in-plane deformation of atomic force microscope (AFM) cantilevers under lateral loading is commonly assumed to have negligible effect in comparison to other deformation modes and ignored. In this article, we present a theoretical study of the behavior of cantilevers under lateral loading, and in so doing establish that in-plane deformation can strongly contribute to the total deformation, particularly for rectangular cantilevers of high aspect ratio (length/width). This has direct implications to lateral force microscopy, where the neglect of in-plane deformation can contribute to significant quantitative errors in force measurements and affect the interpretation of measurements. Consequently, criteria and approaches for minimizing the effects of in-plane deformation are presented, which will be of value to users and designers of AFM cantilevers. Accurate analytical formulas for the in-plane spring constants of both rectangular and V-shaped cantilevers are also presented.
Extended shape evolution of low mismatch Si1−xGex alloy islands on Si(100)
Authors: Sutter E. , Sutter P. , Bernard J. E.
Published: March 2004

The sequence of shape transitions in low mismatch, dilute coherent Si1−xGex (x<0.2) alloy islands was documented by scanning tunneling microscopy and cross-sectional transmission electron microscopy. In dilute Si1−xGex islands we observe an extended shape evolution involving a new “barn” shape formed by introduction of steep {111} facets not observed at higher mismatch strain. This extended shape evolution implies a delayed onset of plastic deformation as a result of an altered competition between strain relaxation via coherent islands and the introduction of dislocations in this regime.
An x-ray confinement cell for studies of complex fluids under shear and confinement
Authors: Nieman Brian , Commeinhes Xavier , Babcock Nathan S. , Frola Ivan , Forgett Rick , Idziak Stefan H. J. , Sutton Mark
Published: March 2004

An x-ray confinement cell is described in this article. Advantages over the previous generation x-ray surface forces apparatus include a stiffer shearing mechanism and improved ease of operation. This completely new device has also been optimized for x-ray diffraction studies of shearing complex fluids under confining gaps ranging from several hundred angstroms to millimeters.
Terahertz-induced lensing and its use for the detection of terahertz pulses in a birefringent crystal
Authors: Schneider Arno , Biaggio Ivan , Günter Peter
Published: March 2004

We demonstrate terahertz-induced lensing (TIL), the focusing and defocusing of an ultrashort “probe” laser pulse induced by a collinearly traveling terahertz pulse in an electro-optic crystal. The intensity change on the axis of the probe beam after the crystal is shown to be linear with the terahertz (THz) electric field and can thus be used to measure the THz wave form. We show that the sensitivity of TIL is comparable to conventional electro-optic sampling, with the advantage of being applicable to all classes of electro-optic crystals, including strongly birefringent ones. The better sensitivity of TIL is demonstrated using the highly birefringent organic salt DAST (4-N,N-dimethylamino-4′-N′-methyl stilbazolium tosylate).
Experimental analysis and theoretical model for anomalously high ideality factors in ZnO/diamond p-n junction diode
Authors: Wang Cheng-Xin , Yang Guo-Wei , Liu Hong-Wu , Han Yong-Hao , Luo Ji-Feng , Gao Chun-Xiao , Zou Guang-Tian
Published: March 2004

High-quality heterojunctions between p-type diamond single-crystalline films and highly oriented n-type ZnO films were fabricated by depositing the p-type diamond single-crystal films on the Io-type diamond single crystal using a hot filament chemical vapor deposition, and later growing a highly oriented n-type ZnO film on the p-type diamond single-crystal film by magnetron sputtering. Interestingly, anomalously high ideality factors (n≫2.0) in the prepared ZnO/diamond p–n junction diode in the interim bias voltage range were measured. For this, detailed electronic characterizations of the fabricated p–n junction were conducted, and a theoretical model was proposed to clarify the much higher ideality factors of the special heterojunction diode.
Double-wall carbon nanotube field-effect transistors: Ambipolar transport characteristics
Authors: Shimada Takashi , Sugai Toshiki , Ohno Yutaka , Kishimoto Shigeru , Mizutani Takashi , Yoshida Hiromichi , Okazaki Toshiya , Shinohara Hisanori
Published: March 2004

Double-wall carbon nanotubes (DWNTs) have been used as channels of field-effect transistors (FETs) to obtain information on their transport characteristics. DWNTs-FETs show metallic or semiconducting behavior depending on the tube diameters. All the semiconducting DWNTs have exhibited both p- and n-type characteristics, the so-called ambipolar behavior which is absent in normal SWNTs-FETs. Comparisons between the subthreshold swing (S) factor of DWNTs and that of SWNTs indicate that DWNTs are better FET channels than SWNTs.
Rotationally selected product pair correlation in F+CD4→DF(ν′)+CD3(ν=0,N)
Authors: Zhou Jingang , Shiu Weicheng , Lin Jim J. , Liu Kopin
Published: March 2004

The title reaction was studied in a crossed-beam experiment by imaging of state-selected products. The rotational state selection of the CD3 products was achieved using (2+1) resonance-enhanced multiphoton ionization. The coincident information on the DF coproducts was revealed in a state-resolved manner from time-sliced velocity map images. Significant dependences of both the correlated differential cross sections and the DF vibrational branching ratios on the “tagged” CD3 rotation states were found. The dynamical implications of one of the major findings are discussed.
Changes in the structure of water deduced from the pressure dependence of the Raman OH frequency
Authors: Kawamoto Tatsuhiko , Ochiai Shukichi , Kagi Hiroyuki
Published: March 2004

We report on the Raman spectra of water under high temperature and pressure conditions and show a discontinuity in the pressure dependence of the OH stretching frequency. As pressure increases, the strength of hydrogen bonding increases rapidly in the pressure ranges up to 0.4±0.1 GPa at 25 °C, 1.0±0.1 GPa at 100 °C, and 1.3±0.1 GPa at 300 °C and slowly above these pressures. This finding clearly demonstrates the existence of discontinuities in the pressure response of the hydrogen bonds of water, which suggests a possible structural change under these conditions.
Structural, magnetic, and transport properties of thin films of the Heusler alloy Co2MnSi
Authors: Singh L. J. , Barber Z. H. , Miyoshi Y. , Bugoslavsky Y. , Branford W. R. , Cohen L. F.
Published: March 2004

Thin films of Co2MnSi have been grown on a-plane sapphire substrates from three elemental targets by dc magnetron cosputtering. These films are single phase, have a strong (110) texture, and a saturation magnetization of 4.95μB/formula unit at 10 K. Films grown at the highest substrate temperature of 715 K showed the lowest resistivity (47 μΩ cm at 4.2 K) and the lowest coercivity (18 Oe). The spin polarization of the transport current was found to be of the order of 54% as determined by point contact Andreev reflection spectroscopy. A decrease in saturation magnetization with a decrease in film thickness and different transport behavior in thinner films indicate graded disorder in these films grown on nonlattice matched substrates.
Direct evidence of ferroelastic participation in 180° polarization switching and fatigue for 111 oriented rhombohedral ferroelectric 0.955 Pb(Zn1/3Nb2/3)O3:0.045 PbTiO3 single crystals
Authors: Zhu Wenyi , Cross L. Eric
Published: March 2004

Direct elastic deformation measurements taken during polarization reversal in 111 oriented 0.955 Pb(Zn1/3Nb2/3)O3–0.045 PbTiO3 single crystals confirm the observation by W. Cao [Ferroelectrics 290, 107 (2003)] that a ferroelastic reorientation of the domain polarization vectors is involved, and the observed strain changes are consistent with the model he proposed. First cycle nonrecoverable fatigue occurring in our crystals and the associated changes of shape in polarization and strain hysteresis are suggested to be due to microcracking associated with the large very rapid strain changes associate with the ferroelastic switching mode.
Vibrational energy levels of ozone up to dissociation revisited
Authors: Lee Hee-Seung , Light John C.
Published: March 2004

Two recent papers presented calculations of the highly excited vibrational states of ozone [J. Chem. Phys. 119, 6512 (2003); 119, 6554 (2003)]. The nature and energies of these states may hold the key to the anomalous isotopic distribution of ozone in the atmosphere. Even though the same potential energy surface of Babikov et al. [J. Chem. Phys. 119, 2577 (2003)] was used in both calculations, the number of bound van der Waals states reported below dissociation differed significantly. In order to resolve the issue we present here the results of an independent computation of all the bound vibrational states of O16O16O16 and O16O16O18 up to dissociation. Our methods differ from both earlier calculations since we use hyperspherical coordinates and a direct product discrete variable representation of the Hamiltonian. The results of present work support the existence of several van der Waals states for J=0 on this potential energy surface.
Molecular orientation via a dynamically induced pulse-train: Wave packet dynamics of NaI in a static electric field
Authors: Marquetand P. , Materny A. , Henriksen N. E. , Engel V.
Published: March 2004

We regard the rovibrational wave packet dynamics of NaI in a static electric field after femtosecond excitation to its first electronically excited state. The following quasibound nuclear wave packet motion is accompanied by a bonding situation changing from covalent to ionic. At times when the charge separation is present, i.e., when the bond-length is large, a strong dipole moment exists and rotational excitation takes place. Upon bond contraction, the then covalently bound molecule does not experience the external field. This scenario repeats itself periodically. Thus, the vibrational dynamics causes a situation which is comparable to the interaction of the molecule with a train of pulses where the pulse separation is determined by the vibrational period.
Molecular clamp mechanism of substrate binding by hydrophobic coiled-coil residues of the archaeal chaperone prefoldin
Authors: Lundin Victor F. , Stirling Peter C. , Gomez-Reino Juan , Mwenifumbo Jill C. , Obst Jennifer M. , Valpuesta José M. , Leroux Michel R.
Published: March 2004

Prefoldin (PFD) is a jellyfish-shaped molecular chaperone that has been proposed to play a general role in
de novo
protein folding in archaea and is known to assist the biogenesis of actins, tubulins, and potentially other proteins in eukaryotes. Using point mutants, chimeras, and intradomain swap variants, we show that the six coiledcoil tentacles of archaeal PFD act in concert to bind and stabilize nonnative proteins near the opening of the cavity they form. Importantly, the interaction between chaperone and substrate depends on the mostly buried interhelical hydrophobic residues of the coiled coils. We also show by electron microscopy that the tentacles can undergo an
en bloc
movement to accommodate an unfolded substrate. Our data reveal how archael PFD uses its unique architecture and intrinsic coiled-coil properties to interact with nonnative polypeptides.
Evolutionary stability of DNA uptake signal sequences in the Pasteurellaceae
Authors: Bakkali M. , Chen T.-Y. , Lee H. C. , Redfield R. J.
Published: March 2004

The DNA-uptake signal sequence (USS) of the bacterium
Haemophilus influenzae
is highly over-represented in its genome (1,471 copies of the core sequence AAGTGCGGT), and DNA fragments containing USS are preferentially taken up by competent cells. Because this bias favors uptake of conspecific DNA, USSs are often considered a kind of mate recognition system in bacteria, acting as species-specific barriers against uptake of unrelated DNA. However, the
H. influenzae
USS is highly over-represented in the genomes of three otherwise-divergent Pasteurellaceae species (
Pasteurella multocida
,
Haemophilus somnus
, and
Actinobacillus actinomycetemcomitans
, 927, 1,205, and 1,760 copies, respectively), suggesting that USSs do not always limit exchange. USSs in all these genomes are mainly in coding regions and show no orientation bias around the chromosome, weakening proposed USS functions in transcription termination and chromosome replication. Alignment of homologous genes was used to determine evolutionary relationships between individual USSs. Most
H. influenzae
USSs were found to have perfect or imperfect homologs (USS at the same location) in at least one other species, and most USSs in the other species had perfect or imperfect homologs in
H. influenzae
. These homologies suggest that the use of a common USS is due to inheritance of the USS-based uptake system from a common ancestor of the Pasteurellaceae, and it indicates that individual USSs can be evolutionarily stable elements of their genomes. The pattern is consistent with a molecular drive model of USS evolution, with new USSs arising by mutation and preferentially spread to new genomes by the biased DNA-uptake system.
Behavioral impairments caused by injections of the protein synthesis inhibitor anisomycin after contextual retrieval reverse with time
Authors: Lattal K. Matthew , Abel Ted
Published: March 2004

Recent accounts of memory suggest that retrieval of a learning experience transforms that memory into a labile state that requires a period of protein synthesis to be reconsolidated into a fixed state. In this article, we show that the impairments in behavior caused by the protein synthesis inhibitor anisomycin given after retrieval are temporary and are thus not likely to reflect disruptions in a protein synthesis-dependent reconsolidation process. Mice received injections of anisomycin after either initial acquisition or retrieval of contextual fear conditioning. When anisomycin injections followed acquisition, freezing was impaired during memory tests the next day and 21 days later. When anisomycin injections followed normal retrieval of contextual fear conditioning, freezing was impaired the next day but recovered to levels of control mice when testing occurred 21 days later. This recovery effect occurred after short or long durations of exposure during the retrieval period and was specific to the conditioning context. These results suggest that anisomycin injections after retrieval do not retroactively affect the memory from conditioning.
Chiral biphenyl diphosphines for asymmetric catalysis: Stereoelectronic design and industrial perspectives
Authors: Jeulin Séverine , de Paule Sébastien Duprat , Ratovelomanana-Vidal Virginie , Genêt Jean-Pierre , Champion Nicolas , Dellis Philippe
Published: March 2004

Two original chiral diphosphines, SYNPHOS and DIFLUORPHOS, have been synthesized on multigram scales. Their steric and electronic profiles have been established in comparison with the commonly used 2,2′-bis(diphenylphosphino)-1,1′-binaphthyl and 6,6′-dimethoxy-2,2′-bis(diphenylphosphino)-1,1′-biphenyl ligands. A screening study of the four ligands in Ru
II
-catalyzed asymmetric hydrogenation of prochiral ketones and olefins has been performed. It revealed that the stereoelectronic features of the ligand and the substrate deeply influenced the enantioselectivities obtained in asymmetric hydrogenation, SYNPHOS and DIFLUORPHOS being fully complementary in terms of enantioselectivity for this reaction.
Suppression of nuclear oscillations in
Saccharomyces cerevisiae
expressing Glu tubulin
Authors: Badin-Larçon A. C. , Boscheron C. , Soleilhac J. M. , Piel M. , Mann C. , Denarier E. , Fourest-Lieuvin A. , Lafanechère L. , Bornens M. , Job D.
Published: March 2004

In most eukaryotic cells, the C-terminal amino acid of α-tubulin is aromatic (Tyr in mammals and Phe in
Saccharomyces cerevisiae
) and is preceded by two glutamate residues. In mammals, the C-terminal Tyr of α-tubulin is subject to cyclic removal from the peptide chain by a carboxypeptidase and readdition to the chain by a tubulin–Tyr ligase. There is evidence that tubulin–Tyr ligase suppression and the resulting accumulation of detyrosinated (Glu) tubulin favor tumor growth, both in animal models and in human cancers. However, the molecular basis for this apparent stimulatory effect of Glu tubulin accumulation on tumor progression is unknown. Here we have developed
S. cerevisiae
strains expressing only Glu tubulin and used them as a model to assess the consequences of Glu tubulin accumulation in cells. We find that Glu tubulin strains show defects in nuclear oscillations. These defects are linked to a markedly decreased association of the yeast ortholog of CLIP170, Bik1p, with microtubule plus-ends. These results indicate that the accumulation of Glu tubulin in cells affects microtubule tip complexes that are important for microtubule interactions with the cell cortex.
Purification and architecture of the ubiquitous Wave complex
Authors: Gautreau Alexis , Ho Hsin-yi H. , Li Jiaxu , Steen Hanno , Gygi Steven P. , Kirschner Marc W.
Published: March 2004

The Wave proteins are major activators of the Arp2/3 complex. The ubiquitous Wave-2 is required for actin polymerization at the leading edge of migrating cells. Here we purify Wave-2 from HeLa cells. Five proteins, Sra, Nap, Wave-2, Abi, and Hspc, are copurified, indicating that they form a tight complex. These proteins are only present in the complexed form, with the exception of Hspc, which displays a free pool. We reconstitute the Wave-2 complex by cotranslating
in vitro
the five subunits and use this system together with specific immunoprecipitations to study the molecular architecture of the complex. The complex is organized around a core of Nap and Abi. Sra is a peripheral subunit recruited on the Nap side, whereas the Wave and Hspc subunits are recruited on the Abi side of the core.
Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota
Authors: Rawls John F. , Samuel Buck S. , Gordon Jeffrey I.
Published: March 2004

Animals have developed the means for supporting complex and dynamic consortia of microorganisms during their life cycle. A transcendent view of vertebrate biology therefore requires an understanding of the contributions of these indigenous microbial communities to host development and adult physiology. These contributions are most obvious in the gut, where studies of gnotobiotic mice have disclosed that the microbiota affects a wide range of biological processes, including nutrient processing and absorption, development of the mucosal immune system, angiogenesis, and epithelial renewal. The zebrafish (
Danio rerio
) provides an opportunity to investigate the molecular mechanisms underlying these interactions through genetic and chemical screens that take advantage of its transparency during larval and juvenile stages. Therefore, we developed methods for producing and rearing germ-free zebrafish through late juvenile stages. DNA microarray comparisons of gene expression in the digestive tracts of 6 days post fertilization germ-free, conventionalized, and conventionally raised zebrafish revealed 212 genes regulated by the microbiota, and 59 responses that are conserved in the mouse intestine, including those involved in stimulation of epithelial proliferation, promotion of nutrient metabolism, and innate immune responses. The microbial ecology of the digestive tracts of conventionally raised and conventionalized zebrafish was characterized by sequencing libraries of bacterial 16S rDNA amplicons. Colonization of germ-free zebrafish with individual members of its microbiota revealed the bacterial species specificity of selected host responses. Together, these studies establish gnotobiotic zebrafish as a useful model for dissecting the molecular foundations of host-microbial interactions in the vertebrate digestive tract.