bluuebunny/crossref_metadata_2025 huggingface dataset:
Actin Organization During Eucalyptus Root Hair Development and Its Response to Fungal Hypaphorine
Authors: Dauphin A. , De Ruijter N. C. A. , Emons A. M. C. , Legué V.
Published: March 2006

Abstract: The fungus Pisolithus microcarpus establishes an ectomycorrhiza with Eucalyptus globulus. This symbiosis involves a fungal synthesis and secretion of hypaphorine, an indolic compound. Previous studies have shown that hypaphorine induces an alteration in the actin cytoskeleton of elongating root hairs and inhibits hair elongation. Using an alternative approved method, we analyzed the effects of hypaphorine on the E. globulus root hair cyto‐architecture and actin configuration in more detail and provide new results. One mM hypaphorine stops root hair elongation within 20 min, and changes the hair cyto‐architecture. Semi‐quantitative analysis of the actin cytoskeleton before and after treatment with hypaphorine shows that hypaphorine induces a shift from fine F‐actin to F‐actin bundles in the sub‐apex of the hair, which occurs first in the mid‐plane of the cell. This creates a sub‐apical cell centre free of filamentous actin, an actin configuration that differs from that during developmental growth arrest. The mechanism of action of hypaphorine is discussed.
Germination of Coffee Seeds and its Significance for Coffee Quality
Authors: Selmar D. , Bytof G. , Knopp S.‐E. , Breitenstein B.
Published: March 2006

Abstract: Besides genotypic characteristics, the crucial factor that determines coffee quality is the mode of post‐harvest treatment, i.e., the wet and dry processing. Up to now, the resulting characteristic flavour differences between these differentially processed coffees were attributed exclusively to differences in starting material. However, as these quality differences are still evident, even when identical coffee samples were processed by the two methods in parallel, the differences must be created by metabolic processes in the coffee beans themselves. Based on expression studies of the germination‐specific isocitrate lyase and the resumption of cell cycle activity, monitored by the abundance of β‐tubulin, we evidence that germination is initiated in coffee seeds during the course of standard coffee post‐harvest treatments. The extent and nature of the germination processes depend on the processing method. The coherence of metabolic events, substantial differences in the chemical composition of the coffee beans, and the generation of specific coffee qualities establishes the basis for a quite novel approach in coffee research.
Rhizosphere Carboxylate Concentrations of Chickpea are Affected by Soil Bulk Density
Authors: Wouterlood M. , Lambers H. , Veneklaas E. J.
Published: March 2006

Abstract: We investigated whether carboxylate exudation by chickpea (Cicer arietinum L.) was affected by soil bulk density and if this effect was local or systemic. We hypothesised that concentrations of carboxylates would increase with distance from the root apex due to continuous and constitutive accumulation of carboxylates, and that exudate accumulation would be greater in a compacted soil than in a loose soil. Plants were grown in split‐root or single cylinders containing loose (1400 kg m‐3) or compacted (1800 kg m‐3) soil. Rhizosphere carboxylate concentrations were measured of whole root systems as well as of sections along the root. The root diameter was greatest of plants grown in the compacted soil; however, root diameters were the same for both root halves in the split‐root design, whether they grew in loose soil or in compacted soil. Similarly, carboxylate concentrations tended to be lower for the whole root system in the compacted soil, but were the same for both root halves in the split‐root design, irrespective of whether the roots were in loose soil or in compacted soil. These results indicate that both root diameter and carboxylate exudation by roots in chickpea is regulated systemically via a signal from the shoot rather than by local signals in the roots. There was no accumulation of carboxylates with increasing distance from the apex, probably because microbial degradation occurred at similar rates as carboxylate exudation. Malonate, previously suggested as deterrent to microorganisms, is likely only a selective deterrent.
Correlation between AS1 Gene Expression and Seed Protein Contents in Different Soybean (Glycine Max [L.] Merr.) Cultivars
Authors: Wan T.‐F. , Shao G.‐H. , Shan X.‐C. , Zeng N.‐Y. , Lam H.‐M.
Published: March 2006

Abstract: In higher plants, asparagine synthetase (AS) plays an important role in regulating the nitrogen sink‐source relationship. We studied the expression of AS genes in five Chinese soybean cultivars exhibiting contrasting seed protein contents. We found that only the AS2 but not the AS1 gene was induced by dark treatment. On the other hand, the expression of AS1 in leaves (especially in trifoliate leaves of young seedlings) showed a positive correlation with seed protein contents in the soybean cultivars tested. Therefore, in spite of the fact that the principle transporting compounds in soybean plants for nitrogen acquired via symbiotic fixation are ureides, AS may still play an important role in the process of nitrogen assimilation.
Comparison of film detectors, charged-coupled devices, and imaging plates in x-ray spectroscopy of hot dense plasma
Authors: Howe J. , Chambers D. M. , Courtois C. , Förster E. , Gregory C. D. , Hall I. M. , Renner O. , Uschmann I. , Woolsey N. C.
Published: March 2006

We present comparative x-ray spectroscopic measurements using an x-ray film, a charged-coupled device (CCD), and imaging plates as the detectors. An aluminum K-shell x-ray emission in the energy range of 1.8–2.15 keV is produced from a laser-produced plasma, and dispersed using a flat crystal spectrometer. Our interest is in the response of these detectors to weak x-ray emission, their suitability for quantitative and absolute measurements, as well of ease of use. We find that scientific-grade CCD detectors offer superior signal-to-noise performance, while imaging plates are a viable alternative particularly if large detection areas or curved surfaces are required. Despite the excellent spatial resolution of an x-ray film, imaging plates are preferred to film for quantitative measurement as signal to noise ratio is greater by an order of magnitude.
Fast valve and nozzle for gas-puff operation of dense plasma focus
Authors: Milanese María M. , Pouzo Jorge O. , Cortázar Osvaldo D. , Moroso Roberto L.
Published: March 2006

A simple and reliable valve and nozzle system for a very fast injection of gas has been designed and constructed for its use in gas-puff mode of dense plasma focus experiments. It delivers a very quick rise time: 55μs. The pressure measured in our setup at a distance of 15 mm from the nozzle output is about 0.285 mbar, with a plenum pressure of 3 bars (absolute). The time between the valve aperture and pressure front arrival is 360μs. This result comes up as an average of about a hundred measurements. The energy input is 95 J (270 V on a 3000μF capacitor bank). The typical dimensions of the valve are 52 mm in diameter and 80 mm in length. The entire volume of the valve is, then, very small. The relative low pressure and voltage operation are significant advantages of this development. The performance of the valve satisfactorily fulfills the objectives of gas-puff plasma focus operation.
Temporal asymmetry of fluctuations in nonequilibrium steady states
Authors: Paneni Carlo , Searles Debra J. , Rondoni Lamberto
Published: March 2006

Temporal asymmetries of fluctuation paths in nonequilibrium microscopic shearing systems are observed for the first time. Inspired by theories that predict asymmetry of fluctuation paths in stochastic dynamics, we focus on deterministic reversible particle models, which represent a small part of a macroscopic system. We have monitored and measured the asymmetry of the fluctuation paths of various observables as they go away from and towards the mean. The understanding of such asymmetries may scatter light on how irreversibility emerges from the microscopic reversible dynamics and on the behavior of mesoscopic (nanoscale) systems.
Crystallographically orientated fcc Co nanocrystals in rutile TiO2 thin films
Authors: Xin Y. , Lu J. , Stampe P. A. , Kennedy R. J.
Published: March 2006

Cobalt nanocrystals dispersed in rutile thin films on (0001) α-Al2O3 substrates are grown by pulsed-laser deposition. Their microstructure is investigated by transmission electron microscopy and their magnetic properties measured at temperatures from 5to350K. The Co nanocrystals have fcc structure with no multi-twin defects and are crystallographically orientated with their (111) planes parallel to the substrate surface having an orientation relationship to TiO2 of (111)Co‖(100)rutile, and in-plane orientations of [112¯]Co‖[010]rutile and [1¯10]Co‖[001]rutile. The diameter of the Co nanocrystals is 4.4±0.15nm. The samples show superparamagnetic behavior at low temperatures. The zero-field-cooled magnetization versus temperature curve has a peak at about 105K. There is strong magnetic dipolar interaction between the particles which might have resulted in the observed hysteresis at room temperature.
Exploring reaction pathways with transition path and umbrella sampling: Application to methyl maltoside
Authors: Dimelow Richard J. , Bryce Richard A. , Masters Andrew J. , Hillier Ian H. , Burton Neil A.
Published: March 2006

The transition path sampling (TPS) method is a powerful approach to study chemical reactions or transitional properties on complex potential energy landscapes. One of the main advantages of the method over potential of mean force methods is that reaction rates can be directly accessed without knowledge of the exact reaction coordinate. We have investigated the complementary nature of these two differing approaches, comparing transition path sampling with the weighted histogram analysis method to study a conformational change in a small model system. In this case study, the transition paths for a transition between two rotational conformers of a model disaccharide molecule, methyl β-D-maltoside, were compared with a free energy surface constrained by the two commonly used glycosidic (ϕ,ψ) torsional angles. The TPS method revealed a reaction channel that was not apparent from the potential of mean force method, and the suitability of ϕ and ψ as reaction coordinates to describe the isomerization in vacuo was confirmed by examination of the transition path ensemble. Using both transition state theory and transition path sampling methods, the transition rate was estimated. We have estimated a characteristic time between transitions of approximately 160 ns for this rare isomerization event between the two conformations of the carbohydrate. We conclude that transition path sampling can extract subtle information about the dynamics not apparent from the potential of mean force method. However, in calculating the reaction rate, the transition path sampling method required 27.5 times the computational effort than was needed by the potential of mean force method.
Implementation of quantum gate operations in molecules with weak laser fields
Authors: Teranishi Yoshiaki , Ohtsuki Yukiyoshi , Hosaka Kouichi , Chiba Hisashi , Katsuki Hiroyuki , Ohmori Kenji
Published: March 2006

We numerically propose a way to perform quantum computations by combining an ensemble of molecular states and weak laser pulses. A logical input state is expressed as a superposition state (a wave packet) of molecular states, which is initially prepared by a designed femtosecond laser pulse. The free propagation of the wave packet for a specified time interval leads to the specified change in the relative phases among the molecular basis states, which corresponds to a computational result. The computational results are retrieved by means of quantum interferometry. Numerical tests are implemented in the vibrational states of the B state of I2 employing controlled-NOT gate, and 2 and 3qubits Fourier transforms. All the steps involved in the computational scheme, i.e., the initial preparation, gate operation, and detection steps, are achieved with extremely high precision.
Near-threshold photoionization of hot isopropyl radicals
Authors: Fan H. , Pratt S. T.
Published: March 2006

A combination of ion imaging and vacuum ultraviolet, single-photon ionization is used to study the internal energy dependence of the photoionization cross section of isopropyl radicals produced by the 266nm photodissociation of isopropyl iodide. The isopropyl radicals so produced have internal energies of ∼0.3–2.0eV. Images recorded for photoionization energies from just below the adiabatic ionization threshold at 7.37±0.02 and 8.04eV are essentially identical both to each other and to that recorded at 9.67eV. These results imply that the photoionization cross section is only weakly dependent on internal energy. Several factors contributing to this observation are discussed, as are the implications for the photoionization of other systems with significant internal excitation.
Real irreducible sesquilinear-quadratic tensor concomitants of complex bivectors
Authors: Carozzi T. D. , Bergman J. E. S.
Published: March 2006

Irreducible tensor concomitants of an arbitrary complex antisymmetric second rank tensor, or bivector, in a Minkowski space-time are presented. These tensors are quadratic in the complex bivector and invariant under an overall multiplicative phase change of the bivector; in other words, they are sesquilinear-quadratic tensor concomitants of the complex bivector. The tensors are real and irreducible under the full real Lorentz group. Particular consideration is given to when the complex bivector is the electromagnetic field strength tensor (complex description is appropriate for radiation), and it is found that some of these irreducible tensors are novel electromagnetic observables not previously mentioned in the literature.
Modeling collective behavior of molecules in nanoscale direct deposition processes
Authors: Lee Nam-Kyung , Hong Seunghun
Published: March 2006

We present a theoretical model describing the collective behavior of molecules in nanoscale direct deposition processes such as dip-pen nanolithography. We show that strong intermolecular interactions combined with nonuniform substrate-molecule interactions can produce various shapes of molecular patterns including fractal-like structures. Computer simulations reveal circular and starlike patterns at low and intermediate densities of preferentially attractive surface sites, respectively. At large density of such surface sites, the molecules form a two-dimensional invasion percolation cluster. Previous experimental results showing anisotropic patterns of various chemical and biological molecules correspond to the starlike regime [P. Manandhar et al., Phys. Rev. Lett. 90, 115505 (2003); J.-H. Lim and C. A. Mirkin, Adv. Mater. (Weinheim, Ger.) 14, 1474 (2002); D. L. Wilson et al., Proc. Natl. Acad. Sci. U.S.A. 98, 13660 (2001); M. Su et al., Appl. Phys. Lett. 84, 4200 (2004); R. McKendry et al., Nano Lett. 2, 713 (2002); H. Zhou et al., Appl. Surf. Sci. 236, 18 (2004); G. Agarwal et al., J. Am. Chem. Soc. 125, 580 (2003)].
Second-order correction to perfect pairing: An inexpensive electronic structure method for the treatment of strong electron-electron correlations
Authors: Beran Gregory J. O. , Head-Gordon Martin , Gwaltney Steven R.
Published: March 2006

We have formulated a second-order perturbative correction for perfect-pairing wave functions [PP(2)] based on similarity-transformed perturbation techniques in coupled cluster theory. The perfect-pairing approximation is used to obtain a simple reference wave function which can qualitatively describe bond breaking, diradicals, and other highly correlated systems, and the perturbative correction accounts for the dynamical correlation. An efficient implementation of this correction using the resolution of the identity approximation enables PP(2) to be computed at a cost only a few times larger than that of canonical MP2 for systems with hundreds of active electrons and tens of heavy atoms. PP(2) significantly improves on MP2 predictions in various systems with a challenging electronic structure.
Two-photon absorption cross sections: An investigation of the accuracy of calculated absolute and relative values
Authors: Nielsen Christian B. , Rettrup Sten , Sauer Stephan P. A.
Published: March 2006

We have studied the basis set and electron correlation effects on the ab initio calculations of two-photon absorption cross sections of water. Various series of correlation consistent basis sets up to triply augmented basis sets of valence pentuple ζ level as well as the popular 6-31G(d) basis set have been employed in combination with several coupled cluster, configuration interaction, and density functional theory methods. We find that it is very difficult to obtain converged values of the cross sections for even a small molecule such as water. Acknowledging these difficulties in obtaining a fully converged cross section for a given state, we also investigated the possibility of determining relative cross sections for a series of organic molecules. However, we did not find consistency between the relative cross sections calculated at the Hartree-Fock level and several coupled-cluster methods using the 6-31G(d) and aug-cc-pVDZ basis sets. However, we could reproduce the relative ordering of the two-photon absorption cross sections of the molecules studied at the Hartree-Fock level.
Solution of the mean spherical approximation for polydisperse multi-Yukawa hard-sphere fluid mixture using orthogonal polynomial expansions
Authors: Kalyuzhnyi Yurij V. , Cummings Peter T.
Published: March 2006

The Blum-Høye [J. Stat. Phys. 19 317 (1978)] solution of the mean spherical approximation for a multicomponent multi-Yukawa hard-sphere fluid is extended to a polydisperse multi-Yukawa hard-sphere fluid. Our extension is based on the application of the orthogonal polynomial expansion method of Lado [Phys. Rev. E 54, 4411 (1996)]. Closed form analytical expressions for the structural and thermodynamic properties of the model are presented. They are given in terms of the parameters that follow directly from the solution. By way of illustration the method of solution is applied to describe the thermodynamic properties of the one- and two-Yukawa versions of the model.
The invariant constrained equilibrium edge preimage curve method for the dimension reduction of chemical kinetics
Authors: Ren Zhuyin , Pope Stephen B. , Vladimirsky Alexander , Guckenheimer John M.
Published: March 2006

This work addresses the construction and use of low-dimensional invariant manifolds to simplify complex chemical kinetics. Typically, chemical kinetic systems have a wide range of time scales. As a consequence, reaction trajectories rapidly approach a hierarchy of attracting manifolds of decreasing dimension in the full composition space. In previous research, several different methods have been proposed to identify these low-dimensional attracting manifolds. Here we propose a new method based on an invariant constrained equilibrium edge (ICE) manifold. This manifold (of dimension nr) is generated by the reaction trajectories emanating from its (nr−1)-dimensional edge, on which the composition is in a constrained equilibrium state. A reasonable choice of the nr represented variables (e.g., nr “major” species) ensures that there exists a unique point on the ICE manifold corresponding to each realizable value of the represented variables. The process of identifying this point is referred to as species reconstruction. A second contribution of this work is a local method of species reconstruction, called ICE-PIC, which is based on the ICE manifold and uses preimage curves (PICs). The ICE-PIC method is local in the sense that species reconstruction can be performed without generating the whole of the manifold (or a significant portion thereof). The ICE-PIC method is the first approach that locally determines points on a low-dimensional invariant manifold, and its application to high-dimensional chemical systems is straightforward. The “inputs” to the method are the detailed kinetic mechanism and the chosen reduced representation (e.g., some major species). The ICE-PIC method is illustrated and demonstrated using an idealized H2∕O system with six chemical species. It is then tested and compared to three other dimension-reduction methods for the test case of a one-dimensional premixed laminar flame of stoichiometric hydrogen/air, which is described by a detailed mechanism containing nine species and 21 reactions. It is shown that the error incurred by the ICE-PIC method with four represented species is small across the whole flame, even in the low temperature region.
Confinement effect of chain dynamics in micrometer thick layers of a polymer melt below the critical molecular weight
Authors: Kausik Ravinath , Mattea Carlos , Fatkullin Nail , Kimmich Rainer
Published: March 2006

Polymer melts confined in micrometer thick layers were examined with the aid of field-cycling NMR relaxometry. It is shown that chain dynamics under such moderate confinement conditions are perceptibly different from those observed in the bulk material. This is considered to be a consequence of the corset effect, which predicts a crossover between Rouse and reptationlike dynamics for molecular weights below the critical value at confinement length scales much larger than 10RF, where RF is the Flory radius of the bulk polymer coil [Fatkullin et al., New J. Phys. 6, 46 (2004)]. For the polymer species studied, a perfluoropolyether with a molecular weight of 11 000, the Flory radius is of the order 10nm, so that the experiment refers to the far end of the predicted crossover region from confined to bulk chain dynamics. Remarkably the confinement effect is shown to reach polymer-wall distances of the order 100 Flory radii.
Ion chemistry of NOO+
Authors: Midey A. J. , Fernandez A. I. , Viggiano A. A. , Zhang P. , Morokuma K.
Published: March 2006

The kinetics for the reactions of NOO+ ions with neutral molecules having ionization potentials (IPs) from 9.27to15.58eV was measured in a selected ion flow tube at 298K. The NOO+ ions are produced from the reaction of N3++O2 and have been reacted with the following: NO, C6F6, CS2, CF3I, C3F6, OCS, C2H6, Xe, SO2, O3, N2O, CO2, Kr, CO, D2, and N2. Numerous types of reactions were observed with the various neutral reagents, including production of NO+ (which may involve loss of an O from the ion or addition of O to the neutral reactant, although the two channels could not be distinguished here), charge transfer, isomerization of NOO+ to ONO+, and hydride abstraction. High level theoretical calculations of the structures and energetics of the various isomers, electronic states, and transition states of NOO and NOO+ were performed to better understand the observed reactivity. All neutral species with an IP⩽11.18eV were observed to react with NOO+ in part by charge transfer. Detailed calculations showed that the recommended adiabatic and vertical IPs of NOO are 10.4 and 11.7eV, respectively, at the MRCISD(Q)/AVQZ level of theory. The observed experimental limit for charge transfer of 11.18eV agreed well with the energetics of the final products obtained from theory if dissociation of the neutral metastable product occurred, i.e., the products were X++[O(P3)+NO(Π2)], where [O(P3)+NO(Π2)] formed via dissociation of metastable NOO. Charge exchange with neutral reagent X would, therefore, be exothermic if IP(X)<[IPad(NOO)−ΔE(O+NO)–NOO]=∼11.1eV, where IPad(NOO) is the adiabatic IP. The potential energy surface for the reaction of NOO+ with C2H6 was also calculated, indicating that two pathways for formation of HNO2+C2H5+ exist.
A theoretical study of molecular conduction. III. A nonequilibrium-Green’s-function-based Hartree-Fock approach
Authors: Shimazaki Tomomi , Xue Yongqiang , Ratner Mark A. , Yamashita Koichi
Published: March 2006

Many recent experimental and theoretical studies have paid attention to the conductivity of single molecule transport junctions, both because it is fundamentally important and because of its significance in the development of molecular-based electronics. In this paper, we discuss a nonequilibrium Green’s function (NEGF)-based Hartree-Fock (HF) approach; the NEGF method can appropriately accommodate charge distributions in molecules connected to electrodes. In addition, we show that a NEGF-based density matrix can reduce to an ordinary HF density matrix for an isolated molecule if the molecule does not interact with electrodes. This feature of the NEGF-based density matrix also means that NEGF-based Mulliken charges can be reduced to ordinary Mulliken charges in those cases. Therefore, the NEGF-based HF approach can directly compare molecules that are connected to electrodes with isolated ones, and is useful in investigating complicated features of molecular conduction. We also calculated the transmission probability and conduction for benzenedithiol under finite electrode biases. The coupling between the electrodes and molecule causes electron transfer from the molecule to the electrodes, and the applied bias modifies this electron transfer. In addition, we found that the molecule responds capacitively to the applied bias, by shifting the molecular orbital energies.
The effect of the incident collision energy on the phase and crystallization kinetics of vapor deposited water films
Authors: Scott Smith R. , Zubkov Tykhon , Kay Bruce D.
Published: March 2006

Molecular beam techniques are used to grow water films on Pt(111) with incident collision energies from 5 to 205kJ∕mole. The effect of the incident collision energy on the phase of vapor deposited water films and their subsequent crystallization kinetics are studied using temperature programed desorption and infrared spectroscopy. We find that for films deposited at substrate temperatures below 110 K, the incident kinetic energy (up to 205kJ∕mole) has no effect on the initial phase of the deposited film or its crystallization kinetics. Above 110 K, the substrate temperature does affect the phase and crystallization kinetics of the deposited films but this result is also independent of the incident collision energy. The presence of a crystalline ice template (underlayer) does affect the crystallization of amorphous solid water, but this effect is also independent of the incident beam energy. These results suggest that the crystallization of amorphous solid water requires cooperative motion of several water molecules.
Electro-osmosis at inhomogeneous charged surfaces: Hydrodynamic versus electric friction
Authors: Kim Yong Woon , Netz Roland R.
Published: March 2006

Electrokinetic methods are efficient in probing the electrostatic surface properties of charged systems. However, anomalies observed in experiments indicate that the classical electrokinetic theory should be reconsidered. Using Green’s function methods and hydrodynamic simulations, we investigate electro-osmosis driven by electric-field-induced ion motion near a charged planar substrate with smooth or rough boundary. First, a reformulation of electro-osmotic theory for planar charged surfaces employing Green’s functions shows that the Helmholtz-Smoluchowski (HS) relation between electrostatic potential and solvent velocity is exact for smooth surfaces, even in the presence of ion correlations. Deviations from HS theory are caused by combined hydrodynamic and electric surface friction, as our hydrodynamic simulations of ions at smooth and corrugated charged surfaces in lateral electric fields demonstrate. Within the simulations, hydrodynamic interactions are treated in the continuum limit and the presence of a no-slip boundary condition at the surface is taken into account. While electrofriction is relevant in highly charged system and/or for multivalent ions, hydrodynamic friction is dominant in systems with moderate surface charge density and/or low ionic valency. We also derive the effective electrokinetic surface charge from the electro-osmotic solvent profiles, which is substantially reduced when compared with the bare value and shows qualitative agreement with the experimental tendency.
Near infrared surface plasmon resonance of gold tabular nanostructures in the HAuCl4–Na2S reaction
Authors: Diao J. J. , Chen Hao
Published: March 2006

We present an unexpected product of the HAuCl4–Na2S reaction, gold tabular nanostructures, which have a surface plasmon resonance peak in near infrared region.
Theory of solvation in polar nematics
Authors: Kapko Vitaly , Matyushov Dmitry V.
Published: March 2006

We develop a linear response theory of solvation of ionic and dipolar solutes in anisotropic, axially symmetric polar solvents. The theory is applied to solvation in polar nematic liquid crystals. The formal theory constructs the solvation response function from projections of the solvent dipolar susceptibility on rotational invariants. These projections are obtained from Monte Carlo simulations of a fluid of dipolar spherocylinders which can exist both in the isotropic and nematic phases. Based on the properties of the solvent susceptibility from simulations and the formal solution, we have obtained a formula for the solvation free energy which incorporates the experimentally available properties of nematics and the length of correlation between the dipoles in the liquid crystal. The theory provides a quantitative framework for analyzing the steady-state and time-resolved optical spectra and makes several experimentally testable predictions. The equilibrium free energy of solvation, anisotropic in the nematic phase, is given by a quadratic function of cosine of the angle between the solute dipole and the solvent nematic director. The sign of solvation anisotropy is determined by the sign of dielectric anisotropy of the solvent: solvation anisotropy is negative in solvents with positive dielectric anisotropy and vice versa. The solvation free energy is discontinuous at the point of isotropic-nematic phase transition. The amplitude of this discontinuity is strongly affected by the size of the solute becoming less pronounced for larger solutes. The discontinuity itself and the magnitude of the splitting of the solvation free energy in the nematic phase are mostly affected by microscopic dipolar correlations in the nematic solvent. Illustrative calculations are presented for the equilibrium Stokes shift and the Stokes shift time correlation function of coumarin-153 in 4-n-pentyl-4′-cyanobiphenyl and 4,4-n-heptyl-cyanopiphenyl solvents as a function of temperature in both the nematic and isotropic phases.
Semiclassical calculation of nonadiabatic thermal rate constants: Application to condensed phase reactions
Authors: Zhao Yi , Li Xiang , Zheng Zilong , Liang WanZhen
Published: March 2006

The nonadiabatic transition state theory proposed recently by Zhao et al. [J. Chem. Phys. 121, 8854 (2004)] is extended to calculate rate constants of complex systems by using the Monte Carlo and umbrella sampling methods. Surface hopping molecular dynamics technique is incorporated to take into account the dynamic recrossing effect. A nontrivial benchmark model of the nonadiabatic reaction in the condensed phase is used for the numerical test. It is found that our semiclassical results agree well with those produced by the rigorous quantum mechanical method. Comparing with available analytical approaches, we find that the simple statistical theory proposed by Straub and Berne [J. Chem. Phys. 87, 6111 (1987)] is applicable for a wide friction region although their formula is obtained using Landau-Zener [Phys. Z. Sowjetunion 2, 46 (1932); Proc. R. Soc. London, Ser. A 137, 696 (1932)] nonadiabatic transition probability along a one-dimensional diffusive coordinate. We also investigate how the nuclear tunneling events affect the dependence of the rate constant on the friction.
Slope parameters of the barrier heights of metal-organic contacts
Authors: Mönch Winfried
Published: March 2006

The continuum of metal-induced gap states (MIGS) determines the barrier heights of ideal metal-semiconductor or Schottky contacts. The charge transfer across such interfaces may be attributed to the partial ionic character of the covalent bonds between the metal and the semiconductor atoms right at the interface. Consequently, the barrier heights are split up into a zero-charge-transfer term, which equals the energy separation between the MIGSs branch point and the majority-carrier band edge, and an electric-dipole term, which varies proportional to the difference of the metal and the semiconductor electronegativities. For Schottky contacts on inorganic semiconductors, the respective slope parameters were found to depend on the square (ϵ∞−1)2 of the optical susceptibility of the semiconductors. It is demonstrated that experimental as well as theoretical slope parameters reported for metal contacts to organic semiconductors follow the same relationship which was observed earlier with Schottky contacts of inorganic semiconductors. This finding is not surprising as the MIGS originate from the quantum-mechanical tunnel effect of the bulk metal electrons in the energy range from the highest occupied electronic energy level of the semiconductor up to the Fermi level, irrespective of whether inorganic or organic semiconductors are considered.
Electrostatic field-adapted molecular fractionation with conjugated caps for energy calculations of charged biomolecules
Authors: Jiang Nan , Ma Jing , Jiang Yuansheng
Published: March 2006

An electrostatic field-adapted molecular fractionation with conjugated caps (EFA-MFCC) approach is implemented for treating macromolecules with several charge centers. The molecular fragmentation is performed in an “electrostatic field,” which is described by putting point charges on charge centers, directly affecting the Hamiltonians of both fragments and conjugated caps. So the present method does not need truncation during the calculation of electrostatic interactions. Our test calculations on a series of charged model systems and biological macromolecules using the HF and B3LYP methods have demonstrated that this approach is capable of describing the electronic structure with accuracy comparable to other fragment-based methods. The EFA-MFCC approach is an alternative way for predicting the total energies of charged macromolecules with acyclic, loop, and intersectional loop structures and interaction energies between two molecules.
Possible ground-state structure of Au26: A highly symmetric tubelike cage
Authors: Fa Wei , Dong Jinming
Published: March 2006

The stable tubelike AuN (N=26–28) has been found using the scalar relativistic all-electron density functional theory calculations, which becomes another powerful candidate for the lowest-energy AuN, competing in energy with those space-filled structures suggested previously. Unlike the icosahedral “golden” fullerene Au32, these tubelike gold clusters may be closely related to the synthesized single-wall gold nanotubes (SWGNTs). The ground-state Au26 has a hollow tubelike structure constructed from the (6, 0) SWGNT, yielding a high-symmetry D6d cage, based upon which the most stable Au27 and Au28 can be obtained by adding one and two more capped atoms on its one end, respectively.
Structural study of gold clusters
Authors: Xiao Li , Tollberg Bethany , Hu Xiankui , Wang Lichang
Published: March 2006

Density functional theory (DFT) calculations were carried out to study gold clusters of up to 55 atoms. Between the linear and zigzag monoatomic Au nanowires, the zigzag nanowires were found to be more stable. Furthermore, the linear Au nanowires of up to 2nm are formed by slightly stretched Au dimers. These suggest that a substantial Peierls distortion exists in those structures. Planar geometries of Au clusters were found to be the global minima till the cluster size of 13. A quantitative correlation is provided between various properties of Au clusters and the structure and size. The relative stability of selected clusters was also estimated by the Sutton-Chen potential, and the result disagrees with that obtained from the DFT calculations. This suggests that a modification of the Sutton-Chen potential has to be made, such as obtaining new parameters, in order to use it to search the global minima for bigger Au clusters.
Evaluation of low-scaling methods for calculation of phosphorescence parameters
Authors: Jansson Emil , Norman Patrick , Minaev Boris , Ågren Hans
Published: March 2006

In order to find a methodology that is a compromise between favorable computational scaling and tolerable errors, a series of nonrelativistic approaches for the calculation of radiative phosphorescence lifetimes are benchmarked against fully relativistic four-component results. The study of the aA23-XA11 transition intensity in the series of H2CX molecules, where X is a chalcogene atom, X={O,S,Se,Te}, indicates a general good agreement between fully relativistic four-component and nonrelativistic perturbation-theoretical calculations. Among the nonrelativistic approaches, the scaled-charge spin-orbit operator approach is recognized as to provide transition matrix elements that are in good agreement with those obtained with the more elaborate Breit-Pauli and atomic mean field spin-orbit operators. This finding supports phosphorescence calculations using the available linear scaling technology for large complexes and, together with effective-core potentials, large complexes including heavy elements.
Optical probing of a silicon integrated circuit using electric-field-induced second-harmonic generation
Authors: Xiao Dong , Ramsay Euan , Reid Derryck T. , Offenbeck Bernd , Weber Norbert
Published: March 2006

By using the electric-field-induced second-harmonic generation effect, we have detected electrical signals present on a complementary metal-oxide-semiconductor (CMOS) integrated circuit in a noncontact geometry. Femtosecond pulses with a wavelength of 2.16μm were incident on the device and the second harmonic at 1.08μm exhibited a field-dependent behavior. The conversion efficiency from the fundamental to the second harmonic was estimated to be −103dB.
Rydberg states with quantum Monte Carlo
Authors: Bande Annika , Lüchow Arne , Della Sala Fabio , Görling Andreas
Published: March 2006

Calculations on Rydberg states are performed using quantum Monte Carlo methods. Excitation energies and singlet-triplet splittings are calculated for two model systems, the carbon atom (P3 and P1) and carbon monoxide (Σ1 and Σ3). Kohn-Sham wave functions constructed from open-shell localized Hartree-Fock orbitals are used as trial and guide functions. The fixed-node diffusion quantum Monte Carlo (FN-DMC) method depends strongly on the wave function’s nodal hypersurface. Nodal artefacts are investigated for the ground state of the carbon atom. Their effect on the FN-DMC results can be analyzed quantitatively. FN-DMC leads to accurate excitation energies but to less accurate singlet-triplet splittings. Variational Monte Carlo calculations are able to reproduce the experimental results for both the excitation energies and the singlet-triplet splittings.
Tailored coupled cluster singles and doubles method applied to calculations on molecular structure and harmonic vibrational frequencies of ozone
Authors: Hino Osamu , Kinoshita Tomoko , Chan Garnet Kin-Lic , Bartlett Rodney J.
Published: March 2006

To assess the separation of dynamic and nondynamic correlations and orbital choice, we calculate the molecular structure and harmonic vibrational frequencies of ozone with the recently developed tailored coupled cluster singles and doubles method (TCCSD). We employ the Hartree-Fock and complete active space (CAS) self-consistent field (SCF) orbitals to perform TCCSD calculations. When using the Hartree-Fock orbitals, it is difficult to reproduce the experimental vibrational frequency of the asymmetric stretching mode. On the other hand, the TCCSD based on the CASSCF orbitals in a correlation consistent polarized valence triple zeta basis yields excellent results with the two symmetric vibrations differing from the experimental harmonic values by 2cm−1 and the asymmetric vibration differing by 9cm−1.
Effects of humidity on unencapsulated poly(thiophene) thin-film transistors
Authors: Chabinyc Michael L. , Endicott Fred , Vogt Bryan D. , DeLongchamp Dean M. , Lin Eric K. , Wu Yiliang , Liu Ping , Ong Beng S.
Published: March 2006

The effects of humidity on unencapsulated polymeric thin-film transistors (TFTs) of poly[5,5’-bis(3-dodecyl-2-thienyl)-2,2’-bithiophene] (PQT-12) were investigated. The field effect mobility of PQT-12 TFTs decreases and the rate of trapping of charge carriers increases under increasing humidity. The amount of water absorbed by the PQT-12 films was measured using a quartz crystal microbalance. Thin films of PQT-12 absorb comparable amounts of water to the carrier concentration in TFTs under routine operating conditions (humidity of 30% relative humidity and gate voltage of −30V); the changes in electrical characteristics under humid atmospheres are attributed to the interaction of absorbed water with the carriers in the film.
Simultaneous control of ion flow energy and electron temperature in magnetized plasmas
Authors: Takahashi K. , Kaneko T. , Hatakeyama R.
Published: March 2006

Ion flow energy along magnetic-field lines is precisely controlled by electrostatic acceleration in magnetized collisional and synthesized plasmas. The source is made up of an ion-production region and a plasma synthesis region; an electron emitter of mesh shape is installed between the regions and supplies the electrons to the synthesis region. The ion flow is generated by an electrostatic potential difference between these regions. Our experimental results demonstrate that only the ion flow energy can be controlled under constant electron density and temperature. Moreover, the electron temperature is also controllable and could be reduced to less than 0.5eV.
Isotope effects in the dissociation of the B̃A11 state of SiH2, SiHD, and SiD2 using three-dimensional wave packet propagation
Authors: Tokue Ikuo , Yamasaki Katsuyoshi , Nanbu Shinkoh
Published: March 2006

Dissociations after the ÃB11→B̃A11 photoexcitation of SiH2, SiHD, and SiD2 were studied to investigate excited-state dynamics and effects of the initial vibrational state. The cross section (σ) for the photodissociation relative to SiH2(B̃)→Si(D1)+H2 and the rovibrational population of the H2 fragment were computed using the wave packet propagation technique based on the three-dimensional potential energy surfaces (PESs) of the Ã and B̃ electronic states and the transition dipole surfaces, which were reported in our previous paper [J. Chem. Phys. 122, 144307 (2005)]. The photodissociation spectrum consists of a broadband and a number of sharp peaks. For SiH2 and SiD2, the sharp peaks correspond to the resonance structure of the vibrational levels of the B̃ state and the broadbands are nearly independent of the photon energy. The broadband for SiHD increases steeply with the photon energy above 30000cm−1. The flux leaving the computational grid for SiH2 and SiD2 consists of at least two components, whereas that for SiHD consists of only a faster component. These large isotope effects were discussed based on the valley to the dissociation channel on PES and the difference in the position of the initial wave packet for three isotopomers.
Piezoelectric property of an epitaxial lead titanate thin film deposited by the hydrothermal method
Authors: Morita Takeshi , Cho Yasuo
Published: March 2006

A PbTiO3 epitaxial thin film was deposited at 150°C at a thickness of 430nm. The domain structure was composed of c domain and small amount of a domain. The DE hysteresis curve and piezoelectric strain curve were asymmetrical because the initial domain structure was stable and difficult to reverse perfectly with an external electric field. The strain has exceptional linearity, and the d33eff coefficient was found to be 97pC∕N, which is larger than the theoretical value.
Electronic control of the polarization of light emitted by polariton lasers
Authors: Malpuech G. , Glazov M. M. , Shelykh I. A. , Bigenwald P. , Kavokin K. V.
Published: March 2006

We propose a mechanism of electronic control of the polarization of the light emitted by polariton lasers. An electric field applied along the growth axis of the microcavity splits the ground polariton state into [110] and [1–1¯0] polarized components. We perform kinetic simulations which show that above a pumping threshold, a condensate of exciton polaritons is formed at the lowest-energy state. In this regime, the emission of the polariton laser is either [110] or [1–1¯0] linearly polarized depending on the direction of the applied field.
Superconductivity of nanometer-size Pb islands studied by low-temperature scanning tunneling microscopy
Authors: Nishio Takahiro , Ono Masanori , Eguchi Toyoaki , Sakata Hideaki , Hasegawa Yukio
Published: March 2006

Using a low-temperature (1.2K) scanning tunneling microscopy, the tunneling spectra showing the superconducting gap was taken on Pb island structures, whose dimension ranges from 80 to 300nm in diameter and 7–12 monolayers in thickness. There is no considerable spatial variation in the tunneling spectra taken on a single island regardless of local geometry (center or peripheral) and thickness of the measured sites. The superconducting gap increases with the island size, and the size dependence is enhanced at higher temperature (3.9K). The behavior of the gap is explained qualitatively by considering the superconducting fluctuation in the small islands.
Extraordinary stability of anisotropic femtosecond direct-written structures embedded in silica glass
Authors: Bricchi Erica , Kazansky Peter G.
Published: March 2006

In this letter we report the different response to temperature displayed by isotropic femtosecond written structures (type I_fs), and anisotropic ones (type II_fs), which are characterized by the presence of a self-assembled subwavelength periodic structure within the irradiated volume. We observe that the anisotropic structures display an extraordinary annealing behavior, namely, their photoinduced change in refractive index increases with the annealing temperature. We explain our experimental results with a theoretical model.
Controllable room-temperature metallic quantum dot
Authors: Bitton L. , Frydman A.
Published: March 2006

We demonstrate a technique for fabricating a controllable metallic dot coupled to metallic electrodes. This techniques enables one to explore the current-voltage characteristics while varying the distance between the dot and the leads. The fabrication technique combines atomic force microscope nanoscribing and nanomanipulation as well as electrochemical methods and enables very fine dot-lead coupling control. The measured current-voltage curves exhibit stable single-charge phenomena such as Coulomb blockade and Coulomb staircase which are clearly observed even at room temperature. This technique may provide an opportunity to study single electron charging effects in regimes that are currently unaccessible.
Admittance of CdS nanowires embedded in porous alumina template
Authors: Varfolomeev A. , Zaretsky D. , Pokalyakin V. , Tereshin S. , Pramanik S. , Bandyopadhyay S.
Published: March 2006

CdS nanowires of 10nm diameter, electrodeposited in porous alumina films, had shown a conductance bistability in the past [Appl. Phys. Lett. 76, 460 (2000)]. The conductance has a high (ON) and a low (OFF) state. In the ON state, different sets of nanowires display qualitatively different relation between the conductance and capacitance. We propose a model to explain this anomalous behavior. Based on this model, we predict that the inelastic mean free path of electrons in the nanowires is 3–3.5nm at room temperature. This short mean free path may be a consequence of acoustic phonon confinement.