bluuebunny/crossref_metadata_2025 huggingface dataset:
The α1L‐adrenoceptor is an alternative phenotype of the α1A‐adrenoceptor
Authors: Nelson C P
Published: June 2008

Despite over two decades of research, the molecular identity of the α1L‐adrenoceptor phenotype has remained elusive. In this issue of theBJP, Grayet al.(2008) provide persuasive evidence that thein vivoα1L‐adrenoceptor phenotype requires the expression of the α1A‐adrenoceptor gene. They have shown that in mice lacking the functional α1A‐adrenoceptor gene, α1L‐mediated responses to noradrenaline in prostate smooth muscle are substantially attenuated. These findings support earlier evidence that the α1L‐adrenoceptor profile represents a functional phenotype of the α1A‐adrenoceptor gene product, but additional cell background‐dependent factors must act in concert with the α1A‐adrenoceptor protein to determine whether an α1L‐ or a classical α1A‐adrenoceptor profile is expressed. The challenge remains to establish the nature of these cellular factors and the mechanism(s) by which they influence G‐protein‐coupled receptor pharmacology.

British Journal of Pharmacology(2008)155, 1–3; doi:fn1; published online 23 June 2008
Comparative Enumeration Gene Expression
Authors: Varuzza Leonardo , Pereira Carlos
Published: June 2008

This paper is about differential gene expression measured by transcript counting methods such as SAGE or MPSS. It introduces two significance tests for detection of differential expressed tags: frequentist and Bayesian. Under the frequentist view, it is proposed a test that computes the critical level as a function of each tag total frequency. Under the Bayesian view the Full Bayesian Significance Test is used considering the logistic normal distribution. The two proposed significance levels, the frequentist and the Bayesian, are compared for a data set with four libraries. The linking function between them is a Beta distribution function with mean 0.39 and standard deviation 0.30.
Covalent immobilization of Drosophila acetylcholinesterase for biosensor applications
Authors: Barshan‐Tashnizi Mohammad , Ahmadian Shahin , Niknam Kaveh , Torabi Seyed‐Fakhreddin , Ranaei‐Siadat Seyed‐Omid
Published: June 2008

The synthesized cDNA coding for AChE (acetylcholinesterase) was subcloned in pENTR™/D‐TOPO® plasmid and expressed using baculovirus expression vector and Sf9 insect cells as host. Purified enzyme (specific activity 36374 μmol·min−1·mg−1) was immobilized on pre‐activated perlite (a porous silica matrix) by silanization and glutaraldehyde treatment. The total enzyme immobilized was then measured, and total and specific activity of immobilized AChE was compared with that of soluble enzyme. Using this perlite support not only resulted in a great amount of maintained immobilized enzyme activity (more than 70%, specific activity 26238 μmol·min−1·mg−1), but also significantly improved stability against temperature (8.7‐ and 17.7‐fold at 50 and 60 °C respectively), urea (2.7‐fold) and acetonitrile (1.7‐fold). Kinetic studies showed that the Km value for immobilized enzyme is very similar to the soluble one (0.088 and 0.081 mM respectively). In addition, immobilized enzymes retained 80% of their initial activity after 16 consecutive reactor batch cycles. A comparison of the inhibitory effect of paraoxon on soluble and immobilized AChE showed that immobilization increased the linearity of the inhibition plot particularly in the range 0.1 nM–0.1 μM.
Dipeptidyl-peptidase I does not functionally compensate for the loss of tripeptidyl-peptidase I in the neurodegenerative disease late-infantile neuronal ceroid lipofuscinosis
Authors: Kim Kwi-Hye , Pham Christine T. , Sleat David E. , Lobel Peter
Published: June 2008

LINCL (late-infantile neuronal ceroid lipofuscinosis) is a fatal neurodegenerative disease resulting from mutations in the gene encoding the lysosomal protease TPPI (tripeptidyl-peptidase I). TPPI is expressed ubiquitously throughout the body but disease appears restricted to the brain. One explanation for the absence of peripheral pathology is that in tissues other than brain, other proteases may compensate for the loss of TPPI. One such candidate is another lysosomal aminopeptidase, DPPI (dipeptidyl-peptidase I), which appears to have overlapping substrate specificity with TPPI and is expressed at relatively low levels in brain. Compensation for the loss of TPPI by DPPI may have therapeutic implications for LINCL and, in the present study, we have investigated this possibility using mouse genetic models. Our rationale was that if DPPI could compensate for the loss of TPPI in peripheral tissues, then its absence should exacerbate disease in an LINCL mouse model but, conversely, increased CNS (central nervous system) expression of DPPI should ameliorate disease. By comparing TPPI and DPPI single mutants with a double mutant lacking both proteases, we found that the loss of DPPI had no effect on accumulation of storage material, disease severity or lifespan of the LINCL mouse. Transgenic expression of DPPI resulted in a ∼2-fold increase in DPPI activity in the brain, but this had no significant effect on survival of the LINCL mouse. These results together indicate that DPPI cannot functionally compensate for the loss of TPPI. Therapeutic approaches to increase neuronal expression of DPPI are therefore unlikely to be effective for treatment of LINCL.
Probability distributions of molecular observables computed from Markov models
Authors: Noé Frank
Published: June 2008

Molecular dynamics (MD) simulations can be used to estimate transition rates between conformational substates of the simulated molecule. Such an estimation is associated with statistical uncertainty, which depends on the number of observed transitions. In turn, it induces uncertainties in any property computed from the simulation, such as free energy differences or the time scales involved in the system’s kinetics. Assessing these uncertainties is essential for testing the reliability of a given observation and also to plan further simulations in such a way that the most serious uncertainties will be reduced with minimal effort. Here, a rigorous statistical method is proposed to approximate the complete statistical distribution of any observable of an MD simulation provided that one can identify conformational substates such that the transition process between them may be modeled with a memoryless jump process, i.e., Markov or Master equation dynamics. The method is based on sampling the statistical distribution of Markov transition matrices that is induced by the observed transition events. It allows physically meaningful constraints to be included, such as sampling only matrices that fulfill detailed balance, or matrices that produce a predefined equilibrium distribution of states. The method is illustrated on μs MD simulations of a hexapeptide for which the distributions and uncertainties of the free energy differences between conformations, the transition matrix elements, and the transition matrix eigenvalues are estimated. It is found that both constraints, detailed balance and predefined equilibrium distribution, can significantly reduce the uncertainty of some observables.
Stokesian dynamics of close particles
Authors: Ekiel-Jeżewska Maria L. , Gubiec Tomasz , Szymczak P.
Published: June 2008

Stokesian dynamics simulations of close particles are reported, taking into account lubrication forces and many-body hydrodynamic interactions between spheres. A periodic trajectory of three particles maintaining a permanent proximity to each other has been found and analyzed. This solution is used as a benchmark to study the accuracy and stability of various numerical integration schemes. In particular, different methods of preventing unphysical overlaps of the particles are considered and potential artifacts discussed.
Explosive cavitation in superheated liquid argon
Authors: Vinogradov V. E. , Pavlov P. A. , Baidakov V. G.
Published: June 2008

The kinetics of explosive boiling-up of liquid argon has been investigated at negative pressures created by the reflection of a compression pulse 3–5μs long from the free surface of a liquid by the method of liquid pulse heating on a thin platinum wire (with a rate of temperature increase of about 1K∕μs). The limiting superheats T* (stretches p*), the effective nucleation rate J*, and the derivative GT=(dlnJ∕dT)T=T* have been determined by experimental data on the thermal perturbation of a wire probe and the results of solution of the problem on the initial stage of explosive boiling-up of a liquid. The experimental data are compared with homogeneous nucleation theory.
Application of magnetically perturbed time-dependent density functional theory to magnetic circular dichroism. II. Calculation of A terms
Authors: Seth Michael , Krykunov Mykhaylo , Ziegler Tom , Autschbach Jochen
Published: June 2008

The magnetically perturbed time-dependent density functional theory is used to derive equations for the magnetic circular dichroism (MCD) of degenerate transitions of closed shell molecules. The MCD of this type of transition can be divided into two contributions. The dominant contribution is usually that from A terms that arise because of the breaking of the degeneracy of the excited state in the presence of the magnetic field. The second contribution comes from B terms that arise because of the perturbation of the transition dipole by the magnetic field. The formalism is applied to ten tetrahedral d0 transition metal oxy- and thioanions. The MCD parameters of these systems are reproduced quite well by the calculations. Simulated spectra derived from the calculated parameters are in good agreement with the observed spectra.
The variational explicit polarization potential and analytical first derivative of energy: Towards a next generation force field
Authors: Xie Wangshen , Song Lingchun , Truhlar Donald G. , Gao Jiali
Published: June 2008

A previous article proposed an electronic structure-based polarizable potential, called the explicit polarization (X-POL) potential, to treat many-body polarization and charge delocalization effects in polypeptides. Here, we present a variational version of the X-POL potential, in which the wave function of the entire molecular system is variationally optimized to yield the minimum total electronic energy. This allows the calculation of analytic gradients, a necessity for efficient molecular dynamics simulations. In this paper, the detailed derivations of the Fock matrix and analytic force are presented and discussed. The calculations involve a double self-consistent-field procedure in which the wave function of each fragment is self-consistently optimized in the presence of other fragments, and in addition the polarization of the entire system is self-consistently optimized. The variational X-POL potential has been implemented in the Chemistry at Harvard Molecular Mechanics (CHARMM) package and tested successfully for small model compounds.
The emergence of vascular design in three dimensions
Authors: Kim S. , Lorente S. , Bejan A. , Miller W. , Morse J.
Published: June 2008

Nature shows that fluids bathe the animal body as trees matched canopy to canopy. The entering streams invade the body as river deltas and the reconstituted streams sweep and exit the body as river basins. Why should this be so? Why is animal vascularization not based on arrays of parallel channels, as in modern heat exchangers? In this paper, we rely on constructal theory to show that the flow architecture that provides greatest access from point to volume and from volume to point is the three-dimensional compounding of trees matched canopy to canopy. This three-dimensional tree architecture is deduced, not assumed. Its flow performance is evaluated at every step relative to the performance of equivalent architectures with parallel channels. This paper also shows that the dendritic design must become more complex (with more levels of branching) as the volume inhabited by the flow design increases. The transition from designs with p branching levels to p+1 levels occurs abruptly as the available flow volume increases. This fundamental development has implications not only in evolutionary animal design but also in animal tissue modeling and the design of new vascular (smart) materials with volumetric functionalities such as self-cooling and self-healing.
Gaussian distribution of inhomogeneous barrier height in Al/SiO2/p-Si Schottky diodes
Authors: Yıldız D. E. , Altındal Ş. , Kanbur H.
Published: June 2008

The forward and reverse bias current-voltage (I-V) characteristics of Al/SiO2/p-Si (metal-insulator-semiconductor) type Schottky diodes (SDs) were measured in the temperature range of 200–400 K. Evaluation of the experimental I-V data reveals a decrease in ΦB0 and Rs but an increase in n, with a decrease in temperature. To explain this behavior of ΦB0 with temperature, we have reported a modification which included n and the tunneling parameter αχ1/2δ in the expression of reverse saturation current I0. Thus, a corrected effective barrier height ΦB eff(I-V) vs T has a negative temperature coefficient (α≈−5×10−4 eV/K), and it is in good agreement with α=−4.73×10−4 eV/K of Si band gap. Such behavior of Rs estimated from Cheung’s method could be expected for semiconductors in the temperature region, where there is no carrier freezing out, which is non-negligible at low temperatures. Also, there is a linear correlation between ΦB0(I-V) and n due to the inhomogeneities of the barrier heights (BHs). The conventional activation energy (Ea) plot exhibits nonlinearity below 320 K with the linear portion corresponding to Ea of 0.275 eV. An A∗ value of 1.45×10−5 A cm−2 K−2,which is much lower than the known value of 32 A cm−2 K−2 for p-type Si, is determined from the intercept at the ordinate of this experimental plot. Such behavior is attributed to Schottky barrier inhomogeneities by assuming a Gaussian distribution (GD) of BHs due to BH inhomogeneities that prevail at the interface. We attempted to draw a ΦB0 vs q/2kT plot to obtain evidence of a GD of the BHs, and the values of Φ¯B0=1.136 eV and σ0=0.159 V for the mean BH and standard deviation at zero bias have been obtained from this plot. Therefore, the modified ln (I0/T2)−q2σ02/2k2T2 vs q/kT plot gives Φ¯B0 and A∗ values of 1.138 eV and 37.23 A cm−2 K−2, respectively, without using the temperature coefficient of the BH. This A∗ value of 37.23 A cm−2 K−2 is very close to the theoretical value of 32 A K−2 cm−2 for p-type Si. Therefore, it has been concluded that the temperature dependence of the forward bias I-V characteristics of the Al/SiO2/p-Si SDs can be successfully explained based on the thermionic emission mechanism with a GD of the BHs.
Modification of the anomalous optical transitions in multilayer AlGaN-based nanoheterostructure using a nonbonding laser lift-off technique
Authors: Elgawadi Amal , Krasinski Jerzy , Gainer Gordon , Usikov Alexander , Dmitriev Vladimir
Published: June 2008

We present a study of the effect of the strain on the anomalous temperature dependence of the photoluminescence (PL) transition energy of three-nanolayer AlxGa1−xN nanoheterostructur∕GaN (0<x⩽0.29) grown on sapphire substrate by hydride vapor phase epitaxy. We proved that this effect is due to the lattice constant and thermal coefficient mismatches among the various layers, especially between the sapphire and GaN epilayers. We separated the nanoheterostructure from its sapphire substrate using a nonbonding laser lift-off technique which we described in details elsewhere. The separation caused the PL peak positions to shift, which proves that a change in the strain took place after the separation and that the mismatches in the physical parameters between the sapphire and the GaN play an essential role in the anomalous behavior. Furthermore, we observed a much better agreement of the transition energy of the temperature dependent PL with the Varshni equation, after the separation.
Langevin dynamics for rigid bodies of arbitrary shape
Authors: Sun Xiuquan , Lin Teng , Gezelter J. Daniel
Published: June 2008

We present an algorithm for carrying out Langevin dynamics simulations on complex rigid bodies by incorporating the hydrodynamic resistance tensors for arbitrary shapes into an advanced rotational integration scheme. The integrator gives quantitative agreement with both analytic and approximate hydrodynamic theories for a number of model rigid bodies and works well at reproducing the solute dynamical properties (diffusion constants and orientational relaxation times) obtained from explicitly solvated simulations.
Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations
Authors: Lei Hongxing , Wu Chun , Wang Zhi-Xiang , Zhou Yaoqi , Duan Yong
Published: June 2008

Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0μs) and two sets of replica exchange (each to 200.0ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80Å Cα root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8Å Cα RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation. In addition to the mechanistic studies, an ab initio structure prediction was also conducted based on both the physical energy and a statistical potential. Based on the lowest physical energy, the predicted structure was 2.0Å Cα RMSD away from the experimentally determined structure.
Initial nucleation of AlN grown directly on sapphire substrates by metal-organic vapor phase epitaxy
Authors: Banal Ryan G. , Funato Mitsuru , Kawakami Yoichi
Published: June 2008

AlN layers were grown directly on sapphire (0001) substrates using three different growth sequences based on metal-organic vapor phase epitaxy with an emphasis on initial nucleation processes. These three methods were simultaneous, alternating supply of aluminum and nitrogen sources, and a combination of the two. In all the methods, nucleation was initiated by three-dimensional (3D) islands with a typical diameter of ∼20nm. Enhanced migration by the alternating source supply caused highly 3D AlN ridge structures at the sapphire molecular steps. These ridge structures prevented a flattened AlN surface and, in addition, moderated lattice relaxation, suggesting the importance of controlling the initial nucleation in determining the film’s properties. In fact, the hybridized method, derived from the simultaneous and alternating supply methods, was able to control the initial nucleation, and provided the best film quality; the 600-nm-thick AlN grown by this method had an atomically flat surface free of pits and particles, and the x-ray diffraction line widths were ∼45 and ∼250arcsec for the (0002) and (101¯2) planes, respectively.
Rarefied gas flow over an in-line array of circular cylinders
Authors: Taguchi Satoshi , Charrier Pierre
Published: June 2008

A steady rarefied gas flow through periodic porous media kept at a uniform temperature is considered on the basis of the Bhatnagar–Gross–Krook equation and the diffuse reflection condition on the solid boundary. Under the assumption that the period is much smaller than the length scale of variation of the global pressure distribution, a macroscopic fluid model describing the pressure distribution and the mass flux of the gas in the medium is derived by the homogenization previously proposed by Charrier and Dubroca [Multiscale Model. Simul. 2, 124 (2003)]. The effective diffusion coefficient contained in the model is constructed numerically as a function of the Knudsen number, in the case of the medium consisting of an in-line array of circular cylinders, with the help of the numerical analysis of a rarefied gas flow in an infinite expanse of the cylinder array driven by a uniform small pressure gradient. An application of the model to an isothermal flow in a porous slab induced by a pressure difference is presented.
Enhanced terahertz radiation from high stacking fault density nonpolar GaN
Authors: Metcalfe Grace D. , Shen Hongen , Wraback Michael , Hirai Asako , Wu Feng , Speck James S.
Published: June 2008

Terahertz emission from high stacking fault density m-GaN has been observed using ultrafast pulse excitation. The terahertz signal exhibits a 360° periodicity with sample rotation and a polarity flip at 180°, characteristic of real carrier transport in an in-plane electric field parallel to the c axis induced by stacking fault (SF)-terminated internal polarization at wurtzite domain boundaries. The terahertz emission can be enhanced by several times relative to that from a SF-free m-GaN sample, for which the terahertz signal emanates from surface surge currents and diffusion-driven carrier transport normal to the surface and is independent of the c-axis orientation.
Ca
(
Al
H
4
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2
, CaAlH5, and CaH2+6LiBH4: Calculated dehydrogenation enthalpy, including zero point energy, and the structure of the phonon spectra
Authors: Marashdeh Ali , Frankcombe Terry J.
Published: June 2008

The dehydrogenation enthalpies of Ca(AlH4)2, CaAlH5, and CaH2+6LiBH4 have been calculated using density functional theory calculations at the generalized gradient approximation level. Harmonic phonon zero point energy (ZPE) corrections have been included using Parlinski’s direct method. The dehydrogenation of Ca(AlH4)2 is exothermic, indicating a metastable hydride. Calculations for CaAlH5 including ZPE effects indicate that it is not stable enough for a hydrogen storage system operating near ambient conditions. The destabilized combination of LiBH4 with CaH2 is a promising system after ZPE-corrected enthalpy calculations. The calculations confirm that including ZPE effects in the harmonic approximation for the dehydrogenation of Ca(AlH4)2, CaAlH5, and CaH2+6LiBH4 has a significant effect on the calculated reaction enthalpy. The contribution of ZPE to the dehydrogenation enthalpies of Ca(AlH4)2 and CaAlH5 calculated by the direct method phonon analysis was compared to that calculated by the frozen-phonon method. The crystal structure of CaAlH5 is presented in the more useful standard setting of P21∕c symmetry and the phonon density of states of CaAlH5, significantly different to other common complex metal hydrides, is rationalized.
A three-terminal spin filter induced by spin-orbit interaction in the presence of an antidot
Authors: Yamamoto Masayuki , Kramer Bernhard
Published: June 2008

The generation of a spin-polarized electric current is one of the key issues in the field of semiconductor spintronics. We show by numerical simulation that a three-terminal conductor with an antidot potential at the junction can be used as a spin filter. In addition, one can control the direction of spin polarization by changing the Fermi energy with respect to the height of antidot potential. This is understood by the interplay between spin-orbit coupling and the curvature of the potential. We also investigate the effect of disorder and an asymmetric confinement potential in order to clarify the validity of the spin filter.
Surface-plasmon enhanced transparent electrodes in organic photovoltaics
Authors: Reilly Thomas H. , van de Lagemaat Jao , Tenent Robert C. , Morfa Anthony J. , Rowlen Kathy L.
Published: June 2008

Random silver nanohole films were created through colloidal lithography techniques and metal vapor deposition. The transparent electrodes were characterized by uv-visible spectroscopy and incorporated into an organic solar cell. The test cells were evaluated for solar power-conversion efficiency and incident photon-to-current conversion efficiency. The incident photon-to-current conversion efficiency spectra displayed evidence that a nanohole film with 92nm diameter holes induces surface-plasmon-enhanced photoconversion. The nanohole silver films demonstrate a promising route to removing the indium tin oxide transparent electrode that is ubiquitous in organic optoelectronics.
Negative refraction with high transmission at visible and near-infrared wavelengths
Authors: Yan Changchun , Cui Yiping , Wang Qiong , Zhuo Shichuang , Li Jianxin
Published: June 2008

A left-handed material, a metal waveguide with arrays of metal rods within it, is investigated in this letter. The simulation results have shown that the refractive indices are negative between 512 and 898nm, while the negative-index band with high transmission ranges roughly from 672to798nm. This is an effective method to the realization of negative refraction at visible frequencies. The mechanism of resonance has been revealed by simulating the distributions of induced current in a unit cell. A wedge-shaped structure has also been designed to provide direct evidence for the negative refraction behavior.
Structural phase transitions in high-pressure wurtzite to rocksalt phase in GaN and SiC
Authors: Xiao H. Y. , Gao F. , Wang L. M. , Zu X. T. , Zhang Y. , Weber W. J.
Published: June 2008

Ab initio molecular dynamics simulations are employed to study the atomistic mechanisms and pathways of high-pressure phase transformation in GaN and SiC. Our simulations bring a fundamental level of understanding of the wurtzite to rocksalt phase transformation that undergoes inhomogeneous displacements via a tetragonal atomic configuration, and suggest that the transition path may be independent of the presence of d electrons on the cation in GaN. The discrepancies between experimental and theoretical studies of transition paths are discussed.
Energy state distributions of the Pb centers at the (100), (110), and (111) Si∕SiO2 interfaces investigated by Laplace deep level transient spectroscopy
Authors: Dobaczewski L. , Bernardini S. , Kruszewski P. , Hurley P. K. , Markevich V. P. , Hawkins I. D. , Peaker A. R.
Published: June 2008

The energy distribution of the Pb centers at the Si∕SiO2 interface has been determined using isothermal laplace deep level transient spectroscopy. For the (111) and (110) interface orientations, the distributions are similar and centered at 0.38eV below the silicon conduction band. This is consistent with only Pb0 states being present. For the (100) orientation, two types of the interface states are observed: one similar to the (111) and (110) orientations while the other has a negative-U character in which the emission rate versus surface potential dependence is qualitatively different from that observed for Pb0 and is presumed to be Pb1.
On the formation of complexes between Mn acceptors and hydrogen in GaP and GaMnP alloys
Authors: Clerjaud B. , Wasik D. , Bouanani-Rahbi R. , Strzelecka G. , Hruban A. , Kamińska M.
Published: June 2008

The observation of the local vibrational stretching mode of the manganese-hydrogen complex in GaP by infrared spectroscopy is reported. It is shown that when manganese is in the impurity regime, the complex only forms in very small concentrations in samples in which the Fermi level is about 0.3 eV above the valence band maximum. The reasons for this behavior are analyzed. It is argued that in GaMnP alloys, the formation of manganese-hydrogen complexes is more likely than in the impurity regime, but a full passivation of the manganese by hydrogen is not possible. However, the fraction of passivated manganese can impede ferromagnetism.
Thermodynamic behavior and structural properties of an aqueous sodium chloride solution upon supercooling
Authors: Corradini D. , Gallo P. , Rovere M.
Published: June 2008

We present the results of a molecular dynamics simulation study of thermodynamic and structural properties upon supercooling of a low concentration sodium chloride solution in TIP4P water and the comparison with the corresponding bulk quantities. We study the isotherms and the isochores for both the aqueous solution and bulk water. The comparison of the phase diagrams shows that thermodynamic properties of the solution are not merely shifted with respect to the bulk. Moreover, from the analysis of the thermodynamic curves, both the spinodal line and the temperatures of maximum density curve can be calculated. The spinodal line appears not to be influenced by the presence of ions at the chosen concentration, while the temperatures of maximum density curve displays both a mild shift in temperature and a shape modification with respect to bulk. Signatures of the presence of a liquid-liquid critical point are found in the aqueous solution. By analyzing the water-ion radial distribution functions of the aqueous solution, we observe that upon changing density, structural modifications appear close to the spinodal. For low temperatures, additional modifications appear also for densities close to that corresponding to a low density configurational energy minimum.
Molecular modeling of surfactant covered oil-water interfaces: Dynamics, microstructure, and barrier for mass transport
Authors: Gupta Ashish , Chauhan Anuj , Kopelevich Dmitry I.
Published: June 2008

Mass transport across surfactant-covered oil-water interfaces of microemulsions plays an important role in numerous applications. In the current work, we use coarse-grained molecular dynamics simulations to investigate model systems containing flat hexadecane-water interfaces covered by monolayers of nonionic surfactants of various lengths. Several properties of the surfactant monolayers relevant to the mass transport are considered, including the monolayer microstructure, dynamics, and a free energy barrier to the solute transport. It is observed that the dominant contribution of a surfactant monolayer to the free energy barrier is a steric repulsion caused by a local density increase inside the monolayer. The local densities, and hence the free energy barriers, are larger for monolayers composed of longer surfactants. Since it is likely that the solute transport mechanism involves a sequence of jumps between short-lived pores within a monolayer, we perform a detailed analysis of structure, size, and lifetime of these pores. We demonstrate that the pore statistics is consistent with predictions of percolation theory and apply this theory to identify the characteristic length scale of the monolayer microstructure. The obtained pore structures are sensitive to minute changes of surfactant configurations occurring on the picosecond time scale. To reduce this sensitivity, the pores are averaged over short time intervals. The optimal duration of these time intervals is estimated from analysis of dynamics of pores with diameters comparable to or exceeding the characteristic percolation length scale. The developed approach allows one to filter out transient events of the pore dynamics and to focus on events leading to substantial changes of the monolayer microstructure.
Laser-induced focused ultrasound for nondestructive testing and evaluation
Authors: Kozhushko Victor V. , Hess Peter
Published: June 2008

Focused ultrasound pulses generated by photoacoustic transformation at a metal surface immersed in water possess a pronounced compression phase on the nanosecond time scale. For 8 ns laser pump pulses, the spectrum of the initially generated ultrasonic pulse covered a frequency range between 0.1 and 150 MHz. A concave spherical geometry of the light-absorbing metal surface can be used to achieve focusing. In the present experiments a conical ultrasound beam was directed at a solid glass plate or silicon wafer, where the tilt of the normal of the metal mirror defined the efficiency of mode conversion at the water-solid interface. Depending on the configuration, focused bulk waves as well as Rayleigh and Lamb waves could be launched in the sample with this setup. The laser probe-beam-deflection method was employed for local detection of elastic disturbances at the sample surface. Due to the nonlinear elastic response of water and harmonics generation, frequencies >100 MHz were realized, despite a strong attenuation in this frequency range. Gradual increase of the laser power density from 5 to 14 MW/cm2 led to shock formation in the compressive pressure pulse in water and shortening of the Rayleigh pulse induced at the surface of the glass plate. The observed transient surface profiles were highly sensitive to nearby mechanical discontinuities such as a microcrack in glass or an edge discontinuity in silicon. Therefore, laser-induced focused ultrasound seems to be a very promising method of accomplishing diverse tasks of nondestructive evaluation.
Simple white organic light emitting diodes with improved color stability and efficiency using phosphorescent and fluorescent emitters
Authors: Baek Heume-Il , Lee Changhee
Published: June 2008

White organic light emitting diodes (WOLEDs) with both phosphorescent and fluorescent emitting layers (EML) usually adopt an interlayer between them to achieve high efficiency by preventing mutual quenching, but insertion of the interlayer causes a higher operating voltage as well as additional fabrication steps. Here, we demonstrate that simple-structure WOLEDs without an interlayer could be achieved using the combination of phosphor-sensitized-fluorescent red and phosphorescent blue EMLs. In addition, the main cause of the color shift with increasing current density was identified, and the color shift of the WOLED was successfully suppressed by properly balancing emission from the red and blue EMLs. Consequently, a maximum external quantum efficiency of 6.2% (a current efficiency of 14.3 cd/A) and very stable color coordinates of (0.32±0.01,0.42±0.002) were achieved. However, the elimination of an interlayer for the combination with a fluorescent blue EML causes about 50% decrease in the efficiency and a large change in the color coordinates with the driving current density.
Effects of collisions and finite ion temperature on the sheath structure of cylindrical probes in low-pressure electronegative discharges
Authors: Chung T. H.
Published: June 2008

The spatial distributions of electric potential and velocity and density of positive ions are calculated in the surroundings of a negatively biased cylindrical probe immersed in electronegative plasmas. The model equations are solved on the scale of the electron Debye length. The solutions provide the variation of plasma variables along the distance from the plasma bulk region to the probe surface. The control parameters are the ratio of the negative ion density to the electron density, the ratios of the electron temperature to the positive and negative ion temperatures, and the ratio of the rate coefficient for the momentum transfer collision to that for the ionization. Especially, the effects of collision and finite temperature of positive ions are investigated. As the positive ion temperature increases, the sheath width decreases and the positive ion current collected by the probe increases. As the ratio of the rate coefficient for the momentum transfer collision to that for the ionization increases, the sheath edge approaches the plasma region, and the positive ion current to the probe decreases.
Analysis of S-rich CuIn(S,Se)2 layers for photovoltaic applications: Influence of the sulfurization temperature on the crystalline properties of electrodeposited and sulfurized CuInSe2 precursors
Authors: Izquierdo-Roca V. , Pérez-Rodríguez A. , Morante J. R. , Álvarez-García J. , Calvo-Barrio L. , Bermudez V. , Grand P. P. , Parissi L. , Broussillon C. , Kerrec O.
Published: June 2008

This paper reports the microstructural analysis of S-rich CuIn(S,Se)2 layers produced by electrodeposition of CuInSe2 precursors and annealing under sulfurizing conditions as a function of the temperature of sulfurization. The characterization of the layers by Raman scattering, scanning electron microscopy, Auger electron spectroscopy, and XRD techniques has allowed observation of the strong dependence of the crystalline quality of these layers on the sulfurization temperature: Higher sulfurization temperatures lead to films with improved crystallinity, larger average grain size, and lower density of structural defects. However, it also favors the formation of a thicker MoS2 interphase layer between the CuInS2 absorber layer and the Mo back contact. Decreasing the temperature of sulfurization leads to a significant decrease in the thickness of this intermediate layer and is also accompanied by significant changes in the composition of the interface region between the absorber and the MoS2 layer, which becomes Cu rich. The characterization of devices fabricated with these absorbers corroborates the significant impact of all these features on device parameters as the open circuit voltage and fill factor that determine the efficiency of the solar cells.
Physical origin of suppressed effective work function modulation at boron segregated NiSi∕SiON interface
Authors: Tsuchiya Yoshinori , Yoshiki Masahiko , Sekine Katsuyuki , Saito Tomohiro , Nakajima Kazuaki , Aoyama Tomonori , Koga Junji , Nishiyama Akira , Koyama Masato , Ogawa Masaki , Zaima Shigeaki
Published: June 2008

In order to elucidate influences of nitrogen on the change of effective work function (ΔΦeff) with impurity segregation, we systematically investigated the ΔΦeff at arsenic (As) and boron (B) segregated NiSi∕SiO2 and NiSi∕SiON interfaces. These impurities are introduced to NiSi∕SiON (SiO2) interfaces by using the conventional predoping process. It was found that increase in Φeff with B segregation is suppressed as low as ΔΦeff=+0.05eV at NiSi∕SiON interface compared to ΔΦeff=+0.14eV at NiSi∕SiO2 interface, though there is little change in decrease of Φeff with As segregation. Moreover, the opposite (negative) Φeff modulation occurred at NiSi∕SiON interface in the case of low B dose. We also performed the B postdoping process, in which B atoms were introduced after Ni silicide gate formation with lower thermal process (∼500°C) than conventional predoping process (∼1000°C). A large ΔΦeff of +0.2eV occurred even at NiSi∕SiON system in the postdoping process. Based on the results of backside x-ray photoelectron spectroscopy (XPS), we revealed that most of B atoms were segregated at SiON side of the interface, which was similar to the case of NiSi∕SiO2 interface, and the B concentration increases with N ratio in SiON in the predoping process. The backside XPS analysis also clarified that the formation of thermally stable B–N bonds in SiON was suppressed in the case of the postdoping process compared to that in the predoping process. The degree of suppression of ΔΦeff is proportional to the B–N state intensity. From these experimental results, we conclude that generation of B–N bonds positively charged in SiON counteracts and suppresses the interface dipole effect of segregated B at NiSi∕SiON interface. The large ΔΦeff at the B postdoped NiSi∕SiON interface seems to be owing to low density of charged B–N bonds, because of suppression of B infiltration into SiON layer with low annealing temperature.
Lower-dimensional reductions of GL(M,C) self-dual Yang Mills equation: Solutions with break of wave profiles
Authors: Zenchuk A. I.
Published: June 2008

Any matrix self-dual-type S-integrable partial differential equation (PDE) possesses a family of lower-dimensional reductions represented by the matrix quasilinear first order PDEs solvable by the method of characteristics. These PDEs admit two types of particular solutions: (a) explicit solutions and (b) implicit solutions represented by a system of nondifferential equations. The latter solutions exhibit the break of wave profile. (2+1)- and (3+1)-dimensional GL(M,C) self-dual Yang–Mills equations have been considered as examples.
Subrepresentation semirings and an analog of 6j-symbols
Authors: Kwon Namhee , Sage Daniel S.
Published: June 2008

Let V be a complex representation of the compact group G. The subrepresentation semiring associated to V is the set of subrepresentations of the algebra of linear endomorphisms of V with operations induced by the matrix operations. The study of these semirings has been motivated by recent advances in materials science, in which the search for microstructure-independent exact relations for physical properties of composites has been reduced to the study of these semirings for the rotation group SO(3). In this case, the structure constants for subrepresentation semirings can be described explicitly in terms of the 6j-symbols familiar from the quantum theory of angular momentum. In this paper, we investigate subrepresentation semirings for the class of quasisimply reducible groups defined by Mackey [“Multiplicity free representations of finite groups,” Pac. J. Math. 8, 503 (1958)]. We introduce a new class of symbols called twisted 6j-symbols for these groups, and we explicitly calculate the structure constants for subrepresentation semirings in terms of these symbols. Moreover, we show that these symbols satisfy analog of the standard properties of classical 6j-symbols.
Effects of interadsorbate interactions on surface resistivity: Oxygen on sulfur-predosed Cu(100)
Authors: Liu Chang , Tobin R. G.
Published: June 2008

Measurements of surface resistivity as a function of coverage for oxygen adsorbed on sulfur-predosed Cu(100) films reveal two types of interactions between sulfur and oxygen: S–O repulsion and short-range suppression of the surface resistivity change induced by oxygen adsorption. The repulsive interaction causes oxygen atoms to first occupy adsorption sites far from the sulfur atoms, beyond second-nearest-neighbor sites, where the oxygen-induced surface resistivity is unaffected by sulfur. As a result the low-coverage variation of surface resistivity with oxygen coverage is indistinguishable from the linear dependence observed for oxygen on clean Cu(100). As the oxygen coverage increases, oxygen begins to occupy sites close to sulfur. At the nearest-neighbor sites, the resistivity change due to added oxygen is completely suppressed, and the sample resistance levels off, remaining unchanged even as oxygen continues to adsorb. This resistivity suppression may involve both a reduction of oxygen’s direct effect on the resistivity and an oxygen-induced reduction in the resistivity due to the already adsorbed sulfur. With increasing sulfur precoverage both the maximum resistivity change and the oxygen coverage at which the leveling occurs decrease, because the number of sites unaffected by sulfur is reduced. Both the sulfur-oxygen repulsion and the resistivity suppression presumably arise from a through-metal coupling involving adsorbate-induced modifications of the local electronic structure.
Tricritical behavior of the smectic-A to smectic-C phase transition in a liquid crystal mixture
Authors: Das Asok K. , Mukherjee Prabir K.
Published: June 2008

A phenomenological approach to the description of the smectic-A to smectic-C phase transition in a liquid crystal mixture is proposed. The problem of the first or second order transition is explored by means of the variation of the concentration. The influence of the concentration on this transition is discussed by varying the coupling between the concentration variable and the order parameters. We show that a tricritical point on the smectic-A to smectic-C phase transition line can be achieved under certain conditions. The theoretical prediction is found to be in good qualitative agreement with experimental results.
Theoretical consideration of bulk free-radical copolymerization with allowance for the preferential sorption of monomers into globular nanoreactors
Authors: Kuchanov S. I. , Pogodin S. G.
Published: June 2008

The thermodynamics of a globular solution of binary copolymer in two-component solvent is theoretically considered. Classification of phase diagrams of such a solution is performed by their topological appearance. Based on the thermodynamic theory, binary bulk free-radical copolymerization under low conversions is examined in systems where macroradicals being in globular conformational state represent isolated nanoreactors. The theoretical results achieved permit an explanation of all qualitative peculiarities observed experimentally under copolymerization in such anomalous systems.
Atomic approximation to the projection on electronic states in the Douglas-Kroll-Hess approach to the relativistic Kohn-Sham method
Authors: Matveev Alexei V. , Rösch Notker
Published: June 2008

We suggest an approximate relativistic model for economical all-electron calculations on molecular systems that exploits an atomic ansatz for the relativistic projection transformation. With such a choice, the projection transformation matrix is by definition both transferable and independent of the geometry. The formulation is flexible with regard to the level at which the projection transformation is approximated; we employ the free-particle Foldy–Wouthuysen and the second-order Douglas-Kroll-Hess variants. The (atomic) infinite-order decoupling scheme shows little effect on structural parameters in scalar-relativistic calculations; also, the use of a screened nuclear potential in the definition of the projection transformation shows hardly any effect in the context of the present work. Applications to structural and energetic parameters of various systems (diatomics AuH, AuCl, and Au2, two structural isomers of Ir4, and uranyl dication UO22+ solvated by 3-6 water ligands) show that the atomic approximation to the conventional second-order Douglas-Kroll-Hess projection (ADKH) transformation yields highly accurate results at substantial computational savings, in particular, when calculating energy derivatives of larger systems. The size-dependence of the intrinsic error of the ADKH method in extended systems of heavy elements is analyzed for the atomization energies of Pdn clusters (n⩽116).
Electromagnetic interactions of metallic reflection gratings with inner gap modification
Authors: Ma Y. G. , Ong C. K. , Rao X. S.
Published: June 2008

In this work the electromagnetic interactions in metallic reflection gratings of subwavelength periods were investigated. The gratings were modified by inner air gaps introduced between the metal slats and conducting ground plane. The Fabry–Pérot-like modes were excited within the grating slits (the cavities between adjacent metal slats), and depending on the gap width, the frequency locations as well as mode orders changed. Additional resonance modes in both evanescent and propagating types would be excited inside the introduced gap. They would interact with the fields inside the grating slits to form hybrid resonance modes in the gap-modified reflection gratings, i.e., mode coupling around the peripherals of the metal slabs. Such coupling interactions could produce a variety of modes and hybrid modes dependent on the sample’s dimensions and the incident wavelength. The unique electromagnetic functions of the gap-modified gratings were highlighted in the end for potential applications in devices.