bluuebunny/crossref_metadata_2025 huggingface dataset:
Absence of iron-regulatory protein Hfe results in hyperproliferation of retinal pigment epithelium: role of cystine/glutamate exchanger
Authors: Gnana-Prakasam Jaya P. , Thangaraju Muthusamy , Liu Kebin , Ha Yonju , Martin Pamela M. , Smith Sylvia B. , Ganapathy Vadivel
Published: September 2009

Haemochromatosis is an iron-overload disorder with age-dependent oxidative stress and dysfunction in a variety of tissues. Mutations in HFE (histocompatability leucocyte antigen class I-like protein involved in iron homoeostasis) are responsible for most cases of haemochromatosis. We demonstrated recently that HFE is expressed exclusively in the basal membrane of RPE (retinal pigment epithelium). In the present study, we used Hfe−/− mice to examine ferritin levels (an indirect readout for iron levels) and morphological changes in retina. We found increased ferritin accumulation in retina in 18-month-old, but not in 2-month-old, mice with considerable morphological damage compared with age-matched controls. The retinal phenotype included hypertrophy and hyperplasia of RPE. RPE cells isolated from Hfe−/− mice exhibited a hyperproliferative phenotype. We also compared the gene expression profile between wild-type and Hfe−/− RPE cells by microarray analysis. These studies showed that many cell cycle-related genes were differentially regulated in Hfe−/− RPE cells. One of the genes up-regulated in Hfe−/− RPE cells was Slc7a11 (where Slc is solute carrier) which codes for the ‘transporter proper’ xCT in the heterodimeric cystine/glutamate exchanger (xCT/4F2hc). This transporter plays a critical role in cellular glutathione status and cell-cycle progression. We confirmed the microarrray data by monitoring xCT mRNA levels by RT (reverse transcription)–PCR and also by measuring transport function. We also found increased levels of glutathione and the transcription factor/cell-cycle promoter AP1 (activator protein 1) in Hfe−/− RPE cells. Wild-type mouse RPE cells and human RPE cell lines, when loaded with iron by exposure to ferric ammonium citrate, showed increased expression and activity of xCT, reproducing the biochemical phenotype observed with Hfe−/− RPE cells.
A survey of proteins encoded by non-synonymous single nucleotide polymorphisms reveals a significant fraction with altered stability and activity
Authors: Allali-Hassani Abdellah , Wasney Gregory A. , Chau Irene , Hong Bum Soo , Senisterra Guillermo , Loppnau Peter , Shi Zhen , Moult John , Edwards Aled M. , Arrowsmith Cheryl H. , Park Hee Won , Schapira Matthieu , Vedadi Masoud
Published: September 2009

On average, each human gene has approximately four SNPs (single nucleotide polymorphisms) in the coding region, half of which are nsSNPs (non-synonymous SNPs) or missense SNPs. Current attention is focused on those that are known to perturb function and are strongly linked to disease. However, the vast majority of SNPs have not been investigated for the possibility of causing disease. We set out to assess the fraction of nsSNPs that encode proteins that have altered stability and activity, for this class of variants would be candidates to perturb cellular function. We tested the thermostability and, where possible, the catalytic activity for the most common variant (wild-type) and minor variants (total of 46 SNPs) for 16 human enzymes for which the three-dimensional structures were known. There were significant differences in the stability of almost half of the variants (48%) compared with their wild-type counterparts. The catalytic efficiency of approx. 14 variants was significantly altered, including several variants of human PKM2 (pyruvate kinase muscle 2). Two PKM2 variants, S437Y and E28K, also exhibited changes in their allosteric regulation compared with the wild-type enzyme. The high proportion of nsSNPs that affect protein stability and function, albeit subtly, underscores the need for experimental analysis of the diverse human proteome.
Conditions of endoplasmic reticulum stress stimulate lipid droplet formation in Saccharomyces cerevisiae
Authors: Fei Weihua , Wang Han , Fu Xin , Bielby Christopher , Yang Hongyuan
Published: September 2009

LDs (lipid droplets) are cellular organelles which can be found in nearly all eukaryotic cells. Despite their importance in cell biology, the mechanism underlying LD biogenesis remains largely unknown. In the present study we report that conditions of ER (endoplasmic reticulum) stress stimulate LD formation in Saccharomyces cerevisiae. We found that LDs accumulated in yeast mutants with compromised protein glycosylation or ER-associated protein degradation. Moreover, tunicamycin and Brefeldin A, agents which induce ER stress, were found to stimulate LD formation. In contrast, the restoration of protein glycosylation reduced LD accumulation. Interestingly, enhanced neutral lipids synthesis and LD formation under conditions of ER stress was not dependent on Ire1p. Lastly, we demonstrated that the absence of LDs did not compromise cell viability under ER stress. Our results suggest that although more LDs are produced, LDs are not essential to cell survival under ER stress.
Regulation of histidine-rich glycoprotein (HRG) function via plasmin-mediated proteolytic cleavage
Authors: Poon Ivan K. H. , Olsson Anna-Karin , Hulett Mark D. , Parish Christopher R.
Published: September 2009

The plasminogen/plasmin system is involved in a variety of normal physiological and pathological processes, including tissue remodelling, angiogenesis and tumour metastasis. Plasminogen activators and receptors for plasminogen/plasminogen activators are essential for the processing of plasminogen to form the active serine protease plasmin. Plasmin can in turn positively or negatively regulate further plasminogen activation via plasminmediated cleavage of receptors and activators. HRG (histidine-rich glycoprotein), a relatively abundant (approx. 100–150 μg/ml) plasma glycoprotein, has a multi-domain structure that can interact with many ligands, including Zn2+, heparin, HS (heparan sulfate) and plasminogen. HRG has been shown to function as an adaptor molecule to tether plasminogen to GAG (glycosaminoglycan)-bearing surfaces and to regulate plasminogen activation via various mechanisms. As HRG itself is sensitive to plasmin cleavage, the present study examines in detail the cleavage of human HRG by plasmin and the effect of this cleavage on various functions of HRG. HRG fragments, generated by plasmin cleavage, are held together by disulfide linkages and are not released from the molecule under non-reducing conditions. Plasmin-mediated cleavage partially inhibited HRG binding to cell surface HS, but enhanced HRG binding to necrotic cells and to plasminogen. However, both intact and plasmin-cleaved HRG enhanced the binding of plasminogen to heparin-coated surfaces to a similar extent. Furthermore, the presence of heparin, Zn2+ or acidic pH was found to protect HRG from plasmin cleavage. Thus proteolytic cleavage of HRG by plasmin may provide a feedback mechanism to regulate the effects of HRG on the plasminogen/plasmin system and other functions of HRG.
Analysis of the dual function of the ESCRT-III protein Snf7 in endocytic trafficking and in gene expression
Authors: Weiss Peter , Huppert Stefanie , Kölling Ralf
Published: September 2009

ESCRT (endosomal sorting complex required for transport)-III mediates the budding and scission of intralumenal vesicles into multivesicular endosomes in yeast. For the main ESCRT-III subunit Snf7, an additional role in activation of the transcription factor Rim101 (the ‘Rim pathway’) is now also firmly established. In the present study, we investigate how these two Snf7 functions are related to each other. By generating SNF7 mutations that severely affect endocytic trafficking, but leave the Rim pathway function intact, we show that the two functions of SNF7 can be separated genetically. We analysed in detail how the SNF7 mutations affect the interaction of Snf7 with its various binding partners. Although the interactions with proteins Rim13 and Rim20, necessary for the Rim-pathway-related functions, were not altered by the mutations, there was a strong effect on interactions with components of the ESCRT pathway. The interactions, as measured by co-immunoprecipitation, with the ESCRT-III subunits Vps20 and Vps24 were strongly increased by the mutations, whereas the interactions with proteins Vps4 and Bro1, acting downstream of ESCRT-III, were reduced. As Vps4 is required for disassembly of ESCRT-III these results suggest that ESCRT-III is more stable in our SNF7 mutants. In line with this notion, a higher fraction of mutant Snf7 protein was detected at the membrane. Upon a shift to alkaline pH, a stronger binding signal for virtually all interaction partners, except Vps4, was observed. This indicates that the ESCRT network at the endosomal membrane is more extensive under these conditions.
Human and mouse trace amine-associated receptor 1 have distinct pharmacology towards endogenous monoamines and imidazoline receptor ligands
Authors: Hu Liaoyuan A. , Zhou Tian , Ahn Jinwoo , Wang Shuli , Zhou Julia , HU Yi , Liu Qingyun
Published: September 2009

TAARs (trace amine-associated receptors) are G-protein-coupled receptors that respond to low abundance, endogenous amines such as tyramine and tryptamine, and represent potential targets for neuropsychiatric diseases. However, some members of this receptor subfamily either have no ligand identified or remain difficult to express and characterize using recombinant systems. In the present paper we report the successful expression of human and mouse TAAR1, and the characterization of their responses to various natural and synthetic agonists. In HEK (human embryonic kidney)-293/CRE-bla cells, mouse TAAR1 showed a robust response to trace amines as measured using either a cAMP assay or a β-lactamase reporter assay, whereas human TAAR1 showed a weaker, but still measurable, response. When certain fragments of human TAAR1 were replaced with the corresponding regions of mouse TAAR1, the chimaeric receptor showed a much stronger response in cAMP production. Examination of a series of agonists on these receptors revealed that the human and the chimaeric receptor are almost identical in pharmacology, but distinct from the mouse receptor. We also screened small libraries of pharmacologically active agents on TAAR1 and identified a series of synthetic agonists, some of which are also ligands of the enigmatic imidazoline receptor. The findings of the present study not only shed light on the pharmacological species difference of TAAR1, but also raise new possibilities about the mechanism of some of the imidazoline-related agents.
Nutrient isothiocyanates covalently modify and inhibit the inflammatory cytokine macrophage migration inhibitory factor (MIF)
Authors: Cross Janet V. , Rady Joshua M. , Foss Frank W. , Lyons Charles E. , Macdonald Timothy L. , Templeton Dennis J.
Published: September 2009

Dietary ITCs (isothiocyanates) prevent cancer and show other bioactivities in vivo. As electrophiles, ITCs may covalently modify cellular proteins. Using a novel proteomics screen, we identified MIF (macrophage migration inhibitory factor) as the principal target of nutrient ITCs in intact cells. ITCs covalently modify the N-terminal proline residue of MIF and extinguish its catalytic tautomerase activity. MIF deficiency does not prevent induction of Phase 2 gene expression, a hallmark of many cancer chemopreventives, including ITCs. Due to the emerging role of MIF in the control of malignant cell growth and its clear involvement in inflammation, inhibition of MIF by nutrient ITCs suggests therapeutic strategies for inflammatory diseases and cancer.
Exercise and muscle dysfunction in COPD: implications for pulmonary rehabilitation
Authors: Man William D.-C. , Kemp Paul , Moxham John , Polkey Michael I.
Published: September 2009

Skeletal muscle dysfunction in COPD (chronic obstructive pulmonary disease) patients, particularly of the quadriceps, is of clinical interest because it not only influences the symptoms that limit exercise, but may also contribute directly to poor exercise performance and health status, increased healthcare utilization, and mortality. Furthermore, unlike the largely irreversible impairment of the COPD lung, skeletal muscles represent a potential site to improve patients' level of function and quality of life. However, despite expanding knowledge of potential contributing factors and greater understanding of molecular mechanisms of muscle wasting, only one intervention has been shown to be effective in reversing COPD muscle dysfunction, namely exercise training. Pulmonary rehabilitation, an intervention based on individually tailored exercise training, has emerged as arguably the most effective non-pharmacological intervention in improving exercise capacity and health status in COPD patients. The present review describes the effects of chronic exercise training on skeletal muscles and, in particular, focuses on the known effects of pulmonary rehabilitation on the quadriceps muscle in COPD. We also describe the current methods to augment the effects of pulmonary rehabilitation and speculate how greater knowledge of the molecular pathways of skeletal muscle wasting may aid the development of novel pharmaceutical agents.
Relationship between circulating progenitor cells, vascular function and oxidative stress with long-term training and short-term detraining in older men
Authors: Witkowski Sarah , Lockard Michael M. , Jenkins Nathan T. , Obisesan Thomas O. , Spangenburg Espen E. , Hagberg James M.
Published: September 2009

Exercise may contribute to the maintenance of vascular function via enhanced liberation and action of bone-marrow-derived progenitor cells. Activity related changes in oxidative stress may also influence the number and function of these cells. In the present study, we sought to determine (i) whether adaptations in reactive hyperaemic FBF (forearm blood flow) response associated with long-term endurance exercise and short-term detraining were related to resting putative progenitor cell number and function, and (ii) whether oxidative stress affected these factors. Participants included men with a history of more than 30 years of moderate-to-high-intensity exercise (HI group) and healthy low-active age- and BMI (body mass index)-matched control subjects (LO group). Vascular reactive hyperaemic FBF response, resting CD34+ and CD34+/VEGFR2+ (vascular endothelial growth factor receptor 2+] cell number, CFU-EC (colony-forming unit-endothelial cell) count and CFU-EC senescence were evaluated. Oxidative stress measures included OxLDL (oxidized low-density lipoprotein) and TAC (total antioxidant capacity). These measures were assessed following 10 days of detraining in the HI group. The HI group had greater peak reactive hyperaemic FBF responses compared with the LO group, despite no difference in resting CD34+ cell number, CD34+/VEGFR2+ cell number, CFU-EC colonies or CFU-EC senescence. With detraining in the HI group, CD34+ cells declined 44%, and the percentage change in CD34+/VEGFR2+ cells was positively correlated with the change in FBF response to reactive hyperaemia. The percentage change in CD34+/VEGFR2+ cells and the percentage change in EPC (endothelial progenitor cell) senescence with detraining were related to the percentage change in TAC. These results reveal that changes in reactive hyperaemic FBF are closely related to activity dependent dynamic changes in CD34+/VEGFR2+ cell number, which may be influenced by alterations in oxidative stress.
Submonolayer growth of BaTiO3 thin film via pulsed laser deposition: A kinetic Monte Carlo simulation
Authors: Zhu Z. , Zheng X. J. , Li W.
Published: September 2009

Distinguishing with the traditional solid-on-solid model, the adatom bonding is specially considered to describe the atom combined according to the perovskite structure, and the pulsed laser deposition growth of the perovskite thin film on the surface of square lattice substrate of homoepitaxial system is considered as three stochastic incidents such as the deposition, diffusion, and bonding of adatoms. We proposed an energy-dependent kinetic Monte Carlo approach to simulate BaTiO3 thin film growth via pulsed laser deposition within the submonolayer regime, in which the coverage θ is less than 1. In the simulation, first- and second-nearest-neighbor interactions are taken into account by the Born–Mayer–Huggins potential. Varying the values of the laser repetition rate and pulse duration, the relative curves of the island density and island size versus coverage were obtained. The simulation results show that the island density increases, while the island size decreases with the pulse frequency. When the pulse repetition rate is less than 1 kHz, there is no obvious variation for the curves of the island density and island size versus coverage. However, when the pulse repetition rate is larger than 1 kHz, the island density does not change for θ<0.1, and with the pulse duration, the island density increases while the island size decreases for θ>0.1. They are in good agreement with the previous experimental observations. It provides an understanding of the evolution of the morphology of the BaTiO3 thin film in submonolayer growth and a basic exploration of the epitaxial growth process of ionic oxides with perovskite-type structures.
High efficiency reflective liquid crystal polarization gratings
Authors: Komanduri R. K. , Escuti M. J.
Published: September 2009

We experimentally demonstrate a reflective-mode liquid crystal polarization grating with high reflectance, small grating period, and subms switching times. This switchable optical element can diffract ∼100% into a single order, have highly polarization-sensitive first orders, and have a polarization-insensitive zero order. Here we introduce an absorbing layer that overcomes the reflection of the (ultraviolet) holographic beams, which otherwise prevents high quality fabrication. At a grating period of 2.1 μm, we report 98% diffraction efficiency, 90% reflectance, ∼600:1 contrast-ratio, and ∼3000:1 polarization contrast. These elements can therefore be configured as polarization-independent modulators or switchable polarizing beam splitters, for use in telecommunications, displays, spatial-light modulators, and polarimetry.
Applicability of acoustic noise correlation for structural health monitoring in nondiffuse field conditions
Authors: Moulin Emmanuel , Abou Leyla Najib , Assaad Jamal , Grondel Sebastien
Published: September 2009

Ambient noise correlation offers an elegant way of passively caracterize a medium. The principle is that in diffuse field condition, Green’s function between two sensors can be retrieved from the cross-correlated received signals. Here, the technique is applied in conditions where convergence toward Green’s function is not ensured. Since the obtained information is sensible to the medium state, it is still exploitable for damage detection provided a baseline version is available for comparison. This requires the identification of the acoustic source characteristics at the instant of measurement, which could be achieved using the signal measured at a “reference” sensor.
Observation of a critical pressure gradient for the stabilization of interchange modes in simple magnetized toroidal plasmas
Authors: Federspiel L. , Labit B. , Ricci P. , Fasoli A. , Furno I. , Theiler C.
Published: September 2009

The existence of a critical pressure gradient needed to drive the interchange instability is experimentally demonstrated in the simple magnetized torus TORoidal Plasma EXperiment [A. Fasoli et al., Phys. Plasmas 13, 055902 (2006)]. This gradient is reached during a scan in the neutral gas pressure pn. Around a critical value for pn, depending on the magnetic configuration and on the injected rf power, a small increase in the neutral gas pressure triggers a transition in the plasma behavior. The pressure profile is locally flattened, stabilizing the interchange mode observed at lower neutral gas densities. The measured value for the critical gradient is close to the linear theory estimate.
Regimes of expansion of a collisional plasma into a vacuum
Authors: Thaury C. , Mora P. , Adam J. C. , Héron A.
Published: September 2009

The effect of elastic Coulomb collisions on the one-dimensional expansion of a plasma slab is studied in the classical limit, using an electrostatic particle-in-cell code. Two regimes of interest are identified. For a collision rate of few hundreds of the inverse of the expansion characteristic time τe, the electron distribution function remains isotropic and Maxwellian with a homogeneous temperature, during all the expansion. In this case, the expansion can be approached by a three-dimensional version of the hybrid model developed by Mora [P. Mora, Phys. Rev. E 72, 056401 (2005)]. When the collision rate becomes somewhat greater than 104τe−1, the plasma is divided in two parts: an inner part which expands adiabatically as an ideal gas and an outer part which undergoes an isothermal expansion.
Scale-dependent behavior of scale equations
Authors: Kim Pilwon
Published: September 2009

We propose a new mathematical framework to formulate scale structures of general systems. Stack equations characterize a system in terms of accumulative scales. Their behavior at each scale level is determined independently without referring to other levels. Most standard geometries in mathematics can be reformulated in such stack equations. By involving interaction between scales, we generalize stack equations into scale equations. Scale equations are capable to accommodate various behaviors at different scale levels into one integrated solution. On contrary to standard geometries, such solutions often reveal eccentric scale-dependent figures, providing a clue to understand multiscale nature of the real world. Especially, it is suggested that the Gaussian noise stems from nonlinear scale interactions.
Two dimensional planar and nonplanar ion acoustic shock waves in electron-positron-ion plasmas
Authors: Masood W. , Rizvi H.
Published: September 2009

Two dimensional ion acoustic shock waves (IASWs) are studied in an unmagnetized plasma consisting of electrons, positrons, and adiabatically hot positive ions. This is done by deriving the nonplanar Kadomstev–Petviashvili–Burgers (KPB) equation under the small amplitude perturbation expansion method. The dissipation is introduced by taking into account the kinematic viscosity among the plasma constituents. The limiting cases of the nonplanar KPB equation are also discussed. The analytical solution of the planar KPB equation is obtained using the tangent hyperbolic method that is used as the initial profile to numerically solve the nonplanar KPB equation. It is found that the strength of IASW is maximum for spherical, intermediate for cylindrical, and minimum for planar geometry. It is observed that the positron concentration and the plasma kinematic viscosity significantly modify the shock structure. Finally, the temporal evolution of the nonplanar IASW is investigated and the results are discussed from the numerical stand point. The results of the present study may be applicable in the study of small amplitude localized electrostatic shock structures in electron-positron-ion plasmas.
Sputtering yields of Si, SiC, and B4C under nanodroplet bombardment at normal incidence
Authors: Gamero-Castaño Manuel , Mahadevan Mahesh
Published: September 2009

Single-crystal silicon and polycrystalline silicon carbide and boron carbide were bombarded with a beam of electrosprayed nanodroplets at normal incidence. The acceleration voltage of the beam ranged between 9.13 and 20.13 kV. The kinetic energy of the nanodroplet molecules varied between 24.1 and 91.2 eV. The volume of sputtered material was measured with a profilometer, and the molecular flux of the beamlet with a time of flight spectrometer. Sputtering yields as high as 2.32, 1.48, and 2.29 atoms per molecule were obtained for Si, SiC, and B4C. The maximum receding rates of the substrates’ surfaces were 448, 172, and 170 nm/min respectively. The significant increase with respect to the sputtering rates of broad-beam atomic ion sources is due to the large molecular flux of electrosprays.
Binding energy of ionized-donor-bound excitons in parabolic quantum-well wires in a magnetic field
Authors: Liu Lei , Liu Jian-Jun
Published: September 2009

The properties of ionized-donor-bound excitons (D+,X) in a parabolic quantum-well wire in the presence of a magnetic field are studied numerically in the framework of effective-mass envelope function theory. The binding energy of (D+,X) structures is calculated as a function of the oscillator length for different values of the magnetic field by using the one-dimensional effective potential model and the finite-difference method. The results show that the binding energy increases as the oscillator length decreases, and that it is also increased by enhancing the magnetic field. The binding energies of the complex for the two different dissociation processes are taken into account, and their behaviors are discussed in detail. The Haynes factor is found to increase rapidly with decreasing oscillator length in the case of strong parabolic potential confinement. In addition, the average interparticle distances and the probability density distributions are investigated for a given set of values of the oscillator lengths and the magnetic field.
Metadynamics simulations of calcite crystallization on self-assembled monolayers
Authors: Quigley D. , Rodger P. M. , Freeman C. L. , Harding J. H. , Duffy D. M.
Published: September 2009

We show that recent developments in the application of metadynamics methods to direct simulations of crystallization make it possible to predict the orientation of crystals grown on self-assembled monolayers. In contrast to previous studies, the method allows for dynamic treatment of the organic component and the inclusion of explicit surface water without the need for computationally intensive interfacial energy calculations or prior knowledge of the interfacial structure. The method is applied to calcite crystallization on carboxylate terminated alkanethiols arrayed on Au (111). We demonstrate that a dynamic treatment of the monolayer is sufficient to reproduce the experimental results without the need to impose epitaxial constraints on the system. We also observe an odd-even effect in the variation of selectivity with organic chain length, reproducing experimentally observed orientations in both cases. Analysis of the ordering process in our simulations suggests a cycle of mutual control in which both the organic and mineral components induce complementary local order across the interface, leading to the formation of a critical crystalline region. The influence of pH, together with some factors that might affect the range of applicability of our method, is discussed.
Extremely high efficient coupling between long range surface plasmon polariton and dielectric waveguide mode
Authors: Liu Fang , Wan Ruiyuan , Li Yunxiang , Huang Yidong , Miura Yoshikatsu , Ohnishi Dai , Peng Jiangde
Published: September 2009

To connect the surface plasmon polariton (SPP) based devices with the conventional dielectric devices is a significant issue for the further development of SPP and related applications. In this paper, extremely high efficient coupling (>99%) between long range SPP (LRSPP) waveguide mode and TM mode of dielectric waveguide has been demonstrated from a hybrid coupler, which composed of an Au (LRSPP) waveguide and a SiN (dielectric) waveguide. Based on this hybrid coupler, a polarization splitter with pure TM mode output from one arm and TE mode output from the other arm with high TE/TM extinction ratio has been realized.
Robust synchronization of chaotic systems subject to parameter uncertainties
Authors: Huang He , Feng Gang , Sun Yonghui
Published: September 2009

The robust synchronization problem is studied in this paper for uncertain chaotic Lur’e systems. It is assumed that the mismatched parameter uncertainties appear in the master system and are norm bounded. An integral sliding mode control approach is developed to address this problem. First, a suitable integral sliding surface is constructed, and a delay-dependent condition by means of linear matrix inequalities is derived under which the resulting error system is globally asymptotically stable in the specified switching surface. Then, an integral sliding mode controller is designed guaranteeing the reachability of the specified sliding surface. When the bounds of the mismatched parameter uncertainties are unknown, an adaptive integral sliding mode controller is further designed. Finally, the Chua’s circuit is provided as an example to demonstrate the effectiveness of the developed approach.
Dispersion-corrected Møller–Plesset second-order perturbation theory
Authors: Tkatchenko Alexandre , DiStasio Robert A. , Head-Gordon Martin , Scheffler Matthias
Published: September 2009

We show that the often unsatisfactory performance of Møller–Plesset second-order perturbation theory (MP2) for the dispersion interaction between closed-shell molecules can be rectified by adding a correction ΔCn/Rn, to its long-range behavior. The dispersion-corrected MP2 (MP2+ΔvdW) results are in excellent agreement with the quantum chemistry “gold standard” [coupled cluster theory with single, double and perturbative triple excitations, CCSD(T)] for a range of systems bounded by hydrogen bonding, electrostatics and dispersion forces. The MP2+ΔvdW method is only mildly dependent on the short-range damping function and consistently outperforms state-of-the-art dispersion-corrected density-functional theory.
Response to “Comment on ‘Mathematical and physical aspects of Kappa velocity distribution’ ” [Phys. Plasmas 16, 094701 (2009)]
Authors: Hau L.-N. , Fu W.-Z. , Chuang S.-H.
Published: September 2009

The comment questions the formulation of the κ velocity distribution function used in our paper as compared to a slightly different form used by the authors. The difference in the distribution function necessarily leads to different number densities, thermal pressures, etc. We show that the restriction with their distribution function is that the macroscopic temperature (or average kinetic energy) is the same for all spatially uniform systems with a family of κ distributions including the Maxwellian case. The distribution function used in our paper and widely adopted in various studies of nonthermal systems, however, does not impose such a constraint; in particular, the temperature has κ dependence reflecting the kinetic nature of different statistical systems. The points made in the comment are trivial and misleading.
Thermal vibrational disorder of a conjugated polymer in charge-transfer complex
Authors: Osotov M. O. , Bruevich V. V. , Paraschuk D. Yu.
Published: September 2009

Temperature dependences of optical absorption and Raman spectra of ground-state charge-transfer complex (CTC) formed in blends of a conjugated polymer, poly[2-methoxy-5-(2′-ethylhexyloxy)-p-phenylenevinylene] (MEH-PPV), and low-molecular-weight acceptor, 2,4,7-trinitrofluorenone, were studied. Upon cooling from 320 to 120 K, the polymer strongest Raman band shows a 0.5 cm−1 low-frequency shift while it demonstrates a 0.5 cm−1 high-frequency shift in the CTC. This behavior is explained by the temperature dependence of polymer-acceptor charge transfer in the CTC: The amount of transferred charge decreases by 25% upon cooling. At the same time, both the pristine polymer and CTC demonstrate a 0.05–0.1 eV redshift of the absorption edge. To account for these temperature shifts, we propose a model that relates temperature variations in the effective conjugation length with thermal torsion vibrations of the conjugated chains. Comparison of the model and experimental data reveals that the torsion rigidity of conjugated chains involved in the CTC is 30% stronger than that of the pristine ones. This enhanced rigidity increases the conjugation length of MEH-PPV chains in the CTC by 20%. However, the major contribution to the MEH-PPV absorption edge shift in the CTC is assigned to a local built-in electric field effect induced by the ground-state charge transfer.
Simulations of non-neutral slab systems with long-range electrostatic interactions in two-dimensional periodic boundary conditions
Authors: Ballenegger V. , Arnold A. , Cerdà J. J.
Published: September 2009

We introduce a regularization procedure to define electrostatic energies and forces in a slab system of thickness h that is periodic in two dimensions and carries a net charge. The regularization corresponds to a neutralization of the system by two charged walls and can be viewed as the extension to the two-dimensional (2D)+h geometry of the neutralization by a homogeneous background in the standard three-dimensional Ewald method. The energies and forces can be computed efficiently by using advanced methods for systems with 2D periodicity, such as MMM2D or P3M/ELC, or by introducing a simple background-charge correction to the Yeh–Berkowitz approach of slab systems. The results are checked against direct lattice sum calculations on simple systems. We show, in particular, that the Madelung energy of a 2D square charge lattice in a uniform compensating background is correctly reproduced to high accuracy. A molecular dynamics simulation of a sodium ion close to an air/water interface is performed to demonstrate that the method does indeed provide consistent long-range electrostatics. The mean force on the ion reduces at large distances to the image-charge interaction predicted by macroscopic electrostatics. This result is used to determine precisely the position of the macroscopic dielectric interface with respect to the true molecular surface.
Damping of linear oscillations in axisymmetric liquid bridges
Authors: Vega E. J. , Montanero J. M.
Published: September 2009

We analyzed experimentally the damping of both axial and lateral free oscillations of small amplitude in axisymmetric liquid bridges. We excited the first oscillation mode in nearly inviscid and in moderately viscous liquid bridges, and measured the parameters which characterize that mode. The axial spatial dependence of those parameters was determined, and the influence of the equilibrium shape on the oscillation frequency and damping rate was analyzed by considering liquid bridges with very different volumes. The experimental results were compared with the solution of the Navier–Stokes equations in the limit of zero viscous Capillary number and of two one-dimensional models. These theoretical approaches predicted accurately the axial spatial dependence of the parameters characterizing the oscillation mode. Comparison with the experimental data showed remarkable agreement for the oscillation frequency, while significant discrepancies were found for the damping rate.
Determination of interaction potentials of colloidal monolayers from the inversion of pair correlation functions: A two-dimensional predictor-corrector method
Authors: Law A. D. , Buzza D. M. A.
Published: September 2009

The structure and stability of colloidal monolayers depend crucially on the effective pair potential u(r) between colloidal particles. In this paper, we develop a two-dimensional (2D) predictor-corrector method for extracting u(r) from the pair correlation function g(r) of dense colloidal monolayers. The method is based on an extension of the three-dimensional scheme of Rajagopalan and Rao [Phys. Rev. E 55, 4423 (1997)] to 2D by replacing the unknown bridge function B(r) with the hard-disk bridge function Bd(r); the unknown hard-disk diameter d is then determined using an iterative scheme. We compare the accuracy of our predictor-corrector method to the conventional one-step inversion schemes of hypernetted chain closure (HNC) and Percus–Yevick (PY) closure. Specifically we benchmark all three schemes against g(r) data generated from Monte Carlo simulation for a range of 2D potentials: exponential decay, Stillinger–Hurd, Lennard-Jones, and Derjaguin–Landau–Verwey–Overbeek. We find that for all these potentials, the predictor-corrector method is at least as good as the most accurate one-step method for any given potential, and in most cases it is significantly better. In contrast the accuracy of the HNC and PY methods relative to each other depends on the potential studied. The proposed predictor-corrector scheme is therefore a robust and more accurate alternative to these conventional one-step inversion schemes.
Quasiclassical trajectory calculations of differential cross sections and product energy distributions for the N+OH→NO+H reaction
Authors: Jorfi Mohamed , Honvault Pascal , Halvick Philippe
Published: September 2009

A detailed quasiclassical trajectory on the N+OH(v=0, j=0,1,5,10)→NO+H reaction is reported at four collision energies from 0.01 to 0.5 eV. The vibrational distributions which are statistical and the angular distributions, which present a forward/backward symmetry, are consistent with the formation of a long-lived intermediate complex. Our results show globally a weak dependence of the angular and rovibrational distributions on the rotational excitation of OH, but a more pronounced effect of the collision energy.
Reversing the temperature dependence of the sensitized Er3+ luminescence intensity
Authors: Lenz F. , Hryciw A. , DeCorby R. , Meldrum A.
Published: September 2009

The temperature-induced quenching of the Er3+ luminescence is a significant problem in silicon-based materials systems ultimately designed for room-temperature applications. Here, we show that amorphous silicon-rich oxide, moderately annealed in order to avoid growth of Si nanocrystals, exhibits a reversed temperature dependence in which the integrated Er3+ luminescence increases in intensity upon heating from 77 up to 300 K. This behavior is attributed to a unique spectrum of interacting defects that efficiently sensitize the Er3+ levels, even in the absence of nanocrystals. The effect could have ramifications in fiber-optic emitters or amplifiers to be operated at noncryogenic temperatures.
Dynamics of carrier recombination and localization in AlGaN quantum wells studied by time-resolved transmission spectroscopy
Authors: Liuolia V. , Marcinkevičius S. , Pinos A. , Gaska R. , Shur M. S.
Published: September 2009

Time-resolved transmission and photoluminescence measurements were performed on Al0.35Ga0.65N/Al0.49Ga0.51N quantum well structures with different well widths. Comparison of transmission and luminescence data shows that dynamics of electrons and holes excited into extended quantum well states are governed by nonradiative recombination. For excita-tion into potential minima formed by band gap fluctuations, localization of electrons was observed. Excitation energy dependence of the pump-probe transient shape allows estimating locali-zation potential, which is about 80 meV independently of the well width, and is prob-ably caused by fluctuations of AlN molar fraction.
Experiments on high-performance beam-scanning antennas made of gradient-index metamaterials
Authors: Ma Hui Feng , Chen Xi , Xu Hong Sheng , Yang Xin Mi , Jiang Wei Xiang , Cui Tie Jun
Published: September 2009

A planar lens made of gradient index metamaterials can transform cylindrical waves to plane waves, and the beam direction of plane waves is controlled by adjusting the refractive-index distributions of the lens. Based on such properties, we present high-performance beam-scanning antennas experimentally using the gradient-index planar lens and horn antenna. The lens is carefully designed with metamaterials to achieve different refractive indices and good matching of impedance. The near-field distributions of antennas are measured using a two-dimensional near-field microwave scanning apparatus, and the radiation patterns are presented to show the high directivity and low sidelobe.
Interdiffusion and crystallization in HfO2/Al2O3 superlattices
Authors: Adelmann C. , Kesters J. , Opsomer K. , Detavernier C. , Kittl J. A. , Van Elshocht S.
Published: September 2009

The interplay of interdiffusion and crystallization in HfO2/Al2O3 superlattices during spike annealing at 1050 °C was studied using x-ray reflectivity and x-ray diffraction. A transition in thermal stability was found as a function of HfO2 thickness between 2.3 and 3.2 nm. This transition is due to a crossover of HfO2 crystallization and amorphous HfO2/Al2O3 interdiffusion kinetics. For thin HfO2, amorphous HfO2 and Al2O3 interdiffuse and subsequently crystallize as HfAlOx into a cubic-HfO2-like phase. For thicker HfO2, HfO2 layers crystallize individually into the monoclinic phase. As a consequence, interdiffusion between HfO2 and Al2O3 is suppressed because of the immiscibility of Al2O3 in monoclinic HfO2.
Directed self-assembly of monodispersed platinum nanoclusters on graphene Moiré template
Authors: Pan Yi , Gao Min , Huang Li , Liu Feng , Gao H.-J.
Published: September 2009

Monodispersed crystalline platinum nanoclusters (NCs) have been grown on a template of graphene Moiré pattern formed on Ru(0001). The Pt NCs are directed to nucleate at a unique site in the Moiré unit cell, and grow in a layer-by-layer mode up to 4-atomic-layer height without coalescence at room temperature. The size of Pt NCs can be controlled by tuning the coverage. This system may find application in the study of Pt nanocatalyst, and the graphene Moiré pattern may be generally applied as template to direct self-assembled growth of metallic or nonmetallic NCs.
High-efficiency plasma display panel based on a high xenon mole fraction
Authors: Uhm Han S. , Son Chang G. , Hong Byung H. , Choi Eun H.
Published: September 2009

The luminance efficiency of a plasma display panel is directly related to the vacuum-ultraviolet (VUV) light emitted from excited xenon atoms and molecules. The emission efficiency of 173 nm VUV light is measured in terms of the xenon mole fraction (χ) and is shown to become considerably enhanced at a high xenon mole fraction. For example, the emission efficiency at χ=0.35 under a pressure of 400 Torr is more than 2.5 times that at χ=0.1. The experimental data agree remarkably well with theoretical predictions.
Changes in soil - plant P under heterogeneous P supply influence C allocation between the shoot and roots
Authors: Ma Qifu , Rengel Zed , Palta Jairo
Published: September 2009

Wheat plants (Triticum aestivum L.) were subjected to varying phosphorus (P) supply and canopy 13CO2 feeding to uncouple the plant and soil factors regulating carbon (C) allocation between the shoot and roots and in the P-enriched v. P-deficient soil zone. In a split-root system, transferring from 200/200 µM P (high/high) to high/nil P or nil/nil P for 7 days was associated with 18–30% increase in the ratio of root-to-total 13C, whereas 8–12% more 13C was retained in the shoot of plants grown under continuous high/high P. Although the C signal between the shoot and roots weakened at day 12, it closely correlated with root P acquisition at both days. In a non-split-root system, plants supplied with 200 μm P (high) for 7 and 12 days had a lower ratio of root-to-total 13C than plants with continuous 20 μm P (low). Preferential C allocation and increased P acquisition occurred before any measurable growth difference. Shoot P status had a greater influence than soil P supply on plant C allocation, and rapid C signalling between the shoot and roots might serve as an important component of plant response to heterogeneous P conditions.
Anthocyanin influence on light absorption within juvenile and senescing sugar maple leaves - do anthocyanins function as photoprotective visible light screens?
Authors: van den Berg Abby K. , Vogelmann Thomas C. , Perkins Timothy D.
Published: September 2009

Foliar anthocyanins are hypothesised to function as photoprotective visible light screens, preventing over-excitation of the photosynthetic system, and decreasing the likelihood of photo-oxidative stress by absorbing green light and reducing the amount of light available to be absorbed by chloroplasts in deeper tissue layers. Chlorophyll fluorescence imaging was used to test the hypothesis that anthocyanins in the palisade mesophyll of juvenile and senescing sugar maple (Acer saccharum Marsh.) leaves function as visible light screens by assessing their influence on light absorption profiles within leaves. We hypothesised that an effective anthocyanic light screen should reduce light absorption, particularly of green wavelengths, by chloroplasts in the spongy mesophyll. Both anthocyanic juvenile and senescing leaves absorbed greater amounts of green light than corresponding nonanthocyanic leaves. However, profiles of green light absorption by chlorophyll within anthocyanic leaves were not shifted to reflect reduced absorption of green light by spongy mesophyll chloroplasts. Further, the spongy mesophyll of both anthocyanic juvenile and senescing leaves absorbed proportions of green light equal to or greater than the spongy mesophyll of corresponding nonanthocyanic leaves. These results indicate that though they may provide a general source of photoprotection by reducing the total quantity of light available to be absorbed by chlorophyll, the anthocyanins in juvenile and senescing sugar maple leaves do not attenuate light in a manner consistent with that expected for an anthocyanic screen in the palisade mesophyll.
R-type anion channel activation is an essential step for ROS-dependent innate immune response in Arabidopsis suspension cells
Authors: Colcombet Jean , Mathieu Yves , Peyronnet Remi , Agier Nicolas , Lelièvre Françoise , Barbier-Brygoo Hélène , Frachisse Jean-Marie
Published: September 2009

Plants are constantly exposed to environmental biotic and abiotic stresses. Plants cells perceive these factors and trigger early responses followed by delayed and complex adaptation processes. Using cell suspensions of Arabidopsis thaliana (L.) as a cellular model, we investigated the role of plasma membrane anion channels in Reactive Oxygen Species (ROS) production and in cell death which occurs during non-host pathogen infection. Protoplasts derived from Arabidopsis suspension cells display two anion currents with characteristics very similar to those of the slow nitrate-permeable (S-type) and rapid sulfate-permeable (R-type) channels previously characterised in hypocotyl cells and other cell types. Using seven inhibitors, we showed that the R-type channel and ROS formation in cell cultures present similar pharmacological profiles. The efficiency of anion channel blockers to inhibit ROS production was independent of the nature of the triggering signal (osmotic stress or general elicitors of plant defence), indicating that the R-type channel represents a crossroad in the signalling pathways leading to ROS production. In a second step, we show that treatment with R-type channel blockers accelerates cell death triggered by the non-specific plant pathogen Xanthomonas campestris. Finally, we discuss the hypothesis that the R-type channel is involved in innate immune response allowing cell defence via antibacterial ROS production.