bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of Bradyrhizobium japonicum nitric oxide reductase in nitric oxide detoxification in soya bean root nodules
Authors: Meakin G.E. , Jepson B.J.N. , Richardson D.J. , Bedmar E.J. , Delgado M.J.
Published: January 2006

The identification of nitric oxide-bound leghaemoglobin within soya bean nodules has led to the question of how Bradyrhizobium japonicum bacteroids overcome the toxicity of this nitric oxide. It has previously been shown that one candidate for nitric oxide detoxification, the respiratory nitric oxide reductase, is expressed in soya bean nodules from plants supplied with nitrate [Mesa, de Dios Alché, Bedmar and Delgado (2004) Physiol. Plant. 120, 205–211]. In this paper, the role of this enzyme in nitric oxide detoxification is assessed and discussion is provided on other possible B. japonicum nitric oxide detoxification systems.
Nitric oxide-sensing mechanisms in Escherichia coli
Authors: Spiro S.
Published: January 2006

Exposure of Escherichia coli to nitric oxide (NO) or nitrosating agents causes significant changes in patterns of gene expression. Three recent studies have used microarrays to analyse the response of the E. coli transcriptome to NO and nitrosative stress. Drawing on the array data, I review our current understanding of the E. coli regulatory systems that are involved.
Clinical relevance of the neurotrophins and their receptors
Authors: Allen Shelley J. , Dawbarn David
Published: January 2006

The neurotrophins are growth factors required by discrete neuronal cell types for survival and maintenance, with a broad range of activities in the central and peripheral nervous system in the developing and adult mammal. This review examines their role in diverse disease states, including Alzheimer's disease, depression, pain and asthma. In addition, the role of BDNF (brain-derived neurotrophic factor) in synaptic plasticity and memory formation is discussed. Unlike the other neurotrophins, BDNF is secreted in an activity-dependent manner that allows the highly controlled release required for synaptic regulation. Evidence is discussed which shows that sequestration of NGF (nerve growth factor) is able to reverse symptoms of inflammatory pain and asthma in animal models. Both pain and asthma show an underlying pathophysiology linked to increases in endogenous NGF and subsequent NGF-dependent increase in BDNF. Conversely, in Alzheimer's disease, there is a role for NGF in the treatment of the disease and a recent clinical trial has shown benefit from its exogenous application. In addition, reductions in BDNF, and changes in the processing and usage of NGF, are evident and it is possible that both NGF and BDNF play a part in the aetiology of the disease process. This highly selective choice of functions and disease states related to neurotrophin function, although in no way comprehensive, illustrates the importance of the neurotrophins in the brain, the peripheral nervous system and in non-neuronal tissues. Ways in which the neurotrophins, their receptors or agonists/antagonists may act therapeutically are discussed.
Effects of angiotensin-converting-enzyme inhibitors in combination with diuretics on blood pressure and renal injury in nitricoxide-deficiency-induced hypertension in rats
Authors: García-Estañ Joaquín , Ortiz M. Clara , O'Valle Francisco , Alcaraz Antonia , Navarro Esther G. , Vargas Félix , Evangelista Stefano , Atucha Noemí M.
Published: January 2006

The present study investigates the effects of chronic administration of ACEIs (angiotensin-converting-enzyme inhibitors; either zofenopril or enalapril) in combination with a diruetic (hydrochlorothiazide) on BP (blood pressure) increase and renal injury induced by L-NAME (NG-nitro-L-arginine methyl ester), an inhibitor of NO (nitric oxide) synthesis. Rats were untreated or received L-NAME alone, L-NAME+zofenopril+hydrochlorothiazide or L-NAME+enalapril+hydrochlorothiazide for 8 weeks. L-NAME treatment resulted in marked elevation in BP and mortality. Treatment with either ACEI and diuretic prevented the increase in BP induced by L-NAME, reduced the death rate and improved excretory parameters. Renal injury in the L-NAME group was severe, but, in the groups treated with either ACEI and diuretic, glomerular and tubulointerstitial lesions were not observed and the intensity, number and size of vessels affected was reduced. However, the efficacy of zofenopril+diuretic was superior to that of enalapril+diuretic in reducing vascular alterations. Oxidative stress indices and the expression of NO synthase and nitrotyrosine were normalized by the treatments. In conclusion, the combined treatment of zofenopril or enalapril with hydrochlorothiazide completely prevented the development of arterial hypertension induced by L-NAME. Renal morphological and functional alterations in the hypertensive animals were also almost completely normalized, but the treatment with zofenopril+diuretic produced a more complete organ protection. The protective effect is related to an activation of endothelial NO synthase expression and to a normalization of the oxidative stress parameters due to the inhibition of angiotensin II.
SARS: clinical presentation, transmission, pathogenesis and treatment options
Authors: Chan Paul K. S. , Tang Julian W. , Hui David S. C.
Published: January 2006

SARS (severe acute respiratory syndrome) appeared as the first emerging infectious disease of this century. It is fortunate that the culprit virus can be grown without much difficulty from a commonly used cell line, allowing an unlimited supply of isolates for further molecular studies and leading to the development of sensitive diagnostic assays. How the virus has successfully jumped the species barrier is still a mystery. The superspreading events that occurred within hospital, hotel and high-density housing estate opens a new chapter in the mechanisms and routes of virus transmission. The old practice of quarantine proved to be still useful in controlling the global outbreak. Despite all the available sophisticated tests, alertness with early recognition by healthcare workers and prompt isolation of suspected cases is still the most important step for containing the spread of the infection. Although the rapidly evolving outbreak did not allow the conducting of systematic clinical trails to evaluate treatment options, the accumulated experience on managing SARS patients will improve the clinical outcome should SARS return. Although SARS led to more than 700 deaths worldwide, the lessons learnt have prepared healthcare systems worldwide to face future emerging and re-emerging infections.
Effect of high altitude and exercise on microvascular parameters in acclimatized subjects
Authors: Bauer Andreas , Demetz Florian , Bruegger Dirk , Schmoelz Martin , Schroepfer Sebastian , Martignoni André , Baschnegger Heiko , Hoelzl Josef , Thiel Manfred , Choukér Alexander , Peter Klaus , Gamble John , Christ Frank
Published: January 2006

The role of microvascular fluid shifts in the adaptation to hypobaric hypoxia and its contribution to the pathophysiology of AMS (acute mountain sickness) is unresolved. In a systematic prospective study, we investigated the effects of hypobaric hypoxia and physical exercise alone, and in combination, on microvascular fluid exchange and related factors. We used computer-assisted VCP (venous congestion plethysmography) on the calves of ten altitude-acclimatized volunteers. We investigated the effects of: (i) actively climbing to an altitude of 3196 m, (ii) airlifting these subjects to the same altitude, and (iii) exercise at low altitude. CFC (capillary filtration capacity), Pvi (isovolumetric venous pressure) and Qa (calf blood flow) were assessed before and after each procedure and then repeated after an overnight rest. Measurements of CFC showed no evidence of increased microvascular permeability after any of the procedures. Pvi was significantly decreased (P<0.001) from 20.3±4.4 to 8.9±4.3 mmHg after active ascent, and was still significantly lower (P=0.009) after overnight rest at high altitude (13.6±5.9 mmHg). No such changes were observed after the passive ascent (16.7±4.0 mmHg at baseline; 17.3±4.5 mmHg after passive ascent; and 19.9±5.3 mmHg after overnight rest) or after exercise at low altitude. After the active ascent, Qa was significantly increased. We also found a significant correlation between Qa, Pvi and the number of circulating white blood cells. In conclusion, we found evidence to support the hypothesis that increased microvascular permeability associated with AMS does not occur in acclimatized subjects. We also observed that the microvascular equilibrium pressure (Pvi) fell in inverse relation to the increase in Qa, especially in hypoxic exercise. We hypothesize that this inverse relationship reflects the haemodynamic changes at the microvascular interface, possibly attributable to the flow-induced increases in endothelial surface shear forces.
Intermolecular interactions in solid benzene
Authors: Kearley G. J. , Johnson M. R. , Tomkinson J.
Published: January 2006

The lattice dynamics and molecular vibrations of benzene and deuterated benzene crystals are calculated from force constants derived from density-functional theory (DFT) calculations and compared with measured inelastic neutron-scattering spectra. A very small change (0.5%) in lattice parameter is required to obtain real lattice-mode frequencies across the Brillouin zone. There is a strong coupling between wagging and breathing modes away from the zone center. This coupling and sensitivity to cell size arises from two basic interactions. Firstly, comparatively strong interactions that hold the benzene molecules together in layers. These include an intermolecular interaction in which H atoms of one molecule link to the center of the aromatic ring of a neighboring molecule. The layers are held to each other by weaker interactions, which also have components that hold molecules together within a layer. Small changes in the lattice parameters change this second type of interaction and account for the changes to the lattice dynamics. The calculations also reveal a small auxetic effect in that elongation of the crystal along the b axis leads to an increase in internal pressure in the ac plane, that is, elongation in the b direction induces expansion in the a and c directions.
Pseudo-Jahn-Teller origin of geometry and pseudorotations in second row tetra-atomic clusters X4 (X=Na,Mg,Al,Si,P,S)
Authors: Garcia-Fernandez Pablo , Bersuker Isaac B. , Boggs James E.
Published: January 2006

Experimentally determined or ab initio calculated molecular geometries carry no information about their origin. Employing the Jahn-Teller (JT) vibronic coupling effects as the only source of instability and consequent distortions of high-symmetry molecular configurations, we have worked out a procedure that allows us to trace the origin of particular geometries and determine the detailed electronic mechanism of their formation. This procedure is illustrated by considering a series of X4 clusters with X=Na, Mg, Al, Si, P, and S. It shows explicitly why Na4, Si4, and Al4 have a rhombic geometry in the ground state, while Mg4 and P4 are tetrahedral, whereas S4 is a trapezium. Even when the minimum-energy geometries are the same (as in the case of rhombic Na4, Si4, and Al4), the electronic mechanism of their formation is quite different. In particular, in Na4 and Si4 the rhombic minima are produced by a strong pseudo JT coupling between two excited states in the square-planar configuration (different in the two cases) that stabilizes one of them and makes it the ground state by rhombic distortions. The rhombic configuration of Al4 is due to the pseudo JT effect in its ground-state square-planar configuration, and the trapezium in S4 is formed by two pseudo JT couplings essentially involving excited states. In several cases this analysis shows also the tunneling paths between equivalent configurations.
Protonated carbonyl sulfide: Prospects for the spectroscopic observation of the elusive HSCO+ isomer
Authors: Wheeler Steven E. , Yamaguchi Yukio , Schaefer Henry F.
Published: January 2006

Spurred by the apparent conflict between ab initio predictions and infrared spectroscopic evidence regarding the relative stability of isomers of protonated carbonyl sulfide, key stationary points on the isomerization surface of HOCS+ have been examined via systematic extrapolations of ab initio energies. Electron correlation has been accounted for using second-order Møller-Plesset perturbation theory and coupled cluster theory through triple excitations [CCSD, CCSD(T), and CCSDT] in conjunction with the correlation consistent hierarchy of basis sets, cc-pVXZ (X=D,T,Q,5,6). HSCO+ is predicted to lie lower in energy than HOCS+ by 4.86kcalmol−1, computed using the focal point extrapolation scheme of Allen and co-workers [J. Chem. Phys. 99, 4638 (1993)] with corrections for anharmonic zero-point vibrational energy, core correlation, non-Born-Oppenheimer, and scalar relativistic effects. A transition state has been located, constituting the barrier to isomerization of HSCO+ to HOCS+, lying 68.9kcalmol−1 higher in energy than HSCO+. This is well above predicted exothermicity [ΔHr°(0K)=48.1kcalmol−1, cc-pVQZ CCSD(T)] for the reaction considered in the experiments (HSCO++H2→OCS+H3+). Though proton tunneling will lead to a lower effective barrier, this prediction is consistent with the lack of HSCO+ in electrical discharges in H2∕OCS, since the relative populations of HOCS+ and HSCO+ will depend on the experimental details of the protonation route rather than the relative thermodynamic stability of the isomers. Anharmonic vibrational frequencies and vibrationally corrected rotational constants from cc-pVTZ CCSD(T) cubic and quartic force constants are provided, to aid in the spectroscopic observation of the energetically favorable but apparently elusive HSCO+ isomer.
Adaptive optimal stochastic state feedback control of resistive wall modes in tokamaks
Authors: Sun Z. , Sen A. K. , Longman R. W.
Published: January 2006

An adaptive optimal stochastic state feedback control is developed to stabilize the resistive wall mode (RWM) instability in tokamaks. The extended least-square method with exponential forgetting factor and covariance resetting is used to identify (experimentally determine) the time-varying stochastic system model. A Kalman filter is used to estimate the system states. The estimated system states are passed on to an optimal state feedback controller to construct control inputs. The Kalman filter and the optimal state feedback controller are periodically redesigned online based on the identified system model. This adaptive controller can stabilize the time-dependent RWM in a slowly evolving tokamak discharge. This is accomplished within a time delay of roughly four times the inverse of the growth rate for the time-invariant model used.
Coupled-cluster response theory with linear-r12 corrections: The CC2-R12 model for excitation energies
Authors: Fliegl Heike , Hättig Christof , Klopper Wim
Published: January 2006

Coupled-cluster response theory for vertical excitation energies within the second-order approximate coupled-cluster singles-and-doubles model CC2, including linear-r12 corrections, is derived and implemented for Ansätze 1 and 2 of R12 theory. An orthonormal auxiliary basis set is used for the resolution-of-the-identity approximation in order to calculate the three- and four-electron integrals needed in R12 theory. The basis set convergence is investigated for a selected set of atoms and small molecules and it is found that in many cases the convergence is not improved. An analysis of the different contributions to excitation energies shows that the present scheme for the construction of the R12 pair functions leads in response theory to an unbalanced description of ground- and excited-state wave functions and needs to be generalized to carry the high accuracy of R12 methods over to response theory.
Density-functional model cluster studies of EPR g tensors of Fs+ centers on the surface of MgO
Authors: Di Valentin Cristiana , Neyman Konstantin M. , Risse Thomas , Sterrer Martin , Fischbach Esther , Freund Hans-Joachim , Nasluzov Vladimir A. , Pacchioni Gianfranco , Rösch Notker
Published: January 2006

We report g tensors of surface color centers, so-called Fs+ centers, of MgO calculated with two density-functional approaches using accurately embedded cluster models. In line with recent UHV measurements on single-crystalline MgO film, we determined only small g-tensor anisotropies and negative shifts Δg≡g−ge for all Fs+ sites considered, namely, (001)-terrace, step, edge, and corner sites. The g values are very sensitive to the local structure of the defect: relaxation reverses the sign of Δg. However, accounting for the spin-orbit interaction either self-consistently or perturbatively yields very similar results. In addition to the values of the tensor components, their direction with respect to the surface was determined. In contrast to edges, significant deviations from ideal C2v symmetry were found for Fs+ centers at steps. Recent data on single-crystalline thin films are reevaluated in the light of these results.
Brownian dynamics simulations with stiff finitely extensible nonlinear elastic-Fraenkel springs as approximations to rods in bead-rod models
Authors: Hsieh Chih-Chen , Jain Semant , Larson Ronald G.
Published: January 2006

A very stiff finitely extensible nonlinear elastic (FENE)-Fraenkel spring is proposed to replace the rigid rod in the bead-rod model. This allows the adoption of a fast predictor-corrector method so that large time steps can be taken in Brownian dynamics (BD) simulations without over- or understretching the stiff springs. In contrast to the simple bead-rod model, BD simulations with beads and FENE-Fraenkel (FF) springs yield a random-walk configuration at equilibrium. We compare the simulation results of the free-draining bead-FF-spring model with those for the bead-rod model in relaxation, start-up of uniaxial extensional, and simple shear flows, and find that both methods generate nearly identical results. The computational cost per time step for a free-draining BD simulation with the proposed bead-FF-spring model is about twice as high as the traditional bead-rod model with the midpoint algorithm of Liu [J. Chem. Phys. 90, 5826 (1989)]. Nevertheless, computations with the bead-FF-spring model are as efficient as those with the bead-rod model in extensional flow because the former allows larger time steps. Moreover, the Brownian contribution to the stress for the bead-FF-spring model is isotropic and therefore simplifies the calculation of the polymer stresses. In addition, hydrodynamic interaction can more easily be incorporated into the bead-FF-spring model than into the bead-rod model since the metric force arising from the non-Cartesian coordinates used in bead-rod simulations is absent from bead-spring simulations. Finally, with our newly developed bead-FF-spring model, existing computer codes for the bead-spring models can trivially be converted to ones for effective bead-rod simulations merely by replacing the usual FENE or Cohen spring law with a FENE-Fraenkel law, and this convertibility provides a very convenient way to perform multiscale BD simulations.
Exploring a small sawtooth regime in Joint European Torus plasmas with counterinjected neutral beams
Authors: Nave M. F. F. , Koslowski H. R. , Coda S. , Graves J. , Brix M. , Buttery R. , Challis C. , Giroud C. , Stamp M. , de Vries P. ,   JET-FEDA contributors
Published: January 2006

During a recent reversed toroidal field (BT) campaign at the Joint European Torus (JET), experiments were performed to investigate the effect on sawteeth of neutral beam injection (NBI)-driven toroidal plasma rotation counter to the direction of the toroidal plasma current and BT. A power scan at constant density has permitted analytical continuation, into the reversed BT domain, of previous experiments with forward field and hence corotation. Earlier JET results were confirmed, indicating that counter-NBI results in sawtooth periods shorter than in the Ohmic regime. This study has demonstrated that, whereas with co-NBI the sawtooth period increases with power, with counter-NBI the sawtooth period initially decreases with power passing through a minimum at 4 MW. Clearly this trend also manifests itself in terms of the toroidal plasma rotation, for which a minimum is observed for counter-rotation frequency ∼3 kHz. Sawteeth smaller than Ohmic sawteeth are found to be easier to obtain with perpendicular counter-NBI, for which heating penetrates deeper into the core. The sign and magnitude of the toroidal rotation, the penetration of heating to the electrons, and the peaking of the fast-ion pressure profile in the core may all play an important role in modifying the sawtooh period.
The influence of ultrafast laser pulses on electron transfer in molecular wires studied by a non-Markovian density-matrix approach
Authors: Welack Sven , Schreiber Michael , Kleinekathöfer Ulrich
Published: January 2006

New features of molecular wires can be observed when they are irradiated by laser fields. These effects can be achieved by periodically oscillating fields but also by short laser pulses. The theoretical foundation used for these investigations is a density-matrix formalism where the full system is partitioned into a relevant part and a thermal fermionic bath. The derivation of a quantum master equation, either based on a time-convolutionless or time-convolution projection-operator approach, incorporates the interaction with time-dependent laser fields nonperturbatively and is valid at low temperatures for weak system-bath coupling. From the population dynamics the electrical current through the molecular wire is determined. This theory including further extensions is used for the determination of electron transport through molecular wires. As examples, we show computations of coherent destruction of tunneling in asymmetric periodically driven quantum systems, alternating currents and the suppression of the directed current by using a short laser pulse.
Theoretical studies of electron transfer through dendrimeric architecture
Authors: Rana Dipankar , Gangopadhyay Gautam
Published: January 2006

We have analyzed the steady-state electron transfer rate through a bridge of dendrimeric architecture. The difference between the linear chain and the dendrimeric architecture has also been demonstrated with steady-state rate as a main observable in the coherent and incoherent regimes of interactions. It is shown that generally the rate of electron transfer in dendrimeric architecture is faster than the rate associated with their linear chain counterpart with similar kind of bonding connectivities. The rate depends upon the size of the molecule, core branching, and the nature of the coupling among the different nodes on the dendrimer molecule. Depending upon the nature of the donor and acceptor, phenomenological dephasing coefficient due to environment and the geometry of the dendrimeric architecture, the modification of electron transfer rate has been studied. In the regime of fully coherent interactions where all quantum effects are considered the rate shows a multiple inversion due to the dendrimer architecture which is neither available in the regime of incoherent interaction nor in the linear chain case in similar condition. We have discussed about the applicability of our model in metal-molecule-metal junction, photoinduced electron transfer process, and molecular conductor.
Equilibrium free energies from fast-switching trajectories with large time steps
Authors: Lechner Wolfgang , Oberhofer Harald , Dellago Christoph , Geissler Phillip L.
Published: January 2006

Jarzynski’s [Phys. Rev. Lett. 78, 2690 (1997)] identity for the free-energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase-space mappings. Solving a system’s equation of motion by approximate means generates a mapping that is perfectly valid for this purpose, regardless of how closely the solution mimics true time evolution. We exploit this fact, using crudely dynamical trajectories to compute free-energy differences that are in principle exact. Numerical simulations show that Newton’s equation can be discretized to low order over very large time steps (limited only by the computer’s ability to represent resulting values of dynamical variables) without sacrificing thermodynamic accuracy. For computing the reversible work required to move a particle through a dense liquid, these calculations are more efficient than conventional fast-switching simulations by more than an order of magnitude. We also explore consequences of the phase-space mapping perspective for systems at equilibrium, deriving an exact expression for the statistics of energy fluctuations in simulated conservative systems.
On the theory underlying the Car-Parrinello method and the role of the fictitious mass parameter
Authors: Tangney Paul
Published: January 2006

The theory underlying the Car-Parrinello extended-Lagrangian approach to ab initio molecular dynamics (CPMD) is reviewed and reexamined using “heavy” ice as a test system. It is emphasized that the adiabatic decoupling in CPMD is not a decoupling of electronic orbitals from the ions but only a decoupling of a subset of the orbital vibrational modes from the rest of the necessarily coupled system of orbitals and ions. Recent work [J. Chem. Phys. 116, 14 (2002)] has pointed out that, due to the orbital-ion coupling that remains once adiabatic decoupling has been achieved, a large value of the fictitious mass μ can lead to systematic errors in the computed forces in CPMD. These errors are further investigated in the present work with a focus on those parts of these errors that are not corrected simply by rescaling the masses of the ions. It is suggested that any comparison of the efficiencies of Born-Oppenheimer molecular dynamics (BOMD) and CPMD should be performed at a similar level of accuracy. If accuracy is judged according to the average magnitude of the systematic errors in the computed forces, the efficiency of BOMD compares more favorably to that of CPMD than previous comparisons have suggested.
Vortex structure in a high-density nonaxisymmetric E×B equilibrium flow
Authors: Davies J. A. , Chen C.
Published: January 2006

An analysis of nonaxisymmetric E×B equilibrium flow in a crossed-field apparatus is made. The apparatus consists of a conducting circular-cylindrical cathode encompassed by either a corrugated conducting anode or by a periodically biased, circular-cylindrical wall. A uniform magnetic field is directed parallel to the cathode axis. With the aid of perturbation theory, the guiding-center approximation, and the assumption of a constant electron density in the electron layer, we determine equipotential surfaces, electron trajectories, and the corrugated boundary of the electron layer. An interesting result is the appearance of vortex structures in regions of negative potential near the cathode surface. The scaling properties of the width and potential depth of the vortex are studied for the small-amplitude corrugation regime. For sufficiently thin electron layers, results are shown to be applicable to relatively high-density regimes as well as to low-density regimes.
Electron energy transport inferences from modulated electron cyclotron heating in DIII-D
Authors: Gentle K. W. , Austin M. E. , DeBoo J. C. , Luce T. C. , Petty C. C.
Published: January 2006

Electron thermal energy transport in high-temperature plasmas is poorly understood. A useful characterization of the transport as energy flux versus temperature gradient may be obtained for a modest range of fluxes and gradients about an equilibrium by using modulated electron cyclotron heating. The transport is rapid and stiff (high χinc) at the outside, becoming slower and more diffusive toward the center.
Frequency control of photonic crystal membrane resonators by monolayer deposition
Authors: Strauf S. , Rakher M. T. , Carmeli I. , Hennessy K. , Meier C. , Badolato A. , DeDood M. J. A. , Petroff P. M. , Hu E. L. , Gwinn E. G. , Bouwmeester D.
Published: January 2006

We study the response of GaAs photonic crystal membrane resonators to thin-film deposition. Slow spectral shifts of the cavity mode of several nanometers are observed at low temperatures, caused by cryo-gettering of background molecules. Heating the membrane resets the drift and shielding will prevent drift altogether. In order to explore the drift as a tool to detect surface layers, or to intentionally shift the cavity resonance frequency, we studied the effect of self-assembled monolayers of polypeptide molecules attached to the membranes. The 2-nm-thick monolayers lead to a discrete step in the resonance frequency and partially passivate the surface.
Effect of viscous loss on mechanical resonators designed for mass detection
Authors: Vignola Joseph F. , Judge John A. , Jarzynski Jacek , Zalalutdinov Maxim , Houston Brian H. , Baldwin Jeffrey W.
Published: January 2006

Simple models are presented for estimating viscous damping of fluid (gas or liquid) loaded mechanical resonators. The models apply to beams in flexural modes of vibration, and to thin beams and plates in longitudinal modes of vibration. Predictions of the associated quality factor are compared with measured values for several macroscale and microscale resonators. The scaling of viscous loss with oscillator size is discussed. The minimum detectable mass is estimated for several oscillator designs and it is shown that, for comparably sized devices, longitudinal resonators have the lowest threshold of detection. This minimum detectable mass is proportional to scale to the power 1.75 for all resonator architectures limited by viscous damping, and it is shown that the viscous loss is 220 times larger in water than in air.
Embodiment of the warm white-light-emitting diodes by using a Ba2+ codoped Sr3SiO5:Eu phosphor
Authors: Park Joung Kyu , Choi Kyoung Jae , Yeon Jeong Ho , Lee Seung Jae , Kim Chang Hae
Published: January 2006

The shifts of the emission band to longer wavelength (yellow-orange) of the Sr3SiO5:Eu yellow phosphor under the 450–470 nm excitation range have been achieved by adding the codoping element (Ba2+) in the host. In order to apply to white-light-emitting diodes (LEDs) with warm white and high color rendering index, we have fabricated white LEDs through the integration of the InGaN blue LED chip and the two phosphor blends (Sr2SiO4:Eu yellow phosphor +Ba2+ co-doped Sr3SiO5:Eu yellow-orange phosphor) into a single package. By employing two phosphors, covering a red region, the white LEDs show a warm white in the range of 2500–5000 K correlated color temperature and a good color rendering of over 85.
Anisotropy effect on heteroepitaxial growth of self-assembled islands
Authors: Liu P. , Zhang Y. W. , Lu C.
Published: January 2006

The formation, self-assembly, and shape transition of heteroepitaxial islands during Stranski-Kranstonov growth are studied by three-dimensional computer simulations. It is shown that calculations considering surface energy anisotropy and elastic anisotropy reproduce many features of experimental results, and demonstrate the significance of their influence on island formation and self-assembly in epitaxial growth.
On the angular distribution of fast electrons generated in intense laser interaction with solid targets
Authors: Chen Min , Sheng Zheng-Ming , Zhang Jie
Published: January 2006

The angular distribution of fast electrons generated during the interaction of an ultrashort intense laser pulse incident obliquely onto solid targets is studied both analytically and numerically. A formula on the emission angles of electrons as a function of the electron kinetic energy, the incidence angle of the laser pulse, and induced quasistatic fields is found by two different methods. The quasistatic fields include electric and magnetic ones, which are generated near the target surface by the fast electrons. The two fields have the opposite contribution to the electron trajectories. In certain conditions, electrons can move near the target surface.
Determination of trap polarity in conjugated electroluminescent polymer by photoexcitation thermally stimulated current method
Authors: Tseng Hao-En , Liu Ching-Yang , Chen Show-An
Published: January 2006

We succeed in using a photoexcitation thermally stimulated current (TSC) technique for a determination of trap states for poly[2-methoxy-5-(2’-ethylhexyloxy)-1,4-phenylene vinylene] (MEH-PPV). By use of this method, the trap polarity can be easily and clearly assigned. We provide direct evidence that molecular oxygen can form electron traps in MEH-PPV, while moisture cannot result in detectable hole traps. An unusual negative field-dependent TSC is observed for detrapping electron current, indicating a lowering of electron mobility under increased electric field. The state of observed hole trap is not affected by an exposure to ambient air and by a change of morphology, but can be attributed to extrinsic impurities or structure defects.
Size-selective high-yield growth of lead telluride (PbTe) nanocrystals using a chemical vapor deposition technique
Authors: Zhang Bo , He J. , Tritt Terry M.
Published: January 2006

Lead telluride (PbTe) nanocrystals have been synthesized using a chemical vapor deposition technique. The size-selective precipitation mechanism enables relatively good control of the particle size distribution by variation of the heating temperature, the Ar gas flow rate, and an admixture with Au particles. As the result, a high yield of several hundred milligrams of nanocrystals that exhibit rather narrow size distributions of 100, 200, and 600nm have been obtained. X-ray diffraction studies confirm the PbTe crystal structure and in addition find that the lattice constant monotonically increases with diminishing particle size.
High carrier mobility on hydrogen terminated ⟨100⟩ diamond surfaces
Authors: Rezek B. , Watanabe H. , Nebel C. E.
Published: January 2006

An increase in carrier mobility from typical values around 100 to more than 300cm2∕Vs at room temperature is detected on hydrogenated undoped ⟨100⟩ diamond layers after annealing at 400 K in a vacuum. As a function of temperature in the range 400 to 125 K the high mobility followed tendencies remarkably close ionized impurity (toward low temperatures) and phonon scattering (toward high temperatures). As a function of annealing time, the high mobility increased with the time constant of about 6.8 h in the range of 1–16 h. A prerequisite for obtaining the largest increase in mobility was optimized surface cleanness. Exposing the samples to air resulted in a complete recovery of the original values of mobility, hole concentration, and conductivity after several days. The data are discussed in terms of interactions between holes in the surface conductive channel and adsorbates on the surface.
Reproduction of mouse-pup ultrasonic vocalizations by nanocrystalline silicon thermoacoustic emitter
Authors: Kihara Takashi , Harada Toshihiro , Kato Masahiro , Nakano Kiyoshi , Murakami Osamu , Kikusui Takefumi , Koshida Nobuyoshi
Published: January 2006

As one of the functional properties of ultrasound generator based on efficient thermal transfer at the nanocrystalline silicon (nc-Si) layer surface, its potential as an ultrasonic simulator of vocalization signals is demonstrated by using the acoustic data of mouse-pup calls. The device composed of a surface-heating thin-film electrode, an nc-Si layer, and a single-crystalline silicon (c-Si) wafer, exhibits an almost completely flat frequency response over a wide range without any mechanical surface vibration systems. It is shown that the fabricated emitter can reproduce digitally recorded ultrasonic mouse-pups vocalizations very accurately in terms of the call duration, frequency dispersion, and sound pressure level. The thermoacoustic nc-Si device provides a powerful physical means for the understanding of ultrasonic communication mechanisms in various living animals.
Enhanced hole transport from Au to Zn-phthalocyanine by an insertion of a thin n-type layer
Authors: Nonomura Makoto , Hiromitsu Ichiro , Tanaka Senku
Published: January 2006

A thin C60 or bathocuproine (BCP) layer of 5 nm thickness is inserted to the Au/Zn-phthalocyanine (ZnPc) interface of a Au/ZnPc/In/Al Schottky-junction cell, and the effect of the insertion on the dark current is investigated. The forward dark current density is increased from 0.5mA∕cm2 to 9.7 and 9.2mA∕cm2 by the insertions of the C60 and BCP layers, respectively. The increase is not attributed to a change in the barrier height for the hole injection, but to a decrease of the concentration of trapped negative charges on the ZnPc surface.
Drift mobility in quantum nanostructures by scanning probe microscopy
Authors: Giannazzo F. , Raineri V. , Mirabella S. , Impellizzeri G. , Priolo F
Published: January 2006

We used scanning capacitance microscopy (SCM) and scanning spreading resistance microscopy (SSRM) to determine the drift hole mobility in nanometer thick Si∕Si0.75Ge0.25∕Si quantum wells (QWs), from the carrier concentration profiles (obtained by SCM) and the local resistivity values (obtained by SSRM). A relevant decrease of the hole mobility at room temperature was observed when reducing the QW width from 10 nm down to 1 nm. This effect has been explained in terms of the increasing role of surface scattering at the Si∕SiGe interface for lower QW widths.
Ferroelectric gate for control of transport properties of two-dimensional electron gas at AlGaN∕GaN heterostructures
Authors: Stolichnov Igor , Malin Lisa , Muralt Paul , Setter Nava
Published: January 2006

The concept of a field-effect transistor with ferroelectric gate has been implemented using the GaN∕AlGaN heterostructure combined with Pb(Zr,Ti)O3 ferroelectric layer. The processing conditions were optimized in a way to obtain textured Pb(Zr,Ti)O3 films without destroying the two-dimensional electron gas (2D gas) situated at 20nm below the interface. Poling the ferroelectric layer through the conductive cantilever of the atomic force microscope results in a stable change of resistance of the 2D gas. Concentration and mobility of electrons in the 2D gas were monitored using Hall effect and four-probe conduction measurements in a wide temperature range from 12to300K. The gate polarization oriented in the direction from bottom to top provokes a partial depletion in the channel, resulting in a conductivity decrease by factor of 2.5–3. The depletion effect is found to be reversible so that the initial conductivity in the 2D gas can be restored by depoling the ferroelectric gate. These results indicate that the ferroelectric gate integrated onto the GaN-based system with 2D gas is potentially interesting for nonvolatile memories. Additionally, direct domain writing on a ferroelectric gate represents a flexible and nondestructive way of making rewritable nanopatterns projected onto low-dimensional semiconductor structures.
Yeast AMID Homologue Ndi1p Displays Respiration-restricted Apoptotic Activity and Is Involved in Chronological Aging
Authors: Li Wei , Sun Libo , Liang Qiuli , Wang Juan , Mo Weike , Zhou Bing
Published: January 2006

Apoptosis-inducing factor (AIF) and AIF-homologous mitochondrion-associated inducer of death (AMID) are both mitochondrial flavoproteins that trigger caspase-independent apoptosis. Phylogenetic analysis suggests that these two proteins evolutionarily diverge back from their common prokaryote ancestor. Compared with AIF, the proapoptotic nature of AMID and its mode of action are much less clarified. Here, we show that overexpression of yeast AMID homologue internal NADH dehydrogenase (NDI1), but not external NADH dehydrogenase (NDE1), can cause apoptosis-like cell death, and this effect can be repressed by increased respiration on glucose-limited media. This result indicates that the regulatory network of energy metabolism, in particular the cross-talk between mitochondria and the rest of the cell, is involved in Ndi1p-induced yeast cell apoptosis. The apoptotic effect of NDI1 overexpression is associated with increased production of reactive oxygen species (ROS) in mitochondria. In addition, NDI1 overexpression in sod2 background causes cell lethality in both fermentable and semifermentable media. Interruption of certain components in the electron transport chain can suppress the growth inhibition from Ndi1p overexpression. We finally show that disruption of NDI1 or NDE1 decreases ROS production and elongates the chronological life span of yeast, accompanied by the loss of survival fitness. Implication of these findings for Ndi1p-induced apoptosis is discussed.
Activity- and Calcineurin-independent Nuclear Shuttling of NFATc1, but Not NFATc3, in Adult Skeletal Muscle Fibers
Authors: Shen Tiansheng , Liu Yewei , Cseresnyés Zoltán , Hawkins Arie , Randall William R. , Schneider Martin F.
Published: January 2006

The transcription factor NFATc1 may be involved in slow skeletal muscle gene expression. NFATc1 translocates from cytoplasm to nuclei during slow fiber type electrical stimulation of skeletal muscle fibers because of activation of the Ca2+-dependent phosphatase calcineurin, resulting in nuclear factor of activated T-cells (NFAT) dephosphorylation and consequent exposure of its nuclear localization signal. Here, we find that unstimulated adult skeletal muscle fibers exhibit a previously unanticipated nucleocytoplasmic shuttling of NFATc1 without appreciable nuclear accumulation. In resting fibers, the nuclear export inhibitor leptomycin B caused nuclear accumulation of NFATc1 (but not of isoform NFATc3) and formation of NFATc1 intranuclear bodies independent of calcineurin. The rate of nuclear uptake of NFATc1 was 4.6 times lower in resting fibers exposed to leptomycin B than during electrical stimulation. Inhibitors of glycogen synthase kinase and protein kinase A or of casein kinase 1 slowed the decay of nuclear NFATc1 after electrical stimulation, but they did not cause NFATc1 nuclear uptake in unstimulated fibers. We propose that two nuclear translocation pathways, one pathway mediated by calcineurin activation and NFAT dephosphorylation and the other pathway independent of calcineurin and possibly independent of NFAT dephosphorylation, determine the distribution of NFATc1 between cytoplasm and nuclei in adult skeletal muscle.
Heterodimeric Capping Protein fromArabidopsisIs Regulated by Phosphatidic Acid
Authors: Huang Shanjin , Gao Lisa , Blanchoin Laurent , Staiger Christopher J.
Published: January 2006

The cytoskeleton is a key regulator of morphogenesis, sexual reproduction, and cellular responses to extracellular stimuli. Changes in the cellular architecture are often assumed to require actin-binding proteins as stimulus-response modulators, because many of these proteins are regulated directly by binding to intracellular second messengers or signaling phospholipids. Phosphatidic acid (PA) is gaining widespread acceptance as a major, abundant phospholipid in plants that is required for pollen tube tip growth and mediates responses to osmotic stress, wounding, and phytohormones; however, the number of identified effectors of PA is rather limited. Here we demonstrate that exogenous PA application leads to significant increases in filamentous actin levels in Arabidopsis suspension cells and poppy pollen grains. To investigate further these lipid-induced changes in polymer levels, we analyzed the properties of a key regulator of actin filament polymerization, the heterodimeric capping protein from Arabidopsis thaliana (AtCP). AtCP binds to PA with a Kdvalue of 17 μM and stoichiometry of ∼1:2. It also binds well to PtdIns(4,5)P2, but not to several other phosphoinositide or acidic phospholipids. The interaction with PA inhibited the actin-binding activity of CP. In the presence of PA, CP is unable to block the barbed or rapidly growing and shrinking end of actin filaments. Precapped filament barbed ends can also be uncapped by addition of PA, allowing rapid filament assembly from an actin monomer pool that is buffered with profilin. The findings support a model in which the inhibition of CP activity in cells by elevated PA results in the stimulation of actin polymerization from a large pool of profilin-actin. Such regulation may be important for the response of plant cells to extracellular stimuli as well as for the normal process of pollen tube tip growth.
DNA Damage Signaling and p53-dependent Senescence after Prolonged β-Interferon Stimulation
Authors: Moiseeva Olga , Mallette Frédérick A. , Mukhopadhyay Utpal K. , Moores Adrian , Ferbeyre Gerardo
Published: January 2006

Interferons are cytokines with potent antiviral and antiproliferative activities. We report that although a transient exposure to β-interferon induces a reversible cell cycle arrest, a sustained treatment triggers a p53-dependent senescence program. β-Interferon switched on p53 in two steps. First, it induced the acetylation of p53 at lysine 320 and its dephosphorylation at serine 392 but not p53 activity. Later on, it triggered a DNA signaling pathway, the phosphorylation of p53 at serine 15 and its transcriptional activity. In agreement, β-interferon–treated cells accumulated γ-H2AX foci and phosphorylated forms of ATM and CHK2. The DNA damage signaling pathway was activated by an increase in reactive oxygen species (ROS) induced by interferon and was inhibited by the antioxidant N-acetyl cysteine. More important, RNA interference against ATM inhibited p53 phosphorylation at serine 15, p53 activity and senescence in response to β-interferon. β-Interferon–induced senescence was more efficient in cells expressing either, p53, or constitutive allele of ERK2 or RasV12. Hence, β-interferon–induced senescence targets preferentially cells with premalignant changes.
Soil structure and soil‐borne diseases: using epidemiological concepts to scale from fungal spread to plant epidemics
Authors: Otten W. , Gilligan C. A.
Published: January 2006

Many epidemics of root diseases involving soil fungi depend on the interplay between fungal growth and the spatial and temporal heterogeneity of the soil environment. Colonization or infection of a root occurs at fine scales with growth and movement of fungal mycelia through soil. However, epidemics are observed at coarser scales, and depend on a cascading spread through populations of roots. We briefly review conventional analyses of soil‐borne epidemics and argue that these treat soil physical conditions at scales too coarse to be meaningful for interactions between soil, plants and fungi, and fail to consider the effect of soil physical conditions on the underlying epidemiological processes. Instead, we propose a conceptual epidemiological framework that integrates spatial scales and use this to review the effect of soil structure on the dynamics of soil‐borne pathogenic fungi. Using the soil‐borne fungal plant pathogenRhizoctonia solanias an example, we demonstrate that invasion of fungi into host populations is critically affected by environmental conditions operating at each of two scales: (i) at the microscopic scale (μm − cm) the fungus preferentially explores certain pathways in soil, and small changes in soil physical conditions make the fungus switch from small, dense colonies to large, sparse and rapidly expanding ones; (ii) at the larger scale (cm − dm) a critical density of susceptible hosts is required, in excess of which fungi switch from non‐invasive to invasive spread. Finally, we suggest that the approach will increase the applicability of research dealing with microscopic soil–plant–microbe interactions towards the solution of large‐scale epidemiological problems.