bluuebunny/crossref_metadata_2025 huggingface dataset:
On the propagation of a quasi‐static disturbance in a heterogeneous, deformable, and porous medium with pressure‐dependent properties
Authors: Vasco D. W.
Published: November 2011

Using an asymptotic technique, valid when the medium properties are smoothly varying, I derive a semianalytic expression for the propagation velocity of a quasi‐static disturbance traveling within a nonlinear‐elastic porous medium. The phase, a function related to the propagation time, depends upon the properties of the medium, including the pressure sensitivities of the medium parameters, and on pressure and displacement amplitude changes. Thus, the propagation velocity of a disturbance depends upon its amplitude, as might be expected for a nonlinear process. As a check, the expression for the phase function is evaluated for a poroelastic medium when the material properties do not depend upon the fluid pressure. In that case, the travel time estimates agree with conventional analytic estimates and with values calculated using a numerical simulator. For a medium with pressure‐dependent permeability I find general agreement between the semianalytic estimates and estimates from a numerical simulation. In this case the pressure amplitude changes are obtained from the numerical simulator.
How Stereological Analysis of Vascular Morphology Can Quantify the Blood Volume Fraction as a Marker for Tumor Vasculature: Comparison with Magnetic Resonance Imaging
Authors: Perles-Barbacaru Adriana T , van der Sanden Boudewijn PJ , Farion Regine , Lahrech Hana
Published: November 2011

To assess angiogenesis noninvasively in a C6 rat brain tumor model, the rapid-steady-state- T1 (RSST1) magnetic resonance imaging (MRI) method was used for microvascular blood volume fraction (BVf) quantification with a novel contrast agent gadolinium per (3,6 anhydro) α-cyclodextrin (Gd-ACX). In brain tissue contralateral to the tumor, equal BVfs were obtained with Gd-ACX and the clinically approved gadoterate meglumine (Gd-DOTA). Contrary to Gd-DOTA, which leaks out of the tumor vasculature, Gd-ACX was shown to remain vascular in the tumor tissue allowing quantification of the tumor BVf. We sought to confirm the obtained tumor BVf using an independent method: instead of using a ‘standard’ two-dimensional histologic method, we study here how vascular morphometry combined with a stereological technique can be used for three-dimensional assessment of the vascular volume fraction ( VV). The VV is calculated from the vascular diameter and length density. First, the technique is evaluated on simulated data and the healthy rat brain vasculature and is then applied to the same C6 tumor vasculature previously quantified by RSST1-MRI with Gd-ACX. The mean perfused VV and the BVf obtained by MRI in tumor regions are practically equal and the technique confirms the spatial heterogeneity revealed by MRI.
Homology modeling and docking studies to explore the novel drug for monocyte differentiation antigen CD14
Authors: Reshma Bhimisetty , Swaragam Sandeep , Umamaheswari Amineni
Published: November 2011

Monocyte differentiation antigen CD14 belongs to the leucine rich family. Elevated levels of monocyte differentiation antigen CD14 and toll-like receptor 4 (TLR4) play a major role in inflammatory response and cause ischemic heart diseases, neuropathic pain and LPS (endotoxin) induced septic shock. IAXO compounds (IAXO-101, IAXO-102 and IAXO-103) inhibit the CD14-dependent and TLR4-independent signaling pathways but they have severe side effects. Due to unavailability of human monocyte differentiation antigen CD14 crystal structure, 3D structure was constructed based on template structure (1WWL) using Modeler 9v9. The modeled structure was refined, energy minimized and validated. Binding site residues of human monocyte differentiation antigen CD14 were predicted using CASTp. The existing compounds were explored in ligand.info database via analog search. Docking analysis was carried out by Schrodinger Maestro 9.2. In the present study, six leads with good pharmacological properties were proposed. Lead 1 (-10.8169 Kcal/mol docking score) has good binding affinity with binding site residues of monocyte differentiation antigen CD14 such as Trp-45, Phe-38, Ala-61, Leu-66, Phe-69, Ile-59, Val-73, Val-96, Ala-99, Ala-100, Val-101, Leu-105, Leu-106, and Leu-126. The lead 1 inhibits CD14-dependent and TLR4-independent signaling pathways which in turn control the inflammatory diseases.
Homology modeling and in silico screening of inhibitors for human CD5 antigen-like protein involved in cardiovascular disease
Authors: Sravani Varala , Rajitha Reddy S , Umamaheswari Amineni
Published: November 2011

CD5L (CD5 antigen -like) is a secreted glycoprotein that belongs to the SRCR (scavenger receptor cysteine rich) group B family of proteins that regulate leukocyte function. Over expression of human CD5L leads to Kawasaki disease and atherosclerosis. In the quest of designing novel inhibitors against CD5L, homology models for the protein were predicted based on crystal structures of 1BY2, 2OYA and 2OY3 as multiple templates using Modeller 9v9. The CD5L homology models were selected using GA341 score, DOPE score, PROCHECK and ProSA to select the best model. The selected CD5L model was analyzed using CASTp to locate the largest ligand binding pocket. Five known inhibitors of human CD5L were searched for structural analogs from Ligand.Info Meta database. The structural analog dataset (2000) was docked with CD5L using the three phased docking protocol of Maestro v9.2 that implements Glide v5.7. Seven lead molecules showed better binding affinity (lower XPGscore) compared to five known CD5L inhibitors. The binding orientations of the seven leads compared favorably with known CD5L inhibitors. The seven leads also revealed good pharmacological properties (following Lipinski Rule of Five; Zero reactive functional group) and hence were proposed as new class of CD5L inhibitors. The proposed inhibitors would be useful for rational drug design towards treatment of cardiovascular disease if synthesized and validated in animal models.
α-Haemoglobin regulates sympathoadrenal cell metabolism to maintain a catecholaminergic phenotype
Authors: Marcos-Almaraz María T. , Rodríguez-Gómez José A. , López-Barneo José , Pascual Alberto
Published: November 2011

Discovery of haemoglobin A expression outside of the erythroid cell lineage suggests that oxygen transport is the main, but not the unique, function of adult haemoglobin chains in mammals. The contribution of haemoglobin A to antioxidant defences has been proposed in the territories where it is expressed. Catecholaminergic cells rely on an active oxidative metabolism to accomplish their biological function, but are exposed to strong oxidative stress due to metabolism of catecholaminergic transmitters. We show in the present study that peripheral catecholaminegic cells express the α- and not the β-haemoglobin A chains, and that α-haemoglobin expression could modulate the antioxidant capabilities of these cells. We also show that α-haemoglobin overexpression in PC12 cells leads to a selective increase of tyrosine hydroxylase synthesis and activity. This is achieved by means of a reorganization of antioxidant defences, decreasing cytoplasmic glutathione peroxidase and superoxide dismutase, and increasing mitochondrial peroxidase. Moreover, α-haemoglobin induces a decrease in lipogenesis and increase in lipid degradation, situations that help save NAD(P)H and favour supply of acetyl-CoA to the tricarboxylic acid cycle and production of reducing equivalents in the cell. All of these results point to a role for α-haemoglobin as a regulator of catecholaminergic cell metabolism required for phenotype acquisition and maintenance.
Diabetes and Incident Depression: Is the Association Mediated or Modified by Sociodemographic Factors or Co-morbidities? A Systematic Review
Authors: Albers B. , Kruse J. , Giani G. , Icks A.
Published: November 2011

Diabetic patients suffer more frequently from depression. Aim was to evaluate sociodemographic parameters and co-morbidities and late complications as potential modifying factors in the occurrence of depression in diabetic individuals.

We performed a systematic review, based on established meta-analyses and additional original publications in 2005–2009 in Medline and PsycINFO. We included articles focusing on longitudinal studies which evaluated the appearance of depression in diabetic and non diabetic individuals and further analyzed interactions or separate additional influences of potential modifying factors.

8 eligible studies were identified. 6 studies were population based. Only 3 studies analyzed the interaction between the variables of interest and diabetes on the incidence of depression. Remaining used diverse other methods to control for associated factors.

The strongest influence was found for a general measure of co-morbidities but this influence was ambiguous. No significant modifying effect or interaction was found for sociodemographic factors.

There seems to be a clear need for more research concerning mediating and modifying factors or a more stringent presentation of results in order to identify groups at risk or to identify treatment strategies.
Effects of Isolated Hyperinsulinaemia on Sensory Function in Healthy Adults
Authors: Søfteland E. , Dimcevski G. , Graversen C. , Nedrebø B. , Drewes A. , Frøkjær J.
Published: November 2011

Gastrointestinal symptoms such as pain, bloating, nausea and vomiting are more frequent in pre-diabetic states as well as established diabetes, compared to healthy individuals. The mechanisms behind these symptoms are multi-factorial and complex. Furthermore, the effect of isolated hyperinsulinaemia on visceral and peripheral sensory function is poorly understood. Thus, the current study aimed to evaluate effects of acute hyperinsulinaemia on sensory function in healthy adults.

The sensitivity to electrical oesophageal and median nerve stimulation was assessed in 15 healthy volunteers together with recording of evoked brain potentials. All subjects were studied both fasting and using a euglycaemic hyperinsulinaemic clamp.

There was on average a 15% increased sensitivity to oesophageal electrical stimulation during hyperinsulinaemia compared to fasting state (P<0.05), but the sensation after median nerve stimulation remained stable (P=0.58). No significant changes in latencies and amplitudes of evoked brain potentials were observed after oesophageal or median nerve stimulation (all P>0.05).

This study suggests that acute isolated hyperinsulinaemia increases visceral sensitivity, but does not influence the somatic sensory function. The lack of changes in the evoked brain potentials may indicate that hyperinsulinaemia affects the visceral sensory system at a peripheral level. Our result suggests distinct functions of insulin in the various parts of the nervous system, and yields further clues to the significance of insulin as a satiety signal.
Relationship between Plasma Aldosterone Concentration and Soluble Cellular Adhesion Molecules in Patients Referred to Coronary Angiography
Authors: Tomaschitz A. , Pilz S. , Ritz E. , Grammer T. , Amrein K. , Merger S. , Meinitzer A. , Winkelmann B. , Boehm B. , März W.
Published: November 2011

Evidence is emerging that aldosterone contributes to the development and progression of atherosclerosis and cardiovascular disease. Little is known, however, regarding an association between circulating aldosterone levels and soluble cellular adhesion molecules in humans.

We investigated the relationship between plasma aldosterone concentration (PAC) and soluble cellular adhesion molecules in a large cohort of patients referred to coronary angiography. After exclusion of patients with ongoing mineralocorticoid receptor blocker use, oral contraceptive or hormone replacement therapy, 1 733 patients (mean age: 62.5±10.8 years; 26.4%% women; mean PAC: 101.5±93.5 pg/mL) remained eligible for analyses.

Pearson correlation analysis as well as age and gender adjusted partial correlation analysis revealed a positive association between PAC and soluble (s) E-, L- and P-selectin levels but not with sICAM-1 and sVCAM-1, respectively. In multivariate adjusted analyses of covariance (ANCOVA) sE- (p=0.026), sL- (p=0.049) and sP-selectin (p<0.001) levels increased steadily from the first (reference) to the third gender-specific tertile of PAC. No significant variation across PAC tertiles was found for sICAM-1 (p=0.767) and sVCAM1 (p=0.425) levels, respectively. Finally, multivariate regression analyses revealed circulating aldosterone as an important predictor for soluble selectin levels.

Our findings in a large cohort of patients indicate that upregulation of selectins might represent a novel mechanism of aldosterone mediated development and progression of atherosclerosis. In view of aldosterone as a novel cardiovascular risk factor independent of angiotensin II, our findings warrant further interventional studies which should evaluate anti-atherosclerotic effects of aldosterone blocking treatment strategies in humans.
Lipid Infiltration in the Parotid Glands: A Clinical Manifestation of Metabolic Syndrome
Authors: Hida A. , Akahoshi M. , Takagi Y. , Imaizumi M. , Sera N. , Soda M. , Maeda R. , Nakashima E. , Ida H. , Kawakami A. , Nakamura T. , Eguchi K.
Published: November 2011

The clinical features of lipid infiltration in the parotid glands (LIPG) have not been studied. Monitoring of atomic-bomb survivors for late effects of radiation exposure has provided the opportunity to review the clinical findings of LIPG.

A total of 992 atomic-bomb survivors in Nagasaki, Japan underwent lachrymal and salivary secretion tests and anthropometric, biochemical, and abdominal ultrasonographic examinations between 2002 and 2004. Among 465 subjects who had reduced tear and/or salivary excretion, 176 subjects took a salivary magnetic resonance imaging (MRI) examination.

LIPG was detected in 53 of the 176 subjects who had salivary MRI. LIPG cases showed a preponderance of females and fatty liver compared with the subjects without LIPG. Age-and-sex-adjusted regression analysis revealed that body mass index (BMI), low-density lipoprotein cholesterol, triglycerides, hemoglobin A1c, and C-reactive protein were higher, whereas high-density lipoprotein cholesterol and adiponectin were lower, in the subjects with LIPG. Multivariate logistic regression analysis showed that BMI and fatty liver were mutually associated with LIPG independently from radiation dose.

LIPG associated with BMI, fatty liver, and coronary risk factors was a clinical manifestation of metabolic syndrome.
Spin-orbit and rotational couplings in radiative association of C(3P) and N(4S) atoms
Authors: Antipov Sergey V. , Gustafsson Magnus , Nyman Gunnar
Published: November 2011

The role of spin-orbit and rotational couplings in radiative association of C(3P) and N(4S) atoms is investigated. Couplings among doublet electronic states of the CN radical are considered, giving rise to a 6-state model of the process. The solution of the dynamical problem is based on the L2 method, where a complex absorbing potential is added to the Hamiltonian operator in order to treat continuum and bound levels in the same manner. Comparison of the energy-dependent rate coefficients calculated with and without spin-orbit and rotational couplings shows that the couplings have a strong effect on the resonance structure and low-energy baseline of the rate coefficient.
Flute instability in the tandem mirror with the divertor/dipole regions
Authors: Katanuma I. , Masaki S. , Sato S. , Sekiya K. , Ichimura M. , Imai T.
Published: November 2011

The numerical simulation is performed in GAMMA10 A-divertor magnetic configuration, which is a candidate of remodeled device of the GAMMA10 tandem mirror [M. Inutake et al., Phys. Rev. Lett. 55, 939 (1985)]. Both divertor and dipole regions are included in the numerical calculation, which is a new point. The electron short circuit effect along x-point, therefore, is not assumed so that it is not used the boundary condition of the electrostatic perturbations being zero at the separatrix on which the magnetic field lines pass through x-point. The simulation results reveal that the dipole field plays a role of a good magnetic field line curvature to the GAMMA10 A-divertor, and so the flute modes are stabilized without help of electron short circuit effects.
Spectral phonon conduction and dominant scattering pathways in graphene
Authors: Singh Dhruv , Murthy Jayathi Y. , Fisher Timothy S.
Published: November 2011

In this paper, we examine the lattice thermal conductivity and dominant phonon scattering mechanisms of graphene. The interatomic interactions are modeled using the Tersoff interatomic potential and perturbation theory is applied to calculate the transition probabilities for three-phonon scattering. The matrix elements of the perturbing Hamiltonian are calculated using the anharmonic interatomic force constants obtained from the interatomic potential as well. The linearized Boltzmann transport equation is applied to compute the thermal conductivity of graphene for a wide range of parameters giving spectral and polarization-resolved information. The complete spectral detail of selection rules, important phonon scattering pathways, and phonon relaxation times in graphene are provided. We also highlight the specific scattering processes that are important in Raman spectroscopy-based measurements of graphene thermal conductivity, and provide a plausible explanation for the observed dependence on laser spot size.
Interaction of large scale flow structures with gyrokinetic turbulence
Authors: McMillan B. F. , Hill P. , Bottino A. , Jolliet S. , Vernay T. , Villard L.
Published: November 2011

Shear flows have a profound influence on turbulence-driven transport in tokamaks. The introduction of arbitrary initial flow profiles into the code ORB5 [Jolliet et al., Comput. Phys. Commun. 177, 409 (2007)] allows the convenient study of how flows on all length scales both influence transport levels and self-consistently evolve. A formulation is presented which preserves the canonical structure of the background particle distribution when either toroidal or poloidal flows are introduced. Turbulence suppression is possible above a certain shearing rate magnitude for homogeneous shear flows, and little evolution of the shearing rate is seen. However, when a flow with a zone boundary, where the shearing rate reverses at mid-radius, is introduced, the shear flow evolves substantially during the simulation. E × B shear flows with a zone boundary of a positive sign decay to a saturation amplitude, consistent with the well known saturation of turbulently generated zonal flows. Unlike the E × B flow, the parallel flows relax diffusively.
Predator prey oscillations in a simple cascade model of drift wave turbulence
Authors: Berionni V. , Gürcan Ö. D.
Published: November 2011

A reduced three shell limit of a simple cascade model of drift wave turbulence, which emphasizes nonlocal interactions with a large scale mode, is considered. It is shown to describe both the well known predator prey dynamics between the drift waves and zonal flows and to reduce to the standard three wave interaction equations. Here, this model is considered as a dynamical system whose characteristics are investigated. The analytical solutions for the purely nonlinear limit are given in terms of the Jacobi elliptic functions. An approximate analytical solution involving Jacobi elliptic functions and exponential growth is computed using scale separation for the case of unstable solutions that are observed when the energy injection rate is high. The fixed points of the system are determined, and the behavior around these fixed points is studied. The system is shown to display periodic solutions corresponding to limit cycle oscillations, apparently chaotic phase space orbits, as well as unstable solutions that grow slowly while oscillating rapidly. The period doubling route to transition to chaos is examined.
Using time-integrated Kα images to study refluxing and the extent of pre-plasmas in intense laser-plasma experiment
Authors: Ovchinnikov V. M. , Schumacher D. W. , Kemp G. E. , Krygier A. G. , Van Woerkom L. D. , Akli K. U. , Freeman R. R. , Stephens R. B. , Link A.
Published: November 2011

We report the results of an experimental and numerical modeling study of the formation of time-integrated Kα images by electrons excited during an intense laser-plasma interaction. We report the use of the spatial structure of time-integrated Kα images to quantitatively characterize the pre-plasma profile near the critical surface and to verify the near elimination of back-surface refluxing from targets when a thick layer of a low-Z material is attached to the back. The time integrated Kα images are found to be sensitive to the relative separation between the critical surface and the bulk target, permitting a single parameter exponential pre-plasma scale length to be determined by fitting to experimental results. The refluxed electrons affect different parts of the Kα images in a manner that varies depending on the location of the refluxing. We use these properties to characterize refluxing also by fitting to experimental results. Experiments were performed using the Titan laser at the Lawrence Livermore National Laboratory and the simulations used a customized version of the hybrid-PIC code, LSP. We find good quantitative match between experiment and simulation.
Magnetic reconnection in partially ionized plasmas
Authors: Zweibel Ellen G. , Lawrence Eric , Yoo Jongsoo , Ji Hantao , Yamada Masaaki , Malyshkin Leonid M.
Published: November 2011

We review the theory of magnetic reconnection in weakly ionized gases. The theory is relevant to reconnection in the interstellar medium, protostellar and protoplanetary disks, the outer envelopes of cool stars, and a new laboratory experiment. In general, partial ionization introduces three effects beyond the obvious one: increased resistivity due to electron-neutral collisions. First, magnetic neutral sheets are steepened by plasma-neutral drift, setting up the conditions for reconnection. Second, when ion-neutral friction is strong, the effective ion mass is increased by ρ/ρi, the ratio of total to plasma mass density. This reduces the Alfven speed vA by a factor of ρ/ρi and increases the ion skin depth δi by ρ/ρi. As a result, entrainment of neutrals slows MHD reconnection but permits the onset of fast collisionless reconnection at a larger Lundquist number S, or for a longer current sheet, than in the fully ionized plasma case. These effects, taken together, promote fast collisionless reconnection when the ionization fraction is of order 10% to 1%, but reconnection is slowed down for much smaller ionization fractions. Finally, ion-neutral friction can be a strong heating mechanism throughout the inflow and outflow regions. These effects are under study at the Magnetic Reconnection Experiment (MRX).
Oblique propagation of electrostatic waves in a magnetized electron-positron-ion plasma with superthermal electrons
Authors: Alinejad H. , Mamun A. A.
Published: November 2011

A theoretical investigation is carried out to understand the basic features of linear and nonlinear propagation of ion-acoustic (IA) waves subjected to an external magnetic field in an electron-positron-ion plasma which consists of a cold magnetized ion fluid, Boltzmann distributed positrons, and superthermal electrons. In the linear regime, the propagation of two possible modes (fast and slow) and their evolution are investigated. It is shown that the electron superthermality and the relative fraction of positrons cause both modes to propagate with smaller phase velocities. Also, two special cases of dispersion relation are found, which are related to the direction of the wave propagation. In the nonlinear regime, the Korteweg-de Vries (KdV) equation describing the propagation of fast and slow IA waves is derived. The latter admits a solitary wave solution with only negative potential in the weak amplitude limit. It is found that the effects of external magnetic field (obliqueness), superthermal electrons, positron concentration, and temperature ratio significantly modify the basic features of solitary waves.
Development of a new dynamic procedure for the Clark model of the subgrid-scale scalar flux using the concept of optimal estimator
Authors: Fabre Y. , Balarac G.
Published: November 2011

Accurate prediction of a scalar advected by a turbulent flow is needed for various applications. In the framework of large-eddy simulation (LES), an accurate subgrid-scale (SGS) model for the subgrid-scale scalar flux has to be used. In this work, the performance of various dynamic SGS models is first evaluated by a priori tests through the concept of optimal estimator. Direct numerical simulation (DNS) in homogeneous isotropic turbulence is performed on 5123 grid points. Filtered quantities are extracted from the DNS data using a box or a spectral cut-off filter. The models’ accuracy is then evaluated in term of structural and functional performances, i.e., the model capacity to locally approximate the SGS unknown term and to reproduce its energetic action, respectively. It is shown that the Clark model has the best set of parameters to describe the SGS scalar flux. However, the classic dynamic procedure usually applied to compute the model coefficient leads to a large error. A new dynamic procedure is thus proposed to reduce this error. The results show that the new dynamic model leads to a good accuracy, which is not expectable from a model based only on the parameters of the classic dynamic Smagorinsky model. To better evaluate the improvement of the new dynamic procedure, a posteriori (large-eddy simulation) tests are performed for three different Schmidt numbers. It is shown that the new model allows to improve substantially the prediction of various scalar statistics.
Resonant three–wave interaction of Holmboe waves in a sharply stratified shear flow with an inflection–free velocity profile
Authors: Churilov S. M.
Published: November 2011

Within the context of the well-known interpretation in terms of the wave interaction [P. G. Baines and H. Mitsudera, J. Fluid Mech. 276, 327 (1994); J. R. Carpenter et al., Phys. Fluids 22, 054104 (2010)], instability of sharply stratified (so that the vertical scale ℓ of density variation is much smaller than the scale Λ of velocity shear) flows with inflection-free velocity profiles should be treated as Holmboe’s instability. In such flows with a relatively weak stratification (when the bulk Richardson number J < (ℓ/Λ)3/2), eigenoscillations (i.e., Holmboe waves) have much the same phase velocities in a broad spectral range. This creates favorable conditions for a wide variety of three-wave interactions, in contrast to the homogeneous boundary layers where subharmonic resonance is the only effective three-wave process. In the paper, evolution equations are derived which describe three-wave interactions of Holmboe waves and have the form of nonlinear integral equations. Analytical and numerical methods are both used to find their solutions in different cases, and it is shown that at the nonlinear stage disturbances increase, as a rule, explosively. Some possible relations of the results obtained with those of numerical simulations and laboratory experiments are briefly discussed.
Optical interference effect on pattern formation in thin liquid films on solid substrates induced by irradiative heating
Authors: Saeki Fumihiro , Fukui Shigehisa , Matsuoka Hiroshige
Published: November 2011

The pattern formation in thin liquid films on solid substrates induced by irradiative heating is investigated. A model to describe the evolution of both the film surface profile and temperature field in the system is developed, in which the energy absorption into the film and substrate, and the energy reflection to which optical absorption and interference contribute are taken into account. The model consists of a thin film equation that describes the time evolution of the film surface profile and a heat equation for the substrate. The former is obtained within the framework of the long-wave approximation, in which the fluid layer is assumed to be sufficiently thin compared to the lateral length scale, while the latter is unconstrained by the substrate thickness. In order to examine the interference effects on the pattern formation, focus is placed on a transparent film/absorbable substrate system irradiated by a monochromatic wave with laterally uniform intensity distribution. In such a case, the energy reflectance varies periodically with the film thickness due to optical interference. Numerical simulation results show that the stability of the film depends on the first derivative of the energy reflectance with respect to the film thickness at a reference point, and the resultant surface patterns, which include phase separation and periodic wavy patterns, differ depending on the reference thickness and initial perturbation. The stability revealed by the numerical results is confirmed by linear stability analysis of a simplified model.
Switching and rectification of a single light-sensitive diarylethene molecule sandwiched between graphene nanoribbons
Authors: Cai Yongqing , Zhang Aihua , Ping Feng Yuan , Zhang Chun
Published: November 2011

The “open” and “closed” isomers of the diarylethene molecule that can be converted between each other upon photo-excitation are found to have drastically different current-voltage characteristics when sandwiched between two graphene nanoribbons (GNRs). More importantly, when one GNR is metallic and another one is semiconducting, strong rectification behavior of the “closed” diarylethene isomer with the rectification ratio >103 is observed. The surprisingly high rectification ratio originates from the band gap of GNR and the bias-dependent variation of the lowest unoccupied molecular orbital of the diarylethene molecule, the combination of which completely shuts off the current at positive biases. Results presented in this paper may form the basis for a new class of molecular electronic devices.
Viscosity sensor using ZnO and AlN thin film bulk acoustic resonators with tilted polar c-axis orientations
Authors: Qin Lifeng , Chen Qingming , Cheng Hongbin , Chen Qian , Li Jing-Feng , Wang Qing-Ming
Published: November 2011

We present a theoretical analysis of liquid viscosity sensors using ZnO and AlN thin film bulk acoustic wave resonators (FBARs) with tilted polar c-axis orientations. Besides the thickness longitudinal mode, the tilted c-axis orientation induces thickness shear mode in the resonator, which allows resonators operated in liquid medium without significant damping for sensory application. The equation for predicting electric impedance of shear mode film bulk acoustic wave resonators (FBARs) with a viscous liquid loading was derived from the basic piezoelectric constitutive equations. The viscosity sensitivity of shear mode ZnO and AlN resonators was achieved by calculation of resonant frequency shift due to viscous liquid loading. In the simulation, it is assumed that all the resonators have 2 μm thickness and 300 μm×300 μm electrode area; three different liquids (water, acetone, and olive oil) were chosen as the liquid loadings; and different tilt c-axis angles for both ZnO FBARs and AlN FBARs have been examined. It was found that the sensitivities of shear mode resonators to the three liquid loading are very close, and do not change much with the c-axis tilt angle with a value rang from 0.91e-3 to 0.97e-3 (kg m−3 Pa·S)−0.5 for ZnO FBARs and from 1.12e−3 to 1.13 e−3 (kg m−3 Pa·S)−0.5 for AlN FBARs. When the resonator’s mechanical quality factor (Q) is changed from 50 to 10 000, viscosity sensitivities are almost same. However, Q has a great effect on resonator impedance; and if Q is too low or the viscosity of the liquid is high, the maximum phase angle of the resonator will be less than 0, which makes excitation of the oscillation difficult if an oscillator circuit is used for sensor measurement. The results can be used for design and application of ZnO or AlN FBARs to monitor liquid viscosity.
Can stimulated Raman pumping cause large population transfers in isolated molecules?
Authors: Mukherjee Nandini , Zare Richard N.
Published: November 2011

When stimulated Raman pumping (SRP) is applied to a stream of isolated molecules, such as found in a supersonic molecular beam expansion, we show that SRP can neither saturate nor power broaden a molecular transition connecting two metastable levels that is resonant with the energy difference between the pump and Stokes laser pulses. Using the optical Bloch-Feynman equations, we discuss the pumping of the hydrogen molecule from H2 (v = 0, J = 0, M = 0) to H2 (v = 1, J =  2, M = 0) as an illustration of how coherent population return severely reduces the SRP pumping efficiency unless the pump and Stokes laser pulses are applied with an appropriate relative delay and ratio of intensities.
Potential of mean force between a large solute and a biomolecular complex: A model analysis on protein flux through chaperonin system
Authors: Amano Ken-ich , Oshima Hiraku , Kinoshita Masahiro
Published: November 2011

Insertion of a large solute into an even larger vessel comprising biopolymers followed by release of the same solute from it is one of the important functions sustaining life. As a typical example, an unfolded protein is inserted into a chaperonin from bulk aqueous solution, a cochaperonin acting as a lid is attached to the chaperonin rim and the protein folds into its native structure within the closed cavity, the cochaperonin is detached after the folding is finished, and the folded protein is released back to the bulk solution. On the basis of the experimental observations manifesting that the basic aspects of the protein flux through the chaperonin system is independent of the chaperonin, cochaperonin, and protein species, we adopt a simple model system with which we can cover the whole cycle of the protein flux. We calculate the spatial distribution of the solvent-mediated potential of mean force (PMF) between a spherical solute and a cylindrical vessel or vessel/lid complex. The calculation is performed using the three-dimensional integral equation theory, and the PMF is decomposed into energetic and entropic components. We argue that an unfolded protein with a larger excluded volume (EV) and weak hydrophobicity is entropically inserted into the chaperonin cavity and constrained within a small space almost in its center. The switch from insertion to release is achieved by decreasing the EV and turning the protein surface hydrophilic in the folding process. For this release, in which the energetic component is a requisite, the feature that the chaperonin inner surface in the absence of the cochaperonin is not hydrophilic plays essential roles. On the other hand, the inner surface of the chaperonin/cochaperonin complex is hydrophilic, and the protein is energetically repelled from it: The protein remains constrained within the small space mentioned above without contacting the inner surface for correct folding. The structural and inner-surface properties of the chaperonin or complex are controlled by the adenosine triphosphate (ATP) binding to the chaperonin, hydrolysis of ATP into adenosine diphosphate (ADP) and Pi, and dissociation of ADP and Pi. The function of the chaperonin system is exhibited by synchronizing the chemical cycle of ATP hydrolysis with hydration properties of a protein in the water confined on the scale of a nanometer which are substantially different from those in the bulk water.
Photodissociation of methyl iodide embedded in a host-guest complex: A full dimensional (189D) quantum dynamics study of CH3I@resorc[4]arene
Authors: Westermann Till , Brodbeck Ralf , Rozhenko Alexander B. , Schoeller Wolfgang , Manthe Uwe
Published: November 2011

Accurate full dimensional quantum dynamics calculations studying the photodissociation of CH3I@resorc[4]arene on an ab initio based potential energy surface (PES) model are reported. The converged 189D quantum dynamics calculations are facilitated by the multilayer multi-configurational time-dependent Hartree (ML-MCTDH) approach combined with the correlation discrete variable representation (CDVR) for the evaluation of potential energy matrix elements. The potential employed combines an established ab initio PES describing the photodissociation of methyl iodide in the A band with a harmonic description of the resorc[4]arene host and a bilinear modeling of the host-guest interaction. All potential parameters required in the description of the vibrations of the host molecule and the host-guest interaction are derived from ab initio calculations on the host-guest complex. Absorption spectra at \documentclass[12pt]{minimal}\begin{document}$0\, \text{K}$\end{document}0K and \documentclass[12pt]{minimal}\begin{document}$300\, \text{K}$\end{document}300K are calculated and the electronic population dynamics during the bond breaking process occurring in the first 20–30 fs after the photoexcitation is investigated. Weak but significant effects resulting from the host-guest interaction on this time scale are found and interpreted. The present study demonstrates that accurate fully quantum mechanical dynamics calculations can be preformed for systems consisting of more than 50 atoms using the ML-MCTDH/CDVR approach. Utilizing an efficient statistical approach for the construction of the ensemble of initial wavepackets, these calculations are not restricted to zero temperature but can also study the dynamics at 300 K.
Solution on the Bethe lattice of a hard core athermal gas with two kinds of particles
Authors: Oliveira Tiago J. , Stilck Jürgen F.
Published: November 2011

Athermal lattice gases of particles with first neighbor exclusion have been studied for a long time as simple models exhibiting a fluid-solid transition. At low concentration the particles occupy randomly both sublattices, but as the concentration is increased one of the sublattices is occupied preferentially. Here, we study a mixed lattice gas with excluded volume interactions only in the grand-canonical formalism with two kinds of particles: small ones, which occupy a single lattice site and large ones, which, when placed on a site, do not allow other particles to occupy its first neighbors also. We solve the model on a Bethe lattice of arbitrary coordination number q. In the parameter space defined by the activities of both particles, at low values of the activity of small particles (z1) we find a continuous transition from the fluid to the solid phase as the activity of large particles (z2) is increased. At higher values of z1 the transition becomes discontinuous, both regimes are separated by a tricritical point. The critical line has a negative slope at z1 = 0 and displays a minimum before reaching the tricritical point, so that a re-entrant behavior is observed for constant values of z2 in the region of low density of small particles. The isobaric curves of the total density of particles as a function of the density or the activity of small particles show a minimum in the fluid phase.
Presence and origin of interface charges at atomic-layer deposited Al2O3/III-nitride heterojunctions
Authors: Ganguly Satyaki , Verma Jai , Li Guowang , Zimmermann Tom , Xing Huili , Jena Debdeep
Published: November 2011

Unlike silicon and traditional III-V semiconductors, the III-nitrides exhibit high spontaneous and piezoelectric polarization charges at epitaxial polar heterojunctions. In the process of investigating scaling properties of gate-stacks consisting atomic-layer deposited Al2O3/III-Nitride heterojunctions, we find interface charges that appear closely linked to the polarization charges of the underlying nitride substrate. Through capacitance-voltage measurement on a series of samples of varying dielectric thicknesses, we find the presence and propose an origin of benign donor-type interface charges (Qit ∼6 × 1013 cm−2) at the AlN/Al2O3 junction. This interface charge is almost equal to the net polarization charge in AlN. The polarization-related dielectric/AlN interface charge and the role of oxygen in the dielectric as a possible modulation dopant potentially offer opportunities for various device applications.
Terahertz coherent acoustic experiments with semiconductor superlattices
Authors: Huynh A. , Perrin B. , Jusserand B. , Lemaître A.
Published: November 2011

We demonstrate the generation, propagation, and detection of coherent acoustic waves at 1 THz. We performed picosecond ultrasonics experiments in an acoustic transmission geometry, which allows a total decoupling of the phonon generation and detection processes, occurring in two different superlattices grown on opposite sides of a substrate, respectively. We show that a 1 ns burst of monochromatic terahertz coherent acoustic waves could be generated on one side of a substrate, propagated over a large distance and detected on the opposite side. We also measured the lattice dispersion owing to the time delay between the terahertz burst and much lower frequency acoustic waves.
Analytical re-derivation of space charge limited current in solids using capacitor model
Authors: Zhu Y. B. , Ang L. K.
Published: November 2011

In this paper, we have used a capacitor model to reproduce the known analytical formulas of space charge limited current transport inside both trap-free and trap-filled solids in planar geometry. It is found that the approach is simple when compared to the traditional method as the latter involves solving second order differential equation. Exact analytical results can also be obtained for cylindrical diode with an outer radius much larger than the inner radius.
Electrical properties of individual self-assembled GeSi quantum rings
Authors: Zhang Shengli , Lv Yi , Jiang Zuimin , Yang Xinju
Published: November 2011

The nanoscale electrical properties of self-assembled GeSi quantum rings (QRs) were investigated by conductive scanning probe microscopy at room temperature. The current distribution of individual GeSi QRs measured by conductive atomic force microscopy (CAFM) shows a low conductivity at the central hole as compared to the rim; however, the QRs’ composition distribution obtained by selective chemical etching combined with AFM observation reveals that within the QRs’ central holes, the Ge content is high, which should lead to a high conductivity instead of a low one as observed. Together with the results obtained by scanning capacitance microscopy (SCM) and electrostatic force microscopy (EFM), it is supposed that the GeSi QRs’ electrical properties are mainly determined by the ring-shaped topography, rather than by the complete oxidation of the QRs’ central hole or their composition distributions.
Simultaneous detection of surface coverage and structure of krypton films on gold by helium atom diffraction and quartz crystal microbalance techniques
Authors: Danışman M. Fatih , Özkan Berrin
Published: November 2011

We describe a quartz crystal microbalance setup that can be operated at low temperatures in ultra high vacuum with gold electrode surfaces acting as substrate surface for helium diffraction measurements. By simultaneous measurement of helium specular reflection intensity from the electrode surface and resonance frequency shift of the crystal during film adsorption, helium diffraction data can be correlated to film thickness. In addition, effects of interfacial viscosity on the helium diffraction pattern could be observed. To this end, first, flat gold films on AT cut quartz crystals were prepared which yield high enough helium specular reflection intensity. Then the crystals were mounted in the helium diffractometer sample holder and driven by means of a frequency modulation driving setup. Different crystal geometries were tested to obtain the best quality factor and preliminary measurements were performed on Kr films on gold surfaces. While the crystal structure and coverage of krypton films as a function of substrate temperature could successfully be determined, no depinning effects could be observed.
Origin of anomalously high exchange field in antiferromagnetically coupled magnetic structures: Spin reorientation versus interface anisotropy
Authors: Ranjbar M. , Piramanayagam S. N. , Wong S. K. , Sbiaa R. , Song W. , Tan H. K. , Gonzaga L. , Chong T. C.
Published: November 2011

Magnetization reorientation from in-plane to perpendicular direction, observed in Co thin film coupled antiferromagnetically to high perpendicular magnetic anisotropy (Co/Pd) multilayers, is studied systematically for Co thickness ranging from 0 to 2.4 nm. The sample with 0.75 nm thick Co showed an exchange coupling field (Hex) exceeding 15 kOe at room temperature and 17.2 kOe at 5 K. With an increase of Co thickness, Hex decreased as expected and beyond certain thickness, magnetization reorientation was not observed. Indeed, three regions were observed in the thickness dependence of magnetization of the thin layer; one in which the thin layer (in the thickness range up to 0.8 nm) had a perpendicular magnetic anisotropy due to interface effects and antiferromagnetic coupling, another in which the thin layer (0.9–1.2 nm) magnetization had no interface or crystallographic anisotropy but was reoriented in the perpendicular direction due to antiferromagnetic coupling, and the third (above 1.2 nm) in which the magnetization was in-plane. In addition, Hall effect measurements were carried out to observe the anomalous and planar Hall voltages and to quantify the perpendicular and in-plane components of magnetization. The sample with thicker Co layer (2.4 nm) showed an in-plane component of magnetization, whereas the sample with 0.75 nm Co showed no in-plane component. The high value of Hex observed in 0.75 nm Co samples can have important implications in spintronics and bit patterned media.
Influence of local atomic configuration in AlGdN phosphor thin films on deep ultra-violet luminescence intensity
Authors: Kitayama Shinya , Yoshitomi Hiroaki , Iwahashi Shinya , Nakamura Junya , Kita Takashi , Chigi Yoshitaka , Nishimoto Tetsuro , Tanaka Hiroyuki , Kobayashi Mikihiro , Ishihara Tsuguo , Izumi Hirokazu
Published: November 2011

We investigated the narrowband ultraviolet emission properties of Al0.94Gd0.06N phosphor thin films pumped by an electron beam. An extremely narrow luminescence line, which was less than 1 nm from the intra-orbital f-f transition in Gd3+ ions, was confirmed at 318 nm. The corresponding emission efficiency was improved by decreasing the growth temperature. The extended X-ray absorption fine structure analysis of the local atomic structure revealed that a low-temperature growth led to the formation of a uniform atomic configuration around Gd, which was found to play a key role in improving the luminescence intensity of the films.
Electrical mobility in organic thin-film transistors determined by noise spectroscopy
Authors: Bonavolontà C. , Albonetti C. , Barra M. , Valentino M.
Published: November 2011

Organic field-effect transistors (OFET) based on both n-type (perylene derivative) and p-type (α-sexithiophene and pentacene) organic thin films are characterized using low-frequency noise spectroscopy to estimate the charge carrier mobility. The power spectral density shows that the exposure of OFET to air affects the thermal noise fluctuations and that the thermal noise RMS value depends on gate voltage. The power spectral density noise proves that the carrier mobility is gate-voltage dependent. Unlike the I-V measurements, the noise spectroscopy analysis demonstrates the dependence of the mobility on the carrier polarity. We discuss the charge mobility and transport mechanism of a pentacene device with and without electrodes functionalized by an octanethiol chain. The results show that in the functionalized device the carrier mobility is improved and does not depend on the high gate voltage.