bluuebunny/crossref_metadata_2025 huggingface dataset:
Health benefits of nuts: potential role of antioxidants
Authors: Blomhoff Rune , Carlsen Monica H. , Andersen Lene Frost , Jacobs David R.
Published: April 2007

A diet rich in fruits, vegetables and minimally refined cereals is associated with lower risk for chronic degenerative diseases. Since oxidative stress is common in chronic degenerative disease, it has been assumed that dietary antioxidants may explain this protective effect. Every dietary plant contains numerous types of antioxidants with different properties. Many of these antioxidants cooperate in oxidative stress reduction in plants, and we hypothesize that many different antioxidants may also be needed for the proper protection of animal cells. To test this hypothesis, it is useful to identify dietary plants with high total antioxidant content. Several nuts are among the dietary plants with the highest content of total antioxidants. Of the tree nuts, walnuts, pecans and chestnuts have the highest contents of antioxidants. Walnuts contain more than 20 mmol antioxidants per 100 g, mostly in the walnut pellicles. Peanuts (a legume) also contribute significantly to dietary intake of antioxidants. These data are in accordance with our present extended analysis of an earlier report on nut intake and death attributed to various diseases in the Iowa Women's Health Study. We observed that the hazard ratio for total death rates showed a U-shaped association with nut/peanut butter consumption. Hazard ratio was 0·89 (CI =0·81–0·97) and 0·81 (CI =0·75–0·88) for nut/peanut butter intake once per week and 1–4 times per week, respectively. Death attributed to cardiovascular and coronary heart diseases showed strong and consistent reductions with increasing nut/peanut butter consumption. Further studies are needed to clarify whether antioxidants contribute to this apparent beneficial health effect of nuts.
Large-eddy simulation of a subsonic cavity flow including asymmetric three-dimensional effects
Authors: LARCHEVÊQUE LIONEL , SAGAUT PIERRE , LABBÉ ODILE
Published: April 2007

Large-eddy simulations of a cavity configuration yielding a mean flow that exhibits spanwise asymmetry are carried out. Results from the computations reveal that the asymmetry is due to a bifurcation of the whole flow field inside the cavity. It is demonstrated that the bifurcation originates in an inviscid confinement effect induced by the lateral walls. The branch of the bifurcation can be selected by slightly altering the incoming mean flow. Further investigations show that underlying steady spanwise modulations of velocity are amplified under the influence of the lateral walls. The modulation of the streamwise velocity component has the largest energy content and its dominant wavelength contaminates both vertical velocity and pressure. Complementary to these linear interactions, nonlinear energy transfers from streamwise velocity to pressure are also found. A transient analysis highlights the stiff transition from a symmetrical two-structure non-bifurcated flow to a stable unsymmetrical one-and-a-half-structure bifurcated flow. The switch to the bifurcated flow induces an alteration of the Rossiter aero–acoustic loop yielding a change in the dominant Rossiter mode and the appearance of a nonlinear harmonic of the first mode.
On the formation and propagation of nonlinear internal boluses across a shelf break
Authors: VENAYAGAMOORTHY SUBHAS K. , FRINGER OLIVER B.
Published: April 2007

High-resolution two- and three-dimensional numerical simulations are performed of first-mode internal gravity waves interacting with a shelf break in a linearly stratified fluid. The interaction of nonlinear incident waves with the shelf break results in the formation of upslope-surging vortex cores of dense fluid (referred to here as internal boluses) that propagate onto the shelf. This paper primarily focuses on understanding the dynamics of the interaction process with particular emphasis on the formation, structure and propagation of internal boluses onshelf. A possible mechanism is identified for the excitation of vortex cores that are lifted over the shelf break, from where (from the simplest viewpoint) they essentially propagate as gravity currents into a linearly stratified ambient fluid.
The effect of wall heating on instability of channel flow
Authors: SAMEEN A. , GOVINDARAJAN RAMA
Published: April 2007

A comprehensive study of the effect of wall heating or cooling on the linear, transient and secondary growth of instability in channel flow is conducted. The effect of viscosity stratification, heat diffusivity and of buoyancy are estimated separately, with some unexpected results. From linear stability results, it has been accepted that heat diffusivity does not affect stability. However, we show that realistic Prandtl numbers cause a transient growth of disturbances that is an order of magnitude higher than at zero Prandtl number. Buoyancy, even at fairly low levels, gives rise to high levels of subcritical energy growth. Unusually for transient growth, both of these are spanwise-independent and not in the form of streamwise vortices. At moderate Grashof numbers, exponential growth dominates, with distinct Poiseuille–Rayleigh–Bénard and Tollmien–Schlichting modes for Grashof numbers up to ∼ 25 000, which merge thereafter. Wall heating has a converse effect on the secondary instability compared to the primary instability, destabilizing significantly when viscosity decreases towards the wall. It is hoped that the work will motivate experimental and numerical efforts to understand the role of wall heating in the control of channel and pipe flows.
Mechanics of merging events for a series of layers in a stratified turbulent fluid
Authors: RADKO TIMOUR
Published: April 2007

This study attempts to explain the evolutionary pattern of a series of well-mixed layers separated by thin high-gradient interfaces frequently observed in stratified fluids. Such layered structures form as a result of the instability of the equilibrium with uniform stratification, and their subsequent evolution is characterized by a sequence of merging events which systematically increase the average layer thickness. The coarsening of layers can take one of two forms, depending on the realized vertical buoyancy flux law. Layers merge either when the high-gradient interfaces drift and collide, or when some interfaces gradually erode without moving vertically. The selection of a preferred pattern of coarsening is rationalized by the analytical theory – the merging theorem – which is based on linear stability analysis for a series of identical layers and strongly stratified interfaces. The merging theorem suggests that the merger by erosion of weak interfaces occurs when the vertical buoyancy flux decreases with the buoyancy variation across the step. If the buoyancy flux increases with step height, then coarsening of a staircase may result from drift and collision of the adjacent interfaces. Our model also quantifies the time scale of merging events and makes it possible to predict whether the layer merging continues indefinitely or whether the coarsening is ultimately arrested. The merging theorem is applied to extant one-dimensional models of turbulent mixing and successfully tested against the corresponding fully nonlinear numerical simulations. It is hypothesized that the upscale cascade of buoyancy variance associated with merging events may be one of the significant sources of the fine-scale (∼ 10m) variability in the ocean.
Liquid sloshing and wave breaking in circular and square-base cylindrical containers
Authors: ROYON-LEBEAUD A. , HOPFINGER E. J. , CARTELLIER A.
Published: April 2007

Near resonance sloshing in containers, filled with a liquid to a given depthh, depends on three parameters, which are the viscous damping, the frequency offset that contains the forcing amplitude and the fluid depth. Experiments have been conducted with low-viscosity liquids mainly in circular cylindrical containers of radiusRsubjected to harmonic horizontal forcing; complementary experiments on wave breaking have been performed in a square-base container. The fluid depth was kept large (h/R> 1) so that it was no longer a variable parameter. The bounds of existence of the different wave regimes, namely planar waves, swirling waves, chaotic sloshing as well as breaking waves, have been determined as a function of forcing frequencies relative to the lowest natural frequency ω1and for a wide range of forcing amplitudes. It is shown that when the forcing frequency ω is slightly larger than the lowest natural frequency ω1, planar wave motion bifurcates to a swirling wave mode at finite wave amplitude, the value of which depends on the offset parameter. The swirl wave amplitude grows exponentially and saturates at a certain value. The swirl has a hard-spring behaviour, is very robust and can generate a vortical flow of the liquid column. Chaotic sloshing and wave breaking occur quasi-periodically: growth of planar wave amplitude at a rate depending on the forcing amplitude, collapse, irregular swirl and again growth of planar wave amplitude. The details and periodicity of the chaotic behaviour and breaking depend on the frequency-offset parameter. Close to the natural frequency, chaotic wave motion is possible without breaking. Planar wave breaking is, in general, associated with spilling caused by the encounter of nearly freely falling lumps of fluid with the upward moving wave crest, in a way demonstrated previously in two-dimensional wave breaking. In three dimensions, the wave crest is destabilized in the crosswise direction so that spilling is not uniform along the wave crest and an irregular swirl is generated following breaking; free fall of fluid lumps occurs over many wave periods. The complementary experiments, performed in a square-base container of base dimensionL, show four different wave patterns of wavelengthsLandL/2 crosswise to the primary wave. This cross-wave instability is interpreted in terms of parametric instability.
Self-similar clustering of inertial particles in homogeneous turbulence
Authors: YOSHIMOTO HIROSHI , GOTO SUSUMU
Published: April 2007

It is shown by direct numerical simulation that the preferential concentration of small heavy particles in homogeneous isotropic developed turbulence has a self-similar multi-scale nature when the particle relaxation time is within the inertial time scales of the turbulence. This is shown by the pair correlation function of the particle distribution extending over the entire inertial range, and the probability density function of the volumes of particle voids taking a power-law form. This self-similar multi-scale nature of particle clustering cannot be explained only by the centrifugal effect of the smallest-scale (i.e. the Kolmogorov scale) eddies, but also by the effect of co-existing self-similar multi-scale coherent eddies in the turbulence at high Reynolds numbers. This explanation implies that the preferential concentration of particles takes place even when the relaxation time of particles is much larger than the Kolmogorov time, provided it is smaller than the longest time scale of the turbulence, since even the largest-scale eddies bring about particle clustering.
Turbulent mixing at a stable density interface: the variation of the buoyancy flux–gradient relation
Authors: GUYEZ E. , FLOR J.-B. , HOPFINGER E. J.
Published: April 2007

Experiments conducted on mixing across a stable density interface in a turbulent Taylor–Couette flow show, for the first time, experimental evidence of an increase in mixing efficiency at large Richardson numbers. With increasing buoyancy gradient the buoyancy flux first passes a maximum, then decreases and at large values of the buoyancy gradient the flux increases again. Thus, the curve of buoyancy flux versus buoyancy gradient tends to be N-shaped (rather than simply bell shaped), a behaviour suggested by the model of Balmforth et al. (J. Fluid Mech. vol. 428, 1998, p. 349). The increase in mixing efficiency at large Richardson numbers is attributed to a scale separation of the eddies active in mixing at the interface; when the buoyancy gradient is large mean kinetic energy is injected at scales much smaller than the eddy size fixed by the gap width, thus decreasing the eddy turnover time. Observations show that there is no noticeable change in interface thickness when the mixing efficiency increases; it is the mixing mechanism that changes. The curves of buoyancy flux versus buoyancy gradient also show a large variability for identical experimental conditions. These variations occur at time scales one to two orders of magnitude larger than the eddy turnover time scale.
Kommunikative Fertigkeiten bei der pränatalen Beratung schwangerer Frauen
Authors: Bitzer  , Tschudin  , Holzgreve  , Tercanli
Published: April 2007

Pränatale Beratung hat einige besondere Merkmale: A) Die Kommunikation betrifft direkt Wertvorstellungen der schwangeren Frau und ihre Beziehung zu ihrem Kind. B) Die Kommunikation betrifft das Bild der Schwangeren von ihrem Kind und ihre Emotionen. C) Es wird über Risiken, Zahlen und Statistiken gesprochen. D) Arzt und Schwangere sind einbezogen in zentrale ethische Fragestellungen. Aus diesen Gründen stellt die spezifische Situation der pränatalen Beratung besondere Lernanforderungen an Ärzte. Diese sollten in der Lage sein eine patientinnenzentrierte Kommunikation mit nicht-direktiver Beratung mit einer umfassenden Aufklärung und einer gemeinsamen Entscheidungsfindung zu vereinigen. Diese Elemente sind integriert in einem Beratungsprozess der folgende Schritte umfasst: 1. Klärung der Ziele der schwangeren Frau und des ärztlichen Auftrages. 2. Individuelle Informationsvermittlung mit Risikoberatung und Darlegung von Vor- und Nachteilen pränataler Tests und Untersuchungen. 3. Gemeinsame Entscheidungsfindung bezüglich Tests und Untersuchungen. 4. Eventuell die Mitteilung schlechter oder unklarer Befunde. 5. Betreuung der Schwangeren mit einem betroffenen Kind.
Scattering of suprathermal electrons in the solar wind: ACE observations
Authors: Pagel Christina , Gary S. Peter , de Koning Curt A. , Skoug Ruth M. , Steinberg John T.
Published: April 2007

Suprathermal electrons in the solar wind have a strahl component with anisotropic velocity distributions which are directed along the background magnetic field away from the Sun. Analyses of strahl distributions from 73.3 eV to 987 eV as measured during the year 2004 by the SWEPAM plasma instrument on the ACE spacecraft are reported here. This manuscript describes 29 events which correspond to times of strahl pitch‐angle distributions which are broader than those observed at earlier or later times and enhanced magnetic field fluctuations at frequencies ≲3 Hz. Although most previously reported observations at energies up to a few hundred eV show that strahl pitch‐angle widths decrease with increasing energy, during the 29 events reported here, this width increased on average as strahl energy increased. This manuscript also develops the hypothesis that this characteristic is due to electron scattering by broadband whistler fluctuations.
Accuracy of tropospheric and stratospheric water vapor measurements by the cryogenic frost point hygrometer: Instrumental details and observations
Authors: Vömel H. , David D. E. , Smith K.
Published: April 2007

The cryogenic frost point hygrometer (CFH), currently built at the University of Colorado, is a new balloon borne hygrometer, which is capable of continuously measuring water vapor between the surface and the middle stratosphere. The design is loosely based on the old NOAA/CMDL frost point hygrometer, with improved accuracy and a number of significant new features that overcome some limitations of the older instrument. The measurement uncertainty of the new instrument depends on altitude and ranges between less than 4% in the tropical lower troposphere to no more than 10% in the middle stratosphere at 28 km. In the tropopause region the uncertainty is less than 9%. This instrument is used routinely at several sites for validation of satellite measurements and process studies in the upper troposphere and lower stratosphere region. It has proved to be particularly well suited for dehydration observations in the tropical upper troposphere, because the effects of cloud contamination have been significantly reduced. Results of this instrument are compared with the old NOAA/CMDL hygrometer, the Russian Fluorescent Lyman Alpha Stratospheric Hygrometer, the Vaisala RS92, the AURA/MLS satellite instrument, a cloud lidar, the NOAA/CSD frost point hygrometer and the Harvard Lyman‐alpha hygrometer, both of the later instruments flown on board the NASA WB‐57F high‐altitude research aircraft. These comparisons demonstrate the level of accuracy of tropospheric and stratospheric water vapor measurements made by this instrument and point to areas where more research and development are needed.
A model of the trajectories and midair collision probabilities of sand particles in a steady state saltation cloud
Authors: Huang Ning , Zhang Yali , D'Adamo Robert
Published: April 2007

To estimate the probability of a midair interparticle collision for a 0.25 mm saltating particle in a steady state saltation cloud, a physical model that can predict this probability is developed. In our model a set of experimentally determined saltation cloud wind profiles, which are notably nonlogarithmic, are employed. First, the trajectories of a saltating particle with different lift‐off velocities and at different free‐stream wind velocities are calculated using the wind profile results, and they are compared to corresponding trajectories calculated by logarithmically distributed wind profiles. Our model yields trajectory heights and lengths that are much different than those calculated by the logarithmically distributed profiles. Second, the midair interparticle collision probability is simulated for its ascending and descending stages, as well as for its entire trajectory. Finally, by considering the probability density function the collision probabilities of a saltating particle with a random lift‐off velocity at several friction velocities of wind are calculated. The results show that the probability of such a collision almost linearly increases with the friction velocity of wind, and it can reach as high as 0.34 when the friction velocity of wind is 1.2 m/s. Therefore the effect of midair collision should not be neglected in the saltation model, especially at high‐friction velocities of wind.
Polar mesospheric cloud mass and the ice budget: 2. Application to satellite data sets
Authors: Stevens Michael H. , Englert Christoph R. , DeLand Matthew T. , Bailey Scott M.
Published: April 2007

We use satellite observations of mid‐UV solar backscattered light from polar mesospheric clouds (PMCs) to constrain the water ice budget. We compare the PMC mass from observations by two instruments: the limb viewing Student Nitric Oxide Explorer (SNOE) and the nadir viewing Solar Backscattered UltraViolet (SBUV) experiments. At 70 ± 2.5°N we find that SNOE measures over three times more PMC mass than the less sensitive SBUV experiment. We directly compare the two data sets by selecting only the brightest 10% of SNOE clouds so that the SNOE and SBUV PMC occurrence frequencies are the same. This comparison shows that the PMC mass averaged over five northern seasons is the same to within uncertainties in the ice particle size distribution. We also find that near midday, the northern SBUV PMC mass is a factor of 2.4 times greater than the southern PMC mass. These results provide new constraints for global climate models of PMC formation.
Neutral cloud interaction with Saturn's main rings
Authors: Jurac S. , Richardson J. D.
Published: April 2007

The dense water cloud just outward of Saturn's main rings could strongly influence the surface composition of main ring constituents. Cassini pictures display brightening toward the outer edges of the main rings, suggesting that the outer edges have more icy material. We show that this enhanced brightening might not be a ring evolutionary feature, but a consequence of water molecules deposited from the dense neutral cloud emanating from Enceladus. We estimate the deposition rate and densities for water‐group neutrals near the main rings, which could be important for determining the surface composition and chemistry of the ring particles.
Mechanical dissociation of human embryonic stem cell colonies by manual scraping after collagenase treatment is much more detrimental to cellular viability than is trypsinization with gentle pipetting
Authors: Heng Boon Chin , Liu Hua , Ge Zigang , Cao Tong
Published: April 2007

Because hESC (human embryonic stem cells) are ‘social cells’ that require co‐operative interactions and intimate physical contact with each other, it is absolutely essential to dissociate hESC colonies into cellular clumps rather than into a single‐cell suspension during serial passage. The present study compared two commonly used protocols for dissociating hESC colonies. The first protocol involved mild enzymatic treatment with collagenase type IV (1 mg/ml) for approx. 5–10 min, prior to mechanical dissociation into cellular clumps through manual scraping with a plastic pipette tip. The second protocol involved a short duration of exposure (2–3 min) to low concentrations of trypsin (0.05%), followed by gentle pipetting. The MTT [3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl‐2H‐tetrazolium bromide] assay was used to compare the recovery of viable cells after dissociating hESC colonies with these two protocols, before and after conventional freeze–thawing with 10% (v/v) DMSO. Besides undifferentiated hESC, the randomly differentiated fibroblastic progenies of hESC at various passages (P0–P4), together with an immortalized cell line (CRL‐1486), were also utilized to compare the two protocols. The results demonstrated that the second protocol (trypsinization with gentle pipetting) is much less detrimental to cellular viability than is the first protocol (collagenase treatment with scratching). This in turn translated to higher freeze–thaw survival rates. It is hypothesized that scratching after collagenase treatment (first protocol) somehow induces physical damage to the cells, thereby leading to a lower recovery of viable cells, both before and after freeze–thawing.
Expression of VCA (viral capsid antigen) and EBNA1 (Epstein–Barr‐virus‐encoded nuclear antigen 1) genes of Epstein–Barr virus in Pichia pastoris and application of the products in a screening test for patients with nasopharyngeal carcinoma
Authors: Hu Bo , Hong Guoqiang , Li Zhaoxia , Xu Jue , Zhu Zhenyu , Li Lin
Published: April 2007

EBV (Epstein–Barr virus) serological tests have been used for many years as accessory diagnostic predictors of NPC (nasopharyngeal carcinoma). To date, IF (indirect immunofluorescence) assays still serve as the ‘gold standard’ for EBV serodiagnosis. However, IF assays are time‐consuming, unsuitable for automatic handling and difficult to standardize. This makes their application in mass screening of populations inconvenient. Some of the technical difficulties associated with IF have been overcome by the development of specific ELISAs, but, at present, high sensitivity and specificity cannot be achieved simultaneously by using recombinant protein‐based ELISAs, as the diagnostic value of different fragments of EBV in NPC is different. In an attempt to determine a suitable recombinant EBV protein for diagnostic purposes, fragments of EBV VCA (viral capsid antigen) and EBNA1 (Epstein–Barr‐virus‐encoded nuclear antigen 1) genes were expressed in the methylotrophic yeast Pichia pastoris, and a novel ELISA was established using P. pastoris‐expressed VCA‐BALF4 [aa (amino acids) 287–623; the BALF4 gene encodes the EBV glycoprotein gp125], EBNA1 (aa 390–641) and VCA‐BFRF3 (the gene BFRF3 encodes a viral structural capsid protein or tegument protein VCA p18) proteins. Serum samples were collected from patients with NPC and healthy controls and were tested using this ELISA. The sensitivity of VCA‐BFRF3, VCA‐BALF4 and EBNA1 tests in the NPC sera were 65.0 (195/300), 76.3 (229/300) and 81.4% (244/300) respectively, whereas the specificity of normal individuals were 92 (460/500), 96 (480/500) and 95.8% (479/500). The optimum combination is VCA‐BALF4 plus EBNA1, which identified 90.3% (271/300) of the NPC patients and had a specificity of 92.8% (464/500) for normal individuals. The results obtained from the evaluation of three antibodies to EBV as markers for detecting NPC suggests that a combination of EBNA1 (aa 390–641) and VCA‐BALF4 (aa 287–623) assays would give better results in screening for NPC.
Translational control of maskin mRNA by its 3′ untranslated region
Authors: Meijer Hedda A. , Radford Helois E. , Wilson Lolita S. , Lissenden Sarah , de Moor Cornelia H.
Published: April 2007

Background information. Maskin is a member of the TACC (transforming acidic coiled‐coil) domain proteins found in Xenopus laevis oocytes and embryos. It has been implicated in the co‐ordination of the spindle and has been reported to mediate translational repression of cyclin B1 mRNA.

Results. In the present study, we report that maskin mRNA is translationally repressed at the level of initiation in stage 4 oocytes and becomes activated in stage 6 oocytes. The translational repression of maskin mRNA correlates with the presence of a short poly(A) tail on this mRNA in stage 4 oocytes. The 3′‐UTR (untranslated region) of maskin can confer the translational regulation to a reporter mRNA, and so can the 3′‐UTR of human TACC3. A conserved GUCU repeat element was found to repress translation in both stage 4 and stage 6 oocytes, but deletion of this element did not abrogate repression in stage 4 oocytes. UV cross‐linking experiments indicated that overlapping sets of proteins bind efficiently to both the maskin and the cyclin B1 3′‐UTRs. As reported previously, CPEB [CPE (cytoplasmic polyadenylation element)‐binding protein] binds to the cyclin B1 3′‐UTR, but its binding to the maskin 3′‐UTR is minimal. By RNA affinity chromatography and MS, we identified the EDEN‐BP [EDEN (embryonic deadenylation element)‐binding protein] as one of the proteins binding to both the maskin and the cyclin B1 3′‐UTRs.

Conclusions. Maskin mRNA is translationally regulated by at least two repressor elements and an activation element. One of the repessor elements is the evolutionarily conserved GUCU repeat. EDEN‐BP binds to both the maskin and cyclin B1 3′‐UTRs, indicating it may be involved in the deadenylation of these mRNAs.
Conserved patterns of nuclear compartmentalization are not observed in the chordate Oikopleura
Authors: Spada Fabio , Koch Jeannette , Sadoni Nicolas , Mitchell Nadine , Ganot Philippe , De Boni Umberto , Zink Daniele , Thompson Eric M.
Published: April 2007

Background information. Recent results from a limited number of eukaryotic model organisms suggest that major principles governing spatial organization of the genome in functionally distinct nuclear compartments are conserved through evolution.

Results. We examined the in situ spatial organization of major nuclear components and nuclear patterns of gene loci with strictly defined expression patterns in endocycling cells of the transparent urochordate Oikopleura dioica, a complex metazoan with a very compact genome. Endocycling cells with different functions and similar DNA content displayed distinct topologies of nuclear components. However, the generation of the diverse nuclear architectures did not involve specific local organization of active genes or their preferential amplification. Interestingly, endocycling cells lacked nuclear‐envelope‐associated heterochromatin and prominent splicing‐factor domains, which in mammalian cells associate with transcriptionally silent and active loci respectively. In addition, no correlation was found between transcriptional activity of a locus and its association with chromatin domains rich in specific histone modifications.

Conclusions. Together, these findings and the absence of typical eukaryotic replication patterns reveal a surprisingly limited functional compartmentalization of O. dioica endocycling nuclei. This indicates that robust cell‐type‐specific gene expression does not necessarily require high levels of spatial genome organization.
In search of CS2(H2O)n=1–4 clusters
Authors: Kirschner Karl N. , Hartt Gregory M. , Evans Timothy M. , Shields George C.
Published: April 2007

Gaussian-3 and MP2/aug-cc-pVnZ methods have been used to calculate geometries and thermochemistry of CS2(H2O)n, where n=1–4. An extensive molecular dynamics search followed by optimization using these two methods located two dimers, six trimers, six tetramers, and two pentamers. The MP2/aug-cc-pVDZ structure matched best with the experimental result for the CS2(H2O) dimer, showing that diffuse functions are necessary to model the interactions found in this complex. For larger CS2(H2O)n clusters, the MP2/aug-cc-pVDZ minima are significantly different from the MP2(full)∕6-31G* structures, revealing that the G3 model chemistry is not suitable for investigation of sulfur containing van der Waals complexes. Based on the MP2/aug-cc-pVTZ free energies, the concentration of saturated water in the atmosphere and the average amount of CS2 in the atmosphere, the concentrations of these clusters are predicted to be on the order of 105 CS2(H2O) clusters∙cm−3 and 102 CS2(H2O)2 clusters∙cm−3 at 298.15K. The MP2/aug-cc-pVDZ scaled harmonic and anharmonic frequencies of the most abundant dimer cluster at 298K are presented, along with the MP2/aug-cc-pVDZ scaled harmonic frequencies for the CS2(H2O)n structures predicted to be present in a low-temperature molecular beam experiment.
First-principles study of structural, electronic, and multiferroic properties in BiCoO3
Authors: Cai Meng-Qiu , Liu Ji-Cheng , Yang Guo-Wei , Cao Yun-Lun , Tan Xin , Chen Xin-Yi , Wang Yan-Guo , Wang Ling-Ling , Hu Wang-Yu
Published: April 2007

Electronic and magnetic properties of BiCoO3 have been investigated using the ab initio density-functional calculations with local spin density approximation (LSDA) and LSDA+U methods. The structural stability and the origin of the multiferroism for ferroelectronic and ferromagnetic existence were addressed. It was shown that the stability of the C-type antiferromagnetic (C-AFM) structure is better than that of other possible configurations. The hybridization between Bi–O and Co–O with interplay and a local magnetic moment on the Co3+ play important roles for the nature of the ferroelectricity and ferromagnetism. Theoretical calculations predict the insulating ground state with a band gap of 2.11eV in the C-AFM ordering for BiCoO3 originated from the antiferromagnetic interaction in the ab plane, which is in well agreement with experiments.
Epitaxial growth of PbFe12O19 thin films by alternating target laser ablation deposition of Fe2O3 and PbO
Authors: Geiler A. L. , He Y. , Yoon S. D. , Yang A. , Chen Y. , Harris V. G. , Vittoria C.
Published: April 2007

Oriented M-type hexaferrite thin films are deposited using the alternating target laser ablation deposition (ATLAD) technique utilizing PbO and Fe2O3 targets. Crystallographic, dc magnetic, and microwave characterization results confirming the presence of a hexagonal PbFe12O19 phase are presented. We conclude that the ATLAD technique holds great promise for layer by layer deposition of various hexaferrite materials, the properties of which can be adjusted by varying the composition of the targets as well as the number of laser shots from each target during the deposition process. This would provide control over the uniaxial anisotropy fields and saturation magnetization values that was not possible in the conventional single target LAD technique.
Closed-form summation of the Dowker and related sums
Authors: Cvijović Djurdje , Srivastava H. M.
Published: April 2007

Finite sums of powers of cosecants appear in a wide range of physical problems. We, through a unified approach which uses contour integrals and residues, establish the summation formulas for two general families of such sums. One of them is the family which was first studied and summed in closed form by Dowker [Phys. Rev. D 36, 3095 (1987)], while the other is related to it and has not been studied before. Our summation formulas of the Dowker sums involve only the Stirling numbers of the first kind and the (ordinary) Bernoulli polynomials and numbers, unlike the earlier summation formulas in which either the higher-order Bernoulli numbers and polynomials or the multiple sums involving the Bernoulli numbers and their products, were used. A great deal of other (known or presumably new) closed-form summations follows as straightforward corollaries to these formulas. Among them are two special cases of the celebrated Verlinde’s formula and numerous sums encountered in various physical problems by McCoy and Orrick [J. Stat. Phys. 83, 839 (1996)], Gervois and Mehta [J. Math. Phys. 36, 5098 (1995)], and Henkel and Lacki [Phys. Lett. A 138, 105 (1989)].
Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states
Authors: Noé Frank , Horenko Illia , Schütte Christof , Smith Jeremy C.
Published: April 2007

Molecular dynamics simulation generates large quantities of data that must be interpreted using physically meaningful analysis. A common approach is to describe the system dynamics in terms of transitions between coarse partitions of conformational space. In contrast to previous work that partitions the space according to geometric proximity, the authors examine here clustering based on kinetics, merging configurational microstates together so as to identify long-lived, i.e., dynamically metastable, states. As test systems microsecond molecular dynamics simulations of the polyalanines Ala8 and Ala12 are analyzed. Both systems clearly exhibit metastability, with some kinetically distinct metastable states being geometrically very similar. Using the backbone torsion rotamer pattern to define the microstates, a definition is obtained of metastable states whose lifetimes considerably exceed the memory associated with interstate dynamics, thus allowing the kinetics to be described by a Markov model. This model is shown to be valid by comparison of its predictions with the kinetics obtained directly from the molecular dynamics simulations. In contrast, clustering based on the hydrogen-bonding pattern fails to identify long-lived metastable states or a reliable Markov model. Finally, an approach is proposed to generate a hierarchical model of networks, each having a different number of metastable states. The model hierarchy yields a qualitative understanding of the multiple time and length scales in the dynamics of biomolecules.
The weak hydrogen bond in the fluorobenzene-ammonia van der Waals complex: Insights into the effects of electron withdrawing substituents on π versus in-plane bonding
Authors: Tonge Nicola M. , MacMahon Ewan C. , Pugliesi Igor , Cockett Martin C. R.
Published: April 2007

The fluorobenzene-ammonia van der Waals complex has been studied using a combination of two-color resonance enhanced multiphoton ionization (REMPI) spectroscopy, counterpoise corrected RICC2 ab initio molecular orbital calculations, and multidimensional Franck-Condon analysis. The experimental REMPI spectrum is characterized by a dominant, blueshifted band origin, and weak activity in intermolecular vibrational modes. RICC2 geometry optimizations and numerical vibrational frequency calculations of the neutral ground and first excited states have been performed on a number of different structural isomers of the complex using basis sets ranging from augmented double-zeta to quadruple-zeta level. Ground state basis set superposition error corrected zero-point binding energies show the in-plane σ complex, forming a pseudo-six-membered ring connecting the fluorine atom and ortho-hydrogen, to be consistently the most stable of all six conformations considered, at all levels of theory. Comparison of computed zero-point excitation energies for the most stable π and σ conformers with fluorobenzene show that the σ complex is the only conformer predicted to exhibit a spectral blueshift upon electronic excitation. The computed neutral ground and first excited state geometries and frequencies were used to perform multidimensional Franck-Condon simulations of the S1-S0 vibronic spectrum for each of the most stable conformers. These simulations yielded null spectra for transitions involving the most stable of the π complexes, πbridge; a spectrum rich in strong intermolecular vibrational structure for the second of the π complexes, in complete contrast to the experimental spectrum; and for the σ complex, a spectrum exhibiting weak intermolecular activity in line with that observed experimentally. This last simulation allowed an almost complete vibrational assignment of the intermolecular structure in the REMPI spectrum. The agreement between computational results and experiment overwhelmingly favors assignment of the spectrum to the in-plane σ complex.
Ferroelectric to relaxor crossover and dielectric phase diagram in the BaTiO3–BaSnO3 system
Authors: Lei C. , Bokov A. A. , Ye Z.-G.
Published: April 2007

The (1−x)BaTiO3–xBaSnO3 (0⩽x⩽0.30) perovskite solid solution ceramics were prepared by solid state reaction and studied by dielectric spectroscopy. The complex dielectric permittivity was measured as a function of frequency (0.1Hz–100kHz) in the temperature (T) range of 123–573K. The transition from the high-temperature paraelectric state where the dielectric constant obeys the Curie-Weiss law to the ergodic cluster state is found to occur at the same temperature of 485K in all the compositions of x⩾0.04 and at lower temperatures in those with a smaller x. For 0⩽x⩽xc=0.19, the temperature of the dielectric peak Tm, corresponding to the diffuse transition from the ergodic polar cluster state to the ferroelectric state, decreases with increasing x and does not depend on frequency. The diffuseness of the peak gradually increases. For x>xc, the permittivity exhibits relaxor behavior with the frequency-dependent Tm satisfying the Vogel-Fulcher law. The temperature variation of the permittivity on the high-temperature slope of the peak (T>Tm) is characterized by the characteristic Lorenz-type quadratic law for relaxors, with the diffuseness increasing with the increase of x. The mechanisms of the dielectric response in different parts of the phase diagram are discussed. In particular, the crossover from diffuse ferroelectric phase transition to relaxor ferroelectric behavior is attributed to the appearance at x>xc of the additional dielectric contribution arising from the flipping of the local polarization of the polar clusters. The temperature-composition phase diagram of the Ba(Ti1−xSnx)O3 system has been established, which delimits the paraelectric, ergodic polar cluster, nonergodic ferroelectric, and relaxor phases (states) and indicates the crossover from ferroelectric to relaxor behavior at x=xc.
Surface tension of the most popular models of water by using the test-area simulation method
Authors: Vega C. , de Miguel E.
Published: April 2007

We consider the calculation of the surface tension from simulations of several models of water, such as the traditional TIP3P, SPC, SPC/E, and TIP4P models, and the new generation of TIP4P-like models including the TIP4P/Ew, TIP4P/Ice, and TIP4P/2005. We employ a thermodynamic route proposed by Gloor et al. [J. Chem. Phys. 123, 134703 (2005)] to determine the surface tension that involves the estimate of the change in free energy associated with a small change in the interfacial area at constant volume. The values of the surface tension computed from this test-area method are found to be fully consistent with those obtained from the standard mechanical route, which is based on the evaluation of the components of the pressure tensor. We find that most models do not reproduce quantitatively the experimental values of the surface tension of water. The best description of the surface tension is given by those models that provide a better description of the vapor-liquid coexistence curve. The values of the surface tension for the SPC/E and TIP4P/Ew models are found to be in reasonably good agreement with the experimental values. From the present investigation, we conclude that the TIP4P/2005 model is able to accurately describe the surface tension of water over the whole range of temperatures from the triple point to the critical temperature. We also conclude that the test area is an appropriate methodological choice for the calculation of the surface tension not only for simple fluids, but also for complex molecular polar fluids, as is the case of water.
Natrolite: A zeolite with negative Poisson’s ratios
Authors: Grima Joseph N. , Gatt Ruben , Zammit Victor , Williams Jennifer J. , Evans Kenneth E. , Alderson Andrew , Walton Richard I.
Published: April 2007

The recently published experimental elastic constants [C. Sanchez-Valle, S. V. Sinogeikin, Z. A. Lethbridge, R. I. Walton, C. W. Smith, K. E. Evans, and J. D. Bass, J. Appl. Phys. 98, 053508 (2005)] for single crystals of the orthorhombic aluminosilicate zeolite NAT (natrolite, Na2(Al2Si3O10)2H2O, Fdd2) throw valuable light on the potential of NAT as a material which exhibits single crystalline negative Poisson’s ratios (auxetic). On performing an off-axis analysis of these elastic constants we confirm that the zeolite natrolite exhibits auxetic behavior in the (001) plane. This supports our preliminary report that NAT-type zeolites exhibit auxetic behavior through a mechanism involving microscopic rotation of semi-rigid structural units.
Magnetic properties of Bi(Fe1−xCrx)O3 synthesized by a combustion method
Authors: Li J.-B. , Rao G. H. , Liang J. K. , Liu Y. H. , Luo J. , Chen J. R.
Published: April 2007

Single-phase samples of Bi(Fe1−xCrx)O3 with x=0, 0.1, and 0.2 were synthesized by a combustion method. X-ray diffraction reveals that the lattice parameters of Bi(Fe1−xCrx)O3 perovskites decrease linearly with the Cr content, indicating that Cr ions substitute for Fe ions to form a solid solution. X-ray photoelectron spectroscopy investigation shows that Cr ions have the Cr3+ valence state in Bi(Fe1−xCrx)O3. The frequency dependence of dielectric constants was investigated at room temperature. Magnetic measurements show hysteresis loops at both 5 and 300K and the substitution of Cr for Fe enhances the magnetization.
Carrier concentration dependence of band gap shift in n-type ZnO:Al films
Authors: Lu J. G. , Fujita S. , Kawaharamura T. , Nishinaka H. , Kamada Y. , Ohshima T. , Ye Z. Z. , Zeng Y. J. , Zhang Y. Z. , Zhu L. P. , He H. P. , Zhao B. H.
Published: April 2007

Al-doped ZnO (AZO) thin films have been prepared by mist chemical vapor deposition and magnetron sputtering. The band gap shift as a function of carrier concentration in n-type zinc oxide (ZnO) was systematically studied considering the available theoretical models. The shift in energy gap, evaluated from optical absorption spectra, did not depend on sample preparations; it was mainly related to the carrier concentrations and so intrinsic to AZO. The optical gap increased with the electron concentration approximately as ne2∕3 for ne≤4.2×1019 cm−3, which could be fully interpreted by a modified Burstein–Moss (BM) shift with the nonparabolicity of the conduction band. A sudden decrease in energy gap occurred at 5.4−8.4×1019 cm−3, consistent with the Mott criterion for a semiconductor-metal transition. Above the critical values, the band gap increased again at a different rate, which was presumably due to the competing BM band-filling and band gap renormalization effects, the former inducing a band gap widening and the latter an offsetting narrowing. The band gap narrowing (ΔEBGN) derived from the band gap renormalization effect did not show a good ne1∕3 dependence predicated by a weakly interacting electron-gas model, but it was in excellent agreement with a perturbation theory considering different many-body effects. Based on this theory a simple expression, ΔEBGN=Ane1∕3+Bne1∕4+Cne1∕2, was deduced for n-type ZnO, as well as p-type ZnO, with detailed values of A, B, and C coefficients. An empirical relation once proposed for heavily doped Si could also be used to describe well this gap narrowing in AZO.
Tests of functionals for systems with fractional electron number
Authors: Vydrov Oleg A. , Scuseria Gustavo E. , Perdew John P.
Published: April 2007

In the exact theory, the ground state energy of an open system varies linearly when the electron number is changed between two adjacent integers. This linear dependence is not reproduced by common approximate density functionals. Deviation from linearity in this dependence has been suggested as a basis for the concept of many-electron self-interaction error (SIE). In this paper, we quantify many-electron SIE of a number of approximations by performing calculations on fractionally charged atoms. We demonstrate the direct relevance of these studies to such problems of common approximate functionals as instabilities of anions, spurious fractional charges on dissociated atoms, and poor description of charge transfer. Semilocal approximations have the largest many-electron SIE, which is only slightly reduced in typical global hybrids. In these approximations the energy versus fractional electron number curves upward, while in Hartree-Fock theory the energy curves downward. Perdew-Zunger self-interaction correction [Phys. Rev. B 23, 5048 (1981)] significantly reduces the many-electron SIE of semilocal functionals but impairs their accuracy for equilibrium properties. In contrast, a long-range corrected hybrid functional can be nearly many-electron SIE-free in many cases (for reasons we discuss) and at the same time performs remarkably well for many molecular properties.
Coupling between grain growth and grain rotation
Authors: Rath Bhakta B. , Winning M. , Li J. C. M.
Published: April 2007

Grain boundary motion during grain growth or recrystallization is considered as a diffusion process of atomic movement across the boundary. It can be accompanied by subgrain rotation or nanograin rotation. However, grain boundary migration can be achieved also by dislocation motion or creep. The evidence is the power law relationship between driving force and boundary velocity for large driving forces and an activation energy which approaches that of self-diffusion at low driving forces and decreases with increasing driving force. The creep mechanism may or may not involve grain rotation. Experimental evidences and dislocation models are discussed in reference to coupling between boundary migration and grain rotation.
Unusual thermal stability of quantum size effect Pb islands grown on Si(111)-In(4×1)
Authors: Yakes M. , Chen J. , Hupalo M. , Tringides M. C.
Published: April 2007

Pb islands grown on the anisotropic Si(111)-In(4×1) were studied using scanning tunneling microscopy and spot profile analysis–low energy electron diffraction. Anisotropic wire shapes with a uniform island height of four layers due to quantum size effects are observed as well as a preferred width of 6.6nm. Unlike islands grown on clean and Pb covered Si(111), Pb islands grown on the Si(111)-In(4×1) reconstructed surface maintain a height of four layers to room temperature. The increased temperature stability enhances the potential use of the grown structures for technological applications.
Phase-sensitive optical coherence elastography for mapping tissue microstrains in real time
Authors: Wang Ruikang K. , Kirkpatrick Sean , Hinds Monica
Published: April 2007

The authors present a phase-sensitive optical coherence elastography (PSOCE) approach to image instantaneous tissue deformations, strain rates, and strains of soft tissue in real time with sensitivity at the nanometer scale. This method exploits the phase information available in the complex optical coherence tomography images and measures the phase changes between the successive B scans to resolve the instantaneous tissue deformations. The PSOCE system described is capable of producing localized microstrain rate and strain maps of tissue subjected to a dynamic compression in real time. They show that this approach is capable of resolving deformations as small as 0.26nm.