bluuebunny/crossref_metadata_2025 huggingface dataset:
‘Non‐neuronopathic’ Gaucher disease reconsidered. Prevalence of neurological manifestations in a Dutch cohort of type I Gaucher disease patients and a systematic review of the literature
Authors: Biegstraaten M. , van Schaik I. N. , Aerts J. M. F. G. , Hollak C. E. M.
Published: April 2008

Gaucher disease is a lysosomal storage disorder, which is classically divided into three types. Type I Gaucher disease is differentiated from types II and III disease by the absence of nervous system involvement. However, an increasing number of reports has emerged on neurological manifestations in patients with type I Gaucher disease. Whether a strict division in three different phenotypes is still valid has been the subject of debate. The main objective of this study was to provide scientific arguments whether a distinction between type I (non‐neuronopathic) and types II and III (neuronopathic) Gaucher disease should be maintained. We investigated retrospectively a large Dutch cohort of type I Gaucher disease patients for the prevalence of neurological manifestations and provide an overview of the literature on this topic. A diagnosis of a neurological disease was made 34 times in 75 patients. Forty‐five patients reported at least one neurological symptom during the median follow‐up time of 11 years. The literature search revealed 86 studies in which type I Gaucher disease patients or carriers of a glucocerebrosidase mutation were described with a neurological disease or a condition which is known to be associated with neurological disease. In conclusion, the term non‐neuronopathic Gaucher disease does not seem to be an appropriate characterization of type I Gaucher disease. However, the neurological signs and symptoms in type I Gaucher disease are of a totally different kind from and, in the majority of cases, of much less severity than the signs and symptoms associated with types II and III disease Therefore, type I disease should be classified as a separate phenotype.
No effect of n-3 long-chain polyunsaturated fatty acid (EPA and DHA) supplementation on depressed mood and cognitive function: a randomised controlled trial – reply by Rogers et al.
Authors: Rogers Peter J. , Appleton Katherine M. , Kessler David , Peters Tim J. , Gunnell David , Hayward Robert C. , Heatherley Susan V. , Christian Leonie M. , McNaughton Sarah A. , Ness Andy R.
Published: April 2008

We recently reported a null outcome from a study of n-3 long-chain PUFA supplementation in depressed mood(1).
Variability within cotton cultivars for yield, fibre quality and physiological traits
Authors: TOKATLIDIS I. S. , TSIKRIKONI C. , TSIALTAS J. T. , LITHOURGIDIS A. S. , BEBELI P. J.
Published: April 2008

Selection within elite cotton cultivars is ineffective; it is believed that they are genetically homogeneous. Research in other crops, however, has verified significant intra-cultivar variation based either on phenotypic differentiation or molecular analysis techniques. The present study primarily investigated possible intra-cultivar variation for seedcotton yield. Honeycomb selection within three elite cotton cultivars, on the basis of single-plant seedcotton yield and under the ultra-low density of 1·2 plants/m2, was performed. From each cultivar, six selfed (hand-pollinated) plants were selected and seed of each selected plant constituted a separate line. The 18 first generation lines were evaluated in three locations at a density of 1·2 plants/m2. Within each line, the 10 selfed plants which yielded the highest were selected. Mixed seed from these selected plants constituted the respective second generation line. Offspring performance of the 18 second generation lines was also tested in three locations at a density of 1·2 plants/m2. The results were indicative of intra-cultivar variation, since significant differentiation between lines of each cultivar was found for seedcotton yield per plant, averaged across two years and three locations. Additionally, significant intra-cultivar variation was found for fibre quality properties (length and micronaire, but not strength and uniformity) averaged across two years in a single location, as well as for physiological traits (leaf carbon isotope discrimination, ash content and K concentration) averaged across two years and three locations. In comparison with the original cultivars the second generation lines had higher seedcotton yields supporting the existence of exploitable genetic variation. The conclusion was that honeycomb selection in the absence of competition could be an effective technique in breeders' seed treatment in order to avoid gradual degeneration and beneficially exploit any latent or newly developed genetic variation.
EDITORIAL REMARKS
Authors: Fowler William R. , McCafferty Geoffrey G.
Published: April 2008

Ancient Mesoamerica does not run editorial remarks very often. In fact, we have done this only once before, in vol. 1, no. 1, when we explained the rationale for the birth of the new journal (Fowler and Houston 1990). We offer these brief remarks to alert readers to an important addition in staff and a significant editorial innovation.
Attenuation of Lg in the western US using the USArray
Authors: Phillips W. Scott , Stead Richard J.
Published: April 2008

The unprecedented breadth and density of the USArray allows us to resolve lateral variations of 1‐Hz Lg attenuation to 0.5 degrees over much of the western United States. We collected over 31,000 Lg amplitudes from 547 events and 408 stations of the initial USArray footprint. Two‐dimensional tomographic inversion yielded Q ranging from 60 to 550, with a variance reduction of 47% relative to the best‐fit constant Q model (Q = 155). Q is low over most of the region, with lowest values associated with recent volcanic activity, and active shear zones. High Q is found in older, stable crust, notably the Colorado and Columbia plateaus, while smaller islands of high Q are associated with batholiths, including the Sierra Nevada, Peninsular, and Bitterroot Ranges, the western Mojave, and Okanogan Highlands, as well as other areas of competent crust such as the Harcuvar range, and two topographically bounded blocks in the Basin and Range.
Evidence for reconnection at Saturn's magnetopause
Authors: McAndrews H. J. , Owen C. J. , Thomsen M. F. , Lavraud B. , Coates A. J. , Dougherty M. K. , Young D. T.
Published: April 2008

Observations of Saturn's magnetopause by the Cassini Plasma Spectrometer (CAPS) and magnetometer have revealed clear instances of magnetic reconnection signatures, two of which are described here. Both encounters occurred at the equator in the prenoon sector as Cassini was exiting the magnetosphere. Evidence of heating in the electrons and ions is highly suggestive of energization comparable to that associated with the reconnection process at Earth. In one case, the fields are strongly antiparallel and the magnetic data indicate the presence of a locally open magnetic field. In the other example, magnetic data indicate a locally closed magnetic field compatible with the field lines being locally parallel, but the particle signatures lead to the conclusion of a distant reconnection site poleward of the cusps being active. The reconnection voltage for the first case is calculated to be 48 kV, which is of the same order as previous estimates at Saturn. This is lower than the corotational voltage but is not insignificant.
Ground‐based transmitter signals observed from space: Ducted or nonducted?
Authors: Clilverd Mark A. , Rodger Craig J. , Gamble Rory , Meredith Nigel P. , Parrot Michel , Berthelier Jean‐Jacques , Thomson Neil R.
Published: April 2008

The principal loss mechanism for electrons from the inner radiation belt (1.2 < L < 2.0) and slot region (2.0 < L < 3.0) is atmospheric precipitation driven by several processes, including coulomb collisions, plasmaspheric hiss, lightning‐generated whistlers, and manmade transmissions. Several studies have shown that ducted and nonducted VLF waves can precipitate radiation belt energetic electrons into the upper atmosphere. Here we investigate the propagation of VLF communication transmitter signals using plasma wave instruments on board the CRRES and DEMETER satellites in order to determine if nonducted transmitter signals are significant in radiation belt loss processes. We investigate the regions where strong transmitter signals are observed in the ionosphere directly above the transmitter, in the magnetosphere near where the signals cross the geomagnetic equator, and in the ionospheric region geomagnetically conjugate to the transmitter. For very low L‐shell transmitters (L < 1.5) there is evidence that a significant proportion of the wave energy propagating into the plasmasphere is nonducted. However, at higher L‐shells the waves become highly ducted in the plasmasphere. Strong evidence for this comes from the lack of significant wave power propagating above the electron half gyrofrequency limit for interhemispherically ducted waves. We conclude that manmade transmissions in the frequency range (18–25 kHz) will be restricted to driving electron precipitation primarily from the inner radiation belt (L = 1.3–2.5). This will come about through a combination of propagation types, partly through nonducted wave propagation at very low L‐shells (L = 1.3–1.5), but predominantly through ducted wave propagation at higher L‐shells (L = 1.5–2.5), ultimately limited by the electron half‐gyrofrequency limit for ducted waves.
A quantitative assessment of empirical magnetic field models at geosynchronous orbit during magnetic storms
Authors: Huang Chia‐Lin , Spence Harlan E. , Singer Howard J. , Tsyganenko Nikolai A.
Published: April 2008

We evaluate the performance of recent empirical magnetic field models (Tsyganenko, 1996, 2002a, 2002b; Tsyganenko and Sitnov, 2005, hereafter referred to as T96, T02 and TS05, respectively) during magnetic storm times including both pre‐ and post‐storm intervals. The model outputs are compared with GOES observations of the magnetic field at geosynchronous orbit. In the case of a major magnetic storm, the T96 and T02 models predict anomalously strong negative Bz at geostationary orbit on the nightside due to input values exceeding the model limits, whereas a comprehensive magnetic field data survey using GOES does not support that prediction. On the basis of additional comparisons using 52 storm events, we discuss the strengths and limitations of each model. Furthermore, we quantify the performance of individual models at predicting geostationary magnetic fields as a function of local time, Dst, and storm phase. Compared to the earlier models (T96 and T02), the most recent storm‐time model (TS05) has the best overall performance across the entire range of local times, storm levels, and storm phases at geostationary orbit. The field residuals between TS05 and GOES are small (≤3 nT) compared to the intrinsic short time‐scale magnetic variability of the geostationary environment even during non‐storm conditions (∼24 nT). Finally, we demonstrate how field model errors may affect radiation belt studies when estimating electron phase space density.
How certain is desiccation in west African Sahel rainfall (1930–1990)?
Authors: Chappell Adrian , Agnew Clive T.
Published: April 2008

Hypotheses for the late 1960s to 1990 period of desiccation (secular decrease in rainfall) in the west African Sahel (WAS) are typically tested by comparing empirical evidence or model predictions against “observations” of Sahelian rainfall. The outcomes of those comparisons can have considerable influence on the understanding of regional and global environmental systems. Inverse‐distance squared area‐weighted (IDW) estimates of WAS rainfall observations are commonly aggregated over space to provide temporal patterns without uncertainty. Spatial uncertainty of WAS rainfall was determined using the median approximation sequential indicator simulation. Every year (1930–1990) 300 equally probable realizations of annual summer rainfall were produced to honor station observations, match percentiles of the observed cumulative distributions and indicator variograms and perform adequately during cross validation. More than 49% of the IDW mean annual rainfall fell outside the 5th and 95th percentiles for annual rainfall realization means. The IDW means represented an extreme realization. Uncertainty in desiccation was determined by repeatedly (100,000) sampling the annual distribution of rainfall realization means and by applying Mann‐Kendall nonparametric slope detection and significance testing. All of the negative gradients for the entire period were statistically significant. None of the negative gradients for the expected desiccation period were statistically significant. The results support the presence of a long‐term decline in annual rainfall but demonstrate that short‐term desiccation (1965–1990) cannot be detected. Estimates of uncertainty for precipitation and other climate variables in this or other regions, or across the globe, are essential for the rigorous detection of spatial patterns and time series trends.
Closing of the Central American Seaway and the Ice Age: A critical review
Authors: Molnar Peter
Published: April 2008

What role did the closing of the Central American Seaway play in enabling continental ice sheets to wax and wane over North America and Fennoscandia? A summary of relevant evidence presented here permits a causal relationship between them but can be interpreted to show none. The common denominator of such evidence is the approximate simultaneity of that closing with global cooling and the first major ice advance. At the resolution of paleoclimate, however, geologic evidence from Central America places only weak constraints on when interchange between Pacific and Caribbean water ceased. The strongest evidence for when North and South America became connected by a continuous land bridge, the “Great American Exchange” of vertebrates, assigns climate change the causal role, for an arid Central American climate, typical of glacial times, seems necessary for animals that inhabited savannas to pass through Panama. Paleoceanographic and geochemical studies of environments and water masses in the eastern Pacific, western Caribbean, and Atlantic in general call for continual change since ∼6 Ma or earlier, if evidence concurrent with global change near 3.5–3 Ma seems more widespread than for other times. Hypothesized connections between a closed seaway and glaciation commonly call for profoundly different North Atlantic Ocean circulation, but simulations using general circulation models provide a spectrum of differences in circulation for open and closed seaways. Might much (not all) of the evidence implicating the closing of the seaway in global climate change in fact be a consequence of that change and blind to Central America's tectonic development?
Distribution of water masses and diapycnal mixing in the Cape Verde Frontal Zone
Authors: Martínez‐Marrero A. , Rodríguez‐Santana A. , Hernández‐Guerra A. , Fraile‐Nuez E. , López‐Laatzen F. , Vélez‐Belchí P. , Parrilla G.
Published: April 2008

The Cape Verde Frontal Zone separates North and South Atlantic Central Waters in the eastern North Atlantic Subtropical Gyre. CTD‐O2 and shipboard ADCP data from three hydrographic sections carried out in September 2003 are used to study the structure of the front. Results show the relation between spatial variations of water masses and currents, demonstrating the importance of advection in the distribution of water masses. Diapycnal diffusivities due to double diffusion and vertical shear instabilities are also estimated. Existence of competition between the two processes through the water column is shown. Depth‐averaged diffusivities suggest that salt fingering dominates diapycnal mixing, except areas of purest South Atlantic Central Water. Here, double diffusion processes are weak and, consequently, shear of the flow is the main process. Results also show that strong mixing induced by vertical shear is associated with a large intrusion found near the front.
Dense shelf water cascading in the northwestern Mediterranean during the cold winter 2005: Quantification of the export through the Gulf of Lion and the Catalan margin
Authors: Ulses C. , Estournel C. , Puig P. , Durrieu de Madron X. , Marsaleix P.
Published: April 2008

Dense shelf water cascading in the northwestern Mediterranean Sea during winter 2005, which was shown to cause large erosion in the canyons and to influence deep benthic ecosystem, was investigated using numerical modeling validated with temperature and current observations. Intense dense water formation took place on the Gulf of Lion and Catalan shelves. Dense shelf water was transferred to the deep basin through three pathways. The Cap de Creus canyon in the western Gulf of Lion already identified as a huge pathway was shown to export about 1000 km3 of dense water during two months. The Palamós and Blanes canyons located on the Catalan margin were shown to be important pathways for water formed locally and for water transiting from the Gulf of Lion. After the cascading period, dense shelf water was transported mostly toward the Balearic Sea.
Historical deforestation patterns and the conservation value of church forests in the northern Ethiopian highlands
Authors: Aerts Raf , Pankhurst Richard , Van Overtveld Koen , November Eva , Hermy Martin , Muys Bart
Published: April 2008

Mountain forest plants have a limited capacity for migration because altitudinal gradients usually set strict limits to plant species’ ranges and often present physical barriers against dispersal. Innate ‘islands’ of biodiversity, mountain forests are therefore particularly vulnerable to the effects of climatic change and habitat fragmentation, both key drivers of global species loss. Conservation of these ecosystems must for that reason rely on protecting not only large fragments but also small habitat patches and relictual vegetation along a wide altitudinal range.When large fragments in such ecosystems are no longer available, small fragments become an environmental priority. Striking examples of small mountain forest fragments are the church forests of the northern Ethiopian highlands. In a landscape dominated by degraded semiarid savanna, sacred groves represent the majority of all remaining patches of Afromontane forest. Previous studies in the region only covered few fragments and could not adequately estimate the conservation value of these forests. For that reason, we digitized 394 church forests in an area of half a million hectares by systematically scanning high spatial resolution satellite images (pixel resolution 0.8 m) in eight blocks in the northern highlands and calculated area, density, shape, isolation and configuration metrics. Forest cover is only 0.2%, much lower than usually estimated in the literature (4%). Fragment shape and spatial configuration in the north and northeast of the surveyed area (irregular forests on northwestern slopes with churches near the forest edge) are consistent with forest conservation after fragmentation, while forests in the south and west (regular round forests surrounding a central church) indicate conservation prior to widespread deforestation. Fragments are small throughout the region (2.5 +- 0.2 ha) and need expansion, but known vegetation differences between church forests related to the two different historical fragmentation processes call for different strategies for forest conservation and restoration.
A new effective method for thermal annealing of magnetic tunnel junctions in air with protective overlayers
Authors: Pong Philip W. T. , Schmoueli Moshe , Li Feifei , Egelhoff William F.
Published: April 2008

Thermal annealing is an important process to enhance greatly the tunneling magnetoresistance (TMR) of magnetic tunnel junctions (MTJs). MTJ annealing is conventionally carried out in vacuum below 10−5Torr. However, this method involves the cost and complications of using a vacuum furnace. Pumping and venting a chamber are time-consuming; moreover, the sample temperature is difficult to measure accurately and therefore not easy to control. We have developed a method and an instrument to perform thermal annealing of MTJs in air. The method is based on protective overlayers, and the instrument has a simple structure composed of an air heat gun, thermocouple with feedback control, permanent magnets for magnetic field, and a sample holder. The influence of thermal annealing in air on MTJs properties was studied systematically on Al2O3 MTJ samples. The samples are successfully protected from oxidation by using Au∕Ru, or Al2O3 films as protective overlayers. The Al2O3 overlayer can be removed easily with NaOH solution. A MgO MTJ sample was annealed with this technique and its TMR increased from 17.5% to 141.3%.
Magnetic anisotropy and reversal mechanisms in dual layer exchanged coupled perpendicular media
Authors: Thomson T. , Lengsfield B. , Do H. , Terris B. D.
Published: April 2008

We report the magnetic properties of perpendicular media with a layered structure in which a high anisotropy, segregated, granular CoCrPt-oxide base layer is capped by a lower anisotropy CoCrPt-based film. Anisotropy field (Hk) data show that for the thickness of oxide media studied here, the measured value of Hk remains constant as cap thickness increases. This provides strong evidence that the anisotropy of the composite grain is controlled by the hard oxide layer and is not a simple average of the anisotropy of the oxide and cap layers. The reversal mechanism is explored by determining the angle dependent switching as a function of cap thickness. In the absence of a cap layer, the media show a Stoner–Wohlfarth-like reversal which becomes more Kondorsky-like [1∕cos(θ)] when a critical cap thickness is reach, which we interpret as indicating greater lateral exchange coupling.
Multiconfiguration optimized effective potential method for a density-functional treatment of static correlation
Authors: Weimer Martin , Della Sala Fabio , Görling Andreas
Published: April 2008

An approach to treat static correlation within a density-functional framework is presented. To that end, a multiconfiguration optimized effective potential (MCOEP) method is derived. In contrast to standard multiconfiguration self-consistent field (MCSCF) methods and previous combinations of MCSCF procedures with density-functional theory, the MCOEP method yields well-defined physically meaningful orbital and eigenvalue spectra. In addition to the electronic ground state also excited electronic states can be described. The MCOEP method is implemented invoking the localized Hartree–Fock approximation, leading to a multiconfiguration localized Hartree–Fock approach. Applications of the new method to the dissociation of the hydrogen molecule and the isomerization of ethene and cyclobutadiene show that it is capable of describing situations that are characterized by strong static correlation
Origin and control of superlinear polarizability scaling in chemical potential equalization methods
Authors: Lee Warren G. , Davis Joseph E. , Patel Sandeep
Published: April 2008

Many common chemical potential equalization (μEq) methods are known to suffer from a superlinear scaling of the polarizability with increasing molecular size that interferes with model transferability and prevents the straightforward application of these methods to large, biochemically relevant molecules. In the present work, we systematically investigate the origins of this scaling and the mechanisms whereby some existing methods successfully temper the scaling. We demonstrate several types of topological charge constraints distinct from the usual single molecular charge constraint that can successfully achieve linear polarizability scaling in atomic charge based equilibration models. We find the use of recently employed charge conservation constraints tied to small molecular units to be an effective and practical approach for modulating the polarizability scaling in atomic μEq schemes. We also analyze the scaling behavior of several μEq schemes in the bond representation and derive closed-form expressions for the polarizability scaling in a linear atomic chain model; for a single molecular charge constraint these expressions demonstrate a cubic dependence of the polarizability on molecular size compared with linear scaling obtainable in the case of the atom-atom charge transfer (AACT) and split-charge equilibration (SQE) schemes. Application of our results to the trans N-alkane series reveals that in certain situations, the AACT and SQE schemes can become unstable due to an indefinite Hessian matrix. Consequently, we discuss sufficient criteria for ensuring stability within these schemes.
Thermodynamics and dynamics of a monoatomic glass former. Constant pressure and constant volume behavior
Authors: Kapko Vitaliy , Matyushov Dmitry V. , Angell C. Austen
Published: April 2008

We report constant-volume and constant-pressure simulations of the thermodynamic and dynamic properties of the low-temperature liquid and crystalline phases of the modified Stillinger–Weber (SW) model. We have found an approximately linear temperature increase of the effective Gaussian width of the distribution of inherent structures. This effect comes from non-Gaussianity of the landscape and is consistent with the predictions of the Gaussian excitations model representing the thermodynamics of the configurational manifold as an ensemble of excitations, each carrying an excitation entropy. The SW model provides us with both the configurational and excess entropies, with the difference mostly attributed to vibrational anharmonicity. We therefore can address the distinction between the excess thermodynamic quantities, often used to interpret experiments, and configurational thermodynamics used to describe the dynamics in the Adam–Gibbs (AG) equation. However we are limited computationally to work at temperatures above the “crossover” temperature at which the breakdown in the Adam–Gibbs relation has been identified in laboratory studies. We find a new break in the slope of the constant pressure AG plot (in the same sense but at much higher temperature than with laboratory data) when the excess entropy is used in the AG equation. This break, which we associate with anharmonic vibrational effects, is not seen when the configurational entropy is used. The simulation diffusivity data are equally well fitted by the AG equation and by a new equation, derived within the Gaussian excitations model, that emphasizes enthalpy over entropy as the thermodynamic control variable for transport in viscous liquids. We show that the modified SW model has close links to the behavior observed for bulk metallic glasses, both in its diffusional and in its thermodynamic properties.
Nature of metal–nonmetal transition in metal–ammonia solutions. II. From uniform metallic state to inhomogeneous electronic microstructure
Authors: Chuev Gennady N. , Quémerais Pascal
Published: April 2008

Applying semianalytical models of nonideal plasma, we evaluate the behavior of the metallic phase in metal–ammonia solutions (MAS). This behavior is mainly controlled by the degenerate electron gas, which remains stable down to 5 MPM due to high solvent polarizability and strong dielectric screening of solvated ions. Comparing the behavior of the metallic state with those of localized solvated electrons, we have estimated the miscibility gap Δn for various alkali metals and found Δn(Na)>Δn(K). It is rather narrow in Rb−NH3 and does not occur in Cs−NH3 solutions, which is in full agreement with the experiments. The case of Li is discussed separately. The difference calculated in the excess free energies of the metallic and nonmetallic phases is in the order of kBT, yielding a thermally fluctuating mixed state at intermediate metal concentrations. It results in a continuous metal–nonmetal (MNM) transition above the consolute point Tc and a phase separation below Tc. We propose a criterion for the MNM transition which may be attributed to the line of the maximum of compressibility above Tc. This line crosses the spinodal one at the critical temperature. Finally, we assert that a new electronic phase similar to microemulsion should also arise between the spinodal and the binodal lines.
Response to “Comment on ‘Markovian approximation in a coarse-grained description of atomic systems’ ” [J. Chem. Phys. 128, 147101 (2008)]
Authors: Hijón Carmen , Serrano Mar , Español Pep
Published: April 2008

We show within the Mori theory of projection operators that the Green-Kubo formula using microscopic rather than projected forces is only valid if the description is Markovian. Therefore, the only way to assess whether a description is Markovian is through examining the predictions of the theory under the Markovian assumption. Although, in principle, the blob description for a unidimensional chain is non-Markovian, in practice the Markovian approximation describes reasonably well the coarse dynamics of the chain.
Theoretical studies on the bonding and thermodynamic properties of GenSim (m+n=5) clusters: The precursors of germanium/silicon nanomaterials
Authors: Wielgus Pawel , Roszak Szczepan , Majumdar D. , Saloni Julia , Leszczynski Jerzy
Published: April 2008

Theoretical studies on the GenSim clusters have been carried out using advanced ab initio approaches. The lowest energy isomers were determined for the clusters with compositions n+m=2–5. All possible isomers arising due to permutations of Ge and Si atoms were investigated. The L-shaped structure for the trimers, tetragonal with diagonal bond for tetramers, and a trigonal bipyramid for pentamers represent the energy optimized ground state geometries. The bonding analyses revealed that the trimers and tetramers are stabilized through multicenter π bonding. In pentamers, this stabilizing factor is eliminated due to the further cluster growth. The ionization of clusters does not change their geometrical characteristics. The agreement of the calculated ionization and atomization energies with those obtained from the mass spectrometric studies (through estimated appearance potential) validated the reported structures of the clusters. The bonding properties of these species are discussed using their molecular orbital characteristics and analysis of natural bond orbital population data.
Protein dynamics from a NMR perspective: Networks of coupled rotators and fractional Brownian dynamics
Authors: Calandrini Vania , Abergel Daniel , Kneller Gerald R.
Published: April 2008

Nuclear magnetic resonance (NMR) has proven to be the most valuable tool for investigating internal dynamics of proteins. In this perspective, the interpretation of NMR relaxation data eventually relies on a model of the motions. In this article, we propose to compare two radically different approaches that aim at describing internal dynamics in proteins. It is shown that the correlation functions predicted by a network of coupled rotators can be interpreted in terms of a heuristic approach based on fractional Brownian dynamics for each of the vectors in the network. Our results are interpreted in terms of the probability distributions of relaxation modes in both processes, the median of which turns out to be the relevant quantity for the comparison of both models.
Unique magnetic coupling between Mn doped stannaspherenes Mn@Sn12
Authors: Kandalam Anil K. , Chen Gang , Jena Puru
Published: April 2008

We report the density functional theory based study of the interaction between two Mn doped stannaspherenes (Mn@Sn12). The calculated results show that Mn@Sn12 cluster is not only highly stable and carry a high magnetic moment, but these clusters retain their structural identity and form a stable dimer cluster. Most importantly, the magnetic coupling between the Mn@Sn12 clusters depends on the relative orientation of the cages. In addition, ab initio molecular dynamics calculations show that the dimer cluster is stable at room temperature. These results are expected to trigger further investigations on highly stable bimetallic magnetic cage complexes.
Molecular dynamics study on low-energy sputtering properties of MgO surfaces
Authors: Ahn Hyo-Shin , Kim Tae-Eun , Cho Eunae , Ji Miran , Lee Choong-Ki , Han Seungwu , Cho Youngmi , Kim Changwook
Published: April 2008

In an effort to understand microscopic processes occurring between MgO protective layers and impinging plasma ions in a discharge cell of plasma-display panel, sputtering properties of MgO(100) surface by He, Ne, and Xe atoms are studied with molecular dynamics simulations. Interatomic potentials between constituent atoms are fitted to first-principles data sets for representative configurations. Various incident directions of ions are considered with kinetic energies under 100eV. It is found that sputtering yields for the Ne atom are largest among tested noble gases. The angle dependence of sputtering yields indicates that (111)-oriented MgO films are much more vulnerable to ion attacks than (100)-oriented layers. A surface model including the monolayer step is also studied and it is found that the yields increase substantially for grazing-angle incidence.
Pseudochaotic poloidal transport in the laminar regime of the resistive ballooning instabilities
Authors: Calvo I. , Garcia L. , Carreras B. A. , Sánchez R. , van Milligen B. Ph.
Published: April 2008

In toroidal geometry, and prior to the establishment of a fully developed turbulent state, the so-called topological instability of the pressure-gradient-driven turbulence is observed. In this intermediate state, a narrow spectral band of modes dominates the dynamics, giving rise to the formation of isosurfaces of electric potential with a complicated topology. Since E×B advection of tracer particles takes place along these isosurfaces, their topological complexity affects the characteristic features of radial and poloidal transport dramatically. In particular, they both become strongly nondiffusive and non-Gaussian. Since radial transport determines the system confinement properties and poloidal transport controls the equilibration dynamics (on any magnetic surface), the development of nondiffusive models in both directions is thus of physical interest. In previous work, a fractional model to describe radial transport was constructed by the authors. In this contribution, recent results on periodic fractional models are exploited for the construction of an effective model of poloidal transport. Numerical computations using a three-dimensional reduced magnetohydrodynamic set of equations are compared with analytical solutions of the fractional periodic model. It is shown that the aforementioned analytical solutions accurately describe poloidal transport, which turns out to be superdiffusive with index α=1.
Broadband electron spin resonance at low frequency without resonant cavity
Authors: Jang Z. H. , Suh B. J. , Corti M. , Cattaneo L. , Hajny D. , Borsa F. , Luban M.
Published: April 2008

We have developed a nonconventional broadband electron spin resonance (ESR) spectrometer operating continuously in the frequency range from 0.5to9GHz. Dual antenna structure and the microwave absorbing environment differentiate the setup from the conventional one and enable broadband operation with any combination of frequency or magnetic field modulation and frequency or magnetic field sweeping. Its performance has been tested with the measurements on a 1,1-diphenyl-2-picrylhydrazyl (DPPH) sample and with the measurements on the single molecular magnet, V6, in solid state at low temperature.
Application of magnetically perturbed time-dependent density functional theory to magnetic circular dichroism: Calculation of B terms
Authors: Seth Michael , Krykunov Mykhaylo , Ziegler Tom , Autschbach Jochen , Banerjee Arup
Published: April 2008

Magnetically perturbed time-dependent density functional theory is applied to the calculation of the magnetic circular dichroism (MCD) B terms of closed shell molecules. Two approaches to evaluating B term parameters are described: a sum-over-states–type approach and an approach based on the direct solution of the matrix equations. The advantages and disadvantages and technical challenges of each approach are described. The interpretation of the parameters in terms of ground and excited state perturbations are discussed. Several applications of the methodology are described. Calculations of the MCD of ethene are used to compare the sum-over-states and direct solution approaches and to illustrate the potential for analysis. The other applications involving azabenzes, sulfur-nitrogen heterocycles and quinone molecules are compared with experiment and other theoretical calculations. For the most part, all important features of the observed spectra are reproduced.
Structural, electronic, and optical properties of ferroelectric KTa1/2Nb1/2O3 solid solutions
Authors: Shen Yanqing , Zhou Zhongxiang
Published: April 2008

The first principles calculations within generalized gradient approximation have been used to determine the structural, electronic, and optical properties of three chemically ordered ferroelectric KTa1/2Nb1/2O3 phases, with B site cations ordered along the [100], [110], and [111] directions. Stable ferroelectric ground states are found in all structures. The energy bands, density of states, complex dielectric function, reflectivity, refractive index, extinction coefficient, optical conductivity, absorption coefficient, and energy loss function are calculated by using the stable ferroelectric structures. The calculated results show good agreement with the available experimental and theoretical data. It is found that the ferroelectric states are particularly sensitive to the chemical ordering of B site cations and the long-range ordering has significant effect on the properties of KTa1/2Nb1/2O3 crystals.
A simply constructed lead phthalocyanine memory diode
Authors: Mukherjee Biswanath , Ray Asim K. , Sharma Ashwani K. , Cook Michael J. , Chambrier Isabelle
Published: April 2008

Random-access memory switches were fabricated by using 70 nm thick spun films of nonperipherally octahexyl substituted lead phthalocyanine (PbPc) molecules sandwiched between indium tin oxide (ITO) substrates and vacuum-deposited aluminum (Al) top electrodes. The reproducible hysteresis behavior in terms of high and low conductance states was observed in the current-voltage characteristics recorded for the device at room temperature, and the on/off ratio for this single layered device was estimated to be as large as 103. The bistable electrical switching effects were attributed to the existence of the depletion layer at the ITO/PbPc and energetically exponential distribution in energy of traps in nonactive region of PbPc films.
Effects of annealing in N2 ambient on traps and persistent conduction in hydrothermally grown ZnO
Authors: Fang Z.-Q. , Claflin B. , Look D. C.
Published: April 2008

Thermally stimulated current (TSC) spectroscopy and temperature–dependent dark current (DC) measurements have been applied to study traps and photoinduced persistent surface conduction in two hydrothermally grown bulk ZnO samples, as-grown, and annealed at 600°C in N2 ambient for 30min, respectively. The as-grown sample had a room-temperature (RT) resistivity of 1.6×103Ωcm, mobility of 2.1×102cm2∕Vs, and carrier concentration of 1.8×1013cm−3, while the annealed sample was highly resistive, with RT resistivity of 3.6×106Ωcm, mobility of 4.4cm2∕Vs, and carrier concentration of 3.9×1011cm−3. The as-grown sample showed strong conduction at low temperatures, which has been shown to be due to near-surface carriers in other studies. The annealed sample did not demonstrate this phenomenon. The dominant trap in the as-grown sample had an activation energy of 0.16eV, was strongest near the surface, and is possibly related to VZn. In the annealed sample, however, the dominant trap had an activation energy of 0.22eV, was of bulk nature, and is tentatively assigned to LiZn. After several routine TSC measurements, the DC for the as-grown sample increased by more than one order of magnitude at low temperatures (T<180K), while for the annealed sample, the DC increased by a factor of 2 at high temperatures (T>200K). These effects are generated by the TSC trap-filling illumination and can persist for many days under vacuum. At RT, the DC in the annealed sample returns to its equilibrium state if the sample is vented to air.
Deep level transient spectroscopy and capacitance-voltage study of dislocations and associated defects in SiGe∕Si heterostructures
Authors: Lu Jinggang , Park Yongkook , Rozgonyi George A.
Published: April 2008

Three SiGe∕Si heterostructures with different Ge contents have been examined by deep level transient spectroscopy (DLTS) and capacitance-voltage techniques. DLTS revealed a broad band of traps from 80to250K in the as-grown samples. Arrhenius plots of a 25% SiGe sample revealed three trap levels at 0.28, 0.31, and 0.43eV above the valance band, respectively. By varying the reverse biases and comparing samples of different Ge contents, it was found that the trap levels shift toward the valance band with increasing Ge concentration. Capacitance-voltage data indicated that the acceptor trap levels in the SiGe graded layer dramatically decreased from 40×1013cm−3 in the as-grown sample to 4×1013cm−3 after annealing at over 800°C. Based on their charge states and thermal annealing behaviors, we suggest that majority of the grown-in acceptor levels are likely due to vacancy clusters generated by dislocation jog dragging, which can be readily annealed out, leaving only the dislocation related deep levels. The density of deep levels along a relatively clean dislocation is estimated to be ∼104cm−1.
Effects of a surrounding elastic medium on flexural waves propagating in carbon nanotubes via nonlocal elasticity
Authors: Li Xian-Fang , Wang Bao-Lin , Mai Yiu-Wing
Published: April 2008

The flexural wave behavior in carbon nanotubes embedded in an elastic medium is analyzed based on the classical and nonlocal theories of the Timoshenko beam. Emphasis is focused on the effects of small scale and the surrounding elastic medium on the phase velocity of the transverse wave. The system of basic equations for transverse deflection and rotation are derived, and further, a single fourth-order governing differential equation is reduced. The characteristic equation and dispersion relation are obtained for single-walled carbon nanotubes (SWCNTs) and double-walled carbon nanotubes (DWCNTs). The number of flexural wave branches depends only on the number of walls, but not on the surrounding elastic medium and the small scale parameter. A SWCNT has two phase velocities and a DWCNT has four phase velocities for extremely high frequencies. Critical or cutoff frequencies are independent of the small scale parameter. However, the lower critical frequencies depend on the surrounding elastic medium and the van der Waals force, and higher critical frequencies depend on the shear rigidity of tubes. Consideration of small scale decreases the corresponding wave speeds, and this effect is negligible for lower frequencies. A surrounding elastic medium affects the acoustic mode of phase velocity for lower frequencies, and hardly affects the optical mode. The classical/nonlocal Euler–Bernoulli and Rayleigh beam theories can be recovered as special cases of the present models. Moreover, the number of wave speeds for both SWCNTs and DWCNTs diminishes by half compared to that of the Timoshenko beam theory.
Experiments on metastable states of three-dimensional trapped particle clusters
Authors: Block D. , Käding S. , Melzer A. , Piel A. , Baumgartner H. , Bonitz M.
Published: April 2008

Small three-dimensional charged-dust clusters, so-called Yukawa balls, are analyzed with regard to their construction principle. For that purpose, in an experimental approach, different (metastable) configurations of clusters with fixed particle number (N<100) have been generated under identical plasma and trapping conditions. Metastable states are frequently observed. In combination with molecular dynamics simulations, it is shown that particle interaction with screening strongly affects the appearance probabilities of metastable configurations. Small clusters show different average density distributions with screened interaction compared to pure Coulomb, although having the same ground state configurations.
Effects of molecular weight on the liquid-liquid transition in polystyrene melts studied by low-frequency anelastic spectroscopy
Authors: Wu X. B. , Shang S. Y. , Xu Q. L. , Zhu Z. G.
Published: April 2008

A substantial internal friction peak associated with the liquid-liquid transition (Tll) has been observed in polystyrene (PS) melts with different molecular weights Mw. The peak is of the relaxation type and suggested to be caused by the cooperative rearrangement of PS chains. The relaxation time follows the Vogel–Fulcher–Tamman equation. With increasing Mw, the PS melt exhibits a higher energy barrier, a smaller concentration of mobile species, and a stronger coupling between mobile species at Tll. In addition, to quantify the strength of the temperature dependence of the relaxation time, a parameter mll is defined for PS melt according to Angell’s fragility concept. The value of mll decreases with increasing Mw, indicating a slower cooperative rearrangement of PS chains toward Tll. Moreover, at Mw⩽52.5kg∕mol, mll rapidly drops with Mw, while it more slowly decreases at Mw>52.5kg∕mol. The fact suggests more topological constraints due to the intrachain interactions in very long chains.
High-temperature relaxor cobalt-doped (1−x)BiScO3-xPbTiO3 piezoelectric ceramics
Authors: Yao Zhonghua , Liu Hanxing , Liu Yang , Wu Zhaohui , Cao Minghe , Hao Hua
Published: April 2008

Cobalt-doped (1−x)BiScO3-xPbTiO3 piezoelectric ceramics were fabricated by conventional solid state synthesis, in which a morphotropic phase boundary (MPB) region was observed in the compositional range of 0.48⩽x⩽0.53 from the phase structure measurement. Co doping in the 0.50BiScO3–0.50PbTiO3 ceramics resulted in a relaxor ferroelectric behavior due to cation disorder. The ferroelectric phase transition of the composition x=0.50 near the MPB was found to be a displacive and first-order transition with excellent piezoelectric properties, Tm=470°C, d33=282pC∕N, Kp=0.49, indicating a future high-temperature piezoelectric application.
Angular distribution of isothermal expansions of non-quasi-neutral plasmas into a vacuum
Authors: Yongsheng Huang , Xiaojiao Duan , Yijin Shi , Xiaofei Lan , Zhixin Tan , Naiyan Wang , Xiuzhang Tang , Yexi He
Published: April 2008

A two dimensional planar model is developed for self-similar isothermal expansions of non-quasi-neutral plasmas into a vacuum of solid targets heated by ultraintense laser pulses. The angular ion distribution and the dependence of the maximum ion velocity on laser parameters and target thicknesses are predicted. Considering the self-generated magnetic field of plasma beams as a perturbation, the ion energy on edge at the ion opening angle has an increase of 2% relative to that on the front center. Therefore, the self-generated magnetic field of plasma beams is not large enough to interpret for the ring structures.
Substitutional-to-interstitial ratio of manganese in nanostructured GaN by electron channeling enhanced microanalysis
Authors: Niermann T. , Mai D. , Roever M. , Kocan M. , Zenneck J. , Malindretos J. , Rizzi A. , Seibt M.
Published: April 2008

Quantitative lattice-site determination of manganese in spatially inhomogeneous low-temperature GaN is performed by channeling enhanced microanalysis. The technique allows one to measure the substitutional-to-interstitial ratio at a spatial resolution suitable to study individual single-crystalline columns. Numerical fitting to full dynamical Bloch wave calculations yields a fraction of (95.6±6.3)% manganese incorporated on substitutional sites.
Extended tuning of an injection-locked diode laser
Authors: Shaffer M. K. , Ranjit G. , Sukenik C. I.
Published: April 2008

We have investigated the application of an electronic feedback technique recently reported by Repasky et al. [Appl. Opt. 45, 9013 (2006)] to an injection-locked semiconductor diode laser. We find that without electronic feedback, the injection-locked slave laser will only follow the master for less than 1GHz, but once the electronic feedback is applied, the slave laser is capable of following for more than 20GHz, corresponding to the full scan range of the master laser.