bluuebunny/crossref_metadata_2025 huggingface dataset:
Geranyl modification on the tryptophan residue of ComXRO‐E‐2 pheromone by a cell‐free system
Authors: Tsuji Fumitada , Ishihara Ayako , Kurata Keiko , Nakagawa Aya , Okada Masahiro , Kitamura Shigeyuki , Kanamaru Kyoko , Masuda Yuichi , Murakami Kazuma , Irie Kazuhiro , Sakagami Youji
Published: December 2011

ComX pheromone is an isoprenoidal oligopeptide containing a modified tryptophan residue, which stimulates natural genetic competence in the gram‐positive bacterium Bacillus. Since posttranslational prenylation on the tryptophan residue has not been reported except in ComX pheromone, the universality of this modification has not yet been elucidated. In this paper, we established a cell‐free system, whereby the tryptophan residue in peptides is modified with a geranyl group by modifying enzyme ComQ. In addition, we investigated enzymatic reaction conditions using an in vitro enzyme reaction system. This is the first report of in vitro geranylation on the tryptophan residue. This system is potentially a useful tool for elucidating the universality of prenylation on the tryptophan residue.
Flapping propulsion using a fin ray
Authors: Alben S.
Published: December 2011

We calculate optimal driving motions for a fin ray in a two-dimensional inviscid fluid, which is a model for caudal fin locomotion. The driving is sinusoidal in time, and consists of heaving, pitching and a less-studied motion called ‘shifting’. The optimal phases of shifting relative to heaving and pitching for maximum thrust power and efficiency are calculated. The optimal phases undergo jumps at resonant combinations of fin ray bending and shear moduli, and are nearly constant in regions between resonances. In two examples, pitching- and heaving-based motions converge with the addition of optimal shifting. Shifting provides an order-one increase in output power and efficiency.
Intra-basaltic soil formation, sedimentary reworking and eodiagenetic K-enrichment in the Middle to Upper Ordovician Dunn Point Formation of eastern Canada: a rare window into early Palaeozoic surface and near-surface conditions
Authors: JUTRAS P. , HANLEY J. J. , QUILLAN R. S. , LEFORTE M. J.
Published: December 2011

Mafic flows of the Middle to Upper Ordovician Dunn Point Formation of eastern Canada were deeply weathered under warm and relatively humid conditions before being buried by subsequent flows. In the absence of superior plants, and in the context of relatively low atmospheric carbon levels, the soils developed alkaline groundwater conditions through mineral–water interactions, which resulted in an enhanced mobility of Al relative to Si in most palaeosols of that formation. Although the vegetation cover was volumetrically insignificant compared with that of subsequent geological times, it was apparently producing very efficient chelates, which, for most palaeosols of the succession, generated a well-defined cheluviation pattern for not only Al and Fe, but also and mainly Ti, which is typically immobile in modern soils. The resulting soils developed an Al–Fe–Ti-depleted upper horizon that was enriched in Si, probably through periodic ground saturation. Long-term climatic variations related to orbital cycles are inferred to have accounted for a second type of soil in the succession, which contrasts with the former by showing a Si-depleted and less Al–Fe–Ti-depleted upper horizon. Some soil material was substantially reworked by surface runoff, but such occurrences can be easily differentiated fromin situsoil material in terms of texture, structure and composition. A thick overlying rhyolite flow is thought to be responsible for providing abundant K in solution, which was incorporated in the underlying basalt palaeosols as exchangeable cations within a probably montmorillonitic clay precursor to the Fe–Mg-rich phengite that later developed during deep burial and orogenic compression.
Perceived foreign accent in first language attrition and second language acquisition: The impact of age of acquisition and bilingualism
Authors: HOPP HOLGER , SCHMID MONIKA S.
Published: December 2011

This study investigates constraints on ultimate attainment in second language (L2) pronunciation in a direct comparison of perceived foreign accent of 40 late L2 learners and 40 late first language (L1) attriters of German. Both groups were compared with 20 predominantly monolingual controls. Contrasting participants who acquired the target language from birth (monolinguals, L1 attriters) with late L2 learners, on the one hand, and bilinguals (L1 attriters, L2ers) with monolinguals, on the other hand, allowed us to disentangle the impacts of age of onset and bilingualism in speech production. At the group level, the attriters performed indistinguishably from controls, and both differed from the L2 group. However, 80% of all L2ers scored within the native (attriter) range. Correlational analyses with background factors further found some effects of use and language aptitude. These results show that acquiring a language from birth is not sufficient to guarantee nativelike pronunciation, and late acquisition does not necessarily prevent it. The results are discussed in the light of models on the role of age and cross-linguistic influence in L2 acquisition.
PDRs and XDRs
Authors: Meijerink Rowin
Published: December 2011

An overview of the important thermal and chemical processes in “photon-dominated regions” or “photo-dissociation regions” (PDRs) and “X-ray dominated regions” (XDRs) is presented. Applications of the models are shown to observations of the ultra-luminous infrared galaxy Mrk 231, and the starburst galaxy M 82.
Turbulence in the Diffuse Interstellar Medium
Authors: Falgarone Edith , Godard Benjamin , Hily-Blant Pierre
Published: December 2011

The diffuse interstellar medium (ISM) hosts the first steps of interstellar chemistry and the seeds of dense structures. Since its turbulent pressure by far exceeds its thermal pressure, turbulence must play a prominent role in its evolution. Fed at galactic scales, turbulent energy cascades down to the dissipation scales, but as in both laboratory and atmospheric turbulence, it does so in an intermittent way : only a tiny fraction of the small-scales is fed by the turbulent cascade, so that dissipation occurs in bursts. In diffuse molecular clouds, where they can be observed, the signatures of intermittency are: (1) the non-Gaussian statistics of velocity increments, and (2) the existence of coherent structures of intense velocity-shear that appear to channel the large-scale turbulent energy down to milliparsec scales. Attempts at modelling the warm chemistry triggered in the diffuse ISM by bursts of turbulent dissipation are promising : in this framework, the so far unexplained molecular richness observed in this medium is naturally understood, in particular its CH+, HCO+ and CO abundances. Turbulent dissipation is also likely at the origin of the H2 rotational line emission of the diffuse ISM and of a significant fraction of its [C II] emission.
Fullerenes in Circumstellar and Interstellar Environments
Authors: Cami Jan , Bernard-Salas Jeronimo , Peeters Els , Malek Sarah E.
Published: December 2011

We recently identified several emission bands in the Spitzer-IRS spectrum of the unusual planetary nebula Tc 1 with the infrared active vibrational modes of the neutral fullerene species C60 and C70. Since then, the fullerene bands have been detected in a variety of sources representing circumstellar and interstellar environments. Abundance estimates suggest that C60 represents ~0.1%–1.5% of the available carbon in those sources. The observed relative band intensities in various sources are not fully compatible with single-photon heating and fluorescent cooling, and are better reproduced by a thermal distribution at least in some sources. The observational data suggests that fullerenes form in the circumstellar environments of evolved stars, and survive in the interstellar medium. Precisely how they form is still a matter of debate.
The Chemistry of the Early Universe
Authors: Glover S. C. O.
Published: December 2011

The chemistry of the early Universe is a fascinating field of study. Even in the absence of any elements heavier than lithium, a surprising degree of chemical complexity proves to be possible, giving the topic considerable interest in its own right. In addition, the fact that molecular hydrogen plays a key role in the formation of the first stars and galaxies means that if we want to understand the formation of these objects, we must first develop a good understanding of the chemical evolution of the gas. In this review, I first give a brief introduction to the chemistry occurring in the gas prior to the formation of the first stars and galaxies, and then go on to discuss in more detail the main chemical processes occurring during the gravitational collapse of gas from intergalactic to protostellar densities, and how these processes influence the final outcome of the collapse.
Gas-Phase Reactions in the ISM: Rate Coefficients, Temperature Dependences, and Reaction Products
Authors: Smith Ian W. M.
Published: December 2011

Information about the rate coefficients and products of processes that occur in the interstellar medium are required as input to computer models that seek to reproduce the abundances of the rich variety of molecules that have been observed in different regions of the interstellar medium. In this brief review, I seek to identify the different kinds of gas-phase processes for which information is required and to consider the experimental, theoretical, and semi-empirical methods which are employed to measure or predict rate coefficients, k(T), and how they depend on temperature (T) – and also how the products of reactions can, in favourable cases, be observed.
Teilnahme am Straßenverkehr und Psychopathologie bei Jugendlichen und jungen Erwachsenen
Authors: Fegert Jörg M. , Kistler Fegert Liliane
Published: December 2011

Zusammenfasssung.Der Erwerb einer Fahrerlaubnis, die Teilnahme am Straßenverkehr als Mofafahrer, Motorradfahrer und insbesondere das Autofahren stellen in der Autonomieentwicklung vieler Jugendlicher und junger Erwachsener wichtige Schritte dar. Der Beitrag gibt eine Übersicht über Alters- und Entwicklungsgrenzen beim Erwerb von Fahrerlaubnissen, psychopathologische Einschränkungen der Fahrtauglichkeit und ihre Beurteilung. Dabei wird insbesondere auf jugendtypische, externalisierende Verhaltensstörungen, welche in der psychiatrischen Fahrtauglichkeitsliteratur eher wenig berücksichtigt werden, eingegangen. Abschließend wird eine Übersicht über die Folge von Medikamenteneinnahmen auf die Fahrtauglichkeit sowie die Gefahren kombinierter Medikamenten- oder Alkohol- bzw. Suchtmitteleinnahme hingewiesen. In der Behandlung und Psychoedukation von jugendlichen Patienten und jungen Erwachsenen stellt die Teilnahme am Straßenverkehr, der Erwerb des Führerscheins etc. ein wichtiges Thema dar, welches behandelnde Ärzte unbedingt proaktiv aufgreifen sollten.
Modeling Within-Person Variance in Reaction Time Data of Older Adults
Authors: Rast Philippe , Zimprich Daniel
Published: December 2011

In order to model within-person (WP) variance in a reaction time task, we applied a mixed location scale model using 335 participants from the second wave of the Zurich Longitudinal Study on Cognitive Aging. The age of the respondents and the performance in another reaction time task were used to explain individual differences in the WP variance. To account for larger variances due to slower reaction times, we also used the average of the predicted individual reaction time (RT) as a predictor for the WP variability. Here, the WP variability was a function of the mean. At the same time, older participants were more variable and those with better performance in another RT task were more consistent in their responses.
Longitudinal Evaluation of the Mental Health Continuum- Short Form (MHC-SF)
Authors: Lamers Sanne M. A. , Glas Cees A. W. , Westerhof Gerben J. , Bohlmeijer Ernst T.
Published: December 2011

This study evaluated the measurement invariance of the Mental Health Continuum-Short Form (MHC-SF), a 14-item self-report questionnaire for measuring emotional, social, and psychological well-being. The study draws on data of a representative panel (Longitudinal Internet Studies for the Social Sciences of CentERdata). 1,932 Dutch adults filled out the MHC-SF at four timepoints over 9 months. We used item response theory analyses with two-parameter models to examine differential item functioning across demographics, health indicators, and timepoints. The results indicated differences in the performance of one item (social well-being) for educational level, one item (social well-being) for sex, and two items (psychological well-being) for age. The MHC-SF is highly reliable over time, as there was no differential item functioning across the four timepoints. Furthermore, the means and reliabilities of the subscales were consistent over time. The MHC-SF is a reliable and valid instrument to measure positive aspects of mental health.
The Measurement of State Work Engagement
Authors: Breevaart Kimberley , Bakker Arnold B. , Demerouti Evangelia , Hetland Jörn
Published: December 2011

While diary studies have gained in popularity, the validity of the measures utilized in such studies remains an underresearched issue. This study examines the factor structure of the Utrecht Work Engagement Scale (UWES) on both between-person (trait) and within-person (state) levels. A multilevel confirmatory factor analysis was performed to confirm that the between-level factor structure also operates on the within-level. Data from 271 employees who filled in a state version of the UWES on five consecutive days were used to perform the analysis. Results showed that the UWES can be used to measure both trait and state work engagement. The three-factor multilevel model appeared to best fit the data. Implications for future research on engagement are discussed.
Global oceanic microseism sources as seen by seismic arrays and predicted by wave action models
Authors: Hillers G. , Graham N. , Campillo M. , Kedar S. , Landès M. , Shapiro N.
Published: December 2011

We analyze global microseism excitation patterns between July 2000 and June 2001. Seismological observations are compared with modeling results to isolate robust activity features of relevant source processes. First, we use observations of microseism source locations estimated by Landès et al. (2010) based on array processing of ambient noise correlations. Second, we construct synthetic activity patterns by coupling sea state estimates derived from wave action models to the excitation theory for microseisms. The overall spatiotemporal evolution of both estimates is characterized by a seasonal character that is associated with strong activity during winter months. The distribution of landmass causes seasonal changes on the Northern Hemisphere (NH) to exceed the variability on the Southern Hemisphere (SH). Our systematic comparison of the two estimates reveals significant microseism excitation along coastlines and in the open ocean. Since coastal reflections are not accounted for in the modeling approach, the consistent mismatch between near‐coastal observations and predictions suggests that relevant microseism energy arriving at the networks is generated in these areas. Simultaneously, systematic coincidence away from coastlines verifies the open ocean generation hypothesis. These conclusions are universal and robust with respect to the seismic network locations on the NH. The spatially homogeneous resolution of our synthetics provides a valuable resource for the assessment of the global microseism weather. Similar to previously identified hot spot areas in the North Atlantic, the modeled distributions hypothesize regions of strong localized activity on the SH, which are only partially confirmed by the analyzed data sets.
Electron acceleration in a geomagnetic Field Line Resonance
Authors: Damiano P. A. , Johnson J. R.
Published: December 2011

A hybrid MHD kinetic‐electron model in dipolar coordinates is used to simulate the upward current region of a geomagnetic Field Line Resonance (FLR) system for a realistic ambient electron temperature of a keV. It is found that mirror force effects result in potential drops sufficient to accelerate electrons to energies in excess of a keV in support of field aligned currents on the order of 0.5μA/m2. The wave energy dissipated in this acceleration would completely damp an undriven FLR with an equatorial width of 0.5 RE within two resonance cycles.
Biochemical role of the collagen-rich tumour microenvironment in pancreatic cancer progression
Authors: Shields Mario A. , Dangi-Garimella Surabhi , Redig Amanda J. , Munshi Hidayatullah G.
Published: December 2011

PDAC (pancreatic ductal adenocarcinoma) is among the most deadly of human malignances. A hallmark of the disease is a pronounced collagen-rich fibrotic extracellular matrix known as the desmoplastic reaction. Intriguingly, it is precisely these areas of fibrosis in which human PDAC tumours demonstrate increased expression of a key collagenase, MT1-MMP [membrane-type 1 MMP (matrix metalloproteinase); also known as MMP-14]. Furthermore, a cytokine known to mediate fibrosis in vivo, TGF-β1 (transforming growth factor-β1), is up-regulated in human PDAC tumours and can promote MT1-MMP expression. In the present review, we examine the regulation of PDAC progression through the interplay between type I collagen (the most common extracellular matrix present in human PDAC tumours), MT1-MMP and TGF-β1. Specifically, we examine the way in which signalling events through these pathways mediates invasion, regulates microRNAs and contributes to chemoresistance.
Outbreak of Hot-Foot Syndrome – Caused by Pseudomonas Aeruginosa
Authors: Michl R. , Rusche T. , Grimm S. , Limpert E. , Beck J. , Dost A.
Published: December 2011

Infections with Pseudomonas aeruginosa can cause the hot-foot syndrome, presenting with painful plantar erythematous nodules. Particularly, the mechanically stressed areas of the foot are affected after contact with contaminated water from saunas, swimming pools, hot tubs, etc. We report an outbreak of hot-foot syndrome caused by Pseudomonas in 10 patients. The therapeutic regimens applied reached from local antiseptic therapy to systemic antibiotics.
An Unusual Case of Ectopic ACTH Syndrome
Authors: Willhauck M. , Pöpperl G. , Rachinger W. , Giese A. , Auernhammer C. , Spitzweg C.
Published: December 2011

Ectopic ACTH-syndrome is a rare cause of Cushing’s disease. Despite extensive diagnostic procedures the source of ACTH secretion often remains occult.

This case describes a 45-year old woman with an ectopic Cushing’s syndrome. Extensive imaging procedures including CT scan of chest and abdomen, octreotide scan and MRI of the chest and pituitary did not reveal the source of ACTH secretion.

In consideration of an occult source of ACTH secretion we started a therapeutic trial with cabergoline (0.5 mg/d), a dopamine receptor agonist, which has been shown to be effective in ectopic Cushing’s syndrome. 2 months after cabergoline treatment had been initiated, ACTH and cortisol levels normalized in association with significant improvement of the clinical symptoms.

During follow-up a [68Ga-DOTA-dPhe1, Tyr3]-octreotate ([68Ga-DOTA]-TATE) PET-CT was performed revealing a somatostatin receptor positive lesion in the right sphenoidal sinus suggesting the source of ACTH secretion. The patient was cured by transnasal resection of the polypoid lesion, which was immunohistochemically characterized as an ACTH-positive neuroendocrine tumor.

This case report demonstrates the management of ectopic ACTH-syndrome by molecularly ­targeted therapy with dopamine receptor ­agonists as well as improved detection of the ectopic ACTH source by novel imaging modalities, such as [68Ga-DOTA]-TATE PET specifically targeting somatostatin receptor subtype-2 with high affinity.
Electron tunneling through atomically flat and ultrathin hexagonal boron nitride
Authors: Lee Gwan-Hyoung , Yu Young-Jun , Lee Changgu , Dean Cory , Shepard Kenneth L. , Kim Philip , Hone James
Published: December 2011

Electron tunneling through atomically flat and ultrathin hexagonal boron nitride (h-BN) on gold-coated mica was investigated using conductive atomic force microscopy. Low-bias direct tunneling was observed in mono-, bi-, and tri-layer h-BN. For all thicknesses, Fowler-Nordheim tunneling (FNT) occurred at high bias, showing an increase of breakdown voltage with thickness. Based on the FNT model, the barrier height for tunneling (3.07 eV) and dielectric strength (7.94 MV/cm) of h-BN are obtained; these values are comparable to those of SiO2.
On relaxation and transport in gyrokinetic drift wave turbulence with zonal flow
Authors: Kosuga Y. , Diamond P. H.
Published: December 2011

We present a theory for relaxation and transport in phase space for gyrokinetic drift wave turbulence with zonal flow. The interaction between phase space eddys and zonal flows is considered in two different limits, namely for K>>1 and K ≃ 1 where K is the Kubo number. For K>>1, the growth of an isolated coherent phase space structure is calculated, including the associated zonal flow dynamics. For K ≃ 1, mean field relaxation dynamics is considered in the presence of phase space granulations and zonal flows. In both limits, it is shown that the evolution equations for phase space structures are structurally similar to a corresponding Charney-Drazin theorem for zonal momentum balance in a potential vorticity conserving, quasi-geostrophic system. The transport flux in phase space is calculated in the presence of phase space density granulations and zonal flows. The zonal flow exerts a dynamical friction on ion phase space density evolution, which is a fundamentally new zonal flow effect.
Large eddy simulation study of scalar transport in fully developed wind-turbine array boundary layers
Authors: Calaf Marc , Parlange Marc B. , Meneveau Charles
Published: December 2011

Wind harvesting is fast becoming an important alternative source of energy. As wind farms become larger, they begin to attain scales at which two-way interactions with the atmospheric boundary layer (ABL) must be taken into account. Several studies have shown that there is a quantifiable effect of wind farms on the local meteorology, mainly through changes in the land-atmosphere fluxes of heat and moisture. In particular, the observed trends suggest that wind farms increase fluxes at the surface and this could be due to increased turbulence in the wakes. Conversely, simulations and laboratory experiments show that underneath wind farms, the friction velocity is decreased due to extraction of momentum by the wind turbines, a factor that could decrease scalar fluxes at the surface. In order to study this issue in more detail, a suite of large eddy simulations of an infinite (fully developed) wind turbine array boundary layer, including scalar transport from the ground surface without stratification, is performed. Results show an overall increase in the scalar fluxes of about 10%–15% when wind turbines are present in the ABL, and that the increase does not strongly depend upon wind farm loading as described by the turbines’ thrust coefficient and the wind turbines spacings. A single-column analysis including scalar transport shows that the presence of wind farms can be expected to increase slightly the scalar transport from the bottom surface and that this slight increase is due to a delicate balance between two strong opposing trends.
Nonlinear behavior of photoluminescence from silicon particles under two-photon excitation
Authors: Xu Xingsheng , Yokoyama Shiyoshi
Published: December 2011

Two-photon excited fluorescence (TPEF) under continuous-wave excitation from silicon particles produced by a pulsed laser is investigated. Spectra and images of TPEF from silicon particles are studied under different excitation intensities and operation modes (continuous wave or pulse). It is found that the photoluminescence depends superlinearly on the excitation intensity and that the spectral shape and peaks vary with different silicon particles. The above phenomena show the nonlinear behavior of TPEF from silicon particles, and stimulated emission is a possible process.
Mechanical stability of ordered droplet packings in microfluidic channels
Authors: Fleury Jean-Baptiste , Claussen Ohle , Herminghaus Stephan , Brinkmann Martin , Seemann Ralf
Published: December 2011

The mechanical response and stability of one and two-row packing of monodisperse emulsion droplets are studied in quasi 2d microchannels under longitudinal compression. Depending on the choice of parameter, a considered droplet arrangement is either transformed continuously into another packing under longitudinal compression or becomes mechanically unstable and segregates into domains of higher and lower packing fraction. Our experimental results are compared to analytical calculations for 2d-droplet arrangements with good quantitative agreement. This study also predicts important consequences for the stability of droplet arrangements in flowing systems.
Depth-profiling of elastic and optical inhomogeneities in transparent materials by picosecond ultrasonic interferometry: Theory
Authors: Gusev V. , Lomonosov A. M. , Ruello P. , Ayouch A. , Vaudel G.
Published: December 2011

The theoretical backgrounds for the depth-profiling of the optically transparent materials by picosecond ultrasonic interferometry are developed. The mathematical description of the light reflection from inhomogeneous transparent films or coatings is proposed. The inhomogeneity can be caused both by the film synthesis (intrinsic stationary inhomogeneity) and by the short acoustic transients launched in the film (time-dependent inhomogeneity). The theory indicates that the measurements of the complex optical reflectivity time evolution, caused by acoustic strain pulse propagation in such films, offer various possibilities to extract the depth profiles of intrinsic inhomogeneous distributions of mechanical/acoustical, optical, and acousto-optical parameters of the films. In particular it is proposed how the measurements of the transient complex optical reflectivity by the femtosecond optical interferometers, operating with light of different polarizations and probing the tested samples at different angles of light incidence, can be used. The spatial resolution of the method is limited by the acoustic spatial scale which, for picosecond acoustic pulses, is much shorter than optical wavelength.
Modelling charge transfer reactions with the frozen density embedding formalism
Authors: Pavanello Michele , Neugebauer Johannes
Published: December 2011

The frozen density embedding (FDE) subsystem formulation of density–functional theory is a useful tool for studying charge transfer reactions. In this work charge-localized, diabatic states are generated directly with FDE and used to calculate electronic couplings of hole transfer reactions in two π-stacked nucleobase dimers of B-DNA: 5′-GG-3′ and 5′-GT-3′. The calculations rely on two assumptions: the two–state model, and a small differential overlap between donor and acceptor subsystem densities. The resulting electronic couplings agree well with benchmark values for those exchange-correlation functionals that contain a high percentage of exact exchange. Instead, when semilocal GGA functionals are used the electronic couplings are grossly overestimated.
Growth propagation of yeast in linear arrays of microfluidic chambers over many generations
Authors: Wang Li , Liu Jiaji , Li Xin , Shi Jian , Hu Jie , Cui Ran , Zhang Zhi-Ling , Pang Dai-Wen , Chen Yong
Published: December 2011

The growth of microorganisms is often confined in restricting geometries. In this work, we designed a device to study the growth propagation of budding yeast along linear arrays of microfluidic chambers. Vacuum assisted cell loading was used to seed cells of limited numbers in the up-most chambers of each linear array. Once loaded, cells grow until confluent and then overgrow, pushing some of the newborns into the neighboring downstream chamber through connection channels. Such a scenario repeats sequentially along the whole linear chamber arrays. We observed that the propagation speed of yeast population along the linear arrays was strongly channel geometry dependent. When the connection channel is narrow and long, the amount of cells delivered into the downstream chamber is small so that cells grow over several generations in the same chamber before passing into the next chamber. Consequently, a population growth of more than 50 generations could be observed along a single linear array. We also provided a mathematical model to quantitatively interpret the observed growth dynamics.
Structure change of β-hairpin induced by turn optimization: An enhanced sampling molecular dynamics simulation study
Authors: Shao Qiang , Yang Lijiang , Gao Yi Qin
Published: December 2011

Our previous study showed that for the tested polypeptides which have similar β-hairpin structures but different sequences, their folding free energy pathways are dominantly determined by the turn conformational propensity. In this study, we study how the turn conformational propensity affects the structure of hairpins. The folding of two mutants of GB1p peptide (GB1m2 and GB1m3), which have the optimized turn sequence (6DDATK11T → 6NPATG11K) with native structures unsolved, were simulated using integrated tempering sampling molecular dynamics simulations and the predicted stable structures were compared to wild-type GB1p. It was observed that the turn optimization of GB1p generates a more favored 5-residue type I′ turn in addition to the 6-residue type I turn in wild-type GB1p. As a result two distinctly different hairpin structures are formed corresponding to the “misfolded” (M) and the “folded” (F) states. M state is a one-residue-shifted asymmetric β-hairpin structure whereas F state has the similar symmetric hairpin structure as wild-type GB1p. The formation of the favored type I′ turn has a small free energy barrier and leads to the shifted β-hairpin structure, following the modified “zipping” model. The presence of disfavored type I turn structure makes the folding of a β-hairpin consistent with the “hydrophobic-core-centric” model. On the other hand, the folding simulations on other two GB1p mutants (GB1r1 and GBr2), which have the position of the hydrophobic core cluster further away from the turn compared to wild-type GB1p, showed that moving the hydrophobic core cluster away from the turn region destabilizes but does not change the hairpin structure. Therefore, the present study showed that the turn conformational propensity is a key factor in affecting not only the folding pathways but also the stable structure of β-hairpins, and the turn conformational change induced by the turn optimization leads to significant changes of β-hairpin structure.
Dielectric and spin relaxation behaviour in DyFeO3 nanocrystals
Authors: Jaiswal Adhish , Das Raja , Maity Tuhin , Poddar Pankaj
Published: December 2011

We report the temperature and frequency dependent dielectric measurements and ac magnetic susceptibility of chemically synthesized DyFeO3 nanoparticles (size ∼50–60 nm). The measurement of the dielectric properties was carried out in a broad temperature (20–325 K) and frequency (1–106 Hz) range. The non-Debye type dipolar relaxation phenomenon was observed in the DyFeO3 nanoparticles, as confirmed by the Cole–Cole plots. The higher values of ɛ′ at the lower frequencies are explained on the basis of the Maxwell–Wagner model. The Cole–Cole analysis enabled us to separate the contribution of relaxation times, resistance and capacitance in grain and grain boundaries in DyFeO3 nanocrystals. We found that with increasing temperature, the contribution of grain boundary resistance increases in comparison to the grain resistance. We also performed spin relaxation studies in a broad temperature and frequency range. Both the in-phase (χ′) and out-of-phase (χ″) components of the ac magnetic susceptibilities of the DyFeO3 nanoparticles show a clear evidence at spin reorientation transition around 70 K and TN (Dy) around 4 K as reported by us in our earlier study using the dc magnetic behaviour.
Enhanced energy filtering and thermopower from synergetic scatterings of electrons at interface potential barriers (or wells) in semiconductor-based nanocomposites dispersed with metallic particles
Authors: Yang X. H. , Qin X. Y.
Published: December 2011

The electron scattering by the mesoscopic interface potentials in semiconductor-based thermoelectric nanocomposites dispersed with spherical metallic nanoparticles was theoretically investigated. The scattering probabilities were analytically calculated by using perturbation theory, and scattering parameter λ was determined through the energy dependence of relaxation time τ = τ0Eλ−1/2 (here, E is the energy). The results indicate that single scattering of electrons by either the interface potential barriers or wells formed due to the nanoparticles embedded in semiconductors cannot yield a magnitude of λ larger than 2.4. In contrast, a magnitude of λ as large as 3.4–4.9 can be achieved if synergetic scattering of electrons at ionized impurities and the potential barriers or wells occurs. In addition, on the whole, the scattering parameter for synergetic scattering is a weak function of temperature in the temperature range (100 K–850 K) investigated, and the magnitude of λ is influenced to a degree by adoption of different energy dispersion relations. Based on the obtained λ values, thermopower was calculated, which shows that thermopower of the nanocomposites was enhanced considerably for synergetic scattering as compared to single scattering, indicating that the synergetic scattering is an effective mechanism that strengthens energy filtering and enhances thermopower in nanocomposites.
Room-temperature, atmospheric plasma needle reduces adenovirus gene expression in HEK 293A host cells
Authors: Xiong Z. , Lu X. , Cao Y. , Ning Q. , Ostrikov K. , Lu Y. , Zhou X. , Liu J.
Published: December 2011

Room-temperature, atmospheric-pressure plasma needle treatment is used to effectively minimize the adenovirus (AdV) infectivity as quantified by the dramatic reduction of its gene expression in HEK 293A primary human embryonic kidney cells studied by green fluorescent protein imaging. The AdV titer is reduced by two orders of magnitude within only 8 min of the plasma exposure. This effect is due to longer lifetimes and higher interaction efficacy of the plasma-generated reactive species in confined space exposed to the plasma rather than thermal effects commonly utilized in pathogen inactivation. This generic approach is promising for the next-generation anti-viral treatments and imunotherapies.
Percolation, phase separation, and gelation in fluids and mixtures of spheres and rods
Authors: Jadrich Ryan , Schweizer Kenneth S.
Published: December 2011

The relationship between kinetic arrest, connectivity percolation, structure and phase separation in protein, nanoparticle, and colloidal suspensions is a rich and complex problem. Using a combination of integral equation theory, connectivity percolation methods, naïve mode coupling theory, and the activated dynamics nonlinear Langevin equation approach, we study this problem for isotropic one-component fluids of spheres and variable aspect ratio rigid rods, and also percolation in rod-sphere mixtures. The key control parameters are interparticle attraction strength and its (short) spatial range, total packing fraction, and mixture composition. For spherical particles, formation of a homogeneous one-phase kinetically stable and percolated physical gel is predicted to be possible, but depends on non-universal factors. On the other hand, the dynamic crossover to activated dynamics and physical bond formation, which signals discrete cluster formation below the percolation threshold, almost always occurs in the one phase region. Rods more easily gel in the homogeneous isotropic regime, but whether a percolation or kinetic arrest boundary is reached first upon increasing interparticle attraction depends sensitively on packing fraction, rod aspect ratio and attraction range. Overall, the connectivity percolation threshold is much more sensitive to attraction range than either the kinetic arrest or phase separation boundaries. Our results appear to be qualitatively consistent with recent experiments on polymer-colloid depletion systems and brush mediated attractive nanoparticle suspensions.
Degenerate p-doping of InP nanowires for large area tunnel diodes
Authors: Wallentin Jesper , Wickert Peter , Ek Martin , Gustafsson Anders , Reine Wallenberg L. , Magnusson Martin H. , Samuelson Lars , Deppert Knut , Borgström Magnus T.
Published: December 2011

We have investigated p-doping of InP nanowires using diethyl zinc. Two-terminal devices showed non-linear source-drain characteristics and p-type gate dependence. Electron beam induced current measurements were employed to determine minority carrier diffusion lengths. We used large-area tunnel diodes to demonstrate degenerate doping, showing peak current densities of up to 0.11 A/cm2 and room temperature peak to valley current ratios of 5.3. These results demonstrate that high p- and n-doping, paired with sharp doping profiles, can be achieved in InP nanowires.
On the validity of a universal solution for viscous capillary jets
Authors: Montanero J. M. , Herrada M. A. , Ferrera C. , Vega E. J. , Gañán-Calvo A. M.
Published: December 2011

In this paper, we assess the validity of a universal solution based on the slenderness approximation to describe the velocity and shape of viscous capillary jets produced by two very different mechanisms: the action of the constant gravity force and the focusing effect of a coflowing gas stream. In the gravitational case, the jet’s velocity distribution given by the universal solution is compared with that calculated numerically from the Navier-Stokes equations. The universal solution provides remarkably good predictions for the wide range of parameters considered in this work. Its accuracy generally improves as the Reynolds number increases and/or the Froude number decreases, probably because the jet viscous region decreases in this case. The flow focusing method was examined experimentally by acquiring and processing images of the tapering liquid meniscus formed between the feeding capillary and the discharge orifice. In this case, the universal solution provides satisfactory results for sufficiently slender liquid meniscus (i.e., for sufficiently large liquid viscosities and flow rates and small applied pressure drops), provided that the ratio capillary-to-orifice distance H to orifice diameter D takes sufficiently small values. If these conditions are not satisfied, the universal solution underestimates the jet radius close to the feeding capillary, but it still provides accurate predictions beyond the discharge orifice. For small H/D values, the accuracy of the universal solution is mainly limited by radial momentum effects associated with the sharp contraction of the meniscus shape, which becomes less slender as the liquid viscosity and flow rate decrease, or the pressure drop increases. For large H/D values, the driving force significantly deviates from its assumed constant value in the universal solution, giving rise to larger discrepancies between that solution and the experimental results even for slender shapes.
Size dependent biexciton binding energies in GaN quantum dots
Authors: Amloy S. , Yu K. H. , Karlsson K. F. , Farivar R. , Andersson T. G. , Holtz P. O.
Published: December 2011

Single GaN/Al(Ga)N quantum dots (QDs) have been investigated by means of microphotoluminescence. Emission spectra related to excitons and biexcitons have been identified by excitation power dependence and polarization resolved spectroscopy. All investigated dots exhibit a strong degree of linear polarization (∼90%). The biexciton binding energy scales with the dot size. However, both positive and negative binding energies are found for the studied QDs. These results imply that careful size control of III-Nitride QDs would enable the emission of correlated photons with identical frequencies from the cascade recombination of the biexciton, with potential applications in the area of quantum information processing.
Transition network based on equilibrium sampling: A new method for extracting kinetic information from Monte Carlo simulations of protein folding
Authors: Klenin Konstantin V. , Wenzel Wolfgang
Published: December 2011

We propose a new type of transition network for modeling of protein dynamics. The nodes of the network correspond to the conformations taken from random sampling of equilibrium ensemble available, e.g., by Monte Carlo simulations. Although this approach does not provide absolute values of folding/unfolding rates, it allows identification of reaction pathways, transition state ensemble, and, eventually, intermediates. The new method is verified by a comparison with direct molecular dynamic simulations performed for a coarse-grained Gō-like model of proteins. As an illustrative example, we analyze kinetics of formation of a small β-hairpin (Trp zipper 1) in the all-atom representation.
Diamond based light-emitting diode for visible single-photon emission at room temperature
Authors: Lohrmann A. , Pezzagna S. , Dobrinets I. , Spinicelli P. , Jacques V. , Roch J.-F. , Meijer J. , Zaitsev A. M.
Published: December 2011

Diamond-based p-i-n light-emitting diodes capable of single-photon emission in the visible spectral region at room temperature are discussed. The diodes were fabricated on a high quality single crystal diamond grown by chemical vapor deposition. Implantation of boron and phosphorus ions followed by annealing at a temperature of 1600 °C has been used for doping p-type and n-type areas, respectively. Electrical characterization of the devices demonstrates clear diode behavior. Spectra of electroluminescence generated in the i-area reveal sole emission from the neutral nitrogen-vacancy (NV) defects. Photon antibunching implies single-photon character of this emission when generated by individual NV defects.
Polarization insensitive and omnidirectional broadband near perfect planar metamaterial absorber in the near infrared regime
Authors: Chen Shuqi , Cheng Hua , Yang Haifang , Li Junjie , Duan Xiaoyang , Gu Changzhi , Tian Jianguo
Published: December 2011

We present the design, characterization, and experimental demonstration of a polarization insensitive and omnidirectional broadband near perfect planar metamaterial absorber (MA) in the near infrared regime, which does not need to stack multilayer composite structures. Experimental result shows that greater than 80% absorption is obtained across a wavelength range of 0.41 μm, which is in reasonable agreement with the simulation. The electromagnetic response of the MA is theoretically investigated. The broadband planar MA is polarization insensitive and the absorption remains high even at large incident angles.
Lorentzian covering space and homotopy classes
Authors: Kim Do-Hyung
Published: December 2011

We analyze structures of covering space over a Lorentzian manifold. By use of this we show that, if a Lorentzian manifold is globally hyperbolic then for any two causally related points p and q, the number of homotopy classes of causal curves from p to q is finite and each of its homotopy classes has a causal geodesic from p to q.
Correlation between the ferromagnetic metal percolation and the sign evolution of angular dependent magnetoresistance in Pr0.7Ca0.3MnO3 film
Authors: Zhang Y. Q. , Meng H. , Wang X. W. , Liu J. J. , Du J. , Zhang Z. D.
Published: December 2011

Angular dependent magnetoresistance (AMR) phenomena in Pr0.7Ca0.3MnO3 film have been investigated. A transition between cos2θ dependent AMR in an insulating state at low fields and sin2θ dependent AMR in a metal state at high fields is observed at intermediate fields, depending on the temperature and/or strength of an applied magnetic field. Although the AMR sign evolution process from cos2θ dependence to sin2θ dependence at low temperature is different from that at high temperature due to existence of ferromagnetic insulator besides charge ordering antiferromagnetic insulator, we believe that such AMR sign evolutions are closely related with magnetic-field-induced ferromagnetic metal percolation behavior.
Enhanced rectifying response from metal-insulator-insulator-metal junctions
Authors: Maraghechi P. , Foroughi-Abari A. , Cadien K. , Elezzabi A. Y.
Published: December 2011

We present on a metal-insulator-insulator-metal quantum electronic tunneling devices suitable for high speed rectifiers. Through the introduction of double oxide layer between similar metallic electrodes, a cascaded potential barrier is formed which alters the electron tunneling mechanism at forward versus the reverse bias. The cascaded potential barrier engineering manifests itself in both a highly nonlinear and asymmetric I-V junction characteristic. It is envisioned that high speed rectifiers and mixers having extraordinary nonlinearity can be realized through the incorporation of the cascaded potential barrier architecture and dissimilar metallic electrodes.
Solid-state sensor incorporated in microfluidic chip and magnetic-bead enzyme immobilization approach for creatinine and glucose detection in serum
Authors: Lin Yen-Heng , Chiang Chien-Hung , Wu Min-Hsien , Pan Tung-Ming , Luo Ji-Dung , Chiou Chiuan-Chian
Published: December 2011

Solid-state sensors are stable and inexpensive electric transducers for biomedical measurement. This study proposes a microfluidic chip incorporated with a solid-state sensor for measuring glucose and creatinine in blood serum. Magnetic beads are employed to immobilize enzymes and deliver them in a micro-channel. Glucose and creatinine can be measured at 2–8 mM and 10−2 to 10 mM, respectively, which is a meaningful range in human blood. The immobilization approach also addresses the issue of the long-term preservation of enzymes in microfluidic devices. The proposed device is suitable for multi-target measurement in a point-of-care system.
High resolution patterning of nanoparticles by evaporative self-assembly enabled by in situ creation and mechanical lift-off of a polymer template
Authors: Demko Michael T. , Choi Sun , Zohdi Tarek I. , Pisano Albert P.
Published: December 2011

High-resolution patterning of nanostructured materials into open templates is limited by the processes of creation and removal of the necessary template. In this work, a process for forming a micropatterned template from cellulose acetate polymer in situ on the substrate is demonstrated. Nanoparticles are patterned by evaporative self-assembly, and the template is removed by mechanical means. The process is demonstrated by patterning zinc oxide nanoparticles on silicon and cyclic olefin copolymer substrates and by creating a highly sensitive ultraviolet light detector.
Near zero temperature coefficient of resistivity in antiperovskite Mn3Ni1−xCuxN
Authors: Ding Lei , Wang Cong , Chu Lihua , Yan Jun , Na Yuanyuan , Huang Qingzhen , Chen Xiaolong
Published: December 2011

The near zero temperature coefficient of resistivity (NZ-TCR) in Mn-based antiperovskite Mn3Ni1−xCuxN is reported. The temperature range of NZ-TCR is controllable by changing Cu content. Further, the TCR value of 0.09 ppm K−1 was obtained in Mn3Ni0.5Cu0.5N over a broad temperature range around room temperature. The anomalous resistivity change of Mn3Ni1−xCuxN from metal-like to NZ-TCR behavioris apparently due to a magnetic transition. The possible reason for the formation of NZ-TCR is interpreted on the basis of spin-disorder scattering.