bluuebunny/crossref_metadata_2025 huggingface dataset:
Edge detection applied to Cassini images reveals no measurable displacement of Ontario Lacus' margin between 2005 and 2010
Authors: Cornet Thomas , Bourgeois Olivier , Le Mouélic Stéphane , Rodriguez Sébastien , Sotin Christophe , Barnes Jason W. , Brown Robert H. , Baines Kevin H. , Buratti Bonnie J. , Clark Roger N. , Nicholson Phillip D.
Published: June 2012

Ontario Lacus is thus far the largest flat‐floored topographic depression of Titan's southern hemisphere interpreted as a permanent or ephemeral lake. From 2005 to 2010, it was imaged several times and at various wavelengths by ISS, VIMS and RADAR instruments onboard Cassini's spacecraft. We analyze the position and uncertainty of Ontario Lacus' margin in all these images using an edge detection method based on image derivation. We find that, given the range of uncertainties in contour locations derived from images, no measurable displacement of Ontario Lacus' margin can be detected between 2005 and 2010 at the actual image spatial resolutions. The discrepancy between this result and previous ones is attributable to differences in (1) the basics behind the methods used, (2) the actual spatial resolutions and contrasts of the available images due to differential atmospheric scattering effects at different wavelengths, and (3) the geomorphological interpretation of contours derived from images acquired at different wavelengths. This lack of measurable displacement in the images suggests that the imaged contour corresponds either (1) to the border of a surface liquid body, provided that potential changes in its extent over five terrestrial years were not sufficiently large to be measured, or (2) to the stationary topographic border between Ontario Lacus' depression and the surrounding alluvial plain. Potential displacements of Ontario Lacus' margin between 2005 and 2010 are thus below the actual resolution of currently available images or have to be sought for within the extent of the topographic depression rather than along its borders.
Assessing the influence of upstream drainage lakes on fluvial organic carbon in a wetland‐rich region
Authors: Lottig Noah R. , Stanley Emily H. , Maxted Jeffrey T.
Published: June 2012

The role of aquatic ecosystems in regional and global carbon cycles is becoming increasingly apparent, and lakes and reservoirs may be particularly important to the retention and processing of organic carbon. If this is the case, then lakes and reservoirs may act as control points that decrease OC concentrations and fluxes in downstream aquatic ecosystems. We tested this hypothesis at a regional scale by comparing dissolved organic carbon (DOC) concentrations and fluxes in 52 randomly selected streams and rivers with and without upstream lakes in the water‐rich Northern Highlands Lake District (NHLD), Wisconsin, USA. DOC concentrations were significantly higher (p < 0.01) in drainage networks that did not contain lakes (25.02 mg/L) than they were in networks with upstream lakes (10.38 mg/L). However, when accounting for differences in wetland extent between watersheds, we were unable to detect a lake effect on downstream DOC concentrations (p > 0.49). Likewise, there were no significant differences in DOC:DON or DOC:DOP ratios, or in yields from watersheds with and without upstream lakes after compensating for wetland influences. We suggest that lake OC storage or processing may be limited by high hydrologic flushing in lakes with stream outlets and overwhelmed by larger scale influences of landscape composition in the NHLD. Consequently, drainage lakes in carbon‐rich regions like the NHLD may have limited influence on terrigenous carbon exports to the ocean.
Capillary trapping of buoyant particles within regions of emergent vegetation
Authors: Peruzzo Paolo , Defina Andrea , Nepf Heidi
Published: June 2012

The seeds of many aquatic plants are buoyant and thus transported at the water surface, where they are subject to surface tension that may enhance their retention within emergent vegetation. Specifically, seeds may be trapped by surface tension (i.e., by the Cheerios effect) at the surface‐piercing interface of the vegetation. In this work we develop a physical model that predicts this mechanism of seed trapping, advancing the model proposed by Defina and Peruzzo (2010) that describes the propagation of floating particles through emergent vegetation. The emergent vegetation is simulated as an array of cylinders, randomly arranged, with the mean gap between cylinders far greater than the particle size, which prevents the trapping of particles between pairs of cylinders, referred to as net trapping. Laboratory experiments are used to guide and validate the model. The model also has good agreement with experimental data available in the literature for real seeds and more complex plant morphology.
Ultimate Answers to Proximate Questions: The Evolutionary Motivations behind Tattoos and Body Piercings in Popular Culture
Authors: Carmen Rachael A. , Guitar Amanda E. , Dillon Haley M.
Published: June 2012

Numerous studies have found that piercing and tattooing the body is an increasingly prevalent trend in modern popular culture; however, this is not only a modern practice. Evidence of various forms of body ornamentation has been found in human societies dating back thousands of years. Although prior research has focused on the potential relationships between various personality traits and the likelihood of piercing or tattooing the body, few have approached this topic from an evolutionary perspective. For instance, the general motivations for getting tattoos and piercings have tended to fall into the same three categories for hundreds of years: (a) a symbol of an important past event, love, or friendship, (b) group membership, and/or (c) a marker of individuality. We argue that these motivations are simply proximate behaviors for an ultimate evolutionary reason: the perpetuation of one's genes. In this article, we propose two new theories about the origins of body ornamentation. First, in our “human canvas” hypothesis, we propose a link between body ornamentation and the human species' historical use of symbolic thought. Second, in our “upping the ante” hypothesis, we suggest that the steady rise in popularity of tattooing and piercing in Western culture has come about due to larger population densities and advancements in healthcare, which has led individuals to seek new and unique displays of fitness (i.e., body ornamentation). We then conclude with proximate examples in popular culture to display the proposed ultimate evolutionary reasoning behind body ornamentation.
Sex Differences in the Creation of Fictional Heroes with Particular Emphasis on Female Heroes and Superheroes in Popular Culture: Insights from Evolutionary Psychology
Authors: Ingalls Victoria
Published: June 2012

Cultural and psychological perspectives have been used to examine the characteristics of modern fictional heroes, but rarely if ever has an evolutionary approach been applied to this topic, an approach that could be quite enlightening. Evolutionary psychology suggests that sexual selection will have shaped differences in the underlying behavioral tendencies of males and females. Specifically, the higher parental investment of females makes establishing dominance more valuable to males and the helping of family members more valuable for females. If this is true, evolved differences manifesting themselves in the subconscious could influence the characteristics of the fictional heroes created by each sex. Here, I use a preliminary examination of female superheroes from the popular media to help frame an exploration of these predicted sex differences, which is followed by a more systematic approach examining heroes found in recent children's fantasy novels. If there are evolved differences, the female heroes created by men are expected to be more physically powerful and exhibit more displays of physical power than those created by women. In addition, the primary goal of the two types should also differ, with female-generated heroes displaying more concern for family members. Analyzing these characters using evolutionary psychology is compared to previous approaches. If the evolutionary approach proves to be valid, this new method of hero comparisons should be of interest to those studying gender issues and role models for girls.
Monsters Evolve: A Biocultural Approach to Horror Stories
Authors: Clasen Mathias
Published: June 2012

Horror fiction is a thriving industry. Many consumers pay hard-earned money to be scared witless by films, books, and computer games. The well-told horror story can affect even the most obstinate skeptic. How and why does horror fiction work? Why are people so fascinated with monsters? Why do horror stories generally travel well across cultural borders, if all they do is encode salient culturally contingent anxieties, as some horror scholars have claimed? I argue that an evolutionary perspective is useful in explaining the appeal of horror, but also that this perspective cannot stand alone. An exhaustive, vertically integrated theory of horror fiction incorporates the cultural dimension. I make the case for a biocultural approach, one that recognizes evolutionary underpinnings and cultural variation.
Panorama of DNA hairpin folding observedviadiffusion-decelerated fluorescence correlation spectroscopy
Authors: Yin Yandong , Wang Peng , Yang Xin Xing , Li Xun , He Chuan , Zhao Xin Sheng
Published: June 2012

A wide kinetic range from ∼0.1 μs to 1 s is offered by diffusion-decelerated FCS, allowing simultaneously monitoring multi-kinetic components.
The C-terminal rod 2 fragment of filamin A forms a compact structure that can be extended
Authors: Ruskamo Salla , Gilbert Robert , Hofmann Gregor , Jiang Pengju , Campbell Iain D. , Ylänne Jari , Pentikäinen Ulla
Published: June 2012

Filamins are large proteins that cross-link actin filaments and connect to other cellular components. The C-terminal rod 2 region of FLNa (filamin A) mediates dimerization and interacts with several transmembrane receptors and intracellular signalling adaptors. SAXS (small-angle X-ray scattering) experiments were used to make a model of a six immunoglobulin-like domain fragment of the FLNa rod 2 (domains 16–21). This fragment had a surprising three-branched structural arrangement, where each branch was made of a tightly packed two-domain pair. Peptides derived from transmembrane receptors and intracellular signalling proteins induced a more open structure of the six domain fragment. Mutagenesis studies suggested that these changes are caused by peptides binding to the CD faces on domains 19 and 21 which displace the preceding domain A-strands (18 and 20 respectively), thus opening the individual domain pairs. A single particle cryo-EM map of a nine domain rod 2 fragment (domains 16–24), showed a relatively compact dimeric particle and confirmed the three-branched arrangement as well as the peptide-induced conformation changes. These findings reveal features of filamin structure that are important for its interactions and mechanical properties.
Differential effects of cyclic uniaxial stretch on human mesenchymal stem cell into skeletal muscle cell
Authors: Haghighipour Nooshin , Heidarian Saeide , Shokrgozar Mohammad Ali , Amirizadeh Naser
Published: June 2012

Both fetal and adult skeletal muscle cells are continually being subjected to biomechanical forces. Biomechanical stimulation during cell growth affects proliferation, differentiation and maturation of skeletal muscle cells. Bone marrow‐derived hMSCs [human MSCs (mesenchymal stem cells)] can differentiate into a variety of cell types, including skeletal muscle cells that are potentially a source for muscle regeneration. Our investigations involved a 10% cyclic uniaxial strain at 1 Hz being applied to hMSCs grown on collagen‐coated silicon membranes with or without IGF‐I (insulin‐like growth factor‐I) for 24 h. Results obtained from morphological studies confirmed the rearrangement of cells after loading. Comparison of MyoD and MyoG mRNA levels between test groups showed that mechanical loading alone can initiate myogenic differentiation. Furthermore, comparison of Myf5, MyoD, MyoG and Myf6 mRNA levels between test groups showed that a combination of mechanical loading and growth factor results in the highest expression of myogenic genes. These results indicate that cyclic strain may be useful in myogenic differentiation of stem cells, and can accelerate the differentiation of hMSCs into MSCs in the presence of growth factor.
Near-interface Si substrate 3d metal contamination during atomic layer deposition processing detected by electron spin resonance
Authors: Nguyen A. P. D. , Stesmans A. , Hiller D. , Zacharias M.
Published: June 2012

A K- and Q-band electron spin resonance (ESR) study has been carried out on (100)Si/SiO2 entities manufactured by low temperature (150 °C) atomic layer deposition (ALD) of a high-quality SiO2 layer on Si using 3-aminopropyltriethoxysilane, H2O, and ozone in a three-step process. Whereas previous work has demonstrated the high quality of the deposited SiO2 layer, the current ESR analysis reports on the tracing of growth-related contamination of near interface Si substrate layers by two transition metals. This includes, first, detection of the signal of interstitial Cr+ (S = 5/2) impurities in c-Si, characterized by an isotropic central g value of 1.9980 ± 0.0002, an isotropic 53Cr (I = 3/2) hyperfine interaction of splitting Aiso = 11.8 G, and cubic crystal field splitting parameter a = +32.2 G, well in agreement with the known bulk c-Si case; A small anisotropic contribution to the hyperfine interaction has additionally been revealed. The total Cr+ defect density is inferred as ∼5 × 1011 cm−2. Second, a single signal is observed at isotropic g = 2.070 ± 0.001, corresponding to interstitial Fe impurities (Fei)0 (S = 1) positioned in a c-Si matrix. Defect density depth profiling reveals the impurities to be confined to a few μm thick Si substrate top layer, the density decaying exponential-like from the Si/SiO2 interface inward the Si substrate. The total of the results points to a contamination of reactor-environment origin, connected with the layer deposition process. It concerns a weak contamination, in which detection the ESR technique emerges as a powerful technique able to unveil very low levels of contamination of near-surface Si substrate layers.
Invited Review Article: Combining scanning probe microscopy with optical spectroscopy for applications in biology and materials science
Authors: Lucas Marcel , Riedo Elisa
Published: June 2012

This is a comprehensive review of the combination of scanning probe microscopy (SPM) with various optical spectroscopies, with a particular focus on Raman spectroscopy. Efforts to combine SPM with optical spectroscopy will be described, and the technical difficulties encountered will be examined. These efforts have so far focused mainly on the development of tip-enhanced Raman spectroscopy, a powerful technique to detect and image chemical signatures with single molecule sensitivity, which will be reviewed. Beyond tip-enhanced Raman spectroscopy and/or topography measurements, combinations of SPM with optical spectroscopy have a great potential in the characterization of structure and quantitative measurements of physical properties, such as mechanical, optical, or electrical properties, in delicate biological samples and nanomaterials. The different approaches to improve the spatial resolution, the chemical sensitivity, and the accuracy of physical properties measurements will be discussed. Applications of such combinations for the characterization of structure, defects, and physical properties in biology and materials science will be reviewed. Due to the versatility of SPM probes for the manipulation and characterization of small and/or delicate samples, this review will mainly focus on the apertureless techniques based on SPM probes.
Replica theory of the rigidity of structural glasses
Authors: Yoshino Hajime
Published: June 2012

We present a first principle scheme to compute the rigidity, i.e., the shear-modulus of structural glasses at finite temperatures using the cloned liquid theory, which combines the replica theory and the liquid theory. With the aid of the replica method which enables disentanglement of thermal fluctuations in liquids into intra-state and inter-state fluctuations, we extract the rigidity of metastable amorphous solid states in the supercooled liquid and glass phases. The result can be understood intuitively without replicas. As a test case, we apply the scheme to the supercooled and glassy state of a binary mixture of soft-spheres. The result compares well with the shear-modulus obtained by a previous molecular dynamic simulation. The rigidity of metastable states is significantly reduced with respect to the instantaneous rigidity, namely, the Born term, due to non-affine responses caused by displacements of particles inside cages at all temperatures down to T = 0. It becomes nearly independent of temperature below the Kauzmann temperature TK. At higher temperatures in the supercooled liquid state, the non-affine correction to the rigidity becomes stronger suggesting melting of the metastable solid state. Inter-state part of the static response implies jerky, intermittent stress-strain curves with static analogue of yielding at mesoscopic scales.
Strain mapping for the silicon-on-insulator generation of semiconductor devices by high-angle annular dark field scanning electron transmission microscopy
Authors: Cooper David , Le Royer Cyrille , Béché Armand , Rouvière Jean-Luc
Published: June 2012

The strain in pMOS p-type metal-oxide-semiconductor devices grown on silicon-on-insulator substrates has been measured by using the geometrical phase analysis of high angle annular dark field scanning electron microscopy. We show that by using the latest generations of electron microscopes, the strain can now be quantitatively measured with a large field of view, a spatial resolution as low as 1 nm with a sensitivity as good as 0.15%. This technique is extremely flexible, provides both structural and strain information, and can be applied to all types of nanoscale materials both quickly and easily.
Structural properties of thermoresponsive poly(N-isopropylacrylamide)-poly(ethyleneglycol) microgels
Authors: Clara-Rahola J. , Fernandez-Nieves A. , Sierra-Martin B. , South A. B. , Lyon L. A. , Kohlbrecher J. , Fernandez Barbero A.
Published: June 2012

We present investigations of the structural properties of thermoresponsive poly(N-isopropylacrylamide) (PNiPAM) microgels dispersed in an aqueous solvent. In this particular work poly(ethyleneglycol) (PEG) units flanked with acrylate groups are employed as cross-linkers, providing an architecture designed to resist protein fouling. Dynamic light scattering (DLS), static light scattering (SLS), and small angle neutron scattering (SANS) are employed to study the microgels as a function of temperature over the range 10 °C ≤ T ≤ 40 °C. DLS and SLS measurements are simultaneously performed and, respectively, allow determination of the particle hydrodynamic radius, Rh, and radius of gyration, Rg, at each temperature. The thermal variation of these magnitudes reveals the microgel deswelling at the PNiPAM lower critical solution temperature (LCST). However, the hydrodynamic radius displays a second transition to larger radii at temperatures T ≤ 20 °C. This feature is atypical in standard PNiPAM microgels and suggests a structural reconfiguration within the polymer network at those temperatures. To better understand this behavior we perform neutron scattering measurements at different temperatures. In striking contrast to the scattering profile of soft sphere microgels, the SANS profiles for T ≤ LCST of our PNiPAM-PEG suspensions indicate that the particles exhibit structural properties characteristic of star polymer configurations. The star polymer radius of gyration and correlation length gradually decrease with increasing temperature despite maintenance of the star polymer configuration. At temperatures above the LCST, the scattered SANS intensity is typical of soft sphere systems.
Extraordinary optical transmission and extinction in a Terahertz wire-grid polarizer
Authors: Cetnar John S. , Middendorf John R. , Brown Elliott R.
Published: June 2012

A THz wire grid polarizer is simulated and demonstrated consisting of 40-μm periodic aluminum strips mounted on a polycarbonate substrate with a variable metal-to-gap ratio. Full-wave numerical simulations were performed from 100 GHz to 550 GHz predicting that the transmission in perpendicular (parallel) polarization is much higher (lower) than that predicted by geometric optics, leading to a very high extinction ratio of ∼60 dB between 100 and 550 GHz when the gaps become very small (<5 μm). This behavior is confirmed qualitatively in experiments between 100 and 530 GHz where extinction ratios exceeding 40 dB are achieved. These results are explained physically as an electromagnetic concentration effect in the gaps consistent with plasmonic-like behavior. The effect depends critically on gap width and weakly on frequency.
Chain-length and mode-delocalization dependent amide-I anharmonicity in peptide oligomers
Authors: Zhao Juan , Wang Jianping
Published: June 2012

The diagonal anharmonicities of the amide-I mode in the alanine oligomers are examined in the normal-mode basis by ab initio calculations. The selected oligomers range from dimer to heptamer, in either the α-helical or β-sheet conformations. It is found that the anharmonicity varies from mode to mode within the same oligomer. For a given amide-I mode, the anharmonicity is closely related to the delocalization extent of the mode: the less it delocalizes, the larger the anharmonicity it has. Thus, the single-mode potential energy distribution (PEDmax) can be used as an indicator of the magnitude of the anharmonicity. It is found that as the peptide chain length increases, the averaged diagonal anharmonicity generally decreases; however, the sum of the averaged diagonal and off-diagonal anharmonicities within a peptide roughly remains a constant for all the oligomers examined, indicating the excitonic characteristics of the amide-I modes. Excitonic coupling tends to decrease the diagonal anharmonicities in a coupled system with multiple chromophores, which explains the observed behavior of the anharmonicities. The excitonic nature of the amide-I band in peptide oligomers is thus verified by the anharmonic computations. Isotopic substitution effect on the anharmonicities and mode localizations of the amide-I modes in peptides is also discussed.
Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum
Authors: Ozer Gungor , Quirk Stephen , Hernandez Rigoberto
Published: June 2012

The potential of mean force (PMF) for stretching decaalanine in vacuum was determined earlier by Park and Schulten [J. Chem. Phys. 120, 5946 (2004)] in a landmark article demonstrating the efficacy of combining steered molecular dynamics and Jarzynski's nonequilibrium relation. In this study, the recently developed adaptive steered molecular dynamics (ASMD) algorithm [G. Ozer, E. Valeev, S. Quirk, and R. Hernandez, J. Chem. Theory Comput. 6, 3026 (2010)] is used to reproduce the PMF of the unraveling of decaalanine in vacuum by averaging over fewer nonequilibrium trajectories. The efficiency and accuracy of the method are demonstrated through the agreement with the earlier work by Park and Schulten, a series of convergence checks compared to alternate SMD pulling strategies, and an analytical proof. The nonequilibrium trajectories obtained through ASMD have also been used to analyze the intrapeptide hydrogen bonds along the stretching coordinate. As the decaalanine helix is stretched, the initially stabilized i → i + 4 contacts (α-helix) is replaced by i → i + 3 contacts (310-helix). No significant formation of i → i + 5 hydrogen bonds (π-helix) is observed.
Mode-splitting-based optical label-free biosensing with a biorecognition-covered microcavity
Authors: Yi Xu , Xiao Yun-Feng , Feng Yin , Qiu Dong-Ying , Fan Jing-Yi , Li Yan , Gong Qihuang
Published: June 2012

A pair of counter-propagating high-Q whispering-gallery modes (WGMs) can couple to each other and produce two new modes with a significant resonance splitting when single or multi-Rayleigh scatterers are adsorbed on the microcavity surface. In this paper, we investigate the mode-splitting-based biosensing by using a biorecognition-covered WGM microcavity because the pre-covering is essentially necessary for label-free detection of specific biological targets. It is shown that the quantitative detection, e.g., nanoparticle sizing, is strongly affected by the biorecognition, and the minimum target size suitable for detection is subjected to the surface pre-covering ratio. To eliminate this degradation induced by biorecognition, we further propose to use the total linewidth broadening of the two new modes as the detection signal, which is immune to thermal fluctuation.
Superradiance from one-dimensionally aligned ZnO nanorod multiple-quantum-well structures
Authors: Yatsui T. , Ishikawa A. , Kobayashi K. , Shojiguchi A. , Sangu S. , Kawazoe T. , Ohtsu M. , Yoo J. , Yi G.-C.
Published: June 2012

Using one-dimensionally aligned ZnO nanorod multiple-quantum-well structures (MQWs), we observed a superradiance, i.e., a cooperative spontaneous emission. We confirmed that the excitation power dependence of the emissions from the MQWs originated from the coherent coupling of the QWs due to the well organization at nanoscale. We identified two QWs with cooperative emission. Additionally, we evaluated the number of coherently coupled QWs sets of four that resulted in the superradiance. Our findings provide criteria for designing nanoscale synergetic devices without the use of an external cavity.
Absolute energy calibration for relativistic electron beams with pointing instability from a laser-plasma accelerator
Authors: Cha H. J. , Choi I. W. , Kim H. T. , Kim I J. , Nam K. H. , Jeong T. M. , Lee J.
Published: June 2012

The pointing instability of energetic electron beams generated from a laser-driven accelerator can cause a serious error in measuring the electron spectrum with a magnetic spectrometer. In order to determine a correct electron spectrum, the pointing angle of an electron beam incident on the spectrometer should be exactly defined. Here, we present a method for absolutely calibrating the electron spectrum by monitoring the pointing angle using a scintillating screen installed in front of a permanent dipole magnet. The ambiguous electron energy due to the pointing instability is corrected by the numerical and analytical calculations based on the relativistic equation of electron motion. It is also possible to estimate the energy spread of the electron beam and determine the energy resolution of the spectrometer using the beam divergence angle that is simultaneously measured on the screen. The calibration method with direct measurement of the spatial profile of an incident electron beam has a simple experimental layout and presents the full range of spatial and spectral information of the electron beams with energies of multi-hundred MeV level, despite the limited energy resolution of the simple electron spectrometer.
Molecular weight distribution effects on the structure of strongly adsorbed polymers by Monte Carlo simulation
Authors: Kuppa Vikram K.
Published: June 2012

Monte Carlo simulations are reported to study the structure of polymers adsorbed from solution onto strongly attractive, perfectly smooth substrates. Six systems spanning a range of molecular weight distributions are investigated with a coarse-grained united atom model for freely rotating chains. By employing a global replica exchange algorithm and topology altering Monte Carlo moves, a range of monomer-surface attraction from weak (0.27kT) to strong (4kT) is simultaneously explored. Thus for the first time ever, equilibrium polymer adsorption on highly attractive surfaces is studied, with all adsorbed molecules displaying similar properties and statistics. The architecture of the adsorbed layers, including density profiles, bond orientation order parameters, radii of gyration, and distribution of the adsorbed chain fractions, is shown to be highly dependent on the polydispersity of the polymer phase. The homology of polymer chains, and the ergodicity of states explored by the molecules is in contrast to the metastable, kinetically constrained paradigm of irreversible adsorption. The structure of more monodisperse systems is qualitatively similar to experimental results and theoretical predictions, but result from very different chain conformations and statistics. The polydispersity-dependent behavior is explained in the context of the competition between polymers to make contact with the surface.
Kinetic and geometric isotope effects originating from different adsorption potential energy surfaces: Cyclohexane on Rh(111)
Authors: Koitaya Takanori , Shimizu Sumera , Mukai Kozo , Yoshimoto Shinya , Yoshinobu Jun
Published: June 2012

Novel isotope effects were observed in desorption kinetics and adsorption geometry of cyclohexane on Rh(111) by the use of infrared reflection absorption spectroscopy, temperature programmed desorption, photoelectron spectroscopy, and spot-profile-analysis low energy electron diffraction. The desorption energy of deuterated cyclohexane (C6D12) is lower than that of C6H12. In addition, the work function change by adsorbed C6D12 is smaller than that by adsorbed C6H12. These results indicate that C6D12 has a shallower adsorption potential than C6H12 (vertical geometric isotope effect). The lateral geometric isotope effect was also observed in the two-dimensional cyclohexane superstructures as a result of the different repulsive interaction between interfacial dipoles. The observed isotope effects should be ascribed to the quantum nature of hydrogen involved in the C–H···metal interaction.
Force-dependent mobility and entropic rectification in tubes of periodically varying geometry
Authors: Dagdug Leonardo , Berezhkovskii Alexander M. , Makhnovskii Yurii A. , Zitserman Vladimir Yu. , Bezrukov Sergey M.
Published: June 2012

We investigate transport of point Brownian particles in a tube formed by identical periodic compartments of varying diameter, focusing on the effects due to the compartment asymmetry. The paper contains two parts. First, we study the force-dependent mobility of the particle. The mobility is a symmetric non-monotonic function of the driving force, F, when the compartment is symmetric. Compartment asymmetry gives rise to an asymmetric force-dependent mobility, which remains non-monotonic when the compartment asymmetry is not too high. The F-dependence of the mobility becomes monotonic in tubes formed by highly asymmetric compartments. The transition of the F-dependence of the mobility from non-monotonic to monotonic behavior results in important consequences for the particle motion under the action of a time-periodic force with zero mean, which are discussed in the second part of the paper: In a tube formed by moderately asymmetric compartments, the particle under the action of such a force moves with an effective drift velocity that vanishes at small and large values of the force amplitude having a maximum in between. In a tube formed by highly asymmetric compartments, the effective drift velocity monotonically increases with the amplitude of the driving force and becomes unboundedly large as the amplitude tends to infinity.
Meniscus and beam halo formation in a tandem-type negative ion source with surface production
Authors: Miyamoto K. , Okuda S. , Hatayama A.
Published: June 2012

A meniscus of plasma-beam boundary in H− ion sources largely affects the extracted H− ion beam optics. Although it is hypothesized that the shape of the meniscus is one of the main reasons for the beam halo observed in experiments, a physical mechanism of the beam halo formation is not yet fully understood. In this letter, it is first shown by the 2D particle in cell simulation that the H− ions extracted from the periphery of the meniscus cause a beam halo since the surface produced H− ions penetrate into the bulk plasma, and, thus, the resultant meniscus has a relatively large curvature.
Formation of nitrogen-vacancy complexes during plasma-assisted nitrogen doping of epitaxial graphene on SiC(0001)
Authors: Rhim S. H. , Qi Y. , Liu Y. , Weinert M. , Li L.
Published: June 2012

Doping epitaxial graphene on SiC(0001) using nitrogen plasma leads to N-vacancy complexes. Based on the calculated energetics by density functional theory and comparison with scanning tunneling microscopy observations, the most probable configuration is determined to be a nonmagnetic complex consisting of substitutional nitrogen next to a carbon vacancy. Further calculations show that other N-vacancy complexes, where the substituted N and the vacancy are the second and third nearest neighbors, do exhibit localized moments. These results indicate that the electronic and magnetic properties of graphene can be further tailored by plasma-assisted nitrogen doping.
Monte Carlo simulation of vapor-liquid equilibrium and critical asymmetry of square-well dimer fluid
Authors: Li Liyan , Tang Kaiwei , Wu Liang , Zhao Wei , Cai Jun
Published: June 2012

The critical behavior of square-well dimer fluid has been investigated using grand canonical ensemble Monte Carlo simulations combined with a histogram reweighting technique, hyper-parallel tempering and finite-size scaling. The critical temperature and density obtained are $T_{\rm c}^* = 1.5495 \pm 0.0009$Tc*=1.5495±0.0009 and $\rho _{\rm c}^* = 0.1473 \pm 0.0007$ρc*=0.1473±0.0007, which are 2.5% lower and 5.2% higher than previous results. Coexistence curves both near to and far from the critical point were obtained. The vapor-liquid equilibrium data far from the critical point are consistent with previous results. Simulation results show that the contribution of |t|1−α to the coexistence diameter of square-well dimer fluid dominates the critical behavior and the contribution of |t|2β is larger than for a hard-core square-well fluid.
Increasing the optical transition oscillator strength in GaSb-based type II quantum wells
Authors: Janiak F. , Sęk G. , Motyka M. , Ryczko K. , Misiewicz J. , Bauer A. , Höfling S. , Kamp M. , Forchel A.
Published: June 2012

The oscillator strength of the fundamental optical transition in GaSb-based type II quantum well structures as one of the crucial parameters for the performance of interband cascade lasers was investigated. Modulation spectroscopy, supported by eight-band k·p calculations, has been employed as a sensitive probing technique allowing to determine the transition intensities of samples with various layer structures. The results show that altering the composition of the valence band well in a type II system can efficiently enhance the transition oscillator strength. Especially, the utilization of a quaternary GaInAsSb material for hole confinement turned out to be highly beneficial.
Strain-induced effects on the dielectric constant for thin, crystalline rare earth oxides on silicon
Authors: Schwendt D. , Osten H. J. , Shekhter P. , Eizenberg M.
Published: June 2012

Thin epitaxial rare earth oxide layers on Si exhibit K values that are much larger than the known bulk values. We investigate the thickness dependence of that enhancement effect for epitaxial Gd2O3 on Si(111). Controlling the oxide composition in ternary (Gd1-xNdx)2O3 thin films enables us to tune the lattice mismatch to silicon and thus the K values of the dielectric layer from 13 (close to the bulk value) up to 20. We show that simple tetragonal distortion of the cubic lattice is not sufficient to explain the enhancement in K. Therefore, we propose more severe strain induced structural phase deformations.
Extreme ultraviolet spectroscopy and modeling of Cu on the SSPX Spheromak and laser plasma “Sparky”
Authors: Weller M. E. , Safronova A. S. , Clementson J. , Kantsyrev V. L. , Safronova U. I. , Beiersdorfer P. , Petkov E. E. , Wilcox P. G. , Osborne G. C.
Published: June 2012

Impurities play a critical role in magnetic fusion research. In large quantities, impurities can cool and dilute plasma creating problems for achieving ignition and burn; however in smaller amounts the impurities could provide valuable information about several plasma parameters through the use of spectroscopy. Many impurity ions radiate within the extreme ultraviolet (EUV) range. Here, we report on spectra from the silver flat field spectrometer, which was implemented at the Sustained Spheromak Physics experiment (SSPX) to monitor ion impurity emissions. The chamber within the SSPX was made of Cu, which makes M-shell Cu a prominent impurity signature. The Spect3D spectral analysis code was utilized to identify spectral features in the range of 115–315 Å and to more fully understand the plasma conditions. A second set of experiments was carried out on the compact laser-plasma x-ray/EUV facility “Sparky” at UNR, with Cu flat targets used. The EUV spectra were recorded between 40–300 Å and compared with results from SSPX.
Magnetism of Cr-doped ZnO with intrinsic defects
Authors: Weng Z. Z. , Huang Z. G. , Lin W. X.
Published: June 2012

The electronic structure and formation energies of defect in Cr-doped ZnO are investigated by the first-principles calculations. The dopant Cr atom and native defects (O vacancy, Zn vacancy, and Zn interstitial) at different charge states are considered. The calculated results indicate that the substitutive Cr in the oxidation state of +3 and the neutral Zn vacancy in the ZnO:Cr sample is the most favorable defect complex to maintain a high stability of ferromagnetic order. Therefore, a p-type ZnO:Cr prepared under O-rich condition could have a higher Curie temperature. The p-d hybridization and the itinerant d-characteristic n-type carriers are suggested to mediate the long range ferromagnetic exchange interaction between Cr atoms.
Extracted current saturation in negative ion sources
Authors: Mochalskyy S. , Lifschitz A. F. , Minea T.
Published: June 2012

The extraction of negatively charged particles from a negative ion source is one of the crucial issues in the development of the neutral beam injector system for future experimental reactor ITER. Full 3D electrostatic particle-in-cell Monte Carlo collision code—ONIX [S. Mochalskyy et al., Nucl. Fusion 50, 105011 (2010)]—is used to simulate the hydrogen plasma behaviour and the extracted particle features in the vicinity of the plasma grid, both sides of the aperture. It is found that the contribution to the extracted negative ion current of ions born in the volume is small compared with that of ions created at the plasma grid walls. The parametric study with respect to the rate of negative ions released from the walls shows an optimum rate. Beyond this optimum, a double layer builds-up by the negative ion charge density close to the grid aperture surface reducing thus extraction probability, and therefore the extracted current. The effect of the extraction potential and magnetic field magnitudes on the extraction is also discussed. Results are in good agreement with available experimental data.
Ion beam synthesis of nanothermochromic diffraction gratings with giant switching contrast at telecom wavelengths
Authors: Zimmer Johannes , Wixforth Achim , Karl Helmut , Krenner Hubert J.
Published: June 2012

Nanothermochromic diffraction gratings based on the metal-insulator transition of VO2 are fabricated by site-selective ion beam implantation in a SiO2 matrix. Gratings were defined either (i) directly by spatially selective ion beam synthesis or (ii) by site-selective deactivation of the phase transition by ion beam induced defects. The strongest increase of the diffracted light intensities was observed at a wavelength of 1550 nm exceeding a factor of 20 for the selectively deactivated gratings. The observed pronounced thermal hysteresis extending down close to room temperature makes this system ideally suited for optical memory applications.
Hard x-ray photoelectron spectroscopy study of the electroforming in Ti/HfO2-based resistive switching structures
Authors: Sowinska M. , Bertaud T. , Walczyk D. , Thiess S. , Schubert M. A. , Lukosius M. , Drube W. , Walczyk Ch. , Schroeder T.
Published: June 2012

The chemical and electronic modifications induced by the electroforming process on the Ti/HfO2/TiN-based resistive switching devices were investigated by non-destructive hard x-ray photoelectron spectroscopy (HAXPES). The results indicate an increase of the titanium top electrode oxidation at the interface with HfO2 after the electroforming process. Additionally, the binding energy values of the HAXPES peaks of the electroformed sample increased as compared to the as-prepared sample. The observed changes between both samples are attributed to the creation of n-type defects, such as oxygen vacancies, in the HfO2 layer near the Ti interface during the electroforming process.
Evolutionary selection of enzymatically synthesized semiconductors from biomimetic mineralization vesicles
Authors: Bawazer Lukmaan A. , Izumi Michi , Kolodin Dmitriy , Neilson James R. , Schwenzer Birgit , Morse Daniel E.
Published: June 2012

The way nature evolves and sculpts materials using proteins inspires new approaches to materials engineering but is still not completely understood. Here, we present a cell-free synthetic biological platform to advance studies of biologically synthesized solid-state materials. This platform is capable of simultaneously exerting many of the hierarchical levels of control found in natural biomineralization, including genetic, chemical, spatial, structural, and morphological control, while supporting the evolutionary selection of new mineralizing proteins and the corresponding genetically encoded materials that they produce. DNA-directed protein expression and enzymatic mineralization occur on polystyrene microbeads in water-in-oil emulsions, yielding synthetic surrogates of biomineralizing cells that are then screened by flow sorting, with light-scattering signals used to sort the resulting mineralized composites differentially. We demonstrate the utility of this platform by evolutionarily selecting newly identified silicateins, biomineralizing enzymes previously identified from the silica skeleton of a marine sponge, for enzyme variants capable of synthesizing silicon dioxide (silica) or titanium dioxide (titania) composites. Mineral composites of intermediate strength are preferentially selected to remain intact for identification during cell sorting, and then to collapse postsorting to expose the encoding genes for enzymatic DNA amplification. Some of the newly selected silicatein variants catalyze the formation of crystalline silicates, whereas the parent silicateins lack this ability. The demonstrated bioengineered route to previously undescribed materials introduces in vitro enzyme selection as a viable strategy for mimicking genetic evolution of materials as it occurs in nature.
Chemotactic adaptation kinetics of individual
Escherichia coli
cells
Authors: Min Taejin L. , Mears Patrick J. , Golding Ido , Chemla Yann R.
Published: June 2012

Escherichia coli
chemotaxis serves as a paradigm for the way living cells respond and adapt to changes in their environment. The chemotactic response has been characterized at the level of individual flagellar motors and in populations of swimming cells. However, it has not been previously possible to quantify accurately the adaptive response of a single, multiflagellated cell. Here, we use our recently developed optical trapping technique to characterize the swimming behavior of individual bacteria as they respond to sudden changes in the chemical environment. We follow the adaptation kinetics of
E. coli
to varying magnitudes of step-up and step-down changes in concentration of chemoattractant. We quantify two features of adaptation and how they vary with stimulus strength: abruptness (the degree to which return to prestimulus behavior occurs within a small number of run/tumble events) and overshoot (the degree of excessive response before the return to prestimulus behavior). We also characterize the asymmetry between step-up and step-down responses, observed at the single-cell level. Our findings provide clues to an improved understanding of chemotactic adaptation.
Patched dependence receptor triggers apoptosis through ubiquitination of caspase-9
Authors: Fombonne Joanna , Bissey Pierre-Antoine , Guix Catherine , Sadoul Rémy , Thibert Chantal , Mehlen Patrick
Published: June 2012

Patched (Ptc), the main receptor for Sonic Hedghog, is a tumor suppressor. Ptc has been shown to be a dependence receptor, and as such triggers apoptosis in the absence of its ligand. This apoptosis induction occurs through the recruitment by the Ptc intracellular domain of a caspase-activating complex, which includes the adaptor proteins DRAL and TUCAN, and the apical caspase-9. We show here that this caspase-activating complex also includes the E3 ubiquitin ligase NEDD4. We demonstrate that Ptc-mediated apoptosis and Ptc-induced caspase-9 activation require NEDD4. We show that Ptc, but not Bax, the prototypical inducer of the intrinsic cell-death pathway, triggers polyubiquitination of caspase-9. Moreover, a caspase-9 mutant that could not be ubiquitinated failed to mediate Ptc-induced apoptosis. Taken together, these data support the view that the Ptc dependence receptor specifically allows the activation of caspase-9 via its ubiquitination, which occurs via the recruitment by Ptc of NEDD4.
Elastic sheet on a liquid drop reveals wrinkling and crumpling as distinct symmetry-breaking instabilities
Authors: King Hunter , Schroll Robert D. , Davidovitch Benny , Menon Narayanan
Published: June 2012

Smooth wrinkles and sharply crumpled regions are familiar motifs in biological or synthetic sheets, such as rapidly growing plant leaves and crushed foils. Previous studies have addressed both morphological types, but the generic route whereby a featureless sheet develops a complex shape remains elusive. Here we show that this route proceeds through an unusual sequence of distinct symmetry-breaking instabilities. The object of our study is an ultrathin circular sheet stretched over a liquid drop. As the curvature is gradually increased, the surface tension stretching the sheet over the drop causes compression along circles of latitude. The compression is relieved first by a transition into a wrinkle pattern, and then into a crumpled state via a continuous transition. Our data provide conclusive evidence that wrinkle patterns in highly bendable sheets are not described by classical buckling methods, but rather by a theory which assumes that wrinkles completely relax the compressive stress. With this understanding we recognize the observed sequence of transitions as distinct symmetry breakings of the shape and the stress field. The axial symmetry of the shape is broken upon wrinkling but the underlying stress field preserves this symmetry. Thus, the wrinkle-to-crumple transition marks symmetry-breaking of the stress in highly bendable sheets. By contrast, other instabilities of sheets, such as blistering and cracking, break the homogeneity of shape and stress simultaneously. The onset of crumpling occurs when the wrinkle pattern grows to half the sheet’s radius, suggesting a geometric, material-independent origin for this transition.