bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced binding to and killing of hepatocellular carcinoma cellsin vitroby melittin when linked with a novel targeting peptide screened from phage display
Authors: Zhao Honglei , Feng Xin , Han Wenyu , Diao Yuwen , Han Dong , Tian Xiaofeng , Gao Yu , Liu Shanshan , Zhu Seng , Yao Cuimei , Gu Jingmin , Sun Changjiang , Lei Liancheng
Published: August 2013

A random phage 12‐mer peptide library and a whole‐cell subtractive biopanning protocol against HepG2 cells were used to select a novel peptide‐specific binding to hepatocellular carcinoma cells. As a result, peptide SLSLITMLKISR (AM‐2) was screened as a novel homing peptide to hepatocellular carcinoma cells, tested by immunofluorescence and immunochemistry assays. Subsequently, peptide AM‐2 was linked to melittin by A(EAAAK)2A, and the antitumor effect of this ligation product was detected by MTT assay, fluorescence‐activated cell sorting, and scanning electron microscopy methods. Results of cell growth inhibition tests confirmed that the affinity of melittin was increased after being incorporated into AM‐2, and AM‐2‐melittin specifically targeted and killed HepG2 cellsin vitro. Thus, AM‐2 is a valuable ligand for tumor targeting, which leads to increased binding and killing effect of hepatocellular carcinoma cellsin vitrowhen ligated to melittin, and AM‐2‐melittin has a clinical potential application as target agents for the treatment of human hepatocellular carcinoma. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
Nucleation and growth of CVD diamond on fused silica optical fibres with titanium dioxide interlayer
Authors: Bogdanowicz Robert , Śmietana Mateusz , Gnyba Marcin , Ficek Mateusz , Straňák Vítězslav , Goluński Łukasz , Sobaszek Michał , Ryl Jacek
Published: August 2013

Nucleation and growth processes of thin diamond films on fused silica optical fibres have been investigated. Fibres were coated with diamond film using microwave plasma enhanced chemical vapour deposition (µPE CVD) system. Since the growth of diamond on the fused silica glass requires high seeding density, two types of glass pre‐treatment were applied: titanium dioxide (TiO2) interlayer deposition and sonication in nanodiamond suspension. In the experiment, high density, thin (∼20 nm) TiO2 films were deposited using high‐power impulse magnetron sputtering. Subsequently, a set of thin diamond films deposited in up to 60 min‐long process was investigated. Results obtained for the two pre‐treatment methods were compared. The nucleation processes were studied and compared using numerical analysis of scanning electron microscopy (SEM) images. The molecular structure of nucleated diamond was examined with micro‐Raman spectroscopy. The sp3/sp2 ratio was calculated using Raman spectra deconvolution method. Thickness, roughness and optical properties of the nanodiamond films in VIS–NIR wavelength range were investigated by means of spectroscopic ellipsometry. It was found that the high density TiO2 interlayer enhances CVD diamond film nucleation processes on fused silica and increases sp3/sp2 ratio of the film. The proposed growth method can be effectively applied in manufacturing of various types of optical fibre sensors. Due to high chemical and mechanical resistance of the diamond films such optical sensors are highly desired.
Graph construction and random graph generation for modeling protein structures
Authors: Wagaman Amy
Published: August 2013

Researchers often model folded protein structures as graphs with amino acids as the vertices and edges representing contacts between amino acids. The vertices in these graphs are naturally ordered in the amino acid sequence order. There are many different graph construction methods and there is no consensus about what construction to use or what the major issues are with each construction in the literature. We investigate different constructions and examine their effect on various graph measures. We also consider the small‐world network model for proteins, discuss its validity under the different constructions, and discuss random protein graph generation. We propose a new graph property for graphs with ordered vertices, the contact distribution, and propose a method of reciprocal attachment to merge neighborhoods for protein graphs. Statistical Analysis and Data Mining Statistical Analysis and Data Mining 2013 DOI: 10.1002/sam.11203
Concentration driven phase transitions in multiphase porous media with application to methane oxidation in landfill cover layers
Authors: Ricken T. , Sindern A. , Bluhm J. , Widmann R. , Denecke M. , Gehrke T. , Schmidt T.C.
Published: August 2013

This study focuses on a formulation within the theory of porus media for continuum multicomponent modeling of bacterial driven methane oxidation in a porous landfill cover layer which consists of a porous solid matrix (soil and bacteria) saturated by a liquid (water) and gas phase. The solid, liquid, and gas phases are considered as immiscible constituents occupying spatially their individual volume fraction. However, the gas phase is composed of three components, namely methane (CH4), oxygen (O2), and carbon dioxide (CO2). A thermodynamically consistent constitutive framework is derived by evaluating the entropy inequality on the basis of Coleman and Noll [8], which results in constitutive relations for the constituent stress and pressure states, interaction forces, and mass exchanges. For the final set of process variables of the derived finite element calculation concept we consider the displacement of the solid matrix, the partial hydrostatic gas pressure and osmotic concentration pressures. For simplicity, we assume a constant water pressure and isothermal conditions. The theoretical formulations are implemented in the finite element code FEAP by Taylor [29]. A new set of experimental batch tests has been created that considers the model parameter dependencies on the process variables; these tests are used to evaluate the nonlinear model parameter set. After presenting the framework developed for the finite element calculation concept, including the representation of the governing weak formulations, we examine representative numerical examples.
A Proposal for Physicochemical Standards and Antioxidant Activity of Portuguese Propolis
Authors: Falcão Soraia I. , Freire Cristina , Vilas‐Boas Miguel
Published: August 2013

Propolis is a complex resinous product gathered by honeybees whose chemical composition is highly variable, depending strongly on the plant sources available to the bees at the site of collection. Propolis from several locations in Portugal, including islands, was fully characterized in terms of physicochemical properties, phenolic composition and antioxidant activity, enabling the establishment of quality standards. Color, frequently used as a commercial parameter, was accessed by the first time in propolis with the CIELAB system, and proposed as a quick and reliable method for quality recognition. The results attested the existence of two different types of propolis within the six regions under study. One, the poplar propolis most common in temperate regions, revealed a high content in phenolics and show high bioactivity. The other, with darker green color is less rich in phenolics and generally less bioactive.
Regeneration of Used Frying Oil
Authors: Turan Semra , Yalcuk Arda
Published: August 2013

Used frying oils were purified in a packed column using different amounts of silica gel (SG), aluminum oxide (AO), activated charcoal (AC), bentonite (B), magnesol XL (M), calcium carbonate (CC), zeolite (Z), bleaching earth (BE) and/or their binary, triple, and quaternary combinations. SG (15 g) improved total polar material (TPM) by 100 %, conjugated diene (CD) content by 84 %, and p‐anisidine value (AV) by 104 %, while AO and M improved free fatty acid (FFA) contents by 103 and 105 %, respectively. On the other hand, AC and M bleached the color by 100 and 90 %, respectively. As the amount of adsorbent in the column increased, FFA, CD, AV, and color improved. When the amount of used sunflower oil (UO1) loaded in the column containing SL was increased, FFA, CD, AV and color values increased, while no change was observed in TPM up to 60 g of UO1. Loading UO1 at 150 °C in the column caused the absorbance values at 460 nm to decrease from 0.740 to 0.240, while the amount of adsorbed tocopherol increased compared to UO1 at 25 °C. The increasing number of adsorbents within the column further improved the physicochemical properties of UO1 when it was used 30 g. However, as the amount of different type of used oils (UO2, UO3 and UO4) was increased to 300 g, improvement ratios of all parameters decreased.
Self-harm induced somatic admission after discharge from psychiatric hospital – a prospective cohort study
Authors: Mellesdal L. , Kroken R.A. , Lutro O. , Wentzel-Larsen T. , Kjelby E. , Oedegaard K.J. , Jørgensen H.A. , Mehlum L.
Published: August 2013

Background:

Few studies have examined rate and predictors of self-harm in discharged psychiatric patients.

Aims:

To investigate the rate, coding, timing, predictors and characteristics of self-harm induced somatic admission after discharge from psychiatric acute admission.

Method:

Cohort study of 2827 unselected patients consecutively admitted to a psychiatric acute ward during three years. Mean observation period was 2.3 years. Combined register linkage and manual data examination. Cox regression was used to investigate covariates for time to somatic admission due to self-harm, with covariates changing during follow-up entered time dependently.

Results:

During the observation period, 10.5% of the patients had 792 somatic self-harm admissions. Strongest risk factors were psychiatric admission due to non-suicidal self-harm, suicide attempt and suicide ideation. The risk was increased throughout the first year of follow-up, during readmission, with increasing outpatient consultations and in patients diagnosed with recurrent depression, personality disorders, substance use disorders and anxiety/stress-related disorders. Only 49% of the somatic self-harm admissions were given hospital self-harm diagnosis.

Conclusions:

Self-harm induced somatic admissions were highly prevalent during the first year after discharge from acute psychiatric admission. Underdiagnosing of self-harm in relation to somatic self-harm admissions may cause incorrect follow-up treatments and unreliable register data.
Unusual Complete Proximal Biceps Tendon Rupture
Authors: Raizah Abdullah F.
Published: August 2013

Proximal biceps brachii tendon rupture is an unusual presentation in young individuals. This report is an extremely rare case of a complete rupture of the proximal biceps brachii tendon in a young patient as a result of a high-energy water-skiing injury. It was associated with displacement of the biceps muscle into the forearm with skin necrosis. The patient was treated successfully by débridement of the skin and complete resection of the biceps brachii muscle.
Devonian volcanism in the Minusa basin in the Altai–Sayan area: geological, geochemical, and Sr–Nd isotopic characteristics of rocks
Authors: Vorontsov A.A. , Fedoseev G.S. , Andryushchenko S.V.
Published: August 2013

Based on geological data and the geochemical and isotopic (Sr, Nd) parameters of the Devonian volcanic associations of the Minusa basin, the main regularities of volcanism development are considered, the composition of magmatic sources is studied, and the geodynamic mechanisms of their involvement in rifting are reconstructed. The early stage of formation of the Minusa basin was characterized by intense volcanism, which resulted in differentiated and, more seldom, bimodal volcanic complexes composed of pyroclastic rocks and dolerite sills. At the late stage, only terrigenous deposits accumulated in the basin. It has been established that the basites are similar in composition and are intermediate in geochemical characteristics between intraplate rocks (OIB) and continent-marginal ones (IAB). The basites, like OIB, have high contents of all lithophile elements, which is typical of enriched mantle sources, and, like IAB, show negative anomalies of Nb, Ta, Ti, and, to a smaller extent, Rb, Th, Zr, and Hf, selective enrichment in Pb and Ba (and, sometimes, Sr), and a weak REE differentiation (7 < (La/Yb)N < 17). In contrast to the basins in other segments of the Devonian Altai–Sayan rift area, the igneous associations in the Minusa basin are characterized by a worse expressed geochemical inhomogeneity of rocks and lack of high-Ti (>2 wt.% TiO2) basites. The Sr and Nd isotope compositions of the Minusa basites deviate from the mantle rock series toward the compositions with high radiogenic-strontium and low REE contents. This points to the melting of a mantle substratum (PREMA-type) and carbonate-rich sedimentary rocks, which were probably assimilated by basaltic magma. The correlations between the contents of trace incompatible elements in rocks with SiO2 = 53–77 wt.% testify to the assimilation of crustal substrata by parental basaltic melts and the subsequent differentiation of contaminated magmas (AFC model). We propose a model for the formation of primary melts with the simultaneous participation of magmatic sources of two types: plume and fluid-saturated suprasubductional, localized beneath the active continental margin.
Biostratigraphy and ammonites of the Middle Oxfordian to lowermost Upper Kimmeridgian in northern Central Siberia
Authors: Wierzbowski A. , Rogov M.A.
Published: August 2013

The Middle Oxfordian to lowermost Upper Kimmeridgian ammonite faunas from northern Central Siberia (Nordvik, Chernokhrebetnaya, and Levaya Boyarka sections) are discussed, giving the basis for distinguishing the ammonite zones based on cardioceratid ammonites of the genus Amoeboceras (Boreal zonation), and, within the Kimmeridgian Stage, faunas–for distinguishing zones based on the aulacostephanid ammonites (Subboreal zonation). The succession of Boreal ammonites is essentially the same as in other areas of the Arctic and NW Europe, but the Subboreal ammonites differ somewhat from those known from NW Europe and Greenland. The Siberian aulacostephanid zones—the Involuta Zone and the Evoluta Zone—are correlated with the Baylei Zone (without its lowermost portion), and the Cymodoce Zone/lowermost part of the Mutabilis Zone (the Askepta Subzone) from NW Europe. The uniform character of the Boreal ammonite faunas in the Arctic makes possible a discussion on their phylogeny during the Late Oxfordian and Kimmeridgian: the succession of particular groups of Amoeboceras species referred to successive subgenera is revealed by the occurrence of well differentiated assemblages of typical normal-sized macro and microconchs, intermittently marked by the occurrence of assemblages of paedomorphic “small-sized microconchs” appearing at some levels preceeding marked evolutionary modifications. Some comments on the paleontology of separate groups of ammonites are also given. These include a discussion on the occurrence of Middle Oxfordian ammonites of the genus Cardioceras in the Nordvik section in relation to the critical review of the paper of Rogov and Wierzbowski (2009) by Nikitenko et al. (2011). The discussion shows that the oldest deposits in the section belong to the Middle Oxfordian, which results in the necessity for some changes in the foraminiferal zonal scheme of Nikitenko et al. (2011). The ammonites of the Pictonia involuta group are distinguished as the new subgenus Mesezhnikovia Wierzbowski and Rogov.
A geosteering tool for horizontal well logging
Authors: Epov M.I. , Mironov V.L. , Muzalevskiy K.V. , Eltsov I.N. , Salomatov U.P.
Published: August 2013

A theoretical study has been performed to check the possibility of using ultrabroadband nanosecond electromagnetic pulses as a geosteering tool for horizontal drilling to estimate the distance to the oil-water contact (OWC) in a floating oil accumulation. The voltage of a microwave-bandwidth pulse at the dipole receiver of a downhole radar was modeled for the case of a horizontal borehole near OWC in a formation saturated with oil and water. Numerical solutions to the boundary problem formulated on the basis of the Maxwell equations were obtained with the Microwave Studio software (www.cst.com). The frequency-dependent dielectric constants of the layered saturated formation and the drilling fluid were assumed according to experimentally tested models. The modeling has demonstrated that nanosecond electromagnetic pulses arriving from a layered oil-water contact can in principle be acquired and the distance from the wellbore to the OWC median can be inferred from the respective time delays recorded by a downhole radar. Additionally, the possible dynamic range and accuracy of sensing have been estimated.
Interfamily Conflict, Reproductive Success, and the Evolution of Male Homosexuality
Authors: Apostolou Menelaos
Published: August 2013

In a preindustrial context, the mate choices of women are controlled by their parents, who require evidence of wealth and of ability to generate wealth from prospective sons-in-law in order to grant access to their daughters’ reproductive capacity. As a consequence, male siblings have to compete among themselves for controlling family resources required for successful reproduction. This competition increases interfamily conflict, decreasing each of the siblings’ inclusive fitness. Moreover, the sharing of resources among brothers reduces the chances that each one will be able to gain access to a high-quality female and/or to mate polygynously. It is proposed that male homosexuality has evolved to increase the reproductive success of male siblings and to decrease interfamily conflict. That is, by having a homosexual orientation, a younger male sibling increases his inclusive fitness by reducing competition over resources, whereas his older brothers enjoy higher reproductive success by having more resources available for reproduction. Finally, the reproductive costs of this sexual orientation are kept low by the elevated probability that a homosexual man will find himself in an arranged marriage where he is likely to have children.
The Analogical Peacock Hypothesis: The Sexual Selection of Mind-Reading and Relational Cognition in Human Communication
Authors: McKeown Gary J.
Published: August 2013

This integrative review presents a novel hypothesis as a basis for integrating two evolutionary viewpoints on the origins of human cognition and communication, the sexual selection of human mental capacities, and the social brain hypothesis. This new account suggests that mind-reading social skills increased reproductive success and consequently became targets for sexual selection. The hypothesis proposes that human communication has three purposes: displaying mind-reading abilities, aligning and maintaining representational parity between individuals to enable displays, and the exchange of propositional information. Intelligence, creativity, language, and humor are mental fitness indicators that signal an individual's quality to potential mates, rivals, and allies. Five features central to the proposed display mechanism unify these indicators, the relational combination of concepts, large conceptual knowledge networks, processing speed, contextualization, and receiver knowledge. Sufficient between-mind alignment of conceptual networks allows displays based upon within-mind conceptual mappings. Creative displays communicate previously unnoticed relational connections and novel conceptual combinations demonstrating an ability to read a receiver's mind. Displays are costly signals of mate quality with costs incurred in the developmental production of the neural apparatus required to engage in complex displays and opportunity costs incurred through time spent acquiring cultural knowledge. Displays that are fast, novel, spontaneous, contextual, topical, and relevant are hard-to-fake for lower quality individuals. Successful displays result in elevated social status and increased mating options. The review addresses literatures on costly signaling, sexual selection, mental fitness indicators, and the social brain hypothesis; drawing implications for nonverbal and verbal communication.
The “Genius” and “Madness” of Bobby Fischer: His Life from Three Psychobiographical Lenses
Authors: Ponterotto Joseph G. , Reynolds Jason D.
Published: August 2013

Robert (Bobby) James Fischer (1943–2008) remains one of the most puzzling and enigmatic personalities in modern American history. In 1972, at the height of Cold War tensions between the Soviet Union and the United States, Bobby Fischer defeated Soviet Boris Spassky to become the first official world chess champion from the United States. Two decades later, after playing a rematch with Spassky in war-torn Yugoslavia, Fischer became a fugitive from U.S. justice. Although always an independent, autonomous, and forthright person, Fischer's behavior after the 1972 championship grew increasingly strange and bizarre. “Who was Bobby Fischer and what happened to him” is a lingering question that has not been adequately answered by psychologists, historians, and biographers. The present article examines the life of Bobby Fischer from three diverse psychobiographical lenses: Erikson's (Erikson, E. H. [1950]. Childhood and society. New York, NY: Norton) psychosocial development model; the clinical diagnostic model of the Shedler-Westen Assessment Procedure (SWAP; Shedler, J. [2009]. Guide to SWAP-200 Interpretation. Shedler-Westen Assessment Procedure: Where Science Meets Practice. www.SWAPassessment.org ); and a strengths-based positive psychology model (Peterson, C., & Seligman, M. E. P. [2004]. Character strengths and virtues: A handbook and classification. Oxford, UK: Oxford University Press.). Suggestions for advancing the science of psychobiography are put forth with particular emphasis on incorporating mixed methods approaches to research.
Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus
Authors: Ebina Hirotaka , Misawa Naoko , Kanemura Yuka , Koyanagi Yoshio
Published: August 2013

Even though highly active anti-retroviral therapy is able to keep HIV-1 replication under control, the virus can lie in a dormant state within the host genome, known as a latent reservoir and poses a threat to re-emerge at any time. However, novel technologies aimed at disrupting HIV-1 provirus may be capable of eradicating viral genomes from infected individuals. In this study, we showed the potential of the CRISPR/Cas9 system to edit the HIV-1 genome and block its expression. When LTR-targeting CRISPR/Cas9 components were transfected into HIV-1 LTR expression-dormant and -inducible T cells, a significant loss of LTR-driven expression was observed after stimulation. Sequence analysis confirmed that this CRISPR/Cas9 system efficiently cleaved and mutated LTR target sites. More importantly, this system was also able to remove internal viral genes from the host cell chromosome. Our results suggest that the CRISPR/Cas9 system may be a useful tool for curing HIV-1 infection.
Chiral domain formation from the mixture of achiral rod-like liquid crystal and tri boomerang-shaped molecule
Authors: Lee Ji-Hoon , Yoon Tae-Hoon
Published: August 2013

Spontaneous formation of chiral domains such as a helical filament and a bent-broom texture was observed from the mixture of a rod-like liquid crystal octylcyano-biphenyl (8CB) and a tri boomerang-shaped 2,4,6-triphenoxy-1,3,5-triazine (triphenoxy) molecule. Although the constituent molecules were achiral, their mixture showed the chiral domains with the equal fraction of the opposite handedness. No tilt of 8CB molecules in the smectic layer was observed, implying the chirality is not due to the polar packing and tilt of the molecules. In addition, the splay and bend elastic constant of 8CB was decreased after doping triphenoxy. A structural conformation of triphenoxy and an orientational coupling between 8CB and triphenoxy are considered to be related to the chiral domain formation.
Hydration of the pyrimidine radical cation and stepwise solvation of protonated pyrimidine with water, methanol, and acetonitrile
Authors: Hamid Ahmed M. , Sharma Pramod , Samy El-Shall M. , Hilal Rifaat , Elroby Shaaban , Aziz Saadullah G. , Alyoubi Abdulrahman O.
Published: August 2013

Equilibrium thermochemical measurements using an ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes associated with the stepwise hydration of the biologically significant ions pyrimidine radical cation and protonated pyrimidine. The binding energy of the hydrated pyrimidine radical cation is weaker than that of the proton-bound dimer pyrimidineH+(H2O) consistent with the formation of a weak carbon-based CHδ+··OH2 hydrogen bond (11.9 kcal/mol) and a stronger NH+··OH2 hydrogen bond (15.6 kcal/mol), respectively. Other proton-bound dimers such as pyrimidineH+(CH3OH) and pyrimidineH+(CH3CN) exhibit higher binding energies (18.2 kcal/mol and 22.8 kcal/mol, respectively) due to the higher proton affinities and dipole moments of acetonitrile and methanol as compared to water. The measured collisional cross sections of the proton-bound dimers provide experimental-based support for the DFT calculated structures at the M06-2x/6-311++G (d,p) level. The calculations show that the hydrated pyrimidine radical cation clusters form internally solvated structures in which the water molecules are bonded to the C4N2H4•+ ion by weak CHδ+··OH2 hydrogen bonds. The hydrated protonated pyrimidine clusters form externally solvated structures where the water molecules are bonded to each other and the ion is external to the water cluster. Dissociative proton transfer reactions C4N2H4•+(H2O)n−1 + H2O → C4N2H3• + (H2O)nH+ and C4N2H5+(H2O)n−1 + H2O → C4N2H4 + (H2O)nH+ are observed for n ≥ 4 where the reactions become thermoneutral or exothermic. The absence of the dissociative proton transfer reaction within the C4N2H5+(CH3CN)n clusters results from the inability of acetonitrile molecules to form extended hydrogen bonding structures such as those formed by water and methanol due to the presence of the methyl groups which block the extension of hydrogen bonding networks.
Time-dependent Marangoni-Bénard instability of an evaporating binary-liquid layer including gas transients
Authors: Machrafi H. , Rednikov A. , Colinet P. , Dauby P. C.
Published: August 2013

We are here concerned with Bénard instabilities in a horizontal layer of a binary liquid, considering as a working example the case of an aqueous solution of ethanol with a mass fraction of 0.1. Both the solvent and the solute evaporate into air (the latter being insoluble in the liquid). The system is externally constrained by imposing fixed “ambient” pressure, humidity, and temperature values at a certain effective transfer distance above the liquid-gas interface, while the ambient temperature is also imposed at the impermeable rigid bottom of the liquid layer. Fully transient and horizontally homogeneous solutions for the reference state, resulting from an instantaneous exposure of the liquid layer to ambient air, are first calculated. Then, the linear stability of these solutions is studied using the frozen-time approach, leading to critical (monotonic marginal stability) curves in the parameter plane spanned by the liquid layer thickness and the elapsed time after initial contact. This is achieved for different ratios of the liquid and gas thicknesses, and in particular yields critical times after which instability sets in (for given thicknesses of both phases). Conversely, the analysis also predicts a critical thickness of the liquid layer below which no instability ever occurs. The nature of such critical thickness is explained in detail in terms of mass fraction profiles in both phases, as it indeed appears that the most important mechanism for instability onset is the solutal Marangoni one. Importantly, as compared to the result obtained previously under the quasi-steady assumption in the gas phase [H. Machrafi, A. Rednikov, P. Colinet, and P. C. Dauby, Eur. Phys. J. Spec. Top. 192, 71 (2011)]10.1140/epjst/e2011-01361-y, it is shown that relaxing this assumption may yield essentially lower values of the critical liquid thickness, especially for large gas-to-liquid thickness ratios. A good-working analytical model is developed for the description of such delicate transient effects in the gas. The analysis reveals that the system considered in this paper is generally highly unstable, the instability setting in even for very small times and liquid thicknesses.
Design and experimental evidence of a flat graded-index photonic crystal lens
Authors: Gaufillet F. , Akmansoy É.
Published: August 2013

We report on the design and the experimental evidence of a flat graded index photonic crystal lens. The gradient has been designed so that the flat slab focuses a plane wave and so that it converts the wave issued from a point source into a plane wave. This graded-index photonic crystal lens operates as a convex lens. The gradient of index results from varying the filling factor of the photonic crystal in the direction perpendicular to that of the propagation of the electromagnetic field. The shape of the gradient of index has been designed by engineering the iso-frequency curves of the photonic crystal. As only a few layers were necessary and as graded photonic crystals may be fabricated by a variety of processes, this shows the ability of graded photonic crystals to efficiently apply for various photonic devices, from microwave range to the optical domain. 42.70.Qs Photonic bandgap materials, 78.67.Pt Optical properties of photonic structures, 41.20.Jb Electromagnetic wave propagation; radiowave propagation 84.40.Ba Antennas.
“Multi-temperature” method for high-pressure sorption measurements on moist shales
Authors: Gasparik Matus , Ghanizadeh Amin , Gensterblum Yves , Krooss Bernhard M.
Published: August 2013

A simple and effective experimental approach has been developed and tested to study the temperature dependence of high-pressure methane sorption in moist organic-rich shales. This method, denoted as “multi-temperature” (short “multi-T”) method, enables measuring multiple isotherms at varying temperatures in a single run. The measurement of individual sorption isotherms at different temperatures takes place in a closed system ensuring that the moisture content remains constant. The multi-T method was successfully tested for methane sorption on an organic-rich shale sample. Excess sorption isotherms for methane were measured at pressures of up to 25 MPa and at temperatures of 318.1 K, 338.1 K, and 348.1 K on dry and moisture-equilibrated samples. The measured isotherms were parameterized with a 3-parameter Langmuir-based excess sorption function, from which thermodynamic sorption parameters (enthalpy and entropy of adsorption) were obtained. Using these, we show that by taking explicitly into account water vapor as molecular species in the gas phase with temperature-dependent water vapor pressure during the experiment, more meaningful results are obtained with respect to thermodynamical considerations. The proposed method can be applied to any adsorbent system (coals, shales, industrial adsorbents) and any supercritical gas (e.g., CH4, CO2) and is particularly suitable for sorption measurements using the manometric (volumetric) method.
Overdoped cuprates with high-temperature superconducting transitions
Authors: Marezio M. , Chmaissem O. , Bougerol C. , Karppinen M. , Yamauchi H. , Geballe T. H.
Published: August 2013

Evidence for high-Tc cuprate superconductivity is found in a region of the phase diagram where non-superconducting Fermi liquid metals are expected. Cu valences estimated independently from both x-ray absorption near-edge spectroscopy and bond valence sum measurements are >2.3, and are in close agreement with each other for structures in the homologous series (Cu0.75Mo0.25)Sr2(Y,Ce)sCu2O5+2s+δ with s = 1, 2, 3, and 4. The record short apical oxygen distance, at odds with current theory, suggests the possibility of a new pairing mechanism. The possibility that the charge reservoir layers are able to screen long range coulomb interactions and thus enhance Tc is discussed.
The effect of water uptake on the mechanical properties of low-k organosilicate glass
Authors: Guo X. , Jakes J. E. , Nichols M. T. , Banna S. , Nishi Y. , Shohet J. L.
Published: August 2013

Water uptake in porous low-k dielectrics has become a significant challenge for both back-end-of-line integration and circuit reliability. The influence of absorbed water on the mechanical properties of plasma-enhanced chemical-vapor-deposited organosilicate glasses (SiCOH) was investigated with nanoindentation. The roles of physisorbed (α-bonded) and chemisorbed (β-bonded) water were examined separately through annealing at different temperatures. Nanoindentation measurements were performed on dehydrated organosilicate glass during exposure to varying humidity conditions. The elastic modulus and hardness for as-deposited SiCOH are intimately linked to the nature and concentration of the absorbed water in the dielectric. Under mild-annealing conditions, the water-related film mechanical property changes were shown to be reversible. The mechanical properties of UV-cured SiCOH were also shown to depend on absorbed water, but to a lesser extent because UV curing depopulates the hydrophilic chemical groups in SiCOH. High-load indentation tests showed that in-diffusion of water in the film/substrate interface can degrade the hardness of SiCOH/Si film stacks significantly, while not significantly changing the elastic modulus.
Effect of MgO(100) support on structure and properties of Pd and Pt nanoparticles with 49-155 atoms
Authors: Kozlov Sergey M. , Aleksandrov Hristiyan A. , Goniakowski Jacek , Neyman Konstantin M.
Published: August 2013

Presently, density functional computational studies of nanostructures in heterogeneous catalysts consider either sufficiently big (“scalable with size”) unsupported metal nanoparticles (NPs) or small supported metal clusters. Both models may not be sufficiently representative of a few nm in size supported transition metal NPs dealt with in experiment. As a first step in closing the gap between theoretical models and prepared systems, we investigate the effect of a rather chemically inert oxide support, MgO(100), on relative energies and various properties of Pd and Pt NPs that consist of 49–155 atoms (1.2–1.6 nm in size) and exhibit bulk-like fcc structural arrangements. Shapes and interface configurations of metal NPs on MgO were obtained as a result of thorough optimization within the fcc motif using interatomic potentials. Then the stability and properties of the NPs were studied with a density functional method. We comprehensively characterize interaction between the NPs and MgO(100) support, their interface and effect of the support on NP properties. While the effect of MgO on relative stabilities of NPs with different shapes is found to be significant, other properties of the NPs such as electronic structure and interatomic distances within NP do not notably change upon deposition. This work paves the way to large-scale first-principles computational studies of more realistic models of oxide-supported metal catalysts.
Validation of single-fluid and two-fluid magnetohydrodynamic models of the helicity injected torus spheromak experiment with the NIMROD code
Authors: Akcay Cihan , Kim Charlson C. , Victor Brian S. , Jarboe Thomas R.
Published: August 2013

We present a comparison study of 3-D pressureless resistive MHD (rMHD) and 3-D presureless two-fluid MHD models of the Helicity Injected Torus with Steady Inductive helicity injection (HIT-SI). HIT-SI is a current drive experiment that uses two geometrically asymmetric helicity injectors to generate and sustain toroidal plasmas. The comparable size of the collisionless ion skin depth di to the resistive skin depth predicates the importance of the Hall term for HIT-SI. The simulations are run with NIMROD, an initial-value, 3-D extended MHD code. The modeled plasma density and temperature are assumed uniform and constant. The helicity injectors are modeled as oscillating normal magnetic and parallel electric field boundary conditions. The simulations use parameters that closely match those of the experiment. The simulation output is compared to the formation time, plasma current, and internal and surface magnetic fields. Results of the study indicate 2fl-MHD shows quantitative agreement with the experiment while rMHD only captures the qualitative features. The validity of each model is assessed based on how accurately it reproduces the global quantities as well as the temporal and spatial dependence of the measured magnetic fields. 2fl-MHD produces the current amplification ItorIinj and formation time τf demonstrated by HIT-SI with similar internal magnetic fields. rMHD underestimates ItorIinj and exhibits much a longer τf. Biorthogonal decomposition (BD), a powerful mathematical tool for reducing large data sets, is employed to quantify how well the simulations reproduce the measured surface magnetic fields without resorting to a probe-by-probe comparison. BD shows that 2fl-MHD captures the dominant surface magnetic structures and the temporal behavior of these features better than rMHD.
Spatial observation and quantification of microwave heating in materials
Authors: Crane C. A. , Pantoya M. L. , Weeks B. L.
Published: August 2013

An electromagnetic exposure chamber was designed to safely deliver electromagnetic power in the range of microwaves between 0.8 and 4.2 GHz to a thin cylindrical materials. This instrumentation is unique because the diagnostics not only measure sample heating with a response time of 1.3 ms, but also energy transmitted and reflected. Energy absorption at different frequencies was quantified via electromagnetic heating using an infrared camera. This in situ IR imaging of the spatial distribution of temperature during microwave exposure coupled with sensors for determining transmitted and reflected energy enables novel new microwave energy experiments. Samples were exposed to a portion of both the electric and magnetic fields inside a waveguide and based on sample dimensions, the field strengths were assumed uniform across the sample. Three materials were examined: two were borosilicate, first coated with graphite paint and a second without the coating; and, the third was a compressed sample of flake graphite pressed to 69% of its bulk density. Results are in agreement with the theories of microwave heating and verify the functionality of this experimental design. This diagnostic will be important in future tests where a variety of different materials can be exposed to weak electromagnetic waves and their efficiency in coupling to the microwaves can be examined.
A boundary correction algorithm for metadynamics in multiple dimensions
Authors: McGovern Michael , de Pablo Juan
Published: August 2013

Metadynamics is an efficient method for simulation of the free energy of many-particle systems. Over the last several years it has been applied to study a wide variety of systems, ranging from simple fluids to biological macromolecules. The method relies on uniform sampling along specified collective variables or order parameters. Such order parameters, however, are often bounded, and metadynamics algorithms as originally developed suffer from systematic errors at the corresponding boundaries. While several approaches have been proposed in the past to correct these errors for unidimensional systems, no method exists to fully correct these errors in multi-dimensional systems at points where multiple boundaries meet. Here we present a correction scheme that circumvents this limitation.
Ion irradiation of Fe-Fe oxide core-shell nanocluster films: Effect of interface on stability of magnetic properties
Authors: McCloy John S. , Jiang Weilin , Droubay Timothy C. , Varga Tamas , Kovarik Libor , Sundararajan Jennifer A. , Kaur Maninder , Qiang You , Burks Edward C. , Liu Kai
Published: August 2013

A cluster deposition method was used to produce films of loosely aggregated nanoclusters (NCs) of Fe core-Fe3O4 shell or fully oxidized Fe3O4. Films of these NC on Si(100) or MgO(100)/Fe3O4(100) were irradiated to 1016 Si2+/cm2 near room temperature using an ion accelerator. Ion irradiation creates structural change in the NC film with corresponding chemical and magnetic changes which depend on the initial oxidation state of the cluster. Films were characterized using magnetometry (hysteresis, first order reversal curves), microscopy (transmission electron, helium ion), and x-ray diffraction. In all cases, the particle sizes increased due to ion irradiation, and when a core of Fe is present, irradiation reduces the oxide shells to lower valent Fe species. These results show that ion irradiated behavior of the NC films depends strongly on the initial nanostructure and chemistry, but in general saturation magnetization decreases slightly.
Possible surface plasmon polariton excitation under femtosecond laser irradiation of silicon
Authors: Derrien Thibault J.-Y. , Itina Tatiana E. , Torres Rémi , Sarnet Thierry , Sentis Marc
Published: August 2013

The mechanisms of ripple formation on silicon surface by femtosecond laser pulses are investigated. We demonstrate the transient evolution of the density of the excited free-carriers. As a result, the experimental conditions required for the excitation of surface plasmon polaritons are revealed. The periods of the resulting structures are then investigated as a function of laser parameters, such as the angle of incidence, laser fluence, and polarization. The obtained dependencies provide a way of better control over the properties of the periodic structures induced by femtosecond laser on the surface of a semiconductor material.
Discovering real lie subalgebras of $\mathfrak {e}_6$e6 using Cartan decompositions
Authors: Wangberg Aaron , Dray Tevian
Published: August 2013

The process of complexification is used to classify Lie algebras and identify their Cartan subalgebras. However, this method does not distinguish between real forms of a complex Lie algebra, which can differ in signature. In this paper, we show how Cartan decompositions of a complexified Lie algebra can be combined with information from the Killing form to identify real forms of a given Lie algebra. We apply this technique to \documentclass[12pt]{minimal}\begin{document}$\mathfrak {sl}(3,\mathbb {O})$\end{document}sl(3,O), a real form of \documentclass[12pt]{minimal}\begin{document}$\mathfrak {e}_6$\end{document}e6 with signature (52, 26), thereby identifying chains of real subalgebras and their corresponding Cartan subalgebras within \documentclass[12pt]{minimal}\begin{document}$\mathfrak {e}_6$\end{document}e6. Motivated by an explicit construction of \documentclass[12pt]{minimal}\begin{document}$\mathfrak {sl}(3,\mathbb {O})$\end{document}sl(3,O), we then construct an Abelian group of order 8 which acts on the real forms of \documentclass[12pt]{minimal}\begin{document}$\mathfrak {e}_6$\end{document}e6, leading to the identification of 8 particular copies of the 5 real forms of \documentclass[12pt]{minimal}\begin{document}$\mathfrak {e}_6$\end{document}e6, which can be distinguished by their relationship to the original copy of \documentclass[12pt]{minimal}\begin{document}$\mathfrak {sl}(3,\mathbb {O})$\end{document}sl(3,O).
Dynamics of the Zakharov-Kuznetsov-Burgers equations in dusty plasmas
Authors: Zhen Hui-Ling , Tian Bo , Zhong Hui , Sun Wen-Rong , Li Min
Published: August 2013

In this paper, we investigate the Zakharov-Kuznetsov-Burgers (ZKB) equations for the dust-ion-acoustic waves in dusty plasmas. Shock-like and soliton solutions are both constructed through the introduction of an auxiliary function and variable. ZKB-soliton propagation is plotted, and from those figures, we find that energy of the solitons increases when the number of electrons in a dust particle decreases or the mass of such dust particle becomes larger. Considering the external perturbations in the dusty plasmas, we study the perturbed ZKB equation via some qualitative and quantitative methods. To corroborate that the perturbed ZKB equation can indeed give rise to the chaos, we make use of the power spectrum and Lyapunov exponents. Then, we investigate the phase projections, and find that both the weak and developed chaos can be observed. Weak chaos occur when the absolute value of damped coefficient (l1) is stronger than the strength of perturbed term (g1), or else, the developed one occurs. Ranges of l1 and g1 are given via the largest Lyapunov exponents when the perturbed ZKB equation is in different chaotic states. Therefore, we can find that the chaotic motion of the perturbed ZKB equation will be enhanced with the number of electrons in a dust particle or the mass of such a dust particle decreasing.
Side chain fluorination and anion effect on the structure of 1-butyl-3-methylimidazolium ionic liquids
Authors: Weber Henry , Hollóczki Oldamur , Pensado Alfonso S. , Kirchner Barbara
Published: August 2013

We present a comprehensive molecular dynamics simulation study on 1-butyl-3-methylimidazolium ionic liquids and their fluorinated analogs. The work focused on the effect of fluorination at varying anions. The main findings are that the fluorination of the cations side chain increases overall structuring, especially the aggregation of cation side chain. Furthermore, large and weakly coordinating anions tend to occupy on-top positions of the cation and decrease the aggregation of cation side chains, most likely due to enhanced alkyl-anion interaction.
Nonlinear scattering term in the gyrokinetic Vlasov equation
Authors: Wang Shaojie
Published: August 2013

Nonlinear scattering term is found from the nonlinear gyrokinetic equation by decoupling the perturbed gyrocenter motion from the unperturbed motion. The gyro-center distribution function is determined by the well-understood unperturbed motion, with the effects of fields perturbation included in the nonlinear scattering term, which explicitly reveals the nonlinear stochastic dissipation on the time scale longer than the wave correlation time.
Phonon mediated loss in a graphene nanoribbon
Authors: Kunal K. , Aluru N. R.
Published: August 2013

Periodic stretching of a string, under adiabatic condition (no thermal coupling with the environment), will increase its temperature. This represents the case of intrinsic damping where the energy associated with stretching motion is converted into thermal energy. We study this phenomenon in a graphene nanoribbon (GNR), a nano-string. We utilize classical molecular dynamics and study the scaling of dissipation rate (Q factor) with frequency. The dissipation is shown to result from strong non-linear coupling between the stretching vibration and the out-of-plane thermal phonons. A Langevin dynamics framework is developed to describe the out-of-plane phonon dynamics under in-plane stretching. The dissipation mechanism is analyzed using this framework. From the analysis, a bi-relaxation time model is obtained to explain the observed scaling of Q factor with frequency. We also compute the size and temperature dependence of Q factor. The decrease in Q factor with decrease in size (width) is shown to result from the elastic softening of GNR.