bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear vibration of a single-walled carbon nanotube embedded in a polymer matrix aroused by interfacial van der Waals forces
Authors: Mahdavi M. H. , Jiang L. Y. , Sun X.
Published: December 2009

This paper studies the nonlinear vibration of a single-walled carbon nanotube (CNT) embedded in a polymer matrix aroused by van der Waals (vdW) forces using elastic beam models. The interfacial vdW forces are described by a nonlinear function in terms of the deflection of the CNT. According to different beam end conditions, the relation between deflection amplitudes and resonant frequencies of free vibrations of the CNT is derived through harmonic balance method. This relation is found to be sensitive to end conditions, diameters, and lengths of the embedded CNT. The axial load effect upon the vibrational behavior of the CNT and postbuckling of the embedded CNT are also discussed. Due to the influence of the surrounding polymer, the prediction on the critical buckling loads and resonant frequencies for embedded CNTs is quite different from that for free-standing CNTs. In addition, the applicability and accuracy of both Euler–Bernoulli and Timoshenko beam models are investigated. It is found that the Euler–Bernoulli beam model may provide comparable results as the Timoshenko beam model even for CNTs with smaller length-to-diameter ratios due to the constraint from the surrounding medium.
Ordering induced direct-indirect transformation in unstrained GaxIn1−xP for 0.76≤x≤0.78
Authors: Bhusal L. , Fluegel B. , Steiner M. A. , Mascarenhas A.
Published: December 2009

Ga x In 1 − x P alloys grown by metalorganic vapor phase epitaxy (MOVPE) are known to exhibit spontaneous long-range ordering that results in a modification of the alloy electronic band structure. Using time resolved and time integrated photoluminescence studies at 9 K, we demonstrate that the change in alloy ordering in GaxIn1−xP alloys can transform the conduction to valence band optical transition from direct to indirect for a given Ga concentration. This finding may enable sequential growth of alternate layers of high bandgap direct and indirect semiconductor alloys with similar lattice constants, opening various possibilities for device applications.
Coarse-grained molecular dynamics study of block copolymer/nanoparticle composites under elongational flow
Authors: Kalra Vibha , Joo Yong Lak
Published: December 2009

Symmetric diblock copolymer/nanoparticle (NP) systems under planar elongational flow have been modeled and simulated using coarse-grained nonequilibrium molecular dynamics. The aim of our present study is to understand how the dispersion of NPs in a block copolymer system is influenced by elongational flow and how the presence of NPs changes the rheology and flow-induced morphology transition in block copolymers. We consider two different kinds of spherical NPs categorized with respect to their interaction potential with the polymeric blocks: (1) selective NPs that show a preference toward one of the blocks of a model diblock copolymer and (2) nonselective NPs that show equal attraction toward both blocks. For unrestricted simulation times during elongational flow, spatially and temporally periodic boundary conditions devised by Kraynik and Reinelt [Int. J. Multiphase Flow 18, 1045 (1992)] have been implemented. Our results show that the concentration peak of both selective NPs at the center of the preferred domain and nonselective NPs at the domain interface becomes broader with increasing elongation rate, suggesting that elongational flow can be used as another parameter to control nanocomposite self-assembly. In addition, our results reveal that the onset of flow-induced transition from lamellar to disordered morphology is greatly influenced by particle-particle and particle-polymer interactions.
Half integer quantum Hall effect in high mobility single layer epitaxial graphene
Authors: Wu Xiaosong , Hu Yike , Ruan Ming , Madiomanana Nerasoa K , Hankinson John , Sprinkle Mike , Berger Claire , de Heer Walt A.
Published: December 2009

The quantum Hall effect, with a Berry’s phase of π is demonstrated here on a single graphene layer grown on the C-face of 4H silicon carbide. The mobility is ∼20 000 cm2/V⋅s at 4 K and 15 000 cm2/V⋅s at 300 K despite contamination and substrate steps. This is comparable to the best exfoliated graphene flakes on SiO2 and an order of magnitude larger than Si-face epitaxial graphene monolayers. These and other properties indicate that C-face epitaxial graphene is a viable platform for graphene-based electronics.
A selective integrated tempering method
Authors: Yang Lijiang , Qin Gao Yi
Published: December 2009

In this paper, based on the integrated tempering sampling we introduce a selective integrated tempering sampling (SITS) method for the efficient conformation sampling and thermodynamics calculations for a subsystem in a large one, such as biomolecules solvated in aqueous solutions. By introducing a potential surface scaled with temperature, the sampling over the configuration space of interest (e.g., the solvated biomolecule) is selectively enhanced but the rest of the system (e.g., the solvent) stays largely unperturbed. The applications of this method to biomolecular systems allow highly efficient sampling over both energy and configuration spaces of interest. Comparing to the popular and powerful replica exchange molecular dynamics (REMD), the method presented in this paper is significantly more efficient in yielding relevant thermodynamics quantities (such as the potential of mean force for biomolecular conformational changes in aqueous solutions). It is more important that SITS but not REMD yielded results that are consistent with the traditional umbrella sampling free energy calculations when explicit solvent model is used since SITS avoids the sampling of the irrelevant phase space (such as the boiling water at high temperatures).
Dissociation of water on oxygen-covered Rh{111}
Authors: Shavorskiy A. , Eralp T. , Ataman E. , Isvoranu C. , Schnadt J. , Andersen J. N. , Held G.
Published: December 2009

The adsorption of water and coadsorption with oxygen on Rh{111} under ultrahigh vacuum conditions was studied using synchrotron-based photoemission and photoabsorption spectroscopy. Water adsorbs intact on the clean surface at temperatures below 154 K. Irradiation with x-rays, however, induces fast dissociation and the formation of a mixed OH+H2O layer indicating that the partially dissociated layer is thermodynamically more stable. Coadsorption of water and oxygen at a coverage below 0.3 monolayers has a similar effect, leading to the formation of a hydrogen-bonded network of water and hydroxyl molecules at a ratio of 3:2. The partially dissociated layers are more stable than chemisorbed intact water with the maximum desorption temperatures up to 30 K higher. For higher oxygen coverage, up to 0.5 monolayers, water does not dissociate and an intact water species is observed above 160 K, which is characterized by an O 1s binding energy 0.6 eV higher than that of chemisorbed water and a high desorption temperature similar to the partially dissociated layer. The extra stabilization is most likely due to hydrogen bonds with atomic oxygen.
Surface profile-controlled close-packed Si nanorod arrays for self-cleaning antireflection coatings
Authors: Lin Yi-Ruei , Wang Hsin-Ping , Lin Chin-An , He Jr-Hau
Published: December 2009

We demonstrate the fabrication of surface profile-controlled close-packed Si nanorod arrays (NRAs), using a scalable and integrated circuit compatible process combining colloidal lithography and reactive ion etching. Si NRAs exhibit broadband, omnidirectional, and polarization-insensitive antireflection (AR) properties and enhance the hydrophobicity. The effect of surface profiles of periodic NRAs on the AR and hydrophobicity was investigated systematically. The Si NRAs function as both self-cleaning and AR layers, which offer a promising approach to enhance the solar cell energy conversion efficiency.
Substrate effects on the interface electronic properties of organic photovoltaic devices with an inverted C60/CuPc junction
Authors: Ng T. W. , Lo M. F. , Liu Z. T. , Wong F. L. , Lai S. L. , Fung M. K. , Lee C. S. , Lee S. T.
Published: December 2009

Deposition sequence and substrate work function in controlling the interface energy level alignment in organic photovoltaic (OPV) devices with copper phthalocyanine (CuPc) as the donor and fullerene (C60) as the acceptor were studied using ultraviolet photoelectron spectroscopy. We found that the energy offset at the highest occupied molecular orbital of donor (HOMOD) and the lowest unoccupied orbital of acceptor (LUMOA), which limits the maximum open-circuit voltage of heterojunction OPV, can be changed from 0.64 (C60 on CuPc) to 0.86 eV (CuPc on C60) by reversing the deposition sequence. Furthermore, by controlling the substrate work function from 2.81 to 5.07 eV, the LUMOA-HOMOD offset can be effectively tuned from 0.86 to 1.27 eV. The results suggest that electrodes in OPV devices can have significant influences on the electronic structures and energy levels of the donor/acceptor interface, and thus provide a viable means for performance enhancement.
The calculation of the static first and second susceptibilities of crystalline urea: A comparison of Hartree–Fock and density functional theory results obtained with the periodic coupled perturbed Hartree–Fock/Kohn–Sham scheme
Authors: Ferrero Mauro , Civalleri Bartolomeo , Rérat Michel , Orlando Roberto , Dovesi Roberto
Published: December 2009

The static polarizability α and first hyperpolarizability β tensors of crystalline urea and the corresponding first-(χ(1)) and second-(χ(2)) susceptibilities are calculated and compared to the same quantities obtained for the molecule by using the same code (a development version of CRYSTAL), basis set, and level of theory. In order to separate geometrical and solid state effects, two geometries are considered for the molecule in its planar conformation: (i) as cut out from the bulk structure and (ii) fully optimized. First, the effect of basis sets on computed properties is explored at the B3LYP level by employing basis sets of increasing complexity, from 6-31G(d,p) to 6-311G(2df,2pd) (Pople’s family) and from DZP to QZVPPP (Thakkar/Ahlrichs/Dunning’s family) on α and β for both the molecule and the bulk. Then, five different levels of theory, namely, SVWN (local density approximation), PBE (generalized gradient approximation), PBE0 and B3LYP (hybrid), and Hartree–Fock are compared in combination with a TZPP basis set. Present results show that hybrid methods, in particular, B3LYP, are remarkably successful in predicting correctly both the first and second susceptibilities of urea bulk when combined at least with a triple-zeta quality basis set containing a double set of polarization functions. It is also shown that diffuse functions that are needed for molecular calculations are less crucial for the crystalline structure, as expected. Indeed, B3LYP/TZPP computed χ(1) and χ(2) tensor components (χaa(1)=1.107, χcc(1)=1.459, and χ(2)=−0.93 a.u.) are in very good agreement with experimental values. At variance with respect to previous periodic ab initio calculations, but in agreement with recent supermolecular results, the negative sign of χ(2) is confirmed. Overall, static linear and nonlinear optical properties such as dielectric constants, refractive, and birefringence indices and second-harmonic generation coefficient of crystalline urea are very well reproduced by present calculations.
Fabrication of controlled volume scattering medium in poly(methyl methacrylate) by focused femtosecond laser pulses
Authors: Matoba Osamu , Kitamura Yuri , Manabe Tomoyuki , Nitta Kouichi , Watanabe Wataru
Published: December 2009

A volume scattering medium was fabricated in a transparent material by focused femtosecond laser pulses. A random distribution of voids fabricated by femotosecond pulsed laser light acted as a volume scattering medium that may be applied to photonic secure data storage. We fabricated a partially random distribution of voids in poly(methyl methacrylate) and then measured the scattering properties. Comparing beam widths of the output intensity distribution through the scattering medium, obtained from both complex amplitude propagation and Monte Carlo simulation, showed that the scattering coefficient can be controlled by the void density.
Fe-based nanocrystalline soft magnetic alloys for high-temperature applications
Authors: Knipling Keith E. , Daniil Maria , Willard Matthew A.
Published: December 2009

We report on improved high-temperature soft magnetic properties in Fe88−2xCoxNixZr7B4Cu1 nanocrystalline alloys. Substituting 5.5 at. % Co and Ni for Fe enhances the magnetization by 5% at ambient temperature and by 30% at 650 °C. The Curie temperature of the residual amorphous phase is also raised significantly (from 67 °C for x=0 to 298 °C for x=5.5), resulting in low coercivities (<30 A m−1) for Fe77Co5.5Ni5.5Zr7B4Cu1 over the temperature range 50–500 °C. The higher magnetization and Curie temperature as compared with other Fe-based alloys, and smaller Co content as compared with (Fe,Co)-based alloys, make this alloy attractive as an affordable high-temperature soft magnetic material.
Microphase separation through competitive hydrogen bonding in self-assembled A-b-B/C diblock copolymer/homopolymer complexes
Authors: Hameed Nishar , Salim Nisa V. , Guo Qipeng
Published: December 2009

We present a study of microphase separation induced by competitive hydrogen bonding in A-b-B/C diblock copolymer/homopolymer complexes where the diblock copolymer A-b-B is immiscible and the homopolymer C can interact unequally with both A and B blocks through hydrogen bonding. A model system containing poly(2-vinyl pyridine)-block-poly(methyl methacrylate) (P2VP-b-PMMA) and poly(4-vinyl phenol) (PVPh) in tetrahydrofuran was investigated. In these self-assembled complexes, microphase separation takes place due to the disparity in intermolecular interactions. Specifically, PVPh and P2VP blocks interact strongly to form complex, whereas PVPh and PMMA blocks interact weakly. The hydrogen bonding interactions were revealed by infrared spectroscopy and analyzed in terms of the difference in interassociation constants (K), i.e., interaction parameters of each blocks of the block copolymer to the homopolymer and according to the random phase approximation. The phase behavior of the complexes was investigated with small-angle x-ray scattering and transmission electron microscopy. A series of morphologies including lamellae, hexagonal cylinders, wormlike microdomains, and hierarchical structures was documented as a function of the copolymer concentration. Moreover, we outlined how hydrogen bonding determines the self-assembly and causes morphological transitions in different A-b-B/C diblock copolymer/homopolymer systems with respect to the K values.
The dynamic formation of low-dimensional inorganic nanotubes by filling carbon nanotubes
Authors: Wilson Mark
Published: December 2009

The filling of groups of carbon nanotubes (CNTs) by a generic molten salt of stoichiometry MX is observed using molecular dynamics computer simulation. The CNTs are grouped in terms of their diameters. The salt fills the CNTs to yield low-dimensional inorganic NT (INT) structures whose morphologies can be understood with reference to the folding of a sheet of percolating hexagons. The use of a relatively simple model to describe the interatomic interactions allows multiple filling events to be observed from the same pressure-temperature state point and so permits a rudimentary statistical analysis (often lacking in experimental investigation) of the formed INT morphologies in terms of fundamental CNT properties. The filling events are characterized in terms of the obtained INT morphologies. The thermodynamic and kinetic factors controlling the INT formation, including potential control over their morphology, are discussed. Kinetics (mechanistic) control is found to be significant compared with entropic effects. The role of the CNTs is discussed in terms of behavior as energy landscape filters. The results indicate that a complete morphological control over INTs formed in this fashion may be problematic even if the encasing CNT morphology can be strongly controlled.
Hierarchical quantum master equation with semiclassical Drude dissipation
Authors: Xu Rui-Xue , Tian Bao-Ling , Xu Jian , Shi Qiang , Yan YiJing
Published: December 2009

We propose a nonperturbative quantum dissipation theory, in term of hierarchical quantum master equation, which may be used with a great degree of confidence to various dynamics systems in condensed phases. The theoretical development is rooted in an improved semiclassical treatment of Drude bath, beyond the conventional high temperature approximations. It leads to the new theory a simple but important improvement over the conventional stochastic Liouville equation theory, without extra numerical cost. Its broad range of validity and applicability is extensively demonstrated with two-level electron transfer model systems, where the new theory can be considered as the modified Zusman equation. Criterion is also proposed to estimate the performance of the hierarchical quantum master equation.
A singularity free surface hopping expansion for the multistate wave function
Authors: Herman Michael F.
Published: December 2009

A version of a surface hopping wave function for nonadiabatic multistate problems, which is free of turning point singularities, is derived and tested. The primitive semiclassical form of the particular surface hopping method considered has been shown to be highly accurate, even for classically forbidden processes. However, this semiclassical wave function displays the usual singular behavior at turning points and caustics in the classical motion. Numerical data has shown that this somewhat reduces its accuracy when the energy is near the crossing energy of the diabatic electronic surfaces. The singularity free version of this surface hopping wave function is derived by partitioning the x-axis into a large number of small steps for one dimensional problems. The adiabatic electronic energy surfaces are approximated to be linear functions within each step. The matching conditions required by the continuity of the wave function and its derivative at each step boundary provide the needed conditions to obtain the amplitudes for changes in electronic state and/or reflection of the trajectory for the motion of the nuclei. This leads to a form of the surface hopping wave function that is free of turning point singularities. The method is tested for a one dimensional model problem, and it is found to be highly accurate at all energies considered, even when the energy is near the crossing energy.
Nonlinear refractive index and three-photon absorption coefficient of poly(9,9-dioctylfluorence)
Authors: Jang J. I. , Mani S. , Ketterson J. B. , Lovera P. , Redmond G.
Published: December 2009

We investigate the optical Kerr effect and third harmonic generation (THG) arising from χ(3) of poly(9,9-dioctylfluorence), which is an emerging organic π-conjugated polymer from the perspective of diverse optoelectronic applications. The measured nonlinear refractive index, obtained with closed-aperture Z-scan, is n2=(2.04±0.10)×10−12 esu at λ=1540 nm. Open-aperture Z-scan yields the three-photon absorption coefficient of γ=(1.88±0.26)×10−3 cm3/GW2 at λ=1064 nm, arising from χ(5) response. The wavelength-dependent THG indicates that this semiconducting polymer can be a potentially useful polymer system for nonlinear-optics applications involving high-order optical processes in the mid-IR range.
Control of polarization and dipole moment in low-dimensional semiconductor nanostructures
Authors: Li L. H. , Mexis M. , Ridha P. , Bozkurt M. , Patriarche G. , Smowton P. M. , Blood P. , Koenraad P. M. , Fiore A.
Published: December 2009

We demonstrate the control of polarization and dipole moment in semiconductor nanostructures, through nanoscale engineering of shape and composition. Rodlike nanostructures, elongated along the growth direction, are obtained by molecular beam epitaxial growth. By varying the aspect ratio and compositional contrast between the rod and the surrounding matrix, we rotate the polarization of the dominant interband transition from transverse-electric to transverse-magnetic, and modify the dipole moment producing a radical change in the voltage dependence of absorption spectra. This opens the way to the optimization of quantum dot amplifiers and electro-optical modulators.
Front waves and complex spatiotemporal patterns in a reaction-diffusion-convection system with thermokinetic autocatalysis
Authors: Trávníčková Tereza , Kohout Martin , Schreiber Igor , Kubíček Milan
Published: December 2009

We analyze dynamics of stationary nonuniform patterns, traveling waves, and spatiotemporal chaos in a simple model of a tubular cross-flow reactor. The reactant is supplied continuously via convective flow and/or by diffusion through permeable walls of the reactor. First order exothermic reaction kinetics is assumed and the system is described by mass and energy balances forming coupled reaction-diffusion-convection equations. Dynamical regimes of the reaction-diffusion subsystem range from pulses and fronts to periodic waves and complex chaotic behavior. Two distinct types of chaotic patterns are identified and characterized by Lyapunov dimension. Next we examine the effects of convection on various types of the reaction-diffusion regimes. Remarkable zigzag fronts and steady state patterns are found despite the absence of differential flow. We employ continuation techniques to elucidate the existence and form of these patterns.
Absolute free energies and equilibrium ensembles of dense fluids computed from a nondynamic growth method
Authors: Bhatt Divesh , Zuckerman Daniel M.
Published: December 2009

We demonstrate a nondynamical Monte Carlo method to compute free energies and generate equilibrium ensembles of dense fluids. In this method, based on step-by-step polymer growth algorithms, an ensemble of n+1 particles is obtained from an ensemble of n particles by generating configurations of the n+1st particle. A statistically rigorous resampling scheme is utilized to remove configurations with low weights and to avoid a combinatorial explosion; the free energy is obtained from the sum of the weights. In addition to the free energy, the method generates an equilibrium ensemble of the full system. We consider two different system sizes for a Lennard-Jones fluid and compare the results with conventional Monte Carlo methods.
Epidemics with multistrain interactions: The interplay between cross immunity and antibody-dependent enhancement
Authors: Bianco Simone , Shaw Leah B. , Schwartz Ira B.
Published: December 2009

This paper examines the interplay of the effect of cross immunity and antibody-dependent enhancement (ADE) in multistrain diseases. Motivated by dengue fever, we study a model for the spreading of epidemics in a population with multistrain interactions mediated by both partial temporary cross immunity and ADE. Although ADE models have previously been observed to cause chaotic outbreaks, we show analytically that weak cross immunity has a stabilizing effect on the system. That is, the onset of disease fluctuations requires a larger value of ADE with small cross immunity than without. However, strong cross immunity is shown numerically to cause oscillations and chaotic outbreaks even for low values of ADE.
Computer simulation of water-mediated forces between gel-phase phospholipid bilayers
Authors: Pertsin Alexander , Fedyanin Ivan , Grunze Michael
Published: December 2009

Water-mediated forces between gel-phase phospholipid bilayers were calculated as a function of interbilayer separation using the grand canonical Monte Carlo technique and all-atom CHARMM force field. The mechanism of the short-range interbilayer repulsion proved to be similar to that calculated previously for the fluid-phase bilayers despite substantial differences in structure and areal density between the gel and fluid phases.
Two-photon excited fluorescence from CdSe quantum dots on SiN photonic crystals
Authors: Xu Xingsheng , Yamada Toshiki , Ueda Rieko , Otomo Akira
Published: December 2009

Two-photon excited fluorescence from CdSe quantum dots on a two-dimensional SiN photonic crystal surface is investigated by using a femtosecond laser. By using a photonic crystal, a 90-fold enhancement in the two-photon excited fluorescence in the vertical direction is achieved. This is the highest enhancement achieved so far in the two-photon excited fluorescence in the vertical direction. The mechanism of the enhancement for two-photon excited fluorescence from quantum dots on photonic crystals is analyzed.
Noninvasive metal contacts in chemically derived graphene devices
Authors: Sundaram Ravi S. , Gomez-Navarro Cristina , Lee Eduardo J. H. , Burghard Marko , Kern Klaus
Published: December 2009

We study the properties of gold contacts on chemically derived graphene devices by scanning photocurrent microscopy and gate-dependent electrical transport measurements. In the as-fabricated devices, negligible potential barriers are found at the gold/graphene interface, reflecting the noninvasive character of the contacts. Device annealing above 300 °C leads to the formation of potential barriers at the contacts concomitant with metal-induced p-type doping of the sheet as a consequence of the diffusion of gold from the electrodes. The transfer characteristics of the chemically derived graphene devices point toward the suppression of Klein tunneling in this material.
Effective condensation coefficient on a nanoparticle
Authors: Yang Hoe-Jin , Lee Ki-Hyun , Choi Min-Seok , Yi Min-Young , Lee Jin-Won
Published: December 2009

Condensation of Ar gas on a nanosized Ar particle was analyzed using a molecular dynamics (MD) simulation, with the results presented in terms of instantaneous condensation coefficient as a function of particle temperature and gas pressure and temperature. Gas temperature was kept constant, but the size and temperature of the particle were allowed to change due to condensation. The calculated condensation coefficient was sensitive to the instantaneous particle temperature and initial gas pressure, but was insensitive to gas temperature. MD results agree well with the kinetic model if the vapor pressure corresponding to the critical supersaturation was used instead of the equilibrium saturation pressure.
Microporous SiO2 with huge electric-double-layer capacitance for low-voltage indium tin oxide thin-film transistors
Authors: Lu Aixia , Sun Jia , Jiang Jie , Wan Qing
Published: December 2009

Electric-double-layer (EDL) effect is observed in microporous SiO2 dielectric films deposited at room temperature by plasma-enhanced chemical vapor deposition method. Indium tin oxide thin-film transistors gated by such microporous SiO2 gate dielectric are fabricated at room temperature, and a low operating voltage of 1.5 V is obtained due to the huge EDL specific capacitance (2.14 μF/cm2). The field-effect electron mobility is estimated to be 118 cm2 V−1 s−1. Current on/off ratio and subthreshold gate voltage swing are estimated to be 5×106 and 92 mV/decade, respectively. Room-temperature deposited microporous SiO2 dielectric is promising for low-power field-effect transistors on temperature sensitive substrates.
Time-resolved studies of a rolled-up semiconductor microtube laser
Authors: Strelow Ch. , Sauer M. , Fehringer S. , Korn T. , Schüller C. , Stemmann A. , Heyn Ch. , Heitmann D. , Kipp T.
Published: December 2009

We report on lasing in rolled-up microtube resonators. Time-resolved studies on these semiconductor lasers containing GaAs quantum wells as optical gain material reveal particularly fast turn-on times and short pulse emissions above the threshold. We observe a strong redshift of the laser mode during the pulse emission which is compared to the time evolution of the charge-carrier density calculated by rate equations.
Augmented stability of hydrogen clathrate hydrates by weakly polar molecules
Authors: Nakayama Takato , Koga Kenichiro , Tanaka Hideki
Published: December 2009

Thermodynamic stability of hydrogen clathrate hydrates has been examined in a wide range of pressure based solely on the intermolecular interactions involved. We show that the stability is indeed augmented by a second guest species (here acetone) called a promoter, a consequence of which is notable reduction in the dissociation pressure of the hydrates encaging hydrogen alone. This evaluation is made by extension of the van der Waals–Platteeuw theory combined with semi-grand-canonical Monte Carlo (GCMC) simulations where the number of hydrogen molecules is allowed to vary while those of host water and promoter acetone molecules are fixed. The GCMC simulations then provide various types of cage occupancies of hydrogen from single to quadruple, from which the chemical potential of water in the clathrate hydrate is obtained as a function of the cage occupancy by acetone and the pressure. These occupancies are used to calculate the chemical potential of water in the clathrate hydrate. The stability is estimated by comparison of the chemical potential of water in the clathrate hydrate with that in hexagonal ice. We show the extent to which the dissociation pressure is reduced with increasing the occupancy of the larger cages by acetone.
Continuum remover-complex absorbing potential: Efficient removal of the nonphysical stabilization points
Authors: Sajeev Y. , Vysotskiy V. , Cederbaum L. S. , Moiseyev N.
Published: December 2009

By adding a negative imaginary potential of variable strength η to the Hamiltonian, the resonance state of a system can be found as complex energy stabilized points in the η-trajectories of the eigenvalues. One problem that arises in practical calculations is the appearance of nonphysical complex energy stabilized points. A new method for separating the physical from the nonphysical complex energy stabilized points is proposed. The method is best illustrated with strongly correlated two-electron systems.
In situ observation of secondary phase formation in Fe implanted GaN annealed in low pressure N2 atmosphere
Authors: Talut G. , Grenzer J. , Reuther H. , Shalimov A. , Baehtz C. , Novikov D. , Walz B.
Published: December 2009

The formation of secondary phases in Fe implanted GaN upon annealing in low pressure N2-atmosphere was detected by means of in situ x-ray diffraction and confirmed by magnetization measurements. A repeatable phase change from Fe3N at room temperature and Fe3−xN at 1023 K was observed in situ. The phase transformation is explained by the change of lattice site and concentration of nitrogen within nitrides. The diffusion of Fe toward sample surface and oxidation with increasing annealing cycles limits the availability of secondary phase and hence the repeatability. At high temperature GaN dissolves and Ga as well as Fe oxidize due to presence of residual oxygen in the process gas. The ferromagnetism in the samples is related to nanometer sized interacting Fe3−xN crystallites.
Investigation of both local and global topological ingredients on transport efficiency in scale-free networks
Authors: Huang Wei , Chow Tommy W. S.
Published: December 2009

This paper investigates the combined effect of local and global topological ingredients for routing packets on transport efficiency in scale-free networks with different degree exponents. Four different transport efficiency measurements, namely, the critical packet generation rate, the average number of overall packet loads, the relative variance of packet number on each node, and the relative variance of transport time from source to destination, are investigated in this paper. The combined effects of global and local ingredients on four measurements are presented and analyzed. We also investigate the effect of degree exponent on four measurements. Based on the results we obtained, we propose an improved routing strategy with memory information. Simulation results show that the critical packet generation rate can be efficiently improved by using the improved routing strategy with memory information, especially when packets are showing strong inclination of being forwarded to low-degree or high-degree nodes in scale-free networks with small degree exponents.
Protein mechanical unfolding: Importance of non-native interactions
Authors: Kouza Maksim , Hu Chin-Kun , Zung Hoang , Li Mai Suan
Published: December 2009

Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin (DDFLN4) was studied by all-atom molecular dynamics simulations, using the GROMOS96 force field 43a1 and the simple point charge explicit water solvent. Our study reveals an important role of non-native interactions in the unfolding process. Namely, the existence of a peak centered at the end-to-end extension ΔR∼22 nm in the force-extension curve is associated with breaking of non-native hydrogen bonds. Such a peak has been observed in experiments but not in Go models, where non-native interactions are neglected. We predict that an additional peak occurs at ΔR∼2 nm using not only GROMOS96 force field 43a1 but also Amber 94 and OPLS force fields. This result would stimulate further experimental studies on elastic properties of DDFLN4.
Phosphorylation by Cdk2 is required for Myc to repress Ras-induced senescence in cotransformation
Authors: Hydbring Per , Bahram Fuad , Su Yingtao , Tronnersjö Susanna , Högstrand Kari , von der Lehr Natalie , Sharifi Hamid Reza , Lilischkis Richard , Hein Nadine , Wu Siqin , Vervoorts Jörg , Henriksson Marie , Grandien Alf , Lüscher Bernhard , Larsson Lars-Gunnar
Published: December 2009

The
MYC
and
RAS
oncogenes are frequently activated in cancer and, together, are sufficient to transform rodent cells. The basis for this cooperativity remains unclear. We found that although Ras interfered with Myc-induced apoptosis, Myc repressed Ras-induced senescence, together abrogating two main barriers of tumorigenesis. Inhibition of cellular senescence required phosphorylation of Myc at Ser-62 by cyclin E/cyclin-dependent kinase (Cdk) 2. Cdk2 interacted with Myc at promoters, where it affected Myc-dependent regulation of genes, including
Bmi-1
,
p16
,
p21
, and
hTERT
, which encode proteins known to control senescence. Repression of senescence by Myc was abrogated by the Cdk inhibitor p27Kip1, which is induced by antiproliferative signals like IFN-γ or by pharmacological inhibitors of Cdk2 but not by inhibitors of other Cdks. In contrast, a phospho-mimicking Myc-S62D mutant was resistant to these manipulations. Inhibition of cyclin E/Cdk2 reversed the senescence-associated gene expression pattern imposed by Myc/cyclin E/Cdk2. This indicates a role of Cdk2 as a transcriptional cofactor and activator of the antisenescence function of Myc and provides mechanistic insight into the Myc-p27Kip1 antagonism. Finally, our findings highlight that pharmacological inhibition of Cdk2 activity is a potential therapeutical principle for cancer therapy, in particular for tumors with activated Myc or Ras.
Cardiac and vascular functions of the zebrafish orthologues of the type I neurofibromatosis gene
NFI
Authors: Padmanabhan Arun , Lee Jeong-Soo , Ismat Fraz A. , Lu Min Min , Lawson Nathan D. , Kanki John P. , Look A. Thomas , Epstein Jonathan A.
Published: December 2009

Von Recklinghausen neurofibromatosis is a common autosomal dominant genetic disorder characterized by benign and malignant tumors of neural crest origin. Significant progress in understanding the pathophysiology of this disease has occurred in recent years, largely aided by the development of relevant animal models. Von Recklinghausen neurofibromatosis is caused by mutations in the
NF1
gene, which encodes neurofibromin, a large protein that modulates the activity of Ras. Here, we describe the identification and characterization of zebrafish
nf1a
and
nf1b
, orthologues of
NF1
, and show neural crest and cardiovascular defects resulting from morpholino knockdown, including vascular and cardiac valvular abnormalities. Development of a zebrafish model of von Recklinghausen neurofibromatosis will allow for structure-function analysis and genetic screens in this tractable vertebrate system.
Isolated C-terminal tail of FGF23 alleviates hypophosphatemia by inhibiting FGF23-FGFR-Klotho complex formation
Authors: Goetz Regina , Nakada Yuji , Hu Ming Chang , Kurosu Hiroshi , Wang Lei , Nakatani Teruyo , Shi Mingjun , Eliseenkova Anna V. , Razzaque Mohammed S. , Moe Orson W. , Kuro-o Makoto , Mohammadi Moosa
Published: December 2009

Fibroblast growth factor (FGF) 23 inhibits renal phosphate reabsorption by activating FGF receptor (FGFR) 1c in a Klotho-dependent fashion. The phosphaturic activity of FGF23 is abrogated by proteolytic cleavage at the RXXR motif that lies at the boundary between the FGF core homology domain and the 72-residue-long C-terminal tail of FGF23. Here, we show that the soluble ectodomains of FGFR1c and Klotho are sufficient to form a ternary complex with FGF23 in vitro. The C-terminal tail of FGF23 mediates binding of FGF23 to a de novo site generated at the composite FGFR1c-Klotho interface. Consistent with this finding, the isolated 72-residue-long C-terminal tail of FGF23 impairs FGF23 signaling by competing with full-length ligand for binding to the binary FGFR-Klotho complex. Injection of the FGF23 C-terminal tail peptide into healthy rats inhibits renal phosphate excretion and induces hyperphosphatemia. In a mouse model of renal phosphate wasting attributable to high FGF23, the FGF23 C-terminal peptide reduces phosphate excretion, leading to an increase in serum phosphate concentration. Our data indicate that proteolytic cleavage at the RXXR motif abrogates FGF23 activity by a dual mechanism: by removing the binding site for the binary FGFR-Klotho complex that resides in the C-terminal region of FGF23, and by generating an endogenous inhibitor of FGF23. We propose that peptides derived from the C-terminal tail of FGF23 or peptidomimetics and small-molecule organomimetics of the C-terminal tail can be used as therapeutics to treat renal phosphate wasting.
PDGF-A interactions with fibronectin reveal a critical role for heparan sulfate in directed cell migration during
Xenopus
gastrulation
Authors: Smith Erin M. , Mitsi Maria , Nugent Matthew A. , Symes Karen
Published: December 2009

Platelet-derived growth factor (PDGF) signaling is essential for processes involving cell motility and differentiation during embryonic development in a wide variety of organisms including the mouse, frog, zebrafish, and sea urchin. In early
Xenopus laevis
embryos, PDGF-AA provides guidance cues for the migration of anterior mesendoderm cells as they move across a fibronectin-rich extracellular matrix. The long form of PDGF-A includes a positively charged carboxyl-terminal retention motif that can interact with the extracellular matrix and heparan sulfate proteoglycans (HSPGs). In this study we demonstrate that PDGF-AA binds directly to fibronectin and that this association is greatly enhanced by heparin. The PDGF-AA-fibronectin binding occurs across a broad range of pHs (5.5–9), which is significant because the PDGF-guided migration of
Xenopus
mesendoderm cells occurs under basic extracellular conditions (pH 8.4). We further demonstrate that endogenous HSPG's are required for the PDGF-AA-guided mesendoderm movement, suggesting an in vivo role for HSPGs in mediating the interaction between PDGF-AA and fibronectin.
Functional muscle regeneration with combined delivery of angiogenesis and myogenesis factors
Authors: Borselli Cristina , Storrie Hannah , Benesch-Lee Frank , Shvartsman Dmitry , Cezar Christine , Lichtman Jeff W. , Vandenburgh Herman H. , Mooney David J.
Published: December 2009

Regenerative efforts typically focus on the delivery of single factors, but it is likely that multiple factors regulating distinct aspects of the regenerative process (e.g., vascularization and stem cell activation) can be used in parallel to affect regeneration of functional tissues. This possibility was addressed in the context of ischemic muscle injury, which typically leads to necrosis and loss of tissue and function. The role of sustained delivery, via injectable gel, of a combination of VEGF to promote angiogenesis and insulin-like growth factor-1 (IGF1) to directly promote muscle regeneration and the return of muscle function in ischemic rodent hindlimbs was investigated. Sustained VEGF delivery alone led to neoangiogenesis in ischemic limbs, with complete return of tissue perfusion to normal levels by 3 weeks, as well as protection from hypoxia and tissue necrosis, leading to an improvement in muscle contractility. Sustained IGF1 delivery alone was found to enhance muscle fiber regeneration and protected cells from apoptosis. However, the combined delivery of VEGF and IGF1 led to parallel angiogenesis, reinnervation, and myogenesis; as satellite cell activation and proliferation was stimulated, cells were protected from apoptosis, the inflammatory response was muted, and highly functional muscle tissue was formed. In contrast, bolus delivery of factors did not have any benefit in terms of neoangiogenesis and perfusion and had minimal effect on muscle regeneration. These results support the utility of simultaneously targeting distinct aspects of the regenerative process.
RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in
Arabidopsis thaliana
Authors: Wang Xian-Bing , Wu Qingfa , Ito Takao , Cillo Fabrizio , Li Wan-Xiang , Chen Xuemei , Yu Jia-Lin , Ding Shou-Wei
Published: December 2009

In diverse eukaryotic organisms, Dicer-processed, virus-derived small interfering RNAs direct antiviral immunity by RNA silencing or RNA interference. Here we show that in addition to core dicing and slicing components of RNAi, the RNAi-mediated viral immunity in
Arabidopsis thaliana
requires host RNA-directed RNA polymerase (
RDR
)
1
or
RDR6
to produce viral secondary siRNAs following viral RNA replication-triggered biogenesis of primary siRNAs. We found that the two antiviral RDRs exhibited specificity in targeting the tripartite positive-strand RNA genome of cucumber mosaic virus (CMV). RDR1 preferentially amplified the 5′-terminal siRNAs of each of the three viral genomic RNAs, whereas an increased production of siRNAs targeting the 3′ half of RNA3 detected in
rdr1
mutant plants appeared to be RDR6-dependent. However, siRNAs derived from a single-stranded 336-nucleotide satellite RNA of CMV were not amplified by either antiviral RDR, suggesting avoidance of the potent RDR-dependent silencing as a strategy for the molecular parasite of CMV to achieve preferential replication. Our work thus identifies a distinct mechanism for the amplification of immunity effectors, which together with the requirement for the biogenesis of endogenous siRNAs, may play a role in the emergence and expansion of eukaryotic RDRs.
Epimorphic regeneration approach to tissue replacement in adult mammals
Authors: Agrawal Vineet , Johnson Scott A. , Reing Janet , Zhang Li , Tottey Stephen , Wang Gang , Hirschi Karen K. , Braunhut Susan , Gudas Lorraine J. , Badylak Stephen F.
Published: December 2009

Urodeles and fetal mammals are capable of impressive epimorphic regeneration in a variety of tissues, whereas the typical default response to injury in adult mammals consists of inflammation and scar tissue formation. One component of epimorphic regeneration is the recruitment of resident progenitor and stem cells to a site of injury. Bioactive molecules resulting from degradation of extracellular matrix (ECM) have been shown to recruit a variety of progenitor and stem cells
in vitro
in adult mammals. The ability to recruit multipotential cells to the site of injury by
in vivo
administration of chemotactic ECM degradation products in a mammalian model of digit amputation was investigated in the present study. Adult, 6- to 8-week-old C57/BL6 mice were subjected to midsecond phalanx amputation of the third digit of the right hind foot and either treated with chemotactic ECM degradation products or left untreated. At 14 days after amputation, mice treated with ECM degradation products showed an accumulation of heterogeneous cells that expressed markers of multipotency, including Sox2, Sca1, and Rex1 (Zfp42). Cells isolated from the site of amputation were capable of differentiation along neuroectodermal and mesodermal lineages, whereas cells isolated from control mice were capable of differentiation along only mesodermal lineages. The present findings demonstrate the recruitment of endogenous stem cells to a site of injury, and/or their generation/proliferation therein, in response to ECM degradation products.
The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation
Authors: Bansal Tarun , Alaniz Robert C. , Wood Thomas K. , Jayaraman Arul
Published: December 2009

Interkingdom signaling is established in the gastrointestinal tract in that human hormones trigger responses in bacteria; here, we show that the corollary is true, that a specific bacterial signal, indole, is recognized as a beneficial signal in intestinal epithelial cells. Our prior work has shown that indole, secreted by commensal
Escherichia coli
and detected in human feces, reduces pathogenic
E. coli
chemotaxis, motility, and attachment to epithelial cells. However, the effect of indole on intestinal epithelial cells is not known. Because intestinal epithelial cells are likely to be exposed continuously to indole, we hypothesized that indole may be beneficial for these cells, and investigated changes in gene expression with the human enterocyte cell line HCT-8 upon exposure to indole. Exposure to physiologically relevant amounts of indole increased expression of genes involved in strengthening the mucosal barrier and mucin production, which were consistent with an increase in the transepithelial resistance of HCT-8 cells. Indole also decreased TNF-α-mediated activation of NF-κB, expression of the proinflammatory chemokine IL-8, and the attachment of pathogenic
E. coli
to HCT-8 cells, as well as increased expression of the antiinflammatory cytokine IL-10. The changes in transepithelial resistance and NF-κB activation were specific to indole: other indole-like molecules did not elicit a similar response. Our results are similar to those observed with probiotic strains and suggest that indole could be important in the intestinal epithelial cells response to gastrointestinal tract pathogens.
Evolution and public health
Authors: Omenn Gilbert S.
Published: December 2009

Evolution and its elements of natural selection, population migration, genetic drift, and founder effects have shaped the world in which we practice public health. Human cultures and technologies have modified life on this planet and have coevolved with myriad other species, including microorganisms; plant and animal sources of food; invertebrate vectors of disease; and intermediate hosts among birds, mammals, and nonhuman primates. Molecular mechanisms of differential resistance or susceptibility to infectious agents or diets have evolved and are being discovered with modern methods. Some of these evolutionary relations require a perspective of tens of thousands of years, whereas other changes are observable in real time. The implications and applications of evolutionary understanding are important to our current programs and policies for infectious disease surveillance, gene–environment interactions, and health disparities globally.