bluuebunny/crossref_metadata_2025 huggingface dataset:
Topological effects on capsomer–polyion co-assembly
Authors: Zhang Ran , Linse Per
Published: June 2014

On the basis of a T = 1 icosahedral capsid model, the capsomer–polyion co-assembly process has been investigated by molecular dynamics simulations using capsomers with different net charge and charge distribution as well as linear, branched, and hyper-branched polyions. The assembly process was characterized in terms of the time-dependent cluster size probabilities, averaged cluster size, encapsulation efficiency, and polyion extension. The kinetics of the capsid formation displayed a two-step process. The first one comprised adsorption of capsomers on the polyion, driven by their electrostatic attraction, whereas the second one involved a relocation and/or reorientation of adsorbed capsomers, which rate is reduced upon increasing electrostatic interaction. We found that increased polyion branching facilitated a more rapid encapsulation process towards a higher yield. Moreover, the hyper-branched polyions were entirely encapsulated at all polyion–capsid charge ratios considered.
Density functional theory based generalized effective fragment potential method
Authors: Nguyen Kiet A. , Pachter Ruth , Day Paul N.
Published: June 2014

We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes.
Vibrational dynamics of thiocyanate and selenocyanate bound to horse heart myoglobin
Authors: Maj Michał , Oh Younjun , Park Kwanghee , Lee Jooyong , Kwak Kyung-Won , Cho Minhaeng
Published: June 2014

The structure and vibrational dynamics of SCN- and SeCN-bound myoglobin have been investigated using polarization-controlled IR pump-probe measurements and quantum chemistry calculations. The complexes are found to be in low and high spin states, with the dominant contribution from the latter. In addition, the Mb:SCN high spin complex exhibits a doublet feature in the thiocyanate stretch IR absorption spectra, indicating two distinct molecular conformations around the heme pocket. The binding mode of the high spin complexes was assigned to occur through the nitrogen atom, contrary to the binding through the sulfur atom that was observed in myoglobin derived from Aplysia Limacina. The vibrational energy relaxation process has been found to occur substantially faster than those of free SCN− and SeCN− ions and neutral SCN- and SeCN-derivatized molecules reported previously. This supports the N-bound configurations of MbNCS and MbNCSe, because S- and Se-bound configurations are expected to have significantly long lifetimes due to the insulation effect by heavy bridge atom like S and Se in such IR probes. Nonetheless, even though their lifetimes are much shorter than those of corresponding free ions in water, the vibrational lifetimes determined for MbNCS and MbNCSe are still fairly long compared to those of azide and cyanide myoglobin systems studied before. Thus, thiocyanate and selenocyanate can be good local probes of local electrostatic environment in the heme pocket. The globin dependence on binding mode and vibrational dynamics is also discussed.
Dynamic density functional theory with hydrodynamic interactions and fluctuations
Authors: Donev Aleksandar , Vanden-Eijnden Eric
Published: June 2014

We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, “Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps,” Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absence of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, “A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law,” J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions.
Interaction of single quantum emitter and dark plasmon supported by a metal nanoring
Authors: Deinega Alexei , Seideman Tamar
Published: June 2014

We explore the interaction between a quantum emitter and a metal nanoring by numerical solution of coupled Maxwell-Liouville equations. When the quantum emitter and nanoring are subjected to an incident plane wave, coupling between the quantum emitter and a dark plasmon supported by the nanoring gives rise to a similar lineshape to the familiar Fano type. It results from the excitation of a dark plasmon via intermediary participation of the quantum emitter. The dark plasmon is characterized through the width and shift parameters of the emitter peak in the absorption spectrum of the nanoparticle. Our results are obtained with the help of finite-difference time-domain method and a recently proposed symmetry-adapted averaging approach.
Spectroscopic analysis of H2/CH4 microwave plasma and fast growth rate of diamond single crystal
Authors: Derkaoui N. , Rond C. , Hassouni K. , Gicquel A.
Published: June 2014

One of the best ways to increase the diamond growth rate is to couple high microwave power to the plasma. Indeed, increasing the power density leads to increase gas temperature the atomic hydrogen density in the plasma bulk, and to produce more hydrogen and methyl at the diamond surface. Experimental and numerical approaches were used to study the microwave plasma under high power densities conditions. Gas temperature was measured by optical emission spectroscopy and H-atom density using actinometry. CH3-radical density was obtained using a 1D model that describes temperatures and plasma composition from the substrate to the top of the reactor. The results show that gas temperature in the plasma bulk, atomic hydrogen, and methyl densities at the diamond surface highly increase with the power density. As a consequence, measurements have shown that diamond growth rate also increases. At very high power density, we measured a growth rate of 40 μm/h with an H-atom density of 5 × 1017 cm−3 which corresponds to a H2 dissociation rate higher than 50%. Finally, we have shown that the growth rate can be framed between a lower and an upper limit as a function depending only on the maximum of H-atom density measured or calculated in the plasma bulk. The results also demonstrated that increasing fresh CH4 by an appropriate injection into the boundary layer is a potential way to increase the diamond growth rates.
Role of strain on electronic and mechanical response of semiconducting transition-metal dichalcogenide monolayers: An ab-initio study
Authors: Guzman David M. , Strachan Alejandro
Published: June 2014

We characterize the electronic structure and elasticity of monolayer transition-metal dichalcogenides MX2 (M  =  Mo, W, Sn, Hf and X  =  S, Se, Te) based on 2H and 1T structures using fully relativistic first principles calculations based on density functional theory. We focus on the role of strain on the band structure and band alignment across the series of materials. We find that strain has a significant effect on the band gap; a biaxial strain of 1% decreases the band gap in the 2H structures, by as a much as 0.2  eV in MoS2 and WS2, while increasing it for the 1T cases. These results indicate that strain is a powerful avenue to modulate their properties; for example, strain enables the formation of, otherwise impossible, broken gap heterostructures within the 2H class. These calculations provide insight and quantitative information for the rational development of heterostructures based on this class of materials accounting for the effect of strain.
Solid phase stability of a double-minimum interaction potential system
Authors: Suematsu Ayumi , Yoshimori Akira , Saiki Masafumi , Matsui Jun , Odagaki Takashi
Published: June 2014

We study phase stability of a system with double-minimum interaction potential in a wide range of parameters by a thermodynamic perturbation theory. The present double-minimum potential is the Lennard-Jones-Gauss potential, which has a Gaussian pocket as well as a standard Lennard-Jones minimum. As a function of the depth and position of the Gaussian pocket in the potential, we determine the coexistence pressure of crystals (fcc and bcc). We show that the fcc crystallizes even at zero pressure when the position of the Gaussian pocket is coincident with the first or third nearest neighbor site of the fcc crystal. The bcc crystal is more stable than the fcc crystal when the position of the Gaussian pocket is coincident with the second nearest neighbor sites of the bcc crystal. The stable crystal structure is determined by the position of the Gaussian pocket. These results show that we can control the stability of the solid phase by tuning the potential function.
Collisionless damping of geodesic acoustic mode in plasma with nonextensive distribution
Authors: Qiu Hui-Bin , Song Hai-Ying , Liu Shi-Bing
Published: June 2014

Geodesic acoustic mode (GAM) in collisionless toroidal plasmas with a constant electrostatic potential around a magnetic surface is investigated based on the linear gyrokinetic theory in context of nonextensive statistics mechanics. The damping rate of GAM is shown to be dependent on the nonextensive parameters of ions, and in the extensive limit, the result in Maxwellian distribution plasma is recovered. The damping rate is found to be enhanced as the nonextensive parameter of ion decreases.
Origin of high propagation loss in electrospun polymer nanofibers
Authors: Ishii Yuya , Satozono Shota , Kaminose Ryohei , Fukuda Mitsuo
Published: June 2014

We evaluate optical propagation loss (α) in electrospun poly(methyl methacrylate) (PMMA) nanofibers with different wavelength (λ) and determine the origin of the loss. Aligned single electrospun nanofibers composed of PMMA and a small amount of an organic dye are fabricated with an average diameter of approximately 640 nm. After cladding seven fiber samples, α is evaluated to be 26–62 dB cm−1 at wavelengths 590−680 nm. Moreover, α depended linearly on λ−4, and from the fitting functions we determined the ratio of the following two possible losses for α: loss at the interface between the fiber-core and cladding because of non-uniformity within the fibers (αun), and loss because of excess light scattering in the fibers resulting from density inhomogeneity of PMMA (αsc). For the fibers, αun is evaluated to be 6.9–22 dB cm−1, which represents 19%–50% of α at λ of 650 nm with α ∼ αun + αsc. Thus, we conclude that the high α in these fibers originates from both their poor uniformity and density inhomogeneity. Furthermore, a quantitative investigation of uniformity in the individual fibers revealed that the root mean square roughness ranges from 5.5 nm to 9.0 nm and the theoretical value of αun was ∼1 dB cm−1 showing reasonable agreement with experimental data. These findings hold for low-loss polymer nanofiber waveguides, which have high aspect ratio and fine patterning even in three dimensions.
The electronic and magnetic properties of La0.85Zr0.15MnO3 deposited on SrTiO3 and MgO substrates
Authors: Deshpande N. G. , Weng C. H. , Wang Y. F. , Shao Y. C. , Cheng C. Q. , Ling D. C. , Hsueh H. C. , Du C. H. , Tsai H. M. , Pao C. W. , Lin H. J. , Lee J. F. , Chiou J. W. , Tsai M. H. , Pong W. F.
Published: June 2014

The electronic and magnetic properties of tetravalent-ion-doped La0.85Zr0.15MnO3 (LZMO) thin films that were epitaxially grown on SrTiO3 (STO) and MgO substrates were studied using temperature-dependent x-ray diffraction (XRD), x-ray absorption near-edge structure, x-ray linear dichroism, and x-ray magnetic circular dichroism at the Mn L3,2- and K-edge. XRD studies reveal that the LZMO thin films have compressive and tensile strains (along the c-axis) on the STO and MgO substrates, respectively. As the temperature is reduced from room temperature to below magnetic transition temperature, the preferentially occupied Mn majority-spin eg orbital changes from the in-plane dx2-y2 to the out-of-plane d3z2-r2 orbital for LZMO/STO, and vice versa for LZMO/MgO. Experimental results suggest that the new hopping path that is mediated by the Mn2+ ions triggers a stronger d3z2-r2 orbital ordering of Mn3+ ions and enhances the ferromagnetic coupling between the Mn spin moments of t2g electrons in LZMO/STO, whereas the strong tensile strain stabilizes the dx2-y2 orbital by inducing lattice distortions of the MnO6 octahedra in LZMO/MgO.
Tailoring interlayer coupling and coercivity in Co/Mn/Co trilayers by controlling the interface roughness
Authors: Zhang Bin , Wu Chii-Bin , Kuch Wolfgang
Published: June 2014

Epitaxial Co/Mn/Co trilayers with a wedged Mn layer were grown on Cu(001) and studied by magneto-optical Kerr effect measurements. The bottom Co film as well as the Mn film exhibits a layer-by-layer growth mode, which allows to modify both interface roughnesses on the atomic scale by tuning the thicknesses of the films to achieve a certain filling of their topmost atomic layers. The onset of antiferromagnetic order in the Mn layer at room temperature was found at thicknesses of 4.1 (4.8) and 3.4 (4.0) atomic monolayers (ML) for a filled (half-filled) topmost atomic layer of the bottom Co film in Mn/Co bilayers and Co/Mn/Co trilayers, respectively. Magnetization loops with only one step were found for a trilayer with half-filled topmost atomic layer of the bottom Co film, while loops with two separate steps have been observed in trilayers with an integer number of atomic layers in the bottom Co film. The coercivity of the top Co film shows an oscillation with 1 ML period as a function of the Mn thickness above 10 ML, which is interpreted as the influence of the atomic-scale control of the interface roughness on the interface exchange coupling between the antiferromagnetic Mn and the top ferromagnetic (FM) Co layer. The strength of the magnetic interlayer coupling between the top and bottom Co layers through the Mn layer for an integer number of atomic layers in the bottom Co layer, deduced from minor-loop measurements, exhibits an oscillation with a period of 2 ML Mn thickness, indicative of direct exchange coupling through the antiferromagnetic Mn layer. In addition, a long-period interlayer coupling of the two FM layers with antiparallel coupling maxima at Mn thicknesses of 2.5, 8.2, and 13.7 ML is observed and attributed to indirect exchange coupling of the Rudermann-Kittel-Kasuya-Yosida type.
Heisenberg picture approach to the stability of quantum Markov systems
Authors: Pan Yu , Amini Hadis , Miao Zibo , Gough John , Ugrinovskii Valery , James Matthew R.
Published: June 2014

Quantum Markovian systems, modeled as unitary dilations in the quantum stochastic calculus of Hudson and Parthasarathy, have become standard in current quantum technological applications. This paper investigates the stability theory of such systems. Lyapunov-type conditions in the Heisenberg picture are derived in order to stabilize the evolution of system operators as well as the underlying dynamics of the quantum states. In particular, using the quantum Markov semigroup associated with this quantum stochastic differential equation, we derive sufficient conditions for the existence and stability of a unique and faithful invariant quantum state. Furthermore, this paper proves the quantum invariance principle, which extends the LaSalle invariance principle to quantum systems in the Heisenberg picture. These results are formulated in terms of algebraic constraints suitable for engineering quantum systems that are used in coherent feedback networks.
Optimization of the ITER electron cyclotron equatorial launcher for improved heating and current drive functional capabilities
Authors: Farina D. , Henderson M. , Figini L. , Saibene G.
Published: June 2014

The design of the ITER Electron Cyclotron Heating and Current Drive (EC H&CD) system has evolved in the last years both in goals and functionalities by considering an expanded range of applications. A large effort has been devoted to a better integration of the equatorial and the upper launchers, both from the point of view of the performance and of the design impact on the engineering constraints. However, from the analysis of the ECCD performance in two references H-mode scenarios at burn (the inductive H-mode and the advanced non-inductive scenario), it was clear that the EC power deposition was not optimal for steady-state applications in the plasma region around mid radius. An optimization study of the equatorial launcher is presented here aiming at removing this limitation of the EC system capabilities. Changing the steering of the equatorial launcher from toroidal to poloidal ensures EC power deposition out to the normalized toroidal radius ρ ≈ 0.6, and nearly doubles the EC driven current around mid radius, without significant performance degradation in the core plasma region. In addition to the improved performance, the proposed design change is able to relax some engineering design constraints on both launchers.
Review of recent experimental and modeling progress in the lower hybrid range of frequencies at ITER relevant parameters
Authors: Bonoli Paul T.
Published: June 2014

Progress in experiment and simulation capability in the lower hybrid range of frequencies at ITER relevant parameters is reviewed. Use of LH power in reactor devices is motivated in terms of its potential for efficient off-axis current profile control. Recent improvements in simulation capability including the development of full-wave field solvers, inclusion of the scrape off layer (SOL) in wave propagation codes, the use of coupled ray tracing/full-wave/3D (r v⊥, v//) Fokker Planck models, and the inclusion of wave scattering as well as nonlinear broadening effects in ray tracing / Fokker Planck codes are discussed. Experimental and modeling results are reviewed which are aimed at understanding the spectral gap problem in LH current drive (LHCD) and the density limit that has been observed and mitigated in LHCD experiments. Physics mechanisms that could be operative in these experiments are discussed, including toroidally induced variations in the parallel wavenumber, nonlinear broadening of the pump wave, scattering of LH waves from density fluctuations in the SOL, and spectral broadening at the plasma edge via full-wave effects.
One-dimensional Dirac operators with zero-range interactions: Spectral, scattering, and topological results
Authors: Pankrashkin Konstantin , Richard Serge
Published: June 2014

The spectral and scattering theory for 1-dimensional Dirac operators with mass m and with zero-range interactions are fully investigated. Explicit expressions for the wave operators and for the scattering operator are provided. These new formulae take place in a representation which links, in a suitable way, the energies −∞ and +∞, and which emphasizes the role of ±m. Finally, a topological version of Levinson's theorem is deduced, with the threshold effects at ±m automatically taken into account.
Near-infrared induced optical quenching effects on mid-infrared quantum cascade lasers
Authors: Guo Dingkai , Cai Hong , Talukder Muhammad Anisuzzaman , Chen Xing , Johnson Anthony M. , Khurgin Jacob B. , Choa Fow-Sen
Published: June 2014

In space communications, atmospheric absorption and Rayleigh scattering are the dominant channel impairments. Transmission using mid-infrared (MIR) wavelengths offers the benefits of lower loss and less scintillation effects. In this work, we report the telecom wavelengths (1.55 μm and 1.3 μm) induced optical quenching effects on MIR quantum cascade lasers (QCLs), when QCLs are operated well above their thresholds. The QCL output power can be near 100% quenched using 20 mW of near-infrared (NIR) power, and the quenching effect depends on the input NIR intensity as well as wavelength. Time resolved measurement was conducted to explore the quenching mechanism. The measured recovery time is around 14 ns, which indicates that NIR generated electron-hole pairs may play a key role in the quenching process. The photocarrier created local field and band bending can effectively deteriorate the dipole transition matrix element and quench the QCL. As a result, MIR QCLs can be used as an optical modulator and switch controlled by NIR lasers. They can also be used as “converters” to convert telecom optical signals into MIR optical signals.
Screening of remote charge scattering sites from the oxide/silicon interface of strained Si two-dimensional electron gases by an intermediate tunable shielding electron layer
Authors: Huang Chiao-Ti , Li Jiun-Yun , Chou Kevin S. , Sturm James C.
Published: June 2014

We report the strong screening of the remote charge scattering sites from the oxide/semiconductor interface of buried enhancement-mode undoped Si two-dimensional electron gases (2DEGs), by introducing a tunable shielding electron layer between the 2DEG and the scattering sites. When a high density of electrons in the buried silicon quantum well exists, the tunneling of electrons from the buried layer to the surface quantum well can lead to the formation of a nearly immobile surface electron layer. The screening of the remote charges at the interface by this newly formed surface electron layer results in an increase in the mobility of the buried 2DEG. Furthermore, a significant decrease in the minimum mobile electron density of the 2DEG occurs as well. Together, these effects can reduce the increased detrimental effect of interface charges as the setback distance for the 2DEG to the surface is reduced for improved lateral confinement by top gates.
Continuous-wave four-wave mixing in a single-mode tellurite fiber
Authors: Cheng Tonglei , Deng Dinghuan , Xue Xiaojie , Suzuki Takenobu , Ohishi Yasutake
Published: June 2014

Four-wave mixing in a 6 -m long single-mode tellurite (78TeO2-5Bi2O3-5ZnO-12Na2O, mol%, TBZN) fiber was experimentally observed with the continuous-wave (CW) pump wavelengths changing from ∼1530 to 1565 nm. Conversion efficiency of ∼−20 dB was obtained with the CW signal input power of ∼5 mW at the pump wavelength of ∼1565 nm. The optical signal gain in the TBZN tellurite fiber was numerically simulated, and the result agreed well with the experiment.
Imaging of buried phosphorus nanostructures in silicon using scanning tunneling microscopy
Authors: Oberbeck Lars , Reusch Thilo C. G. , Hallam Toby , Schofield Steven R. , Curson Neil J. , Simmons Michelle Y.
Published: June 2014

We demonstrate the locating and imaging of single phosphorus atoms and phosphorus dopant nanostructures, buried beneath the Si(001) surface using scanning tunneling microscopy. The buried dopant nanostructures have been fabricated in a bottom-up approach using scanning tunneling microscope lithography on Si(001). We find that current imaging tunneling spectroscopy is suited to locate and image buried nanostructures at room temperature and with residual surface roughness present. From these studies, we can place an upper limit on the lateral diffusion during encapsulation with low-temperature Si molecular beam epitaxy.
High-intensity positron microprobe at the Thomas Jefferson National Accelerator Facility
Authors: Golge S. , Vlahovic B. , Wojtsekhowski B.
Published: June 2014

We present a conceptual design for a novel continuous wave electron-linac based high-intensity high-brightness slow-positron production source with a projected intensity on the order of 1010 e+/s. Reaching this intensity in our design relies on the transport of positrons (T+ below 600 keV) from the electron-positron pair production converter target to a low-radiation and low-temperature area for moderation in a high-efficiency cryogenic rare gas moderator, solid Ne. This design progressed through Monte Carlo optimizations of: electron/positron beam energies and converter target thickness, transport of the e+ beam from the converter to the moderator, extraction of the e+ beam from the magnetic channel, a synchronized raster system, and moderator efficiency calculations. For the extraction of e+ from the magnetic channel, a magnetic field terminator plug prototype has been built and experimental results on the effectiveness of the prototype are presented. The dissipation of the heat away from the converter target and radiation protection measures are also discussed.
Injection and acceleration of electron bunch in a plasma wakefield produced by a chirped laser pulse
Authors: Afhami Saeedeh , Eslami Esmaeil
Published: June 2014

An ultrashort laser pulse propagating in plasma can excite a nonlinear plasma wakefield which can trap and accelerate charged particles up to GeV. One-dimensional analysis of electron injection, trapping, and acceleration by different chirped pulses propagating in plasma is investigated numerically. In this paper, we inject electron bunches in front of the chirped pulses. It is indicated that periodical chirped laser pulse can trap electrons earlier than other pulses. It is shown that periodical chirped laser pulses lead to decrease the minimum momentum necessary to trap the electrons. This is due to the fact that periodical chirped laser pulses are globally much efficient than nonchirped pulses in the wakefield generation. It is found that chirped laser pulses could lead to much larger electron energy than that of nonchirped pulses. Relative energy spread has a lower value in the case of periodical chirped laser pulses.
Non-contact multi-particle annular patterning and manipulation with ultrasound microbeam
Authors: Lee Changyang , Seob Jeong Jong , Youn Hwang Jae , Lee Jungwoo , Kirk Shung K.
Published: June 2014

Multiparticle-trapping offers diverse opportunities and applications in biotechnology. It can be applied to creating various functional materials or organizing reactive particles. In this paper, we demonstrate that it is possible to trap and manipulate multi-particles in an annular pattern with a 24 MHz focused ring-type single element ultrasound transducer. Acoustic ring trap can be useful in undertaking biotropism studies due to an equal-distance condition from the center. Also, this ring trap could serve as a force shield to protect analysis area from other cells. The experimental results showed the capability of the proposed method as a multi-cell manipulator in formatting specific patterns of small cells like sperms.
Local structure underlying anomalous tetragonal distortions in BiFeO3-PbTiO3 ferroelectrics
Authors: Levin I. , Krayzman V. , Tucker M. G. , Woicik J. C.
Published: June 2014

The local structure of tetragonal BiFeO3-PbTiO3 solid solutions featuring anomalous lattice distortions has been determined using simultaneous fitting of neutron total scattering and extended X-ray absorption fine structure data. On the local scale, the large tetragonal distortion, promoted by the displacements of the A-cations (Bi and Pb), is accommodated primarily by the [FeO6] octahedra, even though both Fe and Ti acquire (5+1)-fold coordination. Bi cations exhibit considerably larger displacements than Pb. The combination of the A-cation displacements and the ability of M-cations to adopt 5-fold coordination is suggested as key for stabilizing the large tetragonality in BiMO3-PbTiO3 systems.
Efficient optical absorption enhancement in organic solar cells by using a 2-dimensional periodic light trapping structure
Authors: Zu Feng-Shuo , Shi Xiao-Bo , Liang Jian , Xu Mei-Feng , Lee Chun-Sing , Wang Zhao-Kui , Liao Liang-Sheng
Published: June 2014

We have investigated the effects induced by periodic nanosphere arrays on the performance of organic solar cells (OSCs). Two-dimensional periodic arrays of polystyrene nanospheres were formed by using a colloidal lithography method together with plasma etching to trim down the size to various degrees on the substrates of OSCs. It is found that the devices prepared on such substrates can have improved light harvesting, resulting in as high as 35% enhancement in power conversion efficiency over that of the reference devices. The measured external quantum efficiency and finite-difference time-domain simulation reveal that the controlled periodic morphology of the substrate can efficiently increase light scattering in the device and thus enhance the absorption of incident light.
Analytical solution for the potential distribution in a stripe Schottky contact
Authors: Vostokov N. V. , Shashkin V. I.
Published: June 2014

We consider a model of the stripe Schottky contact with a uniformly doped semiconductor. It is assumed that at the boundary of the semiconductor, the position of the Fermi level is fixed due to the high density of surface states in the band gap. An analytical solution of the problem of the potential distribution, the shape of the depletion region, and the high-frequency capacitance of the contact is found in the full depletion approximation. Based on the approach developed, we study quadratic nonlinear properties of the FET with a Schottky barrier in the high-frequency signal detection mode.
Magnetic resonance imaging analysis on the in-situ mixing zone of CO2 miscible displacement flows in porous media
Authors: Song Yongchen , Yang Wenzhe , Wang Dayong , Yang Mingjun , Jiang Lanlan , Liu Yu , Zhao Yuechao , Dou Binlin , Wang Zhiguo
Published: June 2014

The in-situ mixing zone represents dynamic characteristics of CO2 miscible displacement flows, which is important for carbon dioxide enhanced oil recovery (CO2-EOR) projects. However, the migration characteristics of the in-situ mixing zone under reservoir conditions has been neither well studied nor fully understood. The in-situ mixing zone with the flowing mixture of supercritical CO2 and n-decane (nC10) was investigated by using a magnetic resonance imaging apparatus at a reservoir condition of 8.5 MPa and 37.8 °C in porous media. The experimental results showed that the CO2-frontal velocity was larger than the mixing-frontal velocity. The mixing zone length was linearly declined in the miscible displacement process. And the declining rate of the mixing zone length was increased with injection rate. It indicates that the mixing zone length is not constant in a vertically stable CO2 misible displacement and a volume contraction due to phase behavior effects may occur. Then, an error function based on the convection-dispersion equation was fitted with CO2 miscible displacement experiments. The error function was well fitted both at a series of fixed core positions and a series of fixed displacement times. Furthermore, the longitudinal dispersion coefficients (Klx and Klt) and the longitudinal Peclet numbers (Ped and PeL) were quantified from the fitting results. The evolutions of the longitudinal dispersion coefficient were reduced along the displacement time. And the declining rate was increased with injection rate. And with proceeding, the longitudinal dispersion coefficient was tending towards stability and constant. But the evolutions of the longitudinal Peclet numbers were increased along the displacement time. And the increasing rate was increased with injection rate.
Plasma ionization frequency, edge-to-axis density ratio, and density on axis of a cylindrical gas discharge
Authors: Palacio Mizrahi J. H.
Published: June 2014

A rigorous derivation of expressions, starting from the governing equations, for the ionization frequency, edge-to-axis ratio of plasma density, plasma density at the axis, and radially averaged plasma density in a cylindrical gas discharge has been obtained. The derived expressions are simple and involve the relevant parameters of the discharge: Cylinder radius, axial current, and neutral gas pressure. The found expressions account for ion inertia, ion temperature, and changes in plasma ion collisionality.
Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle
Authors: Feillet Céline , Krusche Peter , Tamanini Filippo , Janssens Roel C. , Downey Mike J. , Martin Patrick , Teboul Michèle , Saito Shoko , Lévi Francis A. , Bretschneider Till , van der Horst Gijsbertus T. J. , Delaunay Franck , Rand David A.
Published: June 2014

Significance

In tissues such as bone marrow, intestinal mucosa, or regenerating liver, the daily rhythm of cell division is controlled by the cell’s circadian clock. Determining how this clock organizes important processes such as cell division, apoptosis, and DNA damage repair is key to understanding the links between circadian dysfunction and malignant cell proliferation. We show that in proliferating mouse fibroblasts there is more than one way in which the clock and cell cycle synchronize their oscillations and that one of them is the biological equivalent of the phase locking first discovered by Huygens in the 17th century when he coupled two clocks together. When phase-locked two coupled oscillators have a fixed relative phase and oscillate with a common frequency.
Single-molecule imaging and kinetic analysis of cooperative cofilin–actin filament interactions
Authors: Hayakawa Kimihide , Sakakibara Shotaro , Sokabe Masahiro , Tatsumi Hitoshi
Published: June 2014

Significance

Cooperative protein–protein interactions are essential for understanding the regulation of enzymes. However, the dynamic interactions that endow proteins with cooperativity in solution have not been directly imaged and analyzed. In this study, we performed super-high-resolution real-time single-molecule imaging of the binding of cofilin to single actin filaments and its subsequent detachment. Results show that long-term binding (>0.4 s) of a single cofilin molecule enhances the binding of additional cofilin within 65 nm (across 24 actin subunits) of the initial binding site. This cooperative binding is presumed to be crucial for the peculiar actin filament-severing action of cofilin.
Occurrence in Mexico, 1998–2008, of
Vibrio cholerae
CTX
+
El Tor carrying an additional truncated CTX prophage
Authors: Alam Munirul , Rashed Shah Manzur , Mannan Shahnewaj Bin , Islam Tarequl , Lizarraga-Partida Marcial Leonardo , Delgado Gabriela , Morales-Espinosa Rosario , Mendez Jose Luis , Navarro Armando , Watanabe Haruo , Ohnishi Makoto , Hasan Nur A. , Huq Anwar , Sack R. Bradley , Colwell Rita R. , Cravioto Alejandro
Published: June 2014

Significance

Vibrio cholerae
classical (CL) biotype was isolated, along with biotype El Tor (ET) and altered ET carrying the cholera toxin (CTX) gene of CL biotype, during the 1991 cholera epidemic in Mexico, subsequently becoming endemic until 1997. Microbiological, molecular, and phylogenetic analyses of
V. cholerae
isolated from both clinical and environmental samples during 1998–2008 confirm important genetic events, namely predominance of ET over CL and altered ET in Mexico. Although altered ET is predominantly associated with cholera globally, progression of CTX
+
V. cholerae
ET with truncated CTX prophage to the predominant pathogen causing endemic cholera in Mexico may prove to be yet another key historical point in the global epidemiology of cholera.
MeCP2 enforces Foxp3 expression to promote regulatory T cells’ resilience to inflammation
Authors: Li Chaoran , Jiang Shan , Liu Si-Qi , Lykken Erik , Zhao Lin-tao , Sevilla Jose , Zhu Bo , Li Qi-Jing
Published: June 2014

Significance

Forkhead box P3
+
(Foxp3
+
) regulatory T cells (Tregs) are important for maintaining immune homeostasis and tolerance. The pivotal role of Tregs in immune tolerance demands that they possess a dedicated molecular machinery to maintain stable Foxp3 expression when challenged by an inflammatory environment. Whereas epigenetic mechanisms acting on the
foxp3
locus have been extensively implicated in Tregs’ stable expression of Foxp3, the detailed molecular machinery remains elusive. In this study, we show that methyl-CpG binding protein 2 (MeCP2), an X-linked multifunctional epigenetic regulator, is a crucial player in the epigenetic machinery that confers Tregs with resilience against inflammation. Our study provides, to our knowledge, the first mechanistic description by which MeCP2, a molecule best known for its function in the central nervous system, regulates Treg function and immune tolerance.
Contact between bird species of different lifespans can promote the emergence of highly pathogenic avian influenza strains
Authors: Wikramaratna Paul S. , Pybus Oliver G. , Gupta Sunetra
Published: June 2014

Significance

The emergence of highly pathogenic avian influenza viruses has received much attention due to the severe consequences of their occasional spread to humans, as well as the large toll they take on the poultry industry. Here we argue that the main barriers to the emergence of these viruses are imposed by immunity to related strains rather than the ability of the virus to acquire the necessary mutations. We show that, under these circumstances, patterns of influenza in different avian species are strongly dependent on their lifespan and that processes that alter the interactions between species of different lifespans—such as changes in farming practices—could promote the emergence of highly pathogenic types.
Activation of Ras overcomes B-cell tolerance to promote differentiation of autoreactive B cells and production of autoantibodies
Authors: Teodorovic Lenka S. , Babolin Chiara , Rowland Sarah L. , Greaves Sarah A. , Baldwin David P. , Torres Raul M. , Pelanda Roberta
Published: June 2014

Significance

Only a fraction of immature B cells enter the mature B-cell pool to produce antibodies. Autoreactive immature B cells expressing antibodies to self remain in the bone marrow to continue immunoglobulin gene rearrangements and are selected into the periphery only if they eliminate their autoreactive specificity. We show that the rat sarcoma (Ras)-Erk pathway, which leads to the generation of mature B cells, is not constitutively activated in autoreactive immature B cells. Furthermore, activation of Ras can alter the selection pattern of autoreactive cells, inhibiting immunoglobulin gene recombination via PI3K, promoting cell differentiation via Erk, and resulting in secretion of autoantibodies. This suggests that changes in the activation of the Ras–Erk/PI3K pathway have the potential to lead to autoimmune manifestations.
mTORC1 maintains renal tubular homeostasis and is essential in response to ischemic stress
Authors: Grahammer Florian , Haenisch Nora , Steinhardt Frederic , Sandner Lukas , Roerden Malte , Arnold Frederic , Cordts Tomke , Wanner Nicola , Reichardt Wilfried , Kerjaschki Dontscho , Ruegg Markus A. , Hall Michael N. , Moulin Pierre , Busch Hauke , Boerries Melanie , Walz Gerd , Artunc Ferruh , Huber Tobias B.
Published: June 2014

Significance

Mammalian target of rapamycin complex 1 (mTORC1) inhibitors are commonly used as immunosuppressants in solid-organ transplantation and as antiproliferative agents in various cancers. Despite indications of serious renal adverse events caused by mTORC1 inhibition, the role of mTORC1 for renal epithelial function and homeostasis has remained elusive. Unexpectedly, tubular mTORC1 controls energy-driven urine-concentrating mechanisms by maintaining mitochondrial biogenesis. Under pathophysiological conditions, mTORC1-dependent mitochondrial biogenesis is essential for energy supply and adaptation in response to ischemia. These findings identify mTORC1 as an important regulator of tubular energy metabolism, transcellular transport processes, and ischemic stress responses.
Ferroelectric switching of elastin
Authors: Liu Yuanming , Cai Hong-Ling , Zelisko Matthew , Wang Yunjie , Sun Jinglan , Yan Fei , Ma Feiyue , Wang Peiqi , Chen Qian Nataly , Zheng Hairong , Meng Xiangjian , Sharma Pradeep , Zhang Yanhang , Li Jiangyu
Published: June 2014

Significance

Ferroelectricity has long been speculated to have important biological functions, although its very existence in biology has never been firmly established. Here, we present, to our knowledge, the first macroscopic observation of ferroelectric switching in a biological system, and we elucidate the origin and mechanism underpinning ferroelectric switching of elastin. It is discovered that the polarization in elastin is intrinsic at the monomer level, analogous to the unit cell level polarization in classical perovskite ferroelectrics. Our findings settle a long-standing question on ferroelectric switching in biology and establish ferroelectricity as an important biophysical property of proteins. We believe this is a critical first step toward resolving its physiological significance and pathological implications.
Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs
Authors: Nguyen Giang Huong , Tang Weiliang , Robles Ana I. , Beyer Richard P. , Gray Lucas T. , Welsh Judith A. , Schetter Aaron J. , Kumamoto Kensuke , Wang Xin Wei , Hickson Ian D. , Maizels Nancy , Monnat Raymond J. , Harris Curtis C.
Published: June 2014

Significance

Bloom syndrome is a rare human genetic disease characterized by proportional dwarfism, immunodeficiency, and an elevated risk of many different cancer types. We used RNA expression profiling to identify networks of mRNAs and microRNAs that are differentially expressed in cells from Bloom syndrome patients and associated with cell proliferation, survival, and molecular pathways promoting cancer. Altered mRNA expression was in some cases strongly correlated with the presence of G4 motifs, which may form G-quadruplex targets that are bound by BLM. Further analysis of the genetic networks we identified may elucidate mechanisms responsible for Bloom syndrome disease pathogenesis and ways to ameliorate or prevent disease in affected individuals.
Double electron–electron resonance reveals cAMP-induced conformational change in HCN channels
Authors: Puljung Michael C. , DeBerg Hannah A. , Zagotta William N. , Stoll Stefan
Published: June 2014

Significance

Hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels play central roles in the heart and the brain. In the heart, they are present in pacemaker cells and contribute to the regulation of the heartbeat. In the brain, they are involved in electrical signaling of neurons. HCN channels are activated by hyperpolarization of the cell membrane and are regulated by binding of cAMP to a site in an intracellular binding domain. This study shows that this binding domain undergoes major structural changes upon binding of cAMP. The results are the first step toward elucidating the molecular mechanism of gating in this important class of ion channels.
Fluid flows created by swimming bacteria drive self-organization in confined suspensions
Authors: Lushi Enkeleida , Wioland Hugo , Goldstein Raymond E.
Published: June 2014

Significance

The collective dynamics of swimming microorganisms exhibits a complex interplay with the surrounding fluid: the motile cells stir the fluid, which in turn can reorient and advect them. This feedback loop can result in long-range interactions between the cells, an effect whose significance remains controversial. We present a computational model that takes into account these cell–fluid interactions and cell–cell forces and that predicts counterintuitive cellular order driven by long-range flows. This prediction is confirmed with experimental studies that track the orientation of cells in a confined, dense bacterial suspension.
Piezo1, a mechanically activated ion channel, is required for vascular development in mice
Authors: Ranade Sanjeev S. , Qiu Zhaozhu , Woo Seung-Hyun , Hur Sung Sik , Murthy Swetha E. , Cahalan Stuart M. , Xu Jie , Mathur Jayanti , Bandell Michael , Coste Bertrand , Li Yi-Shuan J. , Chien Shu , Patapoutian Ardem
Published: June 2014

Significance

Ion channels that are activated by mechanical force have been implicated in numerous physiological systems. In mammals, the identity of these channels remains poorly understood. We recently described Piezos as evolutionarily conserved mechanically activated ion channels and showed that Piezo2 is required for activation of touch receptors in the skin. Here we show that Piezo1 is a critical component of endothelial cell mechanotransduction and is required for embryonic development. Piezo1 is expressed in embryonic endothelial cells and is activated by fluid shear stress. Loss of Piezo1 affects the ability of endothelial cells to alter their alignment when subjected to shear stress. These results suggest a potential role for Piezo1 in mechanotransduction in adult cardiovascular function and disease.
Immunization with a functional protein complex required for erythrocyte invasion protects against lethal malaria
Authors: Srinivasan Prakash , Ekanem Emmanuel , Diouf Ababacar , Tonkin Michelle L. , Miura Kazutoyo , Boulanger Martin J. , Long Carole A. , Narum David L. , Miller Louis H.
Published: June 2014

Significance

Apical membrane antigen 1 (AMA1) is a leading blood-stage vaccine candidate. Despite the vaccine’s ability to elicit high-titer AMA1-specific antibodies, it showed little efficacy in clinical trials against a homologous parasite. AMA1 interacts with a 49-aa region of rhoptry neck protein 2 (RON2), another parasite protein, during merozoite invasion. In this study, we demonstrate that immunization with a functional complex of AMA1-RON2 peptide (RON2L) induces antibody-mediated complete protection against lethal
Plasmodium yoelli
challenge. Interestingly, the qualitative increase in efficacy appears to be related in part to a switch in the proportion of antibodies targeting the RON2-binding site in AMA1. Our data suggest that a multiallele AMA1 (to overcome polymorphisms) in complex with RON2L should be effective in protecting against all
Plasmodium falciparum
parasites.