bluuebunny/crossref_metadata_2025 huggingface dataset:
Explicit expressions of self-diffusion coefficient, shear viscosity, and the Stokes-Einstein relation for binary mixtures of Lennard-Jones liquids
Authors: Ohtori Norikazu , Ishii Yoshiki
Published: October 2015

Explicit expressions of the self-diffusion coefficient, Di, and shear viscosity, ηsv, are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m−3. The scaling equations obtained by multiplying all the single-variable dependences can well express Di and ηsv evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for Di can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the “isotope effect” on Di. The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions.
Integration of RFQ beam coolers and solenoidal magnetic fields
Authors: Cavenago M. , Romé M. , Maggiore M. , Porcellato A. M. , Maero G. , Chiurlotto F. , Comunian M. , Galatà A. , Cavaliere F.
Published: October 2015

Electromagnetic traps are a flexible and powerful method of controlling particle beams, possibly of exotic nuclei, with cooling (of energy spread and transverse oscillations) provided by collisions with light gases as in the Radio Frequency Quadrupole Cooler (RFQC). A RFQC prototype can be placed inside the existing Eltrap solenoid, capable of providing a magnetic flux density component Bz up to 0.2 T, where z is the solenoid axis. Confinement in the transverse plane is provided both by Bz and the rf voltage Vrf (up to 1 kV at few MHz). Transport is provided by a static electric field Ez (order of 100 V/m), while gas collisions (say He at 1 Pa, to be maintained by differential pumping) provide cooling or heating depending on Vrf. The beamline design and the major parameters Vrf, Bz (which affect the beam transmission optimization) are here reported, with a brief description of the experimental setup.
Two-chamber configuration of Bio-Nano electron cyclotron resonance ion source for fullerene modification
Authors: Uchida T. , Rácz R. , Muramatsu M. , Kato Y. , Kitagawa A. , Biri S. , Yoshida Y.
Published: October 2015

We report on the modification of fullerenes with iron and chlorine using two individually controllable plasmas in the Bio-Nano electron cyclotron resonance ion source (ECRIS). One of the plasmas is composed of fullerene and the other one is composed of iron and chlorine. The online ion beam analysis allows one to investigate the rate of the vapor-phase collisional modification process in the ECRIS, while the offline analyses (e.g., liquid chromatography-mass spectrometry) of the materials deposited on the plasma chamber can give information on the surface-type process. Both analytical methods show the presence of modified fullerenes such as fullerene-chlorine, fullerene-iron, and fullerene-chlorine-iron.
Helical modulation of the electrostatic plasma potential due to edge magnetic islands induced by resonant magnetic perturbation fields at TEXTOR
Authors: Ciaccio G. , Schmitz O. , Spizzo G. , Abdullaev S. S. , Evans T. E. , Frerichs H. , White R. B.
Published: October 2015

The electrostatic response of the edge plasma to a magnetic island induced by resonant magnetic perturbations to the plasma edge of the circular limiter tokamak TEXTOR is analyzed. Measurements of plasma potential are interpreted by simulations with the Hamiltonian guiding center code Orbit. We find a strong correlation between the magnetic field topology and the poloidal modulation of the measured plasma potential. The ion and electron drifts yield a predominantly electron driven radial diffusion when approaching the island X-point while ion diffusivities are generally an order of magnitude smaller. This causes a strong radial electric field structure pointing outward from the island O-point. The good agreement found between measured and modeled plasma potential connected to the enhanced radial particle diffusivities supports that a magnetic island in the edge of a tokamak plasma can act as convective cell. We show in detail that the particular, non-ambipolar drifts of electrons and ions in a 3D magnetic topology account for these effects. An analytical model for the plasma potential is implemented in the code Orbit, and analyses of ion and electron radial diffusion show that both ion- and electron-dominated transport regimes can exist, which are known as ion and electron root solutions in stellarators. This finding and comparison with reversed field pinch studies and stellarator literature suggest that the role of magnetic islands as convective cells and hence as major radial particle transport drivers could be a generic mechanism in 3D plasma boundary layers.
Vibrational solvatochromism. III. Rigorous treatment of the dispersion interaction contribution
Authors: Błasiak Bartosz , Cho Minhaeng
Published: October 2015

A rigorous first principles theory of vibrational solvatochromism including the intermolecular dispersion interaction, which is based on the effective fragment potential method, is developed. The present theory is an extended version of our previous vibrational solvatochromism model that took into account the Coulomb, exchange-repulsion, and induction interactions. We show that the frequency shifts of the amide I mode of N-methylacetamide in H2O and CDCl3, when combined with molecular dynamics simulations, can be quantitatively reproduced by the theory, which indicates that the dispersion interaction contribution to the vibrational frequency shift is not always negligibly small. Nonetheless, the reason that the purely Coulombic interaction model for vibrational solvatochromism works well for describing amide I mode frequency shifts in polar solvents is because the electrostatic contribution is strong and highly sensitive to the relative orientation of surrounding solvent molecules, which is in stark contrast with polarization, dispersion, and exchange-repulsion contributions. It is believed that the theory presented and discussed here will be of great use in quantitatively describing vibrational solvatochromism and electrochromism of infrared probes in not just polar solvent environments but also in biopolymers such as proteins.
Yamabe flow and ADM mass on asymptotically flat manifolds
Authors: Cheng Liang , Zhu Anqiang
Published: October 2015

In this paper, we investigate the behavior of ADM mass and Einstein-Hilbert functional under the Yamabe flow. Through studying the Yamabe flow by weighted spaces for parabolic operators, we show that the asymptotically flat property is preserved under the Yamabe flow. We also obtain that ADM mass is invariant under the Yamabe flow and Yamabe flow is the gradient flow of Einstein-Hilbert functional on n-dimensional, n ≥ 3, asymptotically flat manifolds with order τ>n−22 for n = 3,  4 or τ > n − 3 for n > 4. Moreover, we show that ADM mass and Einstein-Hilbert functional are non-increasing under the Yamabe flow on n-dimensional asymptotically flat manifolds if we only assume the order τ>n−22 for n > 4.
Study of interface correlation in W/C multilayer structure by specular and non-specular grazing incidence X-ray reflectivity measurements
Authors: Biswas A. , Maidul Haque S. , Tripathi S. , De Rajnarayan , Rai S. , Bhattacharyya D. , Sahoo N. K.
Published: October 2015

W/C/W tri-layer thin film samples have been deposited on c-Si substrates in a home-built Ion Beam Sputtering system at 1.5 × 10−3 Torr Ar working pressure and 10 mA grid current. The tri-layer samples have been deposited at different Ar+ ion energies between 0.6 and 1.2 keV for W layer deposition and the samples have been characterized by specular and non-specular grazing incidence X-ray reflectivity (GIXR) measurements. By analyzing the GIXR spectra, various interface parameters have been obtained for both W-on-C and C-on-W interfaces and optimum Ar+ ion energy for obtaining interfaces with low imperfections has been found. Subsequently, multilayer W/C samples with 5-layer, 7-layer, 9-layer, and 13-layer have been deposited at this optimum Ar+ ion energy. By fitting the specular and diffused GIXR data of the multilayer samples with the parameters of each interface as fitting variables, different interface parameters, viz., interface width, in-plane correlation length, interface roughness, and interface diffusion have been estimated for each interface and their variation across the depth of the multilayers have been obtained. The information would be useful in realizing W/C multilayers for soft X-ray mirror application in the <100 Å wavelength regime. The applicability of the “restart of the growth at the interface” model in the case of these ion beam sputter deposited W/C multilayers has also been investigated in the course of this study.
Maximum wind turbine performance at low tip speed ratio
Authors: Wood D. H.
Published: October 2015

Wind turbines can approach the Betz-Joukowsky limit on maximum power only at sufficiently high tip speed ratio: in practice, for ratios in excess of about seven. This paper analyses the performance of a turbine with an infinite number of blades as the tip speed ratio decreases to zero, beginning with the two traditional ways of determining the maximum power. The first is the “Glauert” optimization of the power extracted at every radius and the second is the “Betz-Goldstein” optimization of the whole rotor with the wake represented as a rigid helicoidal sheet of constant pitch. At high tip speed ratio, the two methods give very similar power and both asymptote to the Betz-Joukowsky limit. As the ratio approaches zero, the differences become significant. It is shown that Glauert's analysis does not account for effect of the varying pitch on the axial velocity. In addition, there is a large and unphysical energy extraction by a stationary rotor, and an unphysical constant circumferential velocity. Glauert's analysis, however, gives positive torque on a stationary rotor, which is necessary to start a wind turbine, but the torque at very low tip speed ratio seems too high. In contrast, the Betz-Goldstein analysis implies no torque on a stationary rotor but the circumferential velocity is zero on the axis of rotation. A modification is proposed to the Betz-Goldstein analysis to yield positive torque on a stationary rotor. The modified Betz-Goldstein torque coefficient never exceeds 1/2 and the power is less than the Glauert optimum. Finally, the analysis for varying pitch is corrected and the power maximized numerically. The modification applied to the Betz-Goldstein rotor is required to produce torque on the stationary rotor. The maximum torque coefficient was 0.55, and the maximum power was again less than the Glauert maximum. As tip speed ratio increases, the power from all methods asymptotes to the Betz-Joukowsky limit.
Dust particle diffusion in ion beam transport region
Authors: Miyamoto N. , Okajima Y. , Romero C. F. , Kuwata Y. , Kasuya T. , Wada M.
Published: October 2015

Dust particles of μm size produced by a monoplasmatron ion source are observed by a laser light scattering. The scattered light signal from an incident laser at 532 nm wavelength indicates when and where a particle passes through the ion beam transport region. As the result, dusts with the size more than 10 μm are found to be distributed in the center of the ion beam, while dusts with the size less than 10 μm size are distributed along the edge of the ion beam. Floating potential and electron temperature at beam transport region are measured by an electrostatic probe. This observation can be explained by a charge up model of the dust in the plasma boundary region.
Investigating crystalline-polarity-dependent electronic structures of GaN by hard x-ray photoemission and ab-initio calculations
Authors: Ohsawa Takeo , Ueda Shigenori , Suzuki Motohiro , Tateyama Yoshitaka , Williams Jesse R. , Ohashi Naoki
Published: October 2015

Crystalline-polarity-dependent electronic structures of gallium nitride (GaN) were studied by photoemission spectroscopy (PES) using soft and hard x-rays with different linear polarizations. A peak located near the valence band (VB) maximum was enhanced for a (0001) surface compared with that for a (0001¯) surface regardless of photon energy. Comparison of the VB density of states obtained by ab-initio calculations with the observed VB-PES spectra indicates that the crystalline-polarity dependence is associated with the Ga 4p and N 2p states. The most plausible origin of the crystalline-polarity-dependent VB feature is based on the photoemission phenomena of electrons in the pz-orbitals due to spontaneous electric polarization along the c-axis of GaN.
Optimization of barrier layer thickness in MgSe/CdSe quantum wells for intersubband devices in the near infrared region
Authors: Chen Guopeng , Tamargo Maria C. , Shen Aidong
Published: October 2015

The authors report the optimization of MgSe barrier thickness in CdSe/MgSe multiple quantum well structures and its effect on structural, optical qualities and intersubband (ISB) transition characteristics. Three samples with the MgSe thicknesses of 2 nm, 3 nm, and 4 nm were grown on InP substrates by molecular beam epitaxy. X-ray diffraction and photoluminescence measurements showed that the thinner the MgSe barrier thickness the better the structural quality. However, ISB absorption was only observed in the sample with a MgSe thickness of 3 nm. Failing to observe ISB absorption in the sample with a thicker MgSe barrier (≥4 nm) is due to the deteriorated material quality while the missing of ISB transition in the sample with thinner barrier (≤2 nm) is due to the tunneling of electrons out of the CdSe wells. The optimized MgSe barrier thickness of around 3 nm is found to be able to suppress the electron tunneling while maintaining a good material quality of the overall structure.
Superconducting-contact-induced resistance-anomalies in the 3D topological insulator Bi2Te3
Authors: Wang Zhuo , Ye Tianyu , Mani R. G.
Published: October 2015

This study examines the magnetotransport response observed in flakes of the 3D topological insulator (TI) Bi2Te3, including indium superconducting electrodes, and demonstrates two critical transitions in the magnetoresistive response with decreasing temperatures below T=3.4 K. The first transition is attributed to superconductivity in the indium electrodes, and the second transition, with a critical field exceeding the transition field of indium, is attributed to a proximity effect at the 2D planar interface of this hybrid TI/superconductor structure.
The appearance, motion, and disappearance of three-dimensional magnetic null points
Authors: Murphy Nicholas A. , Parnell Clare E. , Haynes Andrew L.
Published: October 2015

While theoretical models and simulations of magnetic reconnection often assume symmetry such that the magnetic null point when present is co-located with a flow stagnation point, the introduction of asymmetry typically leads to non-ideal flows across the null point. To understand this behavior, we present exact expressions for the motion of three-dimensional linear null points. The most general expression shows that linear null points move in the direction along which the magnetic field and its time derivative are antiparallel. Null point motion in resistive magnetohydrodynamics results from advection by the bulk plasma flow and resistive diffusion of the magnetic field, which allows non-ideal flows across topological boundaries. Null point motion is described intrinsically by parameters evaluated locally; however, global dynamics help set the local conditions at the null point. During a bifurcation of a degenerate null point into a null-null pair or the reverse, the instantaneous velocity of separation or convergence of the null-null pair will typically be infinite along the null space of the Jacobian matrix of the magnetic field, but with finite components in the directions orthogonal to the null space. Not all bifurcating null-null pairs are connected by a separator. Furthermore, except under special circumstances, there will not exist a straight line separator connecting a bifurcating null-null pair. The motion of separators cannot be described using solely local parameters because the identification of a particular field line as a separator may change as a result of non-ideal behavior elsewhere along the field line.
A handheld low temperature atmospheric pressure air plasma gun for nanomaterial synthesis in liquid phase
Authors: Yu Shuang , Wang Kaile , Zuo Shasha , Liu Jiahui , Zhang Jue , Fang Jing
Published: October 2015

A handheld low temperature atmospheric pressure air plasma gun based on a dielectric barrier structure with hollow electrodes was proposed. The portable plasma gun with an embedded mini air pump was driven by a 12 V direct voltage battery. The air plasma jet generated from the gun could be touched without a common shock hazard. Besides working in air, the plasma gun can also work in water. The diagnostic result of optical emission spectroscopy showed the difference in reactive species of air plasma jet between in air and in water. The plasma gun was excited in 20 ml chloroauric acid aqueous solution with a concentration of 1.214 mM. A significant amount of gold nanoparticles were synthesized after 2 min continuous discharge. The plasma gun with these unique features is applicable in plasma medicine, etching, and s-nthesis of nanomaterials.
High energy micro electron beam generation using chirped laser pulse in the presence of an axial magnetic field
Authors: Akou H. , Hamedi M.
Published: October 2015

In this paper, the generation of high-quality and high-energy micro electron beam in vacuum by a chirped Gaussian laser pulse in the presence of an axial magnetic field is numerically investigated. The features of energy and angular spectra, emittances, and position distribution of electron beam are compared in two cases, i.e., in the presence and absence of an external magnetic field. The electron beam is accelerated with higher energy and qualified in spatial distribution in the presence of the magnetic field. The presence of an axial magnetic field improves electron beam spatial quality as well as its gained energy through keeping the electron motion parallel to the direction of propagation for longer distances. It has been found that a 64 μm electron bunch with about MeV initial energy becomes a 20 μm electron beam with high energy of the order of GeV, after interacting with a laser pulse in the presence of an external magnetic field.
Study of electron transport in a Hall thruster by axial–radial fully kinetic particle simulation
Authors: Cho Shinatora , Watanabe Hiroki , Kubota Kenichi , Iihara Shigeyasu , Fuchigami Kenji , Uematsu Kazuo , Funaki Ikkoh
Published: October 2015

Electron transport across a magnetic field in a magnetic-layer-type Hall thruster was numerically investigated for the future predictive modeling of Hall thrusters. The discharge of a 1-kW-class magnetic-layer-type Hall thruster designed for high-specific-impulse operation was modeled using an r-z two-dimensional fully kinetic particle code with and without artificial electron-diffusion models. The thruster performance results showed that both electron transport models captured the experimental result within discrepancies less than 20% in thrust and discharge current for all the simulated operation conditions. The electron cross-field transport mechanism of the so-called anomalous diffusion was self-consistently observed in the simulation without artificial diffusion models; the effective electron mobility was two orders of magnitude higher than the value obtained using the classical diffusion theory. To account for the self-consistently observed anomalous transport, the oscillation of plasma properties was speculated. It was suggested that the enhanced random-walk diffusion due to the velocity oscillation of low-frequency electron flow could explain the observed anomalous diffusion within an order of magnitude. The dominant oscillation mode of the electron flow velocity was found to be 20 kHz, which was coupled to electrostatic oscillation excited by global ionization instability.
Non-local magnetoresistance in YIG/Pt nanostructures
Authors: Goennenwein Sebastian T. B. , Schlitz Richard , Pernpeintner Matthias , Ganzhorn Kathrin , Althammer Matthias , Gross Rudolf , Huebl Hans
Published: October 2015

We study the local and non-local magnetoresistance of thin Pt strips deposited onto yttrium iron garnet. The local magnetoresistive response, inferred from the voltage drop measured along one given Pt strip upon current-biasing it, shows the characteristic magnetization orientation dependence of the spin Hall magnetoresistance. We simultaneously also record the non-local voltage appearing along a second, electrically isolated, Pt strip, separated from the current carrying one by a gap of a few 100 nm. The corresponding non-local magnetoresistance exhibits the symmetry expected for a magnon spin accumulation-driven process, confirming the results recently put forward by Cornelissen et al. [“Long-distance transport of magnon spin information in a magnetic insulator at room temperature,” Nat. Phys. (published online 14 September 2015)]. Our magnetotransport data, taken at a series of different temperatures as a function of magnetic field orientation, rotating the externally applied field in three mutually orthogonal planes, show that the mechanisms behind the spin Hall and the non-local magnetoresistance are qualitatively different. In particular, the non-local magnetoresistance vanishes at liquid Helium temperatures, while the spin Hall magnetoresistance prevails.
Energetically consistent collisional gyrokinetics
Authors: Burby J. W. , Brizard A. J. , Qin H.
Published: October 2015

We present a formulation of collisional gyrokinetic theory with exact conservation laws for energy and canonical toroidal momentum. Collisions are accounted for by a nonlinear gyrokinetic Landau operator. Gyroaveraging and linearization do not destroy the operator's conservation properties. Just as in ordinary kinetic theory, the conservation laws for collisional gyrokinetic theory are selected by the limiting collisionless gyrokinetic theory.
Transport diffusion in one dimensional molecular systems: Power law and validity of Fick’s law
Authors: Xu Zhi-cheng , Zheng Dong-qin , Ai Bao-quan , Hu Bambi , Zhong Wei-rong
Published: October 2015

The transport diffusion in one-dimensional molecular systems is investigated through non-equilibrium molecular dynamics and Monte Carlo methods. We have proposed the power law relationship of the transport diffusion coefficient with the temperature, the mass and the transport length, D* ∝ T*m*−1L*β, where β equals to 0.8 for small systems and zero for large systems. It is found that Fick’s law is valid in long transport length but invalid in short transport length. Our results can provide a new perspective for understanding the microscopic mechanism of the molecular transport phenomena in low-dimensional systems.
Organic transistors fabricated by contact coating at liquid-solid interface for nano-structures
Authors: Cheng Yu-Wen , Chen Chao-Hsuan , Meng Hsin-Fei , Zan Hsiao-Wen , Chao Yu-Chiang , Horng Sheng-Fu
Published: October 2015

A contact coating method is developed to cover the nano-channels with 100 nm or 200 nm diameter and 400 nm depth with a poly(4-vinylphenol) (PVP). In such coating the nano-channels faces downwards and its vertical position is controlled by a motor. The surface is first lowered to be in immediate contact with the polyvinylpyrrolidone (PVPY) water solution with concentration from 1 to 5 wt%, then pulled at the speed of 0.004 to 0.4 mm/s. By tuning the pulling speed and concentration we can realize conformal, filled, top-only, as well as floating film morphology. For a reproducible liquid detachment from the solid, the sample has a small tilt angle of 3 degree. Contact coating is used to cover the Al grid base of the vertical space-charge-limited transistor with PVPY. Poly(3-hexylthiophene-2,5-diyl) (P3HT) as the semiconductor. The transistor breakdown voltage is raised due to base coverage achieved by contact coating.
Infield superconductivity of carbon nanotubes-Cu0.5Tl0.5Ba2Ca2Cu3O10−δ superconductor composites
Authors: Mumtaz M. , Hussain Ghulam , Rabbani M. W. , Waqee-ur-Rehman M. , Qasim Irfan , Jabbar Abdul , Khan Nawazish A.
Published: October 2015

We investigated the infield superconducting properties of carbon nanotubes-Cu0.5Tl0.5Ba2Ca2Cu3O10−δ superconductor {(CNTs)x-(CuTl-1223)}; x = 0∼7 wt.% composites. The zero resistivity critical temperature {Tc(0)}, critical superconducting onset transition temperature {Tconset(K)} and glass transition temperature (Tg) have been shifted towards lower values after the addition of carbon nanotubes (CNTs). The double transitions for all concentration of CNTs have indicated the existence of vortex-glass phase. The significant resistive broadening {ΔT = Tconset(K)-Tc(0)} has been observed with increasing values of external applied magnetic field. The more increasing trend in resistive broadening has also been observed after the addition of CNTs in CuTl-1223 matrix. The magnetic field dependent activation energy Uo (H) has been calculated according to thermally activated flux flow (TAFF) model. The overall decreasing rate in pinning energy could be due to diffusion of carbon across the grain-boundaries.
Voltage adjusting characteristics in terahertz transmission through Fabry-Pérot-based metamaterials
Authors: Luo Jun , Lin Jiuning , Zhang Xinyu , Sang Hongshi , Ji An , Xie Changsheng
Published: October 2015

Metallic electric split-ring resonators (SRRs) with featured size in micrometer scale, which are connected by thin metal wires, are patterned to form a periodically distributed planar array. The arrayed metallic SRRs are fabricated on an n-doped gallium arsenide (n-GaAs) layer grown directly over a semi-insulating gallium arsenide (SI-GaAs) wafer. The patterned metal microstructures and n-GaAs layer construct a Schottky diode, which can support an external voltage applied to modify the device properties. The developed architectures present typical functional metamaterial characters, and thus is proposed to reveal voltage adjusting characteristics in the transmission of terahertz waves at normal incidence. We also demonstrate the terahertz transmission characteristics of the voltage controlled Fabry-Pérot-based metamaterial device, which is composed of arrayed metallic SRRs. To date, many metamaterials developed in earlier works have been used to regulate the transmission amplitude or phase at specific frequencies in terahertz wavelength range, which are mainly dominated by the inductance-capacitance (LC) resonance mechanism. However, in our work, the external voltage controlled metamaterial device is developed, and the extraordinary transmission regulation characteristics based on both the Fabry-Pérot (FP) resonance and relatively weak surface plasmon polariton (SPP) resonance in 0.025-1.5 THz range, are presented. Our research therefore shows a potential application of the dual-mode-resonance-based metamaterial for improving terahertz transmission regulation.
Resonance spectra of diabolo optical antenna arrays
Authors: Guo Hong , Simpkins Blake , Caldwell Joshua D. , Guo Junpeng
Published: October 2015

A complete set of diabolo optical antenna arrays with different waist widths and periods was fabricated on a sapphire substrate by using a standard e-beam lithography and lift-off process. Fabricated diabolo optical antenna arrays were characterized by measuring the transmittance and reflectance with a microscope-coupled FTIR spectrometer. It was found experimentally that reducing the waist width significantly shifts the resonance to longer wavelength and narrowing the waist of the antennas is more effective than increasing the period of the array for tuning the resonance wavelength. Also it is found that the magnetic field enhancement near the antenna waist is correlated to the shift of the resonance wavelength.
Particle storage ring enables a role reversal in proton capture
Authors: Miller Johanna L.
Published: October 2015

A novel technique for measuring nuclear reaction cross sections may yield long-sought parameters for short-lived isotopes.
A quantum squeezed state of a mechanical resonator has been realized
Authors: Miller Johanna L.
Published: October 2015

Manipulating zero-point fluctuations may pave the way for ultraprecise measurements of forces and positions.
Slow-growing pebbles lead to fast-growing Jupiters
Authors: Chang Sung
Published: October 2015

Planet-formation simulations produce the right number of gas giants in our outer solar system.
Is US headed for a glut of a critical medical isotope?
Authors: Kramer David
Published: October 2015

Each of four prospective producers of molybdenum-99 says it can satisfy at least half of US demand for the short-lived substance.
A FAIR deal: Member countries break impasse on stalled antiproton and ion research center
Authors: Feder Toni
Published: October 2015

Antiproton researchers—who are responsible for the “A” in FAIR—are especially relieved that the project will stay intact.
NSF reconfigures nanoscience network
Authors: Feder Toni
Published: October 2015

Centers are spread more evenly across the country and include environmental and Earth sciences.
Academies seek regulatory relief for university research
Authors: Kramer David
Published: October 2015

Committee report urges agencies to trim and standardize their grant-application requirements.
Arch and scaffold: How Einstein found his field equations
Authors: Janssen Michel , Renn Jürgen
Published: October 2015

In his later years, Einstein often claimed that he had obtained the field equations of general relativity by choosing the mathematically most natural candidate. His writings during the period in which he developed general relativity tell a different story.
What every physicist should know about string theory
Authors: Witten Edward
Published: October 2015

Some of nature’s rhymes—the appearance of similar structures in different areas of physics—underlie the way that string theory potentially unifies gravity with the other forces of nature and eliminates the ultraviolet divergences that plague quantum gravity.
MMR: a tool for read multi-mapper resolution
Authors: Kahles André , Behr Jonas , Rätsch Gunnar
Published: October 2015

Motivation: Mapping high-throughput sequencing data to a reference genome is an essential step for most analysis pipelines aiming at the computational analysis of genome and transcriptome sequencing data. Breaking ties between equally well mapping locations poses a severe problem not only during the alignment phase but also has significant impact on the results of downstream analyses. We present the multi-mapper resolution (MMR) tool that infers optimal mapping locations from the coverage density of other mapped reads.

Results: Filtering alignments with MMR can significantly improve the performance of downstream analyses like transcript quantitation and differential testing. We illustrate that the accuracy (Spearman correlation) of transcript quantification increases by 15% when using reads of length 51. In addition, MMR decreases the alignment file sizes by more than 50%, and this leads to a reduced running time of the quantification tool. Our efficient implementation of the MMR algorithm is easily applicable as a post-processing step to existing alignment files in BAM format. Its complexity scales linearly with the number of alignments and requires no further inputs.

Availability and implementation: Open source code and documentation are available for download at http://github.com/ratschlab/mmr. Comprehensive testing results and further information can be found at http://bioweb.me/mmr.

Contact:  andre.kahles@ratschlab.org or gunnar.ratsch@ratschlab.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules
Authors: Cestarelli Valerio , Fiscon Giulia , Felici Giovanni , Bertolazzi Paola , Weitschek Emanuel
Published: October 2015

Motivation: Nowadays, knowledge extraction methods from Next Generation Sequencing data are highly requested. In this work, we focus on RNA-seq gene expression analysis and specifically on case–control studies with rule-based supervised classification algorithms that build a model able to discriminate cases from controls. State of the art algorithms compute a single classification model that contains few features (genes). On the contrary, our goal is to elicit a higher amount of knowledge by computing many classification models, and therefore to identify most of the genes related to the predicted class.

Results: We propose CAMUR, a new method that extracts multiple and equivalent classification models. CAMUR iteratively computes a rule-based classification model, calculates the power set of the genes present in the rules, iteratively eliminates those combinations from the data set, and performs again the classification procedure until a stopping criterion is verified. CAMUR includes an ad-hoc knowledge repository (database) and a querying tool.

We analyze three different types of RNA-seq data sets (Breast, Head and Neck, and Stomach Cancer) from The Cancer Genome Atlas (TCGA) and we validate CAMUR and its models also on non-TCGA data. Our experimental results show the efficacy of CAMUR: we obtain several reliable equivalent classification models, from which the most frequent genes, their relationships, and the relation with a particular cancer are deduced.

Availability and implementation:  dmb.iasi.cnr.it/camur.php

Contact:  emanuel@iasi.cnr.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Fit3D: a web application for highly accurate screening of spatial residue patterns in protein structure data
Authors: Kaiser Florian , Eisold Alexander , Bittrich Sebastian , Labudde Dirk
Published: October 2015

Summary: The clarification of linkage between protein structure and function is still a demanding process and can be supported by comparison of spatial residue patterns, so-called structural motifs. However, versatile up-to-date resources to search for local structure similarities are rare. We present Fit3D, an easily accessible web application for highly accurate screening of structural motifs in 3D protein data.

Availability and implementation: The web application is accessible at https://biosciences.hs-mittweida.de/fit3d and program sources of the command line version were released under the terms of GNU GPLv3. Platform-independent binaries and documentations for offline usage are available at https://bitbucket.org/fkaiser/fit3d.

Contact:  florian.kaiser@hs-mittweida.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Riboswitch Scanner: an efficient pHMM-based web-server to detect riboswitches in genomic sequences
Authors: Mukherjee Sumit , Sengupta Supratim
Published: October 2015

Summary: Riboswitches are non-coding RNA located in the 5′ untranslated regions where they bind a target metabolite used to specify the riboswitch class and control the expression of associated genes. Accurate identification of riboswitches is the first step towards understanding their regulatory and functional roles in the cell. In this article, we describe a new web application named Riboswitch Scanner which provides an automated pipeline for pHMM-based detection of riboswitches in partial as well as complete genomic sequences rapidly, with high sensitivity and specificity.

Availability and implementation: Riboswitch Scanner can be freely accessed on the web at http://service.iiserkol.ac.in/∼riboscan/.

Contact:  mukherjee.sumit89@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Dynamic Relationship Between Clinical Symptomatology and Viral Shedding in Naturally Acquired Seasonal and Pandemic Influenza Virus Infections
Authors: Ip Dennis K. M. , Lau Lincoln L. H. , Chan Kwok-Hung , Fang Vicky J. , Leung Gabriel M. , Peiris Malik J. S. , Cowling Benjamin J.
Published: October 2015

Background.  Although the pattern of viral shedding over time has been documented in volunteer challenge studies, understanding of the relationship between clinical symptomatology and viral shedding in naturally acquired influenza infections in humans remains limited.

Methods.  In a community-based study in Hong Kong from 2008 to 2014, we followed up initially healthy individuals and identified 224 secondary cases of natural influenza virus infection in the household setting. We examined the dynamic relationship between patterns of clinical symptomatology and viral shedding as quantified using reverse transcription polymerase chain reaction and viral culture in 127 cases with a clinical picture of acute respiratory infection.

Results.  Viral shedding in influenza A virus infections peaked on the first 1–2 days of clinical illness, and decreased gradually to undetectable levels by day 6–7, matching closely with the dynamics of clinical illness. Viral shedding in influenza B virus infections rose up to 2 days prior to symptom onset and persisted for 6–7 days after onset with a bimodal pattern.

Conclusions.  Our results suggest that while clinical illness profiles may serve as a proxy for clinical infectiousness in influenza A virus infections, patients may potentially be infectious even before symptom onset or after clinical improvement in influenza B virus infections.
Flash-ionization of pre-existing circumstellar material around Nova Oph 2015
Authors: Munari U. , Walter F. M.
Published: October 2015

We have obtained daily high-resolution Echelle spectroscopy of Nova Oph 2015 during its initial evolution. It reveals the presence of pre-existing circumstellar material around the nova, which can be interpreted as the wind of an evolved companion. On earliest observations, the emission line profiles of Nova Oph 2015 displayed a very narrow emission component (full width at half-maximum [FWHM] ∼ 60 km s−1), recombining over a time-scale of 5 days and showing constant low velocity (RV⊙ = −4.5 km s−1), that we interpret as coming from the wind of the secondary recombining after the ionization from the initial UV-flash of the nova. The underlying broad component underwent a marked reduction in both FWHM and width at zero intensity (the latter declining from 4000 to 2000 km s−1 in 10 days) while increasing by six times in flux, that we believe is the result of the high-velocity ejecta of the nova being slowed down while trying to expand within the surrounding wind of the companion. Nova Oph 2015 is possibly unique among novae with evolved companions in having displayed a long rise to maximum brightness and a slow decline from it, an Fe ii-type classification, and a probable sub-giant luminosity class for the secondary.
Genetic counseling and tumor predisposition in neuro-oncology
practice
Authors: Dunbar Erin M. , Eppolito Amanda , Henson John W.
Published: October 2015

Tumor predisposition syndromes may be under-recognized in neuro-oncology practice. Identifying patients with a hereditary tumor predisposition permits appropriate tumor management as well as surveillance and risk-reduction measures for patients and their families. The American College of Medical Genetics and Genomics and the National Society of Genetic Counselors recently published referral guidelines for tumor predisposition assessment, providing an impetus to review the use of genetic counseling in neuro-oncology and to describe features of the less stereotypic conditions from the perspective of neuro-oncology practice. This review also provides a framework for the identification and management of these conditions, as well as references to guidelines and resources for providers and patients.
Evidence for a 36 ks phase modulation in the hard X-ray pulses from the magnetar 1E 1547.0−5408
Authors: Makishima Kazuo , Enoto Teruaki , Murakami Hiroaki , Furuta Yoshihiro , Nakano Toshio , Sasano Makoto , Nakazawa Kazuhiro
Published: October 2015

The Suzaku data for the highly variable magnetar 1E 1547.0−5408, obtained during the 2009 January activity, were reanalyzed. The 2.07 s pulsation, detected in the 15–40 keV HXD data, was found to exhibit phase modulation, which can be modeled by a sinusoid with a period of $36.0^{+4.5}_{-2.5}\:$ks and an amplitude of 0.52 ± 0.14 s. While the effect is also seen in the 10–14 keV XIS data, the modulation amplitude decreased towards lower energies, becoming consistent with 0 below 4 keV. After the case of 4U 0142+61, this makes the second example of this kind of behavior detected from magnetars. The effect can be interpreted as a manifestation of torque-free precession of this magnetar, which is suggested to be prolately deformed under the presence of a strong toroidal field of ∼1016 G.
Radiation mechanisms and physical properties of the γ-ray narrow-line Seyfert 1 galaxies
Authors: Yang Jianping , Zhou Bin
Published: October 2015

We investigate the physical properties and radiation mechanisms of 11 states of five narrow-line Seyfert 1 (NLS1) galaxies detected by the Large Area Telescope on board Fermi through modeling the quasi-simultaneous multi-band observations. We obtain the best-fitting model parameters and their uncertainties for each state with the χ2-minimization procedure and discuss their implications on the characteristics of jet. Similar to blazars, their spectral energy distributions (SEDs) have a two-humped structure and their non-thermal emission can be modelled with the single-zone synchrotron + inverse Compton (IC) model. For all states, the GeV γ-rays may be contributed by the external Compton (EC) emission components. The observations of Fermi are mostly located at the declining stage of the EC humps. Text < 0.5 eV in all cases (Text is the characteristic temperature of external soft photons), suggesting that their radiation zones may be usually located outside of the broad line region (BLR) and the soft photons of Compton scattering mainly come from the dust torus. Compared with the bright Fermi blazars studied by Ghisellini et al. (2014, Nature, 515, 376), the Pjet (the power of the jets) of NLS1 galaxies detected by Fermi is similar to that of the flat spectrum radio quasars (FSRQs) but a little larger than that of the BL Lac objects (BL Lacs). However, a comparison of Pr (the powers of radiations) with the FSRQs and BL Lac objects shows that NLS1 galaxies’ Pr has values comparable to BL Lac objects but lower than FSRQs in spite of having similar Pjet values and the same energy carrier (the cold protons) as the FSRQs. Observations indicate that γ-NLS1 galaxies might have lower η (efficiency of gravitational energy release) values than GeV blazars.
Rotation curve decomposition for size–mass relations of bulge, disk, and dark halo components in spiral galaxies
Authors: Sofue Yoshiaki
Published: October 2015

Rotation curves of more than 100 spiral galaxies were compiled from the literature, and deconvolved into bulge, disk, and dark halo components using χ2 fitting in order to determine their scale radii and masses. Correlation analyses were obtained of the fitting parameters for galaxies that satisfied selection and accuracy criteria. Size–mass relations indicate that the sizes and masses are positively correlated among different components in such a way that the larger or more massive the dark halo, the larger or more massive the disk and bulge. Empirical size–mass relations were obtained for bulge, disk and dark halo by least-squares fitting. The disk-to-halo mass ratio was found to be systematically greater by a factor of three than that predicted by cosmological simulations combined with photometry. A preliminary mass function for the dark halo was obtained, which is represented by the Schechter function followed by a power law.
A Unified Theory of Firm Selection and Growth
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Authors: Arkolakis Costas
Published: October 2015

This article develops an analytical framework to study firm and exporter growth and provides a dynamic foundation for a standard general equilibrium trade model. Firm-level growth is the result of idiosyncratic productivity improvements with a continuous arrival of new potential producers. A firm enters a market if it is profitable to incur the marginal cost to reach the first consumer and pays an increasing marketing cost to reach additional consumers. I calibrate the model using data on the cross section of firm sales and bilateral trade, as well as the rate of incumbent firm exit. The calibrated model predicts that a firm’s growth is inversely related to its initial size, and that the distribution of growth rates of small firms is heavily skewed to the right. These predictions are confirmed by looking at the growth of sales of U.S. firms and Brazilian exporters to the United States. I use this model to study the impact of cross-firm reallocations on economic activity and measured productivity.
Guided Growth Implant Failure is a Result of Cyclic Fatigue: Explant Analysis With Scanning Electron Microscopy
Authors: Clement Anna E.B. , Vanderby Ray , Halanski Matthew A. , Noonan Kenneth J.
Published: October 2015

Background:

Guided growth is often used to correct limb deformity and yet implant screw failure in modular systems has been reported. There have been no reports of plate failure and we do not know the exact mode of failure when screws do break.

Methods:

We report the first published case of a fractured plate in a modular plate and screw construct that was used to correct Blount disease in a child through guided growth. The implants were removed and analyzed for method of failure using scanning electron microscopy.

Results:

Scanning electron microscopy of the explant confirms that the mode of failure was not a result of static tension from growth. Rather, analysis confirms cyclic fatigue that led to crack propagation across the anterior side of the plate until overload caused complete plate failure.

Conclusions:

This analysis confirms an in vivo cyclic compression-relaxation of the growth plate presumably to weight-bearing, and that when excessive may lead to implant failure as seen here in this case.

Level of Evidence:

Level V.