bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrogen-bond vibrational and energetic dynamical properties in sI and sII clathrate hydrates and in ice Ih: Molecular dynamics insights
Authors: Chakraborty Somendra Nath , English Niall J.
Published: October 2015

Equilibrium molecular dynamics (MD) simulations have been performed on cubic (sI and sII) polymorphs of methane hydrate, and hexagonal ice (ice Ih), to study the dynamical properties of hydrogen-bond vibrations and hydrogen-bond self-energy. It was found that hydrogen-bond energies are greatest in magnitude in sI hydrates, followed by sII, and their energies are least in magnitude in ice Ih. This is consistent with recent MD-based findings on thermal conductivities for these various materials [N. J. English and J. S. Tse, Phys. Rev. Lett. 103, 015901 (2009)], in which the lower thermal conductivity of sI methane hydrate was rationalised in terms of more strained hydrogen-bond arrangements. Further, modes for vibration and energy-transfer via hydrogen bonds in sI hydrate were found to occur at higher frequencies vis-à-vis ice Ih and sII hydrate in both the water-librational and OH⋯H regions because of the more strained nature of hydrogen bonds therein.
Motivation of concepts for the negative ion extraction from a single element of the matrix source
Authors: Lishev St. , Shivarova A. , Yordanov D.
Published: October 2015

A single element of a matrix source of negative hydrogen ions (a planar-coil inductively driven small-radius discharge equipped with an extraction system) is studied regarding the ion extraction. Since the spatial distribution of the negative ions obeys that of the dc potential, the latter is controlled by applying a high bias to the plasma electrode of the extraction system. This leads to discharge maintenance by both rf and dc power deposition and, respectively, to similarities with the axial profile of the dc potential in the glow discharges. The discharge length, the applied rf power, and the bias to the plasma electrode and its radius are the parameters varied in determination of proper conditions for the ion extraction.
Microwave frequency sweep interferometer for plasma density measurements in ECR ion sources: Design and preliminary results
Authors: Torrisi Giuseppe , Mascali David , Neri Lorenzo , Leonardi Ornella , Sorbello Gino , Celona Luigi , Castro Giuseppe , Agnello Riccardo , Caruso Antonio , Passarello Santi , Longhitano Alberto , Isernia Tommaso , Gammino Santo
Published: October 2015

The Electron Cyclotron Resonance Ion Sources (ECRISs) development is strictly related to the availability of new diagnostic tools, as the existing ones are not adequate to such compact machines and to their plasma characteristics. Microwave interferometry is a non-invasive method for plasma diagnostics and represents the best candidate for plasma density measurement in hostile environment. Interferometry in ECRISs is a challenging task mainly due to their compact size. The typical density of ECR plasmas is in the range 1011–1013 cm−3 and it needs a probing beam wavelength of the order of few centimetres, comparable to the chamber radius. The paper describes the design of a microwave interferometer developed at the LNS-INFN laboratories based on the so-called “frequency sweep” method to filter out the multipath contribution in the detected signals. The measurement technique and the preliminary results (calibration) obtained during the experimental tests will be presented.
Progress in high-temperature oven development for 28 GHz electron cyclotron resonance ion source
Authors: Ohnishi J. , Higurashi Y. , Nakagawa T.
Published: October 2015

We have been developing a high-temperature oven using UO2 in the 28 GHz superconducting electron cyclotron resonance ion source at RIKEN since 2013. A total of eleven on-line tests were performed. The longest operation time in a single test was 411 h, and the consumption rate of UO2 was approximately 2.4 mg/h. In these tests, we experienced several problems: the ejection hole of a crucible was blocked with UO2 and a crucible was damaged because of the reduction of tungsten strength at high temperature. In order to solve these problems, improvements to the crucible shape were made by simulations using ANSYS.
Ionization and photofragmentation of Ru3(CO)12 and Os3(CO)12
Authors: Schalk Oliver , Josefsson Ida , Richter Robert , Prince Kevin C. , Odelius Michael , Mucke Melanie
Published: October 2015

In this paper, we use a combination of photoelectron spectroscopy, mass spectrometry, and density functional theory calculations to get a detailed understanding of valence single and double ionization and the subsequent dissociation processes. This is exemplified on benchmark systems, trimetallo-dodecacarbonyls M3(CO)12 with M = Ru, Os, where the energy remaining in the molecule after photoionization can be retrieved by measuring the degree of fragmentation of the molecular ion. The intensity of different mass peaks can thus be directly related to ionization cross sections obtained by photoelectron spectroscopy. We find that the M—CO dissociation energy rises as the number of CO ligands decreases due to dissociation. Moreover, ionization of the CO ligands has a higher cross section than that of the metal center for both single and double ionization. After advanced fragmentation, a CO bond can break and the carbon atom remains bonded to the metal core. In addition, we found that the valence ionization cross sections of M3(CO)12 are maximal at about 40 eV photon energy thus showing a more pronounced shape resonance than Ru and Os-complexes with a single metal atom center. Finally, an np → nd giant resonance absorption causes a significant increase of the ionization cross section above 50 eV for Ru3(CO)12.
Simulation study of LEBT for transversely coupled beam from an ECR ion source
Authors: Yang Y. , Dou W. P. , Sun L. T. , Yao Q. G. , Zhang Z. M. , Yuan Y. J. , He Y. , Zh X. Z. , Zhao H. W.
Published: October 2015

A Low-Energy intense-highly charged ion Accelerator Facility (LEAF) program has been launched at Institute of Modern Physics. This accelerator facility consists of a superconducting Electron Cyclotron Resonance (ECR) ion source, a Low Energy Beam Transport (LEBT) system, and a Radio Frequency Quadrupole (RFQ). It is especially of interest for the extracted ion beam from the ECR ion source, which is transversely coupled, and this property will significantly affect the beam transmission in the LEBT line and the matching with the downstream RFQ. In the beam transport design of LEAF, beam decoupling in the LEBT is considered to lower down the projection emittances and the feasibility of the design has been verified by beam simulation with a transversely coupled beam from the ECR ion source.
Thermal-electric coupled-field finite element modeling and experimental testing of high-temperature ion sources for the production of radioactive ion beams
Authors: Manzolaro M. , Meneghetti G. , Andrighetto A. , Vivian G. , D’Agostini F.
Published: October 2015

In isotope separation on line facilities the target system and the related ion source are two of the most critical components. In the context of the selective production of exotic species (SPES) project, a 40 MeV 200 μA proton beam directly impinges a uranium carbide target, generating approximately 1013 fissions per second. The radioactive isotopes produced in this way are then directed to the ion source, where they can be ionized and finally accelerated to the subsequent areas of the facility. In this work both the surface ion source and the plasma ion source adopted for the SPES facility are presented and studied by means of numerical thermal-electric models. Then, numerical results are compared with temperature and electric potential difference measurements, and finally the main advantages of the proposed simulation approach are discussed.
Beam dynamics simulations of post low energy beam transport section in RAON heavy ion accelerator
Authors: Jin Hyunchang , Jang Ji-Ho , Jang Hyojae , Hong In-Seok
Published: October 2015

RAON (Rare isotope Accelerator Of Newness) heavy ion accelerator of the rare isotope science project in Daejeon, Korea, has been designed to accelerate multiple-charge-state beams to be used for various science programs. In the RAON accelerator, the rare isotope beams which are generated by an isotope separation on-line system with a wide range of nuclei and charges will be transported through the post Low Energy Beam Transport (LEBT) section to the Radio Frequency Quadrupole (RFQ). In order to transport many kinds of rare isotope beams stably to the RFQ, the post LEBT should be devised to satisfy the requirement of the RFQ at the end of post LEBT, simultaneously with the twiss parameters small. We will present the recent lattice design of the post LEBT in the RAON accelerator and the results of the beam dynamics simulations from it. In addition, the error analysis and correction in the post LEBT will be also described.
Electron cyclotron resonance heating by magnetic filter field in a negative hydrogen ion source
Authors: Kim June Young , Cho Won-Hwi , Dang Jeong-Jeung , Chung Kyoung-Jae , Hwang Y. S.
Published: October 2015

The influence of magnetic filter field on plasma properties in the heating region has been investigated in a planar-type inductively coupled radio-frequency (RF) H− ion source. Besides filtering high energy electrons near the extraction region, the magnetic filter field is clearly observed to increase the electron temperature in the heating region at low pressure discharge. With increasing the operating pressure, enhancement of electron temperature in the heating region is reduced. The possibility of electron cyclotron resonance (ECR) heating in the heating region due to stray magnetic field generated by a filter magnet located at the extraction region is examined. It is found that ECR heating by RF wave field in the discharge region, where the strength of an axial magnetic field is approximately ∼4.8 G, can effectively heat low energy electrons. Depletion of low energy electrons in the electron energy distribution function measured at the heating region supports the occurrence of ECR heating. The present study suggests that addition of axial magnetic field as small as several G by an external electromagnet or permanent magnets can greatly increase the generation of highly ro-vibrationally excited hydrogen molecules in the heating region, thus improving the performance of H− ion generation in volume-produced negative hydrogen ion sources.
First operation and effect of a new tandem-type ion source based on electron cyclotron resonance
Authors: Kato Yushi , Kimura Daiju , Yano Keisuke , Kumakura Sho , Imai Youta , Nishiokada Takuya , Nagaya Tomoki , Hagino Shogo , Otsuka Takuro , Sato Fuminobu
Published: October 2015

A new tandem type source has been constructed on the basis of electron cyclotron resonance plasma for producing synthesized ion beams in Osaka University. Magnetic field in the first stage consists of all permanent magnets, i.e., cylindrically comb shaped one, and that of the second stage consists of a pair of mirror coil, a supplemental coil and the octupole magnets. Both stage plasmas can be individually operated, and produced ions in which is energy controlled by large bore extractor also can be transported from the first to the second stage. We investigate the basic operation and effects of the tandem type electron cyclotron resonance ion source (ECRIS). Analysis of ion beams and investigation of plasma parameters are conducted on produced plasmas in dual plasmas operation as well as each single operation. We describe construction and initial experimental results of the new tandem type ion source based on ECRIS with wide operation window for aiming at producing synthesized ion beams as this new source can be a universal source in future.
Preliminary results concerning the simulation of beam profiles from extracted ion current distributions for mini-STRIKE
Authors: Agostinetti P. , Giacomin M. , Serianni G. , Veltri P. , Bonomo F. , Schiesko L.
Published: October 2015

The Radio Frequency (RF) negative hydrogen ion source prototype has been chosen for the ITER neutral beam injectors due to its optimal performances and easier maintenance demonstrated at Max-Planck-Institut für Plasmaphysik, Garching in hydrogen and deuterium. One of the key information to better understand the operating behavior of the RF ion sources is the extracted negative ion current density distribution. This distribution—influenced by several factors like source geometry, particle drifts inside the source, cesium distribution, and layout of cesium ovens—is not straightforward to be evaluated. The main outcome of the present contribution is the development of a minimization method to estimate the extracted current distribution using the footprint of the beam recorded with mini-STRIKE (Short-Time Retractable Instrumented Kalorimeter). To accomplish this, a series of four computational models have been set up, where the output of a model is the input of the following one. These models compute the optics of the ion beam, evaluate the distribution of the heat deposited on the mini-STRIKE diagnostic calorimeter, and finally give an estimate of the temperature distribution on the back of mini-STRIKE. Several iterations with different extracted current profiles are necessary to give an estimate of the profile most compatible with the experimental data. A first test of the application of the method to the BAvarian Test Machine for Negative ions beam is given.
Transmission of electrons inside the cryogenic pumps of ITER injector
Authors: Veltri P. , Sartori E.
Published: October 2015

Large cryogenic pumps are installed in the vessel of large neutral beam injectors (NBIs) used to heat the plasma in nuclear fusion experiments. The operation of such pumps can be compromised by the presence of stray secondary electrons that are generated along the beam path. In this paper, we present a numerical model to analyze the propagation of the electrons inside the pump. The aim of the study is to quantify the power load on the active pump elements, via evaluation of the transmission probabilities across the domain of the pump. These are obtained starting from large datasets of particle trajectories, obtained by numerical means. The transmission probability of the electrons across the domain is calculated for the NBI of the ITER and for its prototype Megavolt ITer Injector and Concept Advancement (MITICA) and the results are discussed.
A vacuum spark ion source: High charge state metal ion beams
Authors: Yushkov G. Yu. , Nikolaev A. G. , Oks E. M. , Frolova V. P.
Published: October 2015

High ion charge state is often important in ion beam physics, among other reasons for the very practical purpose that it leads to proportionately higher ion beam energy for fixed accelerating voltage. The ion charge state of metal ion beams can be increased by replacing a vacuum arc ion source by a vacuum spark ion source. Since the voltage between anode and cathode remains high in a spark discharge compared to the vacuum arc, higher metal ion charge states are generated which can then be extracted as an ion beam. The use of a spark of pulse duration less than 10 μs and with current up to 10 kA allows the production of ion beams with current of several amperes at a pulse repetition rate of up to 5 pps. We have demonstrated the formation of high charge state heavy ions (bismuth) of up to 15 + and a mean ion charge state of more than 10 +. The physics and techniques of our vacuum spark ion source are described.
Generalized Bogoliubov transformations versus D-pseudo-bosons
Authors: Bagarello F. , Fring A.
Published: October 2015

We demonstrate that not all generalized Bogoliubov transformations lead to D-pseudo-bosons and prove that a correspondence between the two can only be achieved with the imposition of specific constraints on the parameters defining the transformation. For certain values of the parameters, we find that the norms of the vectors in sets of eigenvectors of two related apparently non-selfadjoint number-like operators possess different types of asymptotic behavior. We use this result to deduce further that they constitute bases for a Hilbert space, albeit neither of them can form a Riesz base. When the constraints are relaxed, they cease to be Hilbert space bases but remain D-quasibases.
Improvement of red light response of Cu2Sn1−xGexS3 solar cells by optimization of CdS buffer layers
Authors: Umehara Mitsutaro , Takeda Yasuhiko , Tajima Shin , Motohiro Tomoyoshi , Sakai Takenobu , Maekawa Ryosuke
Published: October 2015

A cross-over anomaly has been observed in Cu2Sn1−xGexS3 (CTGS) solar cells, which degrades the solar cell performance under red light illumination. This is a critical drawback for bottom cells because it should work under red light illumination, filtered through top cells. We suppressed this cross-over anomaly by optimizing the deposition conditions of CdS buffer layers, which improved the performance of the cells under red light illumination. The mechanism of this phenomenon was discussed, and we concluded the origin of the anomalies was attributed to accepter-like defects in CdS buffer layers. Furthermore, we also inferred a model for the conduction band offset of the CTGS/CdS interface, which will aid the design of high efficiency solar cells.
Investigation of pulsed mode operation with the frequency tuned CAPRICE ECRIS
Authors: Maimone F. , Tinschert K. , Endermann M. , Hollinger R. , Kondrashev S. , Lang R. , Mäder J. , Patchakui P. T. , Spädtke P.
Published: October 2015

In order to increase the intensity of the highly charged ions produced by the Electron Cyclotron Resonance Ion Sources (ECRISs), techniques like the frequency tuning and the afterglow mode have been developed and in this paper the effect on the ion production is shown for the first time when combining both techniques. Recent experimental results proved that the tuning of the operating frequency of the ECRIS is a promising technique to achieve higher ion currents of higher charge states. On the other hand, it is well known that the afterglow mode of the ECRIS operation can provide more intense pulsed ion beams in comparison with the continuous wave (cw) operation. These two techniques can be combined by pulsing the variable frequency signal driving the traveling wave tube amplifier which provides the high microwave power to the ECRIS. In order to analyze the effect of these two combined techniques on the ion source performance, several experiments were carried out on the pulsed frequency tuned CAPRICE (Compacte source A Plusiers Résonances Ionisantes Cyclotron Electroniques)-type ECRIS. Different waveforms and pulse lengths have been investigated under different settings of the ion source. The results of the pulsed mode have been compared with those of cw operation.
Enhanced coupling of optical energy during liquid-confined metal ablation
Authors: Kang Hyun Wook , Welch Ashley J.
Published: October 2015

Liquid-confined laser ablation was investigated with various metals of indium, aluminum, and nickel. Ablation threshold and rate were characterized in terms of surface deformation, transient acoustic responses, and plasma emissions. The surface condition affected the degree of ablation dynamics due to variations in reflectance. The liquid confinement yielded up to an order of larger ablation crater along with stronger acoustic transients than dry ablation. Enhanced ablation performance resulted possibly from effective coupling of optical energy at the interface during explosive vaporization, plasma confinement, and cavitation. The deposition of a liquid layer can induce more efficient ablation for laser metal processing.
Use of nonlocal helium microplasma for gas impurities detection by the collisional electron spectroscopy method
Authors: Kudryavtsev Anatoly A. , Stefanova Margarita S. , Pramatarov Petko M.
Published: October 2015

The collisional electron spectroscopy (CES) method, which lays the ground for a new field for analytical detection of gas impurities at high pressures, has been verified. The CES method enables the identification of gas impurities in the collisional mode of electron movement, where the advantages of nonlocal formation of the electron energy distribution function (EEDF) are fulfilled. Important features of dc negative glow microplasma and probe method for plasma diagnostics are applied. A new microplasma gas analyzer design is proposed. Admixtures of 0.2% Ar, 0.6% Kr, 0.1% N2, and 0.05% CO2 are used as examples of atomic and molecular impurities to prove the possibility for detecting and identifying their presence in high pressure He plasma (50–250 Torr). The identification of the particles under analysis is made from the measurements of the high energy part of the EEDF, where maxima appear, resulting from the characteristic electrons released in Penning reactions of He metastable atoms with impurity particles. Considerable progress in the development of a novel miniature gas analyzer for chemical sensing in gas phase environments has been made.
Renormalized theory of ion temperature gradient instability of the magnetic-field-aligned plasma shear flow with hot ions
Authors: Mikhailenko V. V. , Mikhailenko V. S. , Lee Hae June
Published: October 2015

The developed kinetic theory for the stability of a magnetic-field-aligned (parallel) shear flow with inhomogeneous ion temperature [Mikhailenko et al., Phys. Plasmas 21, 072117 (2014)] predicted that a kinetic instability arises from the coupled reinforcing action of the flow velocity shear and ion temperature gradient in the cases where comparable ion and electron temperatures exist. In the present paper, the nonlinear theory was developed for the instability caused by the combined effects of ion-temperature-gradient and shear-flow (ITG–SF). The level of the electrostatic turbulence is determined for the saturation state of the instability on the basis of the nonlinear dispersion equation, which accounts for a nonlinear scattering of ions by the developed turbulence in a sheared flow. The renormalized quasilinear equation for the ion distribution function, which accounts for the turbulent scattering of ions by ITG–SF driven turbulence, was derived and employed for the estimation of the turbulent ion viscosity, the anomalous ion thermal conductivity, and anomalous ion heating rate at the saturation state of the instability.
Space-time resolved measurements of spontaneous magnetic fields in laser-produced plasma
Authors: Pisarczyk T. , Gus'kov S. Yu. , Dudzak R. , Chodukowski T. , Dostal J. , Demchenko N. N. , Korneev Ph. , Kalinowska Z. , Kalal M. , Renner O. , Smid M. , Borodziuk S. , Krousky E. , Ullschmied J. , Hrebicek J. , Medrik T. , Golasowski J. , Pfeifer M. , Skala J. , Pisarczyk P.
Published: October 2015

The first space-time resolved spontaneous magnetic field (SMF) measurements realized on Prague Asterix Laser System are presented. The SMF was generated as a result of single laser beam (1.315 μm) interaction with massive planar targets made of materials with various atomic numbers (plastic and Cu). Measured SMF confirmed azimuthal geometry and their maximum amplitude reached the value of 10 MG at the laser energy of 250 J for both target materials. It was demonstrated that spatial distributions of these fields are associated with the character of the ablative plasma expansion which clearly depends on the target material. To measure the SMF, the Faraday effect was employed causing rotation of the vector of polarization of the linearly polarized diagnostic beam. The rotation angle was determined together with the phase shift using a novel design of a two-channel polaro-interferometer. To obtain sufficiently high temporal resolution, the polaro-interferometer was irradiated by Ti:Sa laser pulse with the wavelength of 808 nm and the pulse duration of 40 fs. The results of measurements were compared with theoretical analysis.
Resonance Raman spectra of organic molecules absorbed on inorganic semiconducting surfaces: Contribution from both localized intramolecular excitation and intermolecular charge transfer excitation
Authors: Ye ChuanXiang , Zhao Yi , Liang WanZhen
Published: October 2015

The time-dependent correlation function approach for the calculations of absorption and resonance Raman spectra (RRS) of organic molecules absorbed on semiconductor surfaces [Y. Zhao and W. Z. Liang, J. Chem. Phys. 135, 044108 (2011)] is extended to include the contribution of the intermolecular charge transfer (CT) excitation from the absorbers to the semiconducting nanoparticles. The results demonstrate that the bidirectionally interfacial CT significantly modifies the spectral line shapes. Although the intermolecular CT excitation makes the absorption spectra red shift slightly, it essentially changes the relative intensities of mode-specific RRS and causes the oscillation behavior of surface enhanced Raman spectra with respect to interfacial electronic couplings. Furthermore, the constructive and destructive interferences of RRS from the localized molecular excitation and CT excitation are observed with respect to the electronic coupling and the bottom position of conductor band. The interferences are determined by both excitation pathways and bidirectionally interfacial CT.
Nb-doped Gd2O3 as charge-trapping layer for nonvolatile memory applications
Authors: Shi R. P. , Huang X. D. , Sin Johnny K. O. , Lai P. T.
Published: October 2015

The charge-trapping properties of Gd2O3 with different Nb doping levels are investigated using an Al/Al2O3/Gd2O3/SiO2/Si structure. Compared with the memory device with pure Gd2O3, the one with lightly Nb-doped Gd2O3 shows better charge-trapping characteristics, including higher programming speed (6.5 V at +12 V programming voltage for 10 ms) and better retention property (92% retained charge at 85 °C after 104 s), due to its higher trapping efficiency that resulted from higher trap density and suppressed formation of a silicate interlayer at the Gd2O3/SiO2 interface induced by the Nb doping. Moreover, the one with heavily Nb-doped Gd2O3 shows improvement in erasing behavior but worse retention and lower programming speed than the one with lightly Nb-doped Gd2O3. Further analysis reveals that the Nb-doping level determines the type of dominant trap in the Nb-doped Gd2O3, thus leading to different charge-loss mechanisms and charge-trapping characteristics.
Congruent evaporation temperature of molecular beam epitaxy grown GaAs (001) determined by local droplet etching
Authors: Heyn Ch. , Jesson D. E.
Published: October 2015

The congruent evaporation temperature Tc of GaAs (001) is critical for many technological processes and is fundamental to the control and stability of Ga droplets for quantum structure fabrication. We apply the technique of local droplet etching (LDE) to measure Tc for technologically important molecular beam epitaxy (MBE) grown GaAs (001). Below Tc, Ga droplets deposited on the surface shrink and form nanoholes via LDE and thermal widening. Above Tc, droplets grow by capturing excess Ga. From the transition between both regimes, we determine Tc = 680 ± 10 °C. Additionally, we find that the nanohole/droplet densities follow an Arrhenius-type temperature dependence with an activation energy of 1.31 eV. The method probes the stability of pre-existing droplets formed by deposition and so avoids the complication of nucleation barriers and readily allows the measurement of Tc for technologically important planar GaAs surfaces in any standard MBE system.
Binary rare earth element-Ni/Co metallic glasses with distinct β-relaxation behaviors
Authors: Zhu Z. G. , Wang Z. , Wang W. H.
Published: October 2015

We report the formation of a series of rare earth element (RE)-Ni/Co binary metallic glasses (MGs) with unusual distinct β-relaxation peak compared with that of most of the reported MGs which usually exhibit as an excess wing or a shoulder. The β-relaxation behavior of RE-Ni/Co MGs is sensitive to the composition and the atomic radii of the RE and can be tuned through changing the fraction of RE-Ni (or Co) atomic pairs. The novel RE-Ni/Co MGs with distinct β-relaxation can serve as model system to investigate the nature of the β-relaxation as well as its relations with other physical and mechanical properties of MGs.
Torsional properties of hexagonal boron nitride nanotubes, carbon nanotubes and their hybrid structures: A molecular dynamics study
Authors: Xiong Qi-lin , Tian Xiao Geng
Published: October 2015

The torsional mechanical properties of hexagonal single-walled boron nitride nanotubes (SWBNNTs), single-walled carbon nanotubes (SWCNTs), and their hybrid structures (SWBN-CNTs) are investigated using molecular dynamics (MD) simulation. Two approaches - force approach and energy approach, are adopted to calculate the shear moduli of SWBNNTs and SWCNTs, the discrepancy between two approaches is analyzed. The results show that the shear moduli of single-walled nanotubes (SWNTs), including SWBNNTs and SWCNTs are dependent on the diameter, especially for armchair SWNTs. The armchair SWNTs show the better ability of resistance the twisting comparable to the zigzag SWNTs. The effects of diameter and length on the critical values of torque of SWNTs are obtained by comparing the torsional behaviors of SWNTs with different diameters and different lengths. It is observed that the MD results of the effect of diameter and length on the critical values of torque agrees well with the prediction of continuum shell model. The shear modulus of SWBN-CNT has a significant dependence on the percentages of SWCNT and the hybrid style has also an influence on shear modulus. The critical values of torque of SWBN-CNTs increase with the increase of the percentages of SWCNT. This phenomenon can be interpreted by the function relationship between the torque of different bonds (B-N-X, C-C-X, C-B-X, C-N-X) and the angles of bonds.
Single wall carbon nanotube (SWCNT) examination on blood flow through a multiple stenosed artery with variable nanofluid viscosity
Authors: Nadeem S. , Ijaz S.
Published: October 2015

The present theoretical model deals with the analysis of variable viscosity and thermal conductivity of a single wall carbon nanotube within the considered base fluid flowing through multiple stenosed arteries. A mathematical model is presented for the mild stenosis case and then solved by using symmetry boundary conditions to determine the exact solution of temperature, axial velocity and pressure gradient. The main hemodynamics due to multiple stenosis is also computed under the influence of a SWCNT. Numerical simulations are presented for the SWCNT with different values of nanoparticles volume fraction. The behavior of fluid flow for blood based SWCNT is discussed through graphs and streamlines.
Therapeutics to prevent congenital cytomegalovirus during pregnancy: what is available now and in the future?
Authors: Hamilton Stuart T , Hutterer Corina , Marschall Manfred
Published: October 2015

Human cytomegalovirus (CMV) is the leading non-genetic cause of fetal malformation in developed countries. Congenital CMV infection can cause serious clinical sequelae, and in severe cases result in fetal or neonatal death. Despite the clinical and social importance of congenital CMV there is currently no standardised management strategy to prevent or treat maternal/fetal CMV infection during pregnancy and no evidence-based therapeutic for prenatally diagnosed CMV infection or disease. For pregnant women with a primary CMV infection during pregnancy, standard medical practise remains to offer no treatment at all or the option to terminate pregnancy. If intervention is requested, pregnant women may be offered a narrow range of medical therapies with limited evidence for efficacy and some with high risks of toxicity. However, there are several experimental and novel anti-CMV therapeutics currently being investigated that may provide a safe and effective therapeutic for use during pregnancy to prevent both fetal infection and reduce the risk of congenital CMV disease developing in the fetus once infected in utero.
Flooding and geomorphology influence the persistence of the invasive annual herb Noogoora burr (Xanthium occidentale Bertol.) in the riparian zone of the dryland Darling River, Australia
Authors: Parsons Melissa , Southwell Mark
Published: October 2015

The relationship between flooding, and the establishment and persistence of exotic species, is not well understood in highly variable dryland rivers. Increased moisture associated with floods is likely to stimulate establishment and growth of exotic plants, but floods may also act as a stress to exotic plants if floods last for weeks to months. This study examined how physical drivers of dryland rivers – flood inundation and geomorphology – influence the persistence of Xanthium occidentale Bertol. in the dryland Darling River, Australia. The distribution of X. occidentale was associated with flood-related moisture subsidy, moderated by channel geomorphology. Dead stalks and burrs on the ground occurred above the 8-m height of the previous flood. Adult and juvenile plants occurred below 8 m corresponding to smaller flood events. Flatter geomorphic units (floodplains and benches) contained more plants and burrs, whereas steeper geomorphic units (banks) did not retain burrs, limiting plant abundance. Flooding is not a stress to X. occidentale. A glasshouse experiment showed that flood durations of up to 40 days had minimal effect on the germination, survival and growth of X. occidentale burrs, seeds or seedlings. Weed management strategies for X. occidentale in dryland rivers could be enhanced by targeting periods following flooding when moisture availability is increased on the flatter geomorphic units in the river channel.
Emergence of system roles in normative neurodevelopment
Authors: Gu Shi , Satterthwaite Theodore D. , Medaglia John D. , Yang Muzhi , Gur Raquel E. , Gur Ruben C. , Bassett Danielle S.
Published: October 2015

Significance

The human brain is a complex system displaying intricate, dynamic functions. In a multidisciplinary effort, the recent application of tools from network science to characterize the interconnected nature of the brain has enabled a tremendous advance in our understanding of cognition. Here, we develop and apply an extension of these tools to define and characterize the role of cognitive systems in the larger scale brain network, and to map how these roles change during adolescent development, providing an important context for understanding psychopathology. Our results are also consistent with the hypothesis that individual variation in network configuration implies differential vulnerability to cognitive abilities or deficits.
Transgenerational epigenetic programming via sperm microRNA recapitulates effects of paternal stress
Authors: Rodgers Ali B. , Morgan Christopher P. , Leu N. Adrian , Bale Tracy L.
Published: October 2015

Significance

Studies examining paternal exposure to diverse environmental stimuli propose that epigenetic marks in germ cells, including small noncoding RNAs such as microRNA (miR), transmit experience-dependent information from parent to offspring. However, these nongenetic mechanisms of transgenerational inheritance are poorly understood, specifically how these germ-cell marks may act postfertilization to enact long-term changes in offspring behavior or physiology. In this study, through zygote microinjection of nine specific sperm miRs previously identified in our paternal stress mouse model, we demonstrate that sperm miRs function to reduce maternal mRNA stores in early zygotes, ultimately reprogramming gene expression in the offspring hypothalamus and recapitulating the offspring stress dysregulation phenotype.
El Niño−Southern Oscillation frequency cascade
Authors: Stuecker Malte F. , Jin Fei-Fei , Timmermann Axel
Published: October 2015

Significance

This study identifies a mechanism to generate atmospheric variability on near-annual and subannual timescales. Responding nonlinearly to both the El Niño−Southern Oscillation (ENSO) and the annual cycle in sea surface temperatures, the atmosphere develops a wide range of deterministic spectral peaks and corresponding spatial patterns. It is demonstrated that the resulting deterministic variability, which projects onto one of the major modes of East Asian Monsoon variability, exhibits similar predictability as ENSO.
Antipredator defenses predict diversification rates
Authors: Arbuckle Kevin , Speed Michael P.
Published: October 2015

Significance

Prey use a variety of mechanisms to avoid the risk of predation, including chemical defense, camouflage, and conspicuous coloration. Here we show that variation in these forms of protection can have profound effects on macroevolutionary patterns in amphibians. Chemical defense and conspicuous coloration both increase speciation rates, in line with the “escape-and-radiate” hypothesis. However, chemical defense also increases extinction rates, lowering net diversification. We therefore show that alternative defensive strategies have important macroevolutionary consequences but that these are only partially consistent with standard escape-and-radiate interpretations. Hence, we suggest a conceptual expansion of this highly influential evolutionary hypothesis. In addition, our findings may have implications for endangered species conservation by allowing some predictability of extinction risk from knowledge of antipredator defenses.
Deciduous forest responses to temperature, precipitation, and drought imply complex climate change impacts
Authors: Xie Yingying , Wang Xiaojing , Silander John A.
Published: October 2015

Significance

Autumnal phenological shifts (leaf senescence and dormancy) because of climate change bring substantial impacts on community and ecosystem processes (e.g. altered C and N cycling and phenological mismatches) and the fall foliage ecotourism industry. However, the understanding of the environmental control of autumn phenology has changed little over the past 60 y. We found that cold, frost, wet, and high heat-stress lead to earlier dormancy dates across temperate deciduous forest communities, whereas moderate heat- and drought-stress delayed dormancy. Divergent future responses of fall dormancy timing were predicted: later for northern regions and earlier for southern areas. Our findings improve understanding of autumn phenology mechanisms and suggests complex interactions among environmental conditions affecting autumn phenology now and in the future.
Targeted binding of nucleocapsid protein transforms the folding landscape of HIV-1 TAR RNA
Authors: McCauley Micah J. , Rouzina Ioulia , Manthei Kelly A. , Gorelick Robert J. , Musier-Forsyth Karin , Williams Mark C.
Published: October 2015

Significance

The nucleocapsid protein (NC) of the human immunodeficiency virus type 1 (HIV-1) is critical for HIV-1 replication. NC is required for reverse transcription, in which the viral single-stranded RNA genome is converted into double-stranded DNA for replication in the cell. One critical step of reverse transcription that requires NC involves transient destabilization of the transactivation response (TAR) RNA hairpin into a stable double-stranded RNA–DNA hybrid structure. It is not clear how NC is able to destabilize TAR RNA without destabilizing the resulting double-stranded structure. This work shows for the first time to our knowledge that NC binding to specific defects and sequence contexts in TAR RNA dramatically alters the unfolding landscape, preferentially destabilizing TAR RNA relative to other structures to facilitate reverse transcription.
Dystrophin–glycoprotein complex regulates muscle nitric oxide production through mechanoregulation of AMPK signaling
Authors: Garbincius Joanne F. , Michele Daniel E.
Published: October 2015

Significance

Loss of dystrophin in Duchenne muscular dystrophy results in a secondary disruption of muscle nitric oxide (NO) signaling thought to contribute to exaggerated muscle fatigue and cardiac dysfunction in this disease. How muscle NO synthesis is regulated, and how dystrophin and the dystrophin–glycoprotein complex participate, are poorly understood. Using isolated adult mouse cardiomyocytes as a model of striated muscle, we provide evidence for a mechanism in which the dystrophin–glycoprotein complex functions as a mechanosensor to activate AMP-activated protein kinase (AMPK), which then phosphorylates NOS to increase NO production in response to direct mechanical stimulation. This paper also provides proof-of-concept evidence for acute pharmacologic AMPK activation as a therapy to restore NO synthesis in Duchenne muscular dystrophy.
Coevolutionary patterning of teeth and taste buds
Authors: Bloomquist Ryan F. , Parnell Nicholas F. , Phillips Kristine A. , Fowler Teresa E. , Yu Tian Y. , Sharpe Paul T. , Streelman J. Todd
Published: October 2015

Significance

Teeth and taste buds are placode-derived organs studied in isolation because of their separate anatomical locations in mammals. Yet, the mouth and pharynx of many aquatic vertebrates, including bony fishes, are lined with teeth and taste buds, one next to the other. Using a combination of genome mapping, synexpression analysis, and small-molecule manipulation, we identify factors that couple tooth and taste bud density (Wingless signals) and those that differentiate the identity of each organ from a common epithelial lamina (BMP, Hedgehog). Integrating results from fishes and mouse suggests a model wherein the regulatory hierarchies that configure teeth and taste buds on mammalian jaws and tongues may be evolutionary remnants inherited from ancestors whose oral organs were copatterned from common epithelium.
Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon
Authors: Bell Elizabeth A. , Boehnke Patrick , Harrison T. Mark , Mao Wendy L.
Published: October 2015

Significance

Evidence for carbon cycling or biologic activity can be derived from carbon isotopes, because a high
12
C/
13
C ratio is characteristic of biogenic carbon due to the large isotopic fractionation associated with enzymatic carbon fixation. The earliest materials measured for carbon isotopes at 3.8 Ga are isotopically light, and thus potentially biogenic. Because Earth’s known rock record extends only to ∼4 Ga, earlier periods of history are accessible only through mineral grains deposited in later sediments. We report
12
C/
13
C of graphite preserved in 4.1-Ga zircon. Its complete encasement in crack-free, undisturbed zircon demonstrates that it is not contamination from more recent geologic processes. Its
12
C-rich isotopic signature may be evidence for the origin of life on Earth by 4.1 Ga.
Structure of an RNA polymerase II preinitiation complex
Authors: Murakami Kenji , Tsai Kuang-Lei , Kalisman Nir , Bushnell David A. , Asturias Francisco J. , Kornberg Roger D.
Published: October 2015

Significance

RNA polymerase II, the enzyme responsible for all mRNA synthesis in eukaryotes, requires a set of general transcription factors (GTFs) for the initiation of transcription. A complex of the polymerase and GTFs, with a mass of 1.5 MDa, was previously isolated and shown to be stable, homogeneous, and active in transcription. A cryo-electron microscope structure of the complex at a resolution of 6–11 Å reported here explains the requirement for the GTFs and elucidates their roles. The GTFs recognize the region of the gene responsible for initiation and deliver it to the polymerase active center in a form amenable to transcription.
CG gene body DNA methylation changes and evolution of duplicated genes in cassava
Authors: Wang Haifeng , Beyene Getu , Zhai Jixian , Feng Suhua , Fahlgren Noah , Taylor Nigel J. , Bart Rebecca , Carrington James C. , Jacobsen Steven E. , Ausin Israel
Published: October 2015

Significance

Plant traits exhibit variation as a result of genetic and epigenetic change. Genetic variation is used for breeding and crop improvement. Epigenetic variation, especially differences in DNA methylation, also contributes to phenotype. For example, epigenetic alleles of plant genes exist in nature, which are identical in DNA sequence, but show heritable differences in DNA methylation and gene expression. Here we present whole-genome DNA methylation patterns of the agronomically important crop cassava (
Manihot esculenta
), which can serve as the basis for the study of epigenetic variation in this organism. We found that recently duplicated genes have evolved different DNA methylation and expression patterns that likely contribute to important agronomic traits.
Qualitative changes in human γ-secretase underlie familial Alzheimer’s disease
Authors: Szaruga Maria , Veugelen Sarah , Benurwar Manasi , Lismont Sam , Sepulveda-Falla Diego , Lleo Alberto , Ryan Natalie S. , Lashley Tammaryn , Fox Nick C. , Murayama Shigeo , Gijsen Harrie , De Strooper Bart , Chávez-Gutiérrez Lucía
Published: October 2015

Presenilin (PSEN) pathogenic mutations cause familial Alzheimer’s disease (AD [FAD]) in an autosomal-dominant manner. The extent to which the healthy and diseased alleles influence each other to cause neurodegeneration remains unclear. In this study, we assessed γ-secretase activity in brain samples from 15 nondemented subjects, 22 FAD patients harboring nine different mutations in PSEN1, and 11 sporadic AD (SAD) patients. FAD and control brain samples had similar overall γ-secretase activity levels, and therefore, loss of overall (endopeptidase) γ-secretase function cannot be an essential part of the pathogenic mechanism. In contrast, impaired carboxypeptidase-like activity (γ-secretase dysfunction) is a constant feature in all FAD brains. Significantly, we demonstrate that pharmacological activation of the carboxypeptidase-like γ-secretase activity with γ-secretase modulators alleviates the mutant PSEN pathogenic effects. Most SAD cases display normal endo- and carboxypeptidase-like γ-secretase activities. However and interestingly, a few SAD patient samples display γ-secretase dysfunction, suggesting that γ-secretase may play a role in some SAD cases. In conclusion, our study highlights qualitative shifts in amyloid-β (Aβ) profiles as the common denominator in FAD and supports a model in which the healthy allele contributes with normal Aβ products and the diseased allele generates longer aggregation-prone peptides that act as seeds inducing toxic amyloid conformations.
Expression of Mutant Bone Morphogenetic Protein Receptor II Worsens Pulmonary Hypertension Secondary to Pulmonary Fibrosis
Authors: Bryant Andrew J. , Robinson Linda J. , Moore Christy S. , Blackwell Thomas R. , Gladson Santhi , Penner Niki L. , Burman Ankita , McClellan Lucas J. , Polosukhin Vasiliy V. , Tanjore Harikrishna , McConaha Melinda E. , Gleaves Linda A. , Talati Megha A. , Hemnes Anna R. , Fessel Joshua P. , Lawson William E. , Blackwell Timothy S. , West James D.
Published: October 2015

Pulmonary fibrosis is often complicated by pulmonary hypertension (PH), and previous studies have shown a potential link between bone morphogenetic protein receptor II (BMPR2) and PH secondary to pulmonary fibrosis. We exposed transgenic mice expressing mutant BMPR2 and control mice to repetitive intraperitoneal injections of bleomycin for 4 weeks. The duration of transgene activation was too short for mutant BMPR2 mice to develop spontaneous PH. Mutant BMPR2 mice had increased right ventricular systolic pressure compared to control mice, without differences in pulmonary fibrosis. We found increased hypoxia‐inducible factor (HIF) 1‐α stabilization in lungs of mutant‐BMPR2‐expressing mice compared to controls following bleomycin treatment. In addition, expression of the hypoxia response element protein connective tissue growth factor was increased in transgenic mice as well as in a human pulmonary microvascular endothelial cell line expressing mutant BMPR2. In mouse pulmonary vascular endothelial cells, mutant BMPR2 expression resulted in increased HIF1‐α and reactive oxygen species production following exposure to hypoxia, both of which were attenuated with the antioxidant TEMPOL. These data suggest that expression of mutant BMPR2 worsens secondary PH through increased HIF activity in vascular endothelium. This pathway could be therapeutically targeted in patients with PH secondary to pulmonary fibrosis.