bluuebunny/crossref_metadata_2025 huggingface dataset:
miRegulome: a knowledge-base of miRNA regulomics and analysis
Authors: Barh Debmalya , Kamapantula Bhanu , Jain Neha , Nalluri Joseph , Bhattacharya Antaripa , Juneja Lucky , Barve Neha , Tiwari Sandeep , Miyoshi Anderson , Azevedo Vasco , Blum Kenneth , Kumar Anil , Silva Artur , Ghosh Preetam
Published: August 2015

miRNAs regulate post transcriptional gene expression by targeting multiple mRNAs and hence can modulate multiple signalling pathways, biological processes and patho-physiologies. Therefore, understanding of miRNA regulatory networks is essential in order to modulate the functions of a miRNA. The focus of several existing databases is to provide information on specific aspects of miRNA regulation. However, an integrated resource on the miRNA regulome is currently not available to facilitate the exploration and understanding of miRNA regulomics. miRegulome attempts to bridge this gap. The current version of miRegulome v1.0 provides details on the entire regulatory modules of miRNAs altered in response to chemical treatments and transcription factors, based on validated data manually curated from published literature. Modules of miRegulome (upstream regulators, downstream targets, miRNA regulated pathways, functions, diseases, etc) are hyperlinked to an appropriate external resource and are displayed visually to provide a comprehensive understanding. Four analysis tools are incorporated to identify relationships among different modules based on user specified datasets. miRegulome and its tools are helpful in understanding the biology of miRNAs and will also facilitate the discovery of biomarkers and therapeutics. With added features in upcoming releases, miRegulome will be an essential resource to the scientific community. Availability: http://bnet.egr.vcu.edu/miRegulome.
Determination of the Cytosolic NADPH/NADP Ratio in Saccharomyces cerevisiae using Shikimate Dehydrogenase as Sensor Reaction
Authors: Zhang Jinrui , Pierick Angela ten , van Rossum Harmen M. , Maleki Seifar Reza , Ras Cor , Daran Jean-Marc , Heijnen Joseph J. , Aljoscha Wahl S.
Published: August 2015

Eukaryotic metabolism is organised in complex networks of enzyme catalysed reactions which are distributed over different organelles. To quantify the compartmentalised reactions, quantitative measurements of relevant physiological variables in different compartments are needed, especially of cofactors. NADP(H) are critical components in cellular redox metabolism. Currently, available metabolite measurement methods allow whole cell measurements. Here a metabolite sensor based on a fast equilibrium reaction is introduced to monitor the cytosolic NADPH/NADP ratio in Saccharomyces cerevisiae: "Equation missing". The cytosolic NADPH/NADP ratio was determined by measuring the shikimate and dehydroshikimate concentrations (by GC-MS/MS). The cytosolic NADPH/NADP ratio was determined under batch and chemostat (aerobic, glucose-limited, D = 0.1 h−1) conditions, to be 22.0 ± 2.6 and 15.6 ± 0.6, respectively. These ratios were much higher than the whole cell NADPH/NADP ratio (1.05 ± 0.08). In response to a glucose pulse, the cytosolic NADPH/NADP ratio first increased very rapidly and restored the steady state ratio after 3 minutes. In contrast to this dynamic observation, the whole cell NADPH/NADP ratio remained nearly constant. The novel cytosol NADPH/NADP measurements provide new insights into the thermodynamic driving forces for NADP(H)-dependent reactions, like amino acid synthesis, product pathways like fatty acid production or the mevalonate pathway.
Visualizing Non-abrupt Transition of Quantum Well States at Stepped Silver Surfaces
Authors: Kumar Saha Srijan , Manna Sujit , Stepanyuk Valeri S. , Kirschner Jürgen
Published: August 2015

We use scanning tunneling spectroscopy (STS) experiments and first-principles density functional theory (DFT) calculations to address a fundamental question of how quantum well (QW) states for electrons in a metal evolve spatially in the lateral direction when there is a surface step that changes the vertical confinement thickness. This study reveals a clear spatially dependent, nearly continuous trend in the energetic shifts of quantum well (QW) states of thin Ag(111) film grown on Cu(111) substrate, showing the strongest change near the step edge. A large energetic shift equaling up to ~200 meV with a lateral extension of the QW states of the order of ~20 Å is found, even though the step-edge is atomically sharp as evidenced by a line scan. The observed lateral extension and the nearly smooth transition of QW states are understood within the context of step-induced charge oscillation and Smoluchowski-type charge spreading and smoothing.
Molecular mobility on graphene nanoroads
Authors: Jafary-Zadeh Mehdi , Zhang Yong-Wei
Published: August 2015

We study molecular mobility on a graphene nanoroad (GNRD), a pristine graphene strip embedded in between two hydrogenated graphene domains serving as a nanoscale pathway for transporting admolecules. Our molecular dynamics simulations using a prototype physisorbed C60 admolecule demonstrate that the proposed GNRD is able to confine the diffusive motion of the admolecule within the nanoroad up to a certain temperature, depending on its width and edge type. Within the confinement regime, the width and edge-type of the GNRD also play an important role in the molecular motion. Specifically, when the GNRD width is narrower than the admolecule diameter, the admolecule performs one-dimensional hopping motion along the nanoroad. When the GNRD width is larger than the admolecule diameter, the admolecule moves only along one of its edges at low temperatures and shuffle between two edges at high temperatures. We further show the admolecule motion on the zigzag-edged GRND is faster than that on the armchair-edged GRND with the same width and at the same temperature. These results can be well explained by analysing the potential energy surfaces of the systems. Since such hydrogenated graphene nanostructures have been experimentally realized, our results provide a valuable reference for constructing molecular conveyor circuits.
Reduced Expression of Argonaute 1, Argonaute 2 and TRBP Changes Levels and Intracellular Distribution of RNAi Factors
Authors: Matsui Masayuki , Li Liande , Janowski Bethany A. , Corey David R.
Published: August 2015

Until recently, Argonaute 2 (AGO2) and other RNA factors were believed to be restricted to the cytoplasm of mammalian somatic cells. It is now becoming appreciated that RNAi factors can also be found in cell nuclei, but much remains to be learned about their transport, molecular recognition and function. We find that siRNA-mediated reduction of AGO1 or AGO2 increases the proportion of AGO1 or AGO2 in cell nuclei. Inhibition of AGO1 expression led to increased AGO2 levels, while knockdown of AGO2 led to increased levels of AGO1. Blocking AGO1, AGO2, or TRBP expression changed expression levels and nuclear distribution of RNAi factors Dicer, TNRC6A (GW182) and TRBP. These data reveal the expression of RNAi proteins is mutually dependent and that perturbation can affect subcellular distribution of those factors inside cells.
Surface confined self-assembly of polyampholytes generated from charge-shifting polymers
Authors: Garnier T. , Dochter A. , Chau N. T. T. , Schaaf P. , Jierry L. , Boulmedais F.
Published: August 2015

Polyampholyte-based films can be efficiently self-assembled onto a surface in a one-pot manner by using a charge-shifting polyelectrolyte transformed into a polyampholyte by an electrogenerated gradient of protons.
A long-life lithium ion sulfur battery exploiting high performance electrodes
Authors: Moreno Noelia , Agostini Marco , Caballero Alvaro , Morales Julián , Hassoun Jusef
Published: August 2015

A very safe, lithium ion sulfur battery operates at 2 V with capacity of 600 mA h g−1, high energy and remarkable cycle life.
A peptide-based pH-sensitive drug delivery system for targeted ablation of cancer cells
Authors: Jin Yulong , Huang Yanyan , Yang Hua , Liu Guoquan , Zhao Rui
Published: August 2015

A peptide-based pH-sensitive drug delivery system AP2H-hydrazone–DOX was developed for selective recognition and targeted ablation of cancer cells.
Biomimetic synthesis of Tramadol
Authors: Lecerf-Schmidt Florine , Haudecoeur Romain , Peres Basile , Ferreira Queiroz Marcos Marçal , Marcourt Laurence , Challal Soura , Ferreira Queiroz Emerson , Sotoing Taiwe Germain , Lomberget Thierry , Le Borgne Marc , Wolfender Jean-Luc , De Waard Michel , Robins Richard J. , Boumendjel Ahcène
Published: August 2015

The key step in the proposed biosynthesis of tramadol was achieved using mild biomimetic conditions.
The use of carbon monoxide as a probe molecule in spectroscopic studies for determination of exposed gold sites on TiO2
Authors: Lari Giacomo M. , Nowicka Ewa , Morgan David J. , Kondrat Simon A. , Hutchings Graham J.
Published: August 2015

CO used as a probe molecule with infrared and UV-Vis spectroscopy to elucidate effectiveness of metal nanoparticle capping agent removal.
Controlling tunnelling in methane loss from acetone ions by deuteration
Authors: Bodi Andras , Baer Tomas , Wells Nancy K. , Fakhoury Daniel , Klecyngier David , Kercher James P.
Published: August 2015

Methane loss is predominantly a result of quantum tunnelling in acetone cations, and it can be suppressed quantitatively by deuteration.
Nanolubrication by ionic liquids: molecular dynamics simulations reveal an anomalous effective rheology
Authors: Voeltzel Nicolas , Giuliani Andrew , Fillot Nicolas , Vergne Philippe , Joly Laurent
Published: August 2015

All-atom molecular dynamics simulations of an ionic liquid confined between iron oxide surfaces reveal an anomalous effective rheology induced by hydrodynamic and thermal slip at the walls.
Tuning steric and electronic effects in transition-metal β-diketiminate complexes
Authors: Chen Chi , Bellows Sarina M. , Holland Patrick L.
Published: August 2015

We summarize steric and electronic influences on structure, spectroscopy, and reactivity in transition metal β-diketiminate complexes.
MeL2Zn2(μ-1,6-Ph2-N6) – a building block for new hexazene complexes
Authors: Gondzik S. , Wölper C. , Haack R. , Jansen G. , Schulz S.
Published: August 2015

MeL2Zn2(μ-1,6-Ph2-N6) 1 (MeL = HC[C(Me)N(2,4,6-Me3C6H2)]2) serves as hexazene transfer reagent in reactions with main group metal and transition metal complexes containing M–Me units.
Synthesis of g-C3N4/CaIn2S4composites with enhanced photocatalytic activity under visible light irradiation
Authors: Yuan Wenhui , Yang Sai , Li Li
Published: August 2015

A series of graphite-like g-C3N4hybridized CaIn2S4photocatalysts with different g-C3N4contents were fabricatedviaa facile hydrothermal synthetic method.
Salt metathesis versus protonolysis routes for the synthesis of silylamide Hauser base (R2NMgX; X = halogen) and amido-Grignard (R2NMgR) complexes
Authors: Goodwin Conrad A. P. , Smith Alex , Ortu Fabrizio , Vitorica-Yrezabal Iñigo. J. , Mills David P.
Published: August 2015

The effectiveness of simple synthetic routes to access silylamide Hauser base (R2NMgX; X = halogen) and amido-Grignard (R2NMgR) complexes from commercially available Grignard reagents is explored herein.
Higher fluorescence in platinum(iv) orthometallated complexes of perylene imine compared with their platinum(ii) or palladium(ii) analogues
Authors: Expósito J. Emilio , Álvarez-Paíno Marta , Aullón Gabriel , Miguel Jesús A. , Espinet Pablo
Published: August 2015

The synthesis, and structural and photophysical characterization of PtIIand PtIVorthometallated complexes of a perylene imine is reported. The less electron rich PtIVcomplexes show higher quantum yields than their PtIIanalogs.
A low-fat yoghurt supplemented with a rooster comb extract on muscle joint function in adults with mild knee pain: a randomized, double blind, parallel, placebo-controlled, clinical trial of efficacy
Authors: Solà Rosa , Valls Rosa-Maria , Martorell Isabel , Giralt Montserrat , Pedret Anna , Taltavull Núria , Romeu Marta , Rodríguez Àurea , Moriña David , Lopez de Frutos Victor , Montero Manuel , Casajuana Maria-Carmen , Pérez Laura , Faba Jenny , Bernal Gloria , Astilleros Anna , González Roser , Puiggrós Francesc , Arola Lluís , Chetrit Carlos , Martinez-Puig Daniel
Published: August 2015

Preliminary associations of RCE with improved muscle strength.
A wafer-scale graphene and ferroelectric multilayer for flexible and fast-switched modulation applications
Authors: Zhu Minmin , Wu Jing , Du Zehui , Tay Roland Yingjie , Li Hongling , Özyilmaz Barbarous , Teo Edwin Hang Tong
Published: August 2015

Here we report a wafer-scale graphene/P(VDF-TrFE)/graphene multilayer for light-weight, flexible and fast-switched broadband modulation applications.
Facile graphene transfer directly to target substrates with a reusable metal catalyst
Authors: Mafra D. L. , Ming T. , Kong J.
Published: August 2015

We explore a CVD transfer technique that abandons both the intermediate membrane and chemical etching of the metal catalyst. This method is fast, simple and is a necessary route towards roll-to-roll production of large-area CVD graphene sheets at high quality and low cost. Such integration is a step forward to the economical and industrial scale production of graphene and enables technology for flexible electronics and optoelectronics.
Optimization of a silicon wafer texturing process by modifying the texturing temperature for heterojunction solar cell applications
Authors: Jiang Yuanjian , Zhang Xiaodan , Wang Fengyou , Zhao Ying
Published: August 2015

A simple and effective method using a two-step texturing temperature control is proposed to optimize the texturing process of commercial Cz-silicon wafers.
Ligand-induced change of the crystal structure and enhanced stability of the Au11 nanocluster
Authors: Kang Xi , Song Yongbo , Deng Huijuan , Zhang Jun , Liu Bingjie , Pan Chensong , Zhu Manzhou
Published: August 2015

Compared with the Au11(PPh3)7Cl3 and [Au11(PPh3)8Cl2]Cl, [Au11(PPh2(CH2)5Ph2P)4(SePh)2]+ exhibits some structural differences and shows significantly enhanced stability in storage and thiol etching.
Bio-based solvents for the Baylis–Hillman reaction of HMF
Authors: Tan Jia-Neng , Ahmar Mohammed , Queneau Yves
Published: August 2015

The Baylis–Hillman reaction of HMF was investigated in various bio-based solvent systems and in water.
Direct in situ measurement of specific capacitance, monolayer tension, and bilayer tension in a droplet interface bilayer
Authors: Taylor Graham J. , Venkatesan Guru A. , Collier C. Patrick , Sarles Stephen A.
Published: August 2015

Thickness and tension are important physical parameters of model cell membranes.
Smart surfaces based on thermo-responsive polymer brushes prepared from l-alanine derivatives for cell capture and release
Authors: Shen Yong , Li Guannan , Ma Yinan , Yu Deyang , Sun Jing , Li Zhibo
Published: August 2015

We prepared two novel thermo-responsive polymer brushes from l-alanine derivatives and explored the temperature-induced cell capture and release on the polymer brush-based substrates.
Novel fabrication of an efficient solid base: carbon-doped MgO–ZnO composite and its CO2 capture at 473 K
Authors: Li Yan Yan , Wan Mi Mi , Sun Xiao Dan , Zhou Jun , Wang Ying , Zhu Jian Hua
Published: August 2015

A new facile strategy using surface vacancies for fabricating carbon-doped MgO–ZnO composites with unusual strong basicity is first reported, which present good instantaneous CO2 adsorption at 473 K.
Synthesis and catalytic properties of ZSM-5 zeolite with hierarchical pores prepared in the presence of n-hexyltrimethylammonium bromide
Authors: Bai Peng , Wu Pingping , Xing Wei , Liu Daolan , Zhao Lianming , Wang Youhe , Xu Benjing , Yan Zifeng , Zhao Xiu Song
Published: August 2015

ZSM-5 zeolites with hierarchical pores have been synthesized with n-hexyltrimethylammonium bromide and exhibited superior catalytic performance to microporous zeolites.
Efficiency enhancement of top-illuminated ITO-free organic solar cells using plasmonic-assisted nanostructured reflective electrodes
Authors: Xu Wei-Feng , Pan Ming-Yang , Fu Po-Han , Li Shih-Wei , Huang Ding-Wei , Wei Pei-Kuen
Published: August 2015

A nanostructured back reflective electrode with nanobowl-shaped 2D nanohole arrays for enhancing the efficiency of top-illuminated organic solar cells.
Correction: Umbelliferone β-d-galactopyranoside exerts an anti-inflammatory effect by attenuating COX-1 and COX-2
Authors: Kumar Vikas , Al-Abbasi F. A. , Verma Amita , Mujeeb Mohd. , Anwar Firoz
Published: August 2015

Correction for ‘Umbelliferone β-d-galactopyranoside exerts an anti-inflammatory effect by attenuating COX-1 and COX-2’ by Vikas Kumar et al., Toxicol. Res., 2015, 4, 1072–1084.
Real‐time construction and visualisation of drift‐free video mosaics from unconstrained camera motion
Authors: Brzeszcz Mateusz , Breckon Toby P.
Published: August 2015

This work proposes a novel approach for real‐time video mosaicking facilitating drift‐free mosaic construction and visualisation, with integrated frame blending and redundancy management, that is shown to be flexible to a range of varying mosaic scenarios. The approach supports unconstrained camera motion with in‐sequence loop closing, variation in camera focal distance (zoom) and recovery from video sequence breaks. Real‐time performance, over extended duration sequences, is realised via novel aspects of frame management within the mosaic representation and thus avoiding the high data redundancy associated with temporally dense, spatially overlapping video frame inputs. This managed set of image frames is visualised in real time using a dynamic mosaic representation of overlapping textured graphics primitives in place of the traditional globally constructed, and hence frequently reconstructed, mosaic image. Within this formulation, subsequent optimisation occurring during online construction can thus efficiency adjust relative frame positions via simple primitive position transforms. Effective visualisation is similarly facilitated by online inter‐frame blending to overcome the illumination and colour variance associated with modern camera hardware. The evaluation illustrates overall robustness in video mosaic construction under a diverse range of conditions including indoor and outdoor environments, varying illumination and presence of in‐scene motion on varying computational platforms.
Beyond the KdV: Post-explosion development
Authors: Ostrovsky L. , Pelinovsky E. , Shrira V. , Stepanyants Y.
Published: August 2015

Several threads of the last 25 years' developments in nonlinear wave theory that stem from the classical Korteweg–de Vries (KdV) equation are surveyed. The focus is on various generalizations of the KdV equation which include higher-order nonlinearity, large-scale dispersion, and a non-local integral dispersion. We also discuss how relatively simple models can capture strongly nonlinear dynamics and how various modifications of the KdV equation lead to qualitatively new, non-trivial solutions and regimes of evolution observable in the laboratory and in nature. As the main physical example, we choose internal gravity waves in the ocean for which all these models are applicable and have genuine importance. We also briefly outline the authors' view of the future development of the chosen lines of nonlinear wave theory.
Overflow cascades in liquid-infused substrates
Authors: Jacobi I. , Wexler J. S. , Stone H. A.
Published: August 2015

Liquid-infused patterned surfaces offer a promising new platform for generating omniphobic surface coatings. However, the liquid infused in these surfaces is susceptible to shear-driven dewetting. Recent work [Wexler et al., “Shear-driven failure of liquid-infused surfaces,” Phys. Rev. Lett. 114, 168301 (2015)] has shown how the substrate pattern in these surfaces can be designed to exploit capillary forces in order to retain infused lubricants against the action of an immiscible shear flow. In this study, we explore the behavior of the infused lubricant when external shear causes the lubricant to overflow finite or “dead-end” surface features, resulting in either temporary or permanent lubricant loss. Microfluidic experiments illustrate how both geometry and chemical Marangoni stresses within liquid-infused surfaces generate an overflow cascade in which the lubricant escapes from the substrate and forms droplets on the surface, after which the droplets depin and are washed away by the external shear flow, allowing the overflow to repeat. General guidelines are developed to estimate the onset of the different stages of the cascade with the aim of providing additional robustness criteria for the design of future liquid-infused surfaces.
Analytic nuclear forces and molecular properties from full configuration interaction quantum Monte Carlo
Authors: Thomas Robert E. , Opalka Daniel , Overy Catherine , Knowles Peter J. , Alavi Ali , Booth George H.
Published: August 2015

Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, “replica” ensemble of walkers, whose population evolves in imaginary time independently from the first and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the Hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, the present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments, and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where sufficiently large basis sets are available, achieve close agreement with experimental values, expanding the scope of the method to new areas of investigation.
Radial and poloidal correlation reflectometry on Experimental Advanced Superconducting Tokamak
Authors: Qu Hao , Zhang Tao , Han Xiang , Wen Fei , Zhang Shoubiao , Kong Defeng , Wang Yumin , Gao Yu , Huang Canbin , Cai Jianqing , Gao Xiang
Published: August 2015

An X-mode polarized V band (50 GHz–75 GHz) radial and poloidal correlation reflectometry is designed and installed on Experimental Advanced Superconducting Tokamak (EAST). Two frequency synthesizers (12 GHz–19 GHz) are used as sources. Signals from the sources are up-converted to V band using active quadruplers and then coupled together for launching through one single pyramidal antenna. Two poloidally separated antennae are installed to receive the reflected waves from plasma. This reflectometry system can be used for radial and poloidal correlation measurement of the electron density fluctuation. In ohmically heated plasma, the radial correlation length is about 1.5 cm measured by the system. The poloidal correlation analysis provides a means to estimate the fluctuation velocity perpendicular to the main magnetic field. In the present paper, the distance between two poloidal probing points is calculated with ray-tracing code and the propagation time is deduced from cross-phase spectrum. Fluctuation velocity perpendicular to the main magnetic field in the core of ohmically heated plasma is about from −1 km/s to −3 km/s.
Equilibrium and stability of axisymmetric drops on a conical substrate under gravity
Authors: Nurse A. K. , Colbert-Kelly S. , Coriell S. R. , McFadden G. B.
Published: August 2015

Motivated by recent investigations of toroidal tissue clusters that are observed to climb conical obstacles after self-assembly [Nurse et al., “A model of force generation in a three-dimensional toroidal cluster of cells,” J. Appl. Mech. 79, 051013 (2012)], we study a related problem of the determination of the equilibrium and stability of axisymmetric drops on a conical substrate in the presence of gravity. A variational principle is used to characterize equilibrium shapes that minimize surface energy and gravitational potential energy subject to a volume constraint, and the resulting Euler equation is solved numerically using an angle/arclength formulation. The resulting equilibria satisfy a Laplace-Young boundary condition that specifies the contact angle at the three-phase trijunction. The vertical position of the equilibrium drops on the cone is found to vary significantly with the dimensionless Bond number that represents the ratio of gravitational and capillary forces; a global force balance is used to examine the conditions that affect the drop positions. In particular, depending on the contact angle and the cone half-angle, we find that the vertical position of the drop can either increase (“the drop climbs the cone”) or decrease due to a nominal increase in the gravitational force. Most of the equilibria correspond to upward-facing cones and are analogous to sessile drops resting on a planar surface; however, we also find equilibria that correspond to downward facing cones that are instead analogous to pendant drops suspended vertically from a planar surface. The linear stability of the drops is determined by solving the eigenvalue problem associated with the second variation of the energy functional. The drops with positive Bond number are generally found to be unstable to non-axisymmetric perturbations that promote a tilting of the drop. Additional points of marginal stability are found that correspond to limit points of the axisymmetric base state. Drops that are far from the tip are subject to azimuthal instabilities with higher mode numbers that are analogous to the Rayleigh instability of a cylindrical interface. We have also found a range of completely stable solutions that correspond to small contact angles and cone half-angles.
Single proton counting at the RIKEN cell irradiation facility
Authors: Mäckel V. , Puttaraksa N. , Kobayashi T. , Yamazaki Y.
Published: August 2015

We present newly developed tapered capillaries with a scintillator window, which enable us to count single protons at the RIKEN cell irradiation setup. Their potential for performing single proton irradiation experiments at our beamline setup is demonstrated with CR39 samples, showing a single proton detection fidelity of 98%.
Suppression of vapor cell temperature error for spin-exchange-relaxation-free magnetometer
Authors: Lu Jixi , Qian Zheng , Fang Jiancheng , Quan Wei
Published: August 2015

This paper presents a method to reduce the vapor cell temperature error of the spin-exchange-relaxation-free (SERF) magnetometer. The fluctuation of cell temperature can induce variations of the optical rotation angle, resulting in a scale factor error of the SERF magnetometer. In order to suppress this error, we employ the variation of the probe beam absorption to offset the variation of the optical rotation angle. The theoretical discussion of our method indicates that the scale factor error introduced by the fluctuation of the cell temperature could be suppressed by setting the optical depth close to one. In our experiment, we adjust the probe frequency to obtain various optical depths and then measure the variation of scale factor with respect to the corresponding cell temperature changes. Our experimental results show a good agreement with our theoretical analysis. Under our experimental condition, the error has been reduced significantly compared with those when the probe wavelength is adjusted to maximize the probe signal. The cost of this method is the reduction of the scale factor of the magnetometer. However, according to our analysis, it only has minor effect on the sensitivity under proper operating parameters.
Analysis of 440 GeV proton beam–matter interaction experiments at the High Radiation Materials test facility at CERN
Authors: Burkart F. , Schmidt R. , Raginel V. , Wollmann D. , Tahir N. A. , Shutov A. , Piriz A. R.
Published: August 2015

In a previous paper [Schmidt et al., Phys. Plasmas 21, 080701 (2014)], we presented the first results on beam–matter interaction experiments that were carried out at the High Radiation Materials test facility at CERN. In these experiments, extended cylindrical targets of solid copper were irradiated with beam of 440 GeV protons delivered by the Super Proton Synchrotron (SPS). The beam comprised of a large number of high intensity proton bunches, each bunch having a length of 0.5 ns with a 50 ns gap between two neighboring bunches, while the length of this entire bunch train was about 7 μs. These experiments established the existence of the hydrodynamic tunneling phenomenon the first time. Detailed numerical simulations of these experiments were also carried out which were reported in detail in another paper [Tahir et al., Phys. Rev. E 90, 063112 (2014)]. Excellent agreement was found between the experimental measurements and the simulation results that validate our previous simulations done using the Large Hadron Collider (LHC) beam of 7 TeV protons [Tahir et al., Phys. Rev. Spec. Top.--Accel. Beams 15, 051003 (2012)]. According to these simulations, the range of the full LHC proton beam and the hadronic shower can be increased by more than an order of magnitude due to the hydrodynamic tunneling, compared to that of a single proton. This effect is of considerable importance for the design of machine protection system for hadron accelerators such as SPS, LHC, and Future Circular Collider. Recently, using metal cutting technology, the targets used in these experiments have been dissected into finer pieces for visual and microscopic inspection in order to establish the precise penetration depth of the protons and the corresponding hadronic shower. This, we believe will be helpful in studying the very important phenomenon of hydrodynamic tunneling in a more quantitative manner. The details of this experimental work together with a comparison with the numerical simulations are presented in this paper.
Evaluation of machine learning algorithms for prediction of regions of high Reynolds averaged Navier Stokes uncertainty
Authors: Ling J. , Templeton J.
Published: August 2015

Reynolds Averaged Navier Stokes (RANS) models are widely used in industry to predict fluid flows, despite their acknowledged deficiencies. Not only do RANS models often produce inaccurate flow predictions, but there are very limited diagnostics available to assess RANS accuracy for a given flow configuration. If experimental or higher fidelity simulation results are not available for RANS validation, there is no reliable method to evaluate RANS accuracy. This paper explores the potential of utilizing machine learning algorithms to identify regions of high RANS uncertainty. Three different machine learning algorithms were evaluated: support vector machines, Adaboost decision trees, and random forests. The algorithms were trained on a database of canonical flow configurations for which validated direct numerical simulation or large eddy simulation results were available, and were used to classify RANS results on a point-by-point basis as having either high or low uncertainty, based on the breakdown of specific RANS modeling assumptions. Classifiers were developed for three different basic RANS eddy viscosity model assumptions: the isotropy of the eddy viscosity, the linearity of the Boussinesq hypothesis, and the non-negativity of the eddy viscosity. It is shown that these classifiers are able to generalize to flows substantially different from those on which they were trained. Feature selection techniques, model evaluation, and extrapolation detection are discussed in the context of turbulence modeling applications.
Drive of a long-lived vortex-flow pattern by coupling to zonal flows in presence of resonant magnetic perturbations
Authors: Leconte M. , Kim J.-H.
Published: August 2015

The working hypothesis for the origin of edge-localized-mode stabilization is that Resonant Magnetic Perturbations (RMPs) increase transport in the pedestal, thus lowering the pressure gradient below the ideal MHD threshold. Large-scale vortex-flows matching the RMP helicity were observed experimentally [N. Vianello et al., Plasma Phys. Controlled Fusion 57, 014027 (2015)]. We derive and solve numerically a 1D model for the generation of long-lived vortex-flows in presence of RMPs. We show that, in presence of RMPs, zonal flows are damped and partially transfer their energy to a resonant vortex-flow pattern. The resulting vortex-flow has a multiscale nature with a fast-varying fine-structure set by zonal flows and a slowly-varying radial envelope with a resonant character. The model predicts that the saturated vortex-flow energy E scales with RMP amplitude as E∼δBrBα with α≃1.9. This novel type of nonlinearly driven non-axisymmetric flow has a radial—streamer like—component, and is therefore a candidate for increased convective transport.
Nonlinear saturation of the ion-electron Buneman instability in a spherical positively pulsed gridded inertial electrostatic confinement device
Authors: Bandara R. , Khachan J.
Published: August 2015

A pulsed, positively biased gridded inertial electrostatic confinement device has been investigated experimentally, using Doppler broadened spectra and current and voltage traces as primary diagnostics. In the high current and energy regime explored in this paper resulting from the removal of the series ballast resistance from the external biasing circuit, large amplitude oscillations in the plasma current and potential were observed within 100 ns of the discharge onset. These oscillations are attributed to the nonlinear and saturated Buneman instability, characterised by a locked oscillation frequency as a function of increasing anode potential. The saturated Buneman instability is known to exhibit ion mass independent behaviour and cause electron trapping, resulting in a transient spatio-temporal virtual cathode and ponderomotive ion confinement, as evidenced by broadened spectra when operated at high currents.
Orbitals from local RDMFT: Are they Kohn-Sham or natural orbitals?
Authors: Theophilou Iris , Lathiotakis Nektarios N. , Gidopoulos Nikitas I. , Rubio Angel , Helbig Nicole
Published: August 2015

Recently, an approximate theoretical framework was introduced, called local reduced density matrix functional theory (local-RDMFT), where functionals of the one-body reduced density matrix (1-RDM) are minimized under the additional condition that the optimal orbitals satisfy a single electron Schrödinger equation with a local potential. In the present work, we focus on the character of these optimal orbitals. In particular, we compare orbitals obtained by local-RDMFT with those obtained with the full minimization (without the extra condition) by contrasting them against the exact NOs and orbitals from a density functional calculation using the local density approximation (LDA). We find that the orbitals from local-RMDFT are very close to LDA orbitals, contrary to those of the full minimization that resemble the exact NOs. Since local RDMFT preserves the good quality of the description of strong static correlation, this finding opens the way to a mixed density/density matrix scheme, where Kohn-Sham orbitals obtain fractional occupations from a minimization of the occupation numbers using 1-RDM functionals. This will allow for a description of strong correlation at a cost only minimally higher than a density functional calculation.
The dependence of nano-contact magnetoresistance on the bulk scattering spin asymmetry in CoFe alloys with oxidation impurities
Authors: Shiokawa Yohei , Jung JinWon , Otsuka Takahiko , Sahashi Masashi
Published: August 2015

Nano-contact magnetoresistance (NCMR) spin-valves (SVs) using an AlOx nano-oxide-layer (NOL) have numerous nanocontacts in the thin AlOx oxide layer. The NCMR theoretically depends on the bulk scattering spin asymmetry (β) of the ferromagnetic material in the nanocontacts. To determine the relationship between NCMR and β, we investigated the dependence of NCMR on the composition of the ferromagnetic material Co1−xFex. The samples were annealed at 270 °C and 380 °C to enhance the MR ratio. For both annealing temperatures, the magnetorsistance ratio in the low-resistance area product region at less than 1 Ω μm2 was maximized for Co0.5Fe0.5. To evaluate β exactly, we fabricated current-perpendicular-to-plane giant magnetoresistance SVs with Co1−xFex/Cu/Co1−xFex layers and used Valet and Fert's theory to solve the diffusion equation of the spin accumulation for a ferromagnetic layer/non-ferromagnetic layer of five layers with a finite diffusion length. The evaluated β for Co1−xFex was also maximized for Co0.5Fe0.5. Additionally, to determine the difference between the experimental MR ratio of NCMR SVs and the theoretical MR ratio, we fabricated Co0.5Fe0.5 with oxygen impurities and estimated the decrease in β with increasing oxygen impurity concentration. Our Co0.5Fe0.5 nano-contacts fabricated using ion-assisted oxidation may contain oxygen impurities, and the oxygen impurities might cause a decrease in β and the MR ratio.
Global gyrokinetic simulations of trapped-electron mode and trapped-ion mode microturbulence
Authors: Drouot T. , Gravier E. , Reveille T. , Sarrat M. , Collard M. , Bertrand P. , Cartier-Michaud T. , Ghendrih P. , Sarazin Y. , Garbet X.
Published: August 2015

This paper presents a reduced kinetic model, which describes simultaneously trapped-ion (TIM) and trapped-electron (TEM) driven modes. Interestingly, the model enables the study of a full f problem for ion and electron trapped particles at very low numerical cost. The linear growth rate obtained with the full f nonlinear code Trapped Element REduction in Semi Lagrangian Approach is successfully compared with analytical predictions. Moreover, nonlinear results show some basic properties of collisionless TEM and TIM turbulence in tokamaks. A competition between streamer-like structures and zonal flows is observed for TEM and TIM turbulence. Zonal flows are shown to play an important role in suppressing the nonlinear transport and strongly depend on the temperature ratio Te/Ti.
Tunable spin wave spectra in two-dimensional Ni80Fe20 antidot lattices with varying lattice symmetry
Authors: Mandal R. , Barman S. , Saha S. , Otani Y. , Barman A.
Published: August 2015

Ferromagnetic antidot lattices are important systems for magnetic data storage and magnonic devices, and understanding their magnetization dynamics by varying their structural parameters is an important problems in magnetism. Here, we investigate the variation in spin wave spectrum in two-dimensional nanoscale Ni80Fe20 antidot lattices with lattice symmetry. By varying the bias magnetic field values in a broadband ferromagnetic resonance spectrometer, we observed a stark variation in the spin wave spectrum with the variation of lattice symmetry. The simulated mode profiles showed further difference in the spatial nature of the modes between different lattices. While for square and rectangular lattices extended modes are observed in addition to standing spin wave modes, all modes in the hexagonal, honeycomb, and octagonal lattices are either localized or standing waves. In addition, the honeycomb and octagonal lattices showed two different types of modes confined within the honeycomb (octagonal) units and between two such consecutive units. Simulated internal magnetic fields confirm the origin of such a wide variation in the frequency and spatial nature of the spin wave modes. The tunability of spin waves with the variation of lattice symmetry is important for the design of future magnetic data storage and magnonic devices.
Anomalous Hall effect in epitaxial ferrimagnetic anti-perovskite Mn4−xDyxN films
Authors: Meng M. , Wu S. X. , Zhou W. Q. , Ren L. Z. , Wang Y. J. , Wang G. L. , Li S. W.
Published: August 2015

Anomalous Hall effect (AHE) has been studied for ferrimagnetic antiperovskite Mn4−xDyxN films grown by molecular-beam epitaxy. The introduction of Dy changes the AHE dramatically, even changes its sign, while the variations in magnetization are negligible. Two sign reversals of the AHE (negative-positive-negative) are ascribed to the variation of charge carriers as a result of Fermi surface reconstruction. We further demonstrate that the AHE current JAH is dissipationless (independent of the scattering rate), by confirming that anomalous Hall conductivity, σAH, is proportional to the carrier density n at 5 K. Our study may provide a route to further utilize antiperovskite manganese nitrides in spintronics.
Equilibria with incompressible flows from symmetry analysis
Authors: Kuiroukidis Ap , Throumoulopoulos G. N.
Published: August 2015

We identify and study new nonlinear axisymmetric equilibria with incompressible flow of arbitrary direction satisfying a generalized Grad Shafranov equation by extending the symmetry analysis presented by Cicogna and Pegoraro [Phys. Plasmas 22, 022520 (2015)]. In particular, we construct a typical tokamak D-shaped equilibrium with peaked toroidal current density, monotonically varying safety factor, and sheared electric field.
Fermi level pinning in metal/Al2O3/InGaAs gate stack after post metallization annealing
Authors: Winter R. , Krylov I. , Cytermann C. , Tang K. , Ahn J. , McIntyre P. C. , Eizenberg M.
Published: August 2015

The effect of post metal deposition annealing on the effective work function in metal/Al2O3/InGaAs gate stacks was investigated. The effective work functions of different metal gates (Al, Au, and Pt) were measured. Flat band voltage shifts for these and other metals studied suggest that their Fermi levels become pinned after the post-metallization vacuum annealing. Moreover, there is a difference between the measured effective work functions of Al and Pt, and the reported vacuum work function of these metals after annealing. We propose that this phenomenon is caused by charging of indium and gallium induced traps at the annealed metal/Al2O3 interface.
Effect of inclined magnetic field in flow of third grade fluid with variable thermal conductivity
Authors: Hayat T. , Shafiq Anum , Alsaedi A. , Asghar S.
Published: August 2015

This paper examines effects of inclined magnetic field and heat transfer in the flow of a third-grade fluid by an exponentially stretching surface. Formulation and analysis are given with heat source and sink. Thermal conductivity is taken temperature dependent. The governing boundary layer equations and boundary conditions are simplified through appropriate transformations. Resulting equations are solved for the approximate solutions. Convergence of governed problems is explicitly discussed. Influences of various dimensionless parameters such as on the flow and thermal fields are discussed. Local skin friction coefficient and the local Nusselt number are analyzed through tabulated values.
Lattice dynamics of KxRhO2 single crystals
Authors: Zhang Bin-Bin , Zhang NaNa , Dong Song-Tao , Lv Yangyang , Chen Y. B. , Yao Shuhua , Zhang Shan-Tao , Gu Zheng-Bin , Zhou Jian , Guedes Ilde , Yu Dehong , Chen Yan-Feng
Published: August 2015

A series of crystals KxRhO2 (x = 0.72, 0.63, 0.55, 0.39, and 0.24) have been synthesized and their vibrational properties have been studied by first principles calculations, Raman spectroscopy, and inelastic neutron scattering. The measured vibrational spectra of KxRhO2 for x = 0.72 and 0.63 are consistent with the theoretical prediction for the stoichiometric KRhO2. For samples with x = 0.55, 0.39 and 0.24, extra vibrational modes have been observed and they are believed to be due to the symmetry reduction and the loss of translational symmetry induced by K disorder. The good agreement was found for the phonon density of states among the Raman spectroscopic observations, inelastic neutron scattering and the first principles calculations, as an evidence for the generation of structure disorder by K deficiency.
Evaluation of load support capacity of remoulded fine and coarse textured soils as affected by wetting and drying cycles
Authors: Salehian Dastjerdi Maryam , Hemmat Abbas
Published: August 2015

Soils of south of Iran used for sugarcane production are frequently exposed to wetting and drying cycles under flood irrigation. The effects of this process on estimation of the load support capacity (pre-compaction stress; σpc) of two soils using plate sinkage test (PST) and confined compression test (CCT) were studied. Large reconstructed specimens of topsoils were subjected to 5 wetting and drying cycles. The specimens, with/without wetting and drying cycles, were then compressed under two pre-loads (100 and 200 kPa) at two water contents (0.9 PL and 1.1 PL, where PL is plastic limit). The centre section of the preloaded soil specimens was ﬁrstly submitted to a 50 mm PST; then immediately one cylindrical sample was cored for CCT. The results indicated that for both soils, without wetting and drying cycles, σpc estimated from PST did not show any significant difference with the values of preload. This method can, therefore, be used to determine the load support capacity for tilled soils. However, wetting and drying cycles caused a significant over-estimation of σpc by PST. Thus, the concept of pre-compaction stress does not account for the effects of changes in soil structure due to wetting and drying.
Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer
Authors: Fedeles Bogdan I. , Freudenthal Bret D. , Yau Emily , Singh Vipender , Chang Shiou-chi , Li Deyu , Delaney James C. , Wilson Samuel H. , Essigmann John M.
Published: August 2015

Significance

Chronic inflammation is a significant risk factor for cancer and other human diseases. During chronic inflammation, cells exposed to neutrophil-derived hypochlorous acid accumulate in their genomes the DNA lesion 5-chlorocytosine (5ClC). Using a battery of chemical, structural, and genetic tools, the present study demonstrates that 5ClC is a mutagenic lesion, suggesting that genomic 5ClC accumulation could have very serious biological consequences. 5ClC induces C→T transitions, a type of mutation commonly observed in tissues under inflammatory stress as well as in the genomes of inflammation-driven cancers. Thus, the mutagenic properties of 5ClC represent an appealing molecular mechanism by which chronic inflammation induces the genetic changes that potentially enable and stimulate carcinogenesis.