bluuebunny/crossref_metadata_2025 huggingface dataset:
A generic rate equation for catalysed, template‐directed polymerisation
Authors: Hofmeyr Jan-Hendrik S. , Gqwaka Olona P.C. , Rohwer Johann M.
Published: July 2013

Biosynthetic networks link to growth and reproduction processes through template‐directed synthesis of macromolecules such as polynucleotides and polypeptides. No rate equation exists that captures this link in a way that it can effectively be incorporated into a single computational model of the overall process. This paper describes the derivation of such a generic steady‐state rate equation for catalysed, template‐directed polymerisation reactions with varying monomer stoichiometry and varying chain length. The derivation is based on a classical Michaelis–Menten mechanism with template binding and an arbitrary number of chain elongation steps that produce a polymer composed of an arbitrary number of monomer types. The rate equation only requires the identity of the first dimer in the polymer sequence; for the remainder only the monomer composition needs be known. Further simplification of a term in the denominator yielded an equation requiring no positional information at all, only the monomer composition of the polymer; this equation still gave an excellent estimate of the reaction rate provided that either the monomer concentrations are at least half‐saturating, or the polymer is very long.
A century of enzyme kinetic analysis, 1913 to 2013
Authors: Johnson Kenneth A.
Published: July 2013

This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re‐analysis of the original Michaelis–Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function.
‘STRUGGLING BUT FAILING TO MASK’: THE MUSIC OF MARK R. TAYLOR
Authors: Maw David
Published: July 2013

The music of Mark R. Taylor (b. 1961) is as yet little known. In part, this derives from his unusual profile in the current musical scene. The initial characterization of his work given in this article takes his own remarks from a note inscribed at the end of a piano fragment from the mid-1990s as a framework. From his earliest compositions onwards, the handling of musical materials has depended on strictly controlled processes that are conveyed through a notable ‘simplicity of presentation’. This gives the work a semblance of postmodernism; but Taylor distances himself from the allusiveness, playfulness and irony of this movement, preferring to recognize a ‘personal expressivity’ characteristic of ‘the better kind of postmodernism’. These opposing tendencies to objectivity on the one hand and to expressivity on the other are components of a dialectical musical expression in which the music is ‘struggling but failing to mask profound inner turmoil’.
EMILY HOWARD'S LOVELACE TRILOGY: A MUSICAL HOMAGE TO A MATHEMATICAL PIONEER
Authors: Petri-Preis Axel
Published: July 2013

WithAda Sketches, for mezzo-soprano, flute, clarinet and percussion,Mesmerism, for solo piano and chamber orchestra, andCalculus of the Nervous System, for large orchestra, in 2011 the young British composer Emily Howard completed a triptych of works in which she drew decisively on the life and thoughts of Ada Lovelace for inspiration. Today, Lovelace is recognized as a pioneer of 19th-Century mathematics, who in her lifetime attempted to bring together art and mathematics in Charles Babbage's Analytical Engine. She was convinced of the power of mesmerism and believed that there was a possible mathematical calculation for the human nervous system. This article shows how Emily Howard took up and developed musically these central threads of Lovelace's work in her ‘Lovelace Trilogy’.
‘RESONANCE AND DISTANCE’: SIMON BAINBRIDGE IN CONVERSATION
Authors: Miller Malcolm
Published: July 2013

This interview, based on a conversation with Simon Bainbridge at London's City Literary Institute in June 2011, presents something of a rounded portrait of the composer while covering a good deal of ground. We began our conversation with a discussion of a recent work for orchestra, Concerti Grossi, going into some detail in matters of scoring and structure. The discussion then broadened to cover such topics as the creative process, formative influences (for example, his parents' activity in the visual arts, Debussy's Jeux, John Lambert and Gunther Schuller), instrumentation and the relationship of music and text. This led on specifically to Bainbridge's settings of Primo Levi, in for example the cycle Ad Ora Incerta, and to a consideration of the composer's relationship with the audience.
ROBIN WALKER AT 60
Authors: Matthews David
Published: July 2013

The composer Robin Walker is 60 this year. David Matthews, who has known Walker and his music well since the composer was 23, gives an overview of his life and the development of his musical language from serial modernism to what Walker calls ‘modal chromaticism’ – essentially a renewal of tonality, with strong links to both Wagner and Sibelius. The thinking that led to this development, which is linked to Jungian psychology, is discussed, and there is an examination of five major works from Walker's extensive catalogue, including his seminal orchestral piece The Stone Maker.
London, St Paul's Cathedral: Tallis Scholars' 40th Anniversary Concert: Jackson, Whitacre and Walker
Authors: Anderson Martin
Published: July 2013

It seems improbable that the Tallis Scholars can have given their first concert 40 years ago: while the rest of us have crumbled, their conductor, Peter Phillips, hardly seems older now that he did when he founded the group. New music has been an increasingly important part of their repertoire over the decades, rubbing shoulders with the Renaissance stalwarts, and so it was gratifying that their anniversary concert should feature two world premières and one first London hearing. The venue on 7 March could hardly have been more imposing: the singers were stationed under the dome of St Paul's Cathedral, the audience radiating out from them towards three of the four points of the compass; and it seemed that most of the British musical establishment had come to pay homage and say thanks.
London, King's Place: Simon Holt and Jonathan Dove at ‘Britten 100’
Authors: Barlow Jill
Published: July 2013

Since reviewing the opening of London's latest new concert hall complex, King's Place, in 2008 I have welcomed the opportunity to follow this up by reviewing subsequent premières in their purpose-built studio-style concert halls pretty well annually. For 2013 Kings Place celebrates the centenary of the birth of one of the UK's most illustrious composers, in its three-day series ‘Britten at 100’. As one of the involved presenting pianists, Andrew Matthews-Owen, aptly commented in the Kings Place brochure: ‘It's strange that people are still a little scared of Britten – I think he'd enjoy the fact that his music still has the ability to shock and unsettle us today’. Well I'm certainly not scared of any composer I'm reviewing, but on this special ‘Britten’ occasion I was at pains to point out to the powers that be that I was mostly there on 9 February to review the two probably rather more ‘quirky’ world premières by Simon Holt and Jonathan Dove rather than make any major comment about Britten as such.
ATPase‐driven oligomerization of RIG‐I on RNA allows optimal activation of type‐I interferon
Authors: Patel Jenish R , Jain Ankur , Chou Yi‐ying , Baum Alina , Ha Taekjip , García‐Sastre Adolfo
Published: July 2013

The cytosolic pathogen sensor RIG‐I is activated by RNAs with exposed 5′‐triphosphate (5′‐ppp) and terminal double‐stranded structures, such as those that are generated during viral infection. RIG‐I has been shown to translocate on dsRNA in an ATP‐dependent manner. However, the precise role of the ATPase activity in RIG‐I activation remains unclear. Using in vitro‐transcribed Sendai virus defective interfering RNA as a model ligand, we show that RIG‐I oligomerizes on 5′‐ppp dsRNA in an ATP hydrolysis‐dependent and dsRNA length‐dependent manner, which correlates with the strength of type‐I interferon (IFN‐I) activation. These results establish a clear role for the ligand‐induced ATPase activity of RIG‐I in the stimulation of the IFN response.
Bacterial regulatory networks—from self‐organizing molecules to cell shape and patterns in bacterial communities
Authors: Hengge Regine , Sourjik Victor
Published: July 2013

The ESF–EMBO Conference on ‘Bacterial Networks’ (BacNet13) was held in March 2013, in Pultusk, Poland. It brought together 164 molecular microbiologists, bacterial systems biologists and synthetic biologists to discuss the architecture, function and dynamics of regulatory networks in bacteria.
Endless paces of degeneration—applying comparative genomics to study evolution's moulding of longevity
Authors: de Magalhães João Pedro , Kean Michael
Published: July 2013

Why do mice and humans have such different lifespans? Genome sequencing efforts are allowing researchers to pick apart the genetic foundations of longevity, with some promising results beginning to emerge.
The sacredness of human life
Authors: Kováč Ladislav
Published: July 2013

Christian De Duve's decision to voluntarily pass away gives us a pause to consider the value and meaning of death. Biologists have much to contribute to the discussion of dying with dignity.
Conducting linear chains of sulphur inside carbon nanotubes
Authors: Fujimori Toshihiko , Morelos-Gómez Aarón , Zhu Zhen , Muramatsu Hiroyuki , Futamura Ryusuke , Urita Koki , Terrones Mauricio , Hayashi Takuya , Endo Morinobu , Young Hong Sang , Chul Choi Young , Tománek David , Kaneko Katsumi
Published: July 2013

Despite extensive research for more than 200 years, the experimental isolation of monatomic sulphur chains, which are believed to exhibit a conducting character, has eluded scientists. Here we report the synthesis of a previously unobserved composite material of elemental sulphur, consisting of monatomic chains stabilized in the constraining volume of a carbon nanotube. This one-dimensional phase is confirmed by high-resolution transmission electron microscopy and synchrotron X-ray diffraction. Interestingly, these one-dimensional sulphur chains exhibit long domain sizes of up to 160 nm and high thermal stability (~800 K). Synchrotron X-ray diffraction shows a sharp structural transition of the one-dimensional sulphur occurring at ~450–650 K. Our observations, and corresponding electronic structure and quantum transport calculations, indicate the conducting character of the one-dimensional sulphur chains under ambient pressure. This is in stark contrast to bulk sulphur that needs ultrahigh pressures exceeding ~90 GPa to become metallic.
Biochemistry of cardiomyopathy in the mitochondrial disease Friedreich's ataxia
Authors: Lane Darius J. R. , Huang Michael Li-Hsuan , Ting Samantha , Sivagurunathan Sutharshani , Richardson Des R.
Published: July 2013

FRDA (Friedreich's ataxia) is a debilitating mitochondrial disorder leading to neural and cardiac degeneration, which is caused by a mutation in the frataxin gene that leads to decreased frataxin expression. The most common cause of death in FRDA patients is heart failure, although it is not known how the deficiency in frataxin potentiates the observed cardiomyopathy. The major proposed biochemical mechanisms for disease pathogenesis and the origins of heart failure in FRDA involve metabolic perturbations caused by decreased frataxin expression. Additionally, recent data suggest that low frataxin expression in heart muscle of conditional frataxin knockout mice activates an integrated stress response that contributes to and/or exacerbates cardiac hypertrophy and the loss of cardiomyocytes. The elucidation of these potential mechanisms will lead to a more comprehensive understanding of the pathogenesis of FRDA, and will contribute to the development of better treatments and therapeutics.
Notochordal Cell–Derived Therapeutic Strategies for Discogenic Back Pain
Authors: Purmessur D. , Cornejo M. C. , Cho S. K. , Hecht A. C. , Iatridis J. C.
Published: July 2013

An understanding of the processes that occur during development of the intervertebral disk can help inform therapeutic strategies for discogenic pain. This article reviews the literature to identify candidates that are found in or derived from the notochord or notochordal cells and evaluates the theory that such factors could be isolated and used as biologics to target the structural disruption, inflammation, and neurovascular ingrowth often associated with discogenic back pain. A systematic review using PubMed was performed with a primary search using keywords “(notochordal OR notochord) And (nerves OR blood vessels OR SHH OR chondroitin sulfate OR notch OR CTGF) NOT chordoma.” Secondary searches involved keywords associated with the intervertebral disk and pain. Several potential therapeutic candidates from the notochord and their possible targets were identified. Studies are needed to further identify candidates, explore mechanisms for effect, and to validate the theory that these candidates can promote structural restoration and limit or inhibit neurovascular ingrowth using in vivo studies.
‘She Found a Way, Left the Child’: ‘Child-shifting’ as the Plantation's Affects and Love's Paradox in Donna Hemans’ River Woman
Authors: Scafe Suzanne
Published: July 2013

This article proposes a situated reading of maternal love, loss and lovelessness in Donna Hemans’ novel River Woman, locating her text in relation to other contemporary Caribbean women writers and to the early fiction of Toni Morrison. I argue that the complex affects that her representation of ‘child-shifting’ produces, can be articulated both in relation to literary texts that re-imagine historical and contemporary practices leaving a child in order to save her, and in the context of the plantation, where ruptured ties at the level of community and culture continue to be reproduced in the personal, emotional and family spheres. I use the concept of marronage, developed in the work of Glissant and Depestre, to define strategies of survival that necessitated actual and imaginative flight or escape, to contextualise the complex affects of the plantation that are repeated and reproduced in the novel's present—the late twentieth-century Caribbean.
‘These Things not Marked on Paper’: Creolisation, Affect and Tomboyism in Joan Anim-addo's Janie, Cricketing Lady and Margaret Cezair-thompson's The Pirate's Daughter
Authors: Smith Karina
Published: July 2013

This article will look closely at the performance of tomboy identity in Joan Anim-Addo's collection of poetry Janie, Cricketing Lady, written as a tribute to her mother Jane Joseph, and Margaret Cezair-Thompson's novel The Pirate's Daughter, a fiction about Errol Flynn's ‘outside’ Jamaican daughter, May. It will argue that the ongoing affects of colonialism and patriarchy in the islands of Grenada and Jamaica, respectively, shape the life narratives of Janie and May who express their anger, shame, fear, frustration and desire through their ambiguous gender identity and through their determination to intervene in masculinist traditions, such as cricket, piracy and adventure, traditions that underpin Caribbean his/tories. To understand the way in which affect can be expressed through tomboyism in Caribbean societies, it is necessary to look at colour and class alongside gender in the context of Caribbean creolisation.
Glassy boundary layers vs enhanced mobility in capped polymer films
Authors: Batistakis C. , Michels M. A. J. , Lyulin A. V.
Published: July 2013

Molecular-dynamics simulations have been carried out for a coarse-grained model of a random AB-copolymer confined between two crystalline substrates. The strength of substrate-polymer interactions, and the distance between the two substrates have been varied in a wide range. For thick films the film-averaged segmental mobility decreases for intermediate adsorption strengths, but start to increase for very high substrate-polymer attraction strength. We saw that this non-monotonic behavior is caused by a very strong heterogeneity of the segmental dynamics above the glass-transition temperature: the segmental mobility slows down drastically close to adsorbing substrates, but strongly increases in the middle part of the film. This effect, and its sensitive dependence on film thickness, are explained by finite-size effects in confinement, in combination with glassy boundary layers. It is demonstrated that film-averaged mobility as often measured cannot be understood without resolving local mobility in space and time.
Phase behavior of athermal colloid-star polymer mixtures
Authors: Mahynski Nathan A. , Panagiotopoulos Athanassios Z.
Published: July 2013

We investigate the depletion-induced phase behavior of athermal colloid-star polymer mixtures on a fine lattice using grand canonical Monte Carlo simulations in the “protein limit,” that is, where polymer dimensions exceed those of the colloid. We consider the influence of the star's functionality, f, the macroscopic size ratio, qr = 2Rg, s/σc, where Rg, s is the radius of gyration of the star and σc is the colloid diameter, and the microscopic size ratio, d = σm/σc, where σm is the diameter of a Kuhn segment. Recent theoretical predictions concerning the qualitative interplay of qr and f in determining the phase stability of these mixtures [D. Marzi, C. N. Likos, and B. Capone, J. Chem. Phys. 137, 014902 (2012)]10.1063/1.4730751 in the limit of large f are mostly corroborated by our results which span a much lower range of functionalities. Our results suggest a direct connection between the phase behavior and the scaling regimes of single star structure in the classical Daoud-Cotton (DC) description [M. Daoud and J. P. Cotton, J. Phys. 43, 531–538 (1982)]10.1051/jphys:01982004303053100. Using this formalism, we define a “low” functionality limit through scaling arguments, for which our model provides a mapping of the phase behavior of colloidal mixtures with star polymers (f > 2) to linear chains (f = 2). Furthermore, our simulations suggest that as qr increases, both the critical monomer and colloid densities tend to a constant, finite value for all f; thus, we do not find the prediction by Marzi and co-workers of an upper limit to immiscibility (infinite critical densities) in terms of qr to be accurate for the stars we have investigated.
Reflectance modulation by free-carrier exciton screening in semiconducting nanotubes
Authors: Pinto Fabrizio
Published: July 2013

A model of exciton screening by photo-generated free charges in semiconducting single-walled carbon nanotubes is considered to interpret recent data from the only experiment on this phenomenon reported in the literature. The potential of electron-hole interactions on the nanotube surface is computed starting from the derived full two-dimensional expression. The error of screened potential numerical computations is analyzed in detail by also including strategies for convergence acceleration and computing time optimization. The two-dimensional Wannier equation on the nanotube surface is solved by means of variational methods and convergence to published results in the unscreened case is demonstrated. The effect of screening charges on the exciton energy is estimated numerically by taking advantage of memoization algorithms. We show that a firm connection can be made between the present description and data readily available from future similar reflectivity experiments to constrain the linear density of photo-generated carriers. Applications of dielectric function modulation to dispersion force manipulation and nanodevice actuation are briefly discussed.
Synchronous concerted multiple-body photodissociation of oxalyl chloride explored by ab initio-based dynamics simulations
Authors: Fang Qiu , Shen Lin , Fang Wei-Hai
Published: July 2013

Photo-induced multiple body dissociation is of fundamental interest in chemistry and physics. A description of the mechanism associated with n-body (n ⩾ 3) photodissociation has proven to be an intriguing and yet challenging issue in the field of chemical dynamics. Oxalyl chloride, (ClCO)2, is the sole molecule reported up to date that can undergo four-body dissociation following absorption of a single UV photon, with a rich history of mechanistic debate. In the present work, the combined electronic structure calculations and dynamics simulations have been performed at the advanced level, which provides convincing evidence for resolving the mechanistic debate. More importantly, synchronous and asynchronous concertedness were explored for the first time for the (ClCO)2 photodissociation, which is based on the simulated time constants for the C–C and C–Cl bond fissions. Upon photoexcitation of (ClCO)2 to the S1 state, the adiabatic C–C or C–Cl fission takes place with little possibility. The four-body dissociation to 2Cl(2P) and 2CO(1Σ) was determined to a dominant channel with its branch of ∼0.7, while the three-body dissociation to ClCO(2A′) + CO(1Σ) + Cl(2P) was predicted to play a minor role in the (ClCO)2 photodissociation at 193 nm. Both the four-body and three-body dissociations are non-adiabatic processes, which proceed in a synchronous concerted way as a result of the S1 → S0 internal conversion. There is a little possibility for two-body dissociation to occur in the S0 and S1 states.
A new endstation at the Swiss Light Source for ultraviolet photoelectron spectroscopy, X-ray photoelectron spectroscopy, and X-ray absorption spectroscopy measurements of liquid solutions
Authors: Brown Matthew A. , Redondo Amaia Beloqui , Jordan Inga , Duyckaerts Nicolas , Lee Ming-Tao , Ammann Markus , Nolting Frithjof , Kleibert Armin , Huthwelker Thomas , Mächler Jean-Pierre , Birrer Mario , Honegger Juri , Wetter Reto , Wörner Hans Jakob , van Bokhoven Jeroen A.
Published: July 2013

A new liquid microjet endstation designed for ultraviolet (UPS) and X-ray (XPS) photoelectron, and partial electron yield X-ray absorption (XAS) spectroscopies at the Swiss Light Source is presented. The new endstation, which is based on a Scienta HiPP-2 R4000 electron spectrometer, is the first liquid microjet endstation capable of operating in vacuum and in ambient pressures up to the equilibrium vapor pressure of liquid water at room temperature. In addition, the Scienta HiPP-2 R4000 energy analyzer of this new endstation allows for XPS measurements up to 7000 eV electron kinetic energy that will enable electronic structure measurements of bulk solutions and buried interfaces from liquid microjet samples. The endstation is designed to operate at the soft X-ray SIM beamline and at the tender X-ray Phoenix beamline. The endstation can also be operated using a Scienta 5 K ultraviolet helium lamp for dedicated UPS measurements at the vapor-liquid interface using either He I or He II α lines. The design concept, first results from UPS, soft X-ray XPS, and partial electron yield XAS measurements, and an outlook to the potential of this endstation are presented.
Understanding the role of vibrations, exact exchange, and many-body van der Waals interactions in the cohesive properties of molecular crystals
Authors: Reilly Anthony M. , Tkatchenko Alexandre
Published: July 2013

The development and application of computational methods for studying molecular crystals, particularly density-functional theory (DFT), is a large and ever-growing field, driven by their numerous applications. Here we expand on our recent study of the importance of many-body van der Waals interactions in molecular crystals [A. M. Reilly and A. Tkatchenko, J. Phys. Chem. Lett. 4, 1028 (2013)10.1021/jz400226x], with a larger database of 23 molecular crystals. Particular attention has been paid to the role of the vibrational contributions that are required to compare experiment sublimation enthalpies with calculated lattice energies, employing both phonon calculations and experimental heat-capacity data to provide harmonic and anharmonic estimates of the vibrational contributions. Exact exchange, which is rarely considered in DFT studies of molecular crystals, is shown to have a significant contribution to lattice energies, systematically improving agreement between theory and experiment. When the vibrational and exact-exchange contributions are coupled with a many-body approach to dispersion, DFT yields a mean absolute error (3.92 kJ/mol) within the coveted “chemical accuracy” target (4.2 kJ/mol). The role of many-body dispersion for structures has also been investigated for a subset of the database, showing good performance compared to X-ray and neutron diffraction crystal structures. The results show that the approach employed here can reach the demanding accuracy of crystal-structure prediction and organic material design with minimal empiricism.
Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation
Authors: Zhao Yanxiang , Kwan Yuen-Yick , Che Jianwei , Li Bo , McCammon J. Andrew
Published: July 2013

A phase-field variational implicit-solvent approach is developed for the solvation of charged molecules. The starting point of such an approach is the representation of a solute-solvent interface by a phase field that takes one value in the solute region and another in the solvent region, with a smooth transition from one to the other on a small transition layer. The minimization of an effective free-energy functional of all possible phase fields determines the equilibrium conformations and free energies of an underlying molecular system. All the surface energy, the solute-solvent van der Waals interaction, and the electrostatic interaction are coupled together self-consistently through a phase field. The surface energy results from the minimization of a double-well potential and the gradient of a field. The electrostatic interaction is described by the Coulomb-field approximation. Accurate and efficient methods are designed and implemented to numerically relax an underlying charged molecular system. Applications to single ions, a two-plate system, and a two-domain protein reveal that the new theory and methods can capture capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states as found in molecular dynamics simulations. Comparisons of the phase-field and the original sharp-interface variational approaches are discussed.
Meyer-Neldel rule and Poole-Frenkel effect in chalcogenide glasses
Authors: Abdel-Wahab F. , Yelon A.
Published: July 2013

A theoretical model for dc conductivity under high electric field in chalcogenide glasses is developed. This model, of correlated barrier hopping is used to treat both low field conductivity, which obeys Meyer-Neldel rule (MNR), and high field Poole-Frenkel (PF) effect. Both are incorporated in one model because the origin of electronic emission is the same: a deep well in which a polaron is trapped. We show that the characteristic temperatures associated with MNR and PF should be the same, as has been predicted using a rigorous adiabatic polaron hopping model, and previously demonstrated experimentally for fullerene films. We also predict that the extrapolated conductivity prefactors will be the same in the two cases. Experimental evidence from the literature suggests, but does not demonstrate conclusively, that the two predictions are satisfied for chalcogenide glasses. Finally, we interpret the result in terms of the multi-excitation entropy model for MNR.
Near-field optical response of periodically arrayed plasmonic nanogap antennas
Authors: Sakai Kyosuke , Nomura Kensuke , Tanaka Yoshito , Sasaki Keiji
Published: July 2013

We have studied two-dimensional periodically arrayed plasmonic nanogap antennas that exploit a “resonant coupling effect,” efficiently collecting incident light and enhancing the nanogap field. A theoretical investigation was carried out on an infinite array of gold nanoblock dimers in a square-lattice arrangement. Under resonant conditions, the near-field intensity spectra in the gap region showed a narrow peak (full width at half maximum of 50 nm) with a field enhancement that was a factor of ∼5 stronger than that of an isolated single-nanogap antenna. The influence of the geometrical parameters of the array (period, dimer orientation, nanogap size, and number of periods) is discussed.
Carbon nanotubes effects on the relaxation properties and critical current densities of MgB2 superconductor
Authors: Pasquini G. , Serquis A. , Moreno A. J. , Serrano G. , Civale L.
Published: July 2013

Addition of nonsuperconducting phases, such as carbon nanotubes, can modify the superconducting properties of MgB2 samples, improving the critical current density and upper critical field. A full understanding of the flux creep mechanism involved is crucial to the development of superconducting magnets in persistent mode, one of the main thrusts for the development of MgB2 wires. In this paper we present a creep study in bulk MgB2 samples, pure and with different amounts of carbon nanotubes additions. We conclude that the most consistent picture at low temperatures is a single vortex pinning regime, where the correlation length is limited by the grain size. We introduce a novel analysis that allows us to identify the region where the Anderson-Kim model is valid.
Study of surfactant mediated growth of Ni/V superlattices
Authors: Amir S. M. , Gupta Mukul , Potdar Satish , Gupta Ajay , Stahn Jochen
Published: July 2013

The Ni/V multilayers are useful as soft x-ray mirrors, polarizers, and phase retarders. For these applications, it is necessary that the interfaces roughness and interdiffusion must be as small as possible. The V-on-Ni and Ni-on-V interfaces are asymmetric due to the difference in the surface free energy of Ni and V. In this work, we report Ag surfactant mediated growth of Ni/V superlattices prepared using ion beam sputter deposition technique. These superlattices were studied using x-ray and neutron scattering techniques. It was found that when added in an optimum amount, Ag surfactant results in reduced interface roughness and interdiffusion across the interfaces. Obtained results can be understood with the surfactant floating-off mechanism leading to a balance in the surface free energy of Ni and V.
Electrical transport and Al doping efficiency in nanoscale ZnO films prepared by atomic layer deposition
Authors: Wu Y. , Hermkens P. M. , van de Loo B. W. H. , Knoops H. C. M. , Potts S. E. , Verheijen M. A. , Roozeboom F. , Kessels W. M. M.
Published: July 2013

In this work, the structural, electrical, and optical properties as well as chemical bonding state of Al-doped ZnO films deposited by atomic layer deposition have been investigated to obtain insight into the doping and electrical transport mechanisms in the films. The range in doping levels from 0% to 16.4% Al was accomplished by tuning the ratio of ZnO and Al2O3 ALD cycles. With X-ray photoelectron spectroscopy depth profiling and transmission electron microscopy, we could distinguish the individual ZnO and AlOx layers in the films. For films with a thickness of 40 nm, the resistivity improved from 9.8 mΩ cm for intrinsic ZnO to an optimum of 2.4 mΩ cm at 6.9 at. % Al. The binding energy of Zn 2p3/2 increased by 0.44 eV from the intrinsic ZnO to the highest Al-doped ZnO. This shift can be ascribed to an increase of the Fermi level. Ex-situ spectroscopic ellipsometry and Fourier transform infrared spectroscopy were used to measure the optical properties from which the carrier concentration and intra-grain mobility were extracted. The results showed that with increasing Al content, the grain boundary mobility increased at first due to an increased Fermi level, and then decreased mainly due to the scattering at AlOx/ZnO interfaces. For the same reasons, the doping efficiency of Al for highly Al-doped ZnO dropped monotonically with increasing Al. Furthermore, a blue shift of the optical band-gap ΔEg up to 0.48 eV was observed, consistent with the shifts of the Fermi level and the binding energy of the Zn 2p3/2 state.
Functional gradation through preferential crystallisation and interfacial activity in rapidly quenched Fe/Co-based bilayered ribbons for bend sensors
Authors: Panda A. K. , Roy R. K. , Dey Sushmita , Singh Satnam , Mitra A.
Published: July 2013

Rapidly quenched bilayered ribbons comprising one layer as Fe73.5Nb3Cu1Si13.5B9 (FM) and the other layer either as Fe74.5Nb3Si13.5B9 (FNb) or Co72.5Si12.5B15 (CSB) alloy designated as BLFM/FNb and BLFM/CSB, respectively, have been addressed. Phase transformation, thermomagnetic transitions, saturation magnetization, and soft magnetic properties of individual layers were revealed in the functional properties of bilayered ribbons. Properties of bilayer could be endorsed with respect to the single layered Fe73.5Nb3Cu1Si13.5B9, Fe74.5Nb3Si13.5B9, and Co72.5Si12.5B15 alloy ribbons. Selective devitrification of the layers in the bilayers could be induced through optimum heat treatment. Enhanced bend sensitivity was revealed in BLFM/CSB through generation of desirable phases in the bilayers of the bilayered ribbon. Synergistic diffusivity of Fe and Co with its consequent effect on interfacial zone of BLFM/CSB bilayer was observed.
Fabrication of stretchable MoS2 thin-film transistors using elastic ion-gel gate dielectrics
Authors: Pu Jiang , Zhang Yijin , Wada Yoshifumi , Tse-Wei Wang Jacob , Li Lain-Jong , Iwasa Yoshihiro , Takenobu Taishi
Published: July 2013

We fabricated stretchable molybdenum disulfide thin-film transistors (MoS2 TFTs) on poly(dimethylsiloxane) substrates using ion gels as elastic gate dielectrics. The TFTs exhibited an electron mobility of 1.40 cm2/(V·s) and an on/off current ratio of 104 with a notably low threshold voltage (∼1 V). Furthermore, our MoS2 TFTs operated at a mechanical strain of 5% without significant degradation of their electrical properties. These results demonstrate the potential for using MoS2 films for stretchable electronics.
Anisotropy and directional pinning in YBa2Cu3O7−x with BaZrO3 nanorods
Authors: Pompeo N. , Augieri A. , Torokhtii K. , Galluzzi V. , Celentano G. , Silva E.
Published: July 2013

Measurements of anisotropic transport properties (dc and high-frequency regime) of driven vortex matter in YBa2Cu3O7−x with elongated strong-pinning sites (c-axis aligned, self-assembled BaZrO3 nanorods) are used to demonstrate that the effective-mass angular scaling takes place only in intrinsic physical quantities (flux-flow resistivity), and not in pinning-related Labusch parameter and critical currents. Comparison of the dynamics at different time scales shows evidence for a transition of the vortex matter toward a Mott phase, driven by the presence of nanorods. The strong pinning in dc arises partially from a dynamic effect.
A spectroscopic study of ethylene destruction and by-product generation using a three-stage atmospheric packed-bed plasma reactor
Authors: Hübner M. , Guaitella O. , Rousseau A. , Röpcke J.
Published: July 2013

Using a three-stage dielectric packed-bed plasma reactor at atmospheric pressure, the destruction of ethylene, a typical volatile organic compound, and the generation of major by-products have been studied by means of Fourier Transform Infrared Spectroscopy. A test gas mixture air at a gas flow of 1 slm containing 0.12% humidity with 0.1% ethylene has been used. In addition to the fragmentation of the precursor gas, the evolution of the concentration of ten stable reaction products, CO, CO2, O3, NO2, N2O, HCN, H2O, HNO3, CH2O, and CH2O2 has been monitored. The concentrations of the by-products range between 5 ppm, in the case of NO2, and 1200 ppm, for H2O. By the application of three sequentially working discharge cells at a frequency of f = 4 kHz and voltage values between 9 and 12 kV, a nearly complete decomposition of C2H4 could be achieved. Furthermore, the influence of the specific energy deposition (SED) on the destruction process has been studied and the maximum value of SED was about 900 J l−1. The value of the characteristic energy β, characterizing the energy efficiency of the ethylene destruction in the reactor, was found to be 330 J l−1. It was proven that the application of three reactor stages suppresses essentially the production of harmful by-products as formaldehyde, formic acid, and NO2 compared to the use of only one or two stages. Based on the multi-component detection, the carbon balance of the plasma chemical conversion of ethylene has been analyzed. The dependence of the fragmentation efficiencies of ethylene (RF(C2H4) = 5.5 × 1019 molecules J−1) and conversion efficiencies to the produced molecular species (RC = (0.1–3) × 1016 molecules J−1) on the discharge conditions could be estimated in the multistage plasma reactor.
Current injection to free-standing III-N nanowires by bipolar diffusion
Authors: Kivisaari Pyry , Oksanen Jani , Tulkki Jukka
Published: July 2013

Light-emitting diodes (LEDs) based on nanowires are expected to enable a superior alternative to conventional LEDs due to their higher light extraction efficiency, reduced droop, and reduced material consumption. However, efficient current injection to nanowires with conventional current spreading approaches is challenging, because the conventional approach requires doping the wires and using at least partly absorbing top contacts. We show that minority carrier diffusion provides an extremely interesting possibility for current injection to undoped free-standing nanowires that do not require top contacts. To investigate this possibility, we have simulated current transport in selected nanowire structures where the nanowires are located close to a separate pn homojunction. Our results suggest that with bipolar diffusion injection, injection efficiencies exceeding 80% are feasible even for unoptimized free-standing nanowire structures at current densities up to 100 A/cm2, with a maximum injection efficiency of approximately 95% at 0.1 A/cm2. The results suggest that the concept also extends to other near surface nanostructures such as quantum wells coupled to surface plasmons and, under reverse operation, to photovoltaic devices.
Lateral Ge segregation and strain evolution in SiGe alloys during the formation of nickel germano-silicide on a relaxed Si0.73Ge0.27 epilayer
Authors: Tang Mengrao , Lin Guangyang , Li Cheng , Wang Chen , Zhang Maotian , Huang Wei , Lai Hongkai , Chen Songyan
Published: July 2013

Ge segregation and strain evolution in the SiGe alloys during the formation of nickel germano-silicide on a relaxed Si0.73Ge0.27 epilayer are studied in temperature range of 300-900 °C. The continuous NiSiGe film on SiGe epilayer is formed at 500 °C and below, which applies tensile stress on the underlying unreacted SiGe layer. When temperature rises to 600 °C and above, the NiSiGe film begins to agglomerate, resulting in the formation of Ge-rich SiGe regions scattering among NiSiGe grains in the surface due to Ge lateral segregation from NiSiGe. During these processes, Ge is preferentially rejected from the NiSiGe grains giving rise to the transformation of NiSiGe to NiSi with increase of temperature and the increase of Ge content in the Ge-rich SiGe at the NiSiGe grain boundaries. The enlarged lattice constant of Ge-rich SiGe and the volume expansion of NiSiGe grains make the Ge-rich SiGe alloy under compressive strain. No significant Ge segregation is observed between Ni(SiGe) and the underlying SiGe layer even at higher temperature.
Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2
Authors: Reiterer Veronika , Fey Dirk , Kolch Walter , Kholodenko Boris N. , Farhan Hesso
Published: July 2013

Significance

The role of catalytically inactive phosphatases (pseudophosphatases) remains enigmatic. Using a combination of experiments and modeling, we identified the pseudophosphatase serine/threonine/tyrosine-interacting protein (STYX) as a nuclear anchor and modulator of ERK signaling. Thereby, STYX regulates the morphology of the Golgi apparatus and its polarization in migrating cells. Consequently, STYX influences directional cell motility, a process that determines the invasive and metastatic ability of cancer cells. By controlling spatiotemporal ERK signaling, STYX plays a role in cell-fate decisions, such as PC12 cell differentiation.
Empirical intrinsic geometry for nonlinear modeling and time series filtering
Authors: Talmon Ronen , Coifman Ronald R.
Published: July 2013

In this paper, we present a method for time series analysis based on empirical intrinsic geometry (EIG). EIG enables one to reveal the low-dimensional parametric manifold as well as to infer the underlying dynamics of high-dimensional time series. By incorporating concepts of information geometry, this method extends existing geometric analysis tools to support stochastic settings and parametrizes the geometry of empirical distributions. However, the statistical models are not required as priors; hence, EIG may be applied to a wide range of real signals without existing definitive models. We show that the inferred model is noise-resilient and invariant under different observation and instrumental modalities. In addition, we show that it can be extended efficiently to newly acquired measurements in a sequential manner. These two advantages enable us to revisit the Bayesian approach and incorporate empirical dynamics and intrinsic geometry into a nonlinear filtering framework. We show applications to nonlinear and non-Gaussian tracking problems as well as to acoustic signal localization.
Swimming against the tide: a case study of an integrated social studies department
Authors: Fenwick Ashley J.J. , Minty Sarah , Priestley Mark
Published: July 2013

A recent trend in developed countries’ school curricula has been the transition from disciplinary to generic forms of knowledge, resulting in an emphasis on interdisciplinary organisation and more active forms of learning. Subject specialists are increasingly expected to demonstrate how their subject interconnects and equips pupils with key life skills. Such a change requires a major cultural shift and has been controversial, particularly in Scotland where Curriculum for Excellence, the latest curriculum reform, has seen this debate re‐emerge. A detailed empirical case study of one secondary school Social Studies department that has already negotiated these shifts is presented. The case study provides insights into how school and department structures and cultures conducive to a more integrated approach have been developed. Leadership, increased opportunities for teachers to exercise greater autonomy in their work, sources of impetus and support for innovation, and the co‐construction of meaning through dialogue are important themes in this process. This case study connects with current policy and provides an insight into strategies that other schools might employ when seeking to embed integrative practices. The department is identified as a significant locus for innovation and one which appears to challenge the norm.
Exotic smooth structures on topological fiber bundles I
Authors: Goette Sebastian , Igusa Kiyoshi , Williams Bruce
Published: July 2013

When two smooth manifold bundles over the same base are fiberwise tangentially homeomorphic, the difference is measured by a homology class in the total space of the bundle. We call this the relative smooth structure class. Rationally and stably, this is a complete invariant. We give a more or less complete and self-contained exposition of this theory.

An important application is the computation of the Igusa-Klein higher Reidemeister torsion invariants of these exotic smooth structures. Namely, the higher torsion invariant is equal to the Poincaré dual of the image of the smooth structure class in the homology of the base. This is proved in the companion paper written by the first two authors.
SICOP: identifying significant co-interaction patterns
Authors: Spitz Andreas , Zweig Katharina A. , Horvát Emőke-Ágnes
Published: July 2013

Summary: Interactions between various types of molecules that regulate crucial cellular processes are extensively investigated by high-throughput experiments and require dedicated computational methods for the analysis of the resulting data. In many cases, these data can be represented as a bipartite graph because it describes interactions between elements of two different types such as the influence of different experimental conditions on cellular variables or the direct interaction between receptors and their activators/inhibitors. One of the major challenges in the analysis of such noisy datasets is the statistical evaluation of the relationship between any two elements of the same type. Here, we present SICOP (significant co-interaction patterns), an implementation of a method that provides such an evaluation based on the number of their common interaction partners, their so-called co-interaction. This general network analytic method, proved successful in diverse fields, provides a framework for assessing the significance of this relationship by comparison with the expected co-interaction in a suitable null model of the same bipartite graph. SICOP takes into consideration up to two distinct types of interactions such as up- or downregulation. The tool is written in Java and accepts several common input formats and supports different output formats, facilitating further analysis and visualization. Its key features include a user-friendly interface, easy installation and platform independence.

Availability: The software is open source and available at cna.cs.uni-kl.de/SICOP under the terms of the GNU General Public Licence (version 3 or later).

Contact:  agnes.horvat@iwr.uni-heidelberg.de or zweig@cs.uni-kl.de
Despite Differences in Cytosolic Calcium Regulation, Lidocaine Toxicity Is Similar in Adult and Neonatal Rat Dorsal Root Ganglia In Vitro
Authors: Doan Lisa V. , Eydlin Olga , Piskoun Boris , Kline Richard P. , Recio-Pinto Esperanza , Rosenberg Andrew D. , Blanck Thomas J. J. , Xu Fang
Published: July 2013

Background:

Neuraxial local anesthetics may have neurological complications thought to be due to neurotoxicity. A primary site of action of local anesthetics is the dorsal root ganglia (DRG) neuron. Physiologic differences have been noted between young and adult DRG neurons; hence, the authors examined whether there were any differences in lidocaine-induced changes in calcium and lidocaine toxicity in neonatal and adult rat DRG neurons.

Methods:

DRG neurons were cultured from postnatal day 7 (P7) and adult rats. Lidocaine-induced changes in cytosolic calcium were examined with the calcium indicator Fluo-4. Cells were incubated with varying concentrations of lidocaine and examined for viability using calcein AM and ethidium homodimer-1 staining. Live imaging of caspase-3/7 activation was performed after incubation with lidocaine.

Results:

The mean KCl-induced calcium transient was greater in P7 neurons (P < 0.05), and lidocaine significantly inhibited KCl-induced calcium responses in both ages (P < 0.05). Frequency distribution histograms of KCl-evoked calcium increases were more heterogeneous in P7 than in adult neurons. With lidocaine, KCl-induced calcium transients in both ages became more homogeneous but remained different between the groups. Interestingly, cell viability was decreased by lidocaine in a dose-dependent manner similarly in both ages. Lidocaine treatment also activated caspase-3/7 in a dose- and time-dependent manner similarly in both ages.

Conclusions:

Despite physiological differences in P7 and adult DRG neurons, lidocaine cytotoxicity is similar in P7 and adult DRG neurons in vitro. Differences in lidocaine- and KCl-evoked calcium responses suggest the similarity in lidocaine cytotoxicity involves other actions in addition to lidocaine-evoked effects on cytosolic calcium responses.