bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of the intrinsic and the injection dependent charge carrier density in organic solar cells using the Suns-VOC method
Authors: Schiefer Sebastian , Zimmermann Birger , Würfel Uli
Published: January 2014

A method is presented to calculate the intrinsic and injection dependent average charge carrier density from the transport resistance of an organic solar cell. The latter is determined using a combination of a Suns-VOC and a current-voltage measurement under illumination which allows to split the total series resistance of the solar cell into an (ohmic) contribution of the circuitry and an injection dependent part which is caused by the transport of the charge carriers through the photoactive layer. In the derivation of the formula for the average charge carrier density, spatially homogeneous generation rate and gradients of the quasi Fermi levels as well as balanced mobilities had to be assumed. However, numerical simulations revealed that even for strongly inhomogeneous generation and unbalanced mobilities the results are reasonably accurate proving the practical applicability of the presented method. Using an inverted ITO-free P3HT:PCBM solar cell, we determined a value for the intrinsic charge carrier density of ni = 2.88 × 1011 cm−3 at T = 300 K and for the average density of mobile charge carriers at “1 sun” under open circuit conditions we obtained nav = 3.2 × 1016 cm−3.
Exploiting magnetic asymmetry to concentrate diamagnetic particles in ferrofluid microflows
Authors: Wilbanks James J. , Kiessling Garrett , Zeng Jian , Zhang Cheng , Tzeng Tzuen-Rong , Xuan Xiangchun
Published: January 2014

Concentrating particles and cells for measurement or removal is often essential in many chemical and biological applications. Diamagnetic particle concentration has been demonstrated in magnetic fluids using two repulsive or attracting magnets, which in almost all cases are symmetrically positioned on the two sides of the particle-flowing channel. This work studies the effects of magnet asymmetry on the pattern and flow rate of diamagnetic particle concentration in ferrofluid flow through a straight rectangular microchannel. Two attracting permanent magnets with a fixed distance are each embedded on one side of the microchannel with a symmetric or an asymmetric configuration. A pair of symmetric counter-rotating circulations of concentrated particles is formed in the microchannel with a symmetric magnet configuration, which is found to grow in size and progress up the flow. In contrast, the single asymmetric circulation of concentrated particles formed in the microchannel with an asymmetric magnet configuration nearly maintains its size and position. Moreover, the magnet asymmetry is found to increase the ferrofluid flow rate for particle trapping, which is predicted by a three-dimensional theoretical model with a reasonable agreement.
Hall effect and the magnetotransport properties of Co2MnSi1-xAlx Heusler alloys
Authors: Prestigiacomo Joseph C. , Young David P. , Adams Philip W. , Stadler Shane
Published: January 2014

We have investigated the transport properties of the quaternary Heusler alloys Co2MnSi1-xAlx (0≤x≤1), which have been theoretically predicted to develop a half-metallic band structure as x→0. Resistivity versus temperature measurements as a function of Al concentration (x) revealed a systematic reduction in the residual resistivity ratio as well as a transition from weakly localized to half-metallic conduction as x→0. From measurements of the ordinary and anomalous Hall effects, the charge carrier concentration was found to increase, while the anomalous Hall coefficient decreased by nearly an order of magnitude with each sample as x→0 (Δx=0.25.). Scaling of the anomalous Hall effect with longitudinal resistivity reveals that both the skew-scattering and intrinsic contributions grow quickly as x→1, indicating that disorder and band-structure effects cause the large anomalous Hall effect magnitudes observed for Co2MnAl.
The effect of a normal electric field on wave propagation on a fluid film
Authors: Hammerton P. W. , Bassom Andrew P.
Published: January 2014

Long-wavelength, small-amplitude disturbances on the surface of a fluid layer subject to a normal electric field are considered. In our model, a dielectric medium lies above a layer of perfectly conducting fluid, and the electric field is produced by parallel plate electrodes. The Reynolds number of the fluid flow is taken to be large, with viscous effects restricted to a thin boundary layer on the lower plate. The effects of surface tension and electric field enter the governing equation through an inverse Bond number and an electrical Weber number, respectively. The thickness of the lower fluid layer is assumed to be much smaller than the disturbance wavelength, and a unified analysis is presented allowing for the full range of scalings for the thickness of the upper dielectric medium. A variety of different forms of modified Korteweg-de Vries equation are derived, involving Hilbert transforms, convolution terms, higher order spatial derivatives, and fractional derivatives. Critical values are identified for the inverse Bond number and electrical Weber number at which the qualitative nature of the disturbances changes.
Sulfur immobilization and lithium storage on defective graphene: A first-principles study
Authors: Zhao Wen , Chen Pengcheng , Tang Peizhe , Li Yuanchang , Wu Jian , Duan Wenhui
Published: January 2014

Motivated by the recent progresses and remaining technical challenges in Li-S battery, we employ defective graphene as a prototype cathode framework to illustrate how battery performance is influenced by the mesoporous carbon materials. We show that the immobilization of S unavoidably sacrifices its ability to further interact with Li, which leads to an enhanced cycle life but a decreased capacity. Based on our calculated results, we suggest a suitable S binding-energy range of ∼4–5 eV to balance the battery stability and capability under thermodynamic equilibrium conditions. Our results may promote the understanding and architecture design of Li-S battery.
Reduction of electron accumulation at InN(0001) surfaces via saturation of surface states by potassium and oxygen as donor- or acceptor-type adsorbates
Authors: Eisenhardt A. , Reiß S. , Krischok S. , Himmerlich M.
Published: January 2014

The influence of selected donor- and acceptor-type adsorbates on the electronic properties of InN(0001) surfaces is investigated implementing in-situ photoelectron spectroscopy. The changes in work function, surface band alignment, and chemical bond configurations are characterized during deposition of potassium and exposure to oxygen. Although an expected opponent charge transfer characteristic is observed with potassium donating its free electron to InN, while dissociated oxygen species extract partial charge from the substrate, a reduction of the surface electron accumulation occurs in both cases. This observation can be explained by adsorbate-induced saturation of free dangling bonds at the InN resulting in the disappearance of surface states, which initially pin the Fermi level and induce downward band bending.
Effects of pulse polarity on nanosecond pulse driven dielectric barrier discharge plasma actuators
Authors: Dawson Robyn A. , Little Jesse
Published: January 2014

Nanosecond pulse driven dielectric barrier discharge plasma actuators are studied in quiescent air using a power supply capable of producing negative and positive polarity waveforms. High voltage pulses are applied to the exposed electrode of typical asymmetric actuator geometry. In addition to polarity, the effects of pulse amplitude, actuator length, and dielectric thickness are also investigated. Schlieren images are used to estimate the relative near surface gas heating, while electrical measurements are acquired simultaneously. Negative polarity pulses develop slightly more energy per unit length for thin dielectrics, while positive polarity is slightly higher for thick dielectrics. In most cases, the difference in per unit length energy produced by positive and negative pulses on equivalent actuators is not outside the measurement uncertainty. Negative polarity pulses are found to produce a stronger pressure wave for a given peak voltage and pulse energy across the test matrix. Results indicate that the negative polarity pulse more efficiently couples electrical energy to the near surface gas as heat. This suggests negative polarity pulses may be preferred for aerodynamic flow control applications employing this actuator arrangement.
Effect of anionic surfactant concentration on the variable range hopping conduction in polypyrrole nanoparticles
Authors: Rawal Ishpal , Kaur Amarjeet
Published: January 2014

The mechanism of charge transport in polypyrrole (PPy) nanoparticles prepared with different concentrations (5 to 30 mM) of anionic surfactant (sodium dodecyl sulfate) is reported. Transmission electron microscopy technique confirms the formation of PPy nanoparticles of sizes ∼52 to 28 nm under surfactant directed approach. The room temperature electrical conductivity of the prepared nanoparticles found to increase from 3 to 22 S/cm with surfactant concentration. The temperature dependent activation energy rules out the possibility of band conduction mechanism in the prepared PPy nanoparticles and thus the synthesized nanoparticles are analyzed under variable range hopping (VRH) model for conduction mechanism. The PPy nanoparticles, reduced with liquid ammonia, hold 3D VRH conduction mechanism for the charge transport. However, in the doped samples, some deviation from 3D VRH conduction behavior at higher temperatures (>150 K) has been observed. This may be attributed to the presence of anionic surfactant in these samples. The doping of anionic surfactant causes rise in conducting islands, which may lead to the change in the shape/distribution of density of states governed by Gaussian or exponential type near Fermi level.
Dynamical response of liquid bridges to a step change in the mass force magnitude
Authors: Ferrera C. , Herrada M. A. , Montanero J. M. , Torregrosa M. , Shevtsova V.
Published: January 2014

We analyze the dynamical response of an isothermal liquid bridge to a step change in the mass force magnitude by numerically solving the three-dimensional Navier-Stokes equations. We study the free surface oscillations caused by both axial and lateral pulses of the mass force. The oscillation amplitude and the dynamical stability limit are calculated for different values of the parameters characterizing the fluid configuration. We examine the stability of one of the liquid bridges to be analyzed in the Japanese and European Research Experiment on Marangoni Instabilities experiment on board of the International Space Station (ISS). We study the response of that liquid bridge to real g-jitter on board of the ISS.
Charge injection across a metal-organic interface suppressed by thermal diffusion
Authors: Monton C. , Saerbeck T. , Valmianski I. , Schuller Ivan K.
Published: January 2014

We find that the ohmic conductance of Co-phthalocyanine (CoPc) vertical capacitive devices is irreversibly suppressed by orders of magnitude when they are heated above 340 K. Detailed structural and transport studies imply that the changes in the conductance are due to diffusion of the top Pd electrode into the CoPc layer. This leads to a decrease in Pd electrode effective work function, which increases the potential barrier for hole injection.
BiFeO3/poly(methyl methacrylate) nanocomposite films: A study on magnetic and dielectric properties
Authors: Ahlawat Anju , Satapathy S. , Bhartiya Shushmita , Singh M. K. , Choudhary R. J. , Gupta P. K.
Published: January 2014

Utilisation of multiferroic BiFeO3 nanoparticles requires that these be embedded in a suitable matrix. We prepared BiFeO3/poly (methyl methacrylate) nanocomposite films with varying volume fraction of nanoparticles and investigated their magnetic and dielectric properties. The results obtained show that BiFeO3 nanoparticles exhibit superparamagnetic behaviour in nanocomposite films. The magnetization was observed to saturate beyond ∼13 kOe for 2.5% and 5% BFO composite films. The AC conductivity of composite films (∼10−12 Ohm−1cm−1) is also significantly reduced (by four order of magnitude) compared to that of the bulk BFO. The superparamagnetic behavior, reduced conductivity, and flexibility make these composite films attractive candidates for potential applications.
Five-dimensional visualization of phase transition in BiNiO3 under high pressure
Authors: Liu Yijin , Wang Junyue , Azuma Masaki , Mao Wendy L. , Yang Wenge
Published: January 2014

Colossal negative thermal expansion was recently discovered in BiNiO3 associated with a low density to high density phase transition under high pressure. The varying proportion of co-existing phases plays a key role in the macroscopic behavior of this material. Here, we utilize a recently developed X-ray Absorption Near Edge Spectroscopy Tomography method and resolve the mixture of high/low pressure phases as a function of pressure at tens of nanometer resolution taking advantage of the charge transfer during the transition. This five-dimensional (X, Y, Z, energy, and pressure) visualization of the phase boundary provides a high resolution method to study the interface dynamics of high/low pressure phase.
Towards a terahertz direct receiver based on graphene up to 10 THz
Authors: Dragoman Mircea , Aldrigo Martino , Dinescu Adrian , Dragoman Daniela , Costanzo Alessandra
Published: January 2014

We present a study for a THz receiver based on graphene. First, the dipole and the bowtie THz antennas on graphene are designed, and followed by the on-wafer fabrication of a graphene diode matched to the antenna. Finally the responsivity of the receiver up to 10 THz is computed. Our results show that the antenna and the diode behaviors exhibit new properties (e.g., the antennas are acting as high reactive impedance surfaces, the diode is rectifying only due to its geometrical shape). These new properties are due to the physical properties of graphene having the carrier transport described by Dirac equation.
Role of quantum confinement in luminescence efficiency of group IV nanostructures
Authors: Barbagiovanni E. G. , Lockwood D. J. , Rowell N. L. , Costa Filho R. N. , Berbezier I. , Amiard G. , Favre L. , Ronda A. , Faustini M. , Grosso D.
Published: January 2014

Experimental results obtained previously for the photoluminescence efficiency (PLeff) of Ge quantum dots (QDs) are theoretically studied. A log-log plot of PLeff versus QD diameter (D) resulted in an identical slope for each Ge QD sample only when EG∼(D2+D)−1. We identified that above D ≈ 6.2 nm: EG∼D−1 due to a changing effective mass (EM), while below D ≈ 4.6 nm: EG∼D−2 due to electron/hole confinement. We propose that as the QD size is initially reduced, the EM is reduced, which increases the Bohr radius and interface scattering until eventually pure quantum confinement effects dominate at small D.
Comparative Monte Carlo analysis of InP- and GaN-based Gunn diodes
Authors: García S. , Pérez S. , Íñiguez-de-la-Torre I. , Mateos J. , González T.
Published: January 2014

In this work, we report on Monte Carlo simulations to study the capability to generate Gunn oscillations of diodes based on InP and GaN with around 1 μm active region length. We compare the power spectral density of current sequences in diodes with and without notch for different lengths and two doping profiles. It is found that InP structures provide 400 GHz current oscillations for the fundamental harmonic in structures without notch and around 140 GHz in notched diodes. On the other hand, GaN diodes can operate up to 300 GHz for the fundamental harmonic, and when the notch is effective, a larger number of harmonics, reaching the Terahertz range, with higher spectral purity than in InP diodes are generated. Therefore, GaN-based diodes offer a high power alternative for sub-millimeter wave Gunn oscillations.
Picosecond and nanosecond laser annealing and simulation of amorphous silicon thin films for solar cell applications
Authors: Theodorakos I. , Zergioti I. , Vamvakas V. , Tsoukalas D. , Raptis Y. S.
Published: January 2014

In this work, a picosecond diode pumped solid state laser and a nanosecond Nd:YAG laser have been used for the annealing and the partial nano-crystallization of an amorphous silicon layer. These experiments were conducted as an alternative/complementary to plasma-enhanced chemical vapor deposition method for fabrication of micromorph tandem solar cell. The laser experimental work was combined with simulations of the annealing process, in terms of temperature distribution evolution, in order to predetermine the optimum annealing conditions. The annealed material was studied, as a function of several annealing parameters (wavelength, pulse duration, fluence), as far as it concerns its structural properties, by X-ray diffraction, SEM, and micro-Raman techniques.
Controllable sealing of leaky alumina films on NiAl(100) surface by catalytic oxidation
Authors: Liu Kuan-Te , Chen Jian-Wei , Liao Yu-Wen , Lin Wen-Chin , Wu Chii-Bin , Kuo Chien-Cheng , Lin Minn-Tsong , Song Ker-Jar
Published: January 2014

We show the oxide films grown by saturated dosing of oxygen on NiAl(100) is leaky, i.e., it has no apparent effect blocking deposited Co from diffusion into the bulk. We then show the easy paths for diffusion (presumably the boundaries between the oxide stripes) can be sealed by an oxidation process catalyzed by Co nanoparticles. Once sealed, the temperature range in which Co nanoparticles persist on the surface is extended by 400 K (up to 1100 K). Such “leak tight” oxide films could serve as better corrosion barrier and insulting layers.
Deep Co penetration and spin-polarization of C60 molecules at hybridized Co-C60 interfaces
Authors: Cheng Pei-Yu , Chiang Meng-Ruei , Chan Yuet-Loy , Hsu Yao-Jane , Wang Pen-Cheng , Wei D. H.
Published: January 2014

We used near-edge x-ray absorption fine structure spectroscopy to identify the interplays at organic semiconductor-ferromagnet interfaces. When monitoring the L-edge intensity of 0.36 nm Co depositing on C60 films of various thicknesses, we detected weaker Co signal from structures with larger C60 thicknesses. Having determined that the electron mean escape depth in C60 is 4.9 nm, further model analysis indicates that the decline of spectral intensity is due to deep penetration of Co clusters. Finally, C K-edge spectra reveal clear evidences of orbital hybridization between Co and C60 as well as a visible dichroic effect at 125 K.
Direct experimental evidence for the reversal of carrier type upon hydrogen intercalation in epitaxial graphene/SiC(0001)
Authors: Rajput S. , Li Y. Y. , Li L.
Published: January 2014

Raman spectroscopy and scanning tunneling microscopy/spectroscopy measurements are performed to determine the atomic structure and electronic properties of H-intercalated graphene/SiC(0001) obtained by annealing the as-grown epitaxial graphene in hydrogen atmosphere. While the as-grown graphene is found to be n-type with the Dirac point (ED) at 450 and 350 meV below Fermi level for the 1st and 2nd layer, the H-intercalated graphene is p-type with ED at 320 and 200 meV above. In addition, ripples are observed in the now quasi-free standing graphene decoupled from the SiC substrate. This causes fluctuations in the Dirac point that directly follow the undulations of the ripples, resulting in electron and hole puddles in the H-intercalated graphene/SiC(0001).
Percolation network in resistive switching devices with the structure of silver/amorphous silicon/p-type silicon
Authors: Liu Yanhong , Gao Ping , Jiang Xuening , Bi Kaifeng , Xu Hongxia , Peng Wei
Published: January 2014

Conducting pathway of percolation network was identified in resistive switching devices (RSDs) with the structure of silver/amorphous silicon/p-type silicon (Ag/a-Si/p-Si) based on its gradual RESET-process and the stochastic complex impedance spectroscopy characteristics (CIS). The formation of the percolation network is attributed to amounts of nanocrystalline Si particles as well as defect sites embedded in a-Si layer, in which the defect sites supply positions for Ag ions to nucleate and grow. The similar percolation network has been only observed in Ag-Ge-Se based RSD before. This report provides a better understanding for electric properties of RSD based on the percolation network.
Fast and slow stress evolution mechanisms during interruptions of Volmer-Weber growth
Authors: Yu Hang Z. , Leib Jeffrey S. , Boles Steven T. , Thompson Carl V.
Published: January 2014

The evolution of mechanical stress during Volmer-Weber growth of thin films is complex, often including a reversible stress evolution during interruptions of film deposition. The underlying mechanism for stress evolution during growth interruptions has been extensively debated, but remains unclear. In this work, in situ measurements of stress evolution during growth interruptions of various time scales, film thicknesses, and substrate temperatures were made during deposition of gold and nickel films. It was found that at least two mechanisms lead to the observed stress evolution, one fast (time constant ∼102 s) and one slow (time constant ∼104 s). The fast process is reversible and weakly dependent on the film thickness, while the slow process is irreversible and strongly dependent on the film thickness. It is shown that grain growth during growth interruptions can account for a significant portion of the stress change associated with the slow process. The fast reversible process is likely to be associated with reversible changes of the surface structure.
Calcium chloride electron injection/extraction layers in organic electronic devices
Authors: Qu Bo , Gao Zhi , Yang Hongsheng , Xiao Lixin , Chen Zhijian , Gong Qihuang
Published: January 2014

Nontoxic calcium chloride (CaCl2) was introduced into organic electronic devices as cathode buffer layer (CBL). The turn-on voltage and maximum luminance of organic light-emitting diode (OLED) with 1.5 nm CaCl2 was 3.5 V and 21 960 cd/m2, respectively. OLED with 1.5 nm CaCl2 possessed comparable electroluminescent characteristics to that of the commonly used LiF. Moreover, the performance of the organic photovoltaic device with 0.5 nm CaCl2 was comparable to that of the control device with LiF. Therefore, CaCl2 has the potential to be used as the CBL for organic electronic devices.
Improved Photocatalytic Activity of Copper Heterostructure Composites (Cu–Cu2O–CuO/AC) Prepared by Simple Carbothermal Reduction
Authors: Ma Hongchao , Liu Yifeng , Fu Yinghuan , Yu Chunling , Dong Xiaoli , Zhang Xiufang , Zhang Xinxin , Xue Wenping
Published: January 2014

Cu–Cu2O–CuO/activated carbon heterostructure composites with visible-light activity have been successfully synthesized by a simple carbothermal reduction procedure using CuSO4 as a single precursor. The resultant samples were characterized by X-ray diffraction, transmission electron microscopy, and X-ray photoelectron spectroscopy measurements. The results showed that the Cu–Cu2O–CuO composites with size less than 10 nm dispersed well on the surface of activated carbon. Activated carbon played both a reducing agent and support role in the formation of Cu–Cu2O–CuO/activated carbon heterostructure composites. X-ray photoelectron spectroscopy analysis suggests that the outside of the nanoparticles is CuO and the inside of the nanoparticles is Cu metal and Cu2O. Moreover, the composition of Cu–Cu2O–CuO/activated carbon composites can be tailored by varying the Cu loading, heat-treatment temperature, and heat-treatment time. The photocatalytic activities of the catalysts were investigated by degrading reactive brilliant blue KN-R under visible-light irradiation. The Cu–Cu2O–CuO/activated carbon heterostructure composites showed excellent photocatalytic activity compared with other catalysts (pure CuO, Cu2O, Cu2O/activated carbon, CuO/activated carbon, and Cu2O–CuO/activated carbon), which is ascribed to synergistic action between the activated carbon support and photoactive copper species, and the presence of interfacial structures such as a Cu2O/CuO heterostructure, Cu/Cu2O (or CuO) Schottky barrier, and Cu2O/Cu/CuO ohmic heterojunction.
Minimalist Approaches to Protein Labelling: Getting the Most Fluorescent Bang for Your Steric Buck
Authors: Speight Lee C. , Samanta Moumita , Petersson E. James
Published: January 2014

Fluorescence methods allow one to monitor protein conformational changes, protein–protein associations, and proteolysis in real time, at the single molecule level and in living cells. The information gained in such experiments is a function of the spectroscopic techniques used and the strategic placement of fluorophore labels within the protein structure. There is often a trade-off between size and utility for fluorophores, whereby large size can be disruptive to the protein’s fold or function, but valuable characteristics, such as visible wavelength absorption and emission or brightness, require sizable chromophores. Three major types of fluorophore readouts are commonly used: (1) Förster resonance energy transfer (FRET); (2) photoinduced electron transfer (PET); and (3) environmental sensitivity. This review focuses on those probes small enough to be incorporated into proteins during ribosomal translation, which allows the probes to be placed on the interiors of proteins as they are folded during synthesis. The most broadly useful method for doing so is site-specific unnatural amino acid (UAA) mutagenesis. We discuss the use of UAA probes in applications relying on FRET, PET, and environmental sensitivity. We also briefly review other methods of protein labelling and compare their relative merits to UAA mutagenesis. Finally, we discuss small probes that have thus far been used only in synthetic peptides, but which have unusual value and may be candidates for incorporation using UAA methods.
Synchrotron X-ray distinction of seasonal hydrological and temperature patterns in speleothem carbonate
Authors: Wynn Peter M. , Fairchild Ian J. , Spötl Christoph , Hartland Adam , Mattey Dave , Fayard Barbara , Cotte Marine
Published: January 2014

Environmental context Speleothem chemical records are used to reconstruct environmental change on a broad range of timescales. However, one of the biggest challenges is to link the records contained within speleothems at the sub-annual timescale to changing meteorological conditions. Seasonal infiltration patterns and cave ventilation dynamics are reconstructed through high resolution analysis of speleothem trace element content by synchrotron radiation, building towards proxy records of hydrological variability and winter duration as indices of recent climatic change beyond the instrumental period. Abstract Synchrotron micro-X-ray fluorescence (µXRF) spectrometry is used to reveal trace element patterns within speleothem calcite at the sub-annual scale and provide one of the first calibrations to prevailing meteorological conditions. Mapping of Zn and SO42– within speleothem calcite was performed at the European Synchrotron Radiation Facility over three annual cycles (1977–1979). Peaks in µXRF Zn concentrations occur on an annual basis, although banding of lower XRF intensity reveals multiple events at the sub-annual scale. The delivery of Zn to the speleothem was found to be dependent upon the presence of a water excess, the condition of any overlying snowpack and the pH of the soil solution as controlled by microbial activity. This generated a pattern of Zn event laminae that documented increasing concentrations from winter through to the following autumn and complies with existing models inferring surface-active trace metals are delivered to the point of speleothem growth in association with natural organic matter (referred to as NOM–metal complexes). Minimum and maximum concentrations of speleothem SO42– coincide with winter and summer respectively, in contrast to the near constant SO42– concentrations of the drip water. Fluctuations in speleothem SO42– levels closely follow changes in cave external temperatures, thereby validating existing models of sulfate incorporation into carbonate minerals thought to be driven by cave ventilation dynamics and internal cave atmospheric pCO2 (partial pressure). At the current resolution of analysis, this represents some of the first evidence linking event-based meteorological (temperature and precipitation) records to the trace element content of speleothem calcite, building towards reconstruction of indices of climatic change beyond the instrumental period.
Religion and the state in the Arab world: an overview
Authors: Belkeziz Abdelilah
Published: January 2014

This article provides an overview of the issues addressed in a series of papers on the general theme of ‘religion and the state in the Arab world’ published in Contemporary Arab Affairs over the past 12 months. The papers were initially presented at a conference convened by the Center for Arab Unity Studies and the Swedish Alexandria Institute, held in Hamamaat, Tunisia, in November 2012. Further to his own paper on the topic (published in issue 6(4) in this journal) here Abdelilah Belkeziz identifies the purpose of the whole exercise, namely to explore a range of different perspectives on the theme. He positions these perspectives on a spectrum between two extremes: at one, he contends, the case for separation between religion and state verges on hostility to religion itself; and at the other, an exclusivist version of Islam is accorded primacy over all other considerations in the running of a state and thence political discourse. He discusses the dangers inherent in both extremes and makes the case for a model of secularism that accords space to both religion and politics in the national project.
Religion and the state in Turkey and Iran: a comparative overview
Authors: Ahmad Refat Sayed
Published: January 2014

The question of the relationship between religion and the state in the Islamic world is as old as Islam itself. The experiences of Turkey and Iran during the past 30 years qualify among the most instructive applications of the relationship. In these two cases, the interaction between the systems of governance, on the one hand, and the Islamic cultural and legislative heritage, on the other, represents a common factor, whereas they differ in terms of the doctrinal reference on which each of these experiences is based. They also differ in perspective, application mechanisms and their relations with the West. The present research can be encapsulated, in broad outline, under five main headlines which raise questions more than provide answers: (1) the historical background of the relationship between religion and the state in the Turkish and Iranian models; (2) the effect of the ascent of revolutionary Islam in Iran, after the revolution of 1979, on the problematic of state–religion relations; (3) from ‘well-being’ to ‘justice and development’: limitations and prospects of a historical compromise between religion, secularism and the state; (4) points of controversy and commonalities in the Turkish and Iranian experiences from the 1980s to the end of 2012; and (5) looking into the relationship of each of these two models with the Arab Spring revolutions: are they determinants of these revolutions or investing in their development?
Autoequivalences of toric surfaces
Authors: Broomhead Nathan , Ploog David
Published: January 2014

We show that the autoequivalence group of the derived category of any smooth projective toric surface is generated by the standard equivalences and spherical twists obtained from

−
2

-2

-curves. In many cases we give all relations between these generators. We also prove a close link between spherical objects and certain pairs of exceptional objects.
Cofinal maximal chains in the Turing degrees
Authors: Wang Wei , Wu Liuzhen , Yu Liang
Published: January 2014

Assuming

Z
F
C

ZFC

, we prove that

C
H

CH

holds if and only if there exists a cofinal maximal chain of order type

ω
1

\omega _1

in the Turing degrees. However, it is consistent that

Z
F

ZF

+“the reals are not well ordered”+“there exists a cofinal chain in the Turing degrees of order type

ω
1

\omega _1

”.
Tschirnhaus-Weierstrass curves
Authors: Schicho Josef , Sevilla David
Published: January 2014

We define the concept of Tschirnhaus-Weierstrass curve, named after the Weierstrass form of an elliptic curve and Tschirnhaus transformations. Every pointed curve has a Tschirnhaus-Weierstrass form, and this representation is unique up to a scaling of variables. This is useful for computing isomorphisms between curves.
Elliptic curves with full 2-torsion and maximal adelic Galois representations
Authors: Corwin David , Feng Tony , Li Zane , Trebat-Leder Sarah
Published: January 2014

In 1972, Serre showed that the adelic Galois representation associated to a non-CM elliptic curve over a number field has open image in

G
L

2

(

Z

^

)

\mathrm {GL}_2(\widehat {\mathbb {Z}})

. In (2010), Greicius developed necessary and sufficient criteria for determining when this representation is actually surjective and exhibits such an example. However, verifying these criteria turns out to be difficult in practice; Greicius describes tests for them that apply only to semistable elliptic curves over a specific class of cubic number fields. In this paper, we extend Greicius’s methods in several directions. First, we consider the analogous problem for elliptic curves with full 2-torsion. Following Greicius, we obtain necessary and sufficient conditions for the associated adelic representation to be maximal and also develop a battery of computationally effective tests that can be used to verify these conditions. We are able to use our tests to construct an infinite family of curves over

Q

(
α
)

\mathbb {Q}(\alpha )

with maximal image, where

α
\alpha

is the real root of

x
3

+
x
+
1

x^3 + x + 1

. Next, we extend Greicius’s tests to more general settings, such as non-semistable elliptic curves over arbitrary cubic number fields. Finally, we give a general discussion concerning such problems for arbitrary torsion subgroups.
A central role for vimentin in regulating repair function during healing of the lens epithelium
Authors: Menko A. S. , Bleaken B. M. , Libowitz A. A. , Zhang L. , Stepp M. A. , Walker J. L.
Published: January 2014

Mock cataract surgery provides a unique ex vivo model for studying wound repair in a clinically relevant setting. Here wound healing involves a classical collective migration of the lens epithelium, directed at the leading edge by an innate mesenchymal subpopulation of vimentin-rich repair cells. We report that vimentin is essential to the function of repair cells as the directors of the wound-healing process. Vimentin and not actin filaments are the predominant cytoskeletal elements in the lamellipodial extensions of the repair cells at the wound edge. These vimentin filaments link to paxillin-containing focal adhesions at the lamellipodial tips. Microtubules are involved in the extension of vimentin filaments in repair cells, the elaboration of vimentin-rich protrusions, and wound closure. The requirement for vimentin in repair cell function is revealed by both small interfering RNA vimentin knockdown and exposure to the vimentin-targeted drug withaferin A. Perturbation of vimentin impairs repair cell function and wound closure. Coimmunoprecipitation analysis reveals for the first time that myosin IIB is associated with vimentin, linking vimentin function in cell migration to myosin II motor proteins. These studies reveal a critical role for vimentin in repair cell function in regulating the collective movement of the epithelium in response to wounding.
Peptide aptamers define distinct EB1- and EB3-binding motifs and interfere with microtubule dynamics
Authors: Leśniewska Karolina , Warbrick Emma , Ohkura Hiroyuki
Published: January 2014

EB1 is a conserved protein that plays a central role in regulating microtubule dynamics and organization. It binds directly to microtubule plus ends and recruits other plus end–localizing proteins. Most EB1-binding proteins contain a Ser–any residue–Ile-Pro (SxIP) motif. Here we describe the isolation of peptide aptamers with optimized versions of this motif by screening for interaction with the Drosophila EB1 protein. The use of small peptide aptamers to competitively inhibit protein interaction and function is becoming increasingly recognized as a powerful technique. We show that SxIP aptamers can bind microtubule plus ends in cells and functionally act to displace interacting proteins by competitive binding. Their expression in developing flies can interfere with microtubules, altering their dynamics. We also identify aptamers binding to human EB1 and EB3, which have sequence requirements similar to but distinct from each other and from Drosophila EB1. This suggests that EB1 paralogues within one species may interact with overlapping but distinct sets of proteins in cells.
Transportin acts to regulate mitotic assembly events by target binding rather than Ran sequestration
Authors: Bernis Cyril , Swift-Taylor Beth , Nord Matthew , Carmona Sarah , Chook Yuh Min , Forbes Douglass J.
Published: January 2014

The nuclear import receptors importin β and transportin play a different role in mitosis: both act phenotypically as spatial regulators to ensure that mitotic spindle, nuclear membrane, and nuclear pore assembly occur exclusively around chromatin. Importin β is known to act by repressing assembly factors in regions distant from chromatin, whereas RanGTP produced on chromatin frees factors from importin β for localized assembly. The mechanism of transportin regulation was unknown. Diametrically opposed models for transportin action are as follows: 1) indirect action by RanGTP sequestration, thus down-regulating release of assembly factors from importin β, and 2) direct action by transportin binding and inhibiting assembly factors. Experiments in Xenopus assembly extracts with M9M, a superaffinity nuclear localization sequence that displaces cargoes bound by transportin, or TLB, a mutant transportin that can bind cargo and RanGTP simultaneously, support direct inhibition. Consistently, simple addition of M9M to mitotic cytosol induces microtubule aster assembly. ELYS and the nucleoporin 107–160 complex, components of mitotic kinetochores and nuclear pores, are blocked from binding to kinetochores in vitro by transportin, a block reversible by M9M. In vivo, 30% of M9M-transfected cells have spindle/cytokinesis defects. We conclude that the cell contains importin β and transportin “global positioning system”or “GPS” pathways that are mechanistically parallel.
The Cox3p assembly module of yeast cytochrome oxidase
Authors: Su Chen-Hsien , McStay Gavin P. , Tzagoloff Alexander
Published: January 2014

Yeast cytochrome oxidase (COX) was previously inferred to assemble from three modules, each containing one of the three mitochondrially encoded subunits and a different subset of the eight nuclear gene products that make up this respiratory complex. Pull-down assays of pulse-labeled mitochondria enabled us to characterize Cox3p subassemblies that behave as COX precursors and contain Cox4p, Cox7p, and Cox13p. Surprisingly, Cox4p is a constituent of two other complexes, one of which was previously proposed to be an intermediate of Cox1p biogenesis. This suggests that Cox4p, which contacts Cox1p and Cox3p in the holoenzyme, can be incorporated into COX by two alternative pathways. In addition to subunits of COX, some Cox3p intermediates contain Rcf1p, a protein associated with the supercomplex that stabilizes the interaction of COX with the bc1 (ubiquinol-cytochrome c reductase) complex. Finally, our results indicate that although assembly of the Cox1p module is not contingent on the presence of Cox3p, the converse is not true, as none of the Cox3p subassemblies were detected in a mutant blocked in translation of Cox1p. These studies support our proposal that Cox3p and Cox1p are separate assembly modules with unique compositions of ancillary factors and subunits derived from the nuclear genome.
The checkpoint-dependent nuclear accumulation of Rho1p exchange factor Rgf1p is important for tolerance to chronic replication stress
Authors: Muñoz Sofía , Manjón Elvira , García Patricia , Sunnerhagen Per , Sánchez Yolanda
Published: January 2014

Guanine nucleotide exchange factors control many aspects of cell morphogenesis by turning on Rho-GTPases. The fission yeast exchange factor Rgf1p (Rho gef1) specifically regulates Rho1p during polarized growth and localizes to cortical sites. Here we report that Rgf1p is relocalized to the cell nucleus during the stalled replication caused by hydroxyurea (HU). Import to the nucleus is mediated by a nuclear localization sequence at the N-terminus of Rgf1p, whereas release into the cytoplasm requires two leucine-rich nuclear export sequences at the C-terminus. Moreover, Rgf1p nuclear accumulation during replication arrest depends on the 14-3-3 chaperone Rad24p and the DNA replication checkpoint kinase Cds1p. Both proteins control the nuclear accumulation of Rgf1p by inhibition of its nuclear export. A mutant, Rgf1p-9A, that substitutes nine serine potential phosphorylation Cds1p sites for alanine fails to accumulate in the nucleus in response to replication stress, and this correlates with a severe defect in survival in the presence of HU. In conclusion, we propose that the regulation of Rgf1p could be part of the mechanism by which Cds1p and Rad24p promote survival in the presence of chronic replication stress. It will be of general interest to understand whether the same is true for homologues of Rgf1p in budding yeast and higher eukaryotes.
Physical constraints determine the logic of bacterial promoter architectures
Authors: Ezer Daphne , Zabet Nicolae Radu , Adryan Boris
Published: January 2014

Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA) when searching for their target sites. Using computer simulations of this search process, we show that the organization of the binding sites, in conjunction with TF copy number and binding site affinity, plays an important role in determining not only the steady state of promoter occupancy, but also the order at which TFs bind. These effects can be captured by facilitated diffusion-based models, but not by standard thermodynamics. We show that the spacing of binding sites encodes complex logic, which can be derived from combinations of three basic building blocks: switches, barriers and clusters, whose response alone and in higher orders of organization we characterize in detail. Effective promoter organizations are commonly found in the E. coli genome and are highly conserved between strains. This will allow studies of gene regulation at a previously unprecedented level of detail, where our framework can create testable hypothesis of promoter logic.
The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria
Authors: Gunnelius Liisa , Hakkila Kaisa , Kurkela Juha , Wada Hajime , Tyystjärvi Esa , Tyystjärvi Taina
Published: January 2014

The eubacterial RNA polymerase core, a transcription machinery performing DNA-dependent RNA polymerization, consists of two α subunits and β, β′ and ω subunits. An additional σ subunit is recruited for promoter recognition and transcription initiation. Cyanobacteria, a group of eubacteria characterized by oxygenic photosynthesis, have a unique composition of the RNA polymerase (RNAP) core due to splitting of the β′ subunit to N-terminal γ and C-terminal β′ subunits. The physiological roles of the small ω subunit of RNAP, encoded by the rpoZ gene, are not yet completely understood in any bacteria. We found that although ω is non-essential in cyanobacteria, it has a major impact on the overall gene expression pattern. In ΔrpoZ strain, recruitment of the primary σ factor into the RNAP holoenzyme is inefficient, which causes downregulation of highly expressed genes and upregulation of many low-expression genes. Especially, genes encoding proteins of photosynthetic carbon concentrating and carbon fixing complexes were down, and the ΔrpoZ mutant showed low light-saturated photosynthetic activity and accumulated photoprotective carotenoids and α-tocopherol. The results indicate that the ω subunit facilitates the association of the primary σ factor with the RNAP core, thereby allowing efficient transcription of highly expressed genes.
Growth, homeostatic regulation and stem cell dynamics in tissues
Authors: Hannezo E. , Prost J. , Joanny J.-F.
Published: January 2014

The regulation of cell growth in animal tissues is a question of critical importance: most tissues contain different types of cells in interconversion and the fraction of each type has to be controlled in a precise way, by mechanisms that remain unclear. Here, we provide a theoretical framework for the homeostasis of stem-cell-containing epithelial tissues using mechanical equations, which describe the size of the tissue and kinetic equations, which describe the interconversions of the cell populations. We show that several features, such as the evolution of stem cell fractions during intestinal development, the shape of a developing intestinal wall, as well as the increase in the proliferative compartment in cancer initiation, can be studied and understood from generic modelling which does not rely on a particular regulatory mechanism. Finally, inspired by recent experiments, we propose a model where cell division rates are regulated by the mechanical stresses in the epithelial sheet. We show that pressure-controlled growth can, in addition to the previous features, also explain with few parameters the formation of stem cell compartments as well as the morphologies observed when a colonic crypt becomes cancerous. We also discuss optimal strategies of wound healing, in connection with experiments on the cornea.
Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents
Authors: Killer J. , Havlík J. , Vlková E. , Rada V. , Pechar R. , Benada O. , Kopečný J. , Kofroňová O. , Sechovcová H.
Published: January 2014

Three strains of regular, long, Gram-stain-positive bacterial rods were isolated using TPY, M.R.S. and Rogosa agar under anaerobic conditions from the digestive tract of wild mice (Mus musculus). All 16S rRNA gene sequences of these isolates were most similar to sequences of

Lactobacillus gasseri

ATCC 33323T and

Lactobacillus johnsonii

ATCC 33200T (97.3 % and 97.2 % sequence similarities, respectively). The novel strains shared 99.2–99.6 % 16S rRNA gene sequence similarities. Type strains of

L. gasseri

and

L. johnsonii

were also most related to the newly isolated strains according to rpoA (83.9–84.0 % similarities), pheS (84.6–87.8 %), atpA (86.2–87.7 %), hsp60 (89.4–90.4 %) and tuf (92.7–93.6 %) gene sequence similarities. Phylogenetic studies based on 16S rRNA, hsp60, rpoA, atpA and pheS gene sequences, other genotypic and many phenotypic characteristics (results of API 50 CHL, Rapid ID 32A and API ZYM biochemical tests; cellular fatty acid profiles; cellular polar lipid profiles; end products of glucose fermentation) showed that these bacterial strains represent a novel species within the genus

Lactobacillus

. The name Lactobacillus rodentium sp. nov. is proposed to accommodate this group of new isolates. The type strain is MYMRS/TLU1T ( = DSM 24759T = CCM 7945T).