bluuebunny/crossref_metadata_2025 huggingface dataset:
Cantilever deflection associated with hybridization of monomolecular DNA film
Authors: Zhao Yue , Ganapathysubramanian Baskar , Shrotriya Pranav
Published: April 2012

Recent experiments show that specific binding between a ligand and surface immobilized receptor, such as hybridization of single stranded DNA immobilized on a microcantilever surface, leads to cantilever deflection. The binding-induced deflection may be used as a method for detection of biomolecules, such as pathogens and biohazards. Mechanical deformation induced due to hybridization of surface-immobilized DNA strands is a commonly used system to demonstrate the efficacy of microcantilever sensors. To understand the mechanism underlying the cantilever deflections, a theoretical model that incorporates the influence of ligand/receptor complex surface distribution and empirical interchain potential is developed to predict the binding-induced deflections. The cantilever bending induced due to hybridization of DNA strands is predicted for different receptor immobilization densities, hybridization efficiencies, and spatial arrangements. Predicted deflections are compared with experimental reports to validate the modeling assumptions and identify the influence of various components on mechanical deformation. Comparison of numerical predictions and experimental results suggest that, at high immobilization densities, hybridization-induced mechanical deformation is determined, primarily by immobilization density and hybridization efficiency, whereas, at lower immobilization densities, spatial arrangement of hybridized chains need to be considered in determining the cantilever deflection.
Quasilinear evolution of plasma distribution functions and consequences on wave spectrum and perpendicular ion heating in the turbulent solar wind
Authors: Rudakov L. , Crabtree C. , Ganguli G. , Mithaiwala M.
Published: April 2012

The measured spectrum of kinetic Alfven wave fluctuations in the turbulent solar wind plasma is used to calculate the quasi-linear evolution of the initially stable electron and ion distribution functions. The resulting ion distribution function is found to be unstable to electromagnetic left hand polarized ion cyclotron-Alfven waves as well as right hand polarized magnetosonic-whistler waves. These waves can pitch angle scatter the ion super-thermal velocity component to provide perpendicular ion heating. Additionally, right hand polarized waves transfer some part of kinetic Alfven wave flux to whistler waves.
Ab initio calculation of the CdSe/CdTe heterojunction band offset using the local-density approximation-1/2 technique with spin-orbit corrections
Authors: Ribeiro M. , Fonseca L. R. C. , Sadowski T. , Ramprasad R.
Published: April 2012

We performed ab initio calculations of the electronic structures of bulk CdSe and CdTe and of their interface. We employed the local-density approximation-1/2 self-energy correction scheme [L. G. Ferreira, M. Marques, and L. K. Teles, Phys. Rev. B 78, 125116 (2008)] to obtain improved band gaps and band offsets, as well as spin-orbit coupling to further correct the valence band edges. Our results are in good agreement with experimental values for bulk band gaps and reproduce the staggered band alignment characteristic of this system. We found that the spin-orbit effect is of considerable importance for the bulk band gaps, but has little impact on the band offset of this particular system. Moreover, the electronic structure calculated along the 61.4 Å transition region across the CdSe/CdTe interface shows a non-monotonic variation of the bandgap in the range 0.8-1.8 eV. This finding may have important implications to the absorption of light along the interface between these two materials in photovoltaic applications.
Quantum time of arrival Goursat problem
Authors: Sombillo Denny Lane B. , Galapon Eric A.
Published: April 2012

The construction of quantum time of arrival operator conjugate to the system Hamiltonian leads to a particular linear homogeneous Goursat problem. In this work, we demonstrate how to approximate the solution of the mentioned differential equation both semi-analytically and numerically with the goal of calculating the largest eigenvalue of the associated confined time of arrival operator. In the analytical approximation, we used the partial sum expansion of the solution and showed that the resulting largest eigenvalue converges as the number of terms increases. The result shows that for the parameters considered in this paper, the approximation is sufficient up to the fourth order correction term. In the numerical approximation, we develop a non-iterative formula to obtain the numerical solution of the Goursat problem. The performance of the non-iterative method is compared with the known numerical techniques in literature. Numerical results show that the non-iterative algorithm is more accurate and faster compared to the other techniques considered in this paper. Specifically, the proposed algorithm was able to approximate the largest eigenvalue of the confined time of arrival operator up to the third correction term for a particular nonlinear system.
Slow growth of the Rayleigh-Plateau instability in aqueous two phase systems
Authors: Geschiere Sam D. , Ziemecka Iwona , van Steijn Volkert , Koper Ger J. M. , Esch Jan H. van , Kreutzer Michiel T.
Published: April 2012

This paper studies the Rayleigh-Plateau instability for co-flowing immiscible aqueous polymer solutions in a microfluidic channel. Careful vibration-free experiments with controlled actuation of the flow allowed direct measurement of the growth rate of this instability. Experiments for the well-known aqueous two phase system (ATPS, or aqueous biphasic systems) of dextran and polyethylene glycol solutions exhibited a growth rate of 1 s−1, which was more than an order of magnitude slower than an analogous experiment with two immiscible Newtonian fluids with viscosities and interfacial tension that closely matched the ATPS experiment. Viscoelastic effects and adhesion to the walls were ruled out as explanations for the observed behavior. The results are remarkable because all current theory suggests that such dilute polymer solutions should break up faster, not slower, than the analogous Newtonian case. Microfluidic uses of aqueous two phase systems include separation of labile biomolecules but have hitherto be limited because of the difficulty in making droplets. The results of this work teach how to design devices for biological microfluidic ATPS platforms.
Stress-induced VO2 films with M2 monoclinic phase stable at room temperature grown by inductively coupled plasma-assisted reactive sputtering
Authors: Okimura Kunio , Watanabe Tomo , Sakai Joe
Published: April 2012

We report on growth of VO2 films with M2 monoclinic phase stable at room temperature under atmospheric pressure. The films were grown on quartz glass and Si substrates by using an inductively coupled plasma-assisted reactive sputtering method. XRD-sin2Ψ measurements revealed that the films with M2 phase are under compressive stress in contrast to tensile stress of films with M1 phase. Scanning electron microscopy observations revealed characteristic crystal grain aspects with formation of periodical twin structure of M2 phase. Structural phase transition from M2 to tetragonal phases, accompanied by a resistance change, was confirmed to occur as the temperature rises. Growth of VO2 films composed of M2 phase crystalline is of strong interest for clarifying nature of Mott transition of strongly correlated materials.
Magnetic and magnetocaloric properties of ball milled Nd5Ge3
Authors: Maji Bibekananda , Suresh K. G. , Chen X. , Ramanujan R. V.
Published: April 2012

Effect of particle size reduction of the intermetallic compound Nd5Ge3 by ball milling has been studied by investigating the change in the magnetic and magnetocaloric properties. Ball milling is found to enhance the strength of the ferromagnetic component. An analysis based on the Arrott plots shows clear difference in the critical exponents between the bulk and the ball milled samples. Though the maximum entropy change and the relative cooling power are not altered much by the size reduction, magnetic transition temperature is affected.
Different contact formations at the interfaces of C60/LiF/Al and C60/LiF/Ag
Authors: Jeon Pyungeun , Kang Seong Jun , Lee Hyunbok , Lee Jeihyun , Jeong Kwangho , Lee JinWoo , Yi Yeonjin
Published: April 2012

C60 has been used as an electron accepting and transporting material in various organic electronic devices. In such devices, Al and Ag have been adopted as a common cathode in combination with electron injection layers (EIL), e.g., LiF. We found that the initial interface formations of C60/LiF/Al and C60/LiF/Ag are quite different in terms of interfacial electronic structures. We measured the interfacial electronic structures with photoemission spectroscopy and found that LiF works well as an EIL on Al but performs poorly on Ag. The origin of this difference could be attributed to the larger interface dipole on Al, highlighting the importance of the choice of cathode materials.
First-principles calculation of thermodynamic stability of acids and bases under pH environment: A microscopic pH theory
Authors: Kim Yong-Hyun , Kim Kwiseon , Zhang S. B.
Published: April 2012

Despite being one of the most important thermodynamic variables, pH has yet to be incorporated into first-principles thermodynamics to calculate stability of acidic and basic solutes in aqueous solutions. By treating the solutes as defects in homogeneous liquids, we formulate a first-principles approach to calculate their formation energies under proton chemical potential, or pH, based on explicit molecular dynamics. The method draws analogy to first-principle calculations of defect formation energies under electron chemical potential, or Fermi energy, in semiconductors. From this, we propose a simple pictorial representation of the general theory of acid-base chemistry. By performing first-principles molecular dynamics of liquid water models with solutes, we apply the formulation to calculate formation energies of various neutral and charged solutes such as H+, OH−, NH3, NH4+, HCOOH, and HCOO− in water. The deduced auto-dissociation constant of water and the difference in the pKa values of NH3 and HCOOH show good agreement with known experimental values. Our first-principles approach can be further extended and applied to other bio- and electro-chemical molecules such as amino acids and redox reaction couples that could exist in aqueous environments to understand their thermodynamic stability.
Scattering intensity of bicontinuous microemulsions and sponge phases
Authors: Peltomäki Matti , Gompper Gerhard , Kroll Daniel M.
Published: April 2012

Monte Carlo simulations of dynamically triangulated surfaces of variable topology are used to investigate the scattering intensities of bicontinuous microemulsions. The bulk scattering intensity is shown to follow the Teubner-Strey expression. The domain size and the correlation length are extracted from the scattering peaks as a function of the bending rigidity, saddle-splay modulus, and surfactant density. The results are compared to earlier theories based on Ginzburg-Landau and Gaussian random field models. The ratio of the two length scales is shown to be well described by a linear combination of logarithmically renormalized bending rigidity and saddle-splay modulus with universal prefactors. This is in contrast to earlier theoretical predictions in which the scattering intensity is independent of the saddle-splay modulus. The equation of state, and the asymptotics of the bulk and film scattering intensities for high and low wave vectors are determined from simulations and compared with theoretical results.
Amorphization and amorphous stability of Bi2Te3 chalcogenide films
Authors: Ju C. , Cheng X. M. , Miao X. S.
Published: April 2012

Si doping is proposed to be an effective way to improve the amorphous stability of Bi2Te3 thin film. Structural changes in doped crystalline phases are revealed by the bonding nature given by x-ray photoelectron spectroscopy results. Based on ab initio simulations, the energy, electronic and structural changes induced by Si doping are studied. The results show that both nucleation and growth of crystallite are suppressed by Si doping, so that the stability of amorphous Bi2Te3 is improved.
On the evolution and breakup of slender drops in an extensional flow
Authors: Favelukis M. , Lavrenteva O. M. , Nir A.
Published: April 2012

The evolution of the shape of an elongated drop embedded in an extensional flow is studied in the framework of slender body theory. The external flow has a weak but not neglected inertia. The problem is governed by three dimensionless parameters: the capillary number, the external Reynolds number, and the viscosity ratio between the drop and the external fluid, and exhibits a multiplicity of stationary shapes with only one being stable. Evolution of the drop surface from initial shapes was studied when the flow intensity was either kept constant or subjected to a sudden change. It was shown that the dynamics of the shape evolution can lead to a breakup of the drop or to a stable stationary shape. Two modes of breakup are revealed: an indefinite elongation and a center pinching mode. The former appears when the viscous forces dominate the inertia effects, with the typical case being that of a creeping flow. The latter breakup mode takes over in the presence of inertia when the drop viscosity diminishes with the extreme example being that of an inviscid drop.
Statistics and scaling properties of temperature field in symmetrical non-Oberbeck-Boussinesq turbulent convection
Authors: Burnishev Yuri , Steinberg Victor
Published: April 2012

The influence of symmetrical non-Oberbeck-Boussinesq (SNOB) effect on statistical and scaling properties of temperature field in turbulent convection is investigated experimentally in SF6 in the vicinity of its gas-liquid critical point. The main conclusion of the studies is that the most of properties of large scale circulation (LSC) flow in SNOB turbulent convection are the same as in the Oberbeck-Boussinesq (OB) case: (i) the emergence of the main peak frequency fc and the second harmonics frequency 2fc in the temperature power spectra; (ii) the relation between fc and the delay time τsh in the LSC flow between lower and upper regions found from cross correlation functions and their scaling with Ra and Pr agree with those in the OB case and with theoretical predictions. Thus the theory quantitatively describe the properties of the LSC in SNOB turbulent convection as well as in the OB case. (iii) The degree of coherence of the LSC flow oscillations described and the threshold for the onset of the coherent oscillations in the LSC have Pr as well as Ra dependence studied recently in the OB case. However, some differences with the OB case are also identified. Much stronger Ra dependence of the rms of temperature fluctuations normalized by the temperature difference across the cell than in the (OB) case is found. Another distinctive feature observed in the frequency power spectra of the temperature fluctuations is the emergence of strong second harmonics peak at 2fc sometimes even higher than the main one that points out on the strong modulation of the coherent oscillations during the LSC cycle. The peak frequency fp of the dissipation spectra of the temperature fluctuations and its scaling differ significantly from fp in the OB case studied recently. And finally, the dependence of the normalized scaling exponents of the structure functions on the order of the structure functions is qualitatively similar to those for the OB case, and both show strongly intermittent behavior. The results on the scaling exponents of the structure functions in the SNOB case are found close to the theoretical predictions for a passive scalar dependence and quantitatively deviate from the results in the OB case.
On the effect of ion-neutral collisions on dust grain screening in a low-pressure gas discharge plasma
Authors: Semenov I. L. , Zagorodny A. G. , Krivtsun I. V.
Published: April 2012

The effect of ion-neutral collisions on charging of micrometer-sized dust grains immersed in a low-pressure argon discharge plasma is studied on the basis of the Vlasov-Bhatnagar-Gross-Krook kinetic equations. The equations are solved numerically using the method described in our previous work [I. L. Semenov et al., Phys. Plasmas 18, 103707 (2011)]. A modified version of the numerical method is proposed to reduce the required computational time. Numerical calculations are carried out for typical plasma parameters used in laboratory investigations of dusty plasma. On the basis of the obtained results, the influence of collisions on the ion flux and grain charge is analyzed. A comparison of our results with those obtained using different analytical models proposed earlier is presented. In addition, applicability of simple kinetic models describing the influence of collisions on the electric potential around a dust grain [S. A. Khrapak et al., Phys. Rev. Lett. 100, 225003 (2008); A. G. Zagorodny et al. Ukr. J. Phys. 54, 1089 (2009)] is examined. The influence of ion-neutral collisions on the distribution of plasma macroparameters near the grain surface is also demonstrated.
Characteristics of low-aspect ratio, large-diameter, high-density helicon plasmas with variable axial boundary conditions
Authors: Motomura T. , Shinohara S. , Tanikawa T. , Shamrai K. P.
Published: April 2012

A low-aspect ratio, high-density helicon plasma source with a large-diameter of ∼74 cm that utilizes an end-launch flat-spiral antenna has been characterized under three different axial boundary conditions. Whereas one end of the device is a quartz-glass window through which an excitation rf wave is injected, the other end is a movable plasma terminating plate of three different kinds: (1) metal with small holes, (2) solid metal, and (3) solid insulator. Using this movable plate, the device aspect ratio A (device axial length/device diameter) can be reduced to ∼0.075 corresponding to the device axial length of 5.5 cm. The plasma production efficiency (PPE, defined as the ratio of the total number of electrons in the plasma to the input rf power) and helicon wave structures are examined for plasmas with various aspect ratios and boundary conditions to characterize our helicon device. Even for the lowest aspect ratio case (A ∼0.075), a plasma with the electron density of 7.5 × 1011 cm−3 can be produced. The PPE of our device is higher than that of other helicon devices that utilize winding-type antennas. Discrete axial wave modes, which can be explained by a simple model, have been identified for helicon waves excited in our low-aspect ratio helicon plasmas. A comparison between the experimental results and helicon wave theory suggests that second order radial modes must have been excited when the electron density is sufficiently high.
Powerful surface-wave oscillators with two-dimensional periodic structures
Authors: Ginzburg N. S. , Malkin A. M. , Sergeev A. S. , Zaslavsky V. Yu.
Published: April 2012

We propose planar relativistic surface-wave oscillators with two-dimensional periodic gratings. Additional transverse propagating waves emerging on these gratings synchronize the emission from the wide sheet rectilinear electron beam which allows realizing a Cherenkov millimeter wave oscillator with gigawatt output power.
Resistive switching in silicon suboxide films
Authors: Mehonic Adnan , Cueff Sébastien , Wojdak Maciej , Hudziak Stephen , Jambois Olivier , Labbé Christophe , Garrido Blas , Rizk Richard , Kenyon Anthony J.
Published: April 2012

We report a study of resistive switching in a silicon-based memristor/resistive RAM (RRAM) device in which the active layer is silicon-rich silica. The resistive switching phenomenon is an intrinsic property of the silicon-rich oxide layer and does not depend on the diffusion of metallic ions to form conductive paths. In contrast to other work in the literature, switching occurs in ambient conditions, and is not limited to the surface of the active material. We propose a switching mechanism driven by competing field-driven formation and current-driven destruction of filamentary conductive pathways. We demonstrate that conduction is dominated by trap assisted tunneling through noncontinuous conduction paths consisting of silicon nanoinclusions in a highly nonstoichiometric suboxide phase. We hypothesize that such nanoinclusions nucleate preferentially at internal grain boundaries in nanostructured films. Switching exhibits the pinched hysteresis I/V loop characteristic of memristive systems, and on/off resistance ratios of 104:1 or higher can be easily achieved. Scanning tunneling microscopy suggests that switchable conductive pathways are 10 nm in diameter or smaller. Programming currents can be as low as 2 μA, and transition times are on the nanosecond scale.
Metallic nanomesh electrodes with controllable optical properties for organic solar cells
Authors: Zhu Jinfeng , Zhu Xiaodan , Hoekstra Ryan , Li Lu , Xiu Faxian , Xue Mei , Zeng Baoqing , Wang Kang L.
Published: April 2012

We have fabricated a metallic nanomesh using nanosphere lithography and metal evaporation. The metallic nanomesh has a precisely controlled nanostructure showing excellent uniformity with hexagonally arrayed periodic circular holes. A P3HT:PCBM organic solar cell, with the gold nanomesh electrode, demonstrates a high fill factor of 61% and a considerable power conversion efficiency of 3.12%. Electromagnetic simulation indicates that the optical properties of the metallic nanomesh can be optimized for organic photovoltaic devices by tuning the film thickness, hole diameter, and periodicity. These results show the promising potential of using a metallic nanomesh as the transparent electrode in organic solar cells.
Few electron double quantum dot in an isotopically purified 28Si quantum well
Authors: Wild A. , Kierig J. , Sailer J. , Ager J. W. , Haller E. E. , Abstreiter G. , Ludwig S. , Bougeard D.
Published: April 2012

We present a few electron double quantum dot device defined in an isotopically purified 28Si quantum well (QW). An electron mobility of 5.5·104cm2(Vs)-1 is observed in the QW, which is the highest mobility ever reported for a two-dimensional electron system in 28Si. The residual concentration of 29Si nuclei in the 28Si QW is lower than 103ppm, at the verge where the hyperfine interaction is theoretically no longer expected to dominantly limit the T2 spin dephasing time. We also demonstrate a complete suppression of hysteretic gate behavior and charge noise using a negatively biased global top gate.
Omnidirectional broadband acoustic absorber based on metamaterials
Authors: Climente Alfonso , Torrent Daniel , Sánchez-Dehesa José
Published: April 2012

We present the design, construction, and experimental characterization of the acoustic analogue of the so called photonic black-hole. The fabricated sample has cylindrical symmetry and consists of two parts, a shell that bends the sound towards the center and a core that dissipates its energy. The shell is made of a metamaterial that perfectly matches the acoustic impedance of air and behaves like a gradient index lens. The experimental data obtained in a multi-modal impedance chamber demonstrate that the proposed acoustic black-hole acts like an onmidirectional broadband absorber with strong absorbing efficiency.
GaSb/GaAs quantum dot formation and demolition studied with cross-sectional scanning tunneling microscopy
Authors: Smakman E. P. , Garleff J. K. , Young R. J. , Hayne M. , Rambabu P. , Koenraad P. M.
Published: April 2012

We present a cross-sectional scanning tunneling microscopy study of GaSb/GaAs quantum dots grown by molecular beam epitaxy. Various nanostructures are observed as a function of the growth parameters. During growth, relaxation of the high local strain fields of the nanostructures plays an important role in their formation. Pyramidal dots with a high Sb content are often accompanied by threading dislocations above them. GaSb ring formation is favored by the use of a thin GaAs first cap layer and a high growth temperature of the second cap layer. At these capping conditions, strain-driven Sb diffusion combined with As/Sb exchange and Sb segregation remove the center of a nanostructure, creating a ring. Clusters of GaSb without a well defined morphology also appear regularly, often with a highly inhomogeneous structure which is sometimes divided up in fragments.
Effect of molecular p-doping on hole density and mobility in poly(3-hexylthiophene)
Authors: Pingel P. , Schwarzl R. , Neher D.
Published: April 2012

Employing impedance spectroscopy, we have studied the hole density, conductivity, and mobility of poly(3-hexylthiophene), P3HT, doped with the strong molecular acceptor tetrafluorotetracyanoquinodimethane, F4TCNQ. We find that the hole density increases linearly with the F4TCNQ concentration. Furthermore, the hole mobility is decreased upon doping at low-to-medium doping level, which is rationalized by an analytic model of carrier mobility in doped organic semiconductors [V. I. Arkhipov, E. V. Emelianova, P. Heremans, and H. Bässler, Phys. Rev. B 72, 235202 (2005)]. We infer that the presence of ionized F4TCNQ molecules in the P3HT layer increases energetic disorder, which diminishes the carrier mobility.
Structural and optical characterization of SixGe1−x−ySny alloys grown by molecular beam epitaxy
Authors: Lin Hai , Chen Robert , Lu Weisheng , Huo Yijie , Kamins Theodore I. , Harris James S.
Published: April 2012

SixGe1−x−ySny alloys were grown by molecular beam epitaxy at low temperature, followed by ex-situ annealing. The crystal quality of SixGe1−x−ySny layers was characterized by atomic force microscopy and transmission electron microscopy. The compositions and lattice constants of the alloys were studied by x-ray photoelectron spectroscopy and x-ray diffraction. The results show that Vegard’s law is a good approximation for SixGe1−x−ySny alloys. Photoreflectance spectroscopy at room temperature was used to determine the direct bandgap energy of SixGe1−x−ySny layers. Analyzing the relationship between composition and direct bandgap energy reveals a negative energy bowing parameter for SiSn.
Note: Three-dimensional stereolithography for millimeter wave and terahertz applications
Authors: Macor A. , de Rijk E. , Alberti S. , Goodman T. , Ansermet J-Ph.
Published: April 2012

Metal-coated polymers shaped by 3D stereolithography are introduced as a new manufacturing method for passive components for millimeter to terahertz electromagnetic waves. This concept offers increased design capabilities and flexibilities while shortening the manufacturing process of complex shapes, e.g., corrugated horns, mirrors, etc. Tests at 92.5, 140, and 170 GHz are reported.
Observation of room temperature saturated ferroelectric polarization in Dy substituted BiFeO3 ceramics
Authors: Zhang Shuxia , Wang Lei , Chen Yao , Wang Dongliang , Yao Yingbang , Ma Yanwei
Published: April 2012

High quality Bi1−xDyxFeO3 (0 ≤ x ≤ 0.15) ceramics have been fabricated by sintering Dy-doped BiFeO3 (BFO) precursor powders at a low temperature of 780 °C. The magnetic properties of BFO were improved by the introduction of Dy on the Bi-site. More importantly, well saturated ferroelectric hysteresis loops and polarization switching currents have been observed at room temperature. A large remnant polarization (2Pr) value of 62 μC/cm2 is achieved, which is the highest value reported so far for rare-earth-doped BFO ceramics. Moreover, mechanisms for improved multiferroic properties depending on chemical doping-caused structure evolutions have also been discussed.
Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains
Authors: McKee Lauren S. , Peña Maria J. , Rogowski Artur , Jackson Adam , Lewis Richard J. , York William S. , Krogh Kristian B. R. M. , Viksø-Nielsen Anders , Skjøt Michael , Gilbert Harry J. , Marles-Wright Jon
Published: April 2012

The degradation of the plant cell wall by glycoside hydrolases is central to environmentally sustainable industries. The major polysaccharides of the plant cell wall are cellulose and xylan, a highly decorated β-1,4-xylopyranose polymer. Glycoside hydrolases displaying multiple catalytic functions may simplify the enzymes required to degrade plant cell walls, increasing the industrial potential of these composite structures. Here we test the hypothesis that glycoside hydrolase family 43 (GH43) provides a suitable scaffold for introducing additional catalytic functions into enzymes that target complex structures in the plant cell wall. We report the crystal structure of
Humicola insolens
AXHd3 (
Hi
AXHd3), a GH43 arabinofuranosidase that hydrolyses O3-linked arabinose of doubly substituted xylans, a feature of the polysaccharide that is recalcitrant to degradation.
Hi
AXHd3 displays an N-terminal five-bladed β-propeller domain and a C-terminal β-sandwich domain. The interface between the domains comprises a xylan binding cleft that houses the active site pocket. Substrate specificity is conferred by a shallow arabinose binding pocket adjacent to the deep active site pocket, and through the orientation of the xylan backbone. Modification of the rim of the active site introduces endo-xylanase activity, whereas the resultant enzyme variant, Y166A, retains arabinofuranosidase activity. These data show that the active site of
Hi
AXHd3 is tuned to hydrolyse arabinofuranosyl or xylosyl linkages, and it is the topology of the distal regions of the substrate binding surface that confers specificity. This report demonstrates that GH43 provides a platform for generating bespoke multifunctional enzymes that target industrially significant complex substrates, exemplified by the plant cell wall.
Superconductive sodalite-like clathrate calcium hydride at high pressures
Authors: Wang Hui , Tse John S. , Tanaka Kaori , Iitaka Toshiaki , Ma Yanming
Published: April 2012

Hydrogen-rich compounds hold promise as high-temperature superconductors under high pressures. Recent theoretical hydride structures on achieving high-pressure superconductivity are composed mainly of H
2
fragments. Through a systematic investigation of Ca hydrides with different hydrogen contents using particle-swam optimization structural search, we show that in the stoichiometry CaH
6
a body-centered cubic structure with hydrogen that forms unusual “sodalite” cages containing enclathrated Ca stabilizes above pressure 150 GPa. The stability of this structure is derived from the acceptance by two H
2
of electrons donated by Ca forming an “H
4
” unit as the building block in the construction of the three-dimensional sodalite cage. This unique structure has a partial occupation of the degenerated orbitals at the zone center. The resultant dynamic Jahn–Teller effect helps to enhance electron–phonon coupling and leads to superconductivity of CaH
6
. A superconducting critical temperature (T

c

) of 220–235 K at 150 GPa obtained from the solution of the Eliashberg equations is the highest among all hydrides studied thus far.
Atom-by-atom nucleation and growth of graphene nanopores
Authors: Russo Christopher J. , Golovchenko J. A.
Published: April 2012

Graphene is an ideal thin membrane substrate for creating molecule-scale devices. Here we demonstrate a scalable method for creating extremely small structures in graphene with atomic precision. It consists of inducing defect nucleation centers with energetic ions, followed by edge-selective electron recoil sputtering. As a first application, we create graphene nanopores with radii as small as 3 Å, which corresponds to 10 atoms removed. We observe carbon atom removal from the nanopore edge in situ using an aberration-corrected electron microscope, measure the cross-section for the process, and obtain a mean edge atom displacement energy of 14.1 ± 0.1 eV. This approach does not require focused beams and allows scalable production of single nanopores and arrays of monodisperse nanopores for atomic-scale selectively permeable membranes.
Cryo-EM structure of a transcribing cypovirus
Authors: Yang Chongwen , Ji Gang , Liu Hongrong , Zhang Kai , Liu Guangqiao , Sun Fei , Zhu Ping , Cheng Lingpeng
Published: April 2012

Double-stranded RNA viruses in the family
Reoviridae
are capable of transcribing and capping nascent mRNA within an icosahedral viral capsid that remains intact throughout repeated transcription cycles. However, how the highly coordinated mRNA transcription and capping process is facilitated by viral capsid proteins is still unknown. Cypovirus provides a good model system for studying the mRNA transcription and capping mechanism of viruses in the family
Reoviridae
. Here, we report a full backbone model of a transcribing cypovirus built from a near-atomic-resolution density map by cryoelectron microscopy. Compared with the structure of a nontranscribing cypovirus, the major capsid proteins of transcribing cypovirus undergo a series of conformational changes, giving rise to structural changes in the capsid shell: (
i
) an enlarged capsid chamber, which provides genomic RNA with more flexibility to move within the densely packed capsid, and (
ii
) a widened peripentonal channel in the capsid shell, which we confirmed to be a pathway for nascent mRNA. A rod-like structure attributable to a partially resolved nascent mRNA was observed in this channel. In addition, conformational change in the turret protein results in a relatively open turret at each fivefold axis. A GMP moiety, which is transferred to 5’-diphosphorylated mRNA during the mRNA capping reaction, was identified in the pocket-like guanylyltransferase domain of the turret protein.
LOESS correction for length variation in gene set-based genomic sequence analysis
Authors: Aboukhalil Anton , Bulyk Martha L.
Published: April 2012

Motivation: Sequence analysis algorithms are often applied to sets of DNA, RNA or protein sequences to identify common or distinguishing features. Controlling for sequence length variation is critical to properly score sequence features and identify true biological signals rather than length-dependent artifacts.

Results: Several cis-regulatory module discovery algorithms exhibit a substantial dependence between DNA sequence score and sequence length. Our newly developed LOESS method is flexible in capturing diverse score-length relationships and is more effective in correcting DNA sequence scores for length-dependent artifacts, compared with four other approaches. Application of this method to genes co-expressed during Drosophila melanogaster embryonic mesoderm development or neural development scored by the Lever motif analysis algorithm resulted in successful recovery of their biologically validated cis-regulatory codes. The LOESS length-correction method is broadly applicable, and may be useful not only for more accurate inference of cis-regulatory codes, but also for detection of other types of patterns in biological sequences.

Availability: Source code and compiled code are available from http://thebrain.bwh.harvard.edu/LM_LOESS/

Contact:  mlbulyk@receptor.med.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Metab2MeSH: annotating compounds with medical subject headings
Authors: Sartor Maureen A. , Ade Alex , Wright Zach , States David , Omenn Gilbert S. , Athey Brian , Karnovsky Alla
Published: April 2012

Summary: Progress in high-throughput genomic technologies has led to the development of a variety of resources that link genes to functional information contained in the biomedical literature. However, tools attempting to link small molecules to normal and diseased physiology and published data relevant to biologists and clinical investigators, are still lacking. With metabolomics rapidly emerging as a new omics field, the task of annotating small molecule metabolites becomes highly relevant. Our tool Metab2MeSH uses a statistical approach to reliably and automatically annotate compounds with concepts defined in Medical Subject Headings, and the National Library of Medicine's controlled vocabulary for biomedical concepts. These annotations provide links from compounds to biomedical literature and complement existing resources such as PubChem and the Human Metabolome Database.

Availability:  http://metab2mesh.ncibi.org

Contact:  akarnovs@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: systematic approach
Authors: Chen Bor-Sen , Wu Chia-Chou
Published: April 2012

Motivation: The major function of signal transduction pathways in cells is to sense signals from the environment and process the information through signaling molecules in order to regulate the activity of transcription factors. On the molecular level, the information transmitted by a small number of signal molecules is amplified in the internal signaling pathway through enzyme catalysis, molecular modification and via the activation or inhibition of interactions. However, the dynamic system behavior of a signaling pathway can be complex and, despite knowledge of the pathway components and interactions, it is still a challenge to interpret the pathways behavior. Therefore, a systematic method is proposed in this study to quantify the signal transduction ability.

Results: Based on the non-linear signal transduction system, signal transduction ability can be investigated by solving a Hamilton–Jacobi inequality (HJI)-constrained optimization problem. To avoid difficulties associated with solving a complex HJI-constrained optimization problem for signal transduction ability, the Takagi–Sugeno fuzzy model is introduced to approximate the non-linear signal transduction system by interpolating several local linear systems so that the HJI-constrained optimization problem can be replaced by a linear matrix inequality (LMI)-constrained optimization problem. The LMI problem can then be efficiently solved for measuring signal transduction ability. Finally, the signal transduction ability of two important signal transduction pathways was measured by the proposed method and confirmed using experimental data, which is useful for biotechnological and therapeutic application and drug design.

Contact:  bschen@ee.nthu.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
Rknots: topological analysis of knotted biopolymers with R
Authors: Comoglio Federico , Rinaldi Maurizio
Published: April 2012

Motivation: Rknots is a flexible R package providing tools for the detection and characterization of topological knots in biological polymers. The package is well documented and provides a simple syntax for data import and preprocessing, structure reduction, topological analyses and 2D and 3D visualization. Remarkably, Rknots is not limited to protein knots and allows researchers from interdisciplinary fields to analyze different topological structures and to develop simple yet fully custom pipelines.

Availability: Rknots is distributed under the GPL-2 license and is available from the CRAN (the Comprehensive R Archive network) at http://cran.r-project.org/web/packages/Rknots

Contact:  federico.comoglio@bsse.ethz.ch

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Gabapentin Inhibits γ-Amino Butyric Acid Release in the Locus Coeruleus but Not in the Spinal Dorsal Horn after Peripheral Nerve Injury in Rats
Authors: Yoshizumi Masaru , Parker Renee A. , Eisenach James C. , Hayashida Ken-ichiro
Published: April 2012

Background

Gabapentin reduces acute postoperative and chronic neuropathic pain, but its sites and mechanisms of action are unclear. Based on previous electrophysiologic studies, the authors tested whether gabapentin reduced γ-amino butyric acid (GABA) release in the locus coeruleus (LC), a major site of descending inhibition, rather than in the spinal cord.

Methods

Male Sprague-Dawley rats with or without L5-L6 spinal nerve ligation (SNL) were used. Immunostaining for glutamic acid decarboxylase and GABA release in synaptosomes and microdialysates were examined in the LC and spinal dorsal horn.

Results

Basal GABA release and expression of glutamic acid decarboxylase increased in the LC but decreased in the spinal dorsal horn after SNL. In microdialysates from the LC, intravenously administered gabapentin decreased extracellular GABA concentration in normal and SNL rats. In synaptosomes prepared from the LC, gabapentin and other α2δ ligands inhibited KCl-evoked GABA release in normal and SNL rats. In microdialysates from the spinal dorsal horn, intravenous gabapentin did not alter GABA concentrations in normal rats but slightly increased them in SNL rats. In synaptosomes from the spinal dorsal horn, neither gabapentin nor other α2δ ligands affected KCl-evoked GABA release in normal and SNL rats.

Discussion

These results suggest that peripheral nerve injury induces plasticity of GABAergic neurons differently in the LC and spinal dorsal horn and that gabapentin reduces presynaptic GABA release in the LC but not in the spinal dorsal horn. The current study supports the idea that gabapentin activates descending noradrenergic inhibition via disinhibition of LC neurons.
Influence of Shielding TPN From Photooxidation on the Number of Early Blood Transfusions in ELBW Premature Neonates
Authors: Stritzke Amélie , Turcot Valérie , Rouleau Thérèse , Lavoie Jean‐Claude , Chessex Philippe
Published: April 2012

Objectives:

The smallest premature neonates often receive blood transfusions early in life. Nonrestrictive transfusion policies are linked to deleterious outcomes. Exposure of total parenteral nutrition (TPN) to ambient light generates oxidation products associated with haemolysis in vitro. Shielding TPN from light limits oxidation. Our hypothesis was protecting TPN from light decreases haemolysis and therefore the need for early blood transfusions.

Methods:

Comparison of haemolysis between animals fed enterally and those receiving TPN, and exploratory case‐control retrospective analysis of transfusion counts in premature infants receiving light‐exposed or light‐protected TPN. The statistical analysis was analysis of variance and longitudinal binomial regression model adjusting for potential covariables of transfusion counts.

Results:

In animals, TPN is associated with higher (P < 0.05) haemolysis compared with enteral feeds; photoprotection induces lower peroxide load with no effect on the level of haemolysis. In premature infants, light‐exposed (n = 76) or light‐protected (n = 57) populations exhibited similar clinical characteristics. Initial haematocrit, gestational age, and index of disease severity had a significant effect on the number of transfusions. When adjusting for these covariables, photoprotection was no longer significant.

Conclusions:

Even though peroxides are associated in vitro with haemolysis, shielding TPN from light to reduce infused peroxides does not significantly decrease the need for early transfusions in premature infants.
Arenimonas

daechungensis sp. nov., isolated from the sediment of a eutrophic reservoir
Authors: Huy Hangsak , Jin Long , Lee Young-Ki , Lee Keun Chul , Lee Jung-Sook , Yoon Jung-Hoon , Ahn Chi-Yong , Oh Hee-Mock
Published: April 2012

A Gram-negative, non-motile, non-spore-forming and rod-shaped bacterial strain, CH15-1T, was isolated from a sediment sample taken from Daechung Reservoir, South Korea, during the late-blooming period of cyanobacteria. Strain CH15-1T grew optimally at pH 7.0 and 30 °C. A phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain CH15-1T belongs to the genus

Arenimonas

with the similarity range from 92.6–97.4 % and is closely related to

Arenimonas oryziterrae

YC6267T (97.4 %),

Arenimonas composti

TR7-09T (95.4 %),

Arenimonas

metalli CF5-1T (94.7 %),

Arenimonas malthae

CC-JY-1T (94.6 %) and

Arenimonas donghaensis

HO3-R19T (92.6 %). However, the DNA–DNA hybridization between strain CH15-1T and the closest strain,

Arenimonas oryziterrae

YC6267T, was 8.9–12.9 %. The DNA G+C content was 63.9 mol% compared to

A. oryziterrae

YC626T, 65.8 mol%. Strain CH15-1T included Q-8 as the major ubiquinone and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylmonomethylethanolamine as the major polar lipids. The major fatty acids (>5 %) were iso-C15 : 0, iso-C16 : 0, iso-C14 : 0, iso-C11 : 0 3-OH, iso-C17 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). On the basis of phylogenetic, phenotypic and genetic data, strain CH15-1T was classified in the genus

Arenimonas

as a member of a novel species, for which the name
Arenimonas

daechungensis sp. nov. is proposed. The type strain is CH15-1T ( = KCTC 23553T = DSM 24763T).
Amphibacillus indicireducens sp. nov., an alkaliphile that reduces an indigo dye
Authors: Hirota Kikue , Aino Kenichi , Nodasaka Yoshinobu , Morita Naoki , Yumoto Isao
Published: April 2012

Two indigo-reducing alkaliphilic strains, designated strain C40T and strain N214, were isolated from a fermented Polygonum Indigo (Polygonum tinctorium Lour.) liquor sample aged for 10 months and obtained from Date City, Hokkaido, Japan. 16S rRNA gene sequence phylogeny suggested that strains C40T and N214 were members of the genus

Amphibacillus

with the closest relative being

Amphibacillus xylanus

JCM 7361T (97.5 % 16S rRNA gene sequence similarity with strain C40T), which is the only strain having a 16S rRNA gene sequence similarity higher than 97 % with strain C40T. Cells of strain C40T were Gram-stain-positive, facultatively anaerobic, straight rods that were motile by means of peritrichous flagella. The strains grew between 17 and 39 °C (optimum, 35 °C) and in the pH range of 9.0–12.0. No isoprenoid quinone was detected and the DNA G+C content was 37.5–37.7 mol%. The whole-cell fatty acid profile mainly consisted of iso-C15 : 0 and anteiso-C15 : 0. DNA–DNA hybridization of strain C40T with

Amphibacillus xylanus

JCM 7361T revealed a DNA–DNA relatedness value of 10±3 %. Owing to the differences in phenotypic characteristics and phylogenetic analyses based on 16S rRNA gene sequences, as well as DNA–DNA relatedness data from reported species of the genus

Amphibacillus

, the isolates merit classification as a novel species in the genus

Amphibacillus

, for which the name Amphibacillus indicireducens sp. nov. is proposed. The type strain is C40T ( = JCM 17250T = NCIMB 14686T). An additional strain of the species is N214. An emended description of the genus

Amphibacillus

is provided.
Geobacter

luticola sp. nov., an Fe(III)-reducing bacterium isolated from lotus field mud
Authors: Viulu Samson , Nakamura Kohei , Okada Yurina , Saitou Sakiko , Takamizawa Kazuhiro
Published: April 2012

A novel species of Fe(III)-reducing bacterium, designated strain OSK6T, belonging to the genus

Geobacter

, was isolated from lotus field mud in Japan. Strain OSK6T was isolated using a solid medium containing acetate, Fe(III)-nitrilotriacetate (NTA) and gellan gum. The isolate is a strictly anaerobic, Gram-negative, motile, straight rod-shaped bacterium, 0.6–1.9 µm long and 0.2–0.4 µm wide. The growth of the isolate occurred at 20–40 °C with optima of 30–37 °C and pH 6.5–7.5 in the presence of up to 0.5 g NaCl l−1. The G+C content of the genomic DNA was determined by HPLC to be 59.7 mol%. The major respiratory quinone was MK-8. The major fatty acids were 16 : 1ω7c and 16 : 0. Strain OSK6T was able to grow with Fe(III)-NTA, ferric citrate, amorphous iron (III) hydroxide and nitrate, but not with fumarate, malate or sulfate as electron acceptors. Among examined substrates grown with Fe(III)-NTA, the isolate grew on acetate, lactate, pyruvate and succinate. Analysis of the near full-length 16S rRNA gene sequence revealed that strain OSK6T is closely related to

Geobacter daltonii

and

Geobacter toluenoxydans

with 95.6 % similarity to the type strains of these species. On the basis of phylogenetic analysis and physiological tests, strain OSK6T is described as a representative of a novel species,
Geobacter

luticola sp. nov.; the type strain is OSK6T ( = DSM 24905T = JCM 17780T).