bluuebunny/crossref_metadata_2025 huggingface dataset:
Opening gates to oxygen reduction reactions on Cu(111) surface
Authors: Sumer Aslihan , Chaudhuri Santanu
Published: March 2015

Electrocatalytic reduction of oxygen is composed of multiple steps, including the diffusion-adsorption-dissociation of molecular oxygen. This study explores the role of electrical double layer in aqueous medium in quantifying the rate of these coupled electrochemical processes at the electrode interface during oxygen reduction. The electronic, energetic, and configurational aspects of molecular oxygen diffusion and adsorption onto Cu(111) in water are identified through density functional theory based computations. The liquid phase on Cu(111) is modeled with hexagonal-ordered water bilayers, at two slightly different structures, with O–H bonds either facing the vacuum or the metal surface. The results indicate that the energetically preferred structure of water bilayers and adsorption configuration of O2 are different in cathodic and anodic potentials. The diffusion of O2 is found to be heavily hindered at the water/metal interface because of the ordering of water molecules in bilayers as compared to the bulk liquid. The unique correlations of diffusion and adsorption kinetics with water structure identified in this work can provide clues for improving oxygen reduction efficiency.
Numerical simulations of the near wake of a sphere moving in a steady, horizontal motion through a linearly stratified fluid at Re = 1000
Authors: Orr Trevor S. , Domaradzki J. Andrzej , Spedding Geoffrey R. , Constantinescu George S.
Published: March 2015

A numerical investigation of the near wake of a sphere moving horizontally through a linearly stratified fluid is presented. Simulations are first performed on a flow with Reynolds number Re = 200 for a range of internal Froude number, 0.1 ≤ Fr ≤ ∞. The simulations capture buoyant characteristic behavior, the presence of vortex shedding at low Fr, and lee waves. Simulations at higher Reynolds number, Re = 1000, for 1 ≤ Fr ≤ ∞ provide a description and parametrization of the near wake, including the density field. At Re = 1000, the effects of utilizing two different averaging techniques in the unsteady near wake region are discussed. Perturbation quantities in the stratified near wake are anisotropic, and based on the oscillations of the centerline vertical perturbation velocity, the Fr at which the stratified near wake may be considered indistinguishable from the uniform density near wake is suggested to be O(100). Parametrization of the near wake is accomplished using the parameterized vertical wake height, downstream distance from the sphere, and Fr as parameters.
The vibrational dynamics of 3D HOCl above dissociation
Authors: Lin Yi-Der , Reichl L. E. , Jung Christof
Published: March 2015

We explore the classical vibrational dynamics of the HOCl molecule for energies above the dissociation energy of the molecule. Above dissociation, we find that the classical dynamics is dominated by an invariant manifold which appears to stabilize two periodic orbits at energies significantly above the dissociation energy. These stable periodic orbits can hold a large number of quantum states and likely can support a significant quasibound state of the molecule, well above the dissociation energy. The classical dynamics and the lifetime of quantum states on the invariant manifold are determined.
Dependence of FRET efficiency on distance in single donor-acceptor pairs
Authors: Osad’ko I. S.
Published: March 2015

Possibility to create single donor-acceptor (D-A) pairs by attaching dye molecules to various sites of DNA strands with control of the inter-dye distance R enables one to measure average Förster resonance energy transfer (FRET) efficiency E as a function of R. Triplet states of the dyes influence the dependence E(R) considerably. Two types of FRET efficiency are considered: E = EA and E = ED. The efficiency EA(R) = JA(R)/[JA(R) + JD(R)] depends on the donor and the acceptor average intensities JD(R) and JA(R) measured in D- and A-fluorescence, whereas the efficiency ED(R) = 1 − JD(R)/JD(∞) depends only on the intensity of D-fluorescence, so-called the donor quenching method. The shape of the functions ED (R) and EA (R) depends strongly on whether the dyes have blinking fluorescence. FRET efficiencies ED (R) and EA (R) undergo the influence of many experimental factors and therefore, differ considerably from pure FRET efficiencies EDs (R) and EAs (R). Pure FRET efficiencies ED,As (R) are calculated with the help of rate equations for D-A pairs, whose molecules have triplet states. It is shown how the calculated efficiencies ED,As (R) can be compared to FRET efficiencies measured with the help of the intensities ID,A(R) corrected by cross talk and background light.
Marangoni spreading due to a localized alcohol supply on a thin water film
Authors: Hernández-Sánchez José Federico , Eddi Antonin , Snoeijer J. H.
Published: March 2015

Bringing two miscible fluids into contact naturally generates strong gradients in surface tension. Here, we investigate such a Marangoni-driven flow by continuously supplying isopropyl alcohol (IPA) on a film of water, using micron-sized droplets of IPA-water mixtures. These droplets create a localized depression in surface tension that leads to the opening of a circular, thin region in the water film. At the edge of the thin region, there is a growing rim that collects the water of the film, reminiscent of Marangoni spreading due to locally deposited surfactants. In contrast to the surfactant case, the driving by IPA-water drops gives rise to a dynamics of the thin zone that is independent of the initial layer thickness. The radius grows as r ∼ t1/2, which can be explained from a balance between Marangoni and viscous stresses. We derive a scaling law that accurately predicts the influence of the IPA flux as well as the thickness of the thin film at the interior of the spreading front.
On the concept of Bell’s local causality in local classical and quantum theory
Authors: Hofer-Szabó Gábor , Vecsernyés Péter
Published: March 2015

The aim of this paper is to implement Bell’s notion of local causality into a framework, called local physical theory. This framework, based on the axioms of algebraic field theory, is broad enough to integrate both probabilistic and spatiotemporal concepts and also classical and quantum theories. Bell’s original idea of local causality will arise as the classical case of our definition. Classifying local physical theories by whether they obey local primitive causality, a property rendering the dynamics of the theory causal, we then investigate what is needed for a local physical theory to be locally causal. Finally, comparing local causality with the common cause principles and relating both to the Bell inequalities we find a nice parallelism: Bell inequalities cannot be derived neither from local causality nor from a common cause unless the local physical theory is classical or the common cause is commuting, respectively.
Similarity solution to fractional nonlinear space-time diffusion-wave equation
Authors: Costa F. Silva , Marão J. A. P. F. , Soares J. C. Alves , de Oliveira E. Capelas
Published: March 2015

In this article, the so-called fractional nonlinear space-time wave-diffusion equation is presented and discussed. This equation is solved by the similarity method using fractional derivatives in the Caputo, Riesz-Feller, and Riesz senses. Some particular cases are presented and the corresponding solutions are shown by means of 2-D and 3-D plots.
The evolution of a continuously forced shear flow in a closed rectangular domain
Authors: González Vera A. S. , Zavala Sansón L.
Published: March 2015

A shallow, shear flow produced by a constant Lorentz force in a closed rectangular domain is studied by means of laboratory experiments and numerical simulations. We consider different horizontal aspect ratios of the container and magnitudes of the electromagnetic forcing. The shear flow consists of two parallel opposing jets along the long side of the rectangular tanks. Two characteristic stages were observed. First, the flow evolution is dominated by the imposed forcing, producing a linear increase in time of the velocity of the jets. During the second stage, the shear flow becomes unstable and a vortex pattern is generated, which depends on the aspect ratio of the tank. We show that these coherent structures are able to survive during long periods of time, even in the presence of the continuous forcing. Additionally, quasi-regular variations in time of global quantities (two-dimensional (2D) energy and enstrophy) was found. An analysis of the quasi-two-dimensional (Q2D) energy equation reveals that these oscillations are the result of a competition between the injection of energy by the forcing at a localized area and the global bottom friction over the whole domain. The capacity of the system to gain and dissipate energy is in contrast with an exact balance between these two effects, usually assumed in many situations. Numerical simulations based on a quasi-two-dimensional model reproduced the main experimental results, confirming that the essential dynamics of the flow is approximately bidimensional.
Plasma current start-up by the outer ohmic heating coils in the Saskatchewan TORus Modified (STOR-M) iron core tokamak
Authors: Mitarai O. , Xiao C. , McColl D. , Dreval M. , Hirose A. , Peng M.
Published: March 2015

A plasma current up to 15 kA has been driven with outer ohmic heating (OH) coils in the STOR-M iron core tokamak. Even when the inner OH coil is disconnected, the outer OH coils alone can induce the plasma current as primary windings and initial breakdown are even easier in this coil layout. This result suggests a possibility to use an iron core in a spherical tokamak to start up the plasma current without a central solenoid. The effect of the iron core saturation on the extension of the discharge pulse length has been estimated for further experiments in the STOR-M tokamak.
Numerical simulation of Faraday waves oscillated by two-frequency forcing
Authors: Takagi Kentaro , Matsumoto Takeshi
Published: March 2015

We perform a numerical simulation of Faraday waves forced with two-frequency oscillations using a level-set method with Lagrangian-particle corrections (particle level-set method). After validating the simulation with the linear stability analysis, we show that square, hexagonal, and rhomboidal patterns are reproduced in agreement with the laboratory experiments [Arbell and Fineberg, “Two-mode rhomboidal states in driven surface waves,” Phys. Rev. Lett. 84, 654–657 (2000) and “Temporally harmonic oscillons in Newtonian fluids,” Phys. Rev. Lett. 85, 756–759 (2000)]. We also show that the particle level-set’s high degree of conservation of volume is necessary in the simulations. The numerical results of the rhomboidal states are compared with weakly nonlinear analysis. Difficulty in simulating other patterns of the two-frequency forced Faraday waves is discussed.
Coupling of sausage, kink, and magneto-Rayleigh-Taylor instabilities in a cylindrical liner
Authors: Weis M. R. , Zhang P. , Lau Y. Y. , Schmit P. F. , Peterson K. J. , Hess M. , Gilgenbach R. M.
Published: March 2015

This paper analyzes the coupling of magneto-Rayleigh-Taylor (MRT), sausage, and kink modes in an imploding cylindrical liner, using ideal MHD. A uniform axial magnetic field of arbitrary value is included in each region: liner, its interior, and its exterior. The dispersion relation is solved exactly, for arbitrary radial acceleration (-g), axial wavenumber (k), azimuthal mode number (m), liner aspect ratio, and equilibrium quantities in each region. For small k, a positive g (inward radial acceleration in the lab frame) tends to stabilize the sausage mode, but destabilize the kink mode. For large k, a positive g destabilizes both the kink and sausage mode. Using the 1D-HYDRA simulation results for an equilibrium model that includes a pre-existing axial magnetic field and a preheated fuel, we identify several stages of MRT-sausage-kink mode evolution. We find that the m = 1 kink-MRT mode has a higher growth rate at the initial stage and stagnation stage of the implosion, and that the m = 0 sausage-MRT mode dominates at the main part of implosion. This analysis also sheds light on a puzzling feature in Harris' classic paper of MRT [E. G. Harris, Phys. Fluids 5, 1057 (1962)]. An attempt is made to interpret the persistence of the observed helical structures [Awe et al., Phys. Rev. Lett. 111, 235005 (2013)] in terms of non-axisymmetric eigenmode.
A first-principles study of Pt thin films on SrTiO3(100): Support effects on CO adsorption
Authors: Yuk Simuck F. , Asthagiri Aravind
Published: March 2015

Density functional theory was used to study CO adsorption on thin Pt metal films supported on SrO- and TiO2-terminated SrTiO3(100) surfaces. Regardless of substrate-termination, significant enhancement in CO binding occurred on the Pt monolayer compared to the bulk Pt(100) surface. We also observed CO-coverage dependent shifting of Pt atoms, influenced by the nature of underlying oxide atoms. These oxide-induced effects become negligible after depositing more than 2 monolayers of Pt. Evaluating the electronic structures of oxide-supported Pt showed that the interaction of filled Pt dxz+yz and empty Pt dz2 states with CO molecular orbitals can be directly related to CO adsorption on the Pt/SrTiO3(100) surface. A hybrid d-band model is able to capture the CO adsorption trends for systems that do not show large lateral distortion except for the case of Pt adsorbed above the Sr atom on the SrO-termination. For this case, charge transfer from adjacent Pt atoms leads to a large filled dz2 peak below the Fermi level that weakens the Pt–CO σ bonding due to Pauli repulsion.
Urea and deuterium mixtures at high pressures
Authors: Donnelly M. , Bull C. L. , Husband R. J. , Frantzana A. D. , Klotz S. , Loveday J. S.
Published: March 2015

Urea, like many network forming compounds, has long been known to form inclusion (guest-host) compounds. Unlike other network formers like water, urea is not known to form such inclusion compounds with simple molecules like hydrogen. Such compounds if they existed would be of interest both for the fundamental insight they provide into molecular bonding and as potential gas storage systems. Urea has been proposed as a potential hydrogen storage material [T. A. Strobel et al., Chem. Phys. Lett. 478, 97 (2009)]. Here, we report the results of high-pressure neutron diffraction studies of urea and D2 mixtures that indicate no inclusion compound forms up to 3.7 GPa.
Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs
Authors: Wu Yuan-Yan , Bao Lei , Zhang Xi , Tan Zhi-Jie
Published: March 2015

Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5–50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ∼6 bps at each helix end. Correspondingly, the apparent persistence length lp of short DNAs increases gradually from ∼29 nm to ∼45 nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ∼6 bps at each helix end have the similar flexibility with those of kilo bps and can be described by the worm-like chain model with lp ∼ 50 nm.
Electrotransport-induced unmixing and decomposition of ternary oxides
Authors: Chun Jakyu , Martin Manfred , Yoo Han-Ill
Published: March 2015

A general expectation is that in a uniform oxygen activity atmosphere, cation electrotransport induces a ternary or higher oxide, e.g., AB1+ξO3+δ, to kinetically unmix unless the electrochemical mobilities of, say, A2+and B4+ cations are identically equal, and eventually to decompose into the component oxides AO and BO2 once the extent of unmixing exceeds the stability range of its nonmolecularity ξ. It has, however, earlier been reported [Yoo et al., Appl. Phys. Lett. 92, 252103 (2008)] that even a massive cation electrotransport induces BaTiO3 to neither unmix nor decompose even at a voltage far exceeding the so-called decomposition voltage Ud, a measure of the standard formation free energy of the oxide (|ΔGfo| = nFUd). Here, we report that as expected, NiTiO3 unmixes at any voltage and even decomposes if the voltage applied exceeds seemingly a threshold value larger than Ud. We demonstrate experimentally that the electrochemical mobilities of Ni2+ and Ti4+ should be necessarily unequal for unmixing. Also, we show theoretically that equal cation mobilities appear to be a sufficiency for BaTiO3 only for a thermodynamic reason.
Thermal tuning of omnidirectional reflection bands in one-dimensional finite phononic crystals
Authors: Chen Zhaojiang
Published: March 2015

This study investigates the temperature-tuned omnidirectional reflection (ODR) bands in a one-dimensional (1D) finite phononic crystal (PnC), formed by alternating layers of nitinol and epoxy. An analytical model, based on the transfer matrix method, is developed to study reflection and transmission characteristics of the acoustic waves including shear and compressional waves in a 1D PnC. Existence criteria and the sensitive and continuous temperature-tunability of ODR bands in the nitinol/epoxy PnC are demonstrated using the analyses of projected-band structures and reflection spectra. The width and location of the ODR bands shift markedly with temperature variations of nitinol across the phase transition from martensite to austenite. The effects of temperature, filling fraction of nitinol layers, and the Si clad layer on ODR bands are considered. The results will be of benefit in the design and optimization of thermal tuning of omnidirectional acoustic mirrors.
Tiny magnetic wireless pump: Fabrication of magnetic impeller and magnetic wireless manipulation for blood circulation in legs
Authors: Kim Sung Hoon , Yu Chang Ho , Ishiyama K.
Published: March 2015

This paper introduces a wireless pump that uses magnetic wireless manipulation to pump blood in the legs. A compact size and sufficient hydrodynamic performance were the most important requirements. Because the bonded magnet technique allows for a complex shape and various magnetization orientations, we fabricated a magnetic impeller from magnetic SmFeN powder. The impellers demonstrated a magnetic moment of 2772.64 emu and coercive force of 7.55 kOe. Using the impeller, we developed a tiny blood pump with a diameter of 22 mm and height of 6 mm. The pump allows for a maximum flow rate of 2.7 l/min and maximum pump head of approximately 170 mm Hg at a rotating speed of 6000 rpm. This level of hydrodynamic performance is sufficient to circulate blood in the legs. In this paper, we present the magnetic properties of the magnetic impeller and the hydrodynamic performance with wireless operation.
Accurate high level ab initio-based global potential energy surface and dynamics calculations for ground state of CH2+
Authors: Li Y. Q. , Zhang P. Y. , Han K. L.
Published: March 2015

A global many-body expansion potential energy surface is reported for the electronic ground state of CH2+ by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH+(X1Σ+)+H(2S)→C+(2P)+H2(X1Σg+) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C+/H containing systems.
Three-body fragmentation of CO2 driven by intense laser pulses
Authors: Wu Chengyin , Wu Cong , Fan Yameng , Xie Xiguo , Wang Peng , Deng Yongkai , Liu Yunquan , Gong Qihuang
Published: March 2015

Dissociative ionization dynamics were studied experimentally for CO2 driven by intense laser pulses. Three-dimensional momentum vectors of correlated atomic ions were obtained for each three-body fragmentation event using triple ion coincidence measurement. Newton diagram demonstrated that three-body fragmentation of CO2n+ (n = 3-6) can occur through Coulomb explosion process and sequential fragmentation process depending on the fragmentation channels. The experimental data from these two processes were disentangled by using correlation diagram of correlated ions. Based on the accurate Coulomb explosion data, we reconstructed the bond angle distributions of CO2n+ at the moment of fragmentation, which are close to that of neutral CO2 before laser irradiation.
DNA-binding protein searches for its target: Non-monotonic dependence of the search time on the density of roadblocks bound on the DNA chain
Authors: Liu Lin , Luo Kaifu
Published: March 2015

The search of DNA-binding proteins for their target sites positioned on DNA plays a very important role in many cellular processes, and this search process combines 3D excursions in the bulk solution with one-dimensional sliding along the DNA chain. In living cells, there exist roadblocks along DNA chain formed by other proteins; however, the role of the roadblock in search rate is poorly understood. Based on 3D Langevin dynamics simulations, we have investigated the effect of the blocker on the search dynamics. For a pair of symmetrically placed blockers with respect to the target, we find that, with increasing the distance between the blocker and the target, the search time, τ, rapidly decreases and then saturates. For randomly placed blockers with density ϕ, τ may initially increase to its maximum and then unexpectedly decreases with increasing ϕ, or always increase with ϕ, depending on the nonspecific interaction strength and the volume fraction of DNA in the system. The previous contradicted results on the role of the blocker in search time are reconciled by these findings. Particularly, the nonmonotonic behavior of τ with ϕ indicates that blockers may facilitate the search after a critical ϕ.
Quantum entanglement for helium atom in the Debye plasmas
Authors: Lin Yen-Chang , Fang Te-Kuei , Ho Yew Kam
Published: March 2015

In the present work, we present an investigation on quantum entanglement of the two-electron helium atom immersed in weakly coupled Debye plasmas, modeled by the Debye-Hückel, or screened Coulomb, potential to mimic the interaction between two charged particles inside the plasma. Quantum entanglement is related to correlation effects in a multi-particle system. In a bipartite system, a measurement made on one of the two entangled particles affects the outcome of the other particle, even if such two particles are far apart. Employing wave functions constructed with configuration interaction B-spline basis, we have quantified von Neumann entropy and linear entropy for a series of He 1,3Se and 1,3Po states in plasma-embedded helium atom.
Observation of dust torus with poloidal rotation in direct current glow discharge plasma
Authors: Kaur Manjit , Bose Sayak , Chattopadhyay P. K. , Sharma Devendra , Ghosh J. , Saxena Y. C.
Published: March 2015

Observation of dust cloud rotation in parallel-plate DC glow discharge plasma is reported here. The experiments are carried out at high pressures (∼130 Pa) with a metallic ring placed on the lower electrode (cathode). The dust cloud rotates poloidally in the vertical plane near the cathode surface. This structure is continuous toroidally. Absence of magnetic field rules out the possibility of E × B induced ion flow as the cause of dust rotation. The dust rotational structures exist even with water cooled cathode. Therefore, temperature gradient driven mechanisms, such as thermophoretic force, thermal creep flow, and free convection cannot be causing the observed dust rotation. Langmuir probe measurement reveals the existence of a sharp density gradient near the location of the rotating dust cloud. The gradient in the density, giving rise to a gradient in the ion drag force, has been identified as the principal cause behind the rotation of dust particles.
Thin-film encapsulation of the air-sensitive organic-based ferrimagnet vanadium tetracyanoethylene
Authors: Froning I. H. , Harberts M. , Lu Y. , Yu H. , Epstein A. J. , Johnston-Halperin E.
Published: March 2015

The organic-based ferrimagnet vanadium tetracyanoethylene (V[TCNE]x∼2) has demonstrated potential for use in both microwave electronics and spintronics due to the combination of high temperature magnetic ordering (TC > 600 K), extremely sharp ferromagnetic resonance (peak to peak linewidth of 1 G), and low-temperature conformal deposition via chemical vapor deposition (deposition temperature of 50 °C). However, air-sensitivity leads to the complete degradation of the films within 2 h under ambient conditions, with noticeable degradation occurring within 30 min. Here, we demonstrate encapsulation of V[TCNE]x∼2 thin films using a UV-cured epoxy that increases film lifetime to over 710 h (30 days) as measured by the remanent magnetization. The saturation magnetization and Curie temperature decay more slowly than the remanence, and the coercivity is unchanged after 340 h (14 days) of air exposure. Fourier transform infrared spectroscopy indicates that the epoxy does not react with the film, and magnetometry measurements show that the presence of the epoxy does not degrade the magnetic properties. This encapsulation strategy directly enables a host of experimental protocols and investigations not previously feasible for air-sensitive samples and lays the foundation for the development of practical applications for this promising organic-based magnetic material.
Strain-induced gap transition and anisotropic Dirac-like cones in monolayer and bilayer phosphorene
Authors: Wang Can , Xia Qinglin , Nie Yaozhuang , Guo Guanghua
Published: March 2015

The electronic properties of two-dimensional monolayer and bilayer phosphorene subjected to uniaxial and biaxial strains have been investigated using first-principles calculations based on density functional theory. Strain engineering has obvious influence on the electronic properties of monolayer and bilayer phosphorene. By comparison, we find that biaxial strain is more effective in tuning the band gap than uniaxial strain. Interestingly, we observe the emergence of Dirac-like cones by the application of zigzag tensile strain in the monolayer and bilayer systems. For bilayer phosphorene, we induce the anisotropic Dirac-like dispersion by the application of appropriate armchair or biaxial compressive strain. Our results present very interesting possibilities for engineering the electronic properties of phosphorene and pave a way for tuning the band gap of future electronic and optoelectronic devices.
Surface plasmon resonance enhanced light absorption of Au decorated composition-tuned ZnO/ZnxCd1−xSeyTe1−y core/shell nanowires for efficient H2 production
Authors: Zhan Xueying , Bao Yanjun , Wang Fengmei , Wang Qisheng , Cheng Zhongzhou , Wang Zhenxing , Xu Kai , Fang Zheyu , He Jun
Published: March 2015

Efficient solar-to-hydrogen photoelectrodes need harvest sunlight to capacity and improve the separation efficiency of charge carriers for chemical reactions in water. Herein, we demonstrate the merits of type-II heterostructures with component controllable quaternary shells (ZnxCd1−xSeyTe1−y) and the surface plasmon resonance of Au nanoparticles to satisfy photocatalytic requirements. Our ZnO/ZnxCd1−xSeyTe1−y/Au nanostructures display a broad absorption edge from UV to NIR (Near Infrared) and high charge separation efficiency. The finite element method simulation and UV-vis-NIR diffuse reflectance spectroscopy confirm the enhanced absorption of visible light. Furthermore, these ZnO/ZnxCd1−xSeyTe1−y/Au heterostructures show remarkable hydrogen-production ability from water, suggesting a type of photocatalytic paradigm for H2 production.
T-cell receptor α enhancer is inactivated in αβ T lymphocytes
Authors: del Blanco Beatriz , Angulo Úrsula , Krangel Michael S. , Hernández-Munain Cristina
Published: March 2015

Significance

TheTcraenhancer (Eα) is essential during thymocyte development forTcragermline transcription, Vα-to-Jα rearrangement, and the generation of αβ T-lymphocytes. It has been assumed that Eα displays constitutive activity to drive the expression of rearrangedTcragenes in mature T cells. We show that Eα is dramatically inhibited in peripheral T-lymphocytes and is not reactivated in the context of antigen-mediated stimulation or T helper differentiation. We conclude that the major function of Eα is to coordinate the formation of a chromatin hub that drives germline transcription and primaryTcrarearrangements in DP thymocytes. Our results also imply the existence of an Eα-independent molecular mechanism that directs transcription of the rearrangedTcralocus in αβ T cells.
Plexin D1 determines body fat distribution by regulating the type V collagen microenvironment in visceral adipose tissue
Authors: Minchin James E. N. , Dahlman Ingrid , Harvey Christopher J. , Mejhert Niklas , Singh Manvendra K. , Epstein Jonathan A. , Arner Peter , Torres-Vázquez Jesús , Rawls John F.
Published: March 2015

Significance

PLEXIN D1
(
PLXND1
) has been implicated in body fat distribution and type 2 diabetes by genome-wide association studies, but the mechanism is unknown. We show here that Plxnd1 regulates body fat distribution in zebrafish by controlling the visceral adipose tissue (VAT) growth mechanism. Plxnd1 deficiency in zebrafish resulted in induction of a hyperplastic state and reduced lipid deposition in VAT. Regulation of VAT was dependent on the induction of the type V collagen,
col5a1
, suggesting that Plxnd1 controls body fat distribution by determining the status of VAT extracellular matrix. Plxnd1-deficient zebrafish were protected from high-fat-induced insulin resistance, and human
PLXND1
mRNA was positively associated with type 2 diabetes. These results suggest that the role of Plxnd1 in body fat distribution and insulin signaling is conserved from zebrafish to humans.
Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases
Authors: Manthei Kelly A. , Hill Morgan C. , Burke Jordan E. , Butcher Samuel E. , Keck James L.
Published: March 2015

Significance

RecQ DNA helicases catalyze critical genome maintenance reactions in nearly all organisms. This study describes the crystal structure of a bacterial RecQ helicase bound in a productive complex with DNA. Together with biochemical experiments, the structure reveals a conserved coupling mechanism that links DNA binding to ATP hydrolysis in RecQ enzymes. These findings also help explain how structural dynamics could facilitate RecQ’s noted ability to process diverse DNA substrates. A model explaining the physical basis for RecQ substrate binding and unwinding is proposed.
Phosphorylation of ORF1p is required for L1 retrotransposition
Authors: Cook Pamela R. , Jones Charles E. , Furano Anthony V.
Published: March 2015

Significance

All organisms contain transposable DNA elements (TEs) that can be seriously deleterious. The dominant TE in mammals, the L1 (LINE-1) retrotransposon, has generated approximately 40% of the genome. L1 encodes two proteins, ORF1p and ORF2p, that are required for L1 retrotransposition. We show here that phosphorylation of ORF1p is required for this process. These results significantly advance our understanding of retrotransposition and indicate that L1 activity is integrated with, and thus potentially can perturb, host cellular signaling pathways. Thus, the effects of L1 may extend well beyond those of genome alteration as is currently thought.
Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: Insights from DNA complex structures
Authors: Pike Ashley C. W. , Gomathinayagam Shivasankari , Swuec Paolo , Berti Matteo , Zhang Ying , Schnecke Christina , Marino Francesca , von Delft Frank , Renault Ludovic , Costa Alessandro , Gileadi Opher , Vindigni Alessandro
Published: March 2015

Significance

RecQ DNA helicases are critical enzymes for the maintenance of genome integrity. Here, we determined the first DNA complex structures, to our knowledge, of the human RECQ1 helicase. These structures provide new insight into the RecQ helicase mechanism of DNA tracking, strand separation, strand annealing, and Holliday junction (HJ) branch migration. We identified a surface region in the winged-helix domain of RECQ1 that is important for both dsDNA recognition and HJ resolution, and we used a combination of biochemical, analytical ultracentrifugation, and EM experiments to begin elucidating the molecular basis of the distinct HJ resolution activities of human RecQ helicases.
Cross-talk between PKA-Cβ and p65 mediates synergistic induction of PDE4B by roflumilast and NTHi
Authors: Susuki-Miyata Seiko , Miyata Masanori , Lee Byung-Cheol , Xu Haidong , Kai Hirofumi , Yan Chen , Li Jian-Dong
Published: March 2015

Significance

Chronic obstructive pulmonary disease (COPD) is the fourth-leading cause of death worldwide. Roflumilast has been approved for COPD. However, its efficacy has been hampered by the development of tolerance, and the underlying mechanism remains unknown but may be attributed to phosphodiesterase (PDE) 4B up-regulation. Here we found that PDE4B2 is synergistically up-regulated by inflammatory stimuli (e.g. bacteria) and cAMP-elevating agents (e.g. roflumilast) via cross-talk between protein kinase A catalytic subunit β and NF-κB p65 in a cAMP-dependent manner. Up-regulated PDE4B2 contributes to the induction of certain key chemokines in both enzymatic activity-dependent and activity-independent manners. Our findings may explain, at least in part, the development of tolerance and help develop new therapeutics to improve efficacy of roflumilast.
A viral regulator of glycoprotein complexes contributes to human cytomegalovirus cell tropism
Authors: Li Gang , Nguyen Christopher C. , Ryckman Brent J. , Britt William J. , Kamil Jeremy P.
Published: March 2015

Significance

The entry of a virus into a cell is a fundamental step during infection. In certain herpesviruses, including Epstein–Barr virus, human herpesvirus 6, and human cytomegalovirus (HCMV), a viral glycoprotein complex, gH/gL, plays key roles in entry and is found in two different forms on virions. The relative abundance of the two different types of gH/gL complexes is influenced by the type of cell from which the virus is produced and influences the tropism of the virus for different cell types. We have identified a viral glycoprotein, UL148, that influences the cell tropism of HCMV virions by regulating the relative amounts of these two gH/gL complexes. Our findings have implications for understanding how herpesviruses navigate through host tissues.
Insight into the evolution and origin of leprosy bacilli from the genome sequence of
Mycobacterium lepromatosis
Authors: Singh Pushpendra , Benjak Andrej , Schuenemann Verena J. , Herbig Alexander , Avanzi Charlotte , Busso Philippe , Nieselt Kay , Krause Johannes , Vera-Cabrera Lucio , Cole Stewart T.
Published: March 2015

Significance

Leprosy was thought to be exclusively caused by infection of humans by
Mycobacterium leprae
. In 2008, Han et al. proposed that
Mycobacterium lepromatosis
, a separate unculturable species, might be responsible for a rare yet severe form of the disease called diffuse lepromatous leprosy. Here, by using comparative genomics, we show that the two species are very closely related and derived from a common ancestor that underwent genome downsizing and gene decay. Since their separation 13.9 Mya, the two species have continued to lose genes, but from different regions of the genome, and
M. leprae
appears to be more recent. In a phylogeographic survey, by using differential PCR, we found that
M. lepromatosis
was scarce and restricted to patients from Mexico.
A functional role of Rv1738 in
Mycobacterium tuberculosis
persistence suggested by racemic protein crystallography
Authors: Bunker Richard D. , Mandal Kalyaneswar , Bashiri Ghader , Chaston Jessica J. , Pentelute Bradley L. , Lott J. Shaun , Kent Stephen B. H. , Baker Edward N.
Published: March 2015

Significance

Racemic protein crystallography was used to determine the X-ray structure of the predicted
Mycobacterium tuberculosis
protein Rv1738, which had been completely recalcitrant to crystallization in its natural
l
-form. Native chemical ligation was used to synthesize both
l
-protein and
d
-protein enantiomers of Rv1738. Crystallization of the racemic {
d
-protein +
l
-protein} mixture was immediately successful. The resulting crystals diffracted to high resolution and also enabled facile structure determination because of the quantized phases of the data from centrosymmetric crystals. The X-ray structure of Rv1738 revealed striking similarity with bacterial hibernation factors, despite minimal sequence similarity. We predict that Rv1738, which is highly up-regulated in conditions that mimic the onset of persistence, helps trigger dormancy by association with the bacterial ribosome.
Leader emergence through interpersonal neural synchronization
Authors: Jiang Jing , Chen Chuansheng , Dai Bohan , Shi Guang , Ding Guosheng , Liu Li , Lu Chunming
Published: March 2015

Significance

Great leaders are often great communicators. However, little is known about the neural basis of leader–follower communication. Only recently have neuroscientists been able to examine interpersonal neural synchronization (INS) between leaders and followers during social interactions. Here, we show that INS is significantly higher between leaders and followers than between followers and followers, suggesting that leaders emerge by synchronizing their brain activity with that of the followers. Moreover, the quality rather than frequency of the leaders’ communications makes a significant contribution to the increase of INS. This result supports the “quality of communication” hypothesis in leader emergence. Finally, our results show that leadership can be predicted shortly after the onset of a task based on INS as well as communication behaviors.
Unilateral incompatibility gene
ui1.1
encodes an S-locus F-box protein expressed in pollen of
Solanum
species
Authors: Li Wentao , Chetelat Roger T.
Published: March 2015

Significance

Self-incompatibility (SI) in plants prevents inbreeding by rejection of pollen from closely related individuals of the same species. Unilateral interspecific incompatibility (UI) blocks cross-hybridization between related species, typically when the pollen donor is self-compatible and the pistil parent is self-incompatible. In this study, we show that
ui1.1
, a pollen UI factor in tomato, encodes an S-locus F-box protein that is homologous to an SI gene that in
Petunia
determines pollen specificity. We previously showed that another pollen factor,
ui6.1
, encodes a Cullin1 protein that functions in both UI and SI. Cullin1 and F-box proteins are components of SCF-type (Skp1, Cullin1, F-box) ubiquitin ligase complexes. The results provide further evidence that pollen rejection in UI involves biochemical mechanisms related to SI.
Non-native plants add to the British flora without negative consequences for native diversity
Authors: Thomas Chris D. , Palmer G.
Published: March 2015

Significance

Non-native plants dominate global lists of invasive (harmful) species, yet plants introduced to Britain are both less widespread than native species and not increasing any more than native plants, and changes to native and non-native plant diversity are positively associated. The hypothesis that competitive exclusion will eventually enable introduced plants to drive native species extinct receives no support, according to analysis of extensive British data. A more parsimonious explanation is that both native and introduced plants are responding predominantly to other drivers of environmental change. The negative effects of non-native plants on British biodiversity have been exaggerated, and may also have been exaggerated in other parts of the world.
Area burned in the western United States is unaffected by recent mountain pine beetle outbreaks
Authors: Hart Sarah J. , Schoennagel Tania , Veblen Thomas T. , Chapman Teresa B.
Published: March 2015

Significance

Across western North America, abundant susceptible pine hosts and a suitable climate during the early 21st century have promoted widespread mountain pine beetle (MPB) outbreaks, leading to concern that dead fuels may increase wildfire risk. The assumption that outbreaks raise fire risk is driving far-reaching policy decisions involving expenditures of hundreds of millions of dollars. Contrary to the expectation that an MPB outbreak increases fire risk, spatial overlay analysis shows no effect of outbreaks on subsequent area burned during years of extreme burning across the West. These results refute the assumption that increased bark beetle activity has increased area burned; therefore, policy discussions should focus on societal adaptation to the effects of the underlying drivers: warmer temperatures and increased drought.
cGAS-mediated stabilization of IFI16 promotes innate signaling during herpes simplex virus infection
Authors: Orzalli Megan H. , Broekema Nicole M. , Diner Benjamin A. , Hancks Dustin C. , Elde Nels C. , Cristea Ileana M. , Knipe David M.
Published: March 2015

Significance

Interferon γ-inducible protein 16 (IFI16) and cGMP-AMP synthase (cGAS) have both been proposed to directly detect herpesviral DNA in herpes simplex virus (HSV)-infected cells and initiate interferon regulatory factor-3 signaling, but it has been unclear how two DNA sensors could both be required. Both are required in human fibroblasts for detection of HSV and transfected DNAs. We found evidence that IFI16 plays a direct role in HSV DNA sensing, whereas cGAS produces low amounts of cGAMP and promotes the stability of IFI16. Our results demonstrate a new function for cGAS in the maintenance of normal levels of IFI16 and provide an explanation for the multiple proposed DNA sensors.
Emergence of hematopoietic stem and progenitor cells involves a Chd1-dependent increase in total nascent transcription
Authors: Koh Fong Ming , Lizama Carlos O. , Wong Priscilla , Hawkins John S. , Zovein Ann C. , Ramalho-Santos Miguel
Published: March 2015

Significance

Adult hematopoietic stem and progenitor cells (HSPCs) develop from a small number of specialized endothelial cells in the embryo. Very little is known about how this process, known as the endothelial-to-hematopoietic transition, is regulated. In this paper, we used mouse genetic knockout models to establish Chd1 as the first chromatin remodeler, to our knowledge, shown to regulate this transition. Chd1 is not required in the endothelium prior to the transition, nor in the blood system after the transition. We found that the emergence of HSPCs involves an increase in total nascent transcription that is dependent on Chd1. These results reveal a new paradigm of regulation of a developmental transition by modulation of transcriptional output that may be relevant in other stem/progenitor cell contexts.
Carbon monoxide as a metabolic energy source for extremely halophilic microbes: Implications for microbial activity in Mars regolith
Authors: King Gary M.
Published: March 2015

Significance

Increasing evidence indicates that Mars might have been habitable early in its history, and that it might harbor liquid water at present in the form of brines associated with features known as recurrent slope lineae (RSL). However, even if brines do occur, it is unclear what substrates any relict microbes could metabolize. Results presented here show that carbon monoxide, which is abundant in Mars’ atmosphere, could be used at local scales under conditions that occur at RSL, including moderate temperatures, low pressure, high CO
2
, low oxygen concentrations, and extreme water potentials. Halophilic CO-oxidizing Proteobacteria, and recently discovered extremely halophilic CO-oxidizing Euryarchaeota described in this study, represent ideal models for understanding the capacity of Mars’ atmosphere to support microbial communities.
Mechanisms of hematin crystallization and inhibition by the antimalarial drug chloroquine
Authors: Olafson Katy N. , Ketchum Megan A. , Rimer Jeffrey D. , Vekilov Peter G.
Published: March 2015

Significance

Approximately 40% of the global population is at risk for malaria infection and 300–660 million clinical episodes of
Plasmodium falciparum
malaria occur annually. During the malaria parasite lifecycle in human erythrocytes, heme released during hemoglobin catabolism is detoxified by sequestration into crystals. Many of the common antimalarials are believed to suppress the parasite by inhibiting hematin crystallization. We present, to our knowledge, the first evidence of the molecular mechanisms of hematin crystallization and antimalarial drug action as crystal growth inhibitors. These findings enable the identification and optimization of functional moieties that bind to crystal surface sites, thus providing unique guidelines for the discovery of novel antimalarials to combat increased parasite resistance to current drugs.
Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors
Authors: Owen Jeremy G. , Charlop-Powers Zachary , Smith Alexandra G. , Ternei Melinda A. , Calle Paula Y. , Reddy Boojala Vijay B. , Montiel Daniel , Brady Sean F.
Published: March 2015

Significance

Here we use an informatics-based approach to natural product discovery that is broadly applicable to the isolation of medicinally relevant metabolites from environmental microbiomes. Combining metagenome sequencing and bioinformatics approaches with a defined set of metagenomic tools provides a template for the targeted discovery of compounds from the global metagenome. The power of this approach is demonstrated by surveying ketosynthase domain amplicon sequencing data from 185 soil microbiomes for biosynthetic gene clusters encoding epoxyketone proteasome inhibitors, leading to the isolation and characterization of seven epoxyketone natural products, including compounds with unique warhead structures. We believe this approach is applicable to any conserved biosynthetic gene and provides a higher-throughput cost-effective alternative to whole genome sequencing discovery methods.
Development of sedentary communities in the Maya lowlands: Coexisting mobile groups and public ceremonies at Ceibal, Guatemala
Authors: Inomata Takeshi , MacLellan Jessica , Triadan Daniela , Munson Jessica , Burham Melissa , Aoyama Kazuo , Nasu Hiroo , Pinzón Flory , Yonenobu Hitoshi
Published: March 2015

Significance

The results of our research at the lowland Maya site of Ceibal add to the growing archaeological understanding that the transition to sedentism did not necessarily occur simultaneously across different social groups within a region and that monumental constructions did not always postdate fully established sedentism. Whereas sedentary and mobile populations are, in many cases, interpreted to have maintained separate communities, our study suggests that groups with different levels of mobility gathered and collaborated for constructions and public ceremonies. These data indicate that the development of sedentism was a complex process involving interactions among diverse groups, and that collaborative construction projects and communal gatherings played a critical role in this social transformation by facilitating social integration among different groups.