bluuebunny/crossref_metadata_2025 huggingface dataset:
Earthquake recurrence models fail when earthquakes fail to reset the stress field
Authors: Tormann T. , Wiemer S. , Hardebeck J. L.
Published: September 2012

Parkfield's regularly occurring M6 mainshocks, about every 25 years, have over two decades stoked seismologists' hopes to successfully predict an earthquake of significant size. However, with the longest known inter‐event time of 38 years, the latest M6 in the series (28 Sep 2004) did not conform to any of the applied forecast models, questioning once more the predictability of earthquakes in general. Our study investigates the spatial pattern of b‐values along the Parkfield segment through the seismic cycle and documents a stably stressed structure. The forecasted rate of M6 earthquakes based on Parkfield's microseismicity b‐values corresponds well to observed rates. We interpret the observed b‐value stability in terms of the evolution of the stress field in that area: the M6 Parkfield earthquakes do not fully unload the stress on the fault, explaining why time recurrent models fail. We present the 1989 M6.9 Loma Prieta earthquake as counter example, which did release a significant portion of the stress along its fault segment and yields a substantial change in b‐values.
Observation of a gamma‐ray flash at ground level in association with a cloud‐to‐ground lightning return stroke
Authors: Dwyer J. R. , Schaal M. M. , Cramer E. , Arabshahi S. , Liu N. , Rassoul H. K. , Hill J. D. , Jordan D. M. , Uman M. A.
Published: September 2012

Terrestrial gamma‐ray flashes (TGFs) are bright, sub‐millisecond bursts of gamma‐rays, originating within the Earth's atmosphere. Most TGFs have been detected by spacecraft in low‐Earth orbit. Only two TGFs have previously been observed from within our atmosphere: one at ground level and one from an aircraft at 14.1 km. We report on a new TGF‐like gamma‐ray flash observed at ground level, detected by the 19‐station Thunderstorm Energetic Radiation Array (TERA) at the University of Florida/Florida Tech International Center for Lightning Research and Testing (ICLRT). The gamma‐ray flash, which had a duration of 52.7 μs, occurred on June 30, 2009 during a natural negative cloud‐to‐ground lightning return stroke, 191 μs after the start of the stroke. This event is the first definitive association of a gamma‐ray flash with natural CG lightning and is among the most direct links to a specific lightning process so far. For this event, 19 gamma‐rays were recorded, with the highest energy exceeding 20 MeV. The high‐energy radiation exhibited very different behavior from the typical x‐ray emission from lightning. Specifically, the gamma‐ray flash had a much harder energy spectrum, consistent with relativistic runaway electron avalanche (RREA) multiplication; it did not arrive in sub‐microsecond bursts, typical of leader emission from lightning, and it occurred well after the start of the return stroke, which has not been previously observed for the x‐ray emission from lightning. Nevertheless, we present evidence that the source region for the gamma ray flash was the same as that for the preceding leader x‐ray bursts.
Guide field dependence of 3‐D X‐line spreading during collisionless magnetic reconnection
Authors: Shepherd L. S. , Cassak P. A.
Published: September 2012

Theoretical arguments and large‐scale two‐fluid simulations are used to study the spreading of reconnection X‐lines localized in the direction of the current as a function of the strength of the out‐of‐plane (guide) magnetic field. It is found that the mechanism causing the spreading is different for weak and strong guide fields. In the weak guide field limit, spreading is due to the motion of the current carriers, as has been previously established. However, spreading for strong guide fields is bidirectional and is due to the excitation of Alfvén waves along the guide field. In general, we suggest that the X‐line spreads bidirectionally with a speed governed by the faster of the two mechanisms for each direction. A prediction on the strength of the guide field at which the spreading mechanism changes is formulated and verified with three‐dimensional simulations. Solar, magnetospheric, and laboratory applications are discussed.
Seismic structure in central Mexico: Implications for fragmentation of the subducted Cocos plate
Authors: Dougherty Sara L. , Clayton Robert W. , Helmberger Don V.
Published: September 2012

The fine‐scale seismic structure of the central Mexico subduction zone is studied using moderate‐sized (M4‐6) intraslab earthquakes. Regional waveforms from the Mapping the Rivera Subduction Zone (MARS) seismic array are complicated and contain detailed information about the subduction zone structure, including evidence of lateral heterogeneity. This waveform information is used to model the structure of the subducted plates, particularly along the transition from flat to normal subduction, where recent studies have shown evidence for possible slab tearing along the eastern projection of the Orozco Fracture Zone (OFZ). The lateral extent of a thin ultra‐slow velocity layer (USL) imaged atop the Cocos slab in recent studies along the Meso America Subduction Experiment array is examined here using MARS waveforms. We find an edge to this USL which is coincident with the western boundary of the projected OFZ region. Forward modeling of the 2D structure of the subducted Rivera and Cocos plates using a finite difference algorithm provides constraints on the velocity and geometry of each slab's seismic structure in this region and confirms the location of the USL edge. We propose that the Cocos slab is currently fragmenting into a North Cocos plate and a South Cocos plate along the projection of the OFZ, in agreement with observations of variable Cocos plate motion on either side of the OFZ. This tearing event may be a young analogy to the 10 Ma Rivera‐Cocos plate boundary, and may be related to the slab rollback in central Mexico.
Climate variability and phytoplankton composition in the Pacific Ocean
Authors: Rousseaux Cecile S. , Gregg Watson W.
Published: September 2012

The effect of climate variability on the phytoplankton community was assessed for the tropical and sub‐tropical Pacific Ocean between 1998 and 2007 using an established biogeochemical assimilation model. The tropical and sub‐tropical phytoplankton communities exhibited a wide range of responses to climate variability, from radical shifts in the Equatorial Pacific, to changes of only a couple of phytoplankton groups in the North Central Pacific, to no significant changes in the South Pacific. In the Equatorial Pacific, climate variability represented by ENSO dominated the variability of phytoplankton. Here, nitrate, chlorophyll and all of the 4 phytoplankton types (diatoms, cyanobacteria, chlorophytes and coccolithophores) were strongly correlated (p < 0.05) with the Multivariate El Niño Southern Oscillation Index (MEI). During La Niña events, diatoms increased and expanded westward along the cold tongue (correlation with MEI, r = −0.87, p < 0.05), while cyanobacteria concentrations decreased significantly (r = 0.69, p < 0.05). El Niño produced the reverse pattern, with cyanobacteria populations increasing while diatoms plummeted. In the North Central Pacific, the MEI was significantly correlated with diatoms (r = −0.40) and chlorophytes (r = −0.43). Ocean biology in the South Pacific was not significantly correlated with MEI. The phytoplankton composition from the assimilation model was compared to that from a new empirical algorithm using satellite data. Despite differences in the absolute concentration, the relative abundance from the model and the satellite‐derived approach showed a similar shift in phytoplankton community in the Equatorial Pacific. These results highlight the spatially variable nature of the relationship between phytoplankton community structure and climate variability within the Pacific Ocean.
Impact of melt ponds on Arctic sea ice simulations from 1990 to 2007
Authors: Flocco Daniela , Schroeder David , Feltham Daniel L. , Hunke Elizabeth C.
Published: September 2012

The extent and thickness of the Arctic sea ice cover has decreased dramatically in the past few decades with minima in sea ice extent in September 2007 and 2011 and climate models did not predict this decline. One of the processes poorly represented in sea ice models is the formation and evolution of melt ponds. Melt ponds form on Arctic sea ice during the melting season and their presence affects the heat and mass balances of the ice cover, mainly by decreasing the value of the surface albedo by up to 20%. We have developed a melt pond model suitable for forecasting the presence of melt ponds based on sea ice conditions. This model has been incorporated into the Los Alamos CICE sea ice model, the sea ice component of several IPCC climate models. Simulations for the period 1990 to 2007 are in good agreement with observed ice concentration. In comparison to simulations without ponds, the September ice volume is nearly 40% lower. Sensitivity studies within the range of uncertainty reveal that, of the parameters pertinent to the present melt pond parameterization and for our prescribed atmospheric and oceanic forcing, variations of optical properties and the amount of snowfall have the strongest impact on sea ice extent and volume. We conclude that melt ponds will play an increasingly important role in the melting of the Arctic ice cover and their incorporation in the sea ice component of Global Circulation Models is essential for accurate future sea ice forecasts.
Current induced domain wall dynamics in the presence of a transverse magnetic field in out-of-plane magnetized materials
Authors: Boulle O. , Buda-Prejbeanu L. D. , Miron M. , Gaudin G.
Published: September 2012

An analytical model was developed to describe the current induced domain wall (DW) dynamics of a Bloch DW in the presence of an external transverse magnetic field. The model takes into account the DW deformation and the magnetization tilting in the domain. The model is compared to the results of micromagnetic simulation and an excellent agreement is obtained. In the steady state regime, the model shows that the domain tilting does not change the DW mobility. An external or current induced transverse magnetic field such as the Oersted or Rashba field can prevent the Walker breakdown leading to a higher domain wall velocity.
Current-voltage characteristics and ON/OFF ratio in ferroelectric tunnel junctions
Authors: Lu Xiaoyan , Li Hui , Cao Wenwu
Published: September 2012

Current-voltage characteristics of poled ferroelectric tunnel junction have been theoretically studied with the consideration of piezoelectric effect and interface potential due to the depolarization effect. Compared with piezoelectric effect, barrier potential changed by polarization switching is more significant. Tunnel currents with low and high resistances during the reading process are distinct, which have potential applications as low-cost, high-density, and fast-speed ferroelectric memories. The obtained ON/OFF ratio in a symmetry SrRuO3/BaTiO3/SrRuO3 structure is around 50 under a small applied voltage.
As-grown deep-level defects in n-GaN grown by metal–organic chemical vapor deposition on freestanding GaN
Authors: Chen Shang , Honda Unhi , Shibata Tatsunari , Matsumura Toshiya , Tokuda Yutaka , Ishikawa Kenji , Hori Masaru , Ueda Hiroyuki , Uesugi Tsutomu , Kachi Tetsu
Published: September 2012

Traps of energy levels Ec −0.26 and Ec −0.61 eV have been identified as as-grown traps in n-GaN grown by metal–organic chemical vapor deposition by using deep level transient spectroscopy of the Schottky contacts fabricated by resistive evaporation. The additional traps of Ec −0.13 and Ec −0.65 eV have been observed in samples whose contacts are deposited by electron-beam evaporation. An increase in concentration of the Ec −0.13 and Ec −0.65 eV traps when approaching the interface between the contact and the GaN film supports our argument that these traps are induced by electron-beam irradiation. Conversely, the depth profiles of as-grown traps show different profiles between several samples with increased or uniform distribution in the near surface below 50 nm. Similar profiles are observed in GaN grown on a sapphire substrate. We conclude that the growth process causes these large concentrations of as-grown traps in the near-surface region. It is speculated that the finishing step in the growth process should be an essential issue in the investigation of the surface state of GaN.
Independent wavelength and density control of uniform GaAs/AlGaAs quantum dots grown by infilling self-assembled nanoholes
Authors: Atkinson P. , Zallo E. , Schmidt O. G.
Published: September 2012

Very low density growth of GaAs quantum dots in self-assembled nanoholes created by gallium droplet etching is demonstrated. The emission energy of the quantum dots can be accurately controlled by the GaAs deposition amount, from 1.8 to 1.6 eV, independently of the dot density which can be reproducibly controlled over the range 0.2−2×10−8 cm−2 by the gallium deposition rate. The ensemble full-width-half-maximum is <10 meV and single-dot linewidths of 40 μeV (limited by our spectral resolution) have been measured. Additionally, shallow mounds on the sample surface allow the buried GaAs/AlGaAs dots to be located. A simple method to reliably predict the emission energy based on the shape of the nanohole is presented.
An ab initio based full-dimensional global potential energy surface for FH2O(X2A′) and dynamics for the F + H2O → HF + HO reaction
Authors: Li Jun , Dawes Richard , Guo Hua
Published: September 2012

A global potential energy surface (PES) for the ground electronic state of FH2O is constructed based on more than 30 000 ab initio points at the multi-reference configuration interaction level. The PES features a pre-reaction van der Waals well and two post-reaction hydrogen-bonded complexes, as well as a “reactant-like” transition state with a classical barrier of 3.8 kcal/mol. The adiabatic F + H2O → HF + OH reaction dynamics on this PES was investigated using a standard quasi-classical trajectory method. In agreement with experiment, the HF product contains significant vibrational excitation with limited rotational excitation, while the OH product is internally cold, reflecting its spectator role in the reaction. The products are primarily scattered in the backward direction, consistent with a direct abstraction mechanism.
Charge transport in functionalized multi-wall carbon nanotube-Nafion composite
Authors: Suchand Sangeeth C. S. , Kannan R. , Pillai Vijayamohanan K. , Menon Reghu
Published: September 2012

The charge transport in sulfonated multi-wall carbon nanotube (sMWNT)-Nafion composite is reported. The scanning electron microscope images of the composite, at 1 and 10 wt % of sMWNT, show that the nanotubes are well dispersed in polymer matrix, with conductivity values of 0.005 and 3.2 S/cm, respectively; and the percolation threshold is nearly 0.42 wt. %. The exponent (∼0.25) of the temperature dependence of conductivity in both samples indicates Mott's variable range hopping (VRH) transport. The conductance in 1 wt. % sample increases by three orders of magnitude at high electric-fields, consistent with VRH model. The negative magnetoresistance in 10 wt. % sample is attributed to the forward interference scattering mechanism in VRH transport. The ac conductance in 1 wt. % sample is expressed by σ(ω)∝ωs, and the temperature dependence of s follows the correlated barrier hopping model.
Pinned interface dipole-induced tunneling electroresistance in ferroelectric tunnel junctions: A theoretical investigation
Authors: Wu Yin-Zhong
Published: September 2012

Based on the structure predicted in a ferroelectric tunnel junction (FTJ) in the resent density functional theory study [Liu et al., Phys. Rev. B 85, 125407 (2012)], we provide numerical simulations of the electron transport through the FTJ with asymmetric interfaces, i.e., one interface dipole is pinned and the other interface dipole is switchable. Tunneling electroresistance (TER) can be induced due to the nonswitchable interface dipole in FTJs with symmetric electrodes. Compared with the dependence relationship between TER and the polarization of switchable interface, TER is not sensitive to the variation of the polarization of pinned interface. A large TER can be achieved when the pinned polarization points to the ferroelectric film and low interface dielectric constants. In addition, effect of electrode on TER in the structure is also discussed.
Alternating current loss of second-generation high-temperature superconducting coils with magnetic and non-magnetic substrate
Authors: Zhang Min , Kvitkovic J. , Kim Jae-Ho. , Kim C. H. , Pamidi S. V. , Coombs T. A.
Published: September 2012

It is widely believed that the second-generation high-temperature superconducting (2G HTS) tapes with magnetic substrates suffer higher transport loss compared to those with non-magnetic substrates. To test this, we prepared two identical coils with magnetic and non-magnetic substrates, respectively. The experimental result was rather surprising that they generated roughly the same amount of transport loss. We used finite element method to understand this result. It is found that, unlike in the single tape where the magnetic field-dependent critical current characteristic can be neglected and the effect of magnetic substrate dominates, the magnetic field-dependent critical current characteristic of 2G tape plays as an equally important role as magnetic substrate in terms of HTS coils.
Lamb wave band gaps in a homogenous plate with periodic tapered surface
Authors: Zhang Hong-bo , Chen Jiu-jiu , Han Xu
Published: September 2012

In this paper, we present the numerical investigation of Lamb wave propagation in a homogenous plate with periodic tapered surface, which gradually increases the width from the lower base to the upper base. The dispersion relations, the power transmission spectra, and the displacement fields of the eigenmodes are studied by using the finite-element method. We investigate the effects of the geometrical parameters (including the ratio of the lower base width to the upper base width, and the ratio of the upper base width, the thickness of the tapered surface, and the thickness of the homogenous plate, respectively, to the lower base width) on the band gaps. Numerical results show that the band gaps can be effectively shifted by changing the geometrical parameters. Especially, the width of the first band gap changes approximately linearly by changing the ratio of the upper base width to the lower base width and in return. The transmission bands of the structure with the tapered surface are more flat than those of the structure with the stubbed surface. Moreover, the proposed homogenous plate with periodic tapered surface exhibits lower and smaller band gap than that of the homogenous plate with periodic stubbed surface due to weak localized resonance of the tapered surface with the upper base wider than the lower base. These properties of elastic or acoustic waves can potentially be utilized to tune band gaps, slow the group velocity, generate filters, and design acoustic sensors.
Influence of capping layers on CoFeB anisotropy and damping
Authors: Natarajarathinam A. , Tadisina Z. R. , Mewes T. , Watts S. , Chen E. , Gupta S.
Published: September 2012

Magnetic behavior of CoFeB at various thicknesses ranging from 2 nm to 8 nm capped with different materials, such as MgO, Ta, Ru, and V have been studied. The films were sputter-deposited and subsequently characterized by magnetometry and broadband ferromagnetic resonance (FMR). There are magnetically dead layers at the interface observed with Ru and Ta capping layers, while MgO and V have almost no effect on the magnetization of the CoFeB. As the ferromagnetic layer is made thinner, the effective magnetization decreases, indicating an interfacial perpendicular anisotropy. Particularly in the case of MgO, V/Ru, and V/Ta capping layers, interfacial perpendicular anisotropy is induced in CoFeB, and the Gilbert damping parameter is also reduced. The origin of this perpendicular magnetic anisotropy (PMA) is understood to be caused by the interface anisotropy between the free layer and the capping layer. The effect of post-deposition annealing and CoFeB thickness on the anisotropy and damping of V/Ta capped samples are reported. Doping CoFeB with vanadium (V) greatly reduced the 4πMs and 4πMeff values, resulting in an effective increase in the PMA.
Optical absorptions in AlxGa1−xAs/GaAs quantum well for solar energy application
Authors: Yang X. F. , Liu Y. S. , Fu Y.
Published: September 2012

We study the optical transitions among localized and extended states in quantum solar cells based on AlxGa1−xAs/GaAs quantum well (QW). The absorption coefficients of localized-to-localized, ground localized-to-extended, and extended-to-localized transitions are enhanced obviously as the size of the QW decreases. When the wave functions of incident electrons and holes spread along different sides of the structure, the absorption coefficient of extended-to-extended states becomes non-zero value when the QW is inserted. This process has a main contribution to the photocurrents. In addition, our studies also show these optical transitions have different sensitivities to the Fermi levels. Therefore, optical absorptions in AlxGa1−xAs/GaAs solar cells can be optimized by the sizes of QW and Fermi levels.
Delay induced bifurcation of dominant transition pathways
Authors: Jiang Huijun , Hou Zhonghuai
Published: September 2012

We investigate delay effects on dominant transition pathways (DTP) between metastable states of stochastic systems. A modified version of the Maier-Stein model with linear delayed feedback is considered as an example. By a stability analysis of the “on-axis” DTP in trajectory space, we find that a bifurcation of DTPs will be induced when time delay τ is large enough. This finding is soon verified by numerically derived DTPs which are calculated by employing a recently developed minimum action method extended to delayed stochastic systems. Further simulation shows that the delay-induced bifurcation of DTPs also results in a nontrivial dependence of the transition rate constant on the delay time. Finally, the bifurcation diagram is given on the τ−β plane, where β measures the non-conservation of the original Maier-Stein model.
Surface texture and interior residual stress variation induced by thickness of YBa2Cu3O7-δ thin films
Authors: Zeng L. , Lu Y. M. , Liu Z. Y. , Chen C. Z. , Gao B. , Cai C. B.
Published: September 2012

YBa2Cu3O7-δ (YBCO) thin films with various thicknesses from 80 nm to 2000 nm are prepared on single crystal SrTiO3 by means of pulsed laser deposition technique. While it is hard for the x-ray diffraction to observe the evolutions in epitaxial orientation and interior lattice structure, the atomic force microscope shows the degraded surface morphologies and coalesced particles which arise from more misoriented grains with increasing thin film thickness. A detailed Raman spectrum investigation reveals that the a-axis grains exist predominately at the top surface of the films as the total thickness of the film increases up to 2000 nm. It is also evident that the Raman peak corresponding to the O2+/O3− mode emerges with the redshift first and then the blueshift as the film thickness increases. These Raman shifts suggest that the tensile stress in the (a, b) plane arising from the lattice mismatch between the epitaxial film and substrate may release gradually with increasing the film thickness, while the additional tensile stress emerges due to the a-axis grains present at the top surface of thin film. It is believed that the thickness effect of YBCO thin films on the superconducting transition temperature (Tc) and critical current density (Jc) is attributed to the variation of interior residual stress and surface morphology associated with the lattice mismatch and grain orientation, respectively.
Synthesis and upconversion luminescence of N-doped graphene quantum dots
Authors: Li Ming , Wu Wenbin , Ren Wencai , Cheng Hui-Ming , Tang Nujiang , Zhong Wei , Du Youwei
Published: September 2012

A hydrothermal approach was developed for the synthesis of N-doped graphene quantum dots (N-GQDs) by cutting N-doped graphene. The N-GQDs obtained have a N/C atomic ratio of ca. 5.6% and diameter of 1–7 nm. The photoluminescence (PL) properties of the N-GQDs were investigated. It was found that the N-GQDs possess bright blue PL and excellent upconversion PL properties.
Inverted top-emitting blue electrophosphorescent organic light-emitting diodes with high current efficacy
Authors: Knauer K. A. , Najafabadi E. , Haske W. , Kippelen B.
Published: September 2012

Two different types of inverted top-emitting blue electrophosphorescent organic light-emitting diodes (OLEDs) are demonstrated that differ only in the choice of high electron mobility transport layers. The electron transport layer consists of either 1,3,5-tri(p-pyrid-3-yl-phenyl)benzene (TpPyPB) or 1,3,5-tri(m-pyrid-3-yl-phenyl)benzene) (TmPyPB). Devices with TpPyPB exhibit a current efficacy of 5.1 cd/A at 1259 cd/m2. OLEDs with TmPyPB show higher performance with a current efficacy of 33.6 cd/A at 1126 cd/m2. The difference in performance of OLEDs with TmPyPB is due to a combination of TmPyPB's higher triplet energy that decreases exciton transfer to the ETL and altered charge balance.
Hopping photoconductivity in an exponential density of states
Authors: Iacchetti A. , Natali D. , Binda M. , Beverina L. , Sampietro M.
Published: September 2012

Photoconductivity in organic semiconductors is modeled taking into account the hopping nature of charge transport in an exponential density of states and exploiting the transport energy concept. Explicit and analytical expressions describing device behavior are obtained, and a robust procedure is outlined to extract from experimental measurements relevant material parameters, including the charge density dependent bulk mobility, as we show on a prototypical all-organic photoconductor. This qualifies the photoconductor not only as a technologically relevant device but also as a test bed for the optoelectronic characterization of disordered materials.
Effects of growth temperature on Mg-doped GaN grown by ammonia molecular beam epitaxy
Authors: Hurni Christophe A. , Lang Jordan R. , Burke Peter G. , Speck James S.
Published: September 2012

The hole concentration p in Mg-doped GaN films grown by ammonia molecular beam epitaxy depends strongly on the growth temperature TGR. At TGR=760 °C, GaN:Mg films showed a hole concentration of p=1.2 × 1018 cm−3 for [Mg]=4.5×1019 cm−3, while at TGR=840 °C, p=4.4×1016 cm−3 for [Mg]=7×1019 cm−3. Post-growth annealing did not increase p. The sample grown at 760 °C exhibited a low resistivity of 0.7 Ωcm. The mobility for all the samples was around 3−7 cm2/V s. Temperature-dependent Hall measurements and secondary ion mass spectroscopy suggest that the samples grown at TGR>760 °C are compensated by an intrinsic donor rather than hydrogen.
Strain induced lithium functionalized graphane as a high capacity hydrogen storage material
Authors: Hussain Tanveer , De Sarkar Abir , Ahuja Rajeev
Published: September 2012

Strain effects on the stability, electronic structure, and hydrogen storage capacity of lithium-doped graphane have been investigated by state-of-the-art first principles density functional theory. Molecular dynamics simulations have confirmed the stability of Li on graphane sheet when it is subject to 10% of tensile strain. Under biaxial asymmetric strain, the binding energy of Li of graphane (CH) sheet increases by 52% with respect to its bulk’s cohesive energy. With 25% doping concentration of Li on CH sheet, the gravimetric density of hydrogen storage is found to reach up to 12.12 wt. %. The adsorption energies of H2 are found to be within the range of practical H2 storage applications.
Characterization of thin epitaxial emitters for high-efficiency silicon heterojunction solar cells
Authors: Hekmatshoar Bahman , Shahrjerdi Davood , Hopstaken Marinus , Ott John A. , Sadana Devendra K.
Published: September 2012

We report silicon heterojunction solar cells with conversion efficiencies exceeding 21% using appropriately designed emitter structures comprised of highly doped thin epitaxial layers grown by plasma-enhanced chemical vapor deposition at temperatures close to 200 °C. We show that at a given doping concentration, there is an optimum epitaxial layer thickness, above which the conversion efficiency is limited by Auger recombination and bandgap narrowing within the epitaxial layer. In contrast, below the optimum thickness, the conversion efficiency is limited by carrier recombination at the emitter surface of the crystalline silicon substrate.
Role of genes linked to sporadic Alzheimer’s disease risk in the production of β-amyloid peptides
Authors: Bali Jitin , Gheinani Ali Hashemi , Zurbriggen Sebastian , Rajendran Lawrence
Published: September 2012

Alzheimer’s disease (AD) is characterized by the presence of toxic protein aggregates or plaques composed of the amyloid β (Aβ) peptide. Various lengths of Aβ peptide are generated by proteolytic cleavages of the amyloid precursor protein (APP). Mutations in many familial AD-associated genes affect the production of the longer Aβ42 variant that preferentially accumulates in plaques. In the case of sporadic or late-onset AD, which accounts for greater than 95% of cases, several genes are implicated in increasing the risk, but whether they also cause the disease by altering amyloid levels is currently unknown. Through loss of function studies in a model cell line, here RNAi-mediated silencing of several late onset AD genes affected Aβ levels is shown. However, unlike the genes underlying familial AD, late onset AD-susceptibility genes do not specifically alter the Aβ42/40 ratios and suggest that these genes probably contribute to AD through distinct mechanisms.
De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells
Authors: Rodrigo Guillermo , Landrain Thomas E. , Jaramillo Alfonso
Published: September 2012

A grand challenge in synthetic biology is to use our current knowledge of RNA science to perform the automatic engineering of completely synthetic sequences encoding functional RNAs in living cells. We report here a fully automated design methodology and experimental validation of synthetic RNA interaction circuits working in a cellular environment. The computational algorithm, based on a physicochemical model, produces novel RNA sequences by exploring the space of possible sequences compatible with predefined structures. We tested our methodology in
Escherichia coli
by designing several positive riboregulators with diverse structures and interaction models, suggesting that only the energy of formation and the activation energy (free energy barrier to overcome for initiating the hybridization reaction) are sufficient criteria to engineer RNA interaction and regulation in bacteria. The designed sequences exhibit nonsignificant similarity to any known noncoding RNA sequence. Our riboregulatory devices work independently and in combination with transcription regulation to create complex logic circuits. Our results demonstrate that a computational methodology based on first-principles can be used to engineer interacting RNAs with allosteric behavior in living cells.
Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations
Authors: Rudack Till , Xia Fei , Schlitter Jürgen , Kötting Carsten , Gerwert Klaus
Published: September 2012

Members of the Ras superfamily regulate many cellular processes. They are down-regulated by a GTPase reaction in which GTP is cleaved into GDP and P

i

by nucleophilic attack of a water molecule. Ras proteins accelerate GTP hydrolysis by a factor of 10
5
compared to GTP in water. GTPase-activating proteins (GAPs) accelerate hydrolysis by another factor of 10
5
compared to Ras alone. Oncogenic mutations in Ras and GAPs slow GTP hydrolysis and are a factor in many cancers. Here, we elucidate in detail how this remarkable catalysis is brought about. We refined the protein-bound GTP structure and protein-induced charge shifts within GTP beyond the current resolution of X-ray structural models by combining quantum mechanics and molecular mechanics simulations with time-resolved Fourier-transform infrared spectroscopy. The simulations were validated by comparing experimental and theoretical IR difference spectra. The reactant structure of GTP is destabilized by Ras via a conformational change from a staggered to an eclipsed position of the nonbridging oxygen atoms of the γ- relative to the β-phosphates and the further rotation of the nonbridging oxygen atoms of α- relative to the β- and γ-phosphates by GAP. Further, the γ-phosphate becomes more positive although two of its oxygen atoms remain negative. This facilitates the nucleophilic attack by the water oxygen at the phosphate and proton transfer to the oxygen. Detailed changes in geometry and charge distribution in the ligand below the resolution of X-ray structure analysis are important for catalysis. Such high resolution appears crucial for the understanding of enzyme catalysis.
Biased inheritance of the protein PatN frees vegetative cells to initiate patterned heterocyst differentiation
Authors: Risser Douglas D. , Wong Francis C. Y. , Meeks John C.
Published: September 2012

Heterocysts, cells specialized for nitrogen fixation in certain filamentous cyanobacteria, appear singly in a nonrandom spacing pattern along the chain of vegetative cells. A two-stage, biased initiation and competitive resolution model has been proposed to explain the establishment of this spacing pattern. There is substantial evidence that competitive resolution of a subset of cells initiating differentiation occurs by interactions between a self-enhancing activator protein, HetR, and a diffusible pentapeptide inhibitor PatS-5 (RGSGR). Results presented here show that the absence of a unique membrane protein, PatN, in
Nostoc punctiforme
strain ATCC 29133 leads to a threefold increase in heterocyst frequency and a fourfold decrease in the vegetative cell interval between heterocysts. A PatN-GFP translational fusion shows a pattern of biased inheritance in daughter vegetative cells of ammonium-grown cultures. Inactivation of another heterocyst patterning gene,
patA
, is epistatic to inactivation of
patN
, and transcription of
patA
increases in a
patN
-deletion strain, implying that
patN
may function by modulating levels of
patA
. The presence of PatN is hypothesized to decrease the competency of a vegetative cell to initiate heterocyst differentiation, and the cellular concentration of PatN is dependent on cell division that results in cells transiently depleted of PatN. We suggest that biased inheritance of cell-fate determinants is a phylogenetic domain-spanning paradigm in the development of biological patterns.
Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria
Authors: Gasiunas Giedrius , Barrangou Rodolphe , Horvath Philippe , Siksnys Virginijus
Published: September 2012

Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide adaptive immunity against viruses and plasmids in bacteria and archaea. The silencing of invading nucleic acids is executed by ribonucleoprotein complexes preloaded with small, interfering CRISPR RNAs (crRNAs) that act as guides for targeting and degradation of foreign nucleic acid. Here, we demonstrate that the Cas9–crRNA complex of the
Streptococcus thermophilus
CRISPR3/Cas system introduces in vitro a double-strand break at a specific site in DNA containing a sequence complementary to crRNA. DNA cleavage is executed by Cas9, which uses two distinct active sites, RuvC and HNH, to generate site-specific nicks on opposite DNA strands. Results demonstrate that the Cas9–crRNA complex functions as an RNA-guided endonuclease with RNA-directed target sequence recognition and protein-mediated DNA cleavage. These findings pave the way for engineering of universal programmable RNA-guided DNA endonucleases.
Energetics of life on the deep seafloor
Authors: McClain Craig R. , Allen Andrew P. , Tittensor Derek P. , Rex Michael A.
Published: September 2012

With frigid temperatures and virtually no in situ productivity, the deep oceans, Earth’s largest ecosystem, are especially energy-deprived systems. Our knowledge of the effects of this energy limitation on all levels of biological organization is very incomplete. Here, we use the Metabolic Theory of Ecology to examine the relative roles of carbon flux and temperature in influencing metabolic rate, growth rate, lifespan, body size, abundance, biomass, and biodiversity for life on the deep seafloor. We show that the relative impacts of thermal and chemical energy change across organizational scales. Results suggest that individual metabolic rates, growth, and turnover proceed as quickly as temperature-influenced biochemical kinetics allow but that chemical energy limits higher-order community structure and function. Understanding deep-sea energetics is a pressing problem because of accelerating climate change and the general lack of environmental regulatory policy for the deep oceans.
Precursor-centric genome-mining approach for lasso peptide discovery
Authors: Maksimov Mikhail O. , Pelczer István , Link A. James
Published: September 2012

Lasso peptides are a class of ribosomally synthesized posttranslationally modified natural products found in bacteria. Currently known lasso peptides have a diverse set of pharmacologically relevant activities, including inhibition of bacterial growth, receptor antagonism, and enzyme inhibition. The biosynthesis of lasso peptides is specified by a cluster of three genes encoding a precursor protein and two enzymes. Here we develop a unique genome-mining algorithm to identify lasso peptide gene clusters in prokaryotes. Our approach involves pattern matching to a small number of conserved amino acids in precursor proteins, and thus allows for a more global survey of lasso peptide gene clusters than does homology-based genome mining. Of more than 3,000 currently sequenced prokaryotic genomes, we found 76 organisms that are putative lasso peptide producers. These organisms span nine bacterial phyla and an archaeal phylum. To provide validation of the genome-mining method, we focused on a single lasso peptide predicted to be produced by the freshwater bacterium
Asticcacaulis excentricus
. Heterologous expression of an engineered, minimal gene cluster in
Escherichia coli
led to the production of a unique lasso peptide, astexin-1. At 23 aa, astexin-1 is the largest lasso peptide isolated to date. It is also highly polar, in contrast to many lasso peptides that are primarily hydrophobic. Astexin-1 has modest antimicrobial activity against its phylogenetic relative
Caulobacter crescentus
. The solution structure of astexin-1 was determined revealing a unique topology that is stabilized by hydrogen bonding between segments of the peptide.
Fluoride resistance and transport by riboswitch-controlled CLC antiporters
Authors: Stockbridge Randy B. , Lim Hyun-Ho , Otten Renee , Williams Carole , Shane Tania , Weinberg Zasha , Miller Christopher
Published: September 2012

A subclass of bacterial CLC anion-transporting proteins, phylogenetically distant from long-studied CLCs, was recently shown to be specifically up-regulated by F
-
. We establish here that a set of randomly selected representatives from this “CLC
F
” clade protect
Escherichia coli
from F
-
toxicity, and that the purified proteins catalyze transport of F
-
in liposomes. Sequence alignments and membrane transport experiments using
19
F NMR, osmotic response assays, and planar lipid bilayer recordings reveal four mechanistic traits that set CLC
F
proteins apart from all other known CLCs. First, CLC
F
s lack conserved residues that form the anion binding site in canonical CLCs. Second, CLC
F
s exhibit high anion selectivity for F
-
over Cl
-
. Third, at a residue thought to distinguish CLC channels and transporters, CLC
F
s bear a channel-like valine rather than a transporter-like glutamate, and yet are F
-
/H
+
antiporters. Finally, F
-
/H
+
exchange occurs with 1∶1 stoichiometry, in contrast to the usual value of 2∶1.
Sensitization of ultra-long-range excited-state electron transfer by energy transfer in a polymerized film
Authors: Ito Akitaka , Stewart David J. , Fang Zhen , Brennaman M. Kyle , Meyer Thomas J.
Published: September 2012

Distance-dependent energy transfer occurs from the Metal-to-Ligand Charge Transfer (MLCT) excited stateto an anthracene-acrylate derivative (Acr-An) incorporated into the polymer network of a semirigid poly(ethyleneglycol)dimethacrylate monolith. Following excitation,to Acr-An triplet energy transfer occurs followed by long-range, Acr-3An—Acr-An → Acr-An—Acr-3An, energy migration. With methyl viologen dication (MV2+) added as a trap, Acr-3An + MV2+ → Acr-An+ + MV+electron transfer results in sensitized electron transfer quenching over a distance of approximately 90 Å.
Assessing Fit Quality and Testing for Misspecification in Binary-Dependent Variable Models
Authors: Esarey Justin , Pierce Andrew
Published: September 2012

In this article, we present a technique and critical test statistic for assessing the fit of a binary-dependent variable model (e.g., a logit or probit). We examine how closely a model's predicted probabilities match the observed frequency of events in the data set, and whether these deviations are systematic or merely noise. Our technique allows researchers to detect problems with a model's specification that obscure substantive understanding of the underlying data-generating process, such as missing interaction terms or unmodeled nonlinearities. We also show that these problems go undetected by the fit statistics most commonly used in political science.
Effects of the Mycoparasite Sphaerellopsis filum on Overwintering Survival of Stem Rust in Perennial Ryegrass
Authors: Gordon T. C. , Pfender W. F.
Published: September 2012

Sphaerellopsis filum is a mycoparasite of Puccinia graminis subsp. graminicola, a rust fungus that causes widespread crop damage on perennial ryegrass grown for seed. In observations taken over the winter months, S. filum was found naturally colonizing 2% of P. graminis subsp. graminicola uredinia on first-year plantings and 25% of the uredinia on second-year plantings of perennial ryegrass. In controlled experiments conducted in glasshouses and growth chambers, S. filum applied to rust-inoculated plants reduced the lifetime spore production of P. graminis subsp. graminicola pustules by half, from 39,000 to 18,000 spores/pustule. Mist duration, temperature, and P. graminis subsp. graminicola pustule age at the time of S. filum inoculation had significant effects on the proportion of P. graminis subsp. graminicola pustules infected by S. filum. Fifty percent of all P. graminis subsp. graminicola pustules were infected when S. filum was inoculated onto erumpent pustules and incubated above 5°C for 48 h while exposed to mist. Plants inoculated with both fungi under controlled conditions and then planted into the field had a significantly greater proportion of P. graminis subsp. graminicola pustules infected with S. filum, and a significantly reduced P. graminis subsp. graminicola overwintering population, compared with plants inoculated with P. graminis subsp. graminicola only. First-year stands of perennial ryegrass treated in the field with monthly applications of S. filum had more than 10 times the proportion of pustules infected with S. filum and 50% less P. graminis subsp. graminicola disease compared with the nontreated controls. In comparison, plants with one application of fungicide during the winter had 98% lower P. graminis subsp. graminicola severity than the P. graminis subsp. graminicola-only control There were no effects of S. filum or fungicide application on rust severity in 2- or 3-year-old perennial ryegrass stands.
Weyl geometry and the nonlinear mechanics of distributed point defects
Authors: Yavari Arash , Goriely Alain
Published: September 2012

The residual stress field of a nonlinear elastic solid with a spherically symmetric distribution of point defects is obtained explicitly using methods from differential geometry. The material manifold of a solid with distributed point defects—where the body is stress-free—is a flat Weyl manifold, i.e. a manifold with an affine connection that has non-metricity with vanishing traceless part, but both its torsion and curvature tensors vanish. Given a spherically symmetric point defect distribution, we construct its Weyl material manifold using the method of Cartan's moving frames. Having the material manifold, the anelasticity problem is transformed to a nonlinear elasticity problem and reduces the problem of computing the residual stresses to finding an embedding into the Euclidean ambient space. In the case of incompressible neo-Hookean solids, we calculate explicitly this residual stress field. We consider the example of a finite ball and a point defect distribution uniform in a smaller ball and vanishing elsewhere. We show that the residual stress field inside the smaller ball is uniform and hydrostatic. We also prove a nonlinear analogue of Eshelby's celebrated inclusion problem for a spherical inclusion in an isotropic incompressible nonlinear solid.
Major histocompatibility complex class II compatibility, but not class I, predicts mate choice in a bird with highly developed olfaction
Authors: Strandh Maria , Westerdahl Helena , Pontarp Mikael , Canbäck Björn , Dubois Marie-Pierre , Miquel Christian , Taberlet Pierre , Bonadonna Francesco
Published: September 2012

Mate choice for major histocompatibility complex (MHC) compatibility has been found in several taxa, although rarely in birds. MHC is a crucial component in adaptive immunity and by choosing an MHC-dissimilar partner, heterozygosity and potentially broad pathogen resistance is maximized in the offspring. The MHC genotype influences odour cues and preferences in mammals and fish and hence olfactory-based mate choice can occur. We tested whether blue petrels,
Halobaena caerulea
, choose partners based on MHC compatibility. This bird is long-lived, monogamous and can discriminate between individual odours using olfaction, which makes it exceptionally well suited for this analysis. We screened MHC class I and II B alleles in blue petrels using 454-pyrosequencing and quantified the phylogenetic, functional and allele-sharing similarity between individuals. Partners were functionally more dissimilar at the MHC class II B loci than expected from random mating (
p
= 0.033), whereas there was no such difference at the MHC class I loci. Phylogenetic and non-sequence-based MHC allele-sharing measures detected no MHC dissimilarity between partners for either MHC class I or II B. Our study provides evidence of mate choice for MHC compatibility in a bird with a high dependency on odour cues, suggesting that MHC odour-mediated mate choice occurs in birds.