bluuebunny/crossref_metadata_2025 huggingface dataset:
Modification of empirical core loss calculation methods including flux distribution
Authors: Agheb Edris , Høidalen Hans Kristian
Published: July 2013

Using medium‐frequency high‐power transformers leads to significant decrease in size and volume of high‐power converters in different applications such as offshore wind farms and electric traction. However, increasing the operating frequency leads to several challenges such as increase in the core loss. Consequently, estimating magnetic loss with high accuracy is essential especially in thermal modelling point of view and temperature rise calculation. The main contribution of this study is to introduce a novel and accurate model to investigate the spatial distribution of flux density inside the core. The distribution profile depends on the characteristics of the magnetic material and the configuration of the core. The accuracy of this method has been compared with the experimental results of other studies. Variation of flux density and core loss also depend on the operating magnetisation where at higher inductions, the difference between the minimum and maximum will be decreased. Owing to inhomogeneous distribution of flux, higher portion of the core loss will be generated in the inner half of the core. Ultimately, it has been expressed that considering the non‐even distribution of the flux results in higher maximum temperature of the core.
Hybrid successive continuous wave interference cancellation scheme for global positioning system receivers
Authors: Chien Ying‐Ren
Published: July 2013

The authors propose a hybrid successive continuous wave interference (CWI) cancellation scheme for GPS receivers. The proposed hybrid scheme successively detects and estimates CWIs in the time domain and nulls the estimated contaminated frequencies in the frequency domain. An adaptive second‐order infinite impulse response (IIR) filter to perform the CWI detection and estimation is devised. One IIR filter is able to estimate one CWI in each iteration. Then, the detected CWI is fed back to the excision module in the frequency domain. Therefore, the hybrid scheme can successively null multiple CWIs. Moreover, the proposed architecture allows additional cascading of IIR filters to handle multiple CWIs simultaneously. Unlike the existing frequency‐domain approach, CWI estimation does not rely on the statistical values in the frequency domain. Therefore the proposed hybrid scheme can be implemented using a fast Fourier transform (FFT) with fewer points. Simulation results show that the proposed hybrid scheme can operate normally with only a 256‐point FFT and can perform better than the conventional N‐sigma and consecutive mean excision algorithms in terms of the effective signal to interference plus noise ratio of the acquisition results.
Exact spectrum of non‐linear chirp scaling and its application in geosynchronous synthetic aperture radar imaging
Authors: Qi Chen , Dexin Li , Feng He , Diannong Liang
Published: July 2013

Non‐linear chirp scaling (NLCS) is a feasible method to deal with time‐variant frequency modulation (FM) rate problem in synthetic aperture radar (SAR) imaging. However, approximations in derivation of NLCS spectrum lead to performance decline in some cases. Presented is the exact spectrum of the NLCS function. Simulation with a geosynchronous synthetic aperture radar (GEO‐SAR) configuration is implemented. The results show that using the presented spectrum can significantly improve imaging performance, and the NLCS algorithm is suitable for GEO‐SAR imaging after modification.
Tunable plasmonic filter and variable optical attenuator based on ring metal–insulator–metal waveguide
Authors: Guo Jianping , Zhu Jiahu , Zhou Wen
Published: July 2013

A tunable nanoscale plasmonic filter and variable optical attenuator structure based on a rectangular ring metal–insulator–metal waveguide cavity containing electro‐optic (EO) material is proposed and numerically demonstrated by using the finite‐difference time‐domain technique. The simulation results show that the output of the device can be electrically controlled by tuning the refractive index of the EO material and the structure can be used as tunable filter and variable optical attenuator alternatively under very low voltage.
Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method
Authors: Cao Youfang , Liang Jie
Published: July 2013

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape.
Point-form dynamics of quasistable states
Authors: Gadella M. , Gómez-Cubillo F. , Rodriguez L. , Wickramasekara S.
Published: July 2013

We present a field theoretical model of point-form dynamics which exhibits resonance scattering. In particular, we construct point-form Poincaré generators explicitly from field operators and show that in the vector spaces for the in-states and out-states (endowed with certain analyticity and topological properties suggested by the structure of the S-matrix) these operators integrate to furnish differentiable representations of the causal Poincaré semigroup, the semidirect product of the semigroup of spacetime translations into the forward lightcone and the group of Lorentz transformations. We also show that there exists a class of irreducible representations of the Poincaré semigroup defined by a complex mass and a half-integer spin. The complex mass characterizing the representation naturally appears in the construction as the square root of the pole position of the propagator. These representations provide a description of resonances in the same vein as Wigner's unitary irreducible representations of the Poincaré group provide a description of stable particles.
On asymptotic behavior of density functional theory
Authors: Cencek Wojciech , Szalewicz Krzysztof
Published: July 2013

The performance of several previously proposed as well as of some novel approaches for correcting the asymptotic behavior of electron densities in density functional theory (DFT) is evaluated. The comparisons are made for molecular properties that are known to be sensitive to the asymptotic behavior of densities such as polarizabilities, energies of excitations to Rydberg states, and interaction energies (computed using symmetry-adapted perturbation theory). We find that whereas DFT-based methods without asymptotic corrections predict the investigated properties with errors often as large as a dozen or so percent relative to the best known values, the best performing asymptotically corrected hybrid functionals reduce these errors to below 2%. In many cases, the errors are just a fraction of one percent and in a few cases DFT reproduces benchmark values to all figures. These errors are also very close to those produced by the coupled-cluster methods at the highest levels of electron excitations applicable in practice. Such performance is unprecedented for any applications of DFT and is due to high sensitivity of the investigated properties to tails of the electron densities. Range-separated hybrid (RSH) functionals are also examined and found to perform comparably to the asymptotically corrected hybrid functionals for excitation energies and only somewhat worse for polarizabilities. However, very surprisingly, RSH functionals fail completely in interaction energy calculations. We explain the latter problem by showing that, despite some expectations in the literature reflected by the alternative name, long-range corrected, used for the RSH functionals, these methods give densities that are not better in the asymptotic region than those produced by asymptotically uncorrected standard DFT methods. We further show that this failure can be corrected by cutting, displacing, and splicing the exchange-correlation potentials of RSH methods such that these potentials approach the correct value at infinity.
Observations on shock induced chemistry of cyclohexane
Authors: Akin M. C. , Chau R.
Published: July 2013

We use double pass absorption spectroscopy to examine shock induced reactions in situ in cyclohexane and benzene at pressures up to 33.1 GPa. Reactions in cyclohexane begin by 27 GPa and complete by 33.1 GPa. Reactions in benzene are observed to begin by 12 GPa and are complete by 18 GPa. Absorption spectra indicate that the first reaction in cyclohexane occurs within or near the shock front, and that a metastable local equilibrium is reached in the post-shock state. A second process may be observed upon reshock at the lower pressures, suggesting a new equilibrium is reached post-reshock as well. Absorption bands are consistent with the formation of short radicals or fragments upon decomposition; however, spectral resolution is too low to confirm this mechanism.
An enhancement in the low-field electron mobility associated with a ZnMgO/ZnO heterostructure: The role of a two-dimensional electron gas
Authors: Baghani Erfan , O'Leary Stephen K.
Published: July 2013

We determine the role that a two-dimensional electron gas, formed at a ZnMgO/ZnO heterojunction, plays in shaping the corresponding temperature dependence of the low-field electron Hall mobility. This analysis is cast within the framework of the model of Shur et al. [M. Shur et al., J. Electron. Mater. 25, 777 (1996)], and the contributions to the mobility related to the ionized impurity, polar optical phonon, piezoelectric, and acoustic deformation potential scattering processes are considered, the overall mobility being determined through the application of Mathiessen's rule. The best fit to the ZnMgO/ZnO experimental results of Makino et al. [T. Makino et al., Appl. Phys. Lett. 87, 022101 (2005)] is obtained by setting the free electron concentration to 3×1018 cm−3 and the ionized impurity concentration to 1017 cm−3, i.e., within the two-dimensional electron gas formed at the heterojunction, the free electron gas concentration is a factor of 30 times the corresponding ionized impurity concentration. How this enhanced free electron concentration influences the contributions to the low-field electron mobility corresponding to these different scattering processes is also examined. It is found that the enhanced free electron concentration found within the two-dimensional electron gas dramatically decreases the ionized impurity and piezoelectric scattering rates and this is found to increase the overall low-field electron Hall mobility.
Resonance Raman and photoluminescence excitation profiles and excited-state dynamics in CdSe nanocrystals
Authors: Baker Joshua A. , Kelley David F. , Kelley Anne Myers
Published: July 2013

Resonance Raman excitation profiles for the longitudinal optical (LO) phonon fundamental and its first overtone have been measured for organic ligand capped, wurtzite form CdSe nanocrystals of ∼3.2 nm diameter dissolved in chloroform. The absolute differential Raman cross-section for the fundamental is much larger when excited at 532 or 543 nm, on the high-frequency side of the lowest-wavelength absorption maximum, than for excitation in the 458–476 nm range although the absorbance is higher at the shorter wavelengths. That is, the quantum yield for resonance Raman scattering is reduced for higher-energy excitation. In contrast, the photoluminescence quantum yield is relatively constant with wavelength. The optical absorption spectrum and the resonance Raman excitation profiles and depolarization dispersion curves are reproduced with a model for the energies, oscillator strengths, electron-phonon couplings, and dephasing rates of the multiple low-lying electronic excitations. The Huang-Rhys factor for LO phonon in the lowest excitonic transition is found to lie in the range S = 0.04–0.14. The strong, broad absorption feature about 0.5 eV above the lowest excitonic peak, typically labeled as the 1P3/21Pe transition, is shown to consist of at least two significant components that vary greatly in the magnitude of their electron-phonon coupling.
Communication: Spin-free quantum computational simulations and symmetry adapted states
Authors: Whitfield James Daniel
Published: July 2013

The ideas of digital simulation of quantum systems using a quantum computer parallel the original ideas of numerical simulation using a classical computer. In order for quantum computational simulations to advance to a competitive point, many techniques from classical simulations must be imported into the quantum domain. In this article, we consider the applications of symmetry in the context of quantum simulation. Building upon well established machinery, we propose a form of first quantized simulation that only requires the spatial part of the wave function, thereby allowing spin-free quantum computational simulations. We go further and discuss the preparation of N-body states with specified symmetries based on projection techniques. We consider two simple examples, molecular hydrogen and cyclopropenyl cation, to illustrate the ideas. The methods here are the first to explicitly deal with preparing N-body symmetry-adapted states and open the door for future investigations into group theory, chemistry, and quantum simulation.
The effects of the initial stages of native-oxide formation on the surface properties of GaSb (001)
Authors: Bermudez V. M.
Published: July 2013

Atomically clean surfaces of n-type GaSb (001) have been prepared by a combination of ex-situ wet-chemical treatment in HCl and in-situ annealing in a flux of H atoms in ultra-high vacuum (UHV). The surfaces are exposed to “excited” O2 and studied using primarily x-ray photoelectron spectroscopy. Low O2 exposures, up to ∼3 × 103 Langmuirs (L), result in a partial passivation of electrically active defects as shown by a decrease in upward band bending. Adsorption of O2 in this exposure range appears to form mainly Ga+1 sites, with little or no indication of Ga+3, and saturates at an O coverage of ∼0.2–0.3 monolayers. For exposures of ∼104 L or higher, oxidation occurs through insertion into Ga-Sb bonds as indicated by the onset of Ga+3 as well as of Sb+4 and/or Sb+5 together with the appearance of an O 1s feature. Defects resulting from this process cause a reversal of the band-bending change seen for smaller exposures. Data obtained for the composition of a native oxide formed in situ in UHV are compared with those for a “practical” surface produced by processing under ambient conditions. These results suggest an optimum procedure for forming a Ga2O3 layer prior to the growth by atomic layer deposition of an Al2O3 layer.
Quasiclassical trajectory studies of 18O(3P) + NO2 isotope exchange and reaction to O2 + NO on D and D1 potentials
Authors: Fu Bina , Zhang Dong H. , Bowman Joel M.
Published: July 2013

We report quasiclassical trajectory calculations for the bimolecular reaction 18O(3P) + NO2 on the recent potential energy surfaces of the ground (D0) and first excited (D1) states of NO3 [B. Fu, J. M. Bowman, H. Xiao, S. Maeda, and K. Morokuma, J. Chem. Theory. Comput. 9, 893 (2013)]10.1021/ct3009792. The branching ratio of isotope exchange versus O2 + NO formation, as well as the product angular distributions and energy and rovibrational state distributions are presented. The calculations are done at the collision energy of relevance to recent crossed beam experiments [K. A. Mar, A. L. Van Wyngarden, C.-W. Liang, Y. T. Lee, J. J. Lin, and K. A. Boering, J. Chem. Phys. 137, 044302 (2012)]10.1063/1.4736567. Very good agreement is achieved between the current calculations and these experiments for the branching ratio and final translational energy and angular distributions of isotope exchange products 16O(3P) + NO2 and O2 + NO formation products. The reactant 18O atom results in 18O16O but not N18O for the O2 + NO formation product channel, consistent with the experiment. In addition, the detailed vibrational and rotational state information of diatomic molecules calculated currently for the 34O2 + NO formation channel on D0 and D1 states are in qualitative agreement with the previous experimental and theoretical results of the photodissociation of NO3 and are consistent with older thermal bimolecular kinetics measurements.
Application of the extended Lie group analysis to the Hopf functional formulation of the Burgers equation
Authors: Wacławczyk Marta , Oberlack Martin
Published: July 2013

A study concerning the Lie group analysis of the functional differential equations has been performed. This is a continuation of the previous common work of Oberlack and Wacławczyk [“On the extension of Lie group analysis to functional differential equations,” Arch. Mech. 58, 597 (2006)] where Lie group theory has been extended to functional differential equations and a special solution of the functional formulation of the Burgers equation was derived based on the calculated set of infinitesimals. Here we derive an infinite set of symmetry transformations of this equation and find new and more general invariant solutions. With this we get a step closer to solutions of functional differential equations, which, e.g., give a complete statistical description of turbulence in case of the famous Hopf-Novikov-Stokes functional differential equations.
Enhanced p-type conduction of B-doped nanocrystalline diamond films by high temperature annealing
Authors: Gu S. S. , Hu X. J.
Published: July 2013

We report the enhanced p-type conduction with Hall mobility of 53.3 cm2 V−1 s−1 in B-doped nanocrystalline diamond (NCD) films by 1000 °C annealing. High resolution transmission electronic microscopy, uv, and visible Raman spectroscopy measurements show that a part of amorphous carbon grain boundaries (GBs) transforms to diamond phase, which increases the opportunity of boron atoms located at the GBs to enter into the nano-diamond grains. This phase transition doping is confirmed by the secondary ion mass spectrum depth profile results that the concentration of B atoms in nano-diamond grains increases after 1000 °C annealing. It is also observed that 1000 °C annealing improves the lattice perfection, reduces the internal stress, decreases the amount of trans-polyacetylene, and increases the number or size of aromatic rings in the sp2-bonded carbon cluster in B-doped NCD films. These give the contributions to improve the electrical properties of 1000 °C annealed B-doped NCD films.
Quasi-zero lattice mismatch and band alignment of BaTiO3 on epitaxial (110)Ge
Authors: Hudait M. K. , Zhu Y. , Jain N. , Maurya D. , Zhou Y. , Priya S
Published: July 2013

Growth, structural, and band alignment properties of pulsed laser deposited amorphous BaTiO3 on epitaxial molecular beam epitaxy grown (110)Ge layer, as well as their utilization in low power transistor are reported. High-resolution x-ray diffraction demonstrated quasi-zero lattice mismatch of BaTiO3 on (110)Ge. Cross-sectional transmission electron microscopy micrograph confirms the amorphous nature of BaTiO3 layer as well as shows a sharp heterointerface between BaTiO3 and Ge with no traceable interfacial layer. The valence band offset, ΔEv, of 1.99 ± 0.05 eV at the BaTiO3/(110)Ge heterointerface is measured using x-ray photoelectron spectroscopy. The conduction band offset, ΔEc, of 1.14 ± 0.1 eV is calculated using the bandgap energies of BaTiO3 of 3.8 eV and Ge of 0.67 eV. These band offset parameters for carrier confinement and the interface chemical properties of the BaTiO3/(110)Ge system are significant advancement towards designing Ge-based p-and n-channel metal-oxide semiconductor field-effect transistors for low-power application.
Pulsed mid-infrared radiation from spectral broadening in laser wakefield simulations
Authors: Zhu W. , Palastro J. P. , Antonsen T. M.
Published: July 2013

Spectral red-shifting of high power laser pulses propagating through underdense plasma can be a source of ultrashort mid-infrared (MIR) radiation. During propagation, a high power laser pulse drives large amplitude plasma waves, depleting the pulse energy. At the same time, the large amplitude plasma wave provides a dynamic dielectric response that leads to spectral shifting. The loss of laser pulse energy and the approximate conservation of laser pulse action imply that spectral red-shifts accompany the depletion. In this paper, we investigate, through simulation, the parametric dependence of MIR generation on pulse energy, initial pulse duration, and plasma density.
Lasing properties of non-polar GaN quantum dots in cubic aluminum nitride microdisk cavities
Authors: Bürger M. , Callsen G. , Kure T. , Hoffmann A. , Pawlis A. , Reuter D. , As D. J.
Published: July 2013

We demonstrate laser emission from optically pumped non-polar cubic GaN quantum dots embedded in cubic aluminum nitride microdisks. Power dependent micro-photoluminescence studies at low temperature (∼10 K) revealed S-shaped curves of the integral mode intensity. We observed whispering gallery modes with quality factors up to 5000 at the high energy side (4 eV, i.e., ∼310 nm wavelength) in photoluminescence spectra of microdisks with a diameter of 2.5 μm. Furthermore, we have determined the spontaneous emission coupling factors to β = 0.12 and β = 0.42 for resonator modes of different radial orders.
The silicon/zinc oxide interface in amorphous silicon-based thin-film solar cells: Understanding an empirically optimized contact
Authors: Gerlach D. , Wilks R. G. , Wippler D. , Wimmer M. , Lozac'h M. , Félix R. , Mück A. , Meier M. , Ueda S. , Yoshikawa H. , Gorgoi M. , Lips K. , Rech B. , Sumiya M. , Hüpkes J. , Kobayashi K. , Bär M.
Published: July 2013

The electronic structure of the interface between the boron-doped oxygenated amorphous silicon “window layer” (a-SiOx:H(B)) and aluminum-doped zinc oxide (ZnO:Al) was investigated using hard x-ray photoelectron spectroscopy and compared to that of the boron-doped microcrystalline silicon (μc-Si:H(B))/ZnO:Al interface. The corresponding valence band offsets have been determined to be (−2.87 ± 0.27) eV and (−3.37 ± 0.27) eV, respectively. A lower tunnel junction barrier height at the μc-Si:H(B)/ZnO:Al interface compared to that at the a-SiOx:H(B)/ZnO:Al interface is found and linked to the higher device performances in cells where a μc-Si:H(B) buffer between the a-Si:H p-i-n absorber stack and the ZnO:Al contact is employed.
Communication: The distinguishable cluster approximation
Authors: Kats Daniel , Manby Frederick R.
Published: July 2013

We present a method that accurately describes strongly correlated states and captures dynamical correlation. It is derived as a modification of coupled-cluster theory with single and double excitations (CCSD) through consideration of particle distinguishability between dissociated fragments, whilst retaining the key desirable properties of particle-hole symmetry, size extensivity, invariance to rotations within the occupied and virtual spaces, and exactness for two-electron subsystems. The resulting method, called the distinguishable cluster approximation, smoothly dissociates difficult cases such as the nitrogen molecule, with the modest N6 computational cost of CCSD. Even for molecules near their equilibrium geometries, the new model outperforms CCSD. It also accurately describes the massively correlated states encountered when dissociating hydrogen lattices, a proxy for the metal-insulator transition, and the fully dissociated system is treated exactly.
Communication: Spectral representation of the Lamb shift for atomic and molecular calculations
Authors: Dyall Kenneth G.
Published: July 2013

A spectral representation of the self-energy based on hydrogenic atomic data is examined for its usefulness to evaluate the self-energy of many-electron atoms, and thus its potential for molecular calculations. Use of the limited hydrogenic data with a diagonal projection overestimates the valence self-energy by an order of magnitude. The same diagonal projection for the vacuum polarization produces a similar overestimate, but a full projection produces values that are within a factor of 2 of the exact value, as does a density-fitting procedure.
Giant asymmetric transmission of circular polarization in layer-by-layer chiral metamaterials
Authors: Wu Lin , Yang Zhenyu , Cheng Yongzhi , Zhao Ming , Gong Rongzhou , Zheng Yu , Duan Ji'an , Yuan Xiuhua
Published: July 2013

In this paper, two kinds of bi-layered chiral metamaterials were proposed to enhance the asymmetric transmission effects for circular polarized electromagnetic waves which are only found in planar chiral metamaterials according to previous studies. It was found that the magnitude of the asymmetric transmission parameters mainly depends on the distances between the two metal layers. With appropriate distance, the asymmetric transmission parameter for circular polarized electromagnetic waves can increase to 0.6. Moreover, both proposed configurations show no asymmetric transmission for linear polarized electromagnetic waves which is widely studied in other bi-layered metamaterials.
Ultra-wide hysteresis frequency bistability in vertical cavity surface emitting lasers subject to orthogonal optical injection
Authors: Qader Abdulqader A. , Hong Yanhua , Alan Shore K.
Published: July 2013

We report experimental observations of an ultra-wide frequency hysteresis in vertical cavity surface emitting lasers subject to orthogonal optical injection. Polarization bistability and its associated hysteresis are studied by increasing and decreasing the frequency detuning for a fixed injection power when the device operated at high bias current I > 2Ith. The results show that an ultra-wide hysteresis width of about 155 GHz is obtained for positive frequency detuning. The width of the frequency hysteresis is more than four times larger than all previously reported widths.
Interface accommodation mechanism for weakly interacting epitaxial systems
Authors: Danescu A. , Gobaut B. , Penuelas J. , Grenet G. , Favre-Nicolin V. , Blanc N. , Zhou T. , Renaud G. , Saint-Girons G.
Published: July 2013

We report here an interface accommodation mechanism observed by using in situ grazing incidence X-ray diffraction in the very early stages of Ge epitaxial growth on SrTiO3. This mechanism leads to interface-localized misfit accommodation and involves two regimes: very early dislocation emergence followed by a damped collective oscillatory lattice parameter evolution. We show that this behavior is compatible with the simplest nonlinear Frenkel-Kontorova model assuming the weak elastic-chain/substrate interaction.
Economic repercussions of fisheries-induced evolution
Authors: Eikeset Anne Maria , Richter Andries , Dunlop Erin S. , Dieckmann Ulf , Stenseth Nils Chr.
Published: July 2013

Fish stocks experiencing high fishing mortality show a tendency to mature earlier and at a smaller size, which may have a genetic component and therefore long-lasting economic and biological effects. To date, the economic effects of such ecoevolutionary dynamics have not been empirically investigated. Using 70 y of data, we develop a bioeconomic model for Northeast Arctic cod to compare the economic yield in a model in which life-history traits can vary only through phenotypic plasticity with a model in which, in addition, genetic changes can occur. We find that evolutionary changes toward faster growth and earlier maturation occur consistently even if a stock is optimally managed. However, if a stock is managed optimally, the evolutionary changes actually increase economic yield because faster growth and earlier maturation raise the stock’s productivity. The optimal fishing mortality is almost identical for the evolutionary and nonevolutionary model and substantially lower than what it has been historically. Therefore, the costs of ignoring evolution under optimal management regimes are negligible. However, if fishing mortality is as high as it has been historically, evolutionary changes may result in economic losses, but only if the fishery is selecting for medium-sized individuals. Because evolution facilitates growth, the fish are younger and still immature when they are susceptible to getting caught, which outweighs the increase in productivity due to fish spawning at an earlier age.
Community dynamics and ecosystem simplification in a high-CO
2
ocean
Authors: Kroeker Kristy J. , Gambi Maria Cristina , Micheli Fiorenza
Published: July 2013

Disturbances are natural features of ecosystems that promote variability in the community and ultimately maintain diversity. Although it is recognized that global change will affect environmental disturbance regimes, our understanding of the community dynamics governing ecosystem recovery and the maintenance of functional diversity in future scenarios is very limited. Here, we use one of the few ecosystems naturally exposed to future scenarios of environmental change to examine disturbance and recovery dynamics. We examine the recovery patterns of marine species from a physical disturbance across different acidification regimes caused by volcanic CO
2
vents. Plots of shallow rocky reef were cleared of all species in areas of ambient, low, and extreme low pH that correspond to near-future and extreme scenarios for ocean acidification. Our results illustrate how acidification decreases the variability of communities, resulting in homogenization and reduced functional diversity at a landscape scale. Whereas the recovery trajectories in ambient pH were highly variable and resulted in a diverse range of assemblages, recovery was more predictable with acidification and consistently resulted in very similar algal-dominated assemblages. Furthermore, low pH zones had fewer signs of biological disturbance (primarily sea urchin grazing) and increased recovery rates of the dominant taxa (primarily fleshy algae). Together, our results highlight how environmental change can cause ecosystem simplification via environmentally mediated changes in community dynamics in the near future, with cascading impacts on functional diversity and ecosystem function.
Perception of conserved pathogen elicitors at the plasma membrane leads to relocalization of the
Arabidopsis
PEN3 transporter
Authors: Underwood William , Somerville Shauna C.
Published: July 2013

The
Arabidopsis
PENETRATION RESISTANCE 3 (PEN3) ATP binding cassette transporter participates in nonhost resistance to fungal and oomycete pathogens and is required for full penetration resistance to the barley powdery mildew
Blumeria graminis
f. sp.
hordei
. PEN3 resides in the plasma membrane and is recruited to sites of attempted penetration by invading fungal appressoria, where the transporter shows strong focal accumulation. We report that recruitment of PEN3 to sites of pathogen detection is triggered by perception of pathogen-associated molecular patterns, such as flagellin and chitin. PEN3 recruitment requires the corresponding pattern recognition receptors but does not require the BAK1 coreceptor. Pathogen- and pathogen-associated molecular pattern-induced focal accumulation of PEN3 and the PENETRATION RESISTANCE 1 (PEN1) syntaxin show differential sensitivity to specific pharmacological inhibitors, indicating distinct mechanisms for recruitment of these defense-associated proteins to the host–pathogen interface. Focal accumulation of PEN3 requires actin but is not affected by inhibitors of microtubule polymerization, secretory trafficking, or protein synthesis, and plasmolysis experiments indicate that accumulation of PEN3 occurs outside of the plasma membrane within papillae. Our results implicate pattern recognition receptors in the recruitment of defense-related proteins to sites of pathogen detection. Additionally, the process through which PEN3 is recruited to the host–pathogen interface is independent of new protein synthesis and BFA-sensitive secretory trafficking events, suggesting that existing PEN3 is redirected through an unknown trafficking pathway to sites of pathogen detection for export into papillae.
Molecule-hugging graphene nanopores
Authors: Garaj Slaven , Liu Song , Golovchenko Jene A. , Branton Daniel
Published: July 2013

It has recently been recognized that solid-state nanopores in single-atomic-layer graphene membranes can be used to electronically detect and characterize single long charged polymer molecules. We have now fabricated nanopores in single-layer graphene that are closely matched to the diameter of a double-stranded DNA molecule. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were experimentally explored and theoretically modeled. Our experiments show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating molecule’s outer diameter. Such atomically short graphene nanopores can also resolve nanoscale-spaced molecular structures along the length of a polymer, but do so with greatest sensitivity only when the pore and molecule diameters are closely matched. Modeling confirms that our most closely matched pores have an inherent resolution of ≤0.6 nm along the length of the molecule.
Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells
Authors: Kim Jae-Young , Welsh Eric A. , Oguz Umut , Fang Bin , Bai Yun , Kinose Fumi , Bronk Crystina , Remsing Rix Lily L. , Beg Amer A. , Rix Uwe , Eschrich Steven A. , Koomen John M. , Haura Eric B.
Published: July 2013

TANK-binding kinase 1 (TBK1) has emerged as a novel therapeutic target for unspecified subset of lung cancers. TBK1 reportedly mediates prosurvival signaling by activating NF-κB and AKT. However, we observed that TBK1 knockdown also decreased viability of cells expressing constitutively active NF-κB and interferon regulatory factor 3. Basal phospho-AKT level was not reduced after TBK1 knockdown in TBK1-sensitive lung cancer cells, implicating that TBK1 mediates unknown survival mechanisms. To gain better insight into TBK1 survival signaling, we searched for altered phosphoproteins using mass spectrometry following RNAi-mediated TBK1 knockdown. In total, we identified 2,080 phosphoproteins (4,621 peptides), of which 385 proteins (477 peptides) were affected after TBK1 knockdown. A view of the altered network identified a central role of Polo-like kinase 1 (PLK1) and known PLK1 targets. We found that TBK1 directly phosphorylated PLK1 in vitro. TBK1 phosphorylation was induced at mitosis, and loss of TBK1 impaired mitotic phosphorylation of PLK1 in TBK1-sensitive lung cancer cells. Furthermore, lung cancer cell sensitivity to TBK1 was highly correlated with sensitivity to pharmacological PLK inhibition. We additionally found that TBK1 knockdown decreased metadherin phosphorylation at Ser-568. Metadherin was associated with poor outcome in lung cancer, and loss of metadherin caused growth inhibition and apoptosis in TBK1-sensitive lung cancer cells. These results collectively revealed TBK1 as a mitosis regulator through activation of PLK1 and also suggested metadherin as a putative TBK1 downstream effector involved in lung cancer cell survival.
Transducin translocation contributes to rod survival and enhances synaptic transmission from rods to rod bipolar cells
Authors: Majumder Anurima , Pahlberg Johan , Boyd Kimberly K. , Kerov Vasily , Kolandaivelu Saravanan , Ramamurthy Visvanathan , Sampath Alapakkam P. , Artemyev Nikolai O.
Published: July 2013

In rod photoreceptors, several phototransduction components display light-dependent translocation between cellular compartments. Notably, the G protein transducin translocates from rod outer segments to inner segments/spherules in bright light, but the functional consequences of translocation remain unclear. We generated transgenic mice where light-induced transducin translocation is impaired. These mice exhibited slow photoreceptor degeneration, which was prevented if they were dark-reared. Physiological recordings showed that control and transgenic rods and rod bipolar cells displayed similar sensitivity in darkness. After bright light exposure, control rods were more strongly desensitized than transgenic rods. However, in rod bipolar cells, this effect was reversed; transgenic rod bipolar cells were more strongly desensitized than control. This sensitivity reversal indicates that transducin translocation in rods enhances signaling to rod bipolar cells. The enhancement could not be explained by modulation of inner segment conductances or the voltage sensitivity of the synaptic Ca
2+
current, suggesting interactions of transducin with the synaptic machinery.
CTGF antagonism with mAb FG-3019 enhances chemotherapy response without increasing drug delivery in murine ductal pancreas cancer
Authors: Neesse Albrecht , Frese Kristopher K. , Bapiro Tashinga E. , Nakagawa Tomoaki , Sternlicht Mark D. , Seeley Todd W. , Pilarsky Christian , Jodrell Duncan I. , Spong Suzanne M. , Tuveson David A.
Published: July 2013

Pancreatic ductal adenocarcinoma (PDA) is characterized by abundant desmoplasia and poor tissue perfusion. These features are proposed to limit the access of therapies to neoplastic cells and blunt treatment efficacy. Indeed, several agents that target the PDA tumor microenvironment promote concomitant chemotherapy delivery and increased antineoplastic response in murine models of PDA. Prior studies could not determine whether chemotherapy delivery or microenvironment modulation per se were the dominant features in treatment response, and such information could guide the optimal translation of these preclinical findings to patients. To distinguish between these possibilities, we used a chemical inhibitor of cytidine deaminase to stabilize and thereby artificially elevate gemcitabine levels in murine PDA tumors without disrupting the tumor microenvironment. Additionally, we used the FG-3019 monoclonal antibody (mAb) that is directed against the pleiotropic matricellular signaling protein connective tissue growth factor (CTGF/CCN2). Inhibition of cytidine deaminase raised the levels of activated gemcitabine within PDA tumors without stimulating neoplastic cell killing or decreasing the growth of tumors, whereas FG-3019 increased PDA cell killing and led to a dramatic tumor response without altering gemcitabine delivery. The response to FG-3019 correlated with the decreased expression of a previously described promoter of PDA chemotherapy resistance, the X-linked inhibitor of apoptosis protein. Therefore, alterations in survival cues following targeting of tumor microenvironmental factors may play an important role in treatment responses in animal models, and by extension in PDA patients.
Comparison of geomechanical deformation induced by megatonne-scale CO
2
storage at Sleipner, Weyburn, and In Salah
Authors: Verdon James P. , Kendall J.-Michael , Stork Anna L. , Chadwick R. Andy , White Don J. , Bissell Rob C.
Published: July 2013

Significance

The economic and political viability of carbon capture and sequestration (CCS) is dependent on the secure storage of CO
2
in subsurface geologic reservoirs. A key leakage risk is that posed by geomechanical deformation generating fractures in otherwise sealing caprocks. This study examines this risk, comparing and contrasting deformation induced at three large-scale CCS sites—Sleipner (Norwegian North Sea), Weyburn (Canada), and In Salah (Algeria). These sites show very different geomechanical responses, highlighting the importance of systematic geomechanical appraisal prior to injection, and comprehensive, multifaceted monitoring during injection at any future large-scale CCS operations.
Spatiotemporal control and superselectivity in supramolecular polymers using multivalency
Authors: Albertazzi Lorenzo , Martinez-Veracoechea Francisco J. , Leenders Christianus M. A. , Voets Ilja K. , Frenkel Daan , Meijer E. W.
Published: July 2013

Multivalency has an important but poorly understood role in molecular self-organization. We present the noncovalent synthesis of a multicomponent supramolecular polymer in which chemically distinct monomers spontaneously coassemble into a dynamic, functional structure. We show that a multivalent recruiter is able to bind selectively to one subset of monomers (receptors) and trigger their clustering along the self-assembled polymer, behavior that mimics raft formation in cell membranes. This phenomenon is reversible and affords spatiotemporal control over the monomer distribution inside the supramolecular polymer by superselective binding of single-strand DNA to positively charged receptors. Our findings reveal the pivotal role of multivalency in enabling structural order and nonlinear recognition in water-soluble supramolecular polymers, and it offers a design principle for functional, structurally defined supramolecular architectures.
CD22 ligand-binding and signaling domains reciprocally regulate B-cell Ca
2+
signaling
Authors: Müller Jennifer , Obermeier Ingrid , Wöhner Miriam , Brandl Carolin , Mrotzek Sarah , Angermüller Sieglinde , Maity Palash C. , Reth Michael , Nitschke Lars
Published: July 2013

A high proportion of human B cells carry B-cell receptors (BCRs) that are autoreactive. Inhibitory receptors such as CD22 can downmodulate autoreactive BCR responses. With its extracellular domain, CD22 binds to sialic acids in α2,6 linkages
in cis
, on the surface of the same B cell or
in trans
, on other cells. Sialic acids are self ligands, as they are abundant in vertebrates, but are usually not expressed by pathogens. We show that
cis-
ligand binding of CD22 is crucial for the regulation of B-cell Ca
2+
signaling by controlling the CD22 association to the BCR. Mice with a mutated CD22 ligand-binding domain of CD22 showed strongly reduced Ca
2+
signaling. In contrast, mice with mutated CD22 immunoreceptor tyrosine-based inhibition motifs have increased B-cell Ca
2+
responses, increased B-cell turnover, and impaired survival of the B cells. Thus, the CD22 ligand-binding domain has a crucial function in regulating BCR signaling, which is relevant for controlling autoimmunity.
Recycling rice husks for high-capacity lithium battery anodes
Authors: Jung Dae Soo , Ryou Myung-Hyun , Sung Yong Joo , Park Seung Bin , Choi Jang Wook
Published: July 2013

The rice husk is the outer covering of a rice kernel and protects the inner ingredients from external attack by insects and bacteria. To perform this function while ventilating air and moisture, rice plants have developed unique nanoporous silica layers in their husks through years of natural evolution. Despite the massive amount of annual production near 10
8
tons worldwide, so far rice husks have been recycled only for low-value agricultural items. In an effort to recycle rice husks for high-value applications, we convert the silica to silicon and use it for high-capacity lithium battery anodes. Taking advantage of the interconnected nanoporous structure naturally existing in rice husks, the converted silicon exhibits excellent electrochemical performance as a lithium battery anode, suggesting that rice husks can be a massive resource for use in high-capacity lithium battery negative electrodes.
Targeted genetic dependency screen facilitates identification of actionable mutations in FGFR4, MAP3K9, and PAK5 in lung cancer
Authors: Fawdar Shameem , Trotter Eleanor W. , Li Yaoyong , Stephenson Natalie L. , Hanke Franziska , Marusiak Anna A. , Edwards Zoe C. , Ientile Sara , Waszkowycz Bohdan , Miller Crispin J. , Brognard John
Published: July 2013

Approximately 70% of patients with non–small-cell lung cancer present with late-stage disease and have limited treatment options, so there is a pressing need to develop efficacious targeted therapies for these patients. This remains a major challenge as the underlying genetic causes of ∼50% of non–small-cell lung cancers remain unknown. Here we demonstrate that a targeted genetic dependency screen is an efficient approach to identify somatic cancer alterations that are functionally important. By using this approach, we have identified three kinases with gain-of-function mutations in lung cancer, namely FGFR4, MAP3K9, and PAK5. Mutations in these kinases are activating toward the ERK pathway, and targeted depletion of the mutated kinases inhibits proliferation, suppresses constitutive activation of downstream signaling pathways, and results in specific killing of the lung cancer cells. Genomic profiling of patients with lung cancer is ushering in an era of personalized medicine; however, lack of actionable mutations presents a significant hurdle. Our study indicates that targeted genetic dependency screens will be an effective strategy to elucidate somatic variants that are essential for lung cancer cell viability.
Torins are potent antimalarials that block replenishment of
Plasmodium
liver stage parasitophorous vacuole membrane proteins
Authors: Hanson Kirsten K. , Ressurreição Ana S. , Buchholz Kathrin , Prudêncio Miguel , Herman-Ornelas Jonathan D. , Rebelo Maria , Beatty Wandy L. , Wirth Dyann F. , Hänscheid Thomas , Moreira Rui , Marti Matthias , Mota Maria M.
Published: July 2013

Significance

Plasmodium
parasites have two distinct intracellular growth stages inside the mammalian host—the first stage, which is clinically silent, in liver hepatocytes, and the second, which causes the symptoms of malaria, in red blood cells. This study reports the discovery of a class of antimalarial compounds called torins, which are extremely potent inhibitors of both intracellular stages of
Plasmodium
. We show that torins block trafficking of liver stage parasite proteins to the physical host–parasite interface, called the parasitophorous vacuole membrane (PVM), and that without continuous trafficking of PVM-resident proteins, the parasite is subject to elimination by its host hepatocyte.