bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian ensemble refinement by replica simulations and reweighting
Authors: Hummer Gerhard , Köfinger Jürgen
Published: December 2015

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy “ensemble refinement of SAXS” (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the “Bayesian inference of ensembles” method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.
Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)
Authors: Vögele Martin , Holm Christian , Smiatek Jens
Published: December 2015

We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.
Thermal stability of an InAlN/GaN heterostructure grown on silicon by metal-organic chemical vapor deposition
Authors: Watanabe Arata , Freedsman Joseph J. , Urayama Yuya , Christy Dennis , Egawa Takashi
Published: December 2015

The thermal stabilities of metal-organic chemical vapor deposition-grown lattice-matched InAlN/GaN/Si heterostructures have been reported by using slower and faster growth rates for the InAlN barrier layer in particular. The temperature-dependent surface and two-dimensional electron gas (2-DEG) properties of these heterostructures were investigated by means of atomic force microscopy, photoluminescence excitation spectroscopy, and electrical characterization. Even at the annealing temperature of 850 °C, the InAlN layer grown with a slower growth rate exhibited a smooth surface morphology that resulted in excellent 2-DEG properties for the InAlN/GaN heterostructure. As a result, maximum values for the drain current density (IDS,max) and transconductance (gm,max) of 1.5 A/mm and 346 mS/mm, respectively, were achieved for the high-electron-mobility transistor (HEMT) fabricated on this heterostructure. The InAlN layer grown with a faster growth rate, however, exhibited degradation of the surface morphology at an annealing temperature of 850 °C, which caused compositional in-homogeneities and impacted the 2-DEG properties of the InAlN/GaN heterostructure. Additionally, an HEMT fabricated on this heterostructure yielded lower IDS,max and gm,max values of 1 A/mm and 210 mS/mm, respectively.
Correlating hydrodynamic radii with that of two-dimensional nanoparticles
Authors: Yue Yuan , Kan Yuwei , Choi Hyunho , Clearfield Abraham , Liang Hong
Published: December 2015

Dynamic light scattering (DLS) is one of the most adapted methods to measure the size of nanoparticles, as referred to the hydrodynamic radii (Rh). However, the Rh represents only that of three-dimensional spherical nanoparticles. In the present research, the size of two-dimensional (2D) nanoparticles of yttrium oxide (Y2O3) and zirconium phosphate (ZrP) was evaluated through comparing their hydrodynamic diameters via DLS with lateral sizes obtained using scanning and transmission electron microscopy. We demonstrate that the hydrodynamic radii are correlated with the lateral sizes of both square and circle shaped 2D nanoparticles. Two proportional coefficients, i.e., correcting factors, are proposed for the Brownian motion status of 2D nanoparticles. The correction is possible by simplifying the calculation of integrals in the case of small thickness approximation. The correcting factor has great significance for investigating the translational diffusion behavior of 2D nanoparticles in a liquid and in effective and low-cost measurement in terms of size and morphology of shape-specific nanoparticles.
Distributions of experimental protein structures on coarse-grained free energy landscapes
Authors: Sankar Kannan , Liu Jie , Wang Yuan , Jernigan Robert L.
Published: December 2015

Predicting conformational changes of proteins is needed in order to fully comprehend functional mechanisms. With the large number of available structures in sets of related proteins, it is now possible to directly visualize the clusters of conformations and their conformational transitions through the use of principal component analysis. The most striking observation about the distributions of the structures along the principal components is their highly non-uniform distributions. In this work, we use principal component analysis of experimental structures of 50 diverse proteins to extract the most important directions of their motions, sample structures along these directions, and estimate their free energy landscapes by combining knowledge-based potentials and entropy computed from elastic network models. When these resulting motions are visualized upon their coarse-grained free energy landscapes, the basis for conformational pathways becomes readily apparent. Using three well-studied proteins, T4 lysozyme, serum albumin, and sarco-endoplasmic reticular Ca2+ adenosine triphosphatase (SERCA), as examples, we show that such free energy landscapes of conformational changes provide meaningful insights into the functional dynamics and suggest transition pathways between different conformational states. As a further example, we also show that Monte Carlo simulations on the coarse-grained landscape of HIV-1 protease can directly yield pathways for force-driven conformational changes.
On the connection between nonmonotonic taste behavior and molecular conformation in solution: The case of rebaudioside-A
Authors: Chopade Prashant D. , Sarma Bipul , Santiso Erik E. , Simpson Jeffrey , Fry John C. , Yurttas Nese , Biermann Kari L. , Chen Jie , Trout Bernhardt L. , Myerson Allan S.
Published: December 2015

The diterpene steviol glycoside, rebaudioside A, is a natural high potency non-caloric sweetener extracted from the leaves of Stevia rebaudiana. This compound shows a parabolic change in sweet taste intensity with temperature which contrasts with the general finding for other synthetic or natural sweeteners whose sweet taste increases with temperature. The nonmonotonic taste behavior was determined by sensory analysis using large taste panels. The conformational landscape of rebaudioside A was established at a range of temperatures by means of nuclear magnetic resonance and molecular dynamics simulation. The relationship between various conformations and the observed sweetness of rebaudioside A is described.
Interpretation of thermoreflectance measurements with a two-temperature model including non-surface heat deposition
Authors: Regner K. T. , Wei L. C. , Malen J. A.
Published: December 2015

We develop a solution to the two-temperature diffusion equation in axisymmetric cylindrical coordinates to model heat transport in thermoreflectance experiments. Our solution builds upon prior solutions that account for two-channel diffusion in each layer of an N-layered geometry, but adds the ability to deposit heat at any location within each layer. We use this solution to account for non-surface heating in the transducer layer of thermoreflectance experiments that challenge the timescales of electron-phonon coupling. A sensitivity analysis is performed to identify important parameters in the solution and to establish a guideline for when to use the two-temperature model to interpret thermoreflectance data. We then fit broadband frequency domain thermoreflectance (BB-FDTR) measurements of SiO2 and platinum at a temperature of 300 K with our two-temperature solution to parameterize the gold/chromium transducer layer. We then refit BB-FDTR measurements of silicon and find that accounting for non-equilibrium between electrons and phonons in the gold layer does lessen the previously observed heating frequency dependence reported in Regner et al. [Nat. Commun. 4, 1640 (2013)] but does not completely eliminate it. We perform BB-FDTR experiments on silicon with an aluminum transducer and find limited heating frequency dependence, in agreement with time domain thermoreflectance results. We hypothesize that the discrepancy between thermoreflectance measurements with different transducers results in part from spectrally dependent phonon transmission at the transducer/silicon interface.
Negative differential mobility for negative carriers as revealed by space charge measurements on crosslinked polyethylene insulated model cables
Authors: Teyssedre G. , Vu T. T. N. , Laurent C.
Published: December 2015

Among features observed in polyethylene materials under relatively high field, space charge packets, consisting in a pulse of net charge that remains in the form of a pulse as it crosses the insulation, are repeatedly observed but without complete theory explaining their formation and propagation. Positive charge packets are more often reported, and the models based on negative differential mobility(NDM) for the transport of holes could account for some charge packets phenomenology. Conversely, NDM for electrons transport has never been reported so far. The present contribution reports space charge measurements by pulsed electroacoustic method on miniature cables that are model of HVDC cables. The measurements were realized at room temperature or with a temperature gradient of 10 °C through the insulation under DC fields on the order 30–60 kV/mm. Space charge results reveal systematic occurrence of a negative front of charges generated at the inner electrode that moves toward the outer electrode at the beginning of the polarization step. It is observed that the transit time of the front of negative charge increases, and therefore the mobility decreases, with the applied voltage. Further, the estimated mobility, in the range 10−14–10−13 m2 V−1 s−1 for the present results, increases when the temperature increases for the same condition of applied voltage. The features substantiate the hypothesis of negative differential mobility used for modelling space charge packets.
Non-volatile polarization switch of magnetic domain wall velocity
Authors: Huang Z. , Stolichnov I. , Bernand-Mantel A. , Schott Marine , Auffret S. , Gaudin G. , Pizzini S. , Ranno L. , Setter N.
Published: December 2015

Controlled propagation speed of individual magnetic domains in metal channels at the room temperature is obtained via the non-volatile field effect associated with the switchable polarization of P(VDF-TrFE) (polyvinylidene fluoride-trifluoroethylene) ferroelectric polymer. Polarization domains directly written using conducting atomic force microscope probe locally accelerate/decelerate the magnetic domains in the 0.6 nm thick Co film. The change of the magnetic domain wall velocity is consistent with the magnetic anisotropy energy modulation through the polarization upward/downward orientation. Excellent retention is observed. The demonstrated local non-destructive and reversible change of magnetic properties via rewritable patterning of ferroelectric domains could be attractive for exploring the ultimate limit of miniaturization in devices based on ferromagnetic/ferroelectric bilayers.
High power continuous operation of a widely tunable quantum cascade laser with an integrated amplifier
Authors: Slivken S. , Sengupta S. , Razeghi M.
Published: December 2015

Wide electrical tuning and high continuous output power is demonstrated from a single mode quantum cascade laser emitting at a wavelength near 4.8 μm. This is achieved in a space efficient manner by integrating an asymmetric sampled grating distributed feedback tunable laser with an optical amplifier. An initial demonstration of high peak power operation in pulsed mode is demonstrated first, with >5 W output over a 270 nm (113 cm−1) spectral range. Refinement of the geometry leads to continuous operation with a single mode spectral coverage of 300 nm (120 cm−1) and a maximum continuous power of 1.25 W. The output beam is shown to be nearly diffraction-limited, even at high amplifier current.
Nanostructure induced changes in lifetime and enhanced second-harmonic response of organic-plasmonic hybrids
Authors: Leißner Till , Kostiučenko Oksana , Brewer Jonathan R. , Rubahn Horst-Günter , Fiutowski Jacek
Published: December 2015

In this letter we show that the optical response of organic nanofibers, grown from functionalized para-quaterphenylene molecules, can be controlled by forming organic-plasmonic hybrid systems. The interaction between nanofibers and supporting regular arrays of nanostructures leads to a strongly enhanced second harmonic response. At the same time, the fluorescence lifetime of the nanofibers is reduced from 0.32 ns for unstructured gold films to 0.22 ns for gold nanosquare arrays, demonstrating efficient organic–plasmonic interaction. To study the origin of these effects, we applied two-photon laser scanning microscopy and fluorescence lifetime imaging microscopy. These findings provide an effective approach for plasmon-enhanced second-harmonic generation at the nanoscale, which is attractive for nanophotonic circuitry.
Non-axisymmetric equilibrium reconstruction of a current-carrying stellarator using external magnetic and soft x-ray inversion radius measurements
Authors: Ma X. , Maurer D. A. , Knowlton S. F. , ArchMiller M. C. , Cianciosa M. R. , Ennis D. A. , Hanson J. D. , Hartwell G. J. , Hebert J. D. , Herfindal J. L. , Pandya M. D. , Roberds N. A. , Traverso P. J.
Published: December 2015

Non-axisymmetric free-boundary equilibrium reconstructions of stellarator plasmas are performed for discharges in which the magnetic configuration is strongly modified by ohmically driven plasma current. These studies were performed on the compact toroidal hybrid device using the V3FIT reconstruction code with a set of 50 magnetic diagnostics external to the plasma. With the assumption of closed magnetic flux surfaces, the reconstructions using external magnetic measurements allow accurate estimates of the net toroidal flux within the last closed flux surface, the edge safety factor, and the plasma shape of these highly non-axisymmetric plasmas. The inversion radius of standard sawteeth is used to infer the current profile near the magnetic axis; with external magnetic diagnostics alone, the current density profile is imprecisely reconstructed.
Spatially resolved measurements of two-dimensional turbulent structures in DIII-D plasmas
Authors: Zemedkun S. E. , Che S. , Chen Y. , Domier C. W. , Luhmann N. C. , Munsat T. , Parker S. E. , Tobias B. , Wan W. , Yu L.
Published: December 2015

Two-dimensional observations of spatially coherent electron temperature fluctuations at drift-wave scales (k ∼ 1 cm−1) have been made using the electron cyclotron emission imaging diagnostic on the DIII-D tokamak. These measurements enable the extraction of spectral properties, including poloidal dispersion relations. Temperature fluctuation levels are found to be Tẽ/⟨Te⟩=1.2%, and the phase velocity of the fluctuations is found to be constant across frequencies, consistent with modes having real frequencies low compared to the rotation-induced Doppler shifts. Comparisons with radially global linear gyrokinetic simulations suggest that the observed modes may be trapped electron modes.
Intense terahertz field effects on photoexcited carrier dynamics in gated graphene
Authors: Hafez Hassan A. , Lévesque Pierre L. , Al-Naib Ibraheem , Dignam Marc M. , Chai Xin , Choubak Saman , Desjardins Patrick , Martel Richard , Ozaki Tsuneyuki
Published: December 2015

We study nonlinear effects of intense terahertz (THz) field on photoexcited carrier dynamics in gated monolayer graphene. By employing optical-pump/intense-THz-probe spectroscopy on lightly doped graphene, we observe a crossover from negative to positive photo-induced THz differential transmission as the THz probe field is increased. We attribute this qualitative change in the response to a crossover from a regime where the photo-induced increase in the carrier density dominates the differential response to one where a THz-field-induced increase in the scattering rate dominates.
Revisiting the inelastic electron tunneling spectroscopy of single hydrogen atom adsorbed on the Cu(100) surface
Authors: Jiang Zhuoling , Wang Hao , Sanvito Stefano , Hou Shimin
Published: December 2015

Inelastic electron tunneling spectroscopy (IETS) of a single hydrogen atom on the Cu(100) surface in a scanning tunneling microscopy (STM) configuration has been investigated by employing the non-equilibrium Green’s function formalism combined with density functional theory. The electron-vibration interaction is treated at the level of lowest order expansion. Our calculations show that the single peak observed in the previous STM-IETS experiments is dominated by the perpendicular mode of the adsorbed H atom, while the parallel one only makes a negligible contribution even when the STM tip is laterally displaced from the top position of the H atom. This propensity of the IETS is deeply rooted in the symmetry of the vibrational modes and the characteristics of the conduction channel of the Cu-H-Cu tunneling junction, which is mainly composed of the 4s and 4pz atomic orbitals of the Cu apex atom and the 1s orbital of the adsorbed H atom. These findings are helpful for deepening our understanding of the propensity rules for IETS and promoting IETS as a more popular spectroscopic tool for molecular devices.
Actinide chemistry using singlet-paired coupled cluster and its combinations with density functionals
Authors: Garza Alejandro J. , Sousa Alencar Ana G. , Scuseria Gustavo E.
Published: December 2015

Singlet-paired coupled cluster doubles (CCD0) is a simplification of CCD that relinquishes a fraction of dynamic correlation in order to be able to describe static correlation. Combinations of CCD0 with density functionals that recover specifically the dynamic correlation missing in the former have also been developed recently. Here, we assess the accuracy of CCD0 and CCD0+DFT (and variants of these using Brueckner orbitals) as compared to well-established quantum chemical methods for describing ground-state properties of singlet actinide molecules. The f0 actinyl series (UO22+, NpO23+, PuO24+), the isoelectronic NUN, and thorium (ThO, ThO2+) and nobelium (NoO, NoO2) oxides are studied.
Dynamic clustering equivalent model of wind turbines based on spanning tree
Authors: Teng Weijun , Wang Xifan , Meng Yongqing , Shi Wenhui
Published: December 2015

With the increasingly high penetration of wind energy, the dynamic influence of wind farms (WFs) on operation security of power systems gains much more attention. Consisting of hundreds of wind turbines (WTs), dynamic analysis on a detailed model of WFs is complicated and time consuming. In this paper, a simplified dynamic equivalent model of WFs based on the spanning tree (ST) is proposed. First, the clustering method based on the growing ST is first applied to the dynamic equivalent of WFs. Second, according to the mathematical model of doubly fed induction generator (DFIG) and permanent magnetic synchronous generator (PMSG), clustering variables of DFIG and PMSG are classified into internal variables and external variables, reflecting the dynamic characteristics of WTs. Finally, based on the actual WFs and actual wind speed data, simulations were employed in DIGSILENT/PowerFactory. The results demonstrate that the proposed model is able to precisely reflect the dynamic characteristics of WFs in both fault condition and fluctuation of wind speed. With time reducing, the effectiveness and feasibility of the proposed model has been verified.
Background limited mid-infrared photodetection with photovoltaic HgTe colloidal quantum dots
Authors: Guyot-Sionnest Philippe , Roberts John Andris
Published: December 2015

The photovoltaic response of thin films of HgTe colloidal quantum dots in the 3–5 μm range is observed. With no applied bias, internal quantum efficiency exceeding 40%, specific detectivity above 1010 Jones and microseconds response times are obtained at 140 K. The cooled devices detect the ambient thermal radiation. A detector with 5.25 μm cut-off achieves Background Limited Infrared Photodetection at 90 K.
Network analysis of photovoltaic-related Science Citation Index papers in Korea
Authors: Cho Ha Young , Kim Jae Hyun , Lee Ki Jong , Lee Sang Hyon , Park Noeon
Published: December 2015

The Korean Government continues to support the photovoltaic (PV) sector to develop high-efficiency, high-reliability PV technologies. However, considering this R&D investment the level of Korean PV technology is low. In this study, PV-related SCI (Science Citation Index) papers issued from 2009 to 2012 are investigated to understand the trends of the technology and its research network. SCI papers on dye-sensitized solar cells and organic/polymer solar cells are more common than papers on other PV related technologies. A qualitative comparative analysis is also conducted into the impact factor of the journals. Finally, social network analysis is used to investigate indicators, such as density and centrality, to help policy makers direct future R&D investment more effectively. The results reveal that USA and European countries such as Germany, the UK, and Spain published the most influential papers, while Asian countries such as China, Korea, and Japan stood out in terms of quantity. Countries and institutes with more diverse collaborations tend to publish more papers, and the network of countries is becoming stronger and more diverse, while institutes are tending to collaborate more in exclusive subgroups. Korean PV-related research is relatively high in terms of quantity and collaboration, but more effort is necessary to improve its quality and network range.
Nonlinear terahertz coherent excitation of vibrational modes of liquids
Authors: Allodi Marco A. , Finneran Ian A. , Blake Geoffrey A.
Published: December 2015

We report the first coherent excitation of intramolecular vibrational modes via the nonlinear interaction of a TeraHertz (THz) light field with molecular liquids. A terahertz-terahertz-Raman pulse sequence prepares the coherences with a broadband, high-energy, (sub)picosecond terahertz pulse, that are then measured in a terahertz Kerr effect spectrometer via phase-sensitive, heterodyne detection with an optical pulse. The spectrometer reported here has broader terahertz frequency coverage, and an increased sensitivity relative to previously reported terahertz Kerr effect experiments. Vibrational coherences are observed in liquid diiodomethane at 3.66 THz (122 cm−1), and in carbon tetrachloride at 6.50 THz (217 cm−1), in exact agreement with literature values of those intramolecular modes. This work opens the door to 2D spectroscopies, nonlinear in terahertz field, that can study the dynamics of condensed-phase molecular systems, as well as coherent control at terahertz frequencies.
Active power control of direct current smart house using electric vehicles and controllable loads
Authors: Uehara Takahiro , Matayoshi Hidehito , Noorzad Ahmad Samim , Sharma Aditya , Senjyu Tomonobu
Published: December 2015

DC smart house is receiving attention as means for the management of electric power. Since many domestic appliances are also DC devices, the DC smart house can also reduce conversion losses. Recently, the increased introduction of residential photovoltaic generators (PV) has been remarkable. However, since the output power of PV fluctuates according to weather conditions and is commonly allowed to flow into the power grid, it is difficult for the supply side to balance supply and demand. The purpose of this study is to prevent the fluctuations of the PV output power connected to the DC smart house from flowing into the power system. This paper proposes compensation methods for fluctuations in the output power of the PV as well as those caused by consumption power of uncontrollable loads. The proposed scheme achieves a stable constant active power interconnection point between the smart house and the grid by cooperative operation of Electric Vehicle (EV) and Electric Water Heater (EWH). The control scheme of both the EV and the EWH uses the H∞ control method. H∞ control improves the control performance because the gain can be regulated according to the frequency domain. The proposed scheme is tested by comparing with two other cases, of which the control group comprises no-controller for each device and Proportional-Integral (PI) controllers for each device. In the no-control scenario, these devices follow a randomly generated load profile. The effectiveness of the proposed method is verified by simulation results in the MATLAB/Simulink® environment.
Generation of valley-polarized electron beam in bilayer graphene
Authors: Park Changsoo
Published: December 2015

We propose a method to produce valley-polarized electron beams using a bilayer graphene npn junction. By analyzing the transmission properties of electrons through the junction with zigzag interface in the presence of trigonal warping, we observe that there exist a range of incident energies and barrier heights in which transmitted electrons are well polarized and collimated. From this observation and by performing numerical simulations, it is demonstrated that valley-dependent electronic currents with nearly perfect polarization can be generated. We also show that the peak-to-peak separation angle between the polarized currents is tunable either by incident energy or by barrier height each of which is controlled by using top and back gate voltages. The results can be used for constructing an electron beam splitter to produce valley-polarized currents.
Experimental determination of tunneling characteristics and dwell times from temperature dependence of Al/Al2O3/Al junctions
Authors: Patiño Edgar J. , Kelkar N. G.
Published: December 2015

Measurements of current-voltage (I-V) characteristics of a high quality Al/Al2O3/Al junction at temperatures ranging from 3.5 K to 300 K have been used to extract the barrier properties. Fitting results using Simmons's model led to a constant value of barrier width s ∼ 20.8 Å and a continuous increase in the barrier height with decreasing temperature. The latter is used to determine the energy band gap temperature dependence and average phonon frequency ω = 2.05 × 1013 s−1 in Al2O3, which adds confidence to the precision of our measurements. The barrier parameters are used to extract the temperature dependent dwell times in tunneling (τD = 3.6 × 10−16 s at mid-barrier energies) and locate resonances above the barrier.
On-chip dual-comb based on quantum cascade laser frequency combs
Authors: Villares G. , Wolf J. , Kazakov D. , Süess M. J. , Hugi A. , Beck M. , Faist J.
Published: December 2015

Dual-comb spectroscopy is emerging as an appealing application of mid-infrared frequency combs for high-resolution molecular spectroscopy, as it leverages on the unique coherence properties of frequency combs. Here, we present an on-chip dual-comb source based on mid-infrared quantum cascade laser frequency combs. Control of the combs repetition and offset frequencies is obtained by integrating micro-heaters next to each laser. We show that a full control of the dual-comb system is possible, by measuring a multi-heterodyne beating corresponding to an optical bandwidth of 32 cm−1 centered at 1330 cm−1 (7.52 μm), demonstrating that this device represents a critical step towards compact dual-comb systems.
Enhancement of terahertz radiation power from a prebunched electron beam using helical wiggler and ion-channel guiding
Authors: Hasanbeigi A. , Mehdian H. , Gomar P.
Published: December 2015

The generation of coherent Terahertz (THz) radiation from the interaction of a bunched relativistic electron beam with helical wiggler pumped is studied on a basis of fluid model. The relativistic electron beam, modulated by two laser beams, propagates through a helical wiggler with ion-channel guiding. Numerical results show that the Terahertz power increases monotonically with the increasing ion-channel frequency up to a critical point corresponding to the increase in the transverse velocity as the resonance (at ωi≅β||) is approached. The maximum THz power increases with the increasing ion-channel density, the axial velocity, and the radius of the injected beam.
Elimination of carbon vacancies in 4H-SiC employing thermodynamic equilibrium conditions at moderate temperatures
Authors: Ayedh H. M. , Nipoti R. , Hallén A. , Svensson B. G.
Published: December 2015

The carbon vacancy (VC) is a major point defect in high-purity 4H-SiC epitaxial layers limiting the minority charge carrier lifetime. In layers grown by chemical vapor deposition techniques, the VC concentration is typically in the range of 1012 cm−3, and after device processing at temperatures approaching 2000 °C, it can be enhanced by several orders of magnitude. In the present study, both as-grown layers and a high-temperature processed one have been annealed at 1500 °C and the VC concentration is demonstrated to be strongly reduced, exhibiting a value of only a few times 1011 cm−3 as determined by deep-level transient spectroscopy measurements. The value is reached already after annealing times on the order of 1 h and is evidenced to reflect thermodynamic equilibrium under C-rich ambient conditions. The physical processes controlling the kinetics for establishment of the VC equilibrium are estimated to have an activation energy below ∼3 eV and both in-diffusion of carbon interstitials and out-diffusion of VC's are discussed as candidates. This concept of VC elimination is flexible and readily integrated in a materials and device processing sequence.
Femtosecond laser induced tunable surface transformations on (111) Si aided by square grids diffraction
Authors: Han Weina , Jiang Lan , Li Xiaowei , Liu Yang , Lu Yongfeng
Published: December 2015

We report an extra freedom to modulate the femtosecond laser energy distribution to control the surface ablated structures through a copper-grid mask. Due to the reduced deposited pulse energy by changing the scanning speed or the pulse fluence, a sequential evolution of three distinctly different surface patterns with periodic distributions is formed, namely, striped ripple lines, ripple microdots, and surface modification. By changing the scanning speed, the number of the multiple dots in a lattice can be modulated. Moreover, by exploring the ablation process through the copper grid mask, it shows an abnormal enhanced ablation effect with strong dependence of the diffraction-aided fs laser ablated surface structures on polarization direction. The sensitivity shows a quasi-cosinusoid-function with a periodicity of π/2. Particularly, the connection process of striped ripple lines manifests a preferential formation direction with the laser polarization.
Note: Ultra-low birefringence dodecagonal vacuum glass cell
Authors: Brakhane Stefan , Alt Wolfgang , Meschede Dieter , Robens Carsten , Moon Geol , Alberti Andrea
Published: December 2015

We report on an ultra-low birefringence dodecagonal glass cell for ultra-high vacuum applications. The epoxy-bonded trapezoidal windows of the cell are made of SF57 glass, which exhibits a very low stress-induced birefringence. We characterize the birefringence Δn of each window with the cell under vacuum conditions, obtaining values around 10−8. After baking the cell at 150 °C, we reach a pressure below 10−10 mbar. In addition, each window is antireflection coated on both sides, which is highly desirable for quantum optics experiments and precision measurements.
Shaping the fluorescence emission by cavity plasmons in dielectric-metal core-shell resonators
Authors: Li Zhi-Qin , Zhang Chi , Gu Ping , Wan Mingjie , Zhan Peng , Chen Zhuo , Wang Zhenlin
Published: December 2015

We observe experimentally the spectral and spatial reshaping of fluorescence emission in dye-doped dielectric-metal core-shell resonators that support multipolar electric and magnetic-based cavity plasmon resonances. By comparing the experimental fluorescence spectra with analytical calculations based on Mie theory, we are able to demonstrate that the strong reshaping effects are the results of the coupling of dye molecules to those narrow-band cavity plasmon resonances. In addition, we show that the polarization of the fluorescence emission can also be modified by selectively coupling the molecules to the magnetic or electric based cavity plasmons.
Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes
Authors: Holm Christian , Gompper Gerhard , Dill Ken A.
Published: December 2015

This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.
Mitochondrial DNA analyses reveal widespread tardigrade diversity in Antarctica
Authors: Velasco-Castrillón Alejandro , McInnes Sandra J. , Schultz Mark B. , Arróniz-Crespo María , D'Haese Cyrille A. , Gibson John A. E. , Adams Byron J. , Page Timothy J. , Austin Andrew D. , Cooper Steven J. B. , Stevens Mark I.
Published: December 2015

Antarctica contains some of the most challenging environmental conditions on the planet due to freezing temperatures, prolonged winters and lack of liquid water. Whereas 99.7% of Antarctica is permanently covered by ice and snow, some coastal areas and mountain ridges have remained ice-free and are able to sustain populations of microinvertebrates. Tardigrades are one of the more dominant groups of microfauna in soil and limno-terrestrial habitats, but little is known of their diversity and distribution across Antarctica. Here, we examine tardigrades sampled from across an extensive region of continental Antarctica, and analyse and compare their partial mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences with those from the Antarctic Peninsula, maritime and sub-Antarctica, Tierra del Fuego and other worldwide locations in order to recognise operational taxonomic units (OTUs). From 439 new tardigrade COI sequences, we identified 98 unique haplotypes (85 from Antarctica) belonging to Acutuncus, Diphascon, Echiniscus, Macrobiotus, Milnesium and unidentified Parachela. Operational taxonomic units were delimited by Poisson tree processes and general mixed Yule coalescent methods, resulting in 58 and 55 putative species, respectively. Most tardigrades appear to be locally endemic (i.e. restricted to a single geographic region), but some (e.g. Acutuncus antarcticus (Richters, 1904)) are widespread across continental Antarctica. Our molecular results reveal: (i) greater diversity than has previously been appreciated with distinct OTUs that potentially represent undescribed species, and (ii) a lack of connectivity between most OTUs from continental Antarctica and those from other Antarctic geographical zones.
Molecular phylogenetic analyses and morphological variation point to taxonomic problems among four genera of parasitoid doryctine wasps (Hymenoptera : Braconidae)
Authors: Gebiola Marco , Garonna Antonio P. , Bernardo Umberto , Belokobylskij Sergey A.
Published: December 2015

Doryctinae (Hymenoptera : Braconidae) is a large and diverse subfamily of parasitic wasps that has received much attention recently, with new species and genera described and phylogenies based on morphological and/or molecular data that have improved higher-level classification and species delimitation. However, the status of several genera is still unresolved, if not controversial. Here we focus on two related groups of such genera, Dendrosoter Wesmael–Caenopachys Foerster and Ecphylus Foerster–Sycosoter Picard & Lichtenstein. We integrated morphological and molecular (COI and 28S–D2 genes) evidence to highlight, by phylogenetic analyses (maximum likelihood and Bayesian) and a posteriori morphological examination, previously overlooked variation, which is here illustrated and discussed. Monophyly of Dendrosoter and Caenopachys and the presence of synapomorphic morphological characters support synonymy of Caenopachys under Dendrosoter. Low genetic differentiation and high variability for putatively diagnostic morphological characters found in both C. hartigii (Ratzeburg) and C. caenopachoides (Ruschka) supports synonymy of D. caenopachoides under D. hartigii, syn. nov. Morphological and molecular evidence together also indicate independent generic status for Sycosoter, stat. rev., which is here resurrected. This work represents a further advancement in the framework of the ongoing effort to improve systematics and classification of the subfamily Doryctinae.
Transition fronts for inhomogeneous Fisher-KPP reactions and non-local diffusion
Authors: Lim Tau Shean , Zlatoš Andrej
Published: December 2015

We prove existence of and construct transition fronts for a class of reaction-diffusion equations with spatially inhomogeneous Fisher-KPP type reactions and non-local diffusion. Our approach is based on finding these solutions as perturbations of appropriate solutions to the linearization of the PDE at zero. Our work extends a method introduced by one of us to study such questions in the case of classical diffusion.
Growth of nano-dots on the grazing-incidence mirror surface under FEL irradiation
Authors: Kozhevnikov I. V. , Buzmakov A. V. , Siewert F. , Tiedtke K. , Störmer M. , Samoylova L. , Sinn H.
Published: December 2015

A new phenomenon on X-ray optics surfaces has been observed: the growth of nano-dots (40–55 nm diameter, 8–13 nm height, 9.4 dots µm−2surface density) on the grazing-incidence mirror surface under irradiation by the free-electron laser (FEL) FLASH (5–45 nm wavelength, 3° grazing-incidence angle). With a model calculation it is shown that these nano-dots may occur during the growth of a contamination layer due to polymerization of incoming hydrocarbon molecules. The crucial factors responsible for the growth of nano-dots in the model are the incident peak intensity and the reflection angle of the beam. A reduction of the peak intensity (e.g.replacement of the FEL beam by synchrotron radiation) as well as a decrease of the incident angle by just 1° (from 3° to 2°) may result in the total disappearance of the nano-dots. The model calculations are compared with surface analysis of two FLASH mirrors.
Detector developments at DESY
Authors: Wunderer Cornelia B. , Allahgholi Aschkan , Bayer Matthias , Bianco Laura , Correa Jonathan , Delfs Annette , Göttlicher Peter , Hirsemann Helmut , Jack Stefanie , Klyuev Alexander , Lange Sabine , Marras Alessandro , Niemann Magdalena , Pithan Florian , Reza Salim , Sheviakov Igor , Smoljanin Sergej , Tennert Maximilian , Trunk Ulrich , Xia Qingqing , Zhang Jiaguo , Zimmer Manfred , Das Dipayan , Guerrini Nicola , Marsh Ben , Sedgwick Iain , Turchetta Renato , Cautero Giuseppe , Giuressi Dario , Menk Ralf , Khromova Anastasiya , Pinaroli Giovanni , Stebel Luigi , Marchal Julien , Pedersen Ulrik , Rees Nick , Steadman Paul , Sussmuth Mark , Tartoni Nicola , Yousef Hazem , Hyun HyoJung , Kim KyungSook , Rah Seungyu , Dinapoli Roberto , Greiffenberg Dominic , Mezza Davide , Mozzanica Aldo , Schmitt Bernd , Shi Xintian , Krueger Hans , Klanner Robert , Schwandt Joem , Graafsma Heinz
Published: December 2015

With the increased brilliance of state-of-the-art synchrotron radiation sources and the advent of free-electron lasers (FELs) enabling revolutionary science with EUV to X-ray photons comes an urgent need for suitable photon imaging detectors. Requirements include high frame rates, very large dynamic range, single-photon sensitivity with low probability of false positives and (multi)-megapixels. At DESY, one ongoing development project – in collaboration with RAL/STFC, Elettra Sincrotrone Trieste, Diamond, and Pohang Accelerator Laboratory – is the CMOS-based soft X-ray imager PERCIVAL. PERCIVAL is a monolithic active-pixel sensor back-thinned to access its primary energy range of 250 eV to 1 keV with target efficiencies above 90%. According to preliminary specifications, the roughly 10 cm × 10 cm, 3.5k × 3.7k monolithic sensor will operate at frame rates up to 120 Hz (commensurate with most FELs) and use multiple gains within 27 µm pixels to measure 1 to ∼100000 (500 eV) simultaneously arriving photons. DESY is also leading the development of the AGIPD, a high-speed detector based on hybrid pixel technology intended for use at the European XFEL. This system is being developed in collaboration with PSI, University of Hamburg, and University of Bonn. The AGIPD allows single-pulse imaging at 4.5 MHz frame rate into a 352-frame buffer, with a dynamic range allowing single-photon detection and detection of more than 10000 photons at 12.4 keV in the same image. Modules of 65k pixels each are configured to make up (multi)megapixel cameras. This review describes the AGIPD and the PERCIVAL concepts and systems, including some recent results and a summary of their current status. It also gives a short overview over other FEL-relevant developments where the Photon Science Detector Group at DESY is involved.
A table of geometrical ambiguities in powder indexing obtained by exhaustive search
Authors: Oishi-Tomiyasu R.
Published: December 2015

Geometrical ambiguity means the cases in which more than one powder indexing solution exists. Using a new function implemented in the powder indexing softwareCONOGRAPH, unit cells that involve geometrical ambiguity are exhaustively searched. As a result, many unknown cases are obtained, although the number of such unit cells is still rather limited. It is also proven that the number of solutions in powder auto-indexing is not always unique, but generally finite.
Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function
Authors: Prill Dragica , Juhás Pavol , Billinge Simon J. L. , Schmidt Martin U.
Published: December 2015

A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure inP1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.
Beneficial metabolic effects of selected probiotics on diet‐induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota
Authors: Alard Jeanne , Lehrter Véronique , Rhimi Moez , Mangin Irène , Peucelle Véronique , Abraham Anne‐Laure , Mariadassou Mahendra , Maguin Emmanuelle , Waligora‐Dupriet Anne‐Judith , Pot Bruno , Wolowczuk Isabelle , Grangette Corinne
Published: December 2015

Alterations in gut microbiota composition and diversity were suggested to play a role in the development of obesity, a chronic subclinical inflammatory condition. We here evaluated the impact of oral consumption of a monostrain or multi‐strain probiotic preparation in high‐fat diet‐induced obese mice. We observed a strain‐specific effect and reported dissociation between the capacity of probiotics to dampen adipose tissue inflammation and to limit body weight gain. A multi‐strain mixture was able to improve adiposity, insulin resistance and dyslipidemia through adipose tissue immune cell‐remodelling, mainly affecting macrophages. At the gut level, the mixture modified the uptake of fatty acids and restored the expression level of the short‐chain fatty acid receptor GPR43. These beneficial effects were associated with changes in the microbiota composition, such as the restoration of the abundance of Akkermansia muciniphila and Rikenellaceae and the decrease of other taxa like Lactobacillaceae. Using an in vitro gut model, we further showed that the probiotic mixture favours the production of butyrate and propionate. Our findings provide crucial clues for the design and use of more efficient probiotic preparations in obesity management and may bring new insights into the mechanisms by which host–microbe interactions govern such protective effects.