bluuebunny/crossref_metadata_2025 huggingface dataset:
Girsanov reweighting for metadynamics simulations
Authors: Donati Luca , Keller Bettina G.
Published: July 2018

Metadynamics is a computational method to explore the phase space of a molecular system. Gaussian functions are added along relevant coordinates on the fly during a molecular-dynamics simulation to force the system to escape from minima in the potential energy function. The dynamics in the resulting trajectory are however unphysical and cannot be used directly to estimate dynamical properties of the system. Girsanov reweighting is a recent method used to construct the Markov State Model (MSM) of a system subjected to an external perturbation. With the combination of these two techniques—metadynamics/Girsanov-reweighting—the unphysical dynamics in a metadynamics simulation can be reweighted to obtain the MSM of the unbiased system. We demonstrate the method on a one-dimensional diffusion process, alanine dipeptide, and the hexapeptide Val-Gly-Val-Ala-Pro-Gly (VGVAPG). The results are in excellent agreement with the MSMs obtained from direct unbiased simulations of these systems. We also apply metadynamics/Girsanov-reweighting to a β-hairpin peptide, whose dynamics is too slow to efficiently explore its phase space by direct simulation.
Phase retrieval for near-field X-ray imaging beyond linearisation or compact support
Authors: Hagemann J. , Töpperwien M. , Salditt T.
Published: July 2018

X-ray phase contrast imaging based on free space propagation relies on phase retrieval to obtain sharp images of micro- and nanoscale objects, with widespread applications in material science and biomedical research. For high resolution synchrotron experiments, phase retrieval is largely based on the single step reconstruction using the contrast transfer function approach (CTF), as introduced almost twenty years ago [Cloetens et al., Appl. Phys. Lett. 75, 2912 (1999)]. Notwithstanding its tremendous merits, this scheme makes stringent assumptions on the optical properties of the object, requiring, in particular, a weakly varying phase. In this work, we show how significant the loss in image quality becomes if these assumption are violated, and how phase retrieval can be easily improved by a simple scheme of alternating projections. Importantly, the approach demonstrated here uses the same input data and constraint sets as the conventional CTF-based phase retrieval, and is particularly well suited for the holographic regime.
Invited Article: Spectral focusing with asymmetric pulses for high-contrast pump–probe stimulated Raman scattering microscopy
Authors: Ito Terumasa , Obara Yuki , Misawa Kazuhiko
Published: July 2018

Purely label-free imaging to directly monitor small molecules in a biological organism is still challenging despite recent technical advancements. Time-resolved pump–probe coherent Raman scattering microscopy is a promising label-free approach to increase chemical specificity. However, conventional time-resolved methods involve a compromise between three conflicting requirements: high spectral resolution, low background levels, and high sensitivity. Here, we present an advanced spectral-focusing technique using asymmetric pulses produced by nonlinear chirping and demonstrate its performance in pump–probe phase-modulated stimulated Raman scattering microscopy. In addition, we report for the first time a novel frequency-scanning spectral-focusing system using tunable bandpass filters. Our concept uses the filters not only as a frequency allocation tool for the probe pulses but also as a pulse-shaping tool that provides a strong nonlinear chirp. The spectral resolution and signal-to-noise ratio are greatly improved by highly efficient time-resolved detection using asymmetric spectrally focused probe pulses. We achieve a spectral resolution of ∼25 cm−1, a reduced nonresonant background level on the order of 10−8, and a detectable concentration limit of 0.01% dimethyl sulfoxide/water solution (1.5 mM). Using this method, we demonstrate high-contrast imaging of a small-molecule drug in a tissue. These advancements will allow time-resolved coherent Raman microscopy to be used as a practical drug-imaging tool for biomedical sciences.
Invited Article: Coherent Raman and mid-IR microscopy using shaped pulses in a single-beam setup
Authors: Müller Niklas , Brückner Lukas , Motzkus Marcus
Published: July 2018

The possibility to exploit shaped ultrabroadband laser pulses for molecular coherent control offers a unique implementation of numerous nonlinear spectroscopic methods in one setup. Nonlinear processes, such as coherent Raman microscopy, second harmonic generation, or two-photon fluorescence, which have been applied in many different applications in both the material and life sciences, can be selectively addressed and optimized just by changing the phase imprinted by a programmable pulse shaper. Here, the experimental realization of this concept for multimodal nonlinear microscopy is discussed and the successful implementation of adaptive spectral focussing schemes not only for nonlinear Raman but also for difference frequency generation based mid-infrared (Mid-IR) spectroscopy using a single broadband pulse from a Ti:sapphire laser is shown. Flexible pulse shaping enables tuning of the resonance frequency and the spectral width of the excitation. By variation of the instantaneous frequency difference and the amount of chirp, the experiment can be optimized to achieve high resolution spectroscopy reaching up to 20 cm−1. Matching the resolution of the experiment with the linewidths of the sample on the other hand optimizes the contrast for imaging at high signal levels. The combination and flexible switching between Raman or mid-IR excitation for spectroscopy and microscopy is demonstrated on alkynes, polymer films, and skin tissue. The simple addition of this complementary modality to an existing nonlinear microscope is a further step toward an all-purpose laser excitation source for multimodal microscopy.
Note: Electroplating process for connectorizing superconducting NbTi cables
Authors: DeBry Kyle , Lafyatis Gregory
Published: July 2018

Experiments done at cryogenic temperatures below the 4.2 K temperature of liquid helium frequently require superconducting coaxial cables to efficiently transmit high-frequency signals while minimizing heat transfer to the experiment’s cold stage. These cables are often made of niobium-titanium (NbTi) alloy which is difficult to solder directly. This note describes a new electroplating procedure for plating NbTi coax directly with copper, which enables connector attachment matching the structural and electrical properties of standard coaxial cables. Here, a cable is first electrochemically coated with a thin oxide layer and then electroplated with copper in an acidic copper sulfate solution. The procedure has modest safety requirements and may be carried out in a standard vented laboratory fume hood.
Development of polarization consistent basis sets for spin-spin coupling constant calculations for the atoms Li, Be, Na, and Mg
Authors: Aggelund Patrick A. , Sauer Stephan P. A. , Jensen Frank
Published: July 2018

The pcJ-n basis set, optimized for spin-spin coupling constant calculations using density functional theory methods, are expanded to also include the s-block elements Li, Be, Na, and Mg, by studying several small molecules containing these elements. This is done by decontracting the underlying pc-n basis sets, followed by augmentation with additional tight functions. As was the case for the p-block elements, the convergence of the results can be significantly improved by augmentation with tight s-functions. For the p-block elements, additional tight functions of higher angular momentum were also needed, but this is not the case for the s-block elements. A search for the optimum contraction scheme is carried out using the criterion that the contraction error should be lower than the inherent error of the uncontracted pcJ-n relative to the uncontracted pcJ-4 basis set. A large search over possible contraction schemes is done for the Li2 and Na2 molecules, and based on this search contracted pcJ-n basis sets for the four atoms are recommended. This work shows that it is more difficult to contract the pcJ-n basis sets, than the underlying pc-n basis sets. However, it also shows that the pcJ-n basis sets for Li and Be can be more strongly contracted than the pcJ-n basis sets for the p-block elements. For Na and Mg, the contractions are to the same degree as for the p-block elements.
Time-resolved electron spectroscopy for chemical analysis of photodissociation: Photoelectron spectra of Fe(CO)5, Fe(CO)4, and Fe(CO)3
Authors: Leitner T. , Josefsson I. , Mazza T. , Miedema P. S. , Schröder H. , Beye M. , Kunnus K. , Schreck S. , Düsterer S. , Föhlisch A. , Meyer M. , Odelius M. , Wernet Ph.
Published: July 2018

The prototypical photoinduced dissociation of Fe(CO)5 in the gas phase is used to test time-resolved x-ray photoelectron spectroscopy for studying photochemical reactions. Upon one-photon excitation at 266 nm, Fe(CO)5 successively dissociates to Fe(CO)4 and Fe(CO)3 along a pathway where both fragments retain the singlet multiplicity of Fe(CO)5. The x-ray free-electron laser FLASH is used to probe the reaction intermediates Fe(CO)4 and Fe(CO)3 with time-resolved valence and core-level photoelectron spectroscopy, and experimental results are interpreted with ab initio quantum chemical calculations. Changes in the valence photoelectron spectra are shown to reflect changes in the valence-orbital interactions upon Fe–CO dissociation, thereby validating fundamental theoretical concepts in Fe–CO bonding. Chemical shifts of CO 3σ inner-valence and Fe 3p core-level binding energies are shown to correlate with changes in the coordination number of the Fe center. We interpret this with coordination-dependent charge localization and core-hole screening based on calculated changes in electron densities upon core-hole creation in the final ionic states. This extends the established capabilities of steady-state electron spectroscopy for chemical analysis to time-resolved investigations. It could also serve as a benchmark for how charge and spin density changes in molecular dissociation and excited-state dynamics are expressed in valence and core-level photoelectron spectroscopy.
Molecular weight dependence of chain conformation of strong polyelectrolytes
Authors: Xu Guofeng , Yang Jingfa , Zhao Jiang
Published: July 2018

Using sodium polystyrene sulfonate (NaPSS) and quarternized poly 4-vinylpyridine (QP4VP) as model systems, the chain conformation of polyelectrolytes under finite salt concentrations is investigated at a single molecular level. By fluorescence correlation spectroscopy (FCS), the hydrodynamic radius (Rh) of the samples with the molecular weight ranging more than one order of magnitude was measured. The variations of Rh as a function of molecular weight reveal the molecular weight dependence: under moderate salt concentrations (such as 10−4 and 0.1M), the shorter chains of both NaPSS and QP4VP take the rod-like conformation, while the longer chains take the coiled conformation (random coil or swelled random coil conformation, respectively). At high enough salt levels, both the charged chains take the coiled conformations. Photon counting histogram (PCH) measurements of the local pH value at the vicinity of the NaPSS chain expose the higher extent of counterion adsorption for longer chains as well as higher salt concentrations, telling that the charge regularization process is the major governing factor.
On magnetic reconnection as promising driver for future plasma propulsion systems
Authors: Cazzola Emanuele , Curreli Davide , Lapenta Giovanni
Published: July 2018

This work presents a more detailed analysis of the process of magnetic reconnection as a promising ion beam accelerator mechanism with possible applications in laboratory plasmas and, more importantly, in the plasma propulsion field. In a previous work, an introductory study on this subject was already carried out, yet under the adoption of relevant approximations, such as the limitation to 2.5D simulations and especially the use of hydrogen plasma as a propellant, whose element is rarely considered in the real scenario. Also, the analysis mainly focussed on studying the physical content of the outcomes, by leaving out the analysis of more important engineering quantities, such as the mass flow and thrust effectively reached out of such systems. In this work, we intend to fill these gaps in order to provide further insights into the great potentiality of a future technology based on magnetic reconnection. Additionally, one of the possibly limiting features was the inevitable symmetric outflow produced by the reconnection process. Among all the possible adoptable solutions, we propose here a solution based on the particle behavior undertaken for entering the reconnection region according to the initial density profile. We demonstrate that a noticeable net thrust value can be achieved by setting up a longitudinal asymmetric density profile with a relevant drop gradient.
A new approach for the prediction of partition functions using machine learning techniques
Authors: Desgranges Caroline , Delhommelle Jerome
Published: July 2018

Using machine learning (ML), we predict the partition functions and, thus, all thermodynamic properties of atomic and molecular fluids over a wide range of temperatures and pressures. Our approach is based on training neural networks using, as a reference, the results of a few flat-histogram simulations. The neural network weights so obtained are then used to predict fluid properties that are shown to be in excellent agreement with the experiment and with simulation results previously obtained on argon, carbon dioxide, and water. In particular, the ML predictions for the Gibbs free energy, Helmholtz free energy, and entropy are shown to be highly accurate over a wide range of conditions and states for bulk phases as well as for the conditions of phase coexistence. Our ML approach thus provides access instantly to G, A, and S, thereby eliminating the need to carry out any additional simulations to explore the dependence of the fluid properties on the conditions of temperature and pressure. This is of particular interest, for e.g., the screening of new materials, as well as in the parameterization of force fields, for which this ML approach provides a rapid way to assess the impact of new sets of parameters on the system properties.
Trajectory surface hopping study of propane photodissociation dynamics at 157 nm
Authors: Rauta Akshaya Kumar , Maiti Biswajit
Published: July 2018

The photodissociation dynamics of propane molecules has been studied using the quasiclassical trajectory surface hopping (TSH) method in conjunction with Tully’s fewest switches algorithm. The trajectories are propagated on potential energy surfaces computed on-the-fly using the multiconfiguration and multireference ab initio method starting in the lowest excited singlet state (HOMO → 3s Rydberg state) of propane at 157 nm with the emphasis on the site specificity of atomic hydrogen elimination, molecular hydrogen elimination, and their product branching ratios. Our dynamics simulation revealed that there are three primary dissociation channels: the atomic hydrogen elimination, the molecular hydrogen elimination, and the C–C bond scission. The trajectories indicate that the H2 elimination from the internal carbon atom (2,2-H2 elimination) and terminal carbon atom (1,1-H2 elimination) is the major process and follows a three centred synchronous concerted mechanism. 1,2-H2 and 1,3-H2 eliminations on the other hand are minor processes and exclusively follow the roaming mediated nonadiabatic dynamics. The probability of elimination of the hydrogen atom from two terminal groups (terminal hydrogen elimination) is greater than that from the internal CH2 group (internal hydrogen elimination). Almost 83% of atomic hydrogen elimination occurs through the asynchronous concerted mechanism from the terminal carbon atom via triple dissociation leading to CH3 + C2H4 + H products. This finding is in good agreement with a recent experimental observation. The present TSH study indicates that approximately one-third of the trajectories those resulted in a triple dissociation channel, CH3 + C2H4 + H completed in the ground singlet state following a nonadiabatic path (hopping from the first excited singlet S1 to the ground state S0) via the C–C and C–H dissociation coordinate conical intersection S1/S0. The products CH3(1 2A2″) + C2H4(1Ag) + H, obtained are ground state methyl radicals and ground state ethylene. The trajectories those ended in a triple dissociation channel CH3 + C2H4 + H adiabatically in the S1 state lead to CH3(1 2A2″) + C2H4 (1 3B1) + H, where singlet methyl radicals and triplet ethylene are formed in their corresponding lowest electronic state via a spin conserving route. Two channels, CH4 + CH3CH and C2H6 + CH2, are found to have minor contributions. In the case of methane elimination, the trajectories that follow an adiabatic path lead to CH3CH(1 1A″) + CH4,(1 1A1), where ethylidene is in the excited state and methane is in the ground state. Methane elimination via nonadiabatic path leads to CH3CH(11A′) + CH4(1 1A1), where both ethylidene and methane are in the ground electronic state. Ethane eliminations follow the adiabatic path leading to C2H6(1 1A1g) + CH2(1 1B1) where ethane is in the ground state and methylene is in the first excited state.
Head-on collision of ion acoustic shock waves in electron-positron-ion nonextensive plasmas for weakly and highly relativistic regimes
Authors: Alam M. S. , Hafez M. G. , Talukder M. R. , Hossain Ali M.
Published: July 2018

Head-on collision between ion acoustic shock waves (IASWs) and the consequences after collision are investigated considering the plasma system to be consisting of relativistic warm ions and nonextensive electrons and positrons, taking into account the effects of nonlinearity and dispersion. Two-sided KdV-Burger equations are derived employing the extended Poincare´-Lighthill-Kuo method. The results reveal that the plasma parameters are responsible for the modification of the structures along with phase shifts of the shock waves. The nonlinearity effects on IASWs in a highly relativistic regime (HRR) become pronounced rather than the weakly relativistic regime (WRR). The phase shifts of IASWs are enhanced by the relativistic streaming factor and superthermality. The electrostatic IASWs become rarefactive depending on temperatures, kinematic viscosity, and superthermality in both WRR and HRR. The amplitudes of IASWs are increasing for WRR but decreasing for HRR due to increasing ion thermal velocities. Besides, the amplitudes of the solitons are detaining due to the increase in the positron concentration for the depopulation of ions.
Enhancing fluorescence excitation and collection from the nitrogen-vacancy center in diamond through a micro-concave mirror
Authors: Duan Dewen , Kavatamane Vinaya Kumar , Arumugam Sri Ranjini , Rahane Ganesh , Tzeng Yan-Kai , Chang Huan-Cheng , Sumiya Hitoshi , Onoda Shinobu , Isoya Junichi , Balasubramanian Gopalakrishnan
Published: July 2018

We experimentally demonstrate a simple and robust optical fiber based method to achieve simultaneously efficient excitation and fluorescence collection from Nitrogen-Vacancy (NV) defects containing micro-crystalline diamond. We fabricate a suitable micro-concave mirror that focuses scattered excitation laser light into the diamond located at the focal point of the mirror. At the same instance, the mirror also couples the fluorescence light exiting out of the diamond crystal in the opposite direction of the optical fiber back into the optical fiber within its light acceptance cone. This part of fluorescence would have been otherwise lost from reaching the detector. Our proof-of-principle demonstration achieves a 25 times improvement in fluorescence collection compared to the case of not using any mirrors. The increase in light collection favors getting high signal-to-noise ratio optically detected magnetic resonance signals and hence offers a practical advantage in fiber-based NV quantum sensors. Additionally, we compacted the NV sensor system by replacing some bulky optical elements in the optical path with a 1 × 2 fiber optical coupler in our optical system. This reduces the complexity of the system and provides portability and robustness needed for applications like magnetic endoscopy and remote-magnetic sensing.
Stability and dynamics of a chemotaxis system with deformed free-surface in a shallow chamber
Authors: Chakraborty Symphony , Ivancic Filip , Solovchuk Maxim , Wen-Hann Sheu Tony
Published: July 2018

Complex bioconvection patterns have been studied analytically, experimentally, and numerically previously only for a flat free-surface of a suspension of chemotaxis bacteria in a shallow/deep chamber. In this paper, we have considered a two-dimensional chemotaxis-diffusion-convection system with a deformed free-surface. The influence of aggregation of chemotactic cells on the deformed free-surface of a shallow chamber is studied analytically. The aim of this paper is to investigate the nature of the instability in the chemotaxis-diffusion-convection system. We performed a detailed linear stability analysis of a steady-state cell and oxygen concentration distribution. The system becomes dominated by nonlinear convection terms beyond a critical Rayleigh number Raτ, which also depends on the critical wavenumber k as well as the other parameters. We have investigated that how the critical Rayleigh number in this system varies with three different sets of parameters. A weakly nonlinear analysis is carried out as well to determine the relative stability of the pattern formation at the onset of instability. A reactance between rolls, squares, hexagons, and mixed mode pattern is investigated in detail. Further research should link the weakly nonlinear analysis with the bifurcation analysis. Some important direct numerical simulation results have been presented in the support of linear stability analysis. Comparison of the analytical steady-state solution shows good agreement with the numerical result.
Effect of multi-ion-source injection on motional Stark effect diagnostic
Authors: Ko Jinseok
Published: July 2018

Many tokamak devices utilize high-power neutral beams for various beam-based active spectroscopic diagnostics such as the motional Stark effect (MSE). For higher heating performance, it is customary for the neutral beam injection to be made with a multiple number of ion sources, which often makes unfavorable conditions for the active spectroscopic diagnostics. This is mainly because the atomic and molecular emissions taking place from the interactions with multiple beams, or from different flux surfaces, are collected through the front optics at the same time, resulting in systematic errors in the measured quantities. In this work, the effect of the multiple ion source injections on the pitch angle measurements by the MSE diagnostic is quantitatively studied based on both numerical modeling and measurements made from the plasma discharges for the Korea Superconducting Tokamak Advanced Research. The sensitivity of the pitch angle against various combinations of the acceleration voltages of the ion sources is evaluated, yielding the optimum configuration of the beam injection that can maximize the heating efficiency with an acceptable level of the systematic offset in the MSE measurements.
Bifurcations in the Kuramoto model on graphs
Authors: Chiba Hayato , Medvedev Georgi S. , Mizuhara Matthew S.
Published: July 2018

In his classical work, Kuramoto analytically described the onset of synchronization in all-to-all coupled networks of phase oscillators with random intrinsic frequencies. Specifically, he identified a critical value of the coupling strength, at which the incoherent state loses stability and a gradual build-up of coherence begins. Recently, Kuramoto’s scenario was shown to hold for a large class of coupled systems on convergent families of deterministic and random graphs [Chiba and Medvedev, “The mean field analysis of the Kuramoto model on graphs. I. The mean field equation and the transition point formulas,” Discrete and Continuous Dynamical Systems—Series A (to be published); “The mean field analysis of the Kuramoto model on graphs. II. Asymptotic stability of the incoherent state, center manifold reduction, and bifurcations,” Discrete and Continuous Dynamical Systems—Series A (submitted).]. Guided by these results, in the present work, we study several model problems illustrating the link between network topology and synchronization in coupled dynamical systems. First, we identify several families of graphs, for which the transition to synchronization in the Kuramoto model starts at the same critical value of the coupling strength and proceeds in a similar manner. These examples include Erdős-Rényi random graphs, Paley graphs, complete bipartite graphs, and certain stochastic block graphs. These examples illustrate that some rather simple structural properties such as the volume of the graph may determine the onset of synchronization, while finer structural features may affect only higher order statistics of the transition to synchronization. Furthermore, we study the transition to synchronization in the Kuramoto model on power law and small-world random graphs. The former family of graphs endows the Kuramoto model with very good synchronizability: the synchronization threshold can be made arbitrarily low by varying the parameter of the power law degree distribution. For the Kuramoto model on small-world graphs, in addition to the transition to synchronization, we identify a new bifurcation leading to stable random twisted states. The examples analyzed in this work complement the results in Chiba and Medvedev, “The mean field analysis of the Kuramoto model on graphs. I. The mean field equation and the transition point formulas,” Discrete and Continuous Dynamical Systems—Series A (to be published); “The mean field analysis of the Kuramoto model on graphs. II. Asymptotic stability of the incoherent state, center manifold reduction, and bifurcations,” Discrete and Continuous Dynamical Systems—Series A (submitted).
Study of density distribution of electrical exploding tungsten wire in air
Authors: Lu Yihan , Wu Jian , Shi Huantong , Zhang Daoyuan , Li Xingwen , Jia Shenli , Qiu Aici
Published: July 2018

The density distribution is important information in the investigation of electrical exploding wires in the air. In this study, the density profiles of the electrons, tungsten atoms, and air at different instants were reconstructed based on a two-wavelength interferometry method. The experiment was carried out on a 1 kA, 0.1 kA/ns pulsed current generator, with a fine tungsten wire (10 μm in diameter). The laser probing images of the exploding products showed a two-layer structure, exhibiting a shunting discharge scenario. The fitted expanding trajectory of the dense core indicates that the expansion of the wire starts at the instant of the voltage drop. The reconstructed densities show the distribution of particles in the expansion process of the exploding wire. It is found that the wire core has a tube-like structure, and the plasma channel is located around the core boundary.
Comparison of optical absorption spectra of organic molecules and aggregates computed from real frequency dependent polarizability to TD-DFT and the dipole approximation
Authors: Ang Siong Tuan , Pal Amrita , Manzhos Sergei
Published: July 2018

We compare the performance of an approach using real frequency dependent polarizability to compute optical absorption spectra to linear-response time-dependent density functional theory (TD-DFT) for small organic dyes, oligomers of different lengths (oligothiophenes), and molecular clusters representing a molecular crystal (pentacene). For pentacene, the spectra computed with the two methods are also compared to the spectrum computed for clusters and the periodic solid using the dipole approximation. The approach based on real polarizability produces spectra in good agreement with TD-DFT for small molecules. The (artificial) redshift for longer oligomers is slightly more significant with the polarizability-based method than with TD-DFT. For pentacene clusters, TD-DFT produces reasonable spectra with a hybrid functional, but a significant redshift is introduced with a generalized gradient approximation functional due to the presence of charge transfer transitions. This problem is slightly attenuated with the polarizability-based method. The dipole approximation results in spectra much redshifted vs both TD-DFT and the polarizability-based method and in a different trend with cluster size.
Regularization by compressibility of the μ(I) model of dense granular flow
Authors: Goddard J. D. , Lee J.
Published: July 2018

The following article deals with the role of compressibility in regularizing the well-known μ(I) model, i.e., eliminating the short-wavelength (Hadamard) instability revealed by Barker et al. [“Well-posed and ill-posed behaviour of the μ(I)-rheology for granular flow,” J. Fluid Mech. 779, 794–818 (2015)]. In particular, we discuss the compressible-flow models proposed in the recent papers by Heyman et al. [“Compressibility regularizes the μ(I)-rheology for dense granular flows,” J. Fluid Mech. 830, 553–568 (2017)] and Barker et al. [“Well-posed continuum equations for granular flow with compressibility and μ(I)-rheology,” Proc. R. Soc. A 473(2201), 20160846 (2017)]. In addition to a critique of certain aspects of their proposed constitutive models, we show that the main effect of their regularizations is to add viscous effects to the shear response in a way that appears unfortunately to eliminate quasi-static yield stress. Another goal of the present work is to show how the development and analysis of visco-plastic constitutive relations are facilitated by dissipation potentials and the dissipative analog of elastic potentials. We illustrate their utility in Sec. IV of this article, where it is shown that a constant non-zero yield stress leads to loss of convexity that can only be restored by substituting viscous effects or else by adding spatial-gradient effects proposed previously by the present authors [Goddard, J. and Lee, J., “On the stability of the μ(I) rheology for granular flow,” J. Fluid Mech. 833, 302–331 (2017)].
The onset of convective instability of horizontal throughflow in a porous layer with inclined thermal and solutal gradients
Authors: Dubey Rashmi , Murthy P. V. S. N.
Published: July 2018

The double diffusive convective instability of a horizontal throughflow in a fluid-saturated porous layer confined between two infinitely long boundaries is investigated. Inclined thermal and solutal gradients are considered along these impermeable boundaries. The Darcy-Brinkman equation is used for the momentum balance in the porous medium in order to show the contrast in the results as we switch to the Darcy regime from the Brinkman regime through the transition flow regime. The heat generated because of viscous dissipation in the medium is considered to be significant. The basic flow profile is a nonlinear one. The resulting eigenvalue problem is solved numerically using bvp4c in Matlab. More emphasis has been laid on the transition regime and the Brinkman regime. The influence of the viscous dissipation (Ge), horizontal thermal and solutal gradients (RaH and SaH), vertical solutal gradient (Sa), and diffusivity ratio (Le) on the instability of the flow is discussed. The results are validated by comparing them with the existing results in the literature. In the case of pure Hadley flow, the horizontal solutal gradient has a stabilizing effect in the absence of the horizontal thermal gradient, whereas it has a destabilizing effect in the presence of the horizontal thermal gradient. It has a dual effect on the Hadley-Prats flow in the presence of a significant viscous dissipation. The vertical solutal gradient has a linearly destabilizing effect on the flow in all the regimes. The flow is found to be most stable in the Brinkman regime in most of the physical situations.
Implosion shape control of high-velocity, large case-to-capsule ratio beryllium ablators at the National Ignition Facility
Authors: Loomis E. N. , Yi S. A. , Kyrala G. A. , Kline J. , Simakov A. , Ralph J. , Millot M. , Dewald E. , Zylstra A. , Rygg J. R. , Celliers P. , Goyon C. , Lahmann B. , Sio H. , MacLaren S. , Masse L. , Callahan D. , Hurricane O. , Wilson D. C. , Rice N. , Huang H. , Kong C. , Bae J. , Nikroo A. , Batha S. H.
Published: July 2018

Experiments at the National Ignition Facility (NIF) show that the implosion shape of inertial confinement fusion ablators is a key factor limiting performance. To achieve more predictable, shape tunable implosions, we have designed and fielded a large 4.2 case-to-capsule ratio target at the NIF using 6.72 mm diameter Au hohlraums and 1.6 mm diameter Cu-doped Be capsules. Simulations show that at these dimensions during a 10 ns 3-shock laser pulse reaching 275 eV hohlraum temperatures, the plasma flow from the hohlraum wall and ablator is not significant enough to impede beam propagation. Experiments measuring the shock symmetry and in-flight shell symmetry closely matched the simulations. Most notably, in two experiments, we demonstrated symmetry control from negative to positive Legendre P2 space by varying the inner to total laser power cone fraction by 5% below and above the predicted symmetric value. Some discrepancies found in 1st shock arrival times that could affect agreement in late time implosion symmetry suggest hohlraum and capsule modeling uncertainties do remain, but this target design reduces sensitivities to them.
A kinetic description of ion-acoustic waves in collisional dusty plasma: Effects of grain charge fluctuations
Authors: Momot A. I. , Zagorodny A. G. , Momot O. V.
Published: July 2018

The dispersion relation for ion-acoustic waves in collisional weakly ionized dusty (complex) plasma is formulated with due regard to the grain charge fluctuations. Calculations of the dielectric response function are performed using the Bhatnagar-Gross-Krook kinetic equation. The grain charging currents are described by the Khrapak-Morfill interpolation formula [S. A. Khrapak and G. E. Morfill, Phys. Plasmas 15, 114503 (2008)]. The dependencies of the charging frequencies and effective collision frequencies on dusty plasma parameters are studied in detail. The analysis of the ion-acoustic wave spectrum is presented for the wide range of the ion collisionality for both nonisothermal and isothermal plasmas.
On regularizing the ML-MCTDH equations of motion
Authors: Wang Haobin , Meyer Hans-Dieter
Published: July 2018

In a recent paper [H.-D. Meyer and H. Wang, J. Chem. Phys. 148, 124105 (2018)], we have examined the regularization of the equations of motion (EOMs) of the multiconfiguration time-dependent Hartree (MCTDH) approach. We could show that the standard regularization scheme used by almost all researchers in the field is not optimal. The improved regularization allows for larger values of the regularization parameter ϵ, is less sensitive to the actual choice of ϵ, and performs the rotation of initially unoccupied single-particle functions into the “correct” direction in Hilbert space much faster than the old scheme. The latter point increases both the accuracy and efficiency of time propagation for challenging problems. For simple problems, the new scheme requires some additional numerical work as compared with the old scheme, ranging from negligible to almost doubling the total numerical labor. For demanding problems, on the other hand, the additional numerical work of the new scheme is often overcompensated by less steps taken by the integrator. In the present paper, we generalize the new regularization scheme to the multi-layer (ML) extension of MCTDH. Although the principle idea of the new regularization scheme remains unaltered, it was not obvious how the new scheme should be implemented into ML-MCTDH. The ML-MCTDH EOMs are much more complicated than the MCTDH ones, and for optimal numerical performance it was necessary to derive a recursive algorithm for implementing the new regularization scheme.
Monolithic 9 GHz passively mode locked quantum dot lasers directly grown on on-axis (001) Si
Authors: Liu Songtao , Norman Justin C. , Jung Daehwan , Kennedy MJ , Gossard Arthur C. , Bowers John E.
Published: July 2018

Optical frequency comb direct generation on silicon by mode locked lasers (MLLs) is promising as it offers high wavelength channel counts and ultrashort pulses that will benefit future large-scale high capacity silicon photonic integrated circuits. Here, we demonstrate two-section quantum dot (QD) MLLs that are directly grown on a complementary metal–oxide–semiconductor compatible on-axis (001) silicon substrate by employing molecular beam epitaxy. The lasers, incorporating five layers of InAs QDs, operate in the O-band wavelength range with a pulse repetition rate around 9 GHz. A pulsewidth reduction of 48% of the narrowest achievable pulse from each QD MLL is obtained when the saturable absorber (SA) section length ratio is increased from 8% to 23%. The device with the longest SA section exhibits a more than 50 dB fundamental RF peak signal to noise floor ratio with 1.3 ps pulses.
Vibrational enhancement in the dynamics of ammonia dissociative chemisorption on Ru(0001)
Authors: Hu Xixi , Yang Minghui , Xie Daiqian , Guo Hua
Published: July 2018

The vibrationally selective dissociative chemisorption dynamics of ammonia on the Ru(0001) surface is investigated using a quasi-classical trajectory (QCT) method on a new global potential energy surface (PES) with twelve dimensions. The PES is constructed by fitting 92 524 density functional theory points using the permutation invariant polynomial-neural network method, which rigorously enforces the permutation symmetry of the three hydrogen atoms as well as the surface periodicity. The PES enables highly efficient QCT simulations as well as future quantum dynamical studies of the scattering/dissociation dynamics. The QCT calculations yield satisfactory agreement with experiment and suggest strong activation of dissociation by both translational and vibrational excitations.
Phase-sensitive excitability of a limit cycle
Authors: Franović Igor , Omel’chenko Oleh E. , Wolfrum Matthias
Published: July 2018

The classical notion of excitability refers to an equilibrium state that shows under the influence of perturbations a nonlinear threshold-like behavior. Here, we extend this concept by demonstrating how periodic orbits can exhibit a specific form of excitable behavior where the nonlinear threshold-like response appears only after perturbations applied within a certain part of the periodic orbit, i.e., the excitability happens to be phase-sensitive. As a paradigmatic example of this concept, we employ the classical FitzHugh-Nagumo system. The relaxation oscillations, appearing in the oscillatory regime of this system, turn out to exhibit a phase-sensitive nonlinear threshold-like response to perturbations, which can be explained by the nonlinear behavior in the vicinity of the canard trajectory. Triggering the phase-sensitive excitability of the relaxation oscillations by noise, we find a characteristic non-monotone dependence of the mean spiking rate of the relaxation oscillation on the noise level. We explain this non-monotone dependence as a result of an interplay of two competing effects of the increasing noise: the growing efficiency of the excitation and the degradation of the nonlinear response.
First-principles simulation of photonic crystal surface-emitting lasers using rigorous coupled wave analysis
Authors: Song Alex Y. , Kalapala Akhil Raj Kumar , Zhou Weidong , Fan Shanhui
Published: July 2018

We show that the threshold of a photonic crystal surface-emitting laser can be calculated from first-principles by the method of rigorous coupled wave analysis (RCWA), which has been widely used to simulate the response spectra of passive periodic structures. Here, the scattering matrix (S-matrix) of a surface-emitting laser structure with added gain is calculated on the complex frequency plane using RCWA, and the lasing threshold is determined by the value of the gain for which the pole of the S-matrix reaches the real axis. This approach can be used for surface emitting laser structures in general and is particularly useful for those with complex in-plane structures.
Communication: Critical behavior in graphene: Spinodal instability at room temperature
Authors: Ramírez R. , Herrero C. P.
Published: July 2018

At a critical spinodal in-plane stress τC, a planar crystalline graphene layer becomes mechanically unstable. We present a model of the critical behavior of the membrane area near τC and show that it is in complete agreement with path-integral simulations and with recent experiments based on interferometric profilometry and Raman spectroscopy. Close to the critical stress, τC, the in-plane strain behaves as τC−τ1/2 for τ < τC.
Trigonocephalotrema (Digenea : Haplosplanchnidae), a new genus for trematodes parasitising fishes of two Indo-West Pacific acanthurid genera
Authors: Huston Daniel C. , Cutmore Scott C. , Cribb Thomas H.
Published: July 2018

The Great Barrier Reef is the largest coral reef ecosystem on the planet and supports a diverse community of marine fishes, as well as the organisms that parasitise them. Although the digenetic trematodes that parasitise fishes of the Great Barrier Reef have been studied for over a century, the species richness and diversity of many trematode lineages is yet to be explored. Trigonocephalotrema, gen. nov. is proposed to accommodate three new species, Trigonocephalotrema euclidi, sp. nov., T. hipparchi, sp. nov. and T. sohcahtoa, sp. nov., parasitic in fishes of Naso Lacepède and Zebrasoma Swainson (Acanthuridae) in the tropical Pacific. Species of Trigonocephalotrema are characterised with morphological and molecular data (18S rRNA, ITS2 and 28S rRNA). Species of Trigonocephalotrema are morphologically distinguished from all other haplosplanchnid lineages by having terminal, triangular, plate-like oral suckers. With the inclusion of the new molecular data, Bayesian inference and maximum likelihood analyses of the Haplosplanchnidae Poche, 1926 recovered identical tree topologies and demonstrated Trigonocephalotrema as a well-supported monophyletic group. Although species of Trigonocephalotrema are differentiated from all other haplosplanchnid lineages on the basis of morphology, species within the genus are morphologically cryptic; thus, accurate species identification will require inclusion of host and molecular data. Species of Trigonocephalotrema cannot be assigned to a recognised subfamily within the Haplosplanchnidae using either morphological or molecular data and would require the erection of a new subfamily to accommodate them. However, we find little value in the use of subfamilies within the Haplosplanchnidae, given that there are so few taxa in the family, and herein propose that their use be avoided.
A mean field view of the landscape of two-layer neural networks
Authors: Mei Song , Montanari Andrea , Nguyen Phan-Minh
Published: July 2018

Significance

Multilayer neural networks have proven extremely successful in a variety of tasks, from image classification to robotics. However, the reasons for this practical success and its precise domain of applicability are unknown. Learning a neural network from data requires solving a complex optimization problem with millions of variables. This is done by stochastic gradient descent (SGD) algorithms. We study the case of two-layer networks and derive a compact description of the SGD dynamics in terms of a limiting partial differential equation. Among other consequences, this shows that SGD dynamics does not become more complex when the network size increases.
Patterns of persuasion in Hungarian medical discourse domain from the 16th and 17th centuries
Authors: Kuna Agnes
Published: July 2018

This study focuses on the persuasive patterns and conceptual domains of 16th and 17th century Hungarian medical recipes. From a theoretical perspective, the study is set in a functional cognitive framework, with heavy reliance on historical pragmatics and sociolinguistics. From a methodological perspective, the research is based on the concept of genre as script, which is an organized form of everyday knowledge, and on the metonymic model of speech acts. From the qualitative analysis of eight historical and representative collections of recipes, three main conclusions were drawn. First, persuasion can be best described with the help of persuasive intent within linguistic. Second, persuasion cannot be interpreted without its sociocultural context. Last, certain persuasive patterns can be delineated that are closely associated with the norms of the analyzed genre.
Metaphor as a (de-)legitimizing strategy in leadership discourse
Authors: Sebera Jan , Lu Wei-lun
Published: July 2018

This chapter investigates Churchill’s Cold War speeches as a case of how cognitive and corpus linguistics may serve as a useful tool for analyzing how political leaders legitimize their agendas via linguistic means. We find that Churchill’s rhetoric makes extensive use of the source domains person, journey, and building. The argumentative purpose is at least twofold. First, journey and building metaphors give positive value to the country’s prospects. Second, the journey metaphor is found to co-occur with personification, with the purpose of seeking partnership between the United States and the United Kingdom. We conclude by discussing how political leaders linguistically represent and conceptually frame a crisis, especially via metaphorical means, convincing their people of the usefulness of certain proposals and thus legitimizing their agendas, with Churchill as a representative example.
Fictionalizing scenarios in political discourse
Authors: Rosingana Gonzalo Calle
Published: July 2018

This chapter shows how political discourse uses covert fictional construals to persuade audiences. It argues that the use of specific linguistic and conceptual strategies guides their interpretive processes to a point where the distinction between reality and fiction becomes unclear. The study focusses on four areas of a specific discourse event and shows that they can assist in the generation of persuasive effects. The chapter deals with the organization of information in the specific speech event, the way attention patterns and focal adjustment collaborate as potential resources of persuasion, the role of deixis in the speech event, and how the deontic force of modal verbs may be minimized to help engage the audience into the belief of the existence of an alternative reality.
Constructing the ideal organization
Authors: Ng Carl Jon Way
Published: July 2018

This chapter looks at brand communication and how metaphor relates to the cognitive and functional dimensions of this persuasive communication by way of examining how Singapore’s publicly-funded higher education institutions communicate with their audiences. The chapter highlights the role of animate and anthropomorphic metaphors in communicating ideal(ized) representations of these organizations – typically as dynamic, competitive, and purposefully-motivated actors – in the endeavor to forge affinity with audiences and stakeholders. In doing so, the chapter calls for a view of brand communication that considers not just how such communication seeks to persuade audiences in support of the organization, but also how it encourages audiences to subscribe to the attributes and values that the ideal organization supposedly embodies.