bluuebunny/crossref_metadata_2025 huggingface dataset:
An ultrafast programmable electrical tester for enabling time-resolved, sub-nanosecond switching dynamics and programming of nanoscale memory devices
Authors: Shukla Krishna Dayal , Saxena Nishant , Manivannan Anbarasu
Published: December 2017

Recent advancements in commercialization of high-speed non-volatile electronic memories including phase change memory (PCM) have shown potential not only for advanced data storage but also for novel computing concepts. However, an in-depth understanding on ultrafast electrical switching dynamics is a key challenge for defining the ultimate speed of nanoscale memory devices that demands for an unconventional electrical setup, specifically capable of handling extremely fast electrical pulses. In the present work, an ultrafast programmable electrical tester (PET) setup has been developed exceptionally for unravelling time-resolved electrical switching dynamics and programming characteristics of nanoscale memory devices at the picosecond (ps) time scale. This setup consists of novel high-frequency contact-boards carefully designed to capture extremely fast switching transient characteristics within 200 ± 25 ps using time-resolved current-voltage measurements. All the instruments in the system are synchronized using LabVIEW, which helps to achieve various programming characteristics such as voltage-dependent transient parameters, read/write operations, and endurance test of memory devices systematically using short voltage pulses having pulse parameters varied from 1 ns rise/fall time and 1.5 ns pulse width (full width half maximum). Furthermore, the setup has successfully demonstrated strikingly one order faster switching characteristics of Ag5In5Sb60Te30 (AIST) PCM devices within 250 ps. Hence, this novel electrical setup would be immensely helpful for realizing the ultimate speed limits of various high-speed memory technologies for future computing.
Self-organisation of semi-flexible rod-like particles
Authors: de Braaf Bart , Oshima Menegon Mariana , Paquay Stefan , van der Schoot Paul
Published: December 2017

We report on a comprehensive computer simulation study of the liquid-crystal phase behaviour of purely repulsive, semi-flexible rod-like particles. For the four aspect ratios we consider, the particles form five distinct phases depending on their packing fraction and bending flexibility: the isotropic, nematic, smectic A, smectic B, and crystal phase. Upon increasing the particle bending flexibility, the various phase transitions shift to larger packing fractions. Increasing the aspect ratio achieves the opposite effect. We find two different ways in which the layer thickness of the particles in the smectic A phase may respond to an increase in concentration. The layer thickness may either decrease or increase depending on the aspect ratio and flexibility. For the smectic B and the crystalline phases, increasing the concentration always decreases the layer thickness. Finally, we find that the layer spacing jumps to a larger value on transitioning from the smectic A phase to the smectic B phase.
Dynamics and kinetics of reversible homo-molecular dimerization of polycyclic aromatic hydrocarbons
Authors: Mao Qian , Ren Yihua , Luo K. H. , van Duin Adri C. T.
Published: December 2017

Physical dimerization of polycyclic aromatic hydrocarbons (PAHs) has been investigated via molecular dynamics (MD) simulation with the ReaxFF reactive force field that is developed to bridge the gap between the quantum mechanism and classical MD. Dynamics and kinetics of homo-molecular PAH collision under different temperatures, impact parameters, and orientations are studied at an atomic level, which is of great value to understand and model the PAH dimerization. In the collision process, the enhancement factors of homo-molecular dimerizations are quantified and found to be larger at lower temperatures or with smaller PAH instead of size independent. Within the capture radius, the lifetime of the formed PAH dimer decreases as the impact parameter increases. Temperature and PAH characteristic dependent forward and reverse rate constants of homo-molecular PAH dimerization are derived from MD simulations, on the basis of which a reversible model is developed. This model can predict the tendency of PAH dimerization as validated by pyrene dimerization experiments [H. Sabbah et al., J. Phys. Chem. Lett. 1(19), 2962 (2010)]. Results from this study indicate that the physical dimerization cannot be an important source under the typical flame temperatures and PAH concentrations, which implies a more significant role played by the chemical route.
Anisotropy in the hydrophobic and oleophilic characteristics of patterned surfaces
Authors: Fan B. , Bandaru P. R.
Published: December 2017

A significant difference in the wetting angles of water and oil was observed on patterned substrates, combining interstitial spaces along with hydrophobic solid surfaces, as a function of the orientation. The difference was ascribed to a modification of the liquid–interstice interfacial surface energy due to different degrees of penetration of the liquid. A roughness metric related to the extent to which the liquid infiltrates the interstice normalized by the geometrically determined area is proposed. This study has implications in modulating surface slip behavior and would be of importance in guiding liquid droplets.
Self-consistent modeling of laminar electrohydrodynamic plumes from ultra-sharp needles in cyclohexane
Authors: Becerra Marley , Frid Henrik , Vázquez Pedro A.
Published: December 2017

This paper presents a self-consistent model of electrohydrodynamic (EHD) laminar plumes produced by electron injection from ultra-sharp needle tips in cyclohexane. Since the density of electrons injected into the liquid is well described by the Fowler-Nordheim field emission theory, the injection law is not assumed. Furthermore, the generation of electrons in cyclohexane and their conversion into negative ions is included in the analysis. Detailed steady-state characteristics of EHD plumes under weak injection and space-charge limited injection are studied. It is found that the plume characteristics far from both electrodes and under weak injection can be accurately described with an asymptotic simplified solution proposed by Vazquez et al. [“Dynamics of electrohydrodynamic laminar plumes: Scaling analysis and integral model,” Phys. Fluids 12, 2809 (2000)] when the correct longitudinal electric field distribution and liquid velocity radial profile are used as input. However, this asymptotic solution deviates from the self-consistently calculated plume parameters under space-charge limited injection since it neglects the radial variations of the electric field produced by a high-density charged core. In addition, no significant differences in the model estimates of the plume are found when the simulations are obtained either with the finite element method or with a diffusion-free particle method. It is shown that the model also enables the calculation of the current-voltage characteristic of EHD laminar plumes produced by electron field emission, with good agreement with measured values reported in the literature.
Regularizing Feynman path integrals using the generalized Kontsevich-Vishik trace
Authors: Hartung Tobias
Published: December 2017

A fully regulated definition of Feynman’s path integral is presented here. The proposed re-formulation of the path integral coincides with the familiar formulation whenever the path integral is well defined. In particular, it is consistent with respect to lattice formulations and Wick rotations, i.e., it can be used in Euclidean and Minkowski space-time. The path integral regularization is introduced through the generalized Kontsevich-Vishik trace, that is, the extension of the classical trace to Fourier integral operators. Physically, we are replacing the time-evolution semi-group by a holomorphic family of operators such that the corresponding path integrals are well defined in some half space of C. The regularized path integral is, thus, defined through analytic continuation. This regularization can be performed by means of stationary phase approximation or computed analytically depending only on the Hamiltonian and the observable (i.e., known a priori). In either case, the computational effort to evaluate path integrals or expectations of observables reduces to the evaluation of integrals over spheres. Furthermore, computations can be performed directly in the continuum and applications (analytic computations and their implementations) to a number of models including the non-trivial cases of the massive Schwinger model and a φ4 theory.
Nonlinear gyrokinetic simulation of fast ion-driven modes including continuum interaction
Authors: Cole M. D. J. , Borchardt M. , Kleiber R. , Könies A. , Mishchenko A.
Published: December 2017

Energetic particle transport in toroidal magnetic confinement fusion devices can be enhanced by the particles' interaction with electromagnetic global modes. This process has been modelled numerically. The most extensive work has been with reduced models, which may use a simplified description of the bulk plasma, assuming a perturbative approximation for mode structure evolution, restrict simulation to the linear phase, or some combination. In this work, nonlinear non-perturbative simulations are performed using a fully gyrokinetic and reduced models of the bulk plasma. Previous linear investigation of a simple model tokamak case is extended to show that, at least under some conditions, dramatic qualitative differences in mode structure and saturated mode amplitude can exist due to non-perturbative response in the linear and nonlinear phases that depends upon the bulk plasma physics. This supports analytical work which has shown that the non-perturbative energetic particle response should depend upon the magnetic geometry and kinetic physics. It is also shown that energetic particle modes that dominate in the linear phase can be subdominant to a non-perturbative toroidal Alfvén eigenmode-based global structure in the nonlinear phase.
Fluid-fluid interfacial mobility from random walks
Authors: Barclay Paul L. , Lukes Jennifer R.
Published: December 2017

Dual control volume grand canonical molecular dynamics is used to perform the first calculation of fluid-fluid interfacial mobilities. The mobility is calculated from one-dimensional random walks of the interface by relating the diffusion coefficient to the interfacial mobility. Three different calculation methods are employed: one using the interfacial position variance as a function of time, one using the mean-squared interfacial displacement, and one using the time-autocorrelation of the interfacial velocity. The mobility is calculated for two liquid-liquid interfaces and one liquid-vapor interface to examine the robustness of the methods. Excellent agreement between the three calculation methods is shown for all the three interfaces, indicating that any of them could be used to calculate the interfacial mobility.
Exciton dynamics of luminescent defects in aging organic light-emitting diodes
Authors: Ingram Grayson L. , Zhao Yong-Biao , Lu Zheng-Hong
Published: December 2017

Fundamental device physics of exciton dynamics is crucial to the design and fabrication of organic light-emitting diodes (OLEDs) with a long lifetime at high brightness. In this paper, we report a set of analytical equations which describe how and where defects form during exciton-driven degradation of an OLED and their impact on device operation. This set of equations allows us to quantify changes in the exciton and defect populations as a function of time in neat layers of 4,4′-Bis(carbazol-9-yl)biphenyl (CBP) in simple bilayer OLEDs. CBP produces luminescent defects which present a unique opportunity to quantify the exciton capturing dynamics of the defects. Through modeling of the time and current density dependence of both the CBP and defect emission, we clearly identify CBP singlet excitons as the source of OLED degradation. Further analysis of experimental data on devices with precisely positioned exciton capturing layers suggests that defects are formed near organic heterojunctions.
Directly patching high-level exchange-correlation potential based on fully determined optimized effective potentials
Authors: Huang Chen , Chi Yu-Chieh
Published: December 2017

The key element in Kohn-Sham (KS) density functional theory is the exchange-correlation (XC) potential. We recently proposed the exchange-correlation potential patching (XCPP) method with the aim of directly constructing high-level XC potential in a large system by patching the locally computed, high-level XC potentials throughout the system. In this work, we investigate the patching of the exact exchange (EXX) and the random phase approximation (RPA) correlation potentials. A major challenge of XCPP is that a cluster’s XC potential, obtained by solving the optimized effective potential equation, is only determined up to an unknown constant. Without fully determining the clusters’ XC potentials, the patched system’s XC potential is “uneven” in the real space and may cause non-physical results. Here, we developed a simple method to determine this unknown constant. The performance of XCPP-RPA is investigated on three one-dimensional systems: H20, H10Li8, and the stretching of the H19–H bond. We investigated two definitions of EXX: (i) the definition based on the adiabatic connection and fluctuation dissipation theorem (ACFDT) and (ii) the Hartree-Fock (HF) definition. With ACFDT-type EXX, effective error cancellations were observed between the patched EXX and the patched RPA correlation potentials. Such error cancellations were absent for the HF-type EXX, which was attributed to the fact that for systems with fractional occupation numbers, the integral of the HF-type EXX hole is not −1. The KS spectra and band gaps from XCPP agree reasonably well with the benchmarks as we make the clusters large.
Stark tuning and electrical charge state control of single divacancies in silicon carbide
Authors: de las Casas Charles F. , Christle David J. , Ul Hassan Jawad , Ohshima Takeshi , Son Nguyen T. , Awschalom David D.
Published: December 2017

Neutrally charged divacancies in silicon carbide (SiC) are paramagnetic color centers whose long coherence times and near-telecom operating wavelengths make them promising for scalable quantum communication technologies compatible with existing fiber optic networks. However, local strain inhomogeneity can randomly perturb their optical transition frequencies, which degrades the indistinguishability of photons emitted from separate defects and hinders their coupling to optical cavities. Here, we show that electric fields can be used to tune the optical transition frequencies of single neutral divacancy defects in 4H-SiC over a range of several GHz via the DC Stark effect. The same technique can also control the charge state of the defect on microsecond timescales, which we use to stabilize unstable or non-neutral divacancies into their neutral charge state. Using fluorescence-based charge state detection, we show that both 975 nm and 1130 nm excitation can prepare their neutral charge state with near unity efficiency.
Quantitative disentanglement of coherent and incoherent laser-induced surface deformations by time-resolved x-ray reflectivity
Authors: Sander M. , Pudell J.-E. , Herzog M. , Bargheer M. , Bauer R. , Besse V. , Temnov V. , Gaal P.
Published: December 2017

We present time-resolved x-ray reflectivity measurements on laser excited coherent and incoherent surface deformations of thin metallic films. Based on a kinematical diffraction model, we derive the surface amplitude from the diffracted x-ray intensity and resolve transient surface excursions with sub-Å spatial precision and 70 ps temporal resolution. The analysis allows for decomposition of the surface amplitude into multiple coherent acoustic modes and a substantial contribution from incoherent phonons which constitute the sample heating.
Effect of BST film thickness on the performance of tunable interdigital capacitors grown by MBE
Authors: Meyers Cedric J. G. , Freeze Christopher R. , Stemmer Susanne , York Robert A.
Published: December 2017

Voltage-tunable, interdigital capacitors (IDCs) were fabricated on Ba0.29Sr0.71TiO3 grown by hybrid molecular beam epitaxy (MBE). In this growth technique, we utilize the metal-organic precursor titanium tetraisopropoxide rather than solid-source Ti as with conventional MBE. Two samples of varying BaxSr(1−x)TiO3 (BST) thicknesses were fabricated and analyzed. High-quality, epitaxial Pt electrodes were deposited by sputtering from a high-purity Pt target at 825 °C. The Pt electrodes were patterned and etched by argon ion milling, passivated with reactively sputtered SiO2, and then metallized with lift-off Ti/Au. The fabricated devices consisted of two-port IDCs embedded in ground-signal-ground, coplanar waveguide (CPW) transmission lines to enable radio-frequency (RF) probing. The sample included open and thru de-embedding structures to remove pad and CPW parasitic impedances. Two-port RF scattering (S) parameters were measured from 100 MHz to 40 GHz while DC bias was stepped from 0 V to 100 V. The IDCs exhibit a high zero-bias radio-frequency (RF) quality factor (Q) approaching 200 at 1 GHz and better than 2.3:1 capacitance tuning for the 300-nm-thick sample. Differences in the Q(V) and C(V) response with varying thicknesses indicate that unknown higher order material phenomena are contributing to the loss and tuning characteristics of the material.
In vivo oral imaging with integrated portable photoacoustic microscopy and optical coherence tomography
Authors: Qin Wei , Qi Weizhi , Jin Tian , Guo Heng , Xi Lei
Published: December 2017

Oral diseases, especially oral cancers, are becoming serious health problems in humans. To image vasculatures and structures simultaneously in the human oral cavity which are tightly associated with various oral diseases, we develop a dual-modality portable optical resolution photoacoustic microscopy (ORPAM) and optical coherence tomography (OCT) system. This system utilizes a new rotary scanning mechanism and a compact design of the imaging head, making it portable and free of translation of the imaging interface or samples. Through the phantom experiments, both modalities yield high lateral resolutions of 8.1 μm (ORPAM) and 8.56 μm (OCT), respectively. The axial resolutions are measured to be 116.5 μm for ORPAM and 6.1 μm for OCT. In vivo imaging of a mouse ear was carried out to evaluate the performance of the system in biological tissues. In addition, in vivo oral imaging of a healthy human lip and monitoring recovery progress of a lip ulcer demonstrate the clinical potential of this system.
Scanning tunneling microscopy measurements of the spin Hall effect in tungsten films by using iron-coated tungsten tips
Authors: Xie Ting , Dreyer Michael , Bowen David , Hinkel Dan , Butera R. E. , Krafft Charles , Mayergoyz Isaak
Published: December 2017

Scanning tunneling microscopy experiments using iron-coated tungsten tips and current-carrying tungsten films have been conducted. An asymmetry of the tunneling current with respect to the change of the direction of the bias current through a tungsten film has been observed. It is argued that this asymmetry is a manifestation of the spin Hall effect in the current-carrying tungsten film. Nanoscale variations of this asymmetry across the tungsten film have been studied by using the scanning tunneling microscopy technique.
Coexistence of ferromagnetism and spin glass freezing in the site-disordered kagome ferrite SrSn2Fe4O11
Authors: Shlyk Larysa , Strobel S. , Farmer B. , De Long L. E. , Niewa R.
Published: December 2017

Single-crystal x-ray diffraction refinements indicate SrSn2Fe4O11 crystallizes in the hexagonal R-type ferrite structure with non-centrosymmetric space group P63mc and lattice parameters a = 5.9541(2) Å, c = 13.5761(5) Å, Z = 2 (R(F) = 0.034). Octahedrally coordinated sites are randomly occupied by Sn and Fe; whereas tetrahedrally coordinated sites are exclusively occupied by Fe, whose displacement from ideal trigonal-bipyramidal coordination causes the loss of inversion symmetry. DC magnetization data indicate SrSn2Fe4O11 single crystals undergo ferro- or ferri-magnetic order below a transition temperature TC = 630 K with very low coercive fields Hc⊥ = 0.27 Oe and Hc// = 1.5 Oe at 300 K, for applied fields perpendicular and parallel to the c-axis, respectively. The value for TC is exceptionally high, and the coercive fields exceptionally low, among the known R-type ferrites. Enhanced coercivity and thermomagnetic hysteresis suggest the onset of short-range, spin glass order occurs below Tf = 35 K. Optical measurements indicate a band gap of 0.8 eV, consistent with wide-gap semiconducting behavior and a previously established empirical correlation between the semiconducting gap and TC for R-type ferrites based upon Ru.
Linear and nonlinear spectroscopy from quantum master equations
Authors: Fetherolf Jonathan H. , Berkelbach Timothy C.
Published: December 2017

We investigate the accuracy of the second-order time-convolutionless (TCL2) quantum master equation for the calculation of linear and nonlinear spectroscopies of multichromophore systems. We show that even for systems with non-adiabatic coupling, the TCL2 master equation predicts linear absorption spectra that are accurate over an extremely broad range of parameters and well beyond what would be expected based on the perturbative nature of the approach; non-equilibrium population dynamics calculated with TCL2 for identical parameters are significantly less accurate. For third-order (two-dimensional) spectroscopy, the importance of population dynamics and the violation of the so-called quantum regression theorem degrade the accuracy of TCL2 dynamics. To correct these failures, we combine the TCL2 approach with a classical ensemble sampling of slow microscopic bath degrees of freedom, leading to an efficient hybrid quantum-classical scheme that displays excellent accuracy over a wide range of parameters. In the spectroscopic setting, the success of such a hybrid scheme can be understood through its separate treatment of homogeneous and inhomogeneous broadening. Importantly, the presented approach has the computational scaling of TCL2, with the modest addition of an embarrassingly parallel prefactor associated with ensemble sampling. The presented approach can be understood as a generalized inhomogeneous cumulant expansion technique, capable of treating multilevel systems with non-adiabatic dynamics.
A study on arrangement characteristics of microparticles in sedimentation on flat and round substrates
Authors: Yeo Eunju , Son Minhee , Kim Kwanoh , Kim Jeong Hwan , Yoo Yeong-Eun , Choi Doo-Sun , Kim Jungchul , Yoon Seok Ho , Yoon Jae Sung
Published: December 2017

Recent advances of microfabrication techniques have enabled diverse structures and devices on the microscale. This fabrication method using microparticles is one of the most promising technologies because it can provide a cost effective process for large areas. So, many researchers are studying modulation and manipulation of the microparticles in solution to obtain a proper arrangement. However, the microparticles are in sedimentation status during the process in many cases, which makes it difficult to control their arrangement. In this study, droplets containing microparticles were placed on a substrate with minimal force and we investigated the arrangement of these microparticles after evaporation of the liquid. Experiments have been performed with upward and downward substrates to change the direction of gravity. The geometry of substrates was also changed, which were flat or round. The results show that the arrangement depends on the size of particles and gravity and geometry of the substrate. The arrangement also depends on the movement of the contact line of the droplets, which may recede or be pinned during evaporation. This study is expected to provide a method of the fabrication process for microparticles which may not be easily manipulated due to sedimentation.
Forward volume and surface magnetostatic modes in an yttrium iron garnet film for out-of-plane magnetic fields: Theory and experiment
Authors: Lim Jinho , Bang Wonbae , Trossman Jonathan , Amanov Dovran , Ketterson John B.
Published: December 2017

We present experimental and theoretical results on the propagation of magnetostatic spin waves in a film of yttrium iron garnet (YIG) for out-of-plane magnetic fields for which propagation in opposite directions is nonreciprocal in the presence of a metal layer. The plane studied is defined by the film normal n and n × k where k is the wave vector of the mode. Spin waves in this setting are classified as forward volume waves or surface waves and display non-reciprocity in the presence of an adjacent metal layer except for when H//n. The measurements are carried out in a transmission geometry, and a microwave mixer is used to measure the change of phase, and with it the evolution of wavevector, of the arriving spin wave with external magnetic field.
Simulation of a model nanopore sensor: Ion competition underlies device behavior
Authors: Mádai Eszter , Valiskó Mónika , Dallos András , Boda Dezső
Published: December 2017

We study a model nanopore sensor with which a very low concentration of analyte molecules can be detected on the basis of the selective binding of the analyte molecules to the binding sites on the pore wall. The bound analyte ions partially replace the current-carrier cations in a thermodynamic competition. This competition depends both on the properties of the nanopore and the concentrations of the competing ions (through their chemical potentials). The output signal given by the device is the current reduction caused by the presence of the analyte ions. The concentration of the analyte ions can be determined through calibration curves. We model the binding site with the square-well potential and the electrolyte as charged hard spheres in an implicit background solvent. We study the system with a hybrid method in which we compute the ion flux with the Nernst-Planck (NP) equation coupled with the Local Equilibrium Monte Carlo (LEMC) simulation technique. The resulting NP+LEMC method is able to handle both strong ionic correlations inside the pore (including finite size of ions) and bulk concentrations as low as micromolar. We analyze the effect of bulk ion concentrations, pore parameters, binding site parameters, electrolyte properties, and voltage on the behavior of the device.
Synthesis of hard magnetic Mn3Ga micro-islands by e-beam evaporation
Authors: Akdogan O.
Published: December 2017

The permanent magnet industry heavily depends on Nd-Fe-B and Sm-Co alloys because of their high-energy product and high room temperature coercivity. Main ingredient for having such superior magnetic properties compared to other known ferromagnetic materials is rare earth elements (Nd, Sm, Dy…). However recent worldwide reserve and export limitation problem of rare earths, shifted researchers’ focus to rare earth free permanent magnets. Among many alternatives (FePt, Zr2Co11, FeNi …), Mn-based alloys are the most suitable due to abundance of the forming elements and trivial formation of the necessary hard phases. In this study, Mn3Ga micro islands have been prepared. Mn3Ga owes its hard magnetic properties to tetragonal D022 phase with magnetic anisotropy energy of 2 MJ/m3. Thin films and islands of Cr/MnGa/Cr layers have been deposited on Si/SiO2 wafers using combination of e-beam and thermal evaporation techniques. Cr has been used as buffer and cover layer to protect the sample from the substrate and prevent oxidation during annealing. Annealing under Ar/H2 forming gas has been performed at 350oC for 10 min. Nano thick islands of 25, 50 and 100 μm lateral size have been produced by photolithography technique. Room temperature coercivity of 7.5 kOe has been achieved on 100 μm micro islands of Mn3Ga. Produced micro islands could be a rare earth free alternative for magnetic memory and MEMS applications.
Construction of non-Markovian coarse-grained models employing the Mori–Zwanzig formalism and iterative Boltzmann inversion
Authors: Yoshimoto Yuta , Li Zhen , Kinefuchi Ikuya , Karniadakis George Em
Published: December 2017

We propose a new coarse-grained (CG) molecular simulation technique based on the Mori–Zwanzig (MZ) formalism along with the iterative Boltzmann inversion (IBI). Non-Markovian dissipative particle dynamics (NMDPD) taking into account memory effects is derived in a pairwise interaction form from the MZ-guided generalized Langevin equation. It is based on the introduction of auxiliary variables that allow for the replacement of a non-Markovian equation with a Markovian one in a higher dimensional space. We demonstrate that the NMDPD model exploiting MZ-guided memory kernels can successfully reproduce the dynamic properties such as the mean square displacement and velocity autocorrelation function of a Lennard–Jones system, as long as the memory kernels are appropriately evaluated based on the Volterra integral equation using the force-velocity and velocity-velocity correlations. Furthermore, we find that the IBI correction of a pair CG potential significantly improves the representation of static properties characterized by a radial distribution function and pressure, while it has little influence on the dynamic processes. Our findings suggest that combining the advantages of both the MZ formalism and IBI leads to an accurate representation of both the static and dynamic properties of microscopic systems that exhibit non-Markovian behavior.
Density of bunched threading dislocations in epitaxial GaN layers as determined using X-ray diffraction
Authors: Barchuk M. , Holý V. , Rafaja D.
Published: December 2017

X-ray diffraction is one of the most popular experimental methods employed for determination of dislocation densities, as it can recognize both the strain fields and the local lattice rotations produced by dislocations. The main challenge of the quantitative analysis of the dislocation density is the formulation of a suitable microstructure model, which describes the dislocation arrangement and the effect of the interactions between the strain fields from neighboring dislocations reliably in order to be able to determine the dislocation densities precisely. The aim of this study is to prove the capability of X-ray diffraction and two computational methods, which are frequently used for quantification of the threading dislocation densities from X-ray diffraction measurements, in the special case of partially bunched threading dislocations. The first method is based on the analysis of the dislocation-controlled crystal mosaicity, and the other one on the analysis of diffuse X-ray scattering from threading dislocations. The complementarity of both methods is discussed. Furthermore, it is shown how the complementarity of these methods can be used to improve the results of the quantitative analysis of bunched and thus inhomogeneously distributed threading dislocations and to get a better insight into the dislocation arrangement.
Incorporation of soft shaped hydrogel sheets into microfluidic systems using a simple adhesion masking process
Authors: Young Dylan C. , Newsome Isabel G. , Scrimgeour Jan
Published: December 2017

We report the use of simple adhesion masking in fabricating shaped, photo-polymerizable hydrogel sheets with very small elastic moduli on glass substrates. Direct ink masking of surface crosslinking groups allows for low cost hydrogel patterning that is compatible with materials where crosslinking is both photo- and chemically initiated. Mechanical removal of the unwanted polymerized material reveals the shaped hydrogel. The mechanical properties of the shaped hydrogels were characterized by exposure to well-defined shear flow inside the microfluidic device. We show that hydrogel sheets with elastic moduli down to 7.5 Pa can be shaped with millimeter feature sizes using this approach. The shaped hydrogels are suitable for applications such as the detection of shear flow, cell culture, and traction force microscopy.
Hydrodynamic instability of meandering channels
Authors: Ali Sk Zeeshan , Dey Subhasish
Published: December 2017

In this paper, we explore the hydrodynamic instability of meandering channels driven by the turbulent flow. The governing equations of channel dynamics with suitable boundary conditions are closed with the fluid and granular constitutive relationships. A regular expansion of the fundamental variables is employed to linearize the parent equations by superimposing the perturbations on the basic unperturbed flow. The channel dynamics reveal a resonance phenomenon which occurs when the key variables fall in the vicinity of the distinct critical values. The resonance phenomenon preserves its distinctive signature in different flow regimes which are guided by the characteristic values of the shear Reynolds number. The hydrodynamic analysis indicates that the fluid friction and the volumetric sediment flux play a decisive role to characterize the channel instability in different flow regimes. The growths of azimuthal velocity perturbation in phase with curvature, bed topography perturbation, bend amplification rate, and meander propagation speed in different flow regimes are investigated by varying the meander wavenumber, Shields number, channel aspect ratio, and relative roughness number. The analysis is capable to capture the effects of grain size on azimuthal velocity perturbation, bed topography perturbation, bend amplification rate, and meandering propagation speed over a wide range of shear Reynolds numbers. The variations of resonant wavenumbers in different flow regimes with the Shields number, channel aspect ratio, and relative roughness number are addressed. For a specific flow regime, the upstream and downstream migrations of meandering channels are typically governed by the Shields number, channel aspect ratio, and relative roughness number.
Communication: Relationship between local structure and the stability of water in hydrophobic confinement
Authors: Altabet Y. Elia , Debenedetti Pablo G.
Published: December 2017

Liquid water confined between nanoscale hydrophobic objects can become metastable with respect to its vapor at nanoscale separations. While the separations are only several molecular diameters, macroscopic theories are often invoked to interpret the thermodynamics and kinetics of water under confinement. We perform detailed rate and free energy calculations via molecular simulations in order to assess the dependence of the rate of evaporation, free energy barriers, and free energy differences between confined liquid and vapor upon object separation and compare them to the relevant macroscopic theories. At small enough separations, the rate of evaporation appears to deviate significantly from the predictions of classical nucleation theory, and we attribute such deviations to changes in the structure of the confined liquid film. However, the free energy difference between the confined liquid and vapor phases agrees quantitatively with macroscopic theory, and the free energy barrier to condensation displays qualitative agreement. Overall, the present work suggests that theories attempting to capture the kinetic behavior of nanoscale systems should incorporate structural details rather than treating it as a continuum.
Control of the diocotron instability of a hollow electron beam with periodic dipole magnets
Authors: Jo Y. H. , Kim J. S. , Stancari G. , Chung M. , Lee H. J.
Published: December 2017

A method to control the diocotron instability of a hollow electron beam with periodic dipole magnetic fields has been investigated by a two-dimensional particle-in-cell simulation. At first, relations between the diocotron instability and several physical parameters such as the electron number density, the current and shape of the electron beam, and the solenoidal field strength are theoretically analyzed without periodic dipole magnetic fields. Then, we study the effects of the periodic dipole magnetic fields on the diocotron instability using the two-dimensional particle-in-cell simulation. In the simulation, we considered the periodic dipole magnetic field applied along the propagation direction of the beam, as a temporally varying magnetic field in the beam frame. A stabilizing effect is observed when the oscillating frequency of the dipole magnetic field is optimally chosen, which increases with the increasing amplitude of the dipole magnetic field.
Experimental study of Reynolds number effects on performance of thick CAS wind turbine airfoils
Authors: Li Xingxing , Yang Ke , Zhang Lei , Bai Jingyan
Published: December 2017

In this study, the effects of Reynolds number on four thick CAS airfoils of two generations were studied at two different wind tunnels. The results show that in natural transition, increasing Re leads to a reduction of the maximum lift coefficient and stall angle of attack. Furthermore, the results show that increasing Re causes the separation point to move to the leading edge in thick CAS airfoils. This could be reflected by the influence of Re on the separation of the laminar boundary layer. Specifically, it is found that for thick airfoils, the large leading edge radius helps to maintain a laminar boundary layer near the frontal upper surface even at very high angles of attack, whereas the high slope of the rear part of suction surface triggers early separation at small angles of attack. Both of these contribute to a “negative” effect of Reynolds number. The study indicates that the positive effect of Reynolds number on thin airfoils is not suitable for thick airfoils, which is at least highly geometry-dependent. The study also suggests that it may be possible to design special airfoils with desirable Re effects to enhance the efficiency and safety of wind turbines under extreme conditions.
Cyclic AMP-dependent plasticity underlies rapid changes in odor coding associated with reward learning
Authors: Louis Thierry , Stahl Aaron , Boto Tamara , Tomchik Seth M.
Published: December 2017

Significance

Cyclic AMP signaling is involved in learning across taxa, but how cAMP modulation drives coherent plasticity across circuits is unclear. Results of this study demonstrate that cAMP-dependent plasticity in the
Drosophila
brain drives olfactory learning-induced plasticity, which is biased toward appetitive conditioning and modulates motivated behavior.
Unraveling submicron-scale mechanical heterogeneity by three-dimensional X-ray microdiffraction
Authors: Li Runguang , Xie Qingge , Wang Yan-Dong , Liu Wenjun , Wang Mingguang , Wu Guilin , Li Xiaowu , Zhang Minghe , Lu Zhaoping , Geng Chang , Zhu Ting
Published: December 2017

Significance

Shear bands critically control the strength and ductility in a wide range of structural, geological, and biological materials. The nondestructive three-dimensional structural probing of individual shear bands has hitherto not been possible for investigation at the critical mesoscopic length scales. The X-ray microdiffraction study reported in this work reveals the highly localized stress gradients and microscopic damage mechanisms across the fatigue shear bands. The resulting local strain gradients lead to severe stress concentrations at the submicrometer scale, causing an anomalous deviation of the classical Coffin−Manson rule for the high-cycle fatigue failure of metals. This work opens an avenue for harnessing the synchrotron-based, 3D spatially resolved X-ray for studying the heterogeneous deformation and fracture in bulk materials.
Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus
Authors: Baggen Jim , Hurdiss Daniel L. , Zocher Georg , Mistry Nitesh , Roberts Richard W. , Slager Jasper J. , Guo Hongbo , van Vliet Arno L. W. , Wahedi Maryam , Benschop Kimberley , Duizer Erwin , de Haan Cornelis A. M. , de Vries Erik , Casasnovas José M. , de Groot Raoul J. , Arnberg Niklas , Stehle Thilo , Ranson Neil A. , Thibaut Hendrik Jan , van Kuppeveld Frank J. M.
Published: December 2017

Significance

Acute hemorrhagic conjunctivitis (AHC) is a painful and highly contagious infection of the eye, with reported incidence rates of up to 48%. No drugs or vaccines are available for treatment or prevention of AHC. Coxsackievirus A24 variant (CV-A24v) is the main etiological agent of AHC, being responsible for >10 million AHC cases worldwide during the last decades. We have identified the CV-A24v protein receptor and determined the high-resolution structure of the virus–receptor complex. Furthermore, we found that an adaptation which enhances binding to the receptor sialic acid may have contributed to the pathogenicity and pandemic nature of CV-A24v. These findings highlight the importance of sialic acid for viruses with ocular tropism, such as influenza A virus and several adenoviruses.
Localizing softness and stress along loops in 3D topological metamaterials
Authors: Baardink Guido , Souslov Anton , Paulose Jayson , Vitelli Vincenzo
Published: December 2017

Significance

Topological mechanical metamaterials are a type of structure, which can be used to design and control softness. They have been proposed as components for many applications, including for cushioning mechanical shocks and isolation of mechanical deformations as well as controlling actuation and failure. We provide a realization of a specific type of topological structure—a gapped topological lattice in three dimensions. We then use this structure to localize soft deformations either on the surface of the material or in the bulk along line defects called dislocations.
Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling
Authors: Liu Hui , Dong Peng , Ioannou Maria S. , Li Li , Shea Jamien , Pasolli H. Amalia , Grimm Jonathan B. , Rivlin Patricia K. , Lavis Luke D. , Koyama Minoru , Liu Zhe
Published: December 2017

Significance

To circumvent our dependence on photoactivation in single-molecule microscopy, we devise a universal genetic system to precisely control copy number of fluorescently labeled molecules in a cell. Combined with photostable labels, this system enables long-term single-particle tracking of densely packed cellular organelles and proteins. This strategy expands spatiotemporal length scales of live-cell single-molecule measurements to quantitatively understand complex control of molecular dynamics in vivo.
Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite
Leishmania
Authors: Grybchuk Danyil , Akopyants Natalia S. , Kostygov Alexei Y. , Konovalovas Aleksandras , Lye Lon-Fye , Dobson Deborah E. , Zangger Haroun , Fasel Nicolas , Butenko Anzhelika , Frolov Alexander O. , Votýpka Jan , d’Avila-Levy Claudia M. , Kulich Pavel , Moravcová Jana , Plevka Pavel , Rogozin Igor B. , Serva Saulius , Lukeš Julius , Beverley Stephen M. , Yurchenko Vyacheslav
Published: December 2017

Significance

Largely overlooked, the viruses of protists have started to attract more attention. Several viruses of the family
Totiviridae
are currently implicated in the increased pathogenicity of parasitic protozoa such as
Leishmania
to vertebrate hosts. We conducted a broad survey of RNA viruses within trypanosomatids, one of the iconic groups of protists. These revealed several previously unidentified viral taxa including one designated “
Leishbunyaviridae
” and a highly divergent virus termed “Leptomonas pyrrhocoris ostravirus 1.” Our studies provide important information on the origins as well as the diversity and distribution of viruses within a group of protists related to the human parasite
Leishmania
.
Junctional trafficking and restoration of retrograde signaling by the cytoplasmic RyR1 domain
Authors: Polster Alexander , Perni Stefano , Filipova Dilyana , Moua Ong , Ohrtman Joshua D. , Bichraoui Hicham , Beam Kurt G. , Papadopoulos Symeon
Published: December 2017

The type 1 ryanodine receptor (RyR1) in skeletal muscle is a homotetrameric protein that releases Ca2+ from the sarcoplasmic reticulum (SR) in response to an “orthograde” signal from the dihydropyridine receptor (DHPR) in the plasma membrane (PM). Additionally, a “retrograde” signal from RyR1 increases the amplitude of the Ca2+ current produced by CaV1.1, the principle subunit of the DHPR. This bidirectional signaling is thought to depend on physical links, of unknown identity, between the DHPR and RyR1. Here, we investigate whether the isolated cytoplasmic domain of RyR1 can interact structurally or functionally with CaV1.1 by producing an N-terminal construct (RyR11:4300) that lacks the C-terminal membrane domain. In CaV1.1-null (dysgenic) myotubes, RyR11:4300 is diffusely distributed, but in RyR1-null (dyspedic) myotubes it localizes in puncta at SR–PM junctions containing endogenous CaV1.1. Fluorescence recovery after photobleaching indicates that diffuse RyR11:4300 is mobile, whereas resistance to being washed out with a large-bore micropipette indicates that the punctate RyR11:4300 stably associates with PM–SR junctions. Strikingly, expression of RyR11:4300 in dyspedic myotubes causes an increased amplitude, and slowed activation, of Ca2+ current through CaV1.1, which is almost identical to the effects of full-length RyR1. Fast protein liquid chromatography indicates that ∼25% of RyR11:4300 in diluted cytosolic lysate of transfected tsA201 cells is present in complexes larger in size than the monomer, and intermolecular fluorescence resonance energy transfer implies that RyR11:4300 is significantly oligomerized within intact tsA201 cells and dyspedic myotubes. A large fraction of these oligomers may be homotetramers because freeze-fracture electron micrographs reveal that the frequency of particles arranged like DHPR tetrads is substantially increased by transfecting RyR-null myotubes with RyR11:4300. In summary, the RyR1 cytoplasmic domain, separated from its SR membrane anchor, retains a tendency toward oligomerization/tetramerization, binds to SR–PM junctions in myotubes only if CaV1.1 is also present and is fully functional in retrograde signaling to CaV1.1.
Cerebral mitochondrial dysfunction associated with deep hypothermic circulatory arrest in neonatal swine†
Authors: Mavroudis Constantine D , Karlsson Michael , Ko Tiffany , Hefti Marco , Gentile Javier I , Morgan Ryan W , Plyler Ross , Mensah-Brown Kobina G , Boorady Timothy W , Melchior Richard W , Rosenthal Tami M , Shade Brandon C , Schiavo Kellie L , Nicolson Susan C , Spray Thomas L , Sutton Robert M , Berg Robert A , Licht Daniel J , Gaynor J William , Kilbaugh Todd J
Published: December 2017

OBJECTIVES

Controversy remains regarding the use of deep hypothermic circulatory arrest (DHCA) in neonatal cardiac surgery. Alterations in cerebral mitochondrial bioenergetics are thought to contribute to ischaemia–reperfusion injury in DHCA. The purpose of this study was to compare cerebral mitochondrial bioenergetics for DHCA with deep hypothermic continuous perfusion using a neonatal swine model.

METHODS

Twenty-four piglets (mean weight 3.8 kg) were placed on cardiopulmonary bypass (CPB): 10 underwent 40-min DHCA, following cooling to 18°C, 10 underwent 40 min DHCA and 10 remained at deep hypothermia for 40 min; animals were subsequently rewarmed to normothermia. 4 remained on normothermic CPB throughout. Fresh brain tissue was harvested while on CPB and assessed for mitochondrial respiration and reactive oxygen species generation. Cerebral microdialysis samples were collected throughout the analysis.

RESULTS

DHCA animals had significantly decreased mitochondrial complex I respiration, maximal oxidative phosphorylation, respiratory control ratio and significantly increased mitochondrial reactive oxygen species (P < 0.05 for all). DHCA animals also had significantly increased cerebral microdialysis indicators of cerebral ischaemia (lactate/pyruvate ratio) and neuronal death (glycerol) during and after rewarming.

CONCLUSIONS

DHCA is associated with disruption of mitochondrial bioenergetics compared with deep hypothermic continuous perfusion. Preserving mitochondrial health may mitigate brain injury in cardiac surgical patients. Further studies are needed to better understand the mechanisms of neurological injury in neonatal cardiac surgery and correlate mitochondrial dysfunction with neurological outcomes.