Real-space Structure Research Articles

Correlations in the Solute-Solvent Dynamics Reach Beyond the First Hydration Shell of Ions.

While the real-space structure of solvation shells has been explored for decades, a dynamical perspective that directly relies on changes in the H-bond network became accessible more recently mainly via far-infrared (THz) spectroscopies. A remaining key question is how many hydration shells are affected by ion-induced network perturbations. We disclose that theoretical THz difference spectra of aqueous salt solutions can be deciphered in terms of only a handful of dipolar auto- and cross-correlations, including the second solvation shell. This emphasizes the importance of cross-correlations being often neglected in multicomponent models. Analogously, experimental THz responses of simple ions can be deciphered in a similar way. Dramatic intensity cancellations due to large positive and negative contributions are found to effectively shift intensity maxima. Thus, THz spectroscopy provides an unprecedented view on the details of hydration dynamics, which can be understood by a combination of experiment and theory.

勾配曲げモーメントと圧縮軸力を受ける上フランジ連続補剛H形鋼梁の横座屈荷重と連続補剛材の水平・回転拘束効果

When steel moment frames are subjected to seismic forces, H-shaped beams carry the gradient flexural moment. Large cross-section beams are used as main beams to design structural members effectively in real large space structures. Long span beams may not possess the plastic strength due to lateral buckling, so that many lateral braces along the beams should be set up to prevent the lateral bucking deformation (AIJ 1998). Most oy beams in frames are connected by continuous braces such as folded-roof plates, which are effective to prevent the lateral buckling oy beams. However, in the Japanese design code, non-structural members are not considered as the braces. On the other hands, there have been many moment resisting frames with dampers to prevent damages oy main frames recently, and then H-shaped beams connected with dampers are subjected to compressive axial forces in addition to gradient flexural moment. If the beam carries the large axial force induced by the damper during earthquake, the lateral-torsional buckling behavior oy H-shaped beam becomes more unstable than that under flexural moment only. The axial force which the beams carry is possible to exceed 30% oy yield load oy the beam. Therefore, in this paper, the lateral buckling behavior for H-shaped beams with continuous braces under gradient flexural moment and compressive axial force is clarified and elasto-plastic lateral buckling stress oy the beams or lateral stiffing force and rotational stiffing moment oy continuous braces are evaluated by the energy method and numerical analyses. In this study, for H-shaped beams with continuous braces subjected to gradient flexural moment and compressive axial force, two types oy loading conditions and two types oy bracing rigidities are considered. One oy the loading conditions, which is called as Type A, is the case that the upper flange's compressive load is larger than the lower flange's one in the left side oy beam as shown in Fig. 3(a), and another, which is called as Type B, is that the upper flange's compressive load is smaller than the lower flange's one in the left side oy beam as shown in Fig. 3(b). Furthermore, the ratio oy the compressive axial force, P2 to P1 is represented as an axial force ratio ‘p’ in equation oy elastic lateral buckling load. The continuous braces are divided into the lateral braces, ku, and rotational braces, kβ, as shown in Fig. 1. In the case oy TypeA, ku is effective for preventing lateral deformation oy compressive upper flange, whereas in the case oy TypeB, kβ, is effective for preventing torsional deformation. This study is conducted by the following procedures: 1. The equations oy lateral buckling loads oy H-shaped beams with continuous braces under gradient flexural moment and compressive axial force are derived by energy method. To simplify the equations by energy method, the new equations oy lateral buckling loads are suggested with reference to the terms oy the flexural and torsional rigidities oy beams, the rigidities oy braces, and condition oy the loads. 2. The elasto-plastic buckling behaviors oy the beams are simulated by elasto-plastic large deformation analysis. The lower bound oy the elasto-plastic buckling stress oy the beams can be evaluated with the interpolated buckling curve between those oy bending member and compression member, which are provided by Recommendation for Limit State Design oy Steel Structure (AIJ), depending on the axial force ratio. 3. The upper bound oy moment and lateral force which continuous braces carry at the lateral buckling oy beams is evaluated based on the ratio oy the flexural and torsional rigidities oy beams, the rigidities oy braces, the axial force ratio, and the gradient oy flexural moment.

Structure of Plasma Heating in Gyrokinetic Alfvénic Turbulence.

We analyze plasma heating in weakly collisional kinetic Alfvén wave turbulence using high resolution gyrokinetic simulations spanning the range of scales between the ion and the electron gyroradii. Real space structures that have a higher than average heating rate are shown not to be confined to current sheets. This novel result is at odds with previous studies, which use the electromagnetic work in the local electron fluid frame, i.e., J·(E+v_{e}×B), as a proxy for turbulent dissipation to argue that heating follows the intermittent spatial structure of the electric current. Furthermore, we show that electrons are dominated by parallel heating while the ions prefer the perpendicular heating route. We comment on the implications of the results presented here.

Real Space Imaging of Nanoparticle Assembly at Liquid-Liquid Interfaces with Nanoscale Resolution.

Bottom up self-assembly of functional materials at liquid-liquid interfaces has recently emerged as method to design and produce novel two-dimensional (2D) nanostructured membranes and devices with tailored properties. Liquid-liquid interfaces can be seen as a "factory floor" for nanoparticle (NP) self-assembly, because NPs are driven there by a reduction of interfacial energy. Such 2D assembly can be characterized by reciprocal space techniques, namely X-ray and neutron scattering or reflectivity. These techniques have drawbacks, however, as the structural information is averaged over the finite size of the radiation beam and nonperiodic isolated assemblies in 3D or defects may not be easily detected. Real-space in situ imaging methods are more appropriate in this context, but they often suffer from limited resolution and underperform or fail when applied to challenging liquid-liquid interfaces. Here, we study the surfactant-induced assembly of SiO2 nanoparticle monolayers at a water-oil interface using in situ atomic force microscopy (AFM) achieving nanoscale resolved imaging capabilities. Hitherto, AFM imaging has been restricted to solid-liquid interfaces because applications to liquid interfaces have been hindered by their softness and intrinsic dynamics, requiring accurate sample preparation methods and nonconventional AFM operational schemes. Comparing both AFM and grazing incidence X-ray small angle scattering data, we unambiguously demonstrate correlation between real and reciprocal space structure determination showing that the average interfacial NP density is found to vary with surfactant concentration. Additionally, the interaction between the tip and the interface can be exploited to locally determine the acting interfacial interactions. This work opens up the way to studying complex nanostructure formation and phase behavior in a range of liquid-liquid and complex liquid interfaces.

Heuristic Description of Magnetoelectricity of Cu2OSeO3.

CuO2SeO3 is an insulating material that hosts topologically nontrivial spin whirls, so-called skyrmions, and exhibits magnetoelectric coupling allowing to manipulate these skyrmions by means of electric fields. We report magnetic force microscopy imaging of the real-space spin structure on the surface of a bulk single crystal of CuO2SeO3. Based on measurements of the electric polarization using Kelvin-probe force microscopy, we develop a heuristic description of the magnetoelectric properties in CuO2SeO3. The model successfully describes the dependency of the electric polarization on the magnetization in all magnetically modulated phases.

Advancing X-ray scattering metrology using inverse genetic algorithms.

We compare the speed and effectiveness of two genetic optimization algorithms to the results of statistical sampling via a Markov chain Monte Carlo algorithm to find which is the most robust method for determining real space structure in periodic gratings measured using critical dimension small angle X-ray scattering. Both a covariance matrix adaptation evolutionary strategy and differential evolution algorithm are implemented and compared using various objective functions. The algorithms and objective functions are used to minimize differences between diffraction simulations and measured diffraction data. These simulations are parameterized with an electron density model known to roughly correspond to the real space structure of our nanogratings. The study shows that for X-ray scattering data, the covariance matrix adaptation coupled with a mean-absolute error log objective function is the most efficient combination of algorithm and goodness of fit criterion for finding structures with little foreknowledge about the underlying fine scale structure features of the nanograting.

Compact extreme ultraviolet source for laboratory-based photoemission spectromicroscopy

We report on the combination of a state-of-the-art energy-filtering photoemission electron microscope with an intense yet compact laboratory-based gas discharge extreme ultraviolet (EUV) light source. Using a photon energy of 71.7 eV from oxygen plasma (O5+ spectral line), we demonstrate element-selective photoelectron imaging in real space and band structure mapping in reciprocal space. Additionally, the high surface sensitivity of the EUV light was used to study the surface oxidation on islands of the phase-change material Ge1Sb2Te4. The EUV light source allows the extension of spectromicroscopy, previously only feasible at synchrotron beamlines, to laboratory-based work.

Resolving amorphous solid-liquid interfaces by atomic force microscopy

Recent advancements in liquid atomic force microscopy make it an ideal technique for probing the structure of solid-liquid interfaces. Here, we present a structural study of a two-dimensional amorphous silica bilayer immersed in an aqueous solution utilizing liquid atomic force microscopy with sub-nanometer resolution. Structures show good agreement with atomically resolved ultra-high vacuum scanning tunneling microscopy images obtained on the same sample system, owing to the structural stability of the silica bilayer and the imaging clarity from the two-dimensional sample system. Pair distance histograms of ring center positions are utilized to develop quantitative metrics for structural comparison, and the physical origin of pair distance histogram peaks is addressed by direct assessment of real space structures.

Phase and precession evolution in the Burgers equation

We present a phenomenological study of the phase dynamics of the one-dimensional stochastically forced Burgers equation, and of the same equation under a Fourier mode reduction on a fractal set. We study the connection between coherent structures in real space and the evolution of triads in Fourier space. Concerning the one-dimensional case, we find that triad phases show alignments and synchronisations that favour energy fluxes towards small scales --a direct cascade. In addition, strongly dissipative real-space structures are associated with entangled correlations amongst the phase precession frequencies and the amplitude evolution of Fourier triads. As a result, triad precession frequencies show a non-Gaussian distribution with multiple peaks and fat tails, and there is a significant correlation between triad precession frequencies and amplitude growth. Links with dynamical systems approach are briefly discussed, such as the role of unstable critical points in state space. On the other hand, by reducing the fractal dimension D of the underlying Fourier set, we observe: i) a tendency toward a more Gaussian statistics, ii) a loss of alignment of triad phases leading to a depletion of the energy flux, and iii) the simultaneous reduction of the correlation between the growth of Fourier mode amplitudes and the precession frequencies of triad phases.

Some methods to regulate low-bias negative differential resistance in σ barrier separating nanoscale molecular transport systems

Using the first-principles method which combines the nonequilibrium Green’s function (NEGF) with density functional theory (DFT), the role of defect, dopant, barrier length and geometric deformation for low-bias negative differential resistance (NDR) in two capped armchair carbon nanotubes (CNTs) sandwiching [Formula: see text] barrier are systematically analyzed. We found that this method can regulate the negative differential resistance (NDR) effects such as current peak and peak position. The adjusting mechanism may originate from orbital interaction and orbital reconstruction. Our calculations try to manipulate the transport characteristics in energy space by simply manipulating the structure in real space, which may promise the potential applications in nanomolecular-electronics in the future.

Building block analysis of 2D amorphous networks reveals medium range correlation

The random network theory has been the long-accepted structural model for silica glasses. Now, a large bilayer silica sheet that was recently imaged with STM in atomic resolution provides the opportunity for real space structure analysis. General patterns in the formation of amorphous structures may be identified by looking at larger building blocks beyond single rings. Assessments of ring arrangements around each Si atom and ring neighborhoods are compared against uncorrelated structure predictions. A theoretical model of a two-dimensional silica network is investigated in parallel. Significant deviations of the observed structures from the uncorrelated prediction correspond qualitatively with a simple geometric approximation for bond angle frustration.

Structural origins of mechanical properties and hysteresis in SIS triblock copolymers/polystyrene blends with spherical morphology

The mechanical response and the corresponding microstructure of polymer blends composed of styrene-isoprene-styrene block copolymer and deuterated polystyrene are studied via in situ small-angle neutron scattering (SANS) measurements during intermittent uniaxial extension. The initial blend morphologies consist of spherical PS glassy domains arranged in body-centered cubic (BCC) lattices. The spheres rearrange affinely with the macroscopic deformation up to Hencky strains ~0.35. Larger deformation is mechanically characterized by yield and strain hardening. In this regime, SANS measurements reveal a transition from a BCC crystal lattice to chevron-like patterns. Using electron microscopy, we found that the chevrons arise from a real-space structure described as spheres that have been stretched along one axis and aligned parallel to one another. Such configuration is unstable and reverts to BCC structure after stress release. After unloading the blends, remnant nano-deformation is observed, which is fully relaxed only in the transverse direction after more than 10 h. Permanent damage of the internal structure along the stretching direction impedes the full recovery of the initial sphere configuration.

BASDet: Bayesian approach(es) for structure determination from single molecule X-ray diffraction images

X-ray free electron lasers (XFEL) are expected to enable molecular structure determination in single molecule diffraction experiments. In this paper, we describe an implementation of two orthogonal Bayesian approaches, previously introduced in Walczak and Grubmüller (2014), capable of extracting structure information from sparse and noisy diffraction images obtained in these experiments. In the ‘Orientational Bayes’ approach, a ‘seed’ model is used to determine for every recorded diffraction image the underlying molecular orientation. The molecular transform of the irradiated molecule is obtained by aligning and averaging those images in three-dimensional reciprocal space. By contrast, in the ‘Structural Bayes’ approach, a real space structure model is optimized to fit best to an entire set of diffraction images. This approach is used in a Monte Carlo structure refinement procedure.Both presented approaches were implemented in C; previous tests (Walczak and Grubmüller, 2014) suggest that the algorithms are robust against low signal to noise ratios and can deliver high resolution structural information. Program summaryProgram title: BASDetCatalogue identifier: AEZH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEZH_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GPL version 3No. of lines in distributed program, including test data, etc.: 1881590No. of bytes in distributed program, including test data, etc.: 49039580Distribution format: tar.gzProgramming language: C (ANSI 99), Perl.Computer: Workstation (8 CPUs).Operating system: Linux.Classification: 3, 4.13, 16.1.External routines: GNU Scientific Library (GSL), Message Passing Interface (MPI) libraryNature of problem: Extracting structural information from sparse and noisy single molecule XFEL diffraction images.Solution method: Bayes’ formalism is used to calculate either molecular orientation probability distribution with the aim to align individual images; or, alternatively, to calculate directly structure probability given all collected images.Running time: The examples given:Orientation_Bayes—50 h on Ivy Bridge Cores Xeon E3-1270v2 (2×4×3, 5 GHz)Structural_Bayes—These take longer than Orientation_Bayes runs, but can be restarted from checkpoint files.

Real-Space Imaging of the Atomic Structure of Organic-Inorganic Perovskite.

Organic-inorganic perovskite is a promising class of materials for photovoltaic applications and light emitting diodes. However, so far commercialization is still impeded by several drawbacks. Atomic-scale effects have been suggested to be possible causes, but an unequivocal experimental view at the atomic level is missing. Here, we present a low-temperature scanning tunneling microscopy study of single crystal methylammonium lead bromide CH3NH3PbBr3. Topographic images of the in situ cleaved perovskite surface reveal the real-space atomic structure. Compared to the bulk we observe modified arrangements of atoms and molecules on the surface. With the support of density functional theory we explain these by surface reconstruction and a substantial interplay of the orientation of the polar organic cations (CH3NH3)(+) with the position of the hosting anions. This leads to structurally and electronically distinct domains with ferroelectric and antiferroelectric character. We further demonstrate local probing of defects, which may also impact device performance.

Sorting algorithms for single-particle imaging experiments at X-ray free-electron lasers.

Modern X-ray free-electron lasers (XFELs) operating at high repetition rates produce a tremendous amount of data. It is a great challenge to classify this information and reduce the initial data set to a manageable size for further analysis. Here an approach for classification of diffraction patterns measured in prototypical diffract-and-destroy single-particle imaging experiments at XFELs is presented. It is proposed that the data are classified on the basis of a set of parameters that take into account the underlying diffraction physics and specific relations between the real-space structure of a particle and its reciprocal-space intensity distribution. The approach is demonstrated by applying principal component analysis and support vector machine algorithms to the simulated and measured X-ray data sets.

Development of the SSPH Method for Real-Space Electronic Structure Calculations

We have applied symmetric smoothed particle hydrodynamics (SSPH) to real-space electronic structure calculations. The electronic structure of a simple atom such as hydrogen, helium and lithium is calculated. The results of SSPH are compared to that of the higher-order finite difference method (FD), and are in good agreement with that of FD. Our results indicate that SSPH can be applicable to the electronic structure calculations that require high accuracy.

News Article

News Article

Shell-structure-based functionals for the kinetic energy

A new group of shell-structure-based functionals, which rely on proper representation of the atomic shell structure in real space, is introduced. Starting from the model of a perfect piecewise exponential decaying electron density, an analytical expression for the kinetic energy density including two parameters is given. It is shown that parameter values which lead to a proper shell structure in real space give rise to suitable kinetic energy functionals.

Comparative study of the carbide-modified surfacesC/Mo(110)andC/Mo(100)using high-resolution x-ray photoelectron spectroscopy

The preparations of single (monolayer) and bulk carbides on the $\mathrm{Mo}(110)$ and $\mathrm{Mo}(100)$ single crystals are followed in situ at 1200 K using synchrotron-based high-resolution x-ray photoelectron spectroscopy of the $\mathrm{C}\phantom{\rule{0.28em}{0ex}}1s$ and core Mo $3{d}_{5/2}$ levels. By comparing the experimental results to first principles calculations using density functional theory, we suggest real-space surface structures for the carbide-modified surfaces. For a monolayer carbide on $\mathrm{Mo}(110)$, carbon dimers adsorb in the long-bridge site, most likely at a coverage of $3/8\phantom{\rule{0.16em}{0ex}}\mathrm{ML}$ carbon atoms per Mo surface atom. For the bulk carbide, we find a coverage of $\ensuremath{\sim}0.5\phantom{\rule{0.16em}{0ex}}\mathrm{ML}$ on the surface, and the calculations show that single carbon atoms are more stable than dimers on the surface. The monolayer carbide on $\mathrm{Mo}(100)$ exhibits a coverage of $\ensuremath{\sim}1\phantom{\rule{0.16em}{0ex}}\mathrm{ML}$ and agrees with previous studies, while the bulk carbide preparation probably leads to a faceting of the surface.

Application of neutron holography to polycrystalline samples

Neutron holography can be an efficient tool to investigate the local real-space structure of crystalline materials around specific probe nuclei serving as radiation source or detector. The positions of atoms in the neighborhood of such nuclei are observable with high (picometry) accuracy. Measurements of this type require orientational order and, therefore, restrict the range of study essentially to single crystals. However, if the information searched for is limited to the distances between the probe and the surrounding nuclei instead of their positions, holographic techniques can be applied to polycrystalline samples as well. In order to prove this statement, the expected multi-wavelength holographic signal of a polycrystalline sample was calculated. The holographic signal can be obtained by applying time-of-flight techniques, and by using a proper mathematical procedure, the distances between the probe nucleus and the surrounding nuclei can be reconstructed. A model calculation taking into account real instrument parameters confirms this expectation. The experimental verification of the predictions can be undertaken at existing pulsed neutron sources being able to provide the required experimental conditions. This new method opens the way to expand the field of investigation towards gaining information about the local atomic structure of polycrystalline materials which are of importance also in various applications.