Real-space Model Research Articles

Single-photon switching in photonic crystal waveguide with quantum impurity via a control light

We investigate the transmission properties of a single-photon through a three-level quantum impurity embedded in a photonic crystal waveguide. The transmission and reflection spectra are obtained by exactly solving a real-space Hamiltonian model through the S matrix theory. Results show that there is a peak in the reflection spectrum, and the linewidth is dependent on the coupling constant, and the position shifts with the Rabi frequency. Based on this tuning properties of the spectrum, an effective single-photon switching is proposed and analyzed systematically.

A Pedestrian Approach to the Aromaticity of Graphene and Nanographene: Significance of Huckel’s (4n+2)π Electron Rule

In an attempt to describe and rationalize the elusive aromatic properties of graphene by first-principles calculations in a simple and transparent way, we have constructed numerous judicially chosen real-space models of various sizes and symmetries, which lead to the aromaticity pattern of infinite graphene by a process of “spatial” evolution through successive peripheral additions, characterized by fundamental periodicities related to the traditional Huckel (4n+2)π electron rule. In accord with the early expectations of Pauling, we have found that the electronic and aromatic properties of infinite graphene result from the superposition of two complementary primary aromatic configurations, in which full and empty rings are interchanged. The primary pattern consists of a hexagonal superlattice in which each fully aromatic ring is surrounded by six nonaromatic rings, in full agreement with the empirical Clar aromatic sextet theory. We have found that, for finite nanographene(s), aromaticity patterns change ...

Protein-complex structure completion using IPCAS (Iterative Protein Crystal structure Automatic Solution).

Protein complexes are essential components in many cellular processes. In this study, a procedure to determine the protein-complex structure from a partial molecular-replacement (MR) solution is demonstrated using a direct-method-aided dual-space iterative phasing and model-building program suite, IPCAS (Iterative Protein Crystal structure Automatic Solution). The IPCAS iteration procedure involves (i) real-space model building and refinement, (ii) direct-method-aided reciprocal-space phase refinement and (iii) phase improvement through density modification. The procedure has been tested with four protein complexes, including two previously unknown structures. It was possible to use IPCAS to build the whole complex structure from one or less than one subunit once the molecular-replacement method was able to give a partial solution. In the most challenging case, IPCAS was able to extend to the full length starting from less than 30% of the complex structure, while conventional model-building procedures were unsuccessful.

Real-space multiple-scattering Hubbard model calculations for d- and f-state materials.

Calculations are presented of the electronic structure and X-ray spectra of materials with correlated d- and f-electron states based on the Hubbard model, a real-space multiple-scattering formalism and a rotationally invariant local density approximation. Values of the Hubbard parameter are calculated ab initio using the constrained random-phase approximation. The combination of the real-space Green's function with Hubbard model corrections provides an efficient approach to describe localized correlated electron states in these systems, and their effect on core-level X-ray spectra. Results are presented for the projected density of states and X-ray absorption spectra for transition metal- and lanthanide-oxides. Results are found to be in good agreement with experiment.

Anomalous toughening in nanoscale ferroelectrics with polarization vortices

Unusual mechanical behavior of cracks in nanoscale ferroelectrics, where spontaneous polarization characteristically forms closed-flux vortices, is investigated using state-of-the-art real-space phase-field modeling based on the Ginzburg–Landau theory. An anomalously large toughening effect is revealed in nanoscale ferroelectrics due to drastic stress release near the crack tip, which is almost one order of magnitude larger in stress intensity than that observed in macroscale materials. Such anomalous toughening is attributed to an unusual switching behavior of the polarization vortices in nanoscale ferroelectrics, which is no longer localized near the crack tip as in macroscale ferroelectrics, but expands to the entire structure through the splitting and multiplication of vortices. We further demonstrate that this local-to-global switching is intrinsically induced by strong cross-coupling between the ferroelectric polarization and mechanical strain that concentrates to the electro-elastic energy, not only in the vicinity of crack tip, but also to each polarization vortex due to its inhomogeneous distribution. Our finding provides a novel insight into nanoscale polarization vortices and leads to an entirely new strategy for the tailoring and improvement of fracture toughness in ferroelectric materials by engineering the microstructure of polarization vortices.

Interacting bosons in topological optical flux lattices

An interesting route to the realization of topological Chern bands in ultracold atomic gases is through the use of optical flux lattices. These models differ from the tight-binding real-space lattice models of Chern insulators that are conventionally studied in solid-state contexts. Instead, they involve the coherent coupling of internal atomic (spin) states, and can be viewed as tight-binding models in reciprocal space. By changing the form of the coupling and the number $N$ of internal spin states, they give rise to Chern bands with controllable Chern number and with nearly flat energy dispersion. We investigate in detail how interactions between bosons occupying these bands can lead to the emergence of fractional quantum Hall states, such as the Laughlin and Moore-Read states. In order to test the experimental realization of these phases, we study their stability with respect to band dispersion and band mixing. We also probe novel topological phases that emerge in these systems when the Chern number is greater than 1.

Real space electrostatics for multipoles. I. Development of methods.

We have extended the original damped-shifted force (DSF) electrostatic kernel and have been able to derive three new electrostatic potentials for higher-order multipoles that are based on truncated Taylor expansions around the cutoff radius. These include a shifted potential (SP) that generalizes the Wolf method for point multipoles, and Taylor-shifted force (TSF) and gradient-shifted force (GSF) potentials that are both generalizations of DSF electrostatics for multipoles. We find that each of the distinct orientational contributions requires a separate radial function to ensure that pairwise energies, forces, and torques all vanish at the cutoff radius. In this paper, we present energy, force, and torque expressions for the new models, and compare these real-space interaction models to exact results for ordered arrays of multipoles. We find that the GSF and SP methods converge rapidly to the correct lattice energies for ordered dipolar and quadrupolar arrays, while the TSF is too severe an approximation to provide accurate convergence to lattice energies. Because real-space methods can be made to scale linearly with system size, SP and GSF are attractive options for large Monte Carlo and molecular dynamics simulations, respectively.

Real space electrostatics for multipoles. II. Comparisons with the Ewald sum.

We report on tests of the shifted potential (SP), gradient shifted force (GSF), and Taylor shifted force (TSF) real-space methods for multipole interactions developed in Paper I of this series, using the multipolar Ewald sum as a reference method. The tests were carried out in a variety of condensed-phase environments designed to test up to quadrupole-quadrupole interactions. Comparisons of the energy differences between configurations, molecular forces, and torques were used to analyze how well the real-space models perform relative to the more computationally expensive Ewald treatment. We have also investigated the energy conservation, structural, and dynamical properties of the new methods in molecular dynamics simulations. The SP method shows excellent agreement with configurational energy differences, forces, and torques, and would be suitable for use in Monte Carlo calculations. Of the two new shifted-force methods, the GSF approach shows the best agreement with Ewald-derived energies, forces, and torques and also exhibits energy conservation properties that make it an excellent choice for efficient computation of electrostatic interactions in molecular dynamics simulations. Both SP and GSF are able to reproduce structural and dynamical properties in the liquid models with excellent fidelity.

Interpreting the effect of de-solvation on structure of molecular crystals.

The structure effects of varying hydration/solvation levels in molecular crystals can sometimes be difficult to characterize with analytical techniques based solely on Bragg diffraction or other more common methods such as thermal analysis or spectroscopy. It can be demonstrated that supplementary scattering features such as diffuse and satellite intensities can provide insight into these processes even just from a qualitative standpoint. Understanding the nature of these processes is of great importance to many industrial applications (e.g. pharmaceuticals, bulk characterization). One previous caveat is that interpretations for these features are often restricted to experts, yet our work demonstrates this is not the case. For our examples, real-space models can be used to calculate both diffuse diffraction and inter-modulation satellite features. In one case study what we observe when the water leaves the crystal is an incomplete phase transformation and each crystallite in the bulk can be explained as being made up of disordered layers of the different structure phases with an intermediate phase layer resulting in satellite reflections. Another example demonstrates how in a crystal which has one solvent replaced for another, temperature sensitive phase transitional phenomena are induced. Models based on disorder diffraction features not only provide further insight into understanding of the de-solvation process but also could account for observed changes in PXRD from bulk. This can be related to similar material behaviors observed in diffraction patterns from more complex host-guest systems.

Enhancement of magnetic stripe order in iron-pnictide superconductors from the interaction between conduction electrons and magnetic impurities.

Recent experimental studies have revealed several unexpected properties of Mn-doped BaFe(2)As(2). These include extension of the stripelike magnetic (π,0) phase to high temperatures above a critical Mn concentration only, the presence of diffusive and weakly temperature dependent magnetic (π,π) checkerboard scattering, and an apparent absent structural distortion from tetragonal to orthorhombic symmetry. Here, we study the effects of magnetic impurities both below and above the Néel transition temperature within a real-space five-band model appropriate to the iron pnictides. We show how these experimental findings can be explained by a cooperative behavior of the magnetic impurities and the conduction electrons mediating the Ruderman-Kittel-Kasuya-Yosida interactions between them.

Strain-induced polarity switching of magnetic vortex in Fe1−xGax alloys with different compositions

The strain-induced polarity switching of magnetic vortex in the Fe1−xGax nanodots with different compositions is demonstrated by a real-space phase-field model, which explicitly includes the cross-coupling between magnetization and mechanical strain. The composition of Fe1−xGax nanodots has significant influence on the critical shear strain that induces the polarity switching of magnetization vortex. The critical shear strain in the Fe71Ga29 nanodot is one order of magnitude smaller than that of the Fe19Ga81 nanodot, which makes the polarity switching much easier under a mechanical shear strain. In addition, we elucidate that both the magnetostrictive coefficient and exchange stiffness that changes with compositions play the decisive role in the critical behavior; the higher magnetostrictive coefficient (or lower exchange stiffness) decreases critical shear strain.

Multi-Band-Stop Filter for Single-Photon Transport Based on a One-Dimensional Waveguide Side Coupled with Optical Cavities

A model of a multi-band-stop filter is proposed for single-photon transport, using a one-dimensional waveguide side coupled with a series of optical cavities. Its transmission behavior is theoretically studied by a real-space model Hamiltonian and is found to depend on cavity mode frequencies, cavity relative phases, as well as cavity number and the coupling strength between the waveguide and the optical cavities. With proper cavity-mode frequencies and relative phases, the proposed model shows multi-band-stop regions and a rectangular transmission spectrum. Based on these phenomena, optical filters with more than one band-stop regions are simulated with gold material in the THz and communication band.

CRYO-EM Atomic Model of Brome Mosaic Virus Derived from Direct Electron Detection Images and a Real-Space Model Optimization Protocol

Recent advances in cryo-EM have enabled structure determination of macromolecules at near-atomic resolution. However, de novo structure determination remains susceptible to model bias and overfitting, potentially yielding an inaccurate structure even if resolution appears high. Here, we describe a complete workflow for data acquisition, processing, modeling, and validation of an RNA virus, Brome Mosaic Virus (BMV). Data was collected using movies with a direct electron detector in integrating mode with a cumulative exposure beyond the traditional radiation damage limit. Reconstruction based on randomly-generated initial models yielded a map at 3.3 and 3.8 A resolution, with and without subunit averaging, respectively. We used this map to compute a de novo Cα backbone model, which was converted to an all-atom model and optimized with a newly-implemented real-space refinement protocol. The final de novo atomic model ranks in the top 99th percentile when compared to PDB structures at equivalent resolution using statistical scores routinely used in X-ray crystallography.

PDF analysis of ferrihydrite: Critical assessment of the under-constrained akdalaite model

In an effort to shed light on the intricate structure of ferrihydrite, its pair distribution function (PDF) derived from high-energy X-ray scattering (HEXS) data was refined with the single-phase akdalaite model, possessing 20% of the Fe atoms in tetrahedral coordination, and a modified akdalaite model in which Fe has only octahedral coordination. The second model is analogous to the predominant f-phase (ABAC stacking sequence) of classical multi-phase ferrihydrite. The contribution from the disordered d-phase component (randomly stacked ABA and ACA double-layer fragments) of the classical model was recovered in the modified akdalaite description by increasing the atomic motion of the ABAC motif above the double-layer distance 4.2 A to simulate aperiodic stacking faults. Results show that the original and modified akdalaite representations provide near-identical fits to the ferrihydrite PDF. In the original single-phase and periodic model, the plurality of the Fe-O and Fe-Fe distances resulting from phase mixtures and defects are reconciled artificially by taking a large unit cell with three independent Fe sites, two Fe coordinations, and under-constrained atomic positions. Correlation matrices reveal that many fitted parameters are linearly correlated, thus explaining the crystallographic and chemical inconsistencies of the as-refined akdalaite model which have been identified in the literature. Structurally more constrained, the modified akdalaite model does not suffer from bias and provides a more robust description of the PDF data. However, because structural defects and inhomogeneities are not physically present but introduced artificially in PDF modeling, the crystallographic description of ferrihydrite by real-space modeling of HEXS data has an idealized character. To facilitate further understanding of the ferrihydrite structure, the PDF data are provided as supplementary material[1][1] for interlaboratory testing, and as a resource as more sophisticated tools may be brought to bear on this complex problem. [1]: #fn-13

Fractal dynamics in chaotic quantum transport

Despite several experiments on chaotic quantum transport in two-dimensional systems such as semiconductor quantum dots, corresponding quantum simulations within a real-space model have been out of reach so far. Here we carry out quantum transport calculations in real space and real time for a two-dimensional stadium cavity that shows chaotic dynamics. By applying a large set of magnetic fields we obtain a complete picture of magnetoconductance that indicates fractal scaling. In the calculations of the fractality we use detrended fluctuation analysis-a widely used method in time-series analysis-and show its usefulness in the interpretation of the conductance curves. Comparison with a standard method to extract the fractal dimension leads to consistent results that in turn qualitatively agree with the previous experimental data.

Role of grain orientation distribution in the ferroelectric and ferroelastic domain switching of ferroelectric polycrystals

The non-linear electromechanical behavior of ferroelectric polycrystals stems from polarization/domain switching, which are affected by the grain boundaries and grain orientations. The effects of grain orientation distribution on the domain switching and non-linear behavior of a two-dimensional ferroelectric polycrystal subjected to an electric or/and mechanical load are investigated by computer simulations with a real-space phase-field model. Phase-field simulations indicate that the macroscopic coercive field, remanent polarization and remanent strain in the polycrystal with a random distribution of grain orientation are correspondingly smaller than those in the polycrystal with a uniform distribution of grain orientation. However, the polycrystal with randomly distributed grain has a larger strain variation with the electric field than the polycrystal with uniformly distributed grains, which suggests that the random polycrystal has a better piezoelectric property than the uniform one. The different macroscopic non-linear behaviors of the ferroelectric polycrystals are attributed to different microscopic domain switching processes. For the polycrystal with randomly distributed grains, the domain switching takes place from the regions near the large angle grain boundaries, while new domains nucleate from the cross sections between the grain boundaries and the material surface in the polycrystal with uniform grain orientation.

Group delay of single-photon transmission in a waveguide side coupled with a Jaynes-Cummings chain

Using a real-space model Hamiltonian, we have theoretically studied the single-photon transmission in a waveguide side coupled with a Jaynes-Cummings chain (JCC). The JCC can induce the photon group advancement (GA) and group delay (GD) in different frequency ranges determined by JCC eigenmodes. For GA and GD, there exist different optimal JCC lengths. At certain frequency, the GA's maximum value as usual increases with decreasing the cavity dissipation, whereas the GD's eventually reaches saturation. For a 1.55 -μm photon, our calculation indicates that the GD's maximum value is about 400 ps simultaneously with a large transmission.

Small-Angle Neutron Scattering Study of Protein Crowding in Liquid and Solid Phases: Lysozyme in Aqueous Solution, Frozen Solution, and Carbohydrate Powders

The structure, interactions, and interprotein configurations of the protein lysozyme were studied in a variety of phases. These properties have been studied under a variety of solution conditions before, during, and after freezing and after freeze-drying in the presence of glucose and trehalose. Contrast variation experiments have also been performed to determine which features of the scattering in the frozen solutions are from the protein and which are from the ice structure. Data from lysozyme at concentrations ranging from 1 to 100 mg/mL in solution and water ice with NaCl concentrations ranging from 0 to 0.4 mol/L are fit to model small-angle neutron scattering (SANS) intensity functions consisting of an ellipsoidal form factor and either a screened-Coulomb or hard-sphere structure factor. Parameters such as protein volume fraction and long dimension are followed as a function of temperature and salt concentration. The SANS results are compared to real space models of concentrated lysozyme solutions at the same volume fractions obtained from Monte Carlo simulations. A cartoon representation of the frozen lysozyme solution in 0 mol/L NaCl is presented based on the SANS and Monte Carlo results, along with those obtained from other complementary methods.

THE CLUSTERING CHARACTERISTICS OF H I-SELECTED GALAXIES FROM THE 40% ALFALFA SURVEY

The 40% Arecibo Legacy Fast ALFA (ALFALFA) survey catalog (\alpha.40) of approximately 10,150 HI-selected galaxies is used to analyze the clustering properties of gas-rich galaxies. By employing the Landy-Szalay estimator and a full covariance analysis for the two-point galaxy-galaxy correlation function, we obtain the real-space correlation function and model it as a power law, \xi(r) = (r/r_0)^(-\gamma), on scales less than 10 h^{-1} Mpc. As the largest sample of blindly HI-selected galaxies to date, \alpha.40 provides detailed understanding of the clustering of this population. We find \gamma = 1.51 +/- 0.09 and r_0 = 3.3 +0.3, -0.2 h^{-1} Mpc, reinforcing the understanding that gas-rich galaxies represent the most weakly clustered galaxy population known; we also observe a departure from a pure power law shape at intermediate scales, as predicted in \Lambda CDM halo occupation distribution models. Furthermore, we measure the bias parameter for the \alpha.40 galaxy sample and find that HI galaxies are severely antibiased on small scales, but only weakly antibiased on large scales. The robust measurement of the correlation function for gas-rich galaxies obtained via the \alpha.40 sample constrains models of the distribution of HI in simulated galaxies, and will be employed to better understand the role of gas in environmentally-dependent galaxy evolution.

Momentum-space finite-size corrections for quantum Monte Carlo calculations

Extended solids are frequently simulated as finite systems with periodic boundary conditions, which due to the long-range nature of the Coulomb interaction may lead to slowly decaying finite-size errors. In the case of quantum Monte Carlo simulations, which are based on real space, both real-space and momentum-space solutions to this problem exist. Here, we describe a hybrid method which using real-space data models the spherically averaged structure factor in momentum space. We show that (i) by integration our hybrid method exactly maps onto the real-space model periodic Coulomb-interaction (MPC) method and (ii) therefore our method combines the best of both worlds (real space and momentum space). One can use known momentum-resolved behavior to improve convergence where MPC fails (e.g., at surfacelike systems). In contrast to pure momentum-space methods, our method only deals with a simple single-valued function and hence better lends itself to interpolation with exact small-momentum data as no directional information is needed. By virtue of integration, the resulting finite-size corrections can be written as an addition to MPC.