Long-range Component Research Articles

Analysis of long series of longitudinal ordinal data using marginalized models

Marginalized models (Heagerty, 1999, 2002) are often used for short longitudinal series when population averaged effects are of interest. Lee and Daniels (2007, 2008) proposed marginalized models for the analysis of longitudinal ordinal data to permit likelihood-based estimation of marginal mean parameters. In this paper, we extend their work to accommodate the response dependence that we have seen with long series of response data (the functional form of response dependence has both serial and long-range components). Maximum likelihood estimation is proposed utilizing the Quasi-Newton algorithm with a Quasi Monte Carlo method for integration of the random effects. The methods are illustrated on quality of life data from a recent lung cancer clinical trial.

Nanoadhesion of Staphylococcus aureus onto Titanium Implant Surfaces

Adhesion of bacteria to dental implant surfaces is the critical initial step in the process of biofilm colonization; however, the specific nanoadhesive interactions occurring during the first contact between bacterial cells and biomaterial substrates remain poorly understood. In this report, we utilize single-cell force spectroscopy to characterize the dynamics of the initial interaction between living Staphylococcus aureus cells and machined titanium surfaces at the nanoscale. Values for maximum adhesion force were found to increase from 0-s (–0.27 ± 0.30 nN) to 60-s (–9.15 ± 0.78 nN) surface delays, with similar results observed for total adhesion work (7.39 ± 2.38 and 988.06 ± 117.08 aJ, respectively). Single unbinding events observed at higher surface delays were modeled according to the wormlike chain model, obtaining molecular contour-length predictions of 314.06 ± 9.27 nm. Average single-bond rupture forces of −0.95 ± 0.04 nN were observed at increased contact times. Short- and long-range force components of bacterial adhesion were obtained by Poisson analysis of single unbinding event peaks, yielding values of −0.75 ± 0.04 and −0.58 ± 0.15 nN, respectively. Addition of 2-mg/mL chlorhexidine to the buffer solution resulted in the inhibition of specific adhesive events but an increased overall adhesion force and work. These results suggest that initial attachment of S. aureus to smooth titanium is mostly mediated by short-range attractive forces observed at higher surface delays.

Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration.

A challenge in density functional theory is developing functionals that simultaneously describe intermolecular electron correlation and electron delocalization. Recent exchange-correlation functionals address those two issues by adding corrections important at long ranges: an atom-centered pairwise dispersion term to account for correlation and a modified long-range component of the electron exchange term to correct for delocalization. Here we investigate how those corrections influence the accuracy of binding free energy predictions for sodium-water clusters. We find that the dual-corrected ωB97X-D functional gives cluster binding energies closest to high-level ab initio methods (CCSD(T)). Binding energy decomposition shows that the ωB97X-D functional predicts the smallest ion-water (pairwise) interaction energy and larger multibody contributions for a four-water cluster than most other functionals - a trend consistent with CCSD(T) results. Also, ωB97X-D produces the smallest amounts of charge transfer and the least polarizable waters of the density functionals studied, which mimics the lower polarizability of CCSD. When compared with experimental binding free energies, however, the exchange-corrected CAM-B3LYP functional performs best (error <1 kcal/mol), possibly because of its parametrization to experimental formation enthalpies. For clusters containing more than four waters, "split-shell" coordination must be considered to obtain accurate free energies in comparison with experiment.

Forward-backward multiplicity correlations in pp collisions at s $$ \sqrt{s} $$ = 0.9, 2.76 and 7 TeV

The strength of forward-backward (FB) multiplicity correlations is measured by the ALICE detector in proton-proton (pp) collisions at $\sqrt{s}=0.9$, 2.76 and 7 TeV. The measurement is performed in the central pseudorapidity region ($|\eta| < 0.8$) for the transverse momentum $p_{\rm T}>0.3$ GeV/$c$. Two separate pseudorapidity windows of width ($\delta \eta$) ranging from 0.2 to 0.8 are chosen symmetrically around $\eta=0$. The multiplicity correlation strength ($b_{\rm cor}$) is studied as a function of the pseudorapidity gap ($\eta_{\rm gap}$) between the two windows as well as the width of these windows. The correlation strength is found to decrease with increasing $\eta_{\rm gap}$ and shows a non-linear increase with $\delta\eta$. A sizable increase of the correlation strength with the collision energy, which cannot be explained exclusively by the increase of the mean multiplicity inside the windows, is observed. The correlation coefficient is also measured for multiplicities in different configurations of two azimuthal sectors selected within the symmetric FB $\eta$-windows. Two different contributions, the short-range (SR) and the long-range (LR), are observed. The energy dependence of $b_{\rm cor}$ is found to be weak for the SR component while it is strong for the LR component. Moreover, the correlation coefficient is studied for particles belonging to various transverse momentum intervals chosen to have the same mean multiplicity. Both SR and LR contributions to $b_{\rm cor}$ are found to increase with $p_{\rm T}$ in this case. Results are compared to PYTHIA and PHOJET event generators and to a string-based phenomenological model. The observed dependencies of $b_{\rm cor}$ add new constraints on phenomenological models.

Magnetic and thermo-structural design optimization of the Plasma Grid for the MITICA neutral beam injector

MITICA is a prototype of the heating neutral beam (HNB) Injectors for ITER, built with the purpose of validating the injector design and optimizing its operation. Its goal is to produce a focused beam of neutral particles (H or D) with energy up to 1MeV and power of 16MW for 1h. MITICA includes a Radio Frequency (RF) Plasma Source for the production of negative ions, a multi-stage electrostatic accelerator (up to 1MV and 40A), a neutralizer, a residual ion dump and a calorimeter. A transverse magnetic field in the Ion source and accelerator, including both a long-range component and a local component is crucial for obtaining the required Ion current and accelerator efficiency. The long-range component is produced by the current flowing through the plasma grid (PG) and related bus-bars. The PG current distribution and the uniformity of the resulting magnetic field have been optimized by detailed finite element (FEM) models. Hollow volumes in the thick copper part of the PG among beamlet groups allow a more uniform PG current distribution and a consequently uniform magnetic field in front of the grid. The paper describes in detail the PG geometry optimization procedure and the related magnetic and thermo-structural FEM analyses.

The Importance of Short- and Long-Range Exchange on Various Excited State Properties of DNA Monomers, Stacked Complexes, and Watson-Crick Pairs.

We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of nonempirically tuned range-separated functionals, for predicting a diverse set of electronic excitations in DNA nucleobase monomers and dimers. This large and extensive set of excitations comprises a total of 50 different transitions (for each tested DFT functional) that includes several n → π and π → π* valence excitations, long-range charge-transfer excitations, and extended Rydberg transitions (complete with benchmark calculations from high-level EOM-CCSD(T) methods). The presence of localized valence excitations as well as extreme long-range charge-transfer excitations in these systems poses a serious challenge for TD-DFT methods that allows us to assess the importance of both short- and long-range exchange contributions for simultaneously predicting all of these various transitions. In particular, we find that functionals that do not have both short- and full long-range exchange components are unable to predict the different types of nucleobase excitations with the same accuracy. Most importantly, the current study highlights the importance of both short-range exchange and a nonempirically tuned contribution of long-range exchange for accurately predicting the diverse excitations in these challenging nucleobase systems.

Basis convergence of range-separated density-functional theory.

Range-separated density-functional theory (DFT) is an alternative approach to Kohn-Sham density-functional theory. The strategy of range-separated density-functional theory consists in separating the Coulomb electron-electron interaction into long-range and short-range components and treating the long-range part by an explicit many-body wave-function method and the short-range part by a density-functional approximation. Among the advantages of using many-body methods for the long-range part of the electron-electron interaction is that they are much less sensitive to the one-electron atomic basis compared to the case of the standard Coulomb interaction. Here, we provide a detailed study of the basis convergence of range-separated density-functional theory. We study the convergence of the partial-wave expansion of the long-range wave function near the electron-electron coalescence. We show that the rate of convergence is exponential with respect to the maximal angular momentum L for the long-range wave function, whereas it is polynomial for the case of the Coulomb interaction. We also study the convergence of the long-range second-order Møller-Plesset correlation energy of four systems (He, Ne, N2, and H2O) with cardinal number X of the Dunning basis sets cc - p(C)V XZ and find that the error in the correlation energy is best fitted by an exponential in X. This leads us to propose a three-point complete-basis-set extrapolation scheme for range-separated density-functional theory based on an exponential formula.

Coulomb Force Effects in Deuteron--Proton Breakup Reaction

A large set of cross-section data for the H-1 (d,pp)n breakup reaction was measured at 130 MeV deuteron beam energy with the Germanium Wall setup covering the range of very forward polar angles. In the investigated part of the phase-space, the dynamics is dominated by the Coulomb force influence. The data are compared with results of theoretical calculations based on the realistic Argonne V18 potential supplemented with the long-range electromagnetic component. The predictions also include the Urbana IX three nucleon force model. The cross-section data reveal seizable Coulomb force effects.

Pseudorapidity dependence of long-range two-particle correlations in pPb collisions at 5.02 TeV with CMS

CMS measurements of two-particle correlations of charged particles have previously been published for proton–proton (pp), proton–lead (pPb), and lead–lead (PbPb) systems. This analysis studies the pseudorapidity dependency of the two-particle correlations by restricting one of the particles in a narrow η range. The near-side (Δϕ≈0) correlation in high-multiplicity collisions is decomposed into a short-range jet-like component and a long-range ridge component in pseudorapidity. The jet-like correlations are subtracted, and the remaining ridge correlations are studied versus Δη. Furthermore, the Fourier coefficients of the two-particle correlations are extracted for high-multiplicity collisions, with and without subtraction of jet contributions approximated by the scaled low-multiplicity collision data. The η dependence of the azimuthal anisotropy parameters is reported.

An improved classical mapping method for homogeneous electron gases at finite temperature.

We introduce a modified classical mapping method to predict the exchange-correlation free energy and the structure of homogeneous electron gases (HEG) at finite temperature. With the classical map temperature parameterized on the basis of the quantum Monte Carlo simulation data for the correlation energy and exact results at high and low temperature limits, the new theoretical procedure greatly improves the classical mapping method for correlating the energetic properties HEG over a broad range of thermodynamic conditions. Improvement can also be identified in predicting the long-range components of the spin-averaged pair correlation functions.

New Methods for the Visualization of Incommensurately Modulated Structures

While the theory of incommensurate structure and composite crystallography is well established, methods for the visualization of modulated and composite crystal structures are few.[1] At the same time, databases featuring such structures have arisen [2], and there is a growing need for web-based tools that allow users to interactively explore such structures. This presentation is by the principal developer of Jmol, an international open-source collaborative molecular visualization project. It will focus on recent developments that have been made in this area. Jmol provides a flexible and crystallographically rich suite of functionality, including depiction of specific symmetry operations and selective sets of unit cells, selection of specific modes of modulation, use of color to show long-range low-frequency modulation components, and the depiction of relative modulation phasing through animation. From an archival perspective, Jmol development has been an opportunity to test the basic ontology of the IUCr msCIF standard [3], and a number of issues relating to this standard will be discussed, particularly in relation to multidimensional modulation. From an general educational perspective, Jmol for the first time allows easy access to a wide variety of examples of incommensurately and commensurately modulated structures and composite structures. Being accessible on virtually all platforms and within all major browsers, Jmol offers a novel mechanism for the wide-spread dissemination of understanding of this important class of crystal structure.

Spin-cycloid instability as the origin of weak ferromagnetism in the disordered perovskiteBi0.8La0.2Fe0.5Mn0.5O3

Powder neutron diffraction and magnetometry studies have been conducted to investigate the crystallographic and magnetic structure of ${\mathrm{Bi}}_{0.8}{\mathrm{La}}_{0.2}{\mathrm{Fe}}_{0.5}{\mathrm{Mn}}_{0.5}{\mathrm{O}}_{3}$. The compound stabilizes in the $Imma$ orthorhombic crystal symmetry in the measured temperature range of 5 to 380 K, with a transition to antiferromagnetic order at ${T}_{\mathrm{N}}\ensuremath{\approx}240$ K. The spin cycloid present for BiFeO${}_{3}$ is found to be absent with 50% Mn${}^{3+}$ cation substitution, leading to $G$-type antiferromagnetic order with an enhanced out-of-plane canted ferromagnetic component, evident from measurable weak-ferromagnetic hysteresis. Structural modifications do not solely explain this behavior, indicating that modified electron exchange interactions must be taken into account. A classical spin simulation was developed to investigate the effect of random substitution in a disordered pseudocubic perovskite. The calculations took into account the nearest-neighbor, next-nearest-neighbor, and Dzyaloshinskii-Moriya interactions, along with the local spin anisotropy. Using this framework to extend the established Hamiltonian model for BiFeO${}_{3}$, we show that only certain types of perturbations at a magnetic defect and the surrounding molecular fields trigger a simultaneous collapse of cycloidal order and the emergence of the long-range weak-ferromagnetic component. By adopting values for the Mn molecular fields appropriate for $\mathit{RE}$MnO${}_{3}$ ($\mathit{RE}=$ rare earth), simulations of BiMn${}_{0.5}$Fe${}_{0.5}{\mathrm{O}}_{3}$ exhibit the key magnetic properties of our experimental observations.

Spin-orbit coupling as a source of long-range triplet proximity effect in superconductor-ferromagnet hybrid structures

We investigate the proximity effect in diffusive superconducting hybrid structures with a spin-orbit (SO) coupling. Our study is focused on the singlet-triplet conversion and the generation of long-range superconducting correlations in ferromagnetic elements. We derive the quasiclassical equations for the Green's functions including the SO coupling terms in form of a background SU(2) field. With the help of these equations, we first present a complete analogy between the spin diffusion process in normal metals and the generation of the triplet components of the condensate in a diffusive superconducting structure in the presence of SO coupling. From this analogy it turns out naturally that the SO coupling is an additional source of the long-range triplet component (LRTC) besides the magnetic inhomogeneities studied in the past. We demonstrate an explicit connection between an inhomogeneous exchange field and SO coupling mechanisms for the generation of the LRTC and establish the conditions for the appearance of the LRTC in different geometries. We also consider a S/F bilayer in contact with normal metal with SO coupling and show that the latter can be used as a source for the LRTC. Our work gives a global description of the singlet-triplet conversion in hybrids structures in terms of generic spin-fields and our results are particularly important for the understanding of the physics underlying spintronics devices with superconductor elements.

Spatial modelling and uncertainty assessment of pyroclastic cover thickness in the Sorrento Peninsula

Assessing spatial variability of soil thickness is a critical issue for understanding and predicting slope processes. The present work was aimed at estimating the spatial scales at which the variation of pyroclastic cover thickness occurs in a sample area in the Sorrento Peninsula (Italy). Stochastic simulation was used to understand the spatial variability of pyroclastic cover thickness on Mount Pendolo and to assess its spatial uncertainty. In the study area, covering about 0.7 km2, thickness measurements were collected using electrical resistivity tomography profiles, continuous core drillings and steel rod penetrometric tests. Variographic analysis revealed the occurrence of an anisotropic behaviour along the N50 and N140 directions. In the latter anisotropic direction, a nested variogram was fitted including (1) a long-range component which could be related to large-scale factors, like the curvature of the slope and contributing area and (2) a shorter scale variation which is probably associated with the occurrence of denudation processes or to the articulate cover/bedrock interface. To assess the spatial variability and uncertainty of pyroclastic cover thickness, a stochastic simulation algorithm was used and 500 equally probable images of cover thickness were yielded. The results showed that a better thickness distribution map can be drawn by simulating the data collected on the slope and at the footslope separately. The approach also allowed delineating the areas characterized by greater uncertainty, suggesting supplementary measurements to further improve the cover thickness distribution model, thus reducing the uncertainty.

Removal of artifacts in knee joint vibroarthrographic signals using ensemble empirical mode decomposition and detrended fluctuation analysis

High-resolution knee joint vibroarthrographic (VAG) signals can help physicians accurately evaluate the pathological condition of a degenerative knee joint, in order to prevent unnecessary exploratory surgery. Artifact cancellation is vital to preserve the quality of VAG signals prior to further computer-aided analysis. This paper describes a novel method that effectively utilizes ensemble empirical mode decomposition (EEMD) and detrended fluctuation analysis (DFA) algorithms for the removal of baseline wander and white noise in VAG signal processing. The EEMD method first successively decomposes the raw VAG signal into a set of intrinsic mode functions (IMFs) with fast and low oscillations, until the monotonic baseline wander remains in the last residue. Then, the DFA algorithm is applied to compute the fractal scaling index parameter for each IMF, in order to identify the anti-correlation and the long-range correlation components. Next, the DFA algorithm can be used to identify the anti-correlated and the long-range correlated IMFs, which assists in reconstructing the artifact-reduced VAG signals. Our experimental results showed that the combination of EEMD and DFA algorithms was able to provide averaged signal-to-noise ratio (SNR) values of 20.52 dB (standard deviation: 1.14 dB) and 20.87 dB (standard deviation: 1.89 dB) for 45 normal signals in healthy subjects and 20 pathological signals in symptomatic patients, respectively. The combination of EEMD and DFA algorithms can ameliorate the quality of VAG signals with great SNR improvements over the raw signal, and the results were also superior to those achieved by wavelet matching pursuit decomposition and time-delay neural filter.

Analysis of dislocation pile-ups using a dislocation-based continuum theory

The increasing demand for materials with well-defined microstructure, accompanied by the advancing miniaturization of devices, is the reason for the growing interest in physically motivated, dislocation-based continuum theories of plasticity. In recent years, various advanced continuum theories have been introduced, which are able to described the motion of straight and curved dislocation lines. The focus of this paper is the question of how to include fundamental properties of discrete dislocations during their motion and interaction in a continuum dislocation dynamics (CDD) theory. In our CDD model, we obtain elastic interaction stresses for the bundles of dislocations by a mean-field stress, which represents long-range stress components, and a short range corrective stress component, which represents the gradients of the local dislocation density. The attracting and repelling behavior of bundles of straight dislocations of the same and opposite sign are analyzed. Furthermore, considering different dislocation pile-up systems, we show that the CDD formulation can solve various fundamental problems of micro-plasticity. To obtain a mesh size independent formulation (which is a prerequisite for further application of the theory to more complex situations), we propose a discretization dependent scaling of the short range interaction stress. CDD results are compared to analytical solutions and benchmark data obtained from discrete dislocation simulations.

Nematic Phase Emergence in Solutions of Similarly Charged Rodlike Polyelectrolytes

We extend an approximate theory in order to examine the properties of the one-component plasma (OCP) of similarly charged rodlike polyelectrolytes system from the weak- to the strong-coupling regimes. In addition, Monte Carlo simulations are performed in order to verify the approximate theory. The electrostatic interactions are decomposed into short- and long-range components treated within different approximations. In addition to the Coulomb interactions present within the system, the excluded volume interactions between the charged rods are included in our analysis within a second order virial reference system. By theory and numerical simulation, we find that the isotropic phase becomes unstable with reference to the orientational ordering performed by both electrostatic and excluded volume interactions. Good agreement between theory and numerical simulation is obtained for the conditions investigated.

Phonons and related spectra in bulk and monolayerV2O5

The phonons at the zone center are calculated for the layered material ${V}_{2}{\mathrm{O}}_{5}$ using density functional perturbation theory and are compared with experimental infrared and Raman spectra from literature. We find that significantly better agreement is obtained when the pseudopotential treats vanadium semicore states $3s$ and $3p$ as bands. Remaining discrepancies are shown to be related to the local density approximation overestimate of the bond-stretch mode frequencies. The vibrational mode patterns are studied and presented in detail. The same method is then applied to well-separated monolayers. We find significant changes in some phonon frequencies. In particular, the highest-frequency vanadium vanadyl-oxygen stretch modes show a blue-shift of order 6%--8%. The origin of this blue-shift is analyzed in terms of the force-constant changes between bulk and monolayer and is found to arise from a delicate balance of short- and long-range dipolar force components. The latter are affected by the changes in dielectric constants and in the Born-effective charges. The red-shifts of some of the low-frequency modes are found also to be related to a reduction in force constants within the layer, rather than the removal of interlayer bonds. In this case, it is primarily motions along the $x$ direction that are affected. The static and high-frequency dielectric constants are both found to be reduced in the monolayer.

On stocks and interest rates modeling in long-range dependent environment

We consider a multidimensional financial market with stochastic interest rates. The market has a long-range dependent component which is modeled with the help of several fractional Brownian motions with the Hurst indices belonging to (3/4, 1). Interval choice is motivated by both the mathematical and financial reasons. We develop the results of Hitsuda and Cheridito concerning semimartingale properties of the market containing a long-range dependent component with the high-valued Hurst index. We show how to reduce the market model with long-range dependence to semimartingale market and then apply the results of Amin and Jarrow concerning the markets with stochastic interest rates in order to prove the arbitrage-free property as well as to provide option pricing.

Symmetry-preserving mean field theory for electrostatics at interfaces.

We derive an instantaneous symmetry-preserving mean field equation relating the long-ranged component of the intermolecular interaction to an effective single particle potential. We verify the efficiency and accuracy of the symmetry-preserving mean field approach to treat complex nonuniform electrostatics and foresee its application to study self-assembly and disassembly processes at interfaces in many computer simulations.