Atomic Correlation Research Articles

Understanding the Correlation of Crystal Atoms with Photochemistry Property: Zn5(OH)6(CO3)2vs. ZnCO3

AbstractIn this work, Zn5(OH)6(CO3)2 nanosheets are prepared by a simple hydrothermal method, and ZnCO3 are also prepared to compare. It is found that compared with ZnCO3, hydroxyl anion greatly changes energy band structure and oxidation potential of valence band, and improves charge separation efficiency and rates of Zn5(OH)6(CO3)2. The time‐resolved photoluminescence (PL) results show that the average lifetime (τ) of carriers is 1.485 ns for Zn5(OH)6(CO3)2, while 0.380 ns for ZnCO3, illustrating a greatly low carrier recombination rate of Zn5(OH)6(CO3)2; and Zn5(OH)6(CO3)2 has a 20 times photocurrent higher than ZnCO3. Besides, Zn5(OH)6(CO3)2 has a greatly higher oxidation potential (5.05 V) than ZnCO3 (3.17 V), suggesting a high oxidizing ability of Zn5(OH)6(CO3)2. Under ultraviolet light irradiation (λ≤400 nm), 92% of MB can be degraded by Zn5(OH)6(CO3)2 after 80 min, which is 2.31 times as high as that of ZnCO3, although Zn5(OH)6(CO3)2 has a lower BET area (5.8 m2g−1) than ZnCO3 (7.7 m2g−1). This work favors to insight into the correlation of crystal atoms with photochemistry property for a photocatalyst.

Toward Electron Correlation and Electronic Properties from the Perspective of Information Functional Theory.

Over the last years, immense efforts have been made to apply the quantities of information theory to the electronic structure and properties of various systems. In this context, one can make use of one or many of the information theoretic quantities together to describe the total energy, its components, and other electronic properties. Such an idea is feasible through an approach so-called information functional theory, which in turn constitutes the cornerstone of the present investigation. More specifically, in this work several information theoretic quantities like Fisher information, Shannon entropy, Onicescu information energy, and Ghosh-Berkowitz-Parr entropy with the two representations of electron density and shape function are considered for reliable prediction of atomic and molecular correlation energies as well as several electronic properties such as atomization energies, electron affinities, and ionization potentials. It is shown that with more or less different accountabilities of the information theoretic quantities they can be introduced as useful descriptors for estimation of electron correlation energies for a large variety of systems including neutral atoms, cations, isoelectronic series, and molecules. This is also indeed the case for the electronic properties under study. Considering different notions of the information theoretic quantities with various scaling properties and varied physiochemical meanings about the electron density distribution, we find that instead of simulating all data using one of these quantities individually taking all of them together provides a better view for the description of correlation effects and electronic properties of systems.

Dynamics of quantum correlation of atoms immersed in a thermal quantum scalar fields with a boundary

In this paper, we study the behaviors of quantum correlation for two atoms immersed in a thermal bath of quantum scalar fields in the presence of a perfectly reflecting plane boundary. We firstly discuss the solving process of master equation that governs the system evolution. Then, we analyze the creation, revival and degradation of quantum correlation for initial zero-correlation state and initial entangled state. Specially, we discuss in detail the evolution of quantum correlation in certain special conditions and models. The distance from the boundary, besides the bath temperature and the interatomic separation, gives us more freedom in controlling the behaviors of quantum correlation. Compared with the sudden death and birth of entanglement, quantum correlation changes more smoothly and thus is more robust than entanglement.

Radiation-induced extreme elastic and inelastic interactions in concentrated solid solutions

One of the biggest challenges in the radiation induced defect science is to understand the complex nature of ion-atom interactions under highly extreme conditions. Here, we report the irradiation induced non-equilibrium defect formation in NiCoCr single phase concentrated solid solution alloy due to (i) the extreme inelastic and (ii) the coupled inelastic and elastic ion-atom interactions. These two conditions are achieved at 5 and 30μm penetration depths along the paths of swift heavy ions (1.542GeV Bi). In general, the irradiation induced damage consists of interstitial-type dislocation loops and vacancy-type stacking fault tetrahedra (SFT). Near the surface (~5μm) where electronic energy loss is dominating (~62.5keVnm−1), the atomic motion primarily results in the formation of SFT. A noticeable increase of dislocation loop formation is observed at 30μm near the maximum energy deposition from elastic interactions (~4.9keVnm−1), as compared to the near surface region (~0.06keVnm−1). Insights on the complex electronic and atomic correlations of extreme energy deposition and dissipation on defect dynamics and structural stability may pave the way for new design principles of radiation–tolerant structural alloys.

Structure and atomic correlations in molecular systems probed by XAS reverse Monte Carlo refinement

The Reverse Monte Carlo (RMC) algorithm for structure refinement has been applied to x-ray absorption spectroscopy (XAS) multiple-edge data sets for six gas phase molecular systems (SnI2, CdI2, BBr3, GaI3, GeBr4, GeI4). Sets of thousands of molecular replicas were involved in the refinement process, driven by the XAS data and constrained by available electron diffraction results. The equilibrated configurations were analysed to determine the average tridimensional structure and obtain reliable bond and bond-angle distributions. Detectable deviations from Gaussian models were found in some cases. This work shows that a RMC refinement of XAS data is able to provide geometrical models for molecular structures compatible with present experimental evidence. The validation of this approach on simple molecular systems is particularly important in view of its possible simple extension to more complex and extended systems including metal-organic complexes, biomolecules, or nanocrystalline systems.

Lipid Domains at the Plasma Membrane of Red Blood Cells: Organization and Involvement in Deformation

Erythrocytes are highly deformable cells that go through capillaries eight times-narrower than their diameter to deliver oxygen throughout the body. This deformability is linked to erythrocytes specific features such as their biconcave shape, their highly regulated hemoglobin concentration and the strong anchorage of their membrane to the underlying cytoskeleton. Based on our recent evidence for submicrometric lipid domains upon labeling of cholesterol and polar lipids (sphingomyelin, phosphatidylcholine, ganglioside GM1) in erythrocyte outer plasma membrane leaflet, we here explore the mapping of lipid domains in erythrocytes at resting state and under deformation. Thanks to differential properties between cholesterol- and polar lipid-enriched domains (curvature association, lipid order, temperature dependence, cholesterol content dependence) and partial spatial dissociation, we suggest the coexistence of at least two types of lipid domains at the erythrocyte surface at resting state: those enriched in cholesterol and preferentially associated with high-curvature membranes and those mostly enriched in phosphatidylcholine and ganglioside GM1 and associated with low-curvature membranes. Biophysical properties of these domains are currently explored by atomic force microscopy and force correlation spectroscopy. Lipid domains abundance, composition and biophysical properties are differentially modulated by (i) impairment of erythrocyte deformability (energy depletion, modulation of anchorage to the cytoskeleton by pharmacological and genetic approaches), (ii) simulation of deformation (calcium channel activation, stretching in silicon chambers) and (iii) simulation of shape restoration after deformation (stimulation of calcium efflux). Indeed, high-curvature cholesterol-enriched domains gather under deformation while low-curvature domains become enriched in sphingomyelin and lose some of their ganglioside GM1 enrichment. We hypothesize that cholesterol-enriched domains can help to stabilize high curvature membranes during deformation while polar lipid-enriched domains, especially those enriched in sphingomyelin, are involved into calcium balance regulation during or after deformation. This hypothesis is under investigation.

Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics

Since the elucidation of the genetic code almost 50 years ago, many nonrandom aspects of its codon organization remain only partly resolved. Here, we investigate the recent hypothesis of ‘dual-use’ codons which proposes that in addition to allowing adjustment of codon optimization to tRNA abundance, the degeneracy in the triplet-based genetic code also multiplexes information regarding DNA’s helical shape and protein-binding dynamics while avoiding interference with other protein-level characteristics determined by amino acid properties. How such structural optimization of the code within eukaryotic chromatin could have arisen from an RNA world is a mystery, but would imply some preadaptation in an RNA context. We analyzed synonymous (protein-silent) and nonsynonymous (protein-altering) mutational impacts on molecular dynamics in 13823 identically degenerate alternative codon reorganizations, defined by codon transitions in 7680 GPU-accelerated molecular dynamic simulations of implicitly and explicitly solvated double-stranded aRNA and bDNA structures. When compared to all possible alternative codon assignments, the standard genetic code minimized the impact of synonymous mutations on the random atomic fluctuations and correlations of carbon backbone vector trajectories while facilitating the specific movements that contribute to DNA polymer flexibility. This trend was notably stronger in the context of RNA supporting the idea that dual-use codon optimization and informational multiplexing in DNA resulted from the preadaptation of the RNA duplex to resist changes to thermostability. The nonrandom and divergent molecular dynamics of synonymous mutations also imply that the triplet-based code may have resulted from adaptive functional expansion enabling a primordial doublet code to multiplex gene regulatory information via the shape and charge of the minor groove.

Quantum metrology with atom and light correlation

The measurement of physical quantities and measurement units standard promote the development of metrology. Especially, the developments of laser interference and atomic frequency standard bring a revolutionary leap for metrology. Many precision measurement techniques have been proposed and experimentally demonstrated, such as gravitational wave measurements and laser gyroscopes based on laser interferometry, and atomic clocks and atomic gyroscopes based on the atom interferometry. Recently, a new branch of science, quantum metrology, has grown up to further explore and exploit the quantum techniques for precision measurement of physical quantities.#br#This paper will focus on recent developments in quantum metrology and interference based on coherence and correlation of light and atom. Firstly, we briefly review the development of metrology. Then, we introduce our own researches in recent years, including quantum-correlation SU(1,1) optical interferometer based on four wave mixing process in atomic vapor and the atom-light hybrid interferometer based on Raman scattering in atomic vapor.#br#Interferometer is a powerful tool to measure physical quantities sensitive to the inference wave with high precision, and has been widely used in scientific research, industry test, navigation and guidance system. For example, the laser interferometer is able to measure optical phase sensitive quantities, including length, angular velocity, gravitational wave and so on. Meanwhile, the atom interferometer is sensitive to the change of atomic phase caused by the light, gravity, electric and magnetic fields. As a new type of interferometry, the atom-light hybrid interferometer, is sensitive to both the optical phase and atomic phase. Furthermore, SU(1,1) interferometer and nonlinear atom-light hybrid interferometer have the ability to beat the standard quantum limit of phase sensitivity. Quantum interference technology, whose phase measurement accuracy can break through the limit of standard quantum limit, is the core of quantum metrology and quantum measurement technology.

HDL particles incorporate into lipid bilayers \u2013 a combined AFM and single molecule fluorescence microscopy study

The process, how lipids are removed from the circulation and transferred from high density lipoprotein (HDL) – a main carrier of cholesterol in the blood stream – to cells, is highly complex. HDL particles are captured from the blood stream by the scavenger receptor, class B, type I (SR-BI), the so-called HDL receptor. The details in subsequent lipid-transfer process, however, have not yet been completely understood. The transfer has been proposed to occur directly at the cell surface across an unstirred water layer, via a hydrophobic channel in the receptor, or after HDL endocytosis. The role of the target lipid membrane for the transfer process, however, has largely been overlooked. Here, we studied at the single molecule level how HDL particles interact with synthetic lipid membranes. Using (high-speed) atomic force microscopy and fluorescence correlation spectroscopy (FCS) we found out that, upon contact with the membrane, HDL becomes integrated into the lipid bilayer. Combined force and single molecule fluorescence microscopy allowed us to directly monitor the transfer process of fluorescently labelled amphiphilic lipid probe from HDL particles to the lipid bilayer upon contact.

Simulation study of intercalation complexes of kaolinite with simple amides as primary intercalation reagents

Delamination/exfoliation of book-like kaolinite particles is one of the most promising ways to produce aluminosilicate nanoscrolls. For the delamination of the kaolinite layers, multi-step intercalation/deintercalation procedures are used. In the first, direct intercalation step, the intercalation reagents are typically small organic molecules possessing high dipole moment. We modeled, evaluated and compared the incorporation features of formamide, urea and N-methylformamide molecules into the interlayer space of kaolinite by classical molecular simulations using realistic CHARMM-based atomic force fields. Besides the determination of characteristic basal spacings of the intercalation complexes, we compared the density and orientation distributions of the guest molecules, as well as atomic pair correlation functions. From the simulations we also calculated the typical intermolecular interaction energies and estimated the translational mobility of the different substances. Our results show that urea has some preference over the other substances in multi-step, heat-treating intercalation/deintercalation procedures with kaolinite.

Contribution to viscosity from the structural relaxation via the atomic scale Green-Kubo stress correlation function.

We studied the connection between the structural relaxation and viscosity for a binary model of repulsive particles in the supercooled liquid regime. The used approach is based on the decomposition of the macroscopic Green-Kubo stress correlation function into the correlation functions between the atomic level stresses. Previously we used the approach to study an iron-like single component system of particles. The role of vibrational motion has been addressed through the demonstration of the relationship between viscosity and the shear waves propagating over large distances. In our previous considerations, however, we did not discuss the role of the structural relaxation. Here we suggest that the contribution to viscosity from the structural relaxation can be taken into account through the consideration of the contribution from the atomic stress auto-correlation term only. This conclusion, however, does not mean that only the auto-correlation term represents the contribution to viscosity from the structural relaxation. Previously the role of the structural relaxation for viscosity has been addressed through the considerations of the transitions between inherent structures and within the mode-coupling theory by other authors. In the present work, we study the structural relaxation through the considerations of the parent liquid and the atomic level stress correlations in it. The comparison with the results obtained on the inherent structures also is made. Our current results suggest, as our previous observations, that in the supercooled liquid regime, the vibrational contribution to viscosity extends over the times that are much larger than the Einstein's vibrational period and much larger than the times that it takes for the shear waves to propagate over the model systems. Besides addressing the atomic level shear stress correlations, we also studied correlations between the atomic level pressure elements.

Short-range order and correlations of S atoms in thin-layer PbS structures

The correlations of sulfur atoms and vacancies in the planar square and hexagonal nonmetal sublattices formed by the 4(b) and 8(c) sites in thin-layer PbS films with a cubic D03 structure have been studied.

The effects of higher orders of perturbation theory on the correlation energy of atoms and bonds in molecules

AbstractWe examine, for the first time, the effects of higher orders of Møller–Plesset perturbation theory on the individual atoms within a molecule and the bonds between them, via the topological energy partitioning method of interacting quantum atoms. In real terms (i.e., not by absolute value) MP3 decreases the correlation energy of a bond, and MP4SDQ also decreases the energy of the atoms at either end of the bond. In addition, we investigated long‐range through‐space dispersive effects on a H2 oligomer. Overall, MP3 is the largest correction to the correlation energy, and most of that energy is allocated to chemical bonds, reducing their values in actual terms. The MP4SDQ bond correlation correction, despite being relatively small, tends to have two effects: (i) for small or negative correlation energies MP4SDQ tends to decrease the bond correlation values even more, and (ii) for large (positive) bond correlation energies MP4SDQ tends to restore the bond correlation energies from the MP3 back toward the MP2 values. Furthermore, each individual part of a molecule or complex (atom or bond) has a specific convergence pattern for the MPn series: through‐space interactions converge at MP2 but bonds converge at MP3 level. The atomic correlation energy appears to head toward convergence at the MP4 level.

Coupled electronic and atomic effects on defect evolution in silicon carbide under ion irradiation

Understanding energy dissipation processes in electronic/atomic subsystems and subsequent non-equilibrium defect evolution is a long-standing challenge in materials science. In the intermediate energy regime, energetic particles simultaneously deposit a significant amount of energy to both electronic and atomic subsystems of silicon carbide (SiC). Here we show that defect evolution in SiC closely depends on the electronic-to-nuclear energy loss ratio (Se/Sn), nuclear stopping powers (dE/dxnucl), electronic stopping powers (dE/dxele), and the temporal and spatial coupling of electronic and atomic subsystem for energy dissipation. The integrated experiments and simulations reveal that: (1) increasing Se/Sn slows damage accumulation; (2) the transient temperatures during the ionization-induced thermal spike increase with dE/dxele, which causes efficient damage annealing along the ion trajectory; and (3) for more condensed displacement damage within the thermal spike, damage production is suppressed due to the coupled electronic and atomic dynamics. Ionization effects are expected to be more significant in materials with covalent/ionic bonding involving predominantly well-localized electrons. Insights into the complex electronic and atomic correlations may pave the way to better control and predict SiC response to extreme energy deposition.

Pair distribution function analysis applied to decahedral gold nanoparticles

The five-fold symmetry of face-centered cubic (fcc) derived nanoparticles is inconsistent with the translational symmetry of a Bravais lattice and generally explained by multiple twinning of a tetrahedral subunit about a (joint) symmetry axis, with or without structural modification to the fcc motif. Unlike in bulk materials, five-fold twinning in cubic nanoparticles is common and strongly affects their structural, chemical, and electronic properties. To test and verify theoretical approaches, it is therefore pertinent that the local structural features of such materials can be fully characterized. The small size of nanoparticles severely limits the application of traditional analysis techniques, such as Bragg diffraction. A complete description of the atomic arrangement in nanoparticles therefore requires a departure from the concept of translational symmetry, and prevents fully evaluating all the structural features experimentally. We describe how recent advances in instrumentation, together with the increasing power of computing, are shaping the development of alternative analysis methods of scattering data for nanostructures. We present the application of Debye scattering and pair distribution function (PDF) analysis towards modeling of the total scattering data for the example of decahedral gold nanoparticles. PDF measurements provide a statistical description of the pair correlations of atoms within a material, allowing one to evaluate the probability of finding two atoms within a given distance. We explored the sensitivity of existing synchrotron x-ray PDF instruments for distinguishing four different simple models for our gold nanoparticles: a multiply twinned fcc decahedron with either a single gap or multiple distributed gaps, a relaxed body-centered orthorhombic (bco) decahedron, and a hybrid decahedron. The data simulations of the models were then compared with experimental data from synchrotron x-ray total scattering. We present our experimentally derived atomistic models of the gold nanoparticles, with surprising results and a perspective on remaining challenges. Our findings provide evidence for the suitability of PDF analysis in the characterization of other nanosized particles that may have commercial applications.

The detection of low concentrations of water molecules in plasma by methods of actinometry and simulation

Correlations of H2O molecules and atoms of hydrogen concentrations in plasma of humid inert gases are studied. The observed data of water-vapor concentration are compared to the results of simulation of a plasma-chemical process. The scaling of the results is discussed.

Rayleigh scattering in dense fluid helium

Iglesias et al. (2002) showed that the Rayleigh scattering from helium atoms decreases by collective effects in the atmospheres of cool white dwarf stars. Their study is here extended to consider an accurate evaluation of the atomic polarizability and the density effects involved in the Rayleigh cross section over a wide density-temperature region. The dynamic dipole polarizability of helium atoms in the ground state is determinated with the oscillator-strength distribution approach. The spectral density of oscillator strength considered includes most significant single and doubly excited transitions to discrete and continuum energies. Static and dynamic polarizability results are confronted with experiments and other theoretical evaluations shown a very good agreement. In addition, the refractive index of helium is evaluated with the Lorentz-Lorenz equation and shows a satisfactory agreement with the most recent experiments. The effect of spatial correlation of atoms on the Rayleigh scattering is calculated with Monte Carlo simulations and effective energy potentials that represent the particle interactions, covering fluid densities between 0.005 and a few g/cm$^3$ and temperatures between $1000$ K and $15000$ K. We provide analytical fits from which the Rayleigh cross section of fluid helium can be easily calculated at wavelength $\lambda>505.35$ \AA. Collision-induced light scattering was estimated to be the dominant scattering process at densities greater than 1-2 g/cm$^3$ depending on the temperature.

Three-body interactions and the elastic constants of hcp solid 4He.

The effect of three-body interactions on the elastic properties of hexagonal close packed solid 4He is investigated using variational path integral (VPI) Monte Carlo simulations. The solid's nonzero elastic constants are calculated, at T = 0 K and for a range of molar volumes from 7.88 cm3/mol to 20.78 cm3/mol, from the bulk modulus and the three pure shear constants C0, C66, and C44. Three-body interactions are accounted for using our recently reported perturbative treatment based on the nonadditive three-body potential of Cencek et al. Previous studies have attempted to account for the effect of three-body interactions on the elastic properties of solid 4He; however, these calculations have treated zero point motions using either the Einstein or Debye approximations, which are insufficient in the molar volume range where solid 4He is characterized as a quantum solid. Our VPI calculations allow for a more accurate treatment of the zero point motions which include atomic correlation. From these calculations, we find that agreement with the experimental bulk modulus is significantly improved when three-body interactions are considered. In addition, three-body interactions result in non-negligible differences in the calculated pure shear constants and nonzero elastic constants, particularly at higher densities, where differences of up to 26.5% are observed when three-body interactions are included. We compare to the available experimental data and find that our results are generally in as good or better agreement with experiment as previous theoretical investigations.

Radial correlation of the helium atom in the ground state

The model wavefunction of the ground state of the helium atom has been constructed, and the properties of this function have been compared with an analogous function obtained by other authors. The mean values of the quantities determining the matrix elements in the description of atomic processes have been calculated.

Effect of Synthetic Condition on Local Chemical Ordering of Li1.2Mn0.6Ni0.2O2 Investigated By Pair Distribution Function Analysis

INTRODUCTION In the last decade, lithium-rich transition-metal oxides with a monoclinic layered structure have drawn much attention as a cathode of the lithium-ion battery. Among the oxides, Li1.2Mn0.6Ni0.2O2 (LMN) can be regarded as one of promising candidates due to lower cost and environmental load. According to previous works, a synthetic process has much influence on electrochemical properties of LMN and this situation makes the commercial use difficult. In order to uncover an origin of the synthetic-condition effect, it seems that an atomic configuration of LMN must be investigated in detail. As is well known, the Rietveld refinement using the Bragg profile is a typical analytical method, but this technique permits us only to discuss an average structure with periodicity even though a local chemical ordering such as LiMn6cluster is believed to play an important role in a delithiation/lithiation process. In this work, the local chemical orderings of LMN prepared with different synthetic conditions were investigated by the pair distribution function (PDF) analysis, which enables us to discuss longer-range atomic correlation easily than other techniques such as NMR and EXAFS. On the basis of the obtained atomic configurations, an effect of the synthetic condition on the local ordering is discussed. EXPERIMENTAL Li1.2Mn0.6Ni0.2O2was prepared by a co-precipitation method where two kinds of the cooling condition were applied: quenching and slow cooling. The products were characterized by means of X-ray diffraction (XRD) and inductively coupled plasma (ICP) measurements. The average atomic structures (the crystal structures) were refined by the Rietveld method using neutron (SPICA, J-PARC) and synchrotron X-ray (BL02B2 or BL19B2, SPring-8) diffraction patterns. A super cell with 1800 atoms was constructed from the unit cell, and then was used in the Monte Carlo simulation with experimental data, i. e., the reverse Monte Carlo (RMC) modeling. In the modeling, we used simultaneously the Bragg profile, neutron and X-ray structure factors which were obtained by NOVA (J-PARC) and BL04B2 (SPring-8), respectively. We also utilized an inverse Fourier transform of neutron structure factor, which is PDF. The RMC modeling was carried out with the RMCProfile program under the bond-valence-sum (BVS) constraint. RESULTS AND DISCUSSION It was confirmed from XRD and ICP measurements that both the Li1.2Mn0.6Ni0.2O2 had a single phase of the Li2MnO3-type layered structure (S. G.: C2/m) and the analytical metal compositions were almost equal to the nominal value. The Rietveld analysis suggests that a distortion around a Li site is lower in the quenched sample than the other. Such a result is well consistent with the better charge/discharge property of the quenched sample. By using the unit cell refined by the Rietveld analysis, we constructed a super cell and then optimized the atomic configurations on the basis of the RMC algorithm. In the process, neutron and X-ray structure factors were convolved, taking the cell size into account. As an example, Fig. 1 shows neutron D(r) of Li1.2Mn0.6Ni0.2O2 to which the slow cooling process was applied. The obtained atomic configuration snapshot indicates that Li in the transition-metal layer tends to be surrounded by Mn, and Ni at the lithium layer prefer to form a Ni-O domain in the crystal. An effect of the synthetic condition will be discussed. Figure 1