Atomic Density Distribution Research Articles

Molecular structure, vibrational spectra and density functional theory of the spiro-conjugated anticancer active molecule rubrocurcumin

Rubrocurcumin, well-known for its application in photometric determination of boron in various matrices, has attracted substantial attention due to its applications in biological and pharmacological fields. Here, geometrical optimization, diverse bonding features and potential energy surface scans were studied by use of density functional theory. Vibrational analysis of rubrocurcumin was done by Fourier transform infrared and Fourier transform Raman spectroscopies. The electronic density distribution of atoms in the molecule was analyzed by use of natural bond orbital analysis. Conceptual density functional theory-based local reactivity descriptors were used to understand the relationship between structure, stability, and chemical reactivity.

Two-dimensional model for the martian exosphere: Applications to hydrogen and deuterium Lyman α observations

The analysis of Lyman α observations in the exosphere of Mars has become limited by the assumption of spherical symmetry in the modeling process, as the models are being used to analyze increasingly detailed measurements. In order to overcome this limitation, a two-dimensional density model is presented, which better emulates the density distribution of deuterium and hydrogen atoms in the exosphere of Mars. A two-dimensional radiative transfer model developed in order to simulate multiple scattering of solar Lyman α photons by an asymmetric, non-isothermal hydrogen exosphere, is also presented here. The models incorporate changes in density and temperature structure of the martian atmosphere with radial distance and solar zenith angle. The 2-D models were applied to the MAVEN-IUVS echelle observations of deuterium and hydrogen Lyman α as well as HST Lyman α observations of hydrogen at Mars. The asymmetric 2-D model provided better fits to the data and smaller thermal escape rates in comparison to the symmetric 1-D model for the exosphere of Mars. However, intensity differences between both models became small above ~2.5 martian radii indicating that the exosphere of Mars approaches spherical symmetry at higher altitudes, in agreement with earlier studies. In addition, a new cross calibration of the absolute sensitivities of two instruments on the Hubble Space Telescope and the MAVEN-IUVS echelle mode is presented based on near-simultaneous observations of the geocorona and Mars.

All‐Optical Spin–Orbit Coupling of Light in Coherent Media Using Rotating Image

AbstractThe possibility of all‐optical spin–orbit coupling (SOC) of light is investigated based on a rotating spinor image traveling through an electromagnetically induced transparency (EIT) medium. It is shown that the paraxial evolution of the spinor image composed of two Laguerre–Gaussian (LG) modes with different frequencies can be analogous with the quantum dynamics of a spin‐1/2 particle with strong and tunable SOC governed by the Pauli equation, where the spin‐up and ‐down states have different effective masses. Using realistic EIT parameters with cold atoms, both the radial inhomogeneity of the strong control field and the atomic density distribution with comparable size are considered. The results confirm that the large group refractive index varying in the radial dimension mimicking the central potential can greatly enhance the spin–orbit interaction, leading to visible spatial quantization of the oppositely oriented spin states, equivalent to the two LG modes.

Effect of iron doping on the hydrophobicity of titanium dioxide film: experiment and simulation

In this study, we carried out experiments and molecular dynamics simulations to identify the effect of Fe doping on the hydrophobicity of a titanium dioxide film. TiO2 and Fe-doped TiO2 films were fabricated in situ by atomic layer deposition without annealing. X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) were used to characterise the crystal structure and elemental composition. Iron doping resulted in the TiO2 becoming more hydrophobic at a macroscopic level, as estimated by atomic force microscopy observations and static contact angle measurements. Furthermore, the effect of iron doping on the structure and kinetics of water molecules on the exterior of TiO2 were studied by molecular dynamics simulations. On the basis of the XPS results, the Fe-TiO2 surface matrix has a Ti:Fe ratio of 36:5. In addition, the density distribution of oxygen and hydrogen atoms indicate that interfacial water molecules enter the Fe-TiO2 film more easily and hydrogen atoms in the water molecules are oriented upward at the interface. The self-diffusion coefficients indicate that iron doping makes the TiO2 more hydrophobic, which is consistent with the macroscopic test results.

A Quasi-1D Potential for Bose Gas Phase Fluctuations**Supported by the National Natural Science Foundation of China under Grant Nos 61703025, 91736028 and 61673041.

An elongated trap potential for cold atoms is designed based on a quadrupole-Ioffe configuration. Phase fluctuations in a Bose–Einstein condensate (BEC), which is confined by the trap, are studied. We simulate the atom density distribution induced by fluctuation after time of flight from this elongated trap potential and study the temperature measurement method related to the distribution. Furthermore, taking advantage of the tight confinement and radio frequency dressing technique, we propose a double well potential for splitting BECs. Our results are helpful for improving understanding of low-dimensional quantum gases and provide important guidance for atomic interferometry.

Superfluid–Mott-insulator transition of ultracold superradiant bosons in a cavity

We investigate harmonically-trapped, laser-pumped bosons with infinite-range interactions induced by a dissipative high-finesse red-detuned optical cavity with numerical and analytical methods. We obtain multiple cavity and atomic observables as well as the full phase diagram of the system using the multiconfigurational time-dependent Hartree method for indistinguishable particles (MCTDH-X) approach. Besides the transition from an unorganized normal phase to a superradiant phase where atoms self-organize, we focus on an in-depth investigation of the self-organized superfluid to self-organized Mott insulator phase transition in the superradiant phase as a function of the cavity-atom coupling. The numerical results are substantiated by an analytical study of an effective Bose-Hubbard model. We numerically analyze cavity fluctuations and emergent strong correlations between atoms in the many-body state across the Mott transition via the atomic density distributions and Glauber correlation functions. Unexpectedly, the weak harmonic trap leads to features like a lattice switching between the two symmetry-broken $\mathbb{Z}_2$ configurations of the untrapped system and a reentrance of superfluidity in the Mott insulating phase. Our analytical considerations quantitatively explain the numerically observed correlation features.

Superresolving atomic densities

Atomic Physics Quantum gas microscopes provide information about the occupancy of individual optical lattice sites. However, the resolution is limited by the wavelength of the imaging light. Two related superresolution schemes now enable researchers to glean even finer details of the atomic density distribution. McDonald et al. and Subhankar et al. studied one-dimensional arrays of ultracold atoms. A well-chosen perturbation provided a narrow window onto a specific position; when information from different positions was pieced together, the researchers were able to reconstruct the atomic density with a resolution of a fraction of the optical wavelength. The schemes were effective in capturing atomic dynamics and are expected to be applicable to a wide range of atomic and molecular species. Phys. Rev. X 9 , 021001, 021002 (2019).

Exploiting Symmetry Mismatch to Control Magnetism in a Ferroelastic Heterostructure.

In the bulk, LaCoO_{3} (LCO) is a paramagnet, yet the low-temperature ferromagnetism (FM) is observed in tensile strained thin films, and its origin remains unresolved. Here, we quantitatively measured the distribution of atomic density and magnetization in LCO films by polarized neutron reflectometry (PNR) and found that the LCO layers near the heterointerfaces exhibit a reduced magnetization but an enhanced atomic density, whereas the film's interior (i.e., its film bulk) shows the opposite trend. We attribute the nonuniformity to the symmetry mismatch at the interface, which induces a structural distortion related to the ferroelasticity of LCO. This assertion is tested by systematic application of hydrostatic pressure during the PNR experiments. The magnetization can be controlled at a rate of -20.4% per GPa. These results provide unique insights into mechanisms driving FM in strained LCO films while offering a tantalizing observation that tunable deformation of the CoO_{6} octahedra in combination with the ferroelastic order parameter.

Superresolution Microscopy of Cold Atoms in an Optical Lattice

Super-resolution microscopy has revolutionized the fields of chemistry and biology by resolving features at the molecular level. Such techniques can be either "stochastic," gaining resolution through precise localization of point source emitters, or "deterministic," leveraging the nonlinear optical response of a sample to improve resolution. In atomic physics, deterministic methods can be applied to reveal the atomic wavefunction and to perform quantum control. Here we demonstrate super-resolution imaging based on nonlinear response of atoms to an optical pumping pulse. With this technique the atomic density distribution can be resolved with a point spread function FWHM of 32(4) nm and a localization precision below 1 nm. The short optical pumping pulse of 1.4 $\mu$s enables us to resolve fast atomic dynamics within a single lattice site. A byproduct of our scheme is the emergence of moir\'{e} patterns on the atomic cloud, which we show to be immensely magnified images of the atomic density in the lattice. Our work represents a general approach to accessing the physics of cold atoms at the nanometer scale, and can be extended to higher dimensional lattices and bulk systems for a variety of atomic and molecular species.

Zooming in on Ultracold Matter

Ultracold atoms are an exceptionally versatile platform to test novel physical concepts. They have greatly advanced our understanding of the physics of many-body systems and allowed precision measurements of fundamental constants. They are also a promising architecture for quantum computation and quantum simulation. A key to the practicality of ultra-cold atoms is the ability to image them with high spatial resolution. Available microscopy schemes have reached sufficient resolution to detect individual atoms trapped in optical lattices with submicron spacings, but their spatial resolution is typically limited to about half the wavelength of the imaging light. Now, two independent teams—one led by Cheng Chin from the University of Chicago, Illinois, and the other led by Steve Rolston and Trey Porto from the University of Maryland, College Park —have reported subwavelength-resolution imaging techniques for ultracold atoms. The methods, capable of resolving objects up to 50 times smaller than the optical wavelength, have allowed the teams to map the shape of atomic density distributions on nanometer scales. Nanoscale maps of atomic density will be important observables for probing many-body effects in cold atomic and molecular systems.

Measuring spatially extended density profiles using atom-cavity collective strong coupling to higher-order modes

The collective strong coupling of rubidium atoms in a magneto-optical trap (MOT) to the Laguerre-Gaussian (LG) modes of a Fabry-P\'erot cavity is investigated. Bright and dark $^{85}\mathrm{Rb}$ MOT atoms are prepared at the geometric center of the cavity, and the vacuum Rabi splitting (VRS) of the collectively coupled atom-cavity system is measured for ${\mathrm{LG}}_{l0}$ ($l=0,1,2,3$) modes. The atom number coupled to the cavity mode depends on the overlap of the atomic density distribution and the specific spatial mode function, which is reflected in the measured VRS spectrum. The known mode function and the measured VRS can then be used to test whether the atomic density distribution in the experiment is Gaussian or uniform. A simple theoretical model for this process is described, and the experimental measurements are found to be in close agreement with the model.

Phase field crystal study of grain boundary structure and annihilation mechanism in low-angle grain boundary

Using the advantage of phase field crystal model in microstructure evolution, we simulated the details of two-dimensional triangular phase on atomic scale and diffusion time scale. The results show that the annihilation process of grain boundaries can be divided into three stages. The energy changes of the system at different stages are accurately calculated and the process is quantitatively analyzed. By comparing the atomic density distributions at different temperatures and orientation angles, it is shown that the grain boundary is sensitive to temperature. Within the range of low-angle, the increase of orientation angle inhibits the occurrence of annihilation and decreases the grain boundary migration rate. Under the applied stress, the orientation angle has a certain response relationship with the yield strength of the material. This work has some practical significance in the influence of microstructure on the mechanical properties of materials.

Bergman-type medium range order in amorphous Zr77Rh23 alloy studied by ab initio molecular dynamics simulations

In recent years, some arguments about the existence of medium-range order (MRO) in the Zr-Rh system have been put forward. However, research on the structural features of the Zr-Rh binary alloy at the atomic level is still lacking. This study uses ab initio molecular dynamics simulations to systematically study the local structures of Zr77Rh23 from the liquid to the glassy states. Pair correlation function (PCF), coordination number (CN), Honeycutt–Anderson(HA) index, bond-angle distribution functions, and the Voronoi tessellation method are used to reveal a clear icosahedral-like configuration in the amorphous Zr77Rh23 alloy. It is noteworthy that the splitting in the second peak of the partial PDF implies the existence of a medium range order (MRO) in the Zr77Rh23 system. We obtain the local order in three-dimensional atomic density distributions by using a new atomistic cluster alignment (ACA) method. Interestingly, a Bergman-type MRO is observed in the glassy Zr77Rh23. Furthermore, the spatial distribution and connections of icosahedral-like clusters are shown to further demonstrate the MRO network. Our findings shed light on the nature of atomic local structures of amorphous Zr77Rh23 alloy and have important implications to understanding the formation of various MROs in metallic glasses.

Simulation on complex dynamics of hollow cathode discharge in argon

In this paper, the dynamics of hollow cathode discharge in argon is simulated by fluid model. In the numerical model considered are 31 reaction processes, including direct ground state ionization, ground state excitation, stepwise ionization, Penning ionization, de-excitation, two-body collision, three-body collision, radiation transition, elastic collision, and electron-ion recombination reaction. The electron density, Ar<sup>+</sup> density, Ar<sup>4s</sup>, Ar<sup>4p</sup>, Ar<sup>3d </sup>particle density, electric potential and electric field intensity are calculated. At the same time, the contributions of different reaction mechanisms for the generation and consumption of electron, Ar<sup>4s</sup> and Ar<sup>4p </sup>are simulated. The results indicate that hollow cathode effect exists in the discharge, and the Ar<sup>4s</sup> density is much higher than electron density. The penning ionization 2Ar<sup>4s </sup>→ Ar<sup>+</sup> + Ar<sup>+</sup> + e and stepwise ionization involving Ar<sup>4s</sup> make important contributions to the generation of new electrons and the balance of electron energy. In particular, the penning ionization reaction 2Ar<sup>4s </sup>→ Ar<sub>2</sub><sup>+</sup> + e, which is generally ignored in previous simulation, also has an significant influence on electron generation. The spatial distribution of excited state argon atomic density is the result of the balance between the formation and consumption of various particles during discharge. Radiation reaction Ar<sup>4p </sup>→ Ar<sup>4s</sup> + <i>hν</i> is the main source of Ar<sup>4s</sup> generation and the main way to consume Ar<sup>4p</sup>. Ar<sup>4s</sup> + e →Ar<sup>4p</sup> + e is the main way of Ar<sup>4s</sup> consumption and Ar<sup>4p</sup> production. The simulation results also show that the Ar<sup>4p </sup>density distribution can better reflect the optical characteristics in the hollow cathode discharge.

Effect of rough inner wall of nanochannel on fluid flow behavior

Flow system on a nano scale, as an effective and economic system, has been widely employed. While on a macroscopic scale, for the non-slip boundary, the velocity of the fluid at the surface is assumed to be consistent with the surface. This approximation may become invalid on a smaller length scale pertinent to the operation of microfluid devices. The interface slip effect has a significant influence on the flow because of its higher ratio of surface to volume. In this paper, the Poiseuille flow, which is composed of two infinite parallel asymmetric walls, is studied by the molecular dynamics method. The influence of wall roughness and surface wettability of channel on fluid flow in the channel are analyzed. The results show that the asymmetric upper and lower wall can lead to an asymmetric distribution of flow parameters. The change of wall roughness and wettability would affect the flow characteristics of fluid atoms near the wall. Due to the influence of wall grooves, the number density distribution near the rough wall is lower than that on the smooth wall side. As the rib height and wall wettability increase, the number density of fluid atoms in the groove increases gradually, and the change of the rib spacing does not substantially affect the number density distribution of fluid atoms near the rough wall. For different structure types of walls, the real solid-liquid boundary positions are determined by simulating the velocity field distribution in the channel under both Couette flow and Poiseuille flow, which can help us to better analyze the interface slip effect. The variation of wall roughness and wettability can affect the position of the solid-liquid interface. The change of rib height and wettability can greatly influence the velocity distribution in channel, and the position of the solid-liquid boundary as well. Conversely, the rib spacing has a less effect on the boundary position. The difference in boundary position can affect the interface slip effect. We can find the slip velocity and the slip length on one side of the rough wall to be smaller than those on the smooth wall side, and as the rib height and wall wettability increase, the slip velocity and the slip length significantly decrease near the rough wall side. The effect of rib spacing on fluid flow is trivial, and the interface slip velocity and length are relatively stable.

Internal path investigation of the acting electrons during the photocatalysis of panchromatic ruthenium dyes in dye-sensitized solar cells

A series of heteroleptic Ru(II) complexes were theoretically investigated using time-dependent density functional theory. These dyes, including K8 and N3, are based on a common motif formed by Ru center, N C S, and polypyridyl ligands, but differ only by the nature of the added group in para position of each pyridyl. The presence of these ligands will enable the evaluation of the electronic effects ±I and ±M. This work focuses on the localization of the part, among the metal, the N C S, the polypyridyl ligands, and the added group R, which is most actively involved in the photocatalysis process. We dealt with both ground and excited states as well as the electronic transitions between them. To illustrate the effect of each functional group R on its photophysical properties, the geometries of five dyes were optimized in the molecular and univalent cationic states. All molecules are asymmetrical in shape with a distorted octahedral coordination of the RuN6 core. Atomic charge and spin density distributions show that a charge transfer process occurs from the NCS/Ru to polypyridyl ligand. Analysis of the electronic absorption spectra reveals that the band with the highest wavelength value is assigned to metal-to-ligand charge transfer transition. On the contrary, two other bands are assigned to multitransitions Ru/NCS to polypyridyl–π*. These attributions have been confirmed by the localization of all atoms intervening in them. We also introduced an adapted way to estimate the ionization probability values in each atomic center in the ground and first excited states. Phenomenal properties such as mobility, redox potential, electronic spectrum, ionization potential, and optical gap of the most efficient dye, which is the N3, fit well with experimental values.

Solid-to-super-critical phase change and resulting stress wave during internal laser ablation

The phase change, stress wave generation and propagation, and stress-induced structure damage in a model material (argon) during internal picosecond laser ablation are studied by molecular dynamic simulations. The propagation of the stress wave and fluctuations in temperature is periodic and tightly correlated. The phase-change process from solid to liquid and supercritical fluid and then back to solid occurs as a coupled consequence of heat transfer and the tensile stress wave induced by the laser pulse and the limited internal space. The orientation–radial distribution function is applied to provide substantial information about the atomic density and angle distribution of the crystal structure. It reveals the strong material twisting and permanent damaged region induced by the very high stress fields.

Relaxation, chaos, and thermalization in a three-mode model of a Bose–Einstein condensate

We study the complex quantum dynamics of a system of many interacting atoms in an elongated anharmonic trap. The system is initially in a Bose–Einstein condensed state, well described by Thomas–Fermi profile in the elongated direction and the ground state in the transverse directions. After a sudden quench to a coherent superposition of the ground and lowest energy transverse modes, quantum dynamics starts. We describe this process employing a three-mode many-body model. The experimental realization of this system displays decaying oscillations of the atomic density distribution. While a mean-field description predicts perpetual oscillations of the atomic density distribution, our quantum many-body model exhibits a decay of the oscillations for sufficiently strong atomic interactions. We associate this decay with the fragmentation of the condensate during the evolution. The decay and fragmentation are also linked with the approach of the many-body model to the chaotic regime. The approach to chaos lifts degeneracies and increases the complexity of the eigenstates, enabling the relaxation to equilibrium and the onset of thermalization. We verify that the damping time and quantum signatures of chaos show similar dependences on the interaction strength and on the number of atoms.

Representation of DNA environment: Spiral staircase distribution function.

In the present study, we investigated the local structure of DNA and its environment using a new visualization technique. The spiral staircase distribution function (SSDF) is determined as two-dimensional density distribution of atoms of water and ligands in local reference frames linked with each base pair of poly-DNA molecule, either GC or AT. This property of SSDF provides opportunity to study sequence-specific binding of ions, peptides, and other agents derived from a molecular dynamics computer simulation. The spatial structure of double-stranded DNA environment in water solution containing either Mg2+ or Na+ ions was investigated using of SSDF. The distributions of ions around GC and AT base pairs are shown separately. It is observed that Mg2+ ions interact with DNA atoms by means of the layer of water molecules and penetrate into the major groove only. Na+ ions have a direct contact with DNA atoms and penetrate both into the major and minor grooves of DNA. © 2018 Wiley Periodicals, Inc.

Longitudinal variations of the ionospheric trough position

For the first time a comprehensive pattern of the longitudinal effect of the ionospheric trough position was obtained. We present new results with longitudinal variations of the winter trough position as a function of geomagnetic latitude for both hemispheres and conditions of high and low solar activity and all local time hours. We used a large observational data set obtained onboard the Kosmos-900, Interkosmos-19 and CHAMP satellites for quiet geomagnetic conditions. We found that a magnitude of the trough position longitudinal effect averaged for a fixed local time is greater in the daytime (6–8°) than in the nighttime (3–5°). The longitudinal effect magnitude reaches its maximum (16°) in the morning (at 08 LT) in the Southern hemisphere at high solar activity. But on certain days at any solar activity the longitudinal effect magnitude can reach 9–10° even at night. The shape of the longitudinal effect was found to differ significantly in two hemispheres. In the Northern hemisphere the trough is usually closest to the pole in the eastern (American) longitudinal sector, and in the Southern hemisphere the trough is closest in the western (Eurasian) longitudinal sector. The magnitude and shape of the longitudinal effect is also different during low and high solar activity. The Global Self-consistent Model of the Thermosphere, Ionosphere, and Protonosphere (GSM TIP) simulations demonstrate that during low solar activity, the longitudinal variations of the daytime trough position is mainly determined by longitudinal variations of the ionization function, formed due to the longitudinal variations in the solar zenith angle and the atomic oxygen density distribution. The longitudinal variations of the nighttime trough position is formed by the longitudinal variations in ionization of precipitating auroral particles, neutral atmosphere composition, and electric field.