Thermal Motion Of Atoms Research Articles

Energetics of interactions in the solid state of 2-hydroxy-8-X-quinoline derivatives (X = Cl, Br, I, S-Ph): comparison of Hirshfeld atom, X-ray wavefunction and multipole refinements.

In this work, two methods of high-resolution X-ray data refinement: multipole refinement (MM) and Hirshfeld atom refinement (HAR) - together with X-ray wavefunction refinement (XWR) - are applied to investigate the refinement of positions and anisotropic thermal motion of hydrogen atoms, experiment-based reconstruction of electron density, refinement of anharmonic thermal vibrations, as well as the effects of excluding the weakest reflections in the refinement. The study is based on X-ray data sets of varying quality collected for the crystals of four quinoline derivatives with Cl, Br, I atoms and the -S-Ph group as substituents. Energetic investigations are performed, comprising the calculation of the energy of intermolecular interactions, cohesive and geometrical relaxation energy. The results obtained for experimentally derived structures are verified against the values calculated for structures optimized using dispersion-corrected periodic density functional theory. For the high-quality data sets (the Cl and -S-Ph compounds), both MM and XWR could be successfully used to refine the atomic displacement parameters and the positions of hydrogen atoms; however, the bond lengths obtained with XWR were more precise and closer to the theoretical values. In the application to the more challenging data sets (the Br and I compounds), only XWR enabled free refinement of hydrogen atom geometrical parameters, nevertheless, the results clearly showed poor data quality. For both refinement methods, the energy values (intermolecular interactions, cohesive and relaxation) calculated for the experimental structures were in similar agreement with the values associated with the optimized structures - the most significant divergences were observed when experimental geometries were biased by poor data quality. XWR was found to be more robust in avoiding incorrect distortions of the reconstructed electron density as a result of data quality issues. Based on the problem of anharmonic thermal motion refinement, this study reveals that for the most correct interpretation of the obtained results, it is necessary to use the complete data set, including the weak reflections in order to draw conclusions.

Molecular dynamics simulation of helium ion implantation into silicon and its migration

In this paper, a model of helium ion implanted monocrystalline Si was constructed by using molecular dynamics (MD) simulation method to study the interaction mechanism of helium ion with monocrystalline Si and helium ion migration. In order to study the damage effect of helium ion implantation on monocrystalline Si, identify diamond structure (IDS), radial distribution function, temperature analysis were calculated and analyzed. The effects of ion doses, beam currents and energies on the damage were studied. Helium ion implanted Si with ion doses of 1 × 1014/cm2 was subsequently heated to 300 K. MD simulation results indicated that IDS damage induced by ion implantation was positively correlated with ion doses as the ion implantation increased to 1 × 1014/cm2. The mean-square displacement of helium atoms was calculated during the temperature rising to 300 K. It was found that the high permeability of helium atoms in Si and the acceleration of atomic thermal motion owing to elevated temperature as well as the existence of larger stress would be helpful to the migration of implant helium atoms.

Effect of laser-frequency fluctuation on the decay rate of Rydberg coherence

The effect of electromagnetically induced transparency (EIT) combined with Rydberg-state atoms provides high optical nonlinearity to efficiently mediate the photon-photon interaction. However, the decay rate of Rydberg coherence, i.e., the decoherence rate, plays an important role in optical nonlinear efficiency, and can be largely influenced by laser frequency fluctuation. In this work, we carried out a systematic study of the effect of laser frequency fluctuation on the decoherence rate. We derived an analytical formula that quantitatively describes the relationship between the decoherence rate and laser frequency fluctuation. The formula was experimentally verified by using the $\Lambda$-type EIT system of laser-cooled $^{87}$Rb atoms, in which one can either completely eliminate or controllably introduce the effect of laser frequency fluctuation. We also included the effect of Doppler shift caused by the atomic thermal motion in the formula, which can be negligible in the $\Lambda$-type EIT experiment but significant in the Rydberg-EIT experiment. Utilizing the atoms of 350 $\mu$K, we studied the decoherence rate in the Rydberg-EIT system involving with the state of $|32D_{5/2}\rangle$. The experimental data are consistent with the predictions from the formula. We were able to achieve a rather low decoherence rate of $2\pi\times$48 kHz at a moderate coupling Rabi frequency of $2\pi\times$4.3 MHz.

Selective Reflection for a Fabry-Perot Interferometer in Presence of Electromagnetically Induced Transparency

The influence of thermal motion of atoms of alkali metals in a cell with the parallel windows on the formation of electromagnetically induced transparency in the Λ-system is considered. The solution of joint system of equations of density matrix and Maxwell was studied analytically and numerically. The spectra of single and multiple reflections for different optical lengths and parameters of interaction were obtained.

Investigation of the graphene thermal motion by rainbow scattering

The thermal motion of graphene atoms was investigated using angular distributions of transmitted protons. The static proton-graphene interaction potential was constructed applying the Doyle-Turner's expression for the proton-carbon interaction potential. The effects of atom thermal motion were incorporated by averaging the static proton-graphene interaction potential over the distribution of atom displacements. The covariance matrix of graphene displacements was modeled according to the Debye theory, and calculated using Molecular Dynamics approach. Proton trajectories were used for construction of angular yields. We have found that there are lines, called rainbows, along which the angular yield is very large. Their evolution in respect to different sample orientation was examined in detail. Further we found that atom thermal motion has negligible influence on rainbows generated by protons experiencing distant collisions with the carbon atoms forming the graphene hexagon. On the other hand, rainbows generated by protons experiencing close collisions with the carbon atoms can be modeled by ellipses whose parameters are very sensitive to the structure of the covariance matrix. Numerical procedure was developed for extraction of the covariance matrix from the corresponding rainbow patterns in the general case, when atoms perform fully anisotropic and correlated motion.

Fabrication of porous carbons from mesitylene for highly efficient CO2 capture: A rational choice improving the carbon loop

Mesitylene, a representative heavy carbon by-product in the course of C1 chemical downstream processes, is proposed to be employed in this study, as the initial material to synthesize the porous carbons that have played a crucial part in the adsorptive carbon capture process but are generally made from natural carbon resources, instead of fed to the traditional refining process such as hydroprocessing. Based on molecular dynamics calculation, it is proved that once the mesitylene monomers are linked by the flexible methylene groups, the generated polymer can closely mimic the lignin macromolecular behaviors in terms of spatial configuration and atomic thermal motions, which gifts the great potential of the mesitylene-based polymer as applicable a precursor of porous carbon as the biomass-based material. The experimental facts further demonstrate that the porous carbons produced through the routine carbonization of the mesitylene-based polymer can possess desired textural peculiarities, in particular the finely developed micropores that give rise to perfect capacity and selectivity of CO2 capture, of which underlying mechanism is revealed by the first-principle calculation. The porous carbon generated at 700 °C can reach the CO2 capture capacity of 6.16 mmol g−1 at 0 °C and 1 bar, which is much higher than many benchmark materials reported, including some biomass-based porous carbons (2.8 mmol g−1, at 0 °C and 1 bar).

A computational investigation of length-scale effects in the fracture behaviour of a graphene sheet using the atomistic J-integral

The overarching objective of this paper is to investigate the validity of application of continuum-based linear elastic fracture mechanics (LEFM) methodology, which is often employed by researchers to model fracture processes at the “discrete” atomic scale. The potential sources of error in the application of LEFM at the nanoscale are: (a) Length-scale effects, (b) non-local effects due to long range inter-atomic forces, and (c) entropic effects due to random thermal motion of atoms. The material selected for this study is monolayer graphene, primarily because extensive data, both experimental and analytical, already exist for this material in the literature for model validation. Further, an atomistic J-integral is implemented as a nano-scale fracture metric to investigate flaw-tolerance at the nanoscale reported by many researchers, and to develop a methodology to predict the initiation fracture toughness of the material. For this purpose, a bond-order based potential (ReaxFF) available in LAMMPS molecular dynamics (MD) software is utilized to accurately pinpoint bond separation. Predictions obtained using the atomistic J are compared with LEFM predictions for the case of a single (zig-zag) graphene sheet with a center-crack under tensile loading at room temperature, and show significant deviation from LEFM for crack lengths below a certain threshold.

Cavity-Free Optical Isolators and Circulators Using a Chiral Cross-Kerr Nonlinearity.

Optical nonlinearity has been widely used to try to produce optical isolators. However, this is very difficult to achieve due to dynamical reciprocity. Here, we show the use of the chiral cross-Kerr nonlinearity of atoms at room temperature to realize optical isolation, circumventing dynamical reciprocity. In our approach, the chiral cross-Kerr nonlinearity is induced by the thermal motion of N-type atoms. The resulting cross phase shift and absorption of a weak probe field are dependent on its propagation direction. This proposed optical isolator can achieve more than 30dB of isolation ratio, with a low loss of less than 1dB. By inserting this atomic medium in a Mach-Zehnder interferometer, we further propose a four-port optical circulator with a fidelity larger than 0.9 and an average insertion loss less than 1.6dB. Using atomic vapor embedded in an on-chip waveguide, our method may provide chip-compatible optical isolation at the single-photon level of a probe field.

Doppler Frequency Redistribution upon Coherent Photon Emission by Atoms in an Optically Dense Medium

The problem of transfer of line radiation in sodium vapor under photoexcitation by laser radiation of a resonance line with wavelength λ = 589.6 nm is numerically solved. The influence of Doppler frequency shifts on photon emission coherent in the atomic reference system is taken into account in the formation of an emission line profile using the model of partial frequency redistribution. In the case of a small optical thickness of a medium τ0 ≤ 1, the Doppler frequency redistribution in the laboratory reference system yields higher intensity values in the emission line profile core in comparison with the model of complete frequency redistribution. For an optically dense medium, thermal motion of atoms leads to an increase of reabsorption in the emission line core, and intensity increases in the line wings as compared to the complete redistribution model. The dependence of the Holstein trapping factor on optical thickness is closer to the analytic dependence than the complete redistribution model. This is explained by the fact that the frequencies of emitted photons in the laboratory reference system fall into the spectral profile core, which increases the effects of resonance radiation trapping in a dense medium.

Thermal-motion-induced non-reciprocal quantum optical system

Magnetic-free optical non-reciprocal components, such as isolators and circulators, are highly desirable for on-chip optical signal processing1,2 and quantum networks3,4. However, their realization presents a fundamental difficulty due to the Lorentz reciprocity in most optical devices5. In this study, we propose and experimentally realize optical non-reciprocity with atoms embedded in a ring cavity at room temperature. Random thermal motion of atoms, in the presence of a unidirectional control field, creates susceptibility–momentum locking, and subsequently a new type of chiral quantum optical system. Furthermore, we demonstrate strong non-reciprocity based on this chiral quantum system in the regime of collectively strong atom–cavity coupling. Our scheme provides a new routine towards the realization of chiral quantum optics and chip-compatible, non-magnetic optical non-reciprocity.

PySCF-NAO: An efficient and flexible implementation of linear response time-dependent density functional theory with numerical atomic orbitals

We present an algorithm and its implementation to calculate the propertiesof electronic excitations in molecules and clusters from first principles, using time-dependent density functional theory (TDDFT). The algorithm assumes the use of some localized functions as a basis set to represent the spatial degrees of freedom. It relies on an iterative computation of the induced density according to the Dyson-like equation for the linear response function. The current implementation is built upon so-called numerical atomic orbitals. It is suitable for a wide variety of density functional theory (DFT) software. In this work, we demonstrate TDDFT calculations starting from preceding DFT runs with SIESTA, GPAW and PySCF packages, while a coupling with the other DFT packages such as Fireball and OpenMX is planned. The mentioned packages are capable of performing ab initio molecular dynamics simulations, and the speed of our TDDFT implementation makes feasible to perform a configuration average of the optical absorption spectra. Our code is written mostly in Python language allowing for a quick and compact implementation of most numerical methods and data-managing tasks with the help of NumPy/SciPy libraries and Python intrinsic constructs. Part of the code is written in C and Fortran to achieve a competitive speed in particular sections of the algorithm. Many parts of the current algorithm and implementation are useful in other ab initio methods for electronic excited states, such as Hedin’s GW, Bethe–Salpeter equation and DFT with hybrid functionals. Corresponding proof-of-principles implementations are already part of the code. Program summaryProgram Title:PySCF-NAOProgram Files doi:http://dx.doi.org/10.17632/9wgp6255hn.1Licensing provisions: Apache License, Version 2.0Programming language: Python (2 or 3), Fortran90 and CSupplementary material: We provide the source code and input files to organize example and benchmark calculations discussed in the paper.Nature of the problem: The study of the interaction of photons and charged particles with matter depends upon understanding of electronic excitations in matter. A description of the electronic excitations within time-dependent density functional theory (TDDFT) is popular due to the combination of its reasonable accuracy and its relatively low computational cost. Despite the relative simplicity of TDDFT, its application becomes difficult for quantum systems containing several hundreds of atoms. Such microscopically small systems are relevant in organic electronics, plasmonics and surface science. Therefore, much work has been devoted to the development of adequate electronic structure methods. Moreover, thermal motion of atoms and the presence of solvents affects the properties of electronic excited states in a decisive manner. Modeling of the electronic excited states including the system’s dynamics within the Born–Oppenheimer approximation leads to even stronger efficiency requirements from the corresponding electronic structure methods.Solution method: We discretize the Kohn–Sham Hamiltonian using a basis of numerical atomic orbitals. The induced electronic density is determined in response to a dipolar external perturbation, according to linear response TDDFT, using an iterative algorithm. The method takes advantage of the sparsity generated by the finite support of the numerical atomic orbitals. This allows computing the dynamical polarizability of molecules and clusters containing up to several thousands of atoms.Additional comments including Restrictions and Unusual features: The current algorithm is formulated within the formalism of density response functions. Therefore, one needs to know explicitly an exchange–correlation kernel (second-derivative of energy with respect to variation of the density). The exchange–correlation kernel is analytically known for (semi-)local density functionals, but not for the hybrid density functionals. To date, we implemented only the local density approximation (LDA) for the exchange–correlation kernel to be used with the iterative TDDFT in PySCF-NAO. Spin-restricted formalism for finite systems is covered in the current implementation. Moreover, although our code is prepared to compute the electronic response of all-electron systems, our current implementation of an auxiliary product basis (density-fitting basis) is working best in combination with the use of pseudopotentials.

Reversible storage of entangled two-mode wavepacket based on electromagnetically induced transparency

We discuss the reversible storage of an entangled two-mode wavepacket in separated two atomic ensembles based on electromagnetically induced transparency. By introducing wavepacket dark-states, we show the dynamic transfer of quantum information of the wavepacket between the optical field and the atomic ensembles. We examine in detail the performance of the scheme focusing on the reversible storage of an entangled two-photon wavepacket in the case where the effects of the environment and the thermal motions of atoms are taken into consideration.

Observation of Quantum Spin Noise in a 1D Light-Atoms Quantum Interface

We observe collective quantum spin states of an ensemble of atoms in a one-dimensional light-atom interface. Strings of hundreds of cesium atoms trapped in the evanescent fiel of a tapered nanofiber are prepared in a coherent spin state, a superposition of the two clock states. A weak quantum nondemolition measurement of one projection of the collective spin is performed using a detuned probe dispersively coupled to the collective atomic observable, followed by a strong destructive measurement of the same spin projection. For the coherent spin state we achieve the value of the quantum projection noise 40 dB above the detection noise, well above the 3 dB required for reconstruction of the negative Wigner function of nonclassical states. We analyze the effects of strong spatial inhomogeneity inherent to atoms trapped and probed by the evanescent waves. We furthermore study temporal dynamics of quantum fluctuations relevant for measurement-induced spin squeezing and assess the impact of thermal atomic motion. This work paves the road towards observation of spin squeezed and entangled states and many-body interactions in 1D spin ensembles.

Impact of the thermal motion of silicon atoms on the viscosity of nanoconfined aqueous NaCl solution

The properties of nanoconfined fluid are critical for the design and precise control of nanofluidic devices. To understand the fundamental details of the viscosity of nanoconfined aqueous NaCl solution, we investigated the impact of the thermal motion of silicon atoms on the viscosity of nanoconfined aqueous NaCl solution using molecular dynamic simulations. The results show that thermal motion of silicon atoms can decrease the viscosity of NaCl solution, and this impact is significant when the shear rate is small.

Determination of characteristics of a magneto-optical trap by the spectral width of coherent two-photon resonance

A technique is proposed for studying the thermal motion of 7Li atoms in a magneto-optical trap (MOT), based on a comparative analysis of coherent two-photon resonances at the 2S – 2P – nS (n = 38 – 120) transition using counter- and co-propagating laser beams with wavelengths of 671 and 350 nm (differential two-photon spectroscopy). A self-consistent theoretical model is constructed. The dependences of the broadening of two-photon resonance on the frequency detuning of cooling optical beams in the MOT are presented. A good agreement of theory with experimental results is obtained. The developed technique is nondestructive and can be used to determine the parameters of cold atoms in various traps, including the parameters of hydrogen and antihydrogen atoms in magnetic traps.

Crystal structure, phase transition and structural deformations in iron borate (Y0.95Bi0.05)Fe3(BO3)4 in the temperature range 90-500 K.

An accurate X-ray diffraction study of (Y0.95Bi0.05)Fe3(BO3)4 single crystals in the temperature range 90-500 K was performed on a laboratory diffractometer and used synchrotron radiation. It was established that the crystal undergoes a diffuse structural phase transition in the temperature range 350-380 K. The complexity of localization of such a transition over temperature was overcome by means of special analysis of systematic extinction reflections by symmetry. The transition temperature can be considered to be Tstr ≃ 370 K. The crystal has a trigonal structure in the space group P3121 at temperatures of 90-370 K, and it has a trigonal structure in the space group R32 at 375-500 K. There is one type of chain formed by the FeO6 octahedra along the c axis in the R32 phase. When going into the P3121 phase, two types of nonequivalent chains arise, in which Fe atoms are separated from the Y atoms by a different distance. Upon lowering the temperature from 500 to 90 K, a distortion of the Y(Bi)O6, FeO6, B(2,3)O3 coordination polyhedra is observed. The distances between atoms in helical Fe chains and Fe-O-Fe angles change non-uniformly. A sharp jump in the equivalent isotropic displacement parameters of O1 and O2 atoms within the Fe-Fe chains and fluctuations of the equivalent isotropic displacement parameters of B2 and B3 atoms were observed in the region of structural transition as well as noticeable elongation of O1, O2, B2, B3, Fe1, Fe2 atomic displacement ellipsoids. It was established that the helices of electron density formed by Fe, O1 and O2 atoms may be structural elements determining chirality, optical activity and multiferroicity of rare-earth iron borates. Compression and stretching of these helices account for the symmetry change and for the manifestation of a number of properties, whose geometry is controlled by an indirect exchange interaction between iron cations that compete with the thermal motion of atoms in the structure. Structural analysis detected these changes as variations of a number of structural characteristics in the c unit-cell direction, that is, the direction of the helices. Structural results for the local surrounding of the atoms in (Y0.95Bi0.05)Fe3(BO3)4 were confirmed by EXAFS and Mössbauer spectroscopies.

The forward rainbow scattering of low energy protons by a graphene sheet

Abstract This article studies the rainbow scattering of 5-keV protons by the single sheet of free-standing graphene and its possible use as a tool for investigation of the ion-graphene interaction. The proton-graphene interaction potential was constructed by using the Doyle-Turner, ZBL, and Moliere proton-carbon interaction potentials. The thermal motion of carbon atoms was included by averaging the potentials according to the Debye model. Proton trajectories were obtained by numerical solution of the corresponding Newton equations of motion. They were used to obtain the mapping of the proton initial positions to their scattering angles. Morphological properties of the introduced mapping including its multiplicity and the rainbow singularities were used to explain important features of the obtained angular distributions of transmitted protons.

Determination of Anisotropic Ion Velocity Distribution Function in Intrinsic Gas Plasma. Theory.

The first seven coefficients of the expansion of the energy and angular distribution functions in Legendre polynomials for Hg+ ions in Hg vapor plasma with the parameter E/P ≈ 400 V/(cm Torr) are measured for the first time using a planar one-sided probe. The analytic solution to the Boltzmann kinetic equation for ions in the plasma of their parent gas is obtained in the conditions when the resonant charge exchange is the predominant process, and ions acquire on their mean free path a velocity much higher than the characteristic velocity of thermal motion of atoms. The presence of an ambipolar field of an arbitrary strength is taken into account. It is shown that the ion velocity distribution function is determined by two parameters and differs substantially from the Maxwellian distribution. Comparison of the results of calculation of the drift velocity of He+ ions in He, Ar+ in Ar, and Hg+ in Hg with the available experimental data shows their conformity. The results of the calculation of the ion distribution function correctly describe the experimental data obtained from its measurement. Analysis of the result shows that in spite of the presence of the strong field, the ion velocity distribution functions are isotropic for ion velocities lower than the average thermal velocity of atoms. With increasing ion velocity, the distribution becomes more and more extended in the direction of the electric field.

Effects of Vacancy Concentration and Temperature on Mechanical Properties of Single-Crystal γ-TiAl Based on Molecular Dynamics Simulation

Abstract Molecular dynamics simulation is used to analyze tensile strength and elastic modulus under different temperatures and vacancy concentrations. The effects of temperature and vacancy concentration on the mechanical properties of γ-TiAl alloy are investigated. The results show that the ultimate stress, ultimate strain and elastic modulus decrease nonlinearly with increasing temperature and vacancy concentration. As the temperature increases, the plastic of material is reinforced. The influence of temperature on strength and elastic modulus is larger than that of vacancy concentration. The evolution process of vacancy could be observed clearly. Furthermore, vacancies with different concentrations develop into voids first as a function of external forces or other factors, micro cracks evolve from those voids, those micro cracks then converge to a macro crack, and fracture will finally occur. The vacancy evolution process cannot be observed clearly owing to the thermal motion of atoms at high temperature. In addition, potential energy is affected by both temperature and vacancy concentration.

Electron transport in mercury vapor: cross sections, pressure and temperature dependence of transport coefficients and NDC effects

In this work we propose a complete and consistent set of cross sections for electron scattering in mercury vapor. The set is validated through a series of comparisons between swarm data calculated using a multi term theory for solving the Boltzmann equation and Monte Carlo simulations, and the available experimental data. Other sets of cross sections for electron scattering in mercury vapor were also used as input in our numerical codes with the aim of testing their completeness, consistency and accuracy. The calculated swarm parameters are compared with measurements in order to assess the quality of the cross sections in providing data for plasma modeling. In particular, we discuss the dependence of transport coefficients on the pressure and temperature of mercury vapor, and the occurrence of negative differential conductivity (NDC) in the limit of lower values of E∕N. We have shown that the phenomenon of NDC is induced by the presence of mercury dimers and that can be controlled by varying either pressure or temperature of mercury vapor. The effective inelastic cross section for mercury dimers is estimated for a range of pressures and temperatures. It is shown that the measured and calculated drift velocities agree very well only if the effective inelastic cross section for mercury dimers and thermal motion of mercury atoms are carefully considered and implemented in numerical calculations.