Atomic Trajectories Research Articles

Optical collimation of an atomic beam using a white light molasses

We investigate optical collimation of an atomic beam using a spectrally broadened white light molasses. We compare this technique with the standard technique using an atomic collimator and find that, under certain conditions, the white light molasses is preferable. Specifically, a white light molasses is suitable for atomic beams with relatively low mean velocities and broad velocity distributions, for example, a beam effusing from a cryogenically cooled reservoir. This result is demonstrated by numerically modeling the atomic trajectories of argon atoms effusing from a cryogenically cooled reservoir. We find that, given sufficient power, a white light molasses captures a larger fraction of atoms when compared to an atomic collimator, and the velocity distribution of the resulting beam is shifted toward slower velocities. Further, an optical molasses is geometrically relatively simple compared to an atomic collimator; therefore, the complexity of the in-vacuum optical arrangement can be significantly reduced.

Carbon dioxide in monoethanolamine: Interaction and its effect on structural and dynamic properties by molecular dynamics simulation

Molecular dynamics simulation study of carbon dioxide-monoethanolamine, CO2–MEA, was performed at constant pressure and temperature in a spanning range of CO2 mole fraction. Since alkanolamine is an industrial solvent to capture gas impurity, investigating the structural analysis and interaction with gas seems substantial. Force field validation was carried out regarding the thermophysical and transport properties of pure MEA at 313 and 333K. Structural analyses revealed that gas molecules locate among solvent particles by compacting some parts of MEA in order to achieve a position through free spaces of solvent confirmed by atomic Z-density and trajectory. Diffusion coefficient and energy contribution introduced x=0.036 as dissolving point. The orientation of gas molecules among solvent, hydrogen bond interaction, and coordination number calculations demonstrated a stronger interaction of solute and solvent and its involvement with N–H(N) head of MEA.

Atomistic simulation of nanoformed metallic glass

The effects of forming speed and temperature on the forming mechanism and mechanics of Cu50Zr25Ti25 metallic glass are studied using molecular dynamics simulations based on the second-moment approximation of the many-body tight-binding potential. These effects are investigated in terms of atomic trajectories, flow field, slip vectors, internal energy, radial distribution function, and elastic recovery of nanoimprint lithography (NIL) patterns. The simulation results show that a shear transformation zone (STZ) forms at the substrate surface underneath the mold during the forming process. The STZ area increases with mold displacement (D). The movement speed of substrate atoms underneath the mold increases with increasing D value. The movement directions of substrate atoms underneath the mold are more agreeable for a larger D value. The stick-slip phenomenon becomes more obvious with increasing D value and imprint speed. The substrate energy increases with increasing imprint speed and temperature. Great NIL pattern transfer is obtained with unloading at low temperatures (e.g., room temperature).

Shear behaviors of single crystal nickel at different temperatures: molecular dynamics simulations

Shear behaviors of a single crystal nickel along the [\( \overline{1} 10 \)], [\( 1\overline{1} 0 \)], [\( \overline{1}\,\overline{1} 2 \)] and [\( 11\overline{2} \)] directions in the (111) crystallographic plane have been investigated at different temperatures by performing molecular dynamics simulations with an embedded atom method potential. Results show that shear stress–shear strain curves and atomic trajectory during shear process exhibit periodic behaviors, while the periods are varied for different shear directions. It sheds light on the inherent relationship between shear displacement for a period of the curve and the atomic configuration in corresponding crystallographic direction. Furthermore, shear modulus is extracted from the curves over a temperature range from 0 to 1700 K. It is demonstrated that the modulus is independent from the size of shear models and the shear directions, and that the modulus decreases with increasing temperature. In addition, this work also demonstrates that the classical description of shear modulus is still valid at the nanoscale, which might suggest a simple and direct way to obtain shear modulus at the atomic scale.

Studies of crack growth and propagation of single-crystal nickel by molecular dynamics

Abstract The crack growth and propagation of pre-cracked single-crystal nickel under mode I loading conditions are investigated by molecular dynamics simulation based on the many-body tight-binding potential. The effects of temperature, loading rate, and orientations are evaluated in terms of atomic trajectories, von Mises stress, and a centrosymmetry parameter. Simulation results clearly show that partial dislocations begin to slip at the crack tip and propagate along the close-packed (1 1 1) plane until fracture. There are different modes of crack propagation between finite or infinite length in y direction. A brittle-to-ductile transition occurs between temperatures of 50 and 700 K, with the brittle fracture response more obvious at lower temperature. The critical stress increases with increasing strain rate and decreasing temperature. The magnitude of critical stress is σc〈111〉 > σc〈100〉 > σc〈110〉 for difference direction Ni nanoribbons, indicating that the critical stress is strongly dependent on the crystallographic direction.

Influence of liquid environment and bounding wall structure on fluid flow through carbon nanotubes

Flows of different fluids through single-walled carbon nanotubes (SWCNTs) with boundary walls having the perfect and defective graphene structures have been investigated by means of molecular dynamics (MD) simulations. It has been shown that the boundary wall structure has a very strong influence on not only an average fluid flow rate but also on shapes of trajectories of individual fluid atoms (molecules) and fluid centres of mass. The fluid flows through SWCNTs surrounded by different liquid environments have been also simulated and an influence of these environments on the average fluid flow rates have been studied. It has been revealed a strong dependence of the average fluid flow rate on a molecular polarity of fluids flowing through SWCNTs and those surrounding the tubes. It has been shown that, for multi-walled carbon nanotubes (MWCNTs), an effect of liquid environment on the fluid flow can be significantly suppressed.

Thermal conductivity and spectral phonon properties of freestanding and supported silicene

We conduct molecular dynamics (MD) simulations to study the thermal conductivity of freestanding silicene and silicene supported on an amorphous silicon dioxide (SiO2) substrate in the temperature range from 300 to 900 K. The results show that the thermal conductivity decreases with increasing temperature and that the presence of the SiO2 substrate results in a great reduction, up to 78% at 300 K, to the thermal conductivity of silicene. With atomic trajectories from equilibrium MD simulations, we perform spectral energy density analysis to compute the thermal conductivities, spectral phonon relaxation times, and spectral phonon mean free paths (MFPs) of freestanding and supported silicene at 300 K. When silicene is put on a SiO2 substrate, the phonon relaxation times are decreased from 1–13 ps to less than 1 ps, and the phonon MFPs are reduced from 10–120 nm to 0–20 nm. We also calculate the thermal conductivity contributions from all phonon branches and find that the thermal conductivities of freestanding and supported silicene are mainly (>85%) contributed by the longitudinal and transverse acoustic phonons, while the out-of-plane acoustic phonons have a contribution less than 3%. Our study predicts the reduction of the thermal conductivity of silicene due to substrate effects and provides a fundamental understanding of the reduction in terms of the spectral phonon relaxation times and MFPs.

Multipartite model of evaporative cooling in optical dipole traps

We propose and study a model of forced evaporation of atomic clouds in crossed-beam optical dipole traps that explicitly includes the growth of a population in the ``wings'' of the trap and its subsequent impact on dimple temperature and density. It has long been surmised that a large wing population is an impediment to the efficient production of Bose-Einstein condensates in crossed-beam traps. Understanding the effect of the wings is particularly important for $\ensuremath{\lambda}=1.06\phantom{\rule{0.16em}{0ex}}\ensuremath{\mu}\mathrm{m}$ traps, for which a large ratio of Rayleigh range to beam waist results in wings that are large in volume and extend far from the dimple. Key ingredients to our model's realism are (1) our explicit treatment of the nonthermal, time-dependent energy distribution of wing atoms in the full anharmonic potential and (2) our accurate estimations of transition rates among dimple, wing, and free-atom populations, obtained with Monte Carlo simulations of atomic trajectories. We apply our model to trap configurations in which neither, one, or both of the wing potentials are made unbound by applying a ``tipping'' gradient. We find that forced evaporation in a trap with two bound wing potentials produces a large wing population which can collisionally heat the dimple so strongly as to preclude reaching quantum degeneracy. Evaporation in a trap with one unbound wing, such as that made by crossing one vertical beam and one horizontal beam, also leads to a persistent wing population which dramatically degrades the evaporation process. However, a trap with both wings tilted so as to be just unbound enjoys a nearly complete recovery of efficient evaporation. By introducing to our physical model an ad hoc, tunable escape channel for wing atoms, we study the effect of partially filled wings, finding that a wing population caused by single-beam potentials can drastically slow down evaporative cooling and increase the sensitivity to the choice of $\ensuremath{\eta}$.

Ultrafast laser-excited vibration and elastic modulus of individual gold nanorods.

Ultrafast laser irradiation of single gold nanorods of various sizes is simulated for the investigation of the vibrations of the nanorods. The investigation uses a hybrid method that couples molecular dynamics (MD) with the two-temperature model (TTM). The extensional frequencies of the single gold nanorods are extracted from the atomic trajectories obtained by the MD simulations. In combination with continuum elasticity, the elastic moduli of the single gold nanorods are determined, along with the predicted extensional frequencies of the nanorods. It is shown that as the nanorod width increases, the modulus of the single gold nanorods also increases and approaches that of bulk gold. The notable softening of the elastic modulus is clearly shown for the smaller nanorods with widths of ∼8 and ∼12 nm.

Atomistic simulations of nanowelding of single-crystal and amorphous gold nanowires

The mechanism and quality of the welding of single-crystal (SC) and amorphous gold nanowires (NWs) with head-to-head contact are studied using molecular dynamics simulations based on the second-moment approximation of the many-body tight-binding potential. The results are discussed in terms of atomic trajectories, slip vectors, stress, and radial distribution function. Simulation results show that the alignment for the amorphous NWs during welding is easier than that for the SC NWs due to the former's relatively stable geometry. A few dislocations nucleate and propagate on the (111) close-packed plane (slip plane) inside the SC NWs during the welding and stretching processes. During welding, an incomplete jointing area first forms through the interactions of the van der Waals attractive force, and the jointing area increases with increasing extent of contact between the two NWs. A crystallization transition region forms in the jointing area for the welding of SC-amorphous or amorphous-SC NWs. With increasing interference, an amorphous gold NW shortens more than does a SC gold NW due to the former's relatively poor strength. The pressure required for welding decreases with increasing temperature.

Precision measurement of single-atom trajectories in higher-order Laguerre-Gaussian transverse modes of a Fabry-Perot cavity

A coupled quantum system composed of cavity field and atoms is one of the main research contents of cavity quantum electrodynamics. It can be used to realize single atom manipulation and measurement, and has important significance for studying the interaction between light and the atom, preparing quantum states and quantum entanglement. Current research work mainly focuses on two aspects. One is to achieve the atom trapping via the feedback control of the trapping laser intensity. The other is to measure the single atomic motion in a Fabry-Perot cavity by using Hermite-Gaussian transverse modes. The detection of the atomic trajectories has been realized via the observation of transmission spectra of the strong coupling system composed of cold atoms and Hermite-Gaussian transverse modes in a Fabry-Perot cavity. In order to observe the atomic motion trajectories in the cavity, we theoretically study the transmission spectrum of a strong coupling system composed of cold atoms and Laguerre-Gaussian transverse modes in a Fabry-Perot cavity in this paper. We calculate the relationship between the coupling coefficient and the mode number of Laguerre-Gaussian transverse modes. The result shows that with the increase of Laguerre-Gaussian transverse mode number, the maximum coupling coefficient between the atoms and cavity fields is almost unchanged, so the contrast of the detected spectrum is nearly independent of the mode number. Analysis shows that Laguerre-Gaussian transverse mode provides more abundant information about atomic motion trajectory than Hermite-Gaussian transverse mode. The field distribution of Laguerre-Gaussian transverse mode is ring-shaped. Owing to the ring shape, the atoms dropped at different positions experience different electric field intensities, and the detected transmission spectra are changed. Therefore, we can implement the high precision distinguishment of the atomic trajectories by observing the features of the transmission spectra such as the number of the transmission peaks and their positions. Furthermore, a small deviation of the atomic motion trajectories, on the edges of the rings of the electric field, may induce great change in transmission spectrum, and then we can very accurately detect the atomic motion around these positions.

Modeling of Nonthermal Solid‐to‐Solid Phase Transition in Diamond Irradiated with Femtosecond x‐ray FEL Pulse

AbstractIn this contribution we review in detail our recently developed hybrid model able to trace simultaneously nonequilibrium electron kinetics, evolution of an electronic structure, and eventually nonthermal phase transition in solids irradiated with femtosecond free‐electron laser pulses. Diamond irradiated with an ultrashort intense x‐ray pulse serves as an example to show how an irradiated material undergoes an ultrafast phase transition on sub‐picosecond timescales. The transition of diamond into graphite is induced by an excitation of electrons from the valence band into the conduction band, which, in turn, induces a rapid change of the interatomic potential. Our theoretical model incorporates: a Monte‐Carlo method for tracing high‐energy electrons and K‐shell holes in diamond; a temperature equation for the valence‐band and low‐energy conduction‐band electrons; a tight binding method for calculation of the evolving electronic structure of the material and potential energy surfaces; and molecular dynamics propagating atomic trajectories. This unified approach predicts the damage threshold of diamond in a good agreement with experimentally measured values. It reveals a multi‐step nature of nonthermal phase transition being an interplay between electronic excitation, changes of the band structure, and atomic reordering. An effect of pulse parameters, such as photon energy and temporal pulse shape, on the phase transition is discussed in detail. (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Microtubule Electrodynamics Associated with Vibrational Normal Modes

Cytoskeleton is a crucial integrating component of cellular functions. Microtubules, as a part of cytoskeleton, are involved in such functions, serving as transportation tracks, signaling substrate and also are fundamental for cellular division. While chemical, mechanical and electrostatic nature of microtubule function in these cellular processes is being researched, current picture of all underlying types of interactions is far from complete.Here, we introduce a new, electrodynamic aspect of microtubule interaction with its molecular partners from combination of the knowledge of atomic-precision electric charge distribution with fast mechanical fluctuation properties of microtubules.First, a microtubule lattice is reconstructed from combined RCSB Protein DataBank 1TUB and 1JFF tubulin structure and interlocking alpha-tubulin loops between adjacent protofilaments are remodeled to obtain physiological conformation. We analyze normal modes of anisotropic elastic network microtubule model obtained by coarse-graining the atomic model and using rotating block approximation. Further, we map the atomic charge distribution upon atomic trajectories of the first 30 normal modes, which lie in GHz spectral region. Approximating the oscillating atomic charges as a Hertzian dipoles, we calculated and visualized electrodynamic field around the microtubule for each normal mode.Based on the results, we suggest that the electrodynamic field around microtubule can provide interactions of different nature than pure electrostatic interactions since the ionic screening is diminished for frequency the electric >10 MHz.Significance of these unique theoretical predictions is planned to be verified in the upcoming experimental studies. Exploitation of microtubule electrodynamic properties could open paths to novel tools for microtubule manipulation with prospects in new therapeutic and diagnostic methods in the future.

Shear behaviors of single crystal hcp Ti at different temperatures from molecular dynamics simulations

Shear behaviors of single crystal hcp titanium in a close-packed (0001) basal plane along the , [], [], and [] directions at different temperatures were studied via molecular dynamics simulation using an embedded atom method (EAM) potential. Results show that periods of shear stress–shear strain curves along four directions occur, where shear displacement for one period of the curve relates to one period of atomic configuration in the corresponding direction, and that the trajectory of the free atoms also shows periodic characteristics. It is demonstrated that shear behaviors along two orthogonal directions are different, while they perform the same in opposite directions. In addition, the shear modulus can be obtained from the slope of the shear stress–shear strain curves and shows independence from the shear directions and the height of the models. The modulus was extracted over a temperature range of 0 to 1050 K, showing a decreasing trend with increasing temperature. Furthermore, this work also demonstrates that the classical description of shear modulus is still valid on the nanoscale, which might suggest a simple and direct way to obtain the shear modulus on the atomic scale.

The effect of rough surface on nanoscale high speed grinding by a molecular dynamics simulation

Molecular dynamics is employed to study the nanoscale high speed grinding process of single crystal copper with rough surface. Material removal behavior of the cooper workpiece through diamond grinding is studied. The effects of texture density, texture direction, texture shape and the tool with rough or smooth surface are thoroughly investigated in terms of atomic trajectories, temperature distribution, radial distribution function, grinding temperature, grinding force, and friction coefficient. It can be found that a larger texture density results in lowering a surface smoothness of workpiece in the local area, and reduces the partial protrusion, specifically when the texture density is greater than 90%. The material removal and the smoothness of ground surface strongly depend upon the effects of texture orientation and shape. The quality of the ground surface at texture orientation parallel with the x-axis is the best. The texture shape that intensely influences the chip and the groove depends on the size of the contact surface, suggesting that the material removal mechanism is roughly the same under different texture shapes. The smooth prismatic tips generate a more chips than the rough prismatic tip, while the volume of the material pileups is less than that of the rough one, which means that the prismatic diamond tip with smooth surface has an absolute advantage than the rough tip to machine nanostructures and greatly improves the material removal rate. These results show that it is possible to control and tune the grinding parameters according to texture density, direction and shape during machining single crystal copper with rough surface, and provides a potential way to improve a surface integrity and a smoothness of machined surface.

Simulating radiation damage cascades in graphite

Molecular dynamics simulation is used to study radiation damage cascades in graphite. High statistical precision is obtained by sampling a wide energy range (100–2500eV) and a large number of initial directions of the primary knock-on atom. Chemical bonding is described using the Environment Dependent Interaction Potential for carbon. Graphite is found to exhibit a radiation response distinct from metals and oxides primarily due to the absence of a thermal spike which results in point defects and disconnected regions of damage. Other unique attributes include exceedingly short cascade lifetimes and fractal-like atomic trajectories. Unusually for a solid, the binary collision approximation is useful across a wide energy range, and as a consequence residual damage is consistent with the Kinchin–Pease model. The simulations are in agreement with known experimental data and help to clarify substantial uncertainty in the literature regarding the extent of the cascade and the associated damage.

Revisiting the capture velocity of a cesium magneto-optical trap: model, simulation and experiment

In this work, we have explored ab initio the capture process in a magneto-optical trap by theory, simulation and experiment. We measured the capture velocity vc of a cesium vapor cell magneto-optical trap (VCMOT) from its capture rate R and developed an exact model for the capture rate of a VCMOT in terms of its capture velocity, background density and trap laser beam diameter. We measured the capture velocity of a cesium VCMOT for various trap laser intensities and magnetic field gradients. We observed that the capture velocity is a damping force as well as a restoring force phenomenon. We supported our findings by performing simulations for single atom trajectories in a 1D cesium MOT. Finally, we concluded that two MOTs can have the same capture velocities but very different capture rates, thereby revealing that these are two fundamentally different characteristics of the MOT.

Nanomilling mechanism on Cu surfaces investigated using atomistic simulation

The nanoscale milling and scratching processes of copper workpieces are studied using molecular dynamics simulations based on the tight-binding and Morse potentials. The effects of the rotation velocity of the tool and the workpiece temperature are evaluated in terms of atomic trajectories, slip vectors, flow field of chips, cutting forces and groove characteristics. The simulation shows that a slip system in the ⟨110⟩ direction on the workpiece surface occurs for milling with a tool rotation velocity of ω = 0°/fs. However, no apparent slip system appears for ω = 0.005°/fs or higher; instead, the number of amorphous areas increases. At ω = 0°/fs (nanoscratching), most of the removed atoms pile up in front of the tool and some gradually backfill when the tool rotates due to the effects of rotational friction and adhesion between the tool and the removed atoms. The largest number of removed atoms that piled up in front of the tool were obtained for milling with ω = 0°/fs; the number of removed atoms that piled up in front of the tool decreased with the increasing ω value. The component forces corresponding to the feed direction of the tool are the largest for the nanodrilling and nanomilling processes. High-precision grooves can be obtained at a low workpiece temperature (e.g. room temperature) with ω = 0°/fs.

Atomic mirrors for a Λ-type three-level atom

We propose atom mirror schemes for a three-level atom of Λ-type interacting with two evanescent fields, which are generated as a result of the total internal reflection of two coherent Gaussian laser beams at the interface of a dielectric prism with vacuum. The forces acting on the atom are derived by means of optical Bloch equations, based on the atomic density matrix elements. The theory is illustrated by setting up the equations of motion for 23Na atom. Two types of excited schemes are examined, namely the cases in which the evanescent fields have polarization types of and . The equations are solved numerically and we get results for atomic trajectories for different parameters. The performance of the mirror for the two types of polarization schemes is quantified and discussed. The possibility of reflecting atoms at pre-determined directions is also discussed.

Atomistic simulation of nanodrilling mechanics and mechanism on Cu substrates

The nanodrilling process of copper substrates is studied using molecular dynamics simulations. The effects of the rotation velocity of the tool and substrate temperature are evaluated in terms of atomic trajectories, slip vector, thrust force, stress, flow field, and hole characteristics. The simulation shows that the main hole-making mechanism for drilling with low rotation velocities (0.1°/ps or lower) is mechanical indentation. The number of removed atoms and influence area of the substrate increase with increasing rotation velocity of the tool. When the rotation velocity of the tool or substrate temperature increases, the influence area expands more in the radial direction than in the axial direction. The required thrust force for making a hole is lower at a higher rotation velocity of the tool and higher substrate temperature. Undesirable elastic recovery after drilling can be reduced by increasing the rotation velocity of the tool.