Collective Atomic Motion Research Articles

Light-Mediated Collective Atomic Motion in an Optical Lattice Coupled to a Membrane.

We observe effects of collective atomic motion in a one-dimensional optical lattice coupled to an optomechanical system. In this hybrid atom-optomechanical system, the lattice light generates a coupling between the lattice atoms as well as between atoms and a micromechanical membrane oscillator. For large atom numbers we observe an instability in the coupled system, resulting in large-amplitude atom-membrane oscillations. We show that this behavior can be explained by light-mediated collective atomic motion in the lattice, which arises for large atom numbers, small atom-light detunings, and asymmetric pumping of the lattice, in agreement with previous theoretical work. The model connects the optomechanical instability to a phase delay in the global atomic backaction onto the lattice light, which we observe in a direct measurement.

Atomic structure and dynamics properties of Cu50Zr50 films

In this paper, the structural and dynamic properties of Cu50Zr50 films are investigated by molecular dynamics simulations. Our results show that the dynamics of the surface atoms are much faster than those of the bulk. Especially, the diffusion coefficient of the surface atoms is about forty times larger than that of the bulk at 600 K, which qualitatively agrees with the experimental results. Meanwhile, we find that the population of the icosahedral (-like) clusters in the surface region is obviously higher than that of the bulk, which prevents the surface from crystallization. A new method to determine the string-like collective atomic motion is introduced in the paper, and it suggests a possible connection between the glass formation ability and collective atomic motion. By using the method, the effects of surface on collective motion are illustrated. Our results show that the string-like collective atomic motion of surface atoms is weakened while that of the interior atoms is strengthened. The studies clearly explain the effects of surface on the structural and dynamic properties of Cu50Zr50 films from the atomic scale.

An improved model of fission gas atom transport in irradiated uranium dioxide

The hitherto standard approach to predicting fission gas release has been a pure diffusion gas atom transport model based upon Fick's law. An additional mechanism has subsequently been identified from experimental data at high burnup and has been summarised in an empirical model that is considered to embody a so-called fuel matrix ’saturation’ phenomenon whereby the fuel matrix has become saturated with fission gas so that the continued addition of extra fission gas atoms results in their expulsion from the fuel matrix into the fuel rod plenum.The present paper proposes a different approach by constructing an enhanced fission gas transport law consisting of two components: 1) Fick's law and 2) a so-called drift term. The new transport law can be shown to be effectively identical in its predictions to the ’saturation’ approach and is more readily physically justifiable. The method introduces a generalisation of the standard diffusion equation which is dubbed the Drift Diffusion Equation. According to the magnitude of a dimensionless Péclet number, P, the new equation can vary from pure diffusion to pure drift, which latter represents a collective motion of the fission gas atoms through the fuel matrix at a translational velocity.Comparison is made between the saturation and enhanced transport approaches. Because of its dependence on P, the Drift Diffusion Equation is shown to be more effective at managing the transition from one type of limiting transport phenomenon to the other. Thus it can adapt appropriately according to the reactor operation.

Collective-Goldstone-mode-induced ultralow lattice thermal conductivity in Sn-filled skutterudite SnFe4Sb12

We demonstrate that the concept of Goldstone bosons can be exploited for phonon control and thermal conductivity reduction of materials. By studying lattice dynamics of the Sn filled skutterudite ${\mathrm{SnFe}}_{4}{\mathrm{Sb}}_{12}$, we find Sn off-centers in its coordination cage in contrast to the common rare earth fillers. This leads to low-frequency Goldstone-like modes below 1 THz associated mainly with Sn motions. Importantly, these involve collective motion of other atoms, especially Sb, in the host skutterudite lattice. The optical modes transversing to the Sn off-centering direction are identified as Goldstone type modes in association with a three-dimensional Mexican-hat-like potential energy surface. The interaction of these collective Goldstone modes with the host heat-carrying phonons is shown to lead to ultralow lattice thermal conductivity.

Cooperative inter- and intra-layer lattice dynamics of photoexcited multi-walled carbon nanotubes studied by ultrafast electron diffraction.

Optical tuning and probing ultrafast structural response of nanomaterials driven by electronic excitation constitute a challenging but promising approach for understanding microscopic mechanisms and applications in microelectromechanical systems and optoelectrical devices. Here we use pulsed electron diffraction in a transmission electron microscope to investigate laser-induced tubular lattice dynamics of multi-walled carbon nanotubes (MWCNTs) with varying laser fluence and initial specimen temperature. Our photoexcitation experiments demonstrate cooperative and inverse collective atomic motions in intralayer and interlayer directions, whose strengths and rates depend on pump fluence. The electron-driven and thermally driven structural responses with opposite amplitudes cause a crossover between intralayer and interlayer directions. Our ab initio calculations support these findings and reveal that electrons excited from π to π* orbitals in a carbon tube weaken the intralayer bonds while strengthening the interlayer bonds along the radial direction. Moreover, by probing the structural dynamics of MWCNTs at initial temperatures of 300 and 100 K, we uncover the concomitance of thermal and nonthermal dynamical processes and their mutual influence in MWCNTs. Our results illustrate the nature of electron-driven nonthermal process and electron-phonon thermalization in the MWCNTs, and bear implications for the intricate energy conversion and transfer in materials at the nanoscale.

Incidence energy effect and impact assessment during homoepitaxial growth of nickel on (001), (111) and (110) surfaces

In this work, we study homoepitaxial growth of Nickel on low-index (001), (110) and (111) Ni surfaces by means of molecular dynamics simulations based on the embedded atom method. The simulations are performed at 300K using gas precursors with incident energy of 2eV. The deposition of adatoms are done on (001), (110) and (111) surfaces. At low incidence energy, the film growth follows a Stranski-Karstanov mode at a critical film thickness. This aspect depends on the activation energy of the migration process, which affects the lateral diffusion on each surface. The high incidence energy of 2eV shows an effect on the film growth mode where the layers coverage rate increases compared to the low incidence energy for the three mentioned surfaces. Concerning the (111) surface, island coalescence is observed as a consequence of a collective atomic motion. The island geometric shape may be considered as dampers of the incidence energy, which block the exchange mechanism within the (111) surface, whereas in the case of the two other surfaces, the exchange mechanism remains eventual. The anisotropic shape of (110) surface is considered as an exceptional fact that can absorb incidence energy and then reproduces it horizontally, which can promote growth in lateral directions and form 2D islands.

Permanent modifications in silica produced by ion-induced high electronic excitation: experiments and atomistic simulations

The irradiation of silica with ions of specific energy larger than ~0.1 MeV/u produces very high electronic excitations that induce permanent changes in the physical, chemical and structural properties and give rise to defects (colour centres), responsible for the loss of sample transparency at specific bands. This type of irradiation leads to the generation of nanometer-sized tracks around the ion trajectory. In situ optical reflection measurements during systematic irradiation of silica samples allowed us to monitor the irradiation-induced compaction, whereas ex situ optical absorption measurements provide information on colour centre generation. In order to analyse the results, we have developed and validated an atomistic model able to quantitatively explain the experimental results. Thus, we are able to provide a consistent explanation for the size of the nanotracks, the velocity and thresholding effects for track formation, as well as, the colour centre yield per ion and the colour centre saturation density. In this work we will discuss the different processes involved in the permanent modification of silica: collective atomic motion, bond breaking, pressure-driven atom rearrangement and ultra-fast cooling. Despite the sudden lattice energy rise is the triggering and dominant step, all these processes are important for the final atomic configuration.

Large-scale and long-term correlations in collective motions of atoms of liquid argon. Computer simulation

The correlation coefficients of displacements of pairs of neighboring particles located in spheres of a given radius have been studied within the molecular dynamics models of liquid argon including 50000 and 500000 atoms. Atoms separated by distances of about ten diameters from each other are correlated and correlations last nanoseconds. A size effect has been revealed: correlations increase with the size of the model. All these properties indicate that mesoscopic supramolecular structures exist in a liquid.

Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles

Molecular dynamics simulations of ubiquitin in water/glycerol solutions are used to test the suggestion by Karplus and coworkers that proteins in their biologically active state should exhibit a dynamics similar to ‘surface-melted’ inorganic nanoparticles (NPs). Motivated by recent studies indicating that surface-melted inorganic NPs are in a ‘glassy’ state that is an intermediate dynamical state between a solid and liquid, we probe the validity and significance of this proposed analogy. In particular, atomistic simulations of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded Atom Method potential) indicate a common dynamic heterogeneity, along with other features of glass-forming (GF) liquids such as collective atomic motion in the form of string-like atomic displacements, potential energy fluctuations and particle displacements with long range correlations (‘colored’ or ‘pink’ noise), and particle displacement events having a power law scaling in magnitude, as found in earthquakes. On the other hand, we find the dynamics of ubiquitin to be even more like a polycrystalline material in which the α-helix and β-sheet regions of the protein are similar to crystal grains so that the string-like collective atomic motion is concentrated in regions between the α-helix and β-sheet domains.

Observation of coherent delocalized phonon-like modes in DNA under physiological conditions.

Underdamped terahertz-frequency delocalized phonon-like modes have long been suggested to play a role in the biological function of DNA. Such phonon modes involve the collective motion of many atoms and are prerequisite to understanding the molecular nature of macroscopic conformational changes and related biochemical phenomena. Initial predictions were based on simple theoretical models of DNA. However, such models do not take into account strong interactions with the surrounding water, which is likely to cause phonon modes to be heavily damped and localized. Here we apply state-of-the-art femtosecond optical Kerr effect spectroscopy, which is currently the only technique capable of taking low-frequency (GHz to THz) vibrational spectra in solution. We are able to demonstrate that phonon modes involving the hydrogen bond network between the strands exist in DNA at physiologically relevant conditions. In addition, the dynamics of the solvating water molecules is slowed down by about a factor of 20 compared with the bulk.

Step Coalescence by Collective Motion at an Incommensurate Grain Boundary.

Using extended time series scanning transmission electron microscopy, we investigate structural fluctuations at an incommensurate grain boundary in Au. Atomic-resolution imaging reveals the coalescence of two interfacial steps, or disconnections, of different height via coordinated motion of atoms along close-packed directions. Numerical simulations uncover a transition pathway that involves constriction and expansion of a characteristic stacking fault often associated with grain boundaries in face-centered cubic materials. It is found that local atomic fluctuations by enhanced point defect diffusion may play a critical role in initiating this transition. Our results offer new insights into the collective motion of atoms underlying the lateral advance of steps that control the migration of faceted grain boundaries.

Radiation resistance of nano-crystalline iron: Coupling of the fundamental segregation process and the annihilation of interstitials and vacancies near the grain boundaries

Finding novel nuclear materials with high radiation resistance is very important for the nuclear industry and requires the understanding of the self-healing of radiation damage in such novel materials as nano-crystalline iron. Combining molecular dynamics simulations, molecular statics calculations and the object kinetic Monte Carlo method, we found that the self-healing capability of nano-crystalline iron is closely related to the coupling of the individual fundamental segregation and annihilation processes of vacancies and interstitials near the grain boundary (GB). Statically, both near the GB and at the GB, a low-energy-barrier/barrier-free region forms around the interstitial which promotes the annihilation of vacancies. The annihilation process was found to always involve the collective motion of multiple atoms due to the recovery of the strained atoms around the interstitial. Dynamically, the annihilation involves two coupled processes. Before segregating into the GB, the interstitial annihilates lots of vacancies near the GB as it diffuses near the GB together with the low-barrier region. In addition, although the interstitial is tightly bound to the GB after segregation, it efficiently removes the vacancies near the GB while moving along the GB, with the low-barrier region extending into the neighborhood of the GB and even into the grain interior. These two mechanisms were found to work at low temperatures, even temperatures where the vacancy was immobile. This study revealed the interaction of the major radiation defects at different scales and thereby uncovered the origin of the high radiation resistance of nano-crystalline iron.

How Atomic Steps Modify Diffusion and Inter-adsorbate Forces: Empirical Evidence from Hopping Dynamics in Na/Cu(115).

We followed the collective atomic-scale motion of Na atoms on a vicinal Cu(115) surface within a time scale of pico- to nanoseconds using helium spin echo spectroscopy. The well-defined stepped structure of Cu(115) allows us to study the effect that atomic steps have on the adsorption properties, the rate for motion parallel and perpendicular to the step edge, and the interaction between the Na atoms. With the support of a molecular dynamics simulation we show that the Na atoms perform strongly anisotropic 1D hopping motion parallel to the step edges. Furthermore, we observe that the spatial and temporal correlations between the Na atoms that lead to collective motion are also anisotropic, suggesting the steps efficiently screen the lateral interaction between Na atoms residing on different terraces.

Monolayer Transfer Layers During Sliding at the Atomic Scale

One of the fundamental issues in friction is understanding the atomic details of how two materials slide against each other and start to wear. Whether this involves single-atom processes or the collective motion of atoms has been open to debate for some time. Here we report direct observations of this via in situ studies within a transmission electron microscope. We observed for both graphite and molybdenum disulfide that single atomic layers are transferred from the material to a sliding tip to form a transfer layer, and subsequent sliding takes place by sliding of single layers of graphite or molybdenum disulfide against each other. Despite the similarity of the end result, how the single layers are formed is quite different; with graphite, it involves buckling/wrinkling ~3 nm ahead of the tip, whereas with molybdenum disulfide it is via direct transfer of single sheets. Graphite is more like plastic wrap, molybdenum disulfide more like a pack of cards. This difference is attributed to the large difference in the bending modulus and strength of monolayers in the two cases. In both cases, collective processes are taking place.

Collective Atomic Motion at a 90° Tilt Grain Boundary in Gold

Collective Atomic Motion at a 90° Tilt Grain Boundary in Gold

Role of string-like collective atomic motion on diffusion and structural relaxation in glass forming Cu-Zr alloys.

We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by "dynamic heterogeneity" in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ΔGa with temperature of both the Cu and Zr diffusion coefficients D, and the alpha structural relaxation time τα can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract "cooperatively rearranging regions" of AG. We also find coexisting clusters of relatively "immobile" atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of "mobile" atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized ("immobile") and wandering ("mobile") particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations.

Light-wave mixing and scattering with quantum gases

We show that optical processes originating from elementary excitations with dominant collective atomic recoil motion in a quantum gas can profoundly change many nonlinear optical processes routinely observed in a normal gas. Not only multi-photon wave mixing processes all become stimulated Raman or hyper-Raman in nature but the usual forward wave-mixing process, which is the most efficient process in normal gases, is strongly reduced by the condensate structure factor. On the other hand, in the backward direction the Bogoliubov dispersion automatically compensates the optical- wave phase mismatch, resulting in efficient backward light field generation that usually is not supported in normal gases.

Diffusion of point defects, nucleation of dislocation loops, and effect of hydrogen in hcp-Zr: Ab initio and classical simulations

Diffusion of point defects, nucleation of dislocation loops, and the associated dimensional changes of pure and H-loaded hcp-Zr have been investigated by a combination of ab initio calculations and classical simulations. Vacancy diffusion is computed to be anisotropic with Dvac,basal=8.6×10−6e−Q/(RT) (m2/s) and Dvac,axial=9.9×10−6e−Q/(RT) (m2/s), Q=69 and 72kJ/mol for basal and axial diffusion, respectively. At 550K vacancy diffusion is about twice as fast in the basal plane as in a direction parallel to the c-axis. Diffusion of self-interstitials is found to be considerably faster and anisotropic involving collective atomic motions. At 550K diffusion occurs predominantly in the a-directions, but this anisotropy diminishes with increasing temperature. Furthermore, the diffusion anisotropy is very dependent on the local strain (c/a ratio). Interstitial H atoms are found to diffuse isotropically with DH=1.1×10−7e−42/(RT) (m2/s). These results are consistent with experimental data and other theoretical studies. Molecular dynamics simulations at 550K with periodic injection of vacancies and self-interstitial atoms reveal the formation of small nanoclusters, which are sufficient to cause a net expansion of the lattice in the a-directions driven by clusters of self-interstitials and a smaller contraction in the c-direction involving nanoclusters of vacancies. This is consistent with and can explain experimental data of irradiation growth. Energy minimizations show that vacancy c-loops can collapse into stacking-fault pyramids and, somewhat unexpectedly, this is associated with a contraction in the a-directions. This collapse can be impeded by hydrogen atoms. Interstitial hydrogen atoms have no marked influence on self-interstitial diffusion and aggregation. These simulations use a new Zr–H embedded atom potential, which is based on ab initio energies.

Dynamics of βB2-Crystallin Motion Based on Principal Component Analysis and Normal Mode Analysis

The primary function of lens is to focus images perfectly on the retina. Lens crystallins however are flexible nanomachines that frequently accomplish their biological function by collective atomic motions in and/or out the lens. Although genetic and biochemical data on the βB2-crystallin protein are available from several sources, the correlation between conformational changes and dynamic behavior at the atomic level remains to be understood. The βB2-crystallin dimer has studied through a combination of molecular dynamics simulations, principal component analysis (PCA) and normal mode analyses. The changes in interface buried surface shows the mutual orientation of individual domains in βB2-crystallin dimer. The dominant PCA modes for concerted motions of the protein atoms were monitored in a lower-dimensions subspace. Three types of movements found in βB2-crystallin dimer, which are a twist propeller motion, a scissors type hinge motion, and a shear motion between the domains. Both the RMSF and the normal-mode dynamics showed that N-terminal β-sheet is the most correlated segments.

Origin and Nature of Spontaneous Shape Fluctuations in “Small” Nanoparticles

Normally chemically inert materials such as Au have been found to be catalytically active in the form of particles whose size is about 1 nm. Direct and indirect observations of various types of metal nanoparticles (NPs) in this size range, under catalytically relevant conditions for fuel-cell operation and catalysis, have indicated that such “small” particles can exhibit large spontaneous shape fluctuations and significant changes in shape and chemical activity in response to alterations in environmental conditions. NPs also normally exhibit facile coalescence when in proximity, impacting their stability and reactivity in applications. We perform molecular dynamics simulations on Ni nanoparticles, a commonly used NP in catalytic applications and carbon nanotube growth, in the ≈1 nm size regime where large-scale shape fluctuations have been observed experimentally. An analysis of the large-scale shape fluctuations observed in our simulations of these “small” NPs indicates that they are accompanied by collective motion of Ni atoms through the NP center, and we quantify these dynamic structures and their impact on NP shape. In contrast, stringlike collective atomic motion is confined to the NP interfacial region of NPs having a diameter greater than a few nanometers, and correspondingly, the overall NP shape remains roughly spherical, a case studied in our prior Ni NP simulations. Evidently, the large spontaneous NP shape fluctuations reflect a change in character of the collective atomic dynamics when the NPs become critically small in size.