Collective Atomic Motion Research Articles

Dynamical thermal conductivity of argon crystal

The thermal conductivity of a rare-gas crystal (Ar) is computed using equilibrium molecular dynamics in conjunction with the Green-Kubo linear response formalism, and the Lennard-Jones potential with an appropriately long cutoff (4σ). Besides predicting absolute values of the conductivity from low temperature up to the liquid, the approach allows heat conduction to be understood as a dynamical process through the temporal behavior of the heat current correlation function. At low temperatures the correlation function shows a characteristic two-stage decay, a short-time relaxation which we attribute to single-particle motions in a local environment, and a more extended component corresponding to collective atomic motions (phonons). As temperature increases the second correlation component diminishes much faster than the first component, indicating a transition from mainly phase-coherent phonon transport to mainly phase-incoherent interatomic energy transfer in solids.

Shuffling in displacive phase transformations

With the aim to elucidate the transformation paths producing complex martensitic structures, the elementary mechanisms of collective atomic motion in diffusionless phase transformations are investigated using simple geometrical models. Relationships of the structures created by different mechanisms are summarized and the role of various planar crystal defects is examined. It is shown that in addition to intrinsic stacking faults so-called centred stacking faults can be considered and besides single-layer atomic shuffling the shuffling of atomic plane triplets can also occur.

Large-Scale Molecular Dynamics Study of Montmorillonite Clay: Emergence of Undulatory Fluctuations and Determination of Material Properties

Large-scale atomistic simulations, which we define as containing more than 100 000 atoms, are becoming more commonplace as computational resources increase and efficient classical molecular dynamics algorithms are developed. With the advent of grid-computing methods, it is now possible to simulate even larger systems efficiently. Using this new technology, we have simulated montmorillonite clay systems containing up to approximately ten million atoms whose dimensions approach those of a realistic clay platelet. This considerably extends the spatial dimensions of microscopic simulation into a domain normally encountered in mesoscopic simulation. The simulations exhibit emergent behavior with increasing size, manifesting collective thermal motion of clay sheet atoms over lengths greater than 150 Å. This motion produces low-amplitude, long-wavelength undulations of the clay sheets, implicitly inhibited by the small system sizes normally encountered in atomistic simulation. The thermal bending fluctuations allow us to calculate material properties, which are hard to obtain experimentally due to the small size of clay platelets. Montmorillonite is commonly used as a filler in clay−polymer nanocomposites, and estimation of the elastic properties of the composite requires accurate knowledge of the elastic moduli of the components. We estimate the bending modulus to be 1.6 × 10-17 J, corresponding to an in-plane Young's modulus of 230 GPa. We encounter a clay sheet persistence length of approximately 1400 Å, which dampens the undulations at long wavelengths for the largest system in our study.

Atomic-level dynamic behavior of a diffuse interphase boundary in an Au–Cu alloy

This investigation uses in situ high-resolution transmission electron microscopy to quantify the atomic-level dynamic behavior of a diffuse interphase boundary between ordered and disordered phases in an Au–Cu alloy at elevated temperature. It is found that both the interphase boundary position and thickness fluctuate with time and that the behavior of the disordered side of the interphase boundary differs from that of the ordered side. Analysis of the interphase boundary shape shows that it fluctuates by a mechanism involving the collective motion of many atoms rather than by single-atom jumps. These features are explained in terms of the physical properties of the different phases at the interphase boundary.

Collective motion of atoms in grain boundary migration of a bcc metal

Molecular dynamics simulations of grain boundary (GB) migration of a bcc metal, tungsten, have been carried out. The GB is of asymmetrical ⟨ 110⟩ tilt type. Detailed examinations of atomic processes in the migration, show that the GB migration consists mainly of GB dislocation glides. Furthermore, each motion of a GB dislocation involves a cooperative motion of about three atoms on each of the atomic planes perpendicular to the tilt axis, leading to their realignment from the receding grain to the advancing grain. This collective motion is not synchronized in all of the atomic planes, but appears to be in two or three adjacent planes, suggesting a kink mechanism for glides of the GB dislocations.

Elasticity study on collective motion in metallic glasses

The frequency dependence and the strain amplitude dependence of the dynamic Young's modulus in amorphous (a-) Cu 50Ti 50, a-Zr 50Cu 50 and a-Zr 55Cu 30Al 10Ni 5 were investigated at room temperature by means of the vibrating reed method. In the following, f and ɛ denote the frequency and the strain amplitude, respectively. The frequency dependence of the dynamic Young's modulus was measured at ɛ ∼ 10 −6 in the frequency range between 10 1 and 10 4 Hz, where a strong decrease in the dynamic Young's modulus between 10 1 and 10 4 Hz was found. The strain amplitude dependence of the dynamic Young's modulus was measured at f ∼ 10 2 Hz in the strain amplitude range between 10 −5 and 10 −3, where a strong increase in the dynamic Young's modulus with increasing strain amplitude was found. The effect of passing an electric direct-current on the dynamic Young's modulus at ɛ ∼ 10 −6 and f ∼ 10 2 Hz was also investigated, where a net increase in the dynamic Young's modulus with increasing current density in the range of 10 7 A/m 2 was found. These results were discussed from the point of view of the resonant collective motions of many atoms in metallic glasses.

Can Conformational Change Be Described by Only a Few Normal Modes?

We suggest a simple method to assess how many normal modes are needed to map a conformational change. By projecting the conformational change onto a subspace of the normal-mode vectors and using root mean square deviation as a test of accuracy, we find that the first 20 modes only contribute 50% or less of the total conformational change in four test cases (myosin, calmodulin, NtrC, and hemoglobin). In some allosteric systems, like the molecular switch NtrC, the conformational change is localized to a limited number of residues. We find that many more modes are necessary to accurately map this collective displacement. In addition, the normal-mode “spectra” can provide useful information about the details of the conformational change, especially when comparing structures with different bound ligands, in this case, calmodulin. Indeed, this approach presents normal-mode analysis as a useful basis in which to capture the mechanism of conformational change, and shows that the number of normal modes needed to capture the essential collective motions of atoms should be chosen according to the required accuracy.

Self-organization effects and light amplification of collective atomic recoil motion in a harmonic trap

Self-organization effects related to light amplification in the collective atomic recoil laser system with the driven atoms confined in a harmonic trap are investigated further. In the dispersive parametric region, our study reveals that the spontaneously formed structures in the phase space contributes an important role to the light amplification of the probe field under the atomic motion being modified by the trap.

Channels of energy redistribution in short-pulse laser interactions with metal targets

The kinetics and channels of laser energy redistribution in a target irradiated by a short, 1 ps, laser pulse is investigated in computer simulations performed with a model that combines molecular dynamics (MD) simulations with a continuum description of the laser excitation and relaxation of the conduction band electrons, based on the two-temperature model (TTM). The energy transferred from the excited electrons to the lattice splits into several parts, namely the energy of the thermal motion of the atoms, the energy of collective atomic motions associated with the relaxation of laser-induced stresses, the energy carried away from the surface region of the target by a stress wave, the energy of quasi-static anisotropic stresses, and, at laser fluences above the melting threshold, the energy transferred to the latent heat of melting and then released upon recrystallization. The presence of the non-thermal channels of energy redistribution (stress wave and quasi-static stresses), not accounted for in the conventional TTM model, can have important implications for interpretation of experimental results on the kinetics of thermal and mechanical relaxation of a target irradiated by a short laser pulse as well as on the characteristics of laser-induced phase transformations. The fraction of the non-thermal energy in the total laser energy partitioning increases with increasing laser fluence.

Molecular dynamics simulations of evolved collective motions of atoms in the myosin motor domain upon perturbation of the ATPase pocket

A crucial point for mechanical force generation in actomyosin systems is how the energy released by ATP hydrolysis in the myosin motor domain gives rise to the movement of the myosin head along the actin filament. We assumed the signal of the ATP hydrolysis to be transmitted as modulated atomic vibrations from the nucleotide-binding site throughout the myosin head, and carried out 1-ns all-atom molecular dynamics simulations for that signal transmission. We distributed the released energy to atoms located around the ATPase pocket as kinetic energies and examined how the effect of disturbance extended throughout the motor domain. The result showed that the disturbance signal extended over the motor domain in 150 ps and induced slowly varying collective motions of atoms at the actin-binding site and the junction with the neck, both of which are relevant to the movement of the myosin head along the actin filament. We also performed a principal component analysis of thermal atomic motions for the motor domain, and the first principal component was consistent with the response to the disturbance given to the ATPase pocket.

Combined atomistic-continuum model for simulation of laser interaction with metals: application in the calculation of melting thresholds in Ni targets of varying thickness

The threshold laser fluence for the onset of surface melting is calculated for Ni films of different thicknesses and for a bulk Ni target using a combined atomistic-continuum computational model. The model combines the classical molecular dynamics (MD) method for simulation of non-equilibrium processes of lattice superheating and fast phase transformations with a continuum description of the laser excitation and subsequent relaxation of the conduction band electrons based on the two-temperature model (TTM). In the hybrid TTM-MD method, MD substitutes the TTM equation for the lattice temperature, and the diffusion equation for the electron temperature is solved simultaneously with MD integration of the equations of motion of atoms. The dependence of the threshold fluence on the film thickness predicted in TTM-MD simulations qualitatively agrees with TTM calculations, while the values of the thresholds for thick films and bulk targets are ∼10% higher in TTM-MD. The quantitative differences between the predictions of TTM and TTM-MD demonstrate that the kinetics of laser melting as well as the energy partitioning between the thermal energy of atomic vibrations and energy of the collective atomic motion driven by the relaxation of the laser-induced pressure should be taken into account in interpretation of experimental results on surface melting.

Stress-assisted grain boundary sliding and migration at finite temperature: A molecular dynamics study

The sliding in a Ni symmetrical tilt grain boundary, $\ensuremath{\Sigma}5$ (012) [100], is investigated by modified Parrinello-Rahman molecular dynamics which deals with the thermodynamic ensemble characterized by the number of atoms $N$, temperature $T$, and the shear stress $\mathbf{t}$. It is found that the grain boundary can slide in the direction perpendicular to the tilt axis $[02\overline{1}]$ with the aid of shear stress in that direction. The sliding is coupled to the migration involving a collective motion of the third layer atoms hopping into the hollow site in between the first (GB) and second layers. Here, the critical stress necessary to move the grain boundary damps almost exponentially as the temperature is increased. At temperatures above about $820\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, random walk of GB migration occurs without the assistance of stress. On the other hand, it is only at much higher shear stress that the grain boundary can slide in the direction parallel to the tilt axis [001]. This may be because this sliding mechanism does not involve the coupling to the migration mode.

Optical bistability and collective behavior of atoms trapped in a high-Qring cavity

We study the collective motion of atoms confined in an optical lattice operating inside a high-finesse ring cavity. A simplified theoretical model for the dynamics of the system is developed upon the assumption of adiabaticity of the atomic motion. We show that in a regime where the light shift per photon times the number of atoms exceeds the linewidth of the cavity resonance, the otherwise tiny retroaction of the atoms upon the light field becomes a significant feature of the system. As a result dispersive optical bistability can arise and the lattice positions is determined by the strength of the atom-cavity coupling rather than by the phases of the incoupled light beams. Solving the complete set of classical equations of motion confirms these findings, however, additional nonadiabatic phenomena are predicted, such as, for example, self-induced radial breathing oscillations. We compare these results with experiments involving laser-cooled $^{85}\mathrm{Rb}$ atoms trapped in an optical lattice inside a ring cavity with a finesse of $1.8\ifmmode\times\else\texttimes\fi{}{10}^{5}$. Our observations are in excellent agreement with our theoretical predictions.

Light amplification related to collective atomic recoil affected by dipole–dipole collision

We have studied a collective atomic recoil laser (CARL) including atomic dipole–dipole (D–D) collisions. The results simulated under some sets of parametric conditions reveal that this interatomic interaction plays a negative role in the laser process due to its noncoherent characteristic for the collective atomic recoil motions, which greatly reduces the spatial orderliness of the atomic density distribution necessary for the laser operation.

Theory and Modeling of Radiation Damage Processes in Materials

Present knowledge is reviewed of radiation damage processes in materials. These processes cover various time- and length-scales, from ballistic binary collision process to collective atomic motion in the thermal spike stage, followed by the thermally activated processes involved in defect aggregation. It is emphasized that greater researches are required to understand these processes and their interplay in the multiscale modeling approach, before a prediction of a given material’s response to fusion irradiation conditions is possible. In addition, a predictive capability is also needed to develop new, advanced materials.

Light amplification through collective atomic recoil motion modified by a harmonic potential

Light amplification in a collective atomic recoil laser with an active medium confined in an external harmonic trap is investigated. Our study confirms the possibility of a great promotion of the lasing efficiency due to the collective atomic recoil motion being modified by the trapping potential. The physical explanation of this laser behavior is given.

Underlying mechanisms for unique elastic properties of nanocrystalline Au

Abstract In order to get an insight into the grain boundaries (GBs) in nanocrystalline (n-) metal, we prepared the high-density n-Au with ρ / ρ 0 >99% by the gas-deposition method and carried out the vibrating reed measurements, where ρ / ρ 0 is the relative density referring to the bulk density. The strain amplitude dependence (SAMD) of the resonant frequency ( f ) and the internal friction ( Q −1 ) was measured for the strain ( e ) amplitude between 10 −6 and 2×10 −3 and for temperature between 5 and 300 K. No plastic deformations are detected for the present strain range, where f decreases for e up to 10 −4 and then turns to increase, showing saturation for e between 10 −4 and 2×10 −3 . The low temperature irradiation by 2 MeV electrons or 20 MeV protons causes an increase in the Young’s modulus at 6 K, which is surmised to reflect a modification of the anelastic process in the GB regions. In contrast, the SAMD of f is hardly modified by irradiation, suggesting that it is indicative of a collective motion of atoms in n-Au.

Anomalous elastic response of amorphous alloys suggesting collective motions of many atoms

The dynamic Young’s modulus, E , of amorphous (a-) Zr 60 Cu 30 Al 10 (numbers indicate at.%) alloy was measured as a function of frequency, f , with a strain amplitude, ε t , of 10 −6 , E (10 −6 , f ), and also as a function of ε t for f near 10 2 Hz, E ( ε t ,10 2 Hz), by means of the vibrating reed methods. The elasticity study under the passing of electric current (PEC) was carried out too. E (10 −6 , f ) is lower than E 0 for f between 10 and 10 4 Hz showing local minima near 5×10, 5×10 2 and 5×10 3 Hz, which are indicative of the resonant collective motion of many atoms, where E 0 is the static Young’s modulus. E ( ε t ,10 2 Hz) increases showing saturation with increasing ε t . Qualitatively, the outlines of E (10 −6 , f ) and E ( ε t ,10 2 Hz) observed for a-Zr 60 Cu 30 Al 10 are similar to those reported for various a-alloys. Quantitatively, a change in E ( ε t ,10 2 Hz) for a-Zr 60 Cu 30 Al 10 is smallest among that reported for various a-alloys, presumably reflecting that the crystallization volume, (Δ V / V ) x , is smallest for a-Zr 60 Cu 30 Al 10 . The effective charge number, Z ∗ , estimated from the change in E (10 −6 ,10 2 Hz) due to PEC is 3.0×10 5 , which is comparable with Z ∗ reported for various a-alloys. We surmise that the number of atoms in the collective motions excited near 10 2 Hz is similar among various a-alloys. The E (10 −6 , f ) data suggest that the spatial sizes of the density fluctuations may show a distribution.

Elastic vibrations of spheroidal nanometric particles

Particles of nanometric size show low-frequency vibrational modes that can be observed byRaman spectroscopy. These modes involve the collective motion of large numbersof atoms and it is possible to calculate their frequency using elasticity theory.In this work a simple model for oblate-shaped nanoparticles is developed andcompared with experimental results obtained in bismuth nanoparticles. It is foundthat the agreement between theory and experiment is improved in comparison tothe spherical model usually employed. However for the smallest particles theelastic model is no longer valid and lattice discreteness has to be considered.

Collective atomic motion in an optical lattice formed inside a high finesse cavity.

We report on collective nonlinear dynamics in an optical lattice formed inside a high finesse ring cavity in a so far unexplored regime, where the light shift per photon times the number of trapped atoms exceeds the cavity resonance linewidth. We observe bistability and self-induced squeezing oscillations resulting from the retroaction of the atoms upon the optical potential wells. We can well understand most of our observations within a simplified model assuming adiabaticity of the atomic motion. Nonadiabatic aspects of the atomic motion are reproduced by solving the complete system of coupled nonlinear equations of motion.