Collective Atomic Motion Research Articles

Crystal growth in deeply undercooled Ni50Al50: Signature of the ordering sequence at the interface.

Crystal growth of the intermetallic alloy, Ni50Al50, is investigated by molecular dynamics simulations with two different interatomic potentials. The calculated growth rate can be captured by the Wilson-Frenkel or Broughton-Gilmer-Jackson model at small undercoolings but deviates from the theory at deep undercoolings. Failure of the theory is found to be correlated with the dynamic processes that emerged at the interface, but not apparently with the static interface structure. The chemical segregation of Ni and Al atoms occurs before the geometrical ordering upon crystallization at small undercoolings. In contrast, the geometrical ordering precedes the chemical one at deep undercoolings. These two ordering processes show a collapsed time evolution at the crossover temperature consistent with the onset of the theoretical deviation. We rationalize the delayed chemical segregation behavior by the collective atomic motion, which is characterized by the super-Arrhenius transition of the temperature-dependent diffusivity and structural relaxation time at the crossover point.

Relaxation dynamics of Pd–Ni–P metallic glass: decoupling of anelastic and viscous processes

The stress relaxation dynamics of metallic glass Pd40Ni40P20 was studied in both supercooled liquid and glassy states. Time-temperature superposition was found in the metastable liquid, implying an invariant shape of the distribution of times involved in the relaxation. Once in the glass state, the distribution of relaxation times broadens as temperature and fictive temperature decrease, eventually leading to a decoupling of the relaxation in two processes. While the slow one keeps a viscous behavior, the fast one shows an anelastic nature and a time scale similar to that of the collective atomic motion measured by x-ray photon correlation spectroscopy (XPCS). These results suggest that the atomic dynamics of metallic glasses, as determined by XPCS at low temperatures in the glass state, can be related to the rearrangements of particles responsible of the macroscopically reversible anelastic behavior.

Kinetic singularities at transition points from equilibrium to metastable states of the Lennard-Jones particle system

The equilibrium and metastable states of the Lennard-Jones vapor, liquid, and crystal, are studied in the vicinity of the phase transition points. Vapor-liquid, liquid-vapor, liquid-crystal, and crystal-liquid transitions are modeled within the molecular dynamics method. As a research tool, a four-point correlation function is used for the qualitative detection of collective motions of atoms in the equilibrium and metastable states. We use its modification, a correlation coefficient, and find singularities at the transition from equilibrium to metastable states. The nature of these changes, as precursors of nucleation, is discussed.

Structure and dynamics of the Lennard-Jones fcc-solid focusing on melting precursors

The Lennard-Jones potential is taken as a basis to study the structure and dynamics of the face centered cubic (fcc) solid along an isochore from low temperatures up to the solid/fluid transition. The Z method is applied to estimate the melting point. Molecular dynamics simulations are used to calculate the pair distribution function, numbers of nearest neighbors, and the translational order parameter, analyzing the weakening of the fcc-symmetry due to emerging premelting effects. A range of dynamic properties, such as the mean-squared displacement, non-Gaussian parameter, Debye-Waller factor, and vibrational density of states, is considered for the analysis of the solid state. All of these parameters clearly show that bulk mobility is activated at about 2/3 of the melting temperature, known as the Tammann temperature. This indicates that vibrational motion of atoms is not maintained exclusively in the entire stable solid state and that collective atomic motion constitutes a precursor of the melting process.

Wave-Vector Dependence of the Dynamics in Supercooled Metallic Liquids.

We present a detailed investigation of the wave-vector dependence of collective atomic motion in Au_{49}Cu_{26.9}Si_{16.3}Ag_{5.5}Pd_{2.3} and Pd_{42.5}Cu_{27}Ni_{9.5}P_{21} supercooled liquids close to the glass transition temperature. Using x-ray photon correlation spectroscopy in a previously uncovered spatial range of only a few interatomic distances, we show that the microscopic structural relaxation process mimics the structure and presents a marked slowing down at the main average interparticle distance. This behavior is accompanied by dramatic changes in the shape of the intermediate scattering functions, which suggest the presence of large dynamical heterogeneities at length scales corresponding to a few particle diameters. Aballisticlike mechanism of particle motion seems to govern the structural relaxation of the two systems in the highly viscous phase, likely associated with hopping of caged particles in agreement with theoretical studies.

Regular and chaotic behavior of collective atomic motion in two-component Bose-Einstein condensates

We theoretically study binary Bose-Einstein condensates trapped in a single-well harmonic potential to probe the dynamics of collective atomic motion. The idea is to choose tunable scattering lengths through Feshbach resonances such that the ground-state wave function for two types of the condensates are spatially immiscible where one of the condensates, located at the center of the potential trap, can be effectively treated as a potential barrier between bilateral condensates of the second type of atoms. In the case of small wave function overlap between bilateral condensates, one can parametrize their spatial part of the wave functions in the two-mode approximation together with the time-dependent population imbalance $z$ and the phase difference $\phi$ between two wave functions. The condensate in the middle can be approximated by a Gaussian wave function with the displacement of the condensate center $\xi$. As driven by the time-dependent displacement of the central condensate, we find the Josephson oscillations of the collective atomic motion between bilateral condensates as well as their anharmonic generalization of macroscopic self-trapping effects. In addition, with the increase in the wave function overlap of bilateral condensates by properly choosing tunable atomic scattering lengths, the chaotic oscillations are found if the system departs from the state of a fixed point. The Melnikov approach with a homoclinic solution of the derived $z,\,\phi$, and $\xi$ equations can successfully justify the existence of chaos. All results are consistent with the numerical solutions of the full time-dependent Gross-Pitaevskii equations.

Diffuse X-ray scattering from correlated motions in a protein crystal

Protein dynamics are integral to biological function, yet few techniques are sensitive to collective atomic motions. A long-standing goal of X-ray crystallography has been to combine structural information from Bragg diffraction with dynamic information contained in the diffuse scattering background. However, the origin of macromolecular diffuse scattering has been poorly understood, limiting its applicability. We present a finely sampled diffuse scattering map from triclinic lysozyme with unprecedented accuracy and detail, clearly resolving both the inter- and intramolecular correlations. These correlations are studied theoretically using both all-atom molecular dynamics and simple vibrational models. Although lattice dynamics reproduce most of the diffuse pattern, protein internal dynamics, which include hinge-bending motions, are needed to explain the short-ranged correlations revealed by Patterson analysis. These insights lay the groundwork for animating crystal structures with biochemically relevant motions.

Quantum-Enhanced Velocimetry with Doppler-Broadened Atomic Vapor.

Traditionally, measuring the center-of-mass (c.m.) velocity of an atomic ensemble relies on measuring the Doppler shift of the absorption spectrum of single atoms in the ensemble. Mapping out the velocity distribution of the ensemble is indispensable when determining the c.m. velocity using this technique. As a result, highly sensitive measurements require preparation of an ensemble with a narrow Doppler width. Here, we use a dispersive measurement of light passing through a moving room temperature atomic vapor cell to determine the velocity of the cell in a single shot with a short-term sensitivity of 5.5 μm s^{-1} Hz^{-1/2}. The dispersion of the medium is enhanced by creating quantum interference through an auxiliary transition for the probe light under electromagnetically induced transparency condition. In contrast to measurement of single atoms, this method is based on the collective motion of atoms and can sense the c.m. velocity of an ensemble without knowing its velocity distribution. Our results improve the previous measurements by 3 orders of magnitude and can be used to design a compact motional sensor based on thermal atoms.

Collective Motion of Atoms in a Superheated Crystal and a Supercooled Melt of a Simple Metal

Stable and metastable states of a crystal and a melt have been studied near the equilibrium crystal–melt phase transition point using a four-point correlation coefficient previously proposed to reveal collective motions of atoms in a liquid. The embedded copper atom model has been considered as an example with the molecular dynamics method. Strong hysteresis of the correlation coefficient values is detected along the paths of isochoric superheating of the crystal until its melting near the spinodal and the inverse supercooling of the melt to its crystallization. The capabilities of this coefficient for a quantitative estimate of the character of the near-range order, the degree of correlation of the motion of neighboring atoms, and the radius of action of dynamic collective effects in condensed matter are revealed.

EF-X in Silico - Modeling Protein Dynamics in an Electric Field

Protein functions result from local and collective atomic motions that span a wide range of time scales. An integrated analysis of experimental and simulation data can shed light on the detailed mechanism of these motions. Applying a high electric field to protein crystals enables conformational changes that can be captured by time-resolved X-ray crystallography. Such an experiment (referred to as EF-X) carried out on a human PDZ domain obtained a series of atomistic “snapshots” of ensemble averages protein dynamics at 50 to 100 ns time intervals. Here, we present a molecular dynamics (MD) study of the same system and provide a detailed picture of the protein dynamics in between the experimental “snapshots”. We replicated the experimental conditions and system geometry in the presence and absence of an electric field. By constructing a model of the protein crystal as a 3x3x3 supercell with a total of 108 individual proteins, we achieved extensive sampling of the protein conformational ensemble at the sub-millisecond time scale. A number of techniques, including principal component analysis and strain analysis, were utilized to quantify the effects of the electric field on the protein structure and crystal symmetry. This study demonstrates how MD simulations can complement information obtained in EF-X experiments by providing the higher spatial and temporal resolution of underlying dynamical processes.

Molecular dynamics simulation of migration behavior of FCC-BCC atomic terrace-step phase boundary in iron-based alloy

The martensitic transformation between the high-temperature face-centered cubic (FCC) phase and the low-temperature body-centered cubic (BCC) phase in iron-based alloys has been studied for years, which plays a critical role in controlling microstructures and hence properties of the alloys. Generally, the BCC structure martensitic phase forms from the FCC parent phase, involving a collective motions of atoms over a distance less than the interatomic distance in the vicinity of the interphase boundary. Thus the structure of interphase boundary separating the FCC and BCC phases is the key characteristics to quantitatively understanding the mechanism and kinetics of martensitic transformation. Due to the difficulty in observing the atomic motions taking place at a velocity as high as the speed of sound, the experimental investigation on the migration of FCC/BCC interphase boundary during the transformation is as yet limited. Noteworthily, molecular dynamics (MD) simulation has been applied to studying the martensitic transformation, in particular for investigating the mobility of the FCC/BCC interphase boundary in iron. However, in most of the MD studies the atomistically planar interfaces of {111}<sub>FCC</sub> // {110}<sub>BCC</sub> are considered as the initial configuration of the interphase boundary between FCC and BCC phases, which is in contradiction to the high-resolution TEM observations. In fact, the FCC/BCC interphase boundary, which is known as the macroscopic habit plane, is a semi-coherent interface consisting of several steps and terrace planes on an atomic scale. In the present work, the atomic configuration of a terrace-step FCC/BCC interphase boundary of iron is built in terms of the topological model. The MD simulation is conducted to clarify the mechanism of interphase boundary migration in the FCC-to-BCC transformation. The results show that the FCC/BCC boundary migrates along its normal at the expense of FCC phase as a result of the lateral motions of the transformation dislocations. Meanwhile, the interphase boundary maintains the stable terrace-step structure during the transformation. Further examinations reveal that the transformation dislocations move steadily at a velocity as high as (2.8 ± 0.2) × 10<sup>3</sup> m/s, affecting the migration of the interphase boundary with a constant velocity of about (4.4 ± 0.3) × 10<sup>2</sup> m/s. The effective migration velocity of FCC/BCC interface exhibits dynamic properties consistent with the characteristic features commonly observed in a displacive martensitic transformation. Additionally, the motion of transformation dislocations gives rise to the macroscopic shape strain composed of a shear component <inline-formula><tex-math id="M3">\begin{document}$ {\varGamma _{{\rm{yz}}}} = 0.349$\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="13-20191903_M3.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="13-20191903_M3.png"/></alternatives></inline-formula> parallel to the boundary and a dilatation <inline-formula><tex-math id="M4">\begin{document}$ {\varGamma _{{\rm{zz}}}} = 0.053$\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="13-20191903_M4.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="13-20191903_M4.png"/></alternatives></inline-formula> normal to the boundary in the MD simulation, which is close to the crystallographic calculations by the topological model.

Experimental Protein Molecular Dynamics: Broadband Dielectric Spectroscopy coupled with nanoconfinement

Protein dynamics covers multiple spatiotemporal scale processes, among which slow motions, not much understood even though they are underlying protein folding and protein functions. Protein slow motions are associated with structural heterogeneity, short-lived and poorly populated conformations, hard to detect individually. In addition, they involve collective motions of many atoms, not easily tracked by simulation and experimental devices. Here we propose a biophysical approach, coupling geometrical nanoconfinement and broadband dielectric spectroscopy (BDS), which distinguishes protein conformations by their respective molecular dynamics. In particular, protein-unfolding intermediates, usually poorly populated in macroscopic solutions are detected. The protein dynamics is observed under unusual conditions (sample nanoconfinement and dehydration) highlighting the robustness of protein structure and protein dynamics to a variety of conditions consistent with protein sustainability. The protein dielectric signals evolve with the temperature of thermal treatments indicating sensitivity to atomic and molecular interaction changes triggered by the protein thermal unfolding. As dipole fluctuations depend on both collective large-scale motions and local motions, the approach offers a prospect to track in-depth unfolding events.

Temperature dependence of grain boundary excess free volume

Grain boundary energy and mobility are strongly correlated with the grain boundary excess free volume, whose dependence on temperature has yet to be investigated. Using molecular dynamics simulations on face-centered-cubic and body-centered-cubic metals, we found that the boundary free volume decreases with temperature, diminishing the interatomic bond distortion and the grain boundary energy per atom. Interestingly, the free volume shrinks much faster above a critical temperature; meanwhile, the activation energy for grain boundary migration jumps due to collective atomic motion. These insights on the temperature dependence of grain boundary free volume can be instrumental in stabilizing the microstructure of nanocrystals.

Condensation of ground state from a supercooled phase in the Si(111)-(4 × 1) → (8 × 2)-indium atomic wire system.

Strong optical irradiation of indium atomic wires on a Si(111) surface causes the nonthermal structural transition from the (8 × 2) reconstructed ground state to an excited (4 × 1) state. The immediate recovery of the system to the ground state is hindered by an energy barrier for the collective motion of the indium atoms along the reaction coordinate from the (4 × 1) to the (8 × 2) state. This metastable, supercooled state can only recover through nucleation of the ground state at defects like adsorbates or step edges. Subsequently, a recovery front propagates with constant velocity across the surface and the (8 × 2) ground state is reinstated. In a combined femtosecond electron diffraction and photoelectron emission microscopy study, we determined—based on the step morphology—a velocity of this recovery front of ∼100 m/s.

Singularity at the Point of Transition from Equilibrium to Metastable States of a Metallic Melt

Equilibrium and metastable states of a liquid are studied near the liquid-crystal phase transition point in a metallic melt using a time-dependent four-point correlation function. This function was proposed earlier for revealing the collective atomic motion in equilibrium liquids. The characteristic changes in the behavior of liquid when it passes to the region of metastability are found. At the quantitative level, such changes manifest themselves in the specific features of the four-point correlation function in the region of crossover from the equilibrium to metastable state arising on isochoric cooling. As specific examples, the embedded atom models for copper and nickel are considered using the method of molecular dynamics.

Ultrafast Pathways of the Photoinduced Insulator-Metal Transition in a Low-Dimensional Organic Conductor.

Among functional organic materials, low-dimensional molecular crystals represent an intriguing class of solids due to their tunable electronic, magnetic, and structural ground states. This work investigates Cu(Me,Br-dicyanoquinonediimine)2 single crystals, a charge transfer radical ion salt which exhibits a Peierls insulator-to-metal transition at low temperatures. The ultrafast electron diffraction experiments observe collective atomic motions at the photoinduced phase transition with a temporal resolution of 1 ps. These measurements reveal the photoinduced lifting of the insulating phase to happen within 2 ps in the entire crystal volume with an external quantum efficiency of conduction band electrons per absorbed photon of larger than 20. This huge cooperativity of the system, directly monitored during the phase transition, is accompanied by specific intramolecular motions. However, only an additional internal volume expansion, corresponding to a pressure relief, allows the metallic state for long times to be optically locked. The identification of the microscopic molecular pathways that optically drive the structural Peierls transition in Cu(DCNQI)2 highlights the tailored response to external stimuli available in these complex functional materials, a feature enabling high-speed optical sensing and switching with outstanding signal responsivity.

Dynamics of the Formation and Propagation of Nanobands with Elastic Lattice Distortion in Nickel Crystallites

The formation and propagation of localized nanobands with elastic lattice distortion in nickel crystallites have been studied within the molecular dynamics framework. Such nanobands are formed due to the presence of regions with tensile and compressive stresses on the free surface. The nanoband propagation region is characterized by a collective vortex motion of atoms. The effect of different-type grain boundaries on nanoband propagation was investigated. It was shown that grain boundaries do not significantly affect the reorientation angle in the nanoband, but the nanoband propagation direction changes after crossing a grain boundary in accordance with the different crystallographic orientation of grains.

Atomic scale insight into the effects of Aluminum doped Sb2Te for phase change memory application

To date, the unpleasant trade-off between crystallization speed and thermal stability for most phase change materials is detrimental to achieve phase change memory (PCM) with both features of high-speed and good-retention. However, it is proved that Al doping in Sb2Te, served as storage media in PCM, favors both a high writing speed (6 ns) and a good retention (103 °C), as well as a low power consumption. Judging by experimental and theoretical investigations, doped Al atoms prefer to replace Sb in Sb2Te lattice, strongly bonded with 6 Te atoms, to form a homogeneous phase. While in amorphous Al doped Sb2Te (AST), Al atoms are in tetrahedral environment, firmly bonded with four Sb/Te atoms. The strong bonding in Al centered tetrahedron in amorphous AST can obstruct the collective motion of Sb atoms near the matrix boundary, leading to the improvement in thermal stability and the confinement in grain size.

Direct Experimental Characterization of Contributions from Self-Motion of Hydrogen and from Interatomic Motion of Heavy Atoms to Protein Anharmonicity

One fundamental challenge in biophysics is to understand the connection between protein dynamics and its function. Part of the difficulty arises from the fact that proteins often present local atomic motions and collective dynamics on the same time scales, and challenge the experimental identification and quantification of different dynamic modes. Here, by taking lyophilized proteins as the example, we combined deuteration technique and neutron scattering to separate and characterize the self-motion of hydrogen and the collective interatomic motion of heavy atoms (C, O, N) in proteins on the pico-to-nanosecond time scales. We found that hydrogen atoms present an instrument-resolution-dependent onset for anharmonic motions, which can be ascribed to the thermal activation of local side-group motions. However, the protein heavy atoms exhibit an instrument-resolution-independent anharmonicity around 200 K, which results from unfreezing of the relaxation of the protein structures on the laboratory equilibrium time (100-1000 s), softening of the entire bio-macromolecules.

Theoretical description of collective atomic motion in liquid metals describes coupling modes

A theoretical framework explains the existence of an observed mode between the longitudinal and transverse collective wave dynamics as an indirect coupling mechanism.