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This paper develops a homogenization approach, based on the introduction of exact local and integral moments, to investigate the temporal evolution of effective dispersion properties of point-sized and finite-sized particles in periodic media. The proposed method represents a robust and computationally efficient continuous approach, alternative to stochastic dynamic simulations. As a case study, the exact moment method is applied to analyze transient dispersion properties of point-sized and finite-sized particles in sinusoidal tubes under the action of a pressure-driven Stokes flow. The sinusoidal structure of the tube wall induces a significant variation of the axial velocity component along the axial coordinate. This strongly influences the transient behavior of the effective axial velocity V z (t) and of the dispersivity D z (t) , both exhibiting wide and persistent temporal oscillations, even for a steady (not-pulsating) Stokes flow. For a pointwise injection of solute particles on the symmetry axis, many interesting features appear: negative values of the dispersion coefficient D z (t) , values of D z (t) larger than the asymptotic value D z (∞) , and anomalous temporal scaling of the axial variance of the particle distribution. All these peculiar features found a physical and theoretical explanation by adopting simple transport models accounting for the axial and radial variation of the axial velocity field and its interaction with molecular diffusion. [ABSTRACT FROM AUTHOR]

Attractive colloidal glasses are unique as their dynamical arrest is a combination of entropic crowding effects and energetic bonds formation. When such systems are subjected to flow, their dynamics are activated in a way which differs from hard-sphere glasses that melt through a "convective cage release mechanism." Here, we investigate the microscopic dynamics by measuring the relaxation spectrum during flow using orthogonal superposition rheometry. A small amplitude oscillatory strain is imposed perpendicularly to a steady shear flow, and superposition moduli are measured. Brownian dynamic simulations are utilized complementary to extract the moduli from mean-squared displacements using the generalized Stokes–Einstein relation. At low Péclet number, a crossover frequency between elastic and viscous moduli is detected, representing the relaxation time associated with shear-induced particles escape from their frustration (localization) under flow. For the repulsive glass, this is related to shear-induced cage renewal of particles. For attractive glasses, however, when particles escape their localized length (bonds), they move with no further hindrance with the escape time, which is independent of attraction strength and interestingly faster than that in the repulsive glass. This is attributed to particle localization at shorter length scales due to bonding. At high Péclet, a second low frequency crossover is observed and a low frequency elastic dominated response emerges. This elastic response may originate from slow relaxation of hydroclusters or be a consequence of more intricate nature of superposition moduli. At high frequencies, both orthogonal moduli increase relative to quiescent state due to shear-induced cage deformation, which slows down in-cage dynamics. [ABSTRACT FROM AUTHOR]

Molecular dynamic (MD) simulations were used to study threshold displacement energy (TDE) surface and Si displacement cascades in 4H-SiC system. To figure out the role of different Wyckoff sites in determining the TDE values, both Si and C atoms in 2a and 2b Wyckoff sites were separately considered as the primary knocked atoms (PKA). The initial kinetic energy was then distributed along 146 different crystallographic directions at 10 K. TDE surface appeared highly anisotropic for Si and C displacements along different crystallographic directions. The TDE was determined as 41 eV for Si and 16 eV for C. The average values of TDE over two Wyckoff sites were estimated to 66 eV for Si PKA and 24 eV for C PKA. The displacement cascades produced by Si recoils of energies spanning varied from 5 keV to 50 keV at 300 K. To count the number of point defects using Voronoi cell analysis method, the crystal structure of 4H–SiC was transformed from hexagonal to orthorhombic. It was found that the surviving defects at the end of cascades were dominated by C vacancies and interstitials due to low displacement energies of C atoms and greater number of C interstitials when compared to C vacancies. [ABSTRACT FROM AUTHOR]

Through molecular dynamic simulations, a system for investigating the contributions of elastic deformation energy and thermal activation effects to friction has been constructed. In this system, a graphene flake slides on a suspended graphene layer anchored on a bed of springs. The "graphene–spring" system provides a useful ideal approach to model different layers of graphene through changing the stiffness of the springs. The results first indicate that both the friction force and the elastic deformation energy have an exponential dependence on the support stiffness. Second, the observed non-monotonic variation in friction manifested by peaks and plateaus with increasing temperature results from the changing rate of energy dissipation due to the transition of slip regimes. Therefore, we suggest that the friction force emanates from the competition between the interfacial energy barrier and out-of-plane elastic deformation energy, as well as the competition between the thermal activation effects and transition of slip regimes. Therefore, the observation can extend the validity of the Prandtl–Tomlinson model on friction phenomena. Our simulations are intended to provide theoretical guidance when considering the influence of stiffness on the friction between graphene layers in the design of nanodevices. [ABSTRACT FROM AUTHOR]

Molecular dynamics methods are used to investigate the effect of wall wettability and initial fluid density on the nucleation and growth of nanobubbles in a nanochannel with a groove. Surface wettability is controlled by adjusting the parameters of the solid-liquid potential energy and the results show that groove wettability greatly influences the bubble nucleation process. In the case of a groove with a weak solid-liquid interaction, fluid atoms in the groove are strongly affected by repulsive forces attributed to solid atoms, the density of the fluid atoms is low, and atomic collision frequency increases. The local activation energy is concentrated in the groove, resulting in bubble nucleation. In the case of a groove with a stronger solid-liquid interaction, the bubble is formed in the center of the nanochannel. In general, the bubble radius of curvature and contact angle remain unchanged during the growth process in the case of a uniform wettability nanochannel with a groove, while significant changes are observed for a nonuniform wettability nanochannel. The radius of curvature for the generated bubble increases with increasing fluid initial density, while the steady contact angle decreases. [ABSTRACT FROM AUTHOR]

This article shows the capability of using a higher order dynamic mode decomposition (HODMD) algorithm both to identify flow patterns and to extrapolate a transient solution to the attractor region. Numerical simulations are carried out for the three-dimensional flow around a circular cylinder, and both standard dynamic mode decomposition (DMD) and higher order DMD are applied to the nonconverged solution. The good performance of HODMD is proved, showing that this method guesses the converged flow patterns from numerical simulations in the transitional region. The solution obtained can be extrapolated to the attractor region. This fact sheds light on the capability of finding real flow patterns in complex flows and, simultaneously, reducing the computational cost of the numerical simulations or the required quantity of data collected in experiments. [ABSTRACT FROM AUTHOR]

A magnetically driven fast-ion loss detector system for the ASDEX Upgrade tokamak has been designed and will be presented here. The device is feedback controlled to adapt the detector head position to the heat load and physics requirements. Dynamic simulations have been performed taking into account effects such as friction, coil self-induction, and eddy currents. A real time positioning control algorithm to maximize the detector operational window has been developed. This algorithm considers dynamical behavior and mechanical resistance as well as measured and predicted thermal loads. The mechanical design and real time predictive algorithm presented here may be used for other reciprocating systems. [ABSTRACT FROM AUTHOR]

We investigate the phenomenon of delayed yield in reversible colloidal gels via dynamic simulation, with a view toward revealing the microscopic particle dynamics and structural transformations that underlie the rheological behavior before, during, and after yield. Prior experimental studies reveal a pronounced delay period between application of a fixed shear stress and the onset of liquidlike flow, a so-called "delay time." Catastrophic network failure-with sudden, cascading rupture of particle clusters or strands-is the primary model proposed for the structural evolution underlying rheological yield. However, no direct observation of such evolution has been made, owing to the difficulty of obtaining detailed microstructural information during the rapid yield event. Here, we utilize dynamic simulation to examine the microstructural mechanics and rheology of delayed yield. A moderately concentrated dispersion of Brownian hard spheres interacts via a short-range attractive potential of O(kT) that leads to arrested phase separation and the formation of a bicontinuous network of reversibly bonded particles. The linearresponse rheology and coarsening dynamics of this system were characterized in our recent work. In the present study, a step shear stress is imposed on the gel, and its bulk deformation, as well as detailed positions and dynamics of all particles, are monitored over time. Immediately after the stress is imposed, the gel undergoes solidlike creep regardless of the strength of the applied stress. However, a minimum or "critical stress" is required to initiate yield: When the imposed stress is weak compared to the Brownian stress, the gel continues to undergo slow creeping deformation with no transition to liquidlike flow. Under stronger stress, creep is followed by a sudden increase in the strain rate, signaling yield, which then gives way to liquidlike viscous flow. The duration of the creep regime prior to yield is consistent with the delay time identified in prior experimental studies, decreasing monotonically with increasing applied stress. However, when the deformation rate is interrogated as a function of strain (rather than time), we find that a critical strain emerges: Yield occurs at the same extent of deformation regardless of the magnitude of the applied stress. Surprisingly, the gel network can remain fully connected throughout yield, with as few as 0.1% of particle bonds lost during yield, which relieve local glassy frustration and create localized liquidlike regions that enable yield. Brownian motion plays a central role in this behavior: When thermal motion is "frozen out," both the delay time and the critical yield stress increase, showing that Brownian motion facilitates yield. Beyond yield, the long-time behavior depends qualitatively on the strength of the applied stress. In particular, at intermediate stresses, a "re-entrant solid" regime emerges, whereupon a flowing gel resolidifies, owing to flow-enhanced structural coarsening. A nonequilibrium phase diagram is presented that categorizes, and can be used to predict, the ultimate gel fate as a function of imposed stress. We make a connection between these behaviors and the process of ongoing phase separation in arrested colloidal gels. [ABSTRACT FROM AUTHOR]

Large-scale classical molecular dynamics simulations of epitaxial TiN/TiN(001) thin film growth at 1200K are carried out using incident flux ratios N/Ti=1, 2, and 4. The films are analyzed as a function of composition, island size distribution, island edge orientation, and vacancy formation. Results show that N/Ti=1 films are globally understoichiometric with dispersed Ti-rich surface regions which serve as traps to nucleate 111-oriented islands, leading to local epitaxial breakdown. Films grown with N/Ti=2 are approximately stoichiometric and the growth mode is closer to layer-by-layer, while N/Ti=4 films are stoichiometric with N-rich surfaces. As N/Ti is increased from 1 to 4, island edges are increasingly polar, i.e., 110-oriented, and N-terminated to accommodate the excess N flux, some of which is lost by reflection of incident N atoms. N vacancies are produced in the surface layer during film deposition with N/Ti=1 due to the formation and subsequent desorption of N2 molecules composed of a N adatom and a N surface atom, as well as itinerant Ti adatoms pulling up N surface atoms. The N vacancy concentration is significantly reduced as N/Ti is increased to 2; with N/Ti=4, Ti vacancies dominate. Overall, our results show that an insufficient N/Ti ratio leads to surface roughening via nucleation of small dispersed 111 islands, whereas high N/Ti ratios result in surface roughening due to more rapid upper-layer nucleation and mound formation. The growth mode of N/Ti=2 films, which have smoother surfaces, is closer to layer-by-layer. [ABSTRACT FROM AUTHOR]

Impact of energetic nanoparticles on solids produces craters on the surface. We use molecular dynamics simulations to compare crater production on a compact Au solid with that in a porous (foam) target. Our results show a complex picture: (i) At low impact velocities, the nanoparticles produce permanent craters in the foam while they cannot penetrate the compact target. (ii) With increasing velocity and/or projectile mass, the crater depth in the foam target increases less strongly than for the compact target. The plasticity-affected zone in the foam target is of similar size as in the compact target. Our results are relevant for the use of porous structures as shields against nanoparticle impact. [ABSTRACT FROM AUTHOR]

Brownian Dynamics simulations are an important tool for modeling the dynamics of soft matter. However, accurate and rapid computations of the hydrodynamic interactions between suspended, microscopic components in a soft material are a significant computational challenge. Here, we present a new method for Brownian dynamics simulations of suspended colloidal scale particles such as colloids, polymers, surfactants, and proteins subject to a particular and important class of hydrodynamic constraints. The total computational cost of the algorithm is practically linear with the number of particles modeled and can be further optimized when the characteristic mass fractal dimension of the suspended particles is known. Specifically, we consider the so-called “stresslet” constraint for which suspended particles resist local deformation. This acts to produce a symmetric force dipole in the fluid and imparts rigidity to the particles. The presented method is an extension of the recently reported positively split formulation for Ewald summation of the Rotne-Prager-Yamakawa mobility tensor to higher order terms in the hydrodynamic scattering series accounting for force dipoles [A. M. Fiore et al., J. Chem. Phys. 146(12), 124116 (2017)]. The hydrodynamic mobility tensor, which is proportional to the covariance of particle Brownian displacements, is constructed as an Ewald sum in a novel way which guarantees that the real-space and wave-space contributions to the sum are independently symmetric and positive-definite for all possible particle configurations. This property of the Ewald sum is leveraged to rapidly sample the Brownian displacements from a superposition of statistically independent processes with the wave-space and real-space contributions as respective covariances. The cost of computing the Brownian displacements in this way is comparable to the cost of computing the deterministic displacements. The addition of a stresslet constraint to the over-damped particle equations of motion leads to a stochastic differential algebraic equation (SDAE) of index 1, which is integrated forward in time using a mid-point integration scheme that implicitly produces stochastic displacements consistent with the fluctuation-dissipation theorem for the constrained system. Calculations for hard sphere dispersions are illustrated and used to explore the performance of the algorithm. An open source, high-performance implementation on graphics processing units capable of dynamic simulations of millions of particles and integrated with the software package HOOMD-blue is used for benchmarking and made freely available in the supplementary material. [ABSTRACT FROM AUTHOR]

The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002)] for the statically stable structures. [ABSTRACT FROM AUTHOR]

In this paper, we quantitatively investigate with atom probe tomography, the effect of temperature on the interfacial transition layer suboxide species due to the thermal oxidation of silicon. The chemistry at the interface was measured with atomic scale resolution, and the changes in chemistry and intermixing at the interface were identified on a nanometer scale. We find an increase of suboxide (SiOx) concentration relative to SiO2 and increased oxygen ingress with elevated temperatures. Our experimental findings are in agreement with reactive force field molecular dynamics simulations. This work demonstrates the direct comparison between atom probe derived chemical profiles and atomistic-scale simulations for transitional interfacial layer of suboxides as a function of temperature. [ABSTRACT FROM AUTHOR]

We use particle level dynamic simulations, ultrasonic characterization, and rheomicroscopy to investigate the yielding behavior of magnetorheological (MR) fluids under oscillatory shear in both dilute and concentrated regimes. Dilute suspensions exhibit a single peak in the elastic stress that is associated to the breaking of the field-induced structures at the flow point (G' = G"). On the other hand, more concentrated suspensions demonstrate a two-step yielding that is associated to the existence of short-ranged attractions between the particles, possibly coming from remnant magnetization or van der Waals forces. This two-step yielding is demonstrated by introducing additives in the formulation of the MR fluids and performing particle level simulations that include R-shifted Lennard-Jones potentials of interaction. [ABSTRACT FROM AUTHOR]

We study via theory and dynamical simulation the evolving structure, particle dynamics, and time-dependent rheological properties of an aging colloidal gel, with a focus on the micro-mechanics that drive coarsening and age-related changes in linear-response behavior. When colloids in suspension attract one another, the attractions can lead to phase separation into particle-rich and particle-poor regions separated by a single interface. But this transition is sometimes interrupted before full separation occurs. With certain particle concentrations and interparticle potentials, the attractions that promote phase separation also inhibit it, frustrating the separation and "freezing in" a nonequilibrium particle configuration, resulting in a space-spanning gel. With attractions on the order of a few kT, gelation can produce nonfractal bicontinuous morphologies. In such "reversible" gels, thermal fluctuations are strong enough to rupture bonds and reform new ones, allowing restructuring of the gel over time. But, because particle diffusion is dramatically slowed by interparticle attractions, the march toward equilibrium is frustrated. Prior studies of colloidal gels have examined evolution of length scales and dynamics such as decorrelation times or heterogeneity. Left open were additional questions such as how the particle-rich regions are structured (liquidlike, glassy, and crystalline), how restructuring takes place (via bulk diffusion, surface migration, and coalescence of large structures), and the impact of the evolution on rheology. In this study, we conduct dynamic simulations to elucidate the post-gelation evolution of a system of 750 000 Brownian spheres interacting via a hard-sphere repulsion and short-range attractions of order kT, as would be generated by a polymer depletant, for example. We find that the network strands comprise a glassy, immobile interior near random-close packing, enclosed by a liquidlike surface along which the diffusive migration of particles drives coarsening. We show that coarsening is a three-step process of cage forming, cage hopping, and cage arrest, where particles migrate to ever-deeper energy wells via "Smoluchowski's ratchet." Both elastic and viscous high-frequency moduli are found to scale with the square-root of the frequency, similar to the perfectly viscoelastic behavior of nonhydrodynamically interacting, purely repulsive dispersions. But here, the behavior is elastic over all frequencies, with a quantitative offset between elastic and viscous moduli which owes its origin to the hindrance of diffusion by particle attractions. Propagation of this elasticity via the network gives rise to age-stiffening as the gel coarsens. This simple phenomenological model suggests a rescaling of the moduli on network length scale which, when carried out, collapses each modulus for all gel ages onto a single universal curve. A theoretical model inspired by the Rouse model is advanced and, from it, we have obtained an analytical expression that captures the effects of (finite) structural aging on rheology: The moduli are linear in the network size, suggesting that linear mechanical response can be determined at any age by measurement of dominant network length scale--or vice versa. [ABSTRACT FROM AUTHOR]

The translocation process of star polymers through a nanochannel is investigated by dissipative particle dynamics simulations. The translocation process is strongly influenced by the star arm arrangement as the polymer enters the channel, and a scaling relation between the translocation time s and the total number of beads Ntot is obtained. Qualitative agreements are found with predictions of the nucleation and growth model for linear block co-polymer translocation. In the intermediate stage where the center of the star polymer is at the channel entrance, the translocation time is found to have power law-dependence on the number of arms outside the channel and very weakly dependent on the number of arms in the channel. Increasing the total number of star arms also increases the star translocation time. [ABSTRACT FROM AUTHOR]

We examine the accuracy of dissipative particle dynamics (DPD) simulations of polymers in dilute solutions with hydrodynamic interaction (HI), at the theta point, modeled by setting the DPD conservative interaction between beads to zero. We compare the first normal-mode relaxation time extracted from the DPD simulations with theoretical predictions from a normal-mode analysis for theta chains. We characterize the influence of bead inertia within the coil by a ratio Lm/Rg, where Lm is the ballistic distance over which bead inertia is lost, and Rg is the radius of gyration of the polymer coil, while the HI strength per bead h* is determined by the ratio of bead hydrodynamic radius (rH) to the equilibrium spring length. We show how to adjust h* through the spring length and monomer mass, and how to optimize the accuracy of DPD for fixed h* by increasing the friction coefficient (γ≥9) and by incorporating a nonlinear distance dependence into the frictional interaction. Even with this optimization, DPD simulations exhibit deviations of over 20% from the theoretical normal-mode predictions for high HI strength with h*≥0.20, for chains with as many as 100 beads, which is a larger deviation than is found for Stochastic rotation dynamics simulations for similar chains lengths and values of h*. [ABSTRACT FROM AUTHOR]

Electron channeling contrast imaging (ECCI) is used to characterize misfit dislocations in heteroepitaxial layers of GaP grown on Si(100) substrates. Electron channeling patterns serve as a guide to tilt and rotate sample orientation so that imaging can occur under specific diffraction conditions. This leads to the selective contrast of misfit dislocations depending on imaging conditions, confirmed by dynamical simulations, similar to using standard invisibility criteria in transmission electron microscopy (TEM). The onset and evolution of misfit dislocations in GaP films with varying thicknesses (30 to 250 nm) are studied. This application simultaneously reveals interesting information about misfit dislocations in GaP/Si layers and demonstrates a specific measurement for which ECCI is preferable versus traditional plan-view TEM. [ABSTRACT FROM AUTHOR]

The authors wish to retract the referenced publication.[1] In the simulation cases of I i =0.3 and I i =0.4, the temperature control method is incorrect, resulting in flawed simulation results in Figs. 1 L. Zhang, J. Xu, and J. Lei, "Molecular dynamic simulation of bubble nucleation in a nanochannel with a groove", AIP Adv. 9, 035044 (2019).10.1063/1.5081728. [Extracted from the article]

When suspensions containing colloidal particles of two different sizes are coated on substrates to form films by evaporating the host fluids, the smaller particles can segregate to the top surface of the films. We investigate the effects of the evaporation rate on the segregation by use of Langevin dynamics simulations. The evaporation rate is scaled by the Brownian diffusion rate of the particles, yielding a dimensionless number which we define as the particle drying Péclet number. We show that there is a Péclet number at which the segregation is the most enhanced. Our result indicates the need for the regulation of the evaporation rate to control the segregation. [ABSTRACT FROM AUTHOR]