Tracer diffusion in colloidal suspensions under dilute and crowded conditions with hydrodynamic interactions.

We consider tracer diffusion in colloidal suspensions under solid loading conditions, where hydrodynamic interactions play an important role. To this end, we carry out computer simulations based on the hybrid stochastic rotation dynamics-molecular dynamics (SRD-MD) technique. Many details of the simulation method are discussed in detail. In particular, our choices for the SRD-MD parameters and for the different scales are adapted to simulating colloidal suspensions under realistic conditions. Our simulation data are compared with published theoretical, experimental and numerical results and compared to Brownian dynamics simulation data. We demonstrate that our SRD-MD simulations reproduce many features of the hydrodynamics in colloidal fluids under finite loading. In particular, finite-size effects and the diffusive behavior of colloids for a range of volume fractions of the suspension show that hydrodynamic interactions are correctly included within the SRD-MD technique.

Interplay between steps and nonequilibrium effects in surface diffusion for a lattice-gas model of OW(110).

The authors consider the influence of steps and nonequilibrium conditions on surface diffusion in a strongly interacting surface adsorbate system. This problem is addressed through Monte Carlo simulations of a lattice-gas model of OW(110), where steps are described by an additional binding energy EB at the lower step edge positions. Both equilibrium fluctuation and Boltzmann-Matano spreading studies indicate that the role of steps for diffusion across the steps is prominent in the ordered phases at intermediate coverages. The strongest effects are found in the p(2x1) phase, whose periodicity Lp is 2. The collective diffusion then depends on two competing factors: domain growth within the ordered phase, which on a flat surface has two degenerate orientations [p(2x1) and p(1x2)], and the step-induced ordering due to the enhanced binding at the lower step edge position. The latter case favors the p(2x1) phase, in which all adsorption sites right below the step edge are occupied. When these two factors compete, two possible scenarios emerge. First, when the terrace width L does not match the periodicity of the ordered adatom layer (LLp is noninteger), the mismatch gives rise to frustration, which eliminates the effect of steps provided that EB is not exceptionally large. Under these circumstances, the collective diffusion coefficient behaves largely as on a flat surface. Second, however, if the terrace width does match the periodicity of the ordered adatom layer (LLp is an integer), collective diffusion is strongly affected by steps. In this case, the influence of steps is manifested as the disappearance of the major peak associated with the ordered p(2x1) and p(1x2) structures on a flat surface. This effect is particularly strong for narrow terraces, yet it persists up to about L approximately 25Lp for small EB and up to about L approximately 500Lp for EB, which is of the same magnitude as the bare potential of the surface. On real surfaces, similar competition is expected, although the effects are likely to be smaller due to fluctuations in terrace widths. Finally, Boltzmann-Matano spreading simulations indicate that even slight deviations from equilibrium conditions may give rise to transient peaks in the collective diffusion coefficient. These transient structures are due to the interplay between steps and nonequilibrium conditions and emerge at coverages, which do not correspond to the ideal ordered phases.

Dielectrophoresis of nanocolloids: a molecular dynamics study.

Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In this article we present, to our knowledge, the first molecular dynamics simulations of DEP of nanometer-sized colloidal particles. We introduce a simplified model for a polarizable nanoparticle, consisting of a large charged macroion and oppositely charged microions, in an explicit solvent. The model is then used to study DEP motion of the particle at different combinations of temperature and electric field strength. In accord with linear response theory, the particle drift velocities are shown to be proportional to the DEP force. Analysis of the colloid DEP mobility shows a clear time dependence, demonstrating the variation of friction under non-equilibrium. The time dependence of the mobility further results in an apparent weak variation of the DEP displacements with temperature.

Nonequilibrium effects in diffusion of interacting particles on vicinal surfaces.

We study the influence of nonequilibrium conditions on the collective diffusion of interacting particles on vicinal surfaces. To this end, we perform Monte Carlo simulations of a lattice-gas model of an ideal stepped surface, where adatoms have nearest-neighbor attractive or repulsive interactions. Applying the Boltzmann-Matano method to spreading density profiles of the adatoms allows the definition of an effective, time-dependent collective diffusion coefficient D(C) (t)(theta) for all coverages theta. In the case of diffusion across the steps and strong binding at lower step edges we observe three stages in the behavior of the corresponding D(xx,C) (t)(theta). At early times when the adatoms have not yet crossed the steps, D(xx,C) (t)(theta) is influenced by the presence of steps only weakly. At intermediate times, where the adatoms have crossed several steps, there are sharp peaks at coverages theta<1L and theta>1-1L, where L is the terrace width. These peaks are due to different rates of relaxation of the density at successive terraces. At late stages of spreading, these peaks vanish and D(xx,C) (t)(theta) crosses over to its equilibrium value, where for strong step edge binding there is a maximum at theta=1L. In the case of diffusion in direction along the steps the nonequilibrium effects in D(yy,C) (t)(theta) are much weaker, and are apparent only when diffusion along ledges is strongly suppressed or enhanced.

Dynamics and scaling of polymers in a dilute solution: analytical treatment in two and higher dimensions.

We consider the dynamical scaling of a single polymer chain in good solvent. In the case of two-dimensional systems, Shannon and Choy [Phys. Rev. Lett. 79, 1455 (1997)] have suggested that the dynamical scaling for a dilute polymer solution breaks down. Using scaling arguments and analytical calculations based on the Zimm model, we show that the dynamical scaling of a dilute two-dimensional polymer system holds when the relevant dynamical quantities are properly extracted from finite systems. Most important, the polymer diffusion coefficient in two dimensions scales logarithmically with system size, in excellent agreement with our extensive computer simulations. This scaling is the reason for the failure of the previous attempts to resolve the dynamical scaling of dilute two-dimensional polymer systems. In three and higher dimensions our analytic calculations are in agreement with previous results in the literature.

Influence of hydrodynamics on many-particle diffusion in 2D colloidal suspensions.

We study many-particle diffusion in 2D colloidal suspensions with full hydrodynamic interactions through a novel mesoscopic simulation technique. We focus on the behaviour of the effective scaled tracer and collective-diffusion coefficients DT(rho)/D0 and DC(rho)/D0 respectively, where D0 is the single-particle diffusion coefficient, as a function of the density of the colloids rho. At low Schmidt numbers Sc - 1, we find that hydrodynamics has essentially no effect on the behaviour of DT (rho)/D0. At larger Sc, DT (rho)/D0 seems to be enhanced at all densities, although the differences compared to the case without hydrodynamics are rather minor. The collective-diffusion coefficient, on the other hand, is much more strongly coupled to hydrodynamical conservation laws and is distinctly different from the purely dissipative case without hydrodynamic interactions.

Dynamics and scaling of two-dimensional polymers in a dilute solution.

The breakdown of dynamical scaling for a dilute polymer solution in two dimensions has been suggested by Shannon and Choy [Phys. Rev. Lett. 79, 1455 (1997)]. However, we show here through extensive computer simulations that dynamical scaling holds when the relevant dynamical quantities are properly extracted from finite systems. To verify dynamical scaling, we present results based on mesoscopic simulations in two dimensions for a polymer chain in a good solvent with full hydrodynamic interactions. We also present analytical arguments for the size dependence of the diffusion coefficient and find excellent agreement with the present large-scale simulations.

Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions.

We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using the particle-mesh Ewald (PME) technique. All examined truncation distances (1.8-2.5 nm) lead to major effects on the bilayer properties, such as enhanced order of acyl chains together with decreased areas per lipid. The results obtained using PME, on the other hand, are consistent with experiments. These artifacts are interpreted in terms of radial distribution functions g(r) of molecules and molecular groups in the bilayer plane. Pronounced maxima or minima in g(r) appear exactly at the cutoff distance indicating that the truncation gives rise to artificial ordering between the polar phosphatidyl and choline groups of the DPPC molecules. In systems described using PME, such artificial ordering is not present.

Towards better integrators for dissipative particle dynamics simulations

Coarse-grained models that preserve hydrodynamics provide a natural approach to study collective properties of soft-matter systems. Here, we demonstrate that commonly used integration schemes in dissipative particle dynamics give rise to pronounced artifacts in physical quantities such as the compressibility and the diffusion coefficient. We assess the quality of these integration schemes, including variants based on a recently suggested self-consistent approach, and examine their relative performance. Implications of integrator-induced effects are discussed.

Framework for testing random numbers in parallel calculations.

We propose a framework for testing the quality of random numbers in parallel calculations. The key idea is to study cross-correlations between distinct sequences of random numbers via correlations between various diffusing random walkers, each of which is governed by a distinct random number sequence. The asymptotic power-law behavior of the corresponding correlation functions yields exponents, which can be compared with exact theoretical results. Correlations prior to the asymptotic regime can be further investigated by other complementary methods. We demonstrate this approach by three efficient tests, which find correlations in various commonly used pseudorandom number generators. Finally, we discuss some ideas for applying this framework in other contexts.