Transport coefficients of a mesoscopic fluid dynamics model

Two-dimensional fluctuating vesicles in linear shear flow

The stochastic motion of a two-dimensional vesicle in linear shear flow is studied at finite temperature. In the limit of small deformations from a circle, Langevin-type equations of motion are derived, which are highly nonlinear due to the constraint of constant perimeter length. These equations are solved in the low-temperature limit and using a mean-field approach, in which the length constraint is satisfied only on average. The constraint imposes non-trivial correlations between the lowest deformation modes at low temperature. We also simulate a vesicle in a hydrodynamic solvent by using the multi-particle collision dynamics technique, both in the quasi-circular regime and for larger deformations, and compare the stationary deformation correlation functions and the time autocorrelation functions with theoretical predictions. Good agreement between theory and simulations is obtained.

Ejection dynamics of polymeric chains from viral capsids: effect of solvent quality

We present simulations investigating the effects of solvent quality on the dynamics of flexible (RNA-like) and semiflexible (DNA-like) polymers ejecting from spherical viral capsids. We find that the mean ejection time increases and the ejection time distributions are broadened as the solvent quality decreases. Our results thus suggest that DNA ejection may be very efficiently controlled by tuning the salt concentration in the environment, in agreement with recent experimental findings. We also observe random pauses in the ejection. These become extremely long for semiflexible polymers at lower solvent quality, and we interpret this as a signature of a low driving force for ejection. We find that, for most polymers, ejection is an all-or-nothing process at the solvent conditions we investigated: polymers normally completely eject once the process is initiated.

Interplay between hydrodynamic and Brownian fluctuations in sedimenting colloidal suspensions

We apply a hybrid molecular dynamics and mesoscopic simulation technique to study the steady-state sedimentation of hard sphere particles for Peclet number (Pe) ranging from 0.08 to 12. Hydrodynamic backflow causes a reduction of the average sedimentation velocity relative to the Stokes velocity. We find that this effect is independent of Pe number. Velocity fluctuations show the expected effects of thermal fluctuations at short correlation times. At longer times, nonequilibrium hydrodynamic fluctuations are visible, and their character appears to be independent of the thermal fluctuations. The hydrodynamic fluctuations dominate the diffusive behavior even for modest Pe number, while conversely the short-time fluctuations are dominated by thermal effects for surprisingly large Pe numbers. Inspired by recent experiments, we also study finite sedimentation in a horizontal planar slit. In our simulations distinct lateral patterns emerge, in agreement with observations in the experiments.

Relevance of angular momentum conservation in mesoscale hydrodynamics simulations

The angular momentum is conserved in fluids with a few exceptions such as ferrofluids. However, it can be violated locally in fluid simulations to reduce computational costs. The effects of this violation are investigated using a particle-based simulation method, multiparticle collision dynamics, which can switch on or off angular-momentum conservation. To this end, we study circular Couette flows between concentric and eccentric cylinders, where nonphysical torques due to the lack of the angular-momentum conservation are found whereas the velocity field is not affected. In addition, in simulations of fluids with different viscosities in contact and star polymers in solvent, incorrect angular velocities occur. These results quantitatively agree with the theoretical predictions based on the macroscopic stress tensor.

Hydrodynamic screening of star polymers in shear flow

The mutual effects of the conformations of a star polymer in simple shear flow and the deformation of the solvent flow field are investigated by a hybrid mesoscale simulation technique. We characterize the flow field near the star polymer as a function of its functionality (arm number) f . A strong screening of the imposed flow is found inside the star polymer, which increases with increasing f . To elucidate the importance of hydrodynamic screening, we compare results for hydrodynamic and random solvents. The dependence of the polymer orientation angle on the Weissenberg number shows a power law behavior with super-universal exponent --independent of hydrodynamic and excluded-volume interactions. In contrast, the polymer rotation frequency changes qualitatively when hydrodynamic interactions are switched on.

Chemically powered nanodimers

Self-propelled motion of a chemically powered nanodimer is discussed. The nanodimer comprises two linked spheres, one of which has equal interactions with A and B solvent species but catalyzes the reaction A-->B. The other sphere is not chemically active but interacts differently with the two species. The nonequilibrium concentration gradient generated at the catalytic end, in conjunction with the force difference at the noncatalytic end, leads to directed motion. The model mimics features of experimentally studied synthetic nanorod motion. Particle-based simulations and analytical estimates of the velocity provide insight into the nature of nanomotor directed motion.

Simulation of DNA motion in a microchannel using stochastic rotation dynamics

The authors propose a method to simulate the DNA motion in microchannels of complex geometry. It is based on stochastic rotation dynamics using a new scheme for the boundary condition. The method enables them to define a boundary wall of arbitrary shape and to describe a wall moving at an arbitrary velocity. As an application, they simulate the motion of DNA in Poiseuille flow between two parallel planes and show that DNA molecules tend to concentrate near the center of the channel in agreement with experimental results.

Dynamics of polymer packaging

We use the stochastic rotation dynamics algorithm to investigate the packaging of flexible and semiflexible polymers into a capsid that is permeable to solvent molecules. The model takes into account hydrodynamic interactions arising due to local flow. The flexible chain maintains a random configuration as it is being fed into the capsid, in contrast to the semiflexible chain, whose configuration is initially spool-like, becoming more random at high packing. We measure the packing rate, which is found to decrease with the percentage of the chain packed and highlight the difference between the flexible and semiflexible chains. Reflecting experiments, we find pauses in the packing process for individual chains as the motor loses grip of the fluctuating beads. We also find that hydrodynamics is important, in that the packaging rate is faster when flow is included.

Shear thinning in dilute polymer solutions

We use bead-spring models for a polymer coupled to a solvent described by multiparticle collision dynamics to investigate shear thinning effects in dilute polymer solutions. First, we consider the polymer motion and configuration in a shear flow. For flexible polymer models we find a sharp increase in the polymer radius of gyration and the fluctuations in the radius of gyration at a Weissenberg number approximately 1. We then consider the polymer viscosity and the effect of solvent quality, excluded volume, hydrodynamic coupling between the beads, and finite extensibility of the polymer bonds. We conclude that the excluded volume effect is the major cause of shear thinning in polymer solutions. Comparing the behavior of semiflexible chains, we find that the fluctuations in the radius of gyration are suppressed when compared to the flexible case. The shear thinning is greater and, as the rigidity is increased, the viscosity measurements tend to those for a multibead rod.

Dynamic correlations in stochastic rotation dynamics

The dynamic structure factor, vorticity and entropy density dynamic correlation functions are measured for stochastic rotation dynamics (SRD), a particle based algorithm for fluctuating fluids. This allows us to obtain unbiased values for the longitudinal transport coefficients such as thermal diffusivity and bulk viscosity. The results are in good agreement with earlier numerical and theoretical results, and it is shown for the first time that the bulk viscosity is indeed zero for this algorithm. In addition, corrections to the self-diffusion coefficient and shear viscosity arising from the breakdown of the molecular chaos approximation at small mean free paths are analyzed. In addition to deriving the form of the leading correlation corrections to these transport coefficients, the probabilities that two and three particles remain collision partners for consecutive time steps are derived analytically in the limit of small mean free path. The results of this paper verify that we have an excellent understanding of the SRD algorithm at the kinetic level and that analytic expressions for the transport coefficients derived elsewhere do indeed provide a very accurate description of the SRD fluid.

Dynamics of vesicle self-assembly and dissolution

The dynamics of membranes is studied on the basis of a particle-based meshless surface model, which was introduced earlier [Phys. Rev. E 73, 021903 (2006)]. The model describes fluid membranes with bending energy and-in the case of membranes with boundaries-line tension. The effects of hydrodynamic interactions are investigated by comparing Brownian dynamics with a particle-based mesoscale solvent simulation (multiparticle collision dynamics). Particles self-assemble into vesicles via disk-shaped membrane patches. The time evolution of assembly is found to consist of three steps: particle assembly into discoidal clusters, aggregation of clusters into larger membrane patches, and finally vesicle formation. The time dependence of the cluster distribution and the mean cluster size is evaluated and compared with the predictions of Smoluchowski rate equations. On the other hand, when the line tension is suddenly decreased (or the temperature is increased), vesicles dissolve via pore formation in the membrane. Hydrodynamic interactions are found to speed up the dynamics in both cases. Furthermore, hydrodynamics makes vesicle more spherical in the membrane-closure process.

Dissipative particle dynamics simulation of flow generated by two rotating concentric cylinders: boundary conditions

The dissipative particle dynamics (DPD) method was used to simulate the flow in a system comprised of a fluid occupying the space between two cylinders rotating with equal angular velocities. The fluid, initially at rest, ultimately reaches a steady, linear velocity distribution (a rigid-body rotation). Since the induced flow field is solely associated with the no-slip boundary condition at the walls, we employed this system as a benchmark to examine the effect of bounce-back reflections, specular reflections, and Pivkin-Karniadakis no-slip boundary conditions, upon the steady-state velocity, density, and temperature distributions. An additional advantage of the foregoing system is that the fluid occupies inherently a finite bounded domain so that the results are affected by the prescribed no-slip boundary conditions only. Past benchmark systems such as Couette flow between two infinite parallel plates or Poiseuille flow in an infinitely long cylinder must employ artificial periodic boundary conditions at arbitrary upstream and downstream locations, a possible source of spurious effects. In addition, the effect of the foregoing boundary conditions on the time evolution of the simulated velocity profile was compared with that of the known, time-dependent analytical solution. It was shown that bounce-back reflection yields the best results for the velocity distributions with small fluctuations in density and temperature at the inner fluid domain and larger deviations near the walls. For the unsteady solutions a good fit is obtained if the DPD friction coefficient is proportional to the kinematic viscosity. Based on dimensional analysis and the numerical results a universal correlation is suggested between the friction coefficient and the kinematic viscosity.

Hydrodynamic interactions and Brownian forces in colloidal suspensions: coarse-graining over time and length scales

We describe in detail how to implement a coarse-grained hybrid molecular dynamics and stochastic rotation dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The importance of carefully tuning the simulation parameters to correctly resolve the multiple time and length scales of this problem is emphasized. We systematically analyze how our coarse-graining scheme resolves dimensionless hydrodynamic numbers such as the Reynolds number Re, which indicates the importance of inertial effects, the Schmidt number Sc, which indicates whether momentum transport is liquidlike or gaslike, the Mach number, which measures compressibility effects, the Knudsen number, which describes the importance of noncontinuum molecular effects, and the Peclet number, which describes the relative effects of convective and diffusive transport. With these dimensionless numbers in the correct regime the many Brownian and hydrodynamic time scales can be telescoped together to maximize computational efficiency while still correctly resolving the physically relevant processes. We also show how to control a number of numerical artifacts, such as finite-size effects and solvent-induced attractive depletion interactions. When all these considerations are properly taken into account, the measured colloidal velocity autocorrelation functions and related self-diffusion and friction coefficients compare quantitatively with theoretical calculations. By contrast, these calculations demonstrate that, notwithstanding its seductive simplicity, the basic Langevin equation does a remarkably poor job of capturing the decay rate of the velocity autocorrelation function in the colloidal regime, strongly underestimating it at short times and strongly overestimating it at long times. Finally, we discuss in detail how to map the parameters of our method onto physical systems and from this extract more general lessons-keeping in mind that there is no such thing as a free lunch-that may be relevant for other coarse-graining schemes such as lattice Boltzmann or dissipative particle dynamics.

Mesoscopic description of solvent effects on polymer dynamics

Solvent effects on polymer dynamics and structure are investigated using a mesoscopic solvent model that accounts for hydrodynamic interactions among the polymer beads. The simulation method combines molecular dynamics of the polymer chain, interacting with the solvent molecules through intermolecular forces, with mesoscopic multiparticle collision dynamics for the solvent molecules. Changes in the intermolecular forces between the polymer beads and mesoscopic solvent molecules are used to vary the solvent conditions from those for good to poor solvents. Polymer collapse and expansion dynamics following changes in solvent conditions are studied for homopolymer and block copolymer solutions. The frictional properties of polymers are also investigated.

Polymer packaging and ejection in viral capsids: shape matters

We use a mesoscale simulation approach to explore the impact of different capsid geometries on the packaging and ejection dynamics of polymers of different flexibility. We find that both packing and ejection times are faster for flexible polymers. For such polymers a sphere packs more quickly and ejects more slowly than an ellipsoid. For semiflexible polymers, however, the case relevant to DNA, a sphere both packs and ejects more easily. We interpret our results by considering both the thermodynamics and the relaxational dynamics of the polymers. The predictions could be tested with biomimetic experiments with synthetic polymers inside artificial vesicles. Our results suggest that phages may have evolved to be roughly spherical in shape to optimize the speed of genome ejection, which is the first stage in infection.

Star polymers in shear flow

Linear and star polymers in solution are studied in the presence of shear flow. The solvent is described by a particle-based mesoscopic simulation technique, which accounts for hydrodynamic interactions. The scaling properties of the average gyration tensor, the orientation angle, and the rotation frequency are investigated for various arm lengths and arm numbers. With increasing functionality f, star polymers exhibit a crossover in their flow properties from those of linear polymers to a novel behavior, which resembles the tank-treading motion of elastic capsules.

Polymer translocation: The effect of backflow

We investigate the effect of backflow on the translocation dynamics of short, flexible polymer chains threading through a small hole in a wall. We find that hydrodynamic interactions between polymer beads play an important role in determining the translocation time distribution: as a monomer moves through the hole it sets up a flow field which transfers momentum to neighboring monomers, thus helping them to move in the same direction. Translocation times are calculated by using the velocity-Verlet algorithm to solve the equations of motion of a polymer which moves in a fluid described by the stochastic rotation algorithm, a particle-based Navier-Stokes solver.

Dynamics of polymers in a particle-based mesoscopic solvent

We study the dynamics of flexible polymer chains in solution by combining multiparticle-collision dynamics (MPCD), a mesoscale simulation method, and molecular-dynamics simulations. Polymers with and without excluded-volume interactions are considered. With an appropriate choice of the collision time step for the MPCD solvent, hydrodynamic interactions build up properly. For the center-of-mass diffusion coefficient, scaling with respect to polymer length is found to hold already for rather short chains. The center-of-mass velocity autocorrelation function displays a long-time tail which decays algebraically as (Dt)(-3/2) as a function of time t, where D is the diffusion coefficient. The analysis of the intramolecular dynamics in terms of Rouse modes yields excellent agreement between simulation data and results of the Zimm model for the mode-number dependence of the mode-amplitude correlation functions.

Equilibrium calculation of transport coefficients for a fluid-particle model

A recently introduced particle-based model for fluid flow, called stochastic rotation dynamics, can be made Galilean invariant by introducing a random shift of the computational grid before collisions. In this paper, it is shown how the Green-Kubo relations derived previously can be resummed to obtain exact expressions for the collisional contributions to the transport coefficients. It is also shown that the collisional contribution to the microscopic stress tensor is not symmetric, and that this leads to an additional viscosity. The resulting identification of the transport coefficients for the hydrodynamic modes is discussed in detail, and it is shown that this does not impose restrictions on the applicability of the model. The collisional contribution to the thermal conductivity, which becomes important for small mean free path and small average particle number per cell, is also derived.

Shape transitions of fluid vesicles and red blood cells in capillary flows

The dynamics of fluid vesicles and red blood cells (RBCs) in cylindrical capillary flow is studied by using a three-dimensional mesoscopic simulation approach. As flow velocity increases, a model RBC is found to transit from a nonaxisymmetric discocyteto an axisymmetric parachute shape (coaxial with the flow axis), while a fluid vesicle is found to transit from a discocyte to a prolate ellipsoid. Both shape transitions reduce the flow resistance. The critical velocities of the shape transitions are linearly dependent on the bending rigidity and on the shear modulus of the membrane. Slipper-like shapes of the RBC model are observed around the transition velocities. Our results are in good agreement with experiments on RBCs.

Dynamics of fluid vesicles in shear flow: effect of membrane viscosity and thermal fluctuations

The dynamical behavior of vesicles is investigated in simple shear flow. A simulation technique is presented that combines a three-dimensional particle-based mesoscopic model (multiparticle collision dynamics) for the solvent with a dynamically triangulated surface model for the membrane. In this model, thermal fluctuations of the solvent and of the membrane are consistently taken into account. The membrane viscosity can be varied by changing the bond-flip rate of the dynamically triangulated surface. Vesicles are found to transit from steady tank-treading to unsteady tumbling motion with increasing membrane viscosity. At small reduced volumes, the shear induces a transformation from a discocyte to a prolate shape at low membrane viscosity. On the other hand, at high membrane viscosity, the shear induces a transformation from prolate to discocyte, or tumbling motion accompanied by shape oscillations between these two states. Thermal fluctuations induce intermittent tumbling and smooth out the transitions. This effect can be understood from a simplified stochastic model.

Dynamic regimes of fluids simulated by multiparticle-collision dynamics

We investigate the hydrodynamic properties of a fluid simulated with a mesoscopic solvent model. Two distinct regimes are identified, the "particle regime" in which the dynamics is gaslike and the "collective regime" where the dynamics is fluidlike. This behavior can be characterized by the Schmidt number, which measures the ratio between viscous and diffusive transport. Analytical expressions for the tracer diffusion coefficient, which have been derived on the basis of a molecular-chaos assumption, are found to describe the simulation data very well in the particle regime, but important deviations are found in the collective regime. These deviations are due to hydrodynamic correlations. The model is then extended in order to investigate self-diffusion in colloidal dispersions. We study first the transport properties of heavy pointlike particles in the mesoscopic solvent, as a function of their mass and number density. Second, we introduce excluded-volume interactions among the colloidal particles and determine the dependence of the diffusion coefficient on the colloidal volume fraction for different solvent mean-free paths. In the collective regime, the results are found to be in good agreement with previous theoretical predictions based on Stokes hydrodynamics and the Smoluchowski equation.

Simulation of claylike colloids

We investigate the properties of dense suspensions and sediments of small spherical silt particles by means of a combined molecular dynamics and stochastic rotation dynamics (SRD) simulation. We include van der Waals and effective electrostatic interactions between the colloidal particles, as well as Brownian motion and hydrodynamic interactions which are calculated in the SRD part. We present the simulation technique and first results. We have measured velocity distributions, diffusion coefficients, sedimentation velocity, spatial correlation functions, and we have explored the phase diagram depending on the parameters of the potentials and on the volume fraction.

Kinetics of the polymer collapse transition: the role of hydrodynamics

We investigate numerically the dynamical behavior of a polymer chain collapsing in a dilute solution. The rate of collapse is measured with and without the presence of hydrodynamic interactions. We find that hydrodynamic interactions accelerate polymer collapse. We present a scaling theory describing the physical process responsible for the collapse kinetics. Predicted collapse times in a hydrodynamic (tauH approximately N(4/3)) and a Brownian heat bath (tauB approximately N2) agree well with the numerical results (tauH approximately N(1.40+/-0.08) and tauB approximately N(1.89+/-0.09)) where N denotes chain length. The folding kinetics of Go models of proteins is also examined. We show that for these systems, where many free energy minima compete, hydrodynamics has little effect on the kinetics.

Combining molecular dynamics with Lattice Boltzmann: A hybrid method for the simulation of (charged) colloidal systems

We present a hybrid method for the simulation of colloidal systems that combines molecular dynamics (MD) with the Lattice Boltzmann (LB) scheme. The LB method is used as a model for the solvent in order to take into account the hydrodynamic mass and momentum transport through the solvent. The colloidal particles are propagated via MD and they are coupled to the LB fluid by viscous forces. With respect to the LB fluid, the colloids are represented by uniformly distributed points on a sphere. Each such point [with a velocity V(r) at any off-lattice position r] is interacting with the neighboring eight LB nodes by a frictional force F = xi0(V(r)-u(r)), with xi0 being a friction coefficient and u(r) being the velocity of the fluid at the position r. Thermal fluctuations are introduced in the framework of fluctuating hydrodynamics. This coupling scheme has been proposed recently for polymer systems by Ahlrichs and Dunweg [J. Chem. Phys. 111, 8225 (1999)]. We investigate several properties of a single colloidal particle in a LB fluid, namely, the effective Stokes friction and long-time tails in the autocorrelation functions for the translational and rotational velocity. Moreover, a charged colloidal system is considered consisting of a macroion, counterions, and coions that are coupled to a LB fluid. We study the behavior of the ions in a constant electric field. In particular, an estimate of the effective charge of the macroion is yielded from the number of counterions that move with the macroion in the direction of the electric field.

Modeling a tethered polymer in Poiseuille flow

We investigate the behavior of a tethered polymer in Poiseuille flow using a multiscale algorithm. The polymer, treated using molecular dynamics, is coupled to a solvent modeled by the stochastic rotation algorithm, a particle-based Navier-Stokes integrator. The expected series of morphological transitions of the polymer: sphere to distorted sphere to trumpet to stem and flower to rod are recovered, and we discuss how the polymer extension depends on the flow velocity. Backflow effects cause an effective increase in viscosity, which appears to be primarily due to the fluctuations of the free end of the polymer.

Poiseuille flow to measure the viscosity of particle model fluids

The most important property of a fluid is its viscosity, it determines the flow properties. If one simulates a fluid using a particle model, calculating the viscosity accurately is difficult because it is a collective property. In this article we describe a new method that has a better signal to noise ratio than existing methods. It is based on using periodic boundary conditions to simulate counter-flowing Poiseuille flows without the use of explicit boundaries. The viscosity is then related to the mean flow velocity of the two flows. We apply the method to two quite different systems. First, a simple generic fluid model, dissipative particle dynamics, for which accurate values of the viscosity are needed to characterize the model fluid. Second, the more realistic Lennard-Jones fluid. In both cases the values we calculated are consistent with previous work but, for a given simulation time, they are more accurate than those obtained with other methods.

Kinetic Theory Derivation of the Transport Coefficients of Stochastic Rotation Dynamics

We use a kinetic theory approach to derive the continuum Navier-Stokes and heat conduction equations for stochastic rotation dynamics, a particle based algorithm for simulating a fluid. Hence we obtain expressions for the viscosity and thermal conductivity in two and three dimensions. The predictions are tested numerically and good agreement is found.

Fluid vesicles with viscous membranes in shear flow

The effect of membrane viscosity on the dynamics of vesicles in shear flow is studied. We present a new simulation technique, which combines three-dimensional multiparticle collision dynamics for the solvent with a dynamically triangulated membrane model. Vesicles are found to transit from steady tank treading to unsteady tumbling motion with increasing membrane viscosity. Depending on the reduced volume and membrane viscosity, shear can induce both discocyte-to-prolate and prolate-to-discocyte transformations. This behavior can be understood from a simplified model.

Hydrodynamic and brownian fluctuations in sedimenting suspensions

We use a mesoscopic computer simulation method to study the interplay between hydrodynamic and Brownian fluctuations during steady-state sedimentation of hard sphere particles for Peclet numbers (Pe) ranging from 0.1-15. Even when the hydrodynamic interactions are an order of magnitude weaker than Brownian forces, they still induce backflow effects that dominate the reduction of the average sedimentation velocity with increasing particle packing fraction. Velocity fluctuations, on the other hand, begin to show nonequilibrium hydrodynamic character for Pe>1.

Resummed Green-Kubo relations for a fluctuating fluid-particle model

A recently introduced stochastic model for fluid flow can be made Galilean invariant by introducing a random shift of the computational grid before collisions. This grid shifting procedure accelerates momentum transfer between cells and leads to a collisional contribution to transport coefficients. By resumming the Green-Kubo relations derived in a previous paper, it is shown that this collisional contribution to the transport coefficients can be determined exactly. The resummed Green-Kubo relations also show that there are no mixed kinetic-collisional contributions to the transport coefficients. The leading correlation corrections to the transport coefficients are discussed, and explicit expressions for the transport coefficients are presented and compared with simulation data.

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.