Non-equilibrium hydrodynamics of a rotating filament

The nonlinear dynamics of an elastic filament that is forced to rotate at its base is studied by hydrodynamic simulation techniques; coupling between stretch, bend, twist elasticity and thermal fluctuations is included. The twirling-overwhirling transition is located and found to be strongly discontinuous. For finite bend and twist persistence length, thermal fluctuations lower the threshold rotational frequency, for infinite persistence length the threshold agrees with previous analytical predictions

Particles held by springs in a linear shear flow exhibit oscillatory motion

The dynamics of small spheres, which are held by linear springs in a low Reynolds number shear flow at neighboring locations is investigated. The flow elongates the beads and the interplay of the shear gradient with the nonlinear behavior of the hydrodynamic interaction among the spheres causes in a large range of parameters a bifurcation to a surprising oscillatory bead motion. The parameter ranges, wherein this bifurcation is either super- or subcritical, are determined.Comment: 4 pages, 5 figure

The Effect of the Third Dimension on Rough Surfaces Formed by Sedimenting Particles in Quasi-Two-Dimensions

The roughness exponent of surfaces obtained by dispersing silica spheres into a quasi-two-dimensional cell is examined. The cell consists of two glass plates separated by a gap, which is comparable in size to the diameter of the beads. Previous work has shown that the quasi-one-dimensional surfaces formed have two distinct roughness exponents in two well-defined length scales, which have a crossover length about 1cm. We have studied the effect of changing the gap between the plates to a limit of about twice the diameter of the beads.Comment: 4 pages, 4 figures, submitted to IJMP

Stick boundary conditions and rotational velocity auto-correlation functions for colloidal particles in a coarse-grained representation of the solvent

We show how to implement stick boundary conditions for a spherical colloid in a solvent that is coarse-grained by the method of stochastic rotation dynamics. This allows us to measure colloidal rotational velocity auto-correlation functions by direct computer simulation. We find quantitative agreement with Enskog theory for short times and with hydrodynamic mode-coupling theory for longer times. For aqueous colloidal suspensions, the Enskog contribution to the rotational friction is larger than the hydrodynamic one when the colloidal radius drops below 35nm.Comment: new version with some minor change

Wetting and particle adsorption in nanoflows

Molecular dynamics simulations are used to study the behavior of closely-fitting spherical and ellipsoidal particles moving through a fluid-filled cylinder at nanometer scales. The particle, the cylinder wall and the fluid solvent are all treated as atomic systems, and special attention is given to the effects of varying the wetting properties of the fluid. Although the modification of the solid-fluid interaction leads to significant changes in the microstructure of the fluid, its transport properties are found to be the same as in bulk. Independently of the shape and relative size of the particle, we find two distinct regimes as a function of the degree of wetting, with a sharp transition between them. In the case of a highly-wetting suspending fluid, the particle moves through the cylinder with an average axial velocity in agreement with that obtained from the solution of the continuum Stokes equations. In contrast, in the case of less-wetting fluids, only the early-time motion of the particle is consistent with continuum dynamics. At later times, the particle is eventually adsorbed onto the wall and subsequently executes an intermittent stick-slip motion.We show that van der Walls forces are the dominant contribution to the particle adsorption phenomenon and that depletion forces are weak enough to allow, in the highly-wetting situation, an initially adsorbed particle to spontaneously desorb

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, the Schmidt number, the Mach number, the Knudsen number, and the Peclet number. The many Brownian and hydrodynamic time-scales can be telescoped together to maximize computational efficiency while still correctly resolving the physically relevant physical 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 auto-correlation 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 auto-correlation 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 that may be relevant for other coarse-graining schemes such as Lattice Boltzmann or Dissipative Particle Dynamics.Comment: 31 pages, 14 figure

Active particles in periodic lattices

Both natural and artificial small-scale swimmers may often self-propel in environments subject to complex geometrical constraints. While most past theoretical work on low-Reynolds number locomotion addressed idealised geometrical situations, not much is known on the motion of swimmers in heterogeneous environments. As a first theoretical model, we investigate numerically the behaviour of a single spherical micro-swimmer located in an infinite, periodic body-centred cubic lattice consisting of rigid inert spheres of the same size as the swimmer. Running a large number of simulations we uncover the phase diagram of possible trajectories as a function of the strength of the swimming actuation and the packing density of the lattice. We then use hydrodynamic theory to rationalise our computational results and show in particular how the far-field nature of the swimmer (pusher vs. puller) governs even the behaviour at high volume fractions

Cluster algebras in algebraic Lie theory

We survey some recent constructions of cluster algebra structures on coordinate rings of unipotent subgroups and unipotent cells of Kac-Moody groups. We also review a quantized version of these results.Comment: Invited survey; to appear in Transformation Group

Simulating (electro)hydrodynamic effects in colloidal dispersions: smoothed profile method

Previously, we have proposed a direct simulation scheme for colloidal dispersions in a Newtonian solvent [Phys.Rev.E 71,036707 (2005)]. An improved formulation called the ``Smoothed Profile (SP) method'' is presented here in which simultaneous time-marching is used for the host fluid and colloids. The SP method is a direct numerical simulation of particulate flows and provides a coupling scheme between the continuum fluid dynamics and rigid-body dynamics through utilization of a smoothed profile for the colloidal particles. Moreover, the improved formulation includes an extension to incorporate multi-component fluids, allowing systems such as charged colloids in electrolyte solutions to be studied. The dynamics of the colloidal dispersions are solved with the same computational cost as required for solving non-particulate flows. Numerical results which assess the hydrodynamic interactions of colloidal dispersions are presented to validate the SP method. The SP method is not restricted to particular constitutive models of the host fluids and can hence be applied to colloidal dispersions in complex fluids