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We introduce methods for large scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and it square root are available for the given boundary conditions. We address a major challenge in large-scale BD simulations, capturing the stochastic drift term that arises because of the configuration-dependent mobility. Unlike the widely-used Fixman midpoint scheme, our methods utilize random finite differences and do not require the solution of resistance problems or the computation of the action of the inverse square root of the RPY mobility matrix. We construct two temporal schemes which are viable for large scale simulations, an Euler-Maruyama traction scheme and a Trapezoidal Slip scheme, which minimize the number of mobility solves per time step while capturing the required stochastic drift terms. We validate and compare these schemes numerically by modeling suspensions of boomerang shaped particles sedimented near a bottom wall. Using the trapezoidal scheme, we investigate the steady-state active motion in a dense suspensions of confined microrollers, whose height above the wall is set by a combination of thermal noise and active flows. We find the existence of two populations of active particles, slower ones closer to the bottom and faster ones above them, and demonstrate that our method provides quantitative accuracy even with relatively coarse resolutions of the particle geometry.
We develop efficient numerical methods for performing many-body Brownian dynamics simulations of a recently-observed fingering instability in an active suspension of colloidal rollers sedimented above a wall [M. Driscoll, B. Delmotte, M. Youssef, S.
We derive an analytic expression for the mechanical pressure of a generic one-dimensional model of confined active Brownian particles (ABPs) that is valid for all values of Peclet number Pe and all confining scenarios. Our model reproduces the known
The systematic errors due to the practical implementation of the Contact Dynamics method for simulation of dense granular media are examined. It is shown that, using the usual iterative solver to simulate a chain of rigid particles, effective elastic
We simulate cluster formation of model colloidal particles interacting via DLVO (Derjaguin, Landau, Vervey, Overbeek) potentials. The interaction potentials can be related to experimental conditions, defined by the pH-value, the salt concentration an
Recent experimental studies have demonstrated that cellular motion can be directed by topographical gradients, such as those resulting from spatial variations in the features of a micropatterned substrate. This phenomenon, known as topotaxis, is espe