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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 [F. Balboa Usabiaga et al., Commun. Appl. Math. Comput. Sci. 11(2), 217-296 (2016)] 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 its "square" root are available for the given boundary conditions. These kernel operations can be computed with near linear scaling for periodic domains using the positively split Ewald method. Here we study particles partially confined by gravity above a noslip bottom wall using a graphical processing unit implementation of the mobility matrix-vector product, combined with a preconditioned Lanczos iteration for generating Brownian displacements. 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 problems to be solved 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 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. [ABSTRACT FROM AUTHOR]

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. Sacanna, A. Donev, and P. Chaikin, Nat. Phys. (2016), preprint arXiv:1609.08673.We present a stochastic Adams-Bashforth integrator for the equations of Brownian dynamics, which has the same cost but is more accurate than the widely used Euler-Maruyama scheme, and use a random finite difference to capture the stochastic drift proportional to the divergence of the configuration-dependent mobility matrix. We generate the Brownian increments using a Krylov method and show that for particles confined to remain in the vicinity of a no-slip wall by gravity or active flows, the number of iterations is independent of the number of particles. Our numerical experiments with active rollers show that the thermal fluctuations set the characteristic height of the colloids above the wall, both in the initial condition and the subsequent evolution dominated by active flows. The characteristic height in turn controls the time scale and wavelength for the development of the fingering instability. [ABSTRACT FROM AUTHOR]

We formulate and study computationally the fluctuating compressible Navier-Stokes equations for reactive multi-species fluid mixtures. We contrast two different expressions for the covariance of the stochastic chemical production rate in the Langevin formulation of stochastic chemistry, and compare both of them to predictions of the chemical master equation for homogeneous well-mixed systems close to and far from thermodynamic equilibrium. We develop a numerical scheme for inhomogeneous reactive flows, based on our previous methods for non-reactive mixtures [Balakrishnan, Phys. Rev. E 89, 013017 (2014)]. We study the suppression of non-equilibrium long-ranged correlations of concentration fluctuations by chemical reactions, as well as the enhancement of pattern formation by spontaneous fluctuations. Good agreement with available theory demonstrates that the formulation is robust and a useful tool in the study of fluctuations in reactive multi-species fluids. At the same time, several problems with Langevin formulations of stochastic chemistry are identified, suggesting that future work should examine combining Langevin and master equation descriptions of hydrodynamic and chemical fluctuations. [ABSTRACT FROM AUTHOR]

We present a finite element discretization of a non-linear diffusion equation used in the field of critical phenomena and, more recently, in the context of dynamic density functional theory. The discretized equation preserves the structure of the continuum equation. Specifically, it conserves the total number of particles and fulfills an H-theorem as the original partial differential equation. The discretization proposed suggests a particular definition of the discrete hydrodynamic variables in microscopic terms. These variables are then used to obtain, with the theory of coarse-graining, their dynamic equations for both averages and fluctuations. The hydrodynamic variables defined in this way lead to microscopically derived hydrodynamic equations that have a natural interpretation in terms of discretization of continuum equations. Also, the theory of coarse-graining allows to discuss the introduction of thermal fluctuations in a physically sensible way. The methodology proposed for the introduction of thermal fluctuations in finite element methods is general and valid for both regular and irregular grids in arbitrary dimensions. We focus here on simulations of the Ginzburg-Landau free energy functional using both regular and irregular 1D grids. Convergence of the numerical results is obtained for the static and dynamic structure factors as the resolution of the grid is increased. [ABSTRACT FROM AUTHOR]

We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, "Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps," Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior.We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions.We find that, for an incompressible fluid and in the absence of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, "A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law," J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions. [ABSTRACT FROM AUTHOR]

We develop a Fluctuating Immersed Boundary (FIB) method for performing Brownian dynamics simulations of confined particle suspensions. Unlike traditional methods which employ analytical Green's functions for Stokes flow in the confined geometry, the FIB method uses a fluctuating finitevolume Stokes solver to generate the action of the response functions "on the fly." Importantly, we demonstrate that both the deterministic terms necessary to capture the hydrodynamic interactions among the suspended particles, as well as the stochastic terms necessary to generate the hydrodynamically correlated Brownian motion, can be generated by solving the steady Stokes equations numerically only once per time step. This is accomplished by including a stochastic contribution to the stress tensor in the fluid equations consistent with fluctuating hydrodynamics. We develop novel temporal integrators that account for the multiplicative nature of the noise in the equations of Brownian dynamics and the strong dependence of the mobility on the configuration for confined systems. Notably, we propose a random finite difference approach to approximating the stochastic drift proportional to the divergence of the configuration-dependent mobility matrix. Through comparisons with analytical and existing computational results, we numerically demonstrate the ability of the FIB method to accurately capture both the static (equilibrium) and dynamic properties of interacting particles in flow. [ABSTRACT FROM AUTHOR]

We develop an immersed boundary approach to modeling reaction-diffusion processes in dispersions of reactive spherical particles, from the diffusion-limited to the reaction-limited setting. We represent each reactive particle with a minimally-resolved 'blob' using many fewer degrees of freedom per particle than standard discretization approaches. More complicated or more highly resolved particle shapes can be built out of a collection of reactive blobs. We demonstrate numerically that the blob model can provide an accurate representation at low to moderate packing densities of the reactive particles, at a cost not much larger than solving a Poisson equation in the same domain. Unlike multipole expansion methods, our method does not require analytically computed Green's functions, but rather, computes regularized discrete Green's functions on the fly by using a standard grid-based discretization of the Poisson equation. This allows for great flexibility in implementing different boundary conditions, coupling to fluid flow or thermal transport, and the inclusion of other effects such as temporal evolution and even nonlinearities. We develop multigrid-based preconditioners for solving the linear systems that arise when using implicit temporal discretizations or studying steady states. In the diffusion-limited case the resulting linear system is a saddle-point problem, the efficient solution of which remains a challenge for suspensions of many particles. We validate our method by comparing to published results on reaction-diffusion in ordered and disordered suspensions of reactive spheres. [ABSTRACT FROM AUTHOR]

The Stokes-Einstein relation for the self-diffusion coefficient of a spherical particle suspended in an incompressible fluid is an asymptotic result in the limit of large Schmidt number, that is, when momentum diffuses much faster than the particle. When the Schmidt number is moderate, which happens in most particle methods for hydrodynamics, deviations from the Stokes-Einstein prediction are expected. We study these corrections computationally using a recently developed minimally resolved method for coupling particles to an incompressible fluctuating fluid in both two and three dimensions. We find that for moderate Schmidt numbers the diffusion coefficient is reduced relative to the Stokes-Einstein prediction by an amount inversely proportional to the Schmidt number in both two and three dimensions. We find, however, that the Einstein formula is obeyed at all Schmidt numbers, consistent with linear response theory. The mismatch arises because thermal fluctuations affect the drag coefficient for a particle due to the nonlinear nature of the fluid-particle coupling. The numerical data are in good agreement with an approximate self-consistent theory, which can be used to estimate finite-Schmidt number corrections in a variety of methods. Our results indicate that the corrections to the Stokes-Einstein formula come primarily from the fact that the particle itself diffuses together with the momentum. Our study separates effects coming from corrections to no-slip hydrodynamics from those of finite separation of time scales, allowing for a better understanding of widely observed deviations from the Stokes-Einstein prediction in particle methods such as molecular dynamics. [ABSTRACT FROM AUTHOR]

To overcome the reversible nature of low-Reynolds-number flow, a variety of biomimetic microrobotic propulsion schemes and devices capable of rapid transport have been developed. However, these approaches have been typically optimized for a specific function or environment and do not have the flexibility that many real organisms exhibit to thrive in complex microenvironments. Here, inspired by adaptable microbes and using a combination of experiment and simulation, we demonstrate that one-dimensional colloidal chains can fold into geometrically complex morphologies, including helices, plectonemes, lassos, and coils, and translate via multiple mechanisms that can be varied with applied magnetic field. With chains of multiblock asymmetry, the propulsion mode can be switched from bulk to surface-enabled, mimicking the swimming of microorganisms such as flagella-rotating bacteria and tail-whipping sperm and the surface-enabled motion of arching and stretching inchworms and sidewinding snakes. We also demonstrate that reconfigurability enables navigation through three-dimensional and narrow channels simulating capillary blood vessels. Our results show that flexible microdevices based on simple chains can transform both shape and motility under varying magnetic fields, a capability we expect will be particularly beneficial in complex in vivo microenvironments. [ABSTRACT FROM AUTHOR]

We study the cyclic dynamics of a single polymer tethered to a hard wall in shear flow using Brownian dynamics, the lattice Boltzmann method, and a recent stochastic event-driven molecular dynamics algorithm. We focus on the dynamics of the free end (last bead) of the tethered chain and we examine the cross-correlation function and power spectral density of the chain extensions in the flow and gradient directions as a function of chain length N and dimensionless shear rate Wi. Extensive simulation results suggest a classical fluctuation-dissipation stochastic process and question the existence of periodicity of the cyclic dynamics, as previously claimed. We support our numerical findings with a simple analytical calculation for a harmonic dimer in shear flow. [ABSTRACT FROM AUTHOR]

We study the thermodynamics of a binary hard-disk mixture in which the ratio of disk diameters is κ=1.4. We use a recently developed molecular dynamics algorithm to calculate the free-volume entropy of glassy configurations and obtain the configurational entropy (degeneracy) of the supercompressed liquid as a function of density. We find that the configurational entropy of the glasses near the kinetic glass transition is very close to the mixing entropy, suggesting that the degeneracy is zero only for the phase-separated crystal. We explicitly construct an exponential number of jammed packings with densities spanning the spectrum from the accepted “amorphous” glassy state to the phase-separated crystal, thus showing that there is no ideal glass transition in binary hard-disk mixtures. This construction also demonstrates that the ideal glass, defined as having zero configurational entropy, is not amorphous, but instead is nothing more than a phase-separated crystal. This critique of the presumed existence of an ideal glass parallels our previous critique of the idea that there is a most-dense random (close) packing for hard spheres [Torquato et al., Phys. Rev. Lett. 84, 2064 (2000)]. We also perform free-energy calculations to determine the equilibrium phase behavior of the system. The calculations predict a first-order freezing transition at a density below the kinetic glass transition. However, this transition appears to be strongly kinetically suppressed and is not observed directly. New simulation techniques are needed in order to gain a more complete understanding of the thermodynamic and kinetic behavior of the binary disk mixture and, in particular, of the demixing process during crystallization. [ABSTRACT FROM AUTHOR]

Hard-particle packings have provided a rich source of outstanding theoretical problems and served as useful starting points to model the structure of granular media, liquids, living cells, glasses, and random media. The nature of “jammed” hard-particle packings is a current subject of keen interest. Elsewhere, we introduced rigorous and efficient linear-programming algorithms to assess whether a hard-sphere packing is locally, collectively, or strictly jammed, as defined by Torquato and Stillinger [J. Phys. Chem. B 105, 11849 (2001)]. One algorithm applies to ideal packings in which particles form perfect contacts. Another algorithm treats the case of jamming in packings with significant interparticle gaps. We have applied these algorithms to test jamming categories of ordered lattices as well as random packings of circular disks and spheres under periodic boundary conditions. The random packings were produced computationally with a variety of packing generation algorithms, all of which should, in principle, produce at least collectively jammed packings. Our results highlight the importance of jamming categories in characterizing particle packings. One important and interesting conclusion is that the amorphous monodisperse sphere packings with density φ≈0.64 were for practical purposes strictly jammed in three dimensions, but in two dimensions the monodisperse disk packings at previously reported “random close packed” densities of φ≈0.83 were not even collectively jammed. On the other hand, amorphous bidisperse disk packings with density of φ≈0.84 were virtually strictly jammed. This clearly demonstrates one cannot judge “stability” in packings based solely on local criteria. Numerous interactive visualization models are provided on the authors’ webpage.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]