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We present a novel computational framework for the simulation of rigid spherical Janus particle suspensions in Stokes flow. For a wide array of Janus particle types, we show long-range interactions may be resolved using fast, spectrally accurate boundary integral methods. We incorporate this to our rigid body Stokes platform, which resolves hydrodynamic interactions and contact. Our approach features the use of spherical harmonic expansions for spectrally accurate integral operator evaluation, complementarity-based collision resolution, and optimal O (n) scaling with the number of particles when accelerated via fast summation techniques. We demonstrate the versatility of our simulation platform through three test cases involving Janus particle systems prominent in applications: amphiphilic, bipolar electric and phoretic particles. For each test case, we formulate Janus particle interactions in boundary integral form and use our framework to demonstrate examples of self-assembly and complex collective behavior characteristic of these systems. [ABSTRACT FROM AUTHOR]

This paper presents a computational approach for finding the optimal shapes of peristaltic pumps transporting rigid particles in Stokes flow. In particular, we consider shapes that minimize the rate of energy dissipation while pumping a prescribed volume of fluid, number of particles, and/or distance traversed by the particles over a set time period. Our approach relies on a recently developed fast and accurate boundary integral solver for simulating multiphase flows through periodic geometries of arbitrary shapes. In order to fully capitalize on the dimensionality reduction feature of the boundary integral methods, shape sensitivities must ideally involve evaluating the physical variables on the particle or pump boundaries only. We show that this can indeed be accomplished owing to the linearity of Stokes flow. The forward problem solves for the particle motion in a slip-driven pipe flow while the adjoint problems in our construction solve quasi-static Dirichlet boundary value problems backwards in time, retracing the particle evolution. The shape sensitivities simply depend on the solution of one forward and one adjoint (for each shape functional) problems. We validate these analytic shape derivative formulas by comparing against finite-difference based gradients and present several examples showcasing optimal pump shapes under various constraints. [ABSTRACT FROM AUTHOR]

We show that the standard boundary integral operators, defined on the unit sphere, for the Stokes equations diagonalize on a specific set of vector spherical harmonics and provide formulas for their spectra. We also derive analytical expressions for evaluating the operators away from the boundary. When two particle are located close to each other, we use a truncated series expansion to compute the hydrodynamic interaction. On the other hand, we use the standard spectrally accurate quadrature scheme to evaluate smooth integrals on the far-field, and accelerate the resulting discrete sums using the fast multipole method (FMM). We employ this discretization scheme to analyze several boundary integral formulations of interest including those arising in porous media flow, active matter and magneto-hydrodynamics of rigid particles. We provide numerical results verifying the accuracy and scaling of their evaluation. [ABSTRACT FROM AUTHOR]

This paper presents a new boundary integral equation (BIE) method for simulating particulate and multiphase flows through periodic channels of arbitrary smooth shape in two dimensions. The authors consider a particular system--multiple vesicles suspended in a periodic channel of arbitrary shape--to describe the numerical method and test its performance. Rather than relying on the periodic Green's function as classical BIE methods do, the method combines the free-space Green's function with a small auxiliary basis and imposes periodicity as an extra linear condition. As a result, we can exploit existing free-space solver libraries, quadratures, and fast algorithms and handle a large number of vesicles in a geometrically complex channel. Spectral accuracy in space is achieved using the periodic trapezoid rule and product quadratures, while a first-order semi-implicit scheme evolves particles by treating the vesicle-channel interactions explicitly. New constraint-correction formulas are introduced that preserve reduced areas of vesicles, independent of the number of time steps taken. By using two types of fast algorithms--(i) the fast multipole method for the computation of the vesicle-vesicle and the vesicle-channel hydrodynamic interaction, and (ii) a fast direct solver for the BIE on the fixed channel geometry--the computational cost is reduced to O(N) per time step, where N is the spatial discretization size. Moreover, the direct solver inverts the wall BIE operator at t = 0, stores its compressed representation, and applies it at every time step to evolve the vesicle positions, leading to dramatic cost savings compared to classical approaches. Numerical experiments illustrate that a simulation with N = 128;000 can be evolved in less than a minute per time step on a laptop. [ABSTRACT FROM AUTHOR]

We propose numerical algorithms for the simulation of the dynamics of three-dimensional vesicles suspended in viscous Stokesian fluid. Our method is an extension of our previous work (S.K. Veerapaneni et al., 2011) [37] to flows with viscosity contrast. This generalization requires a change in the boundary integral formulation of the solution, in which a double-layer Stokes integral is introduced, and leads to changes in the fluid dynamics due to the viscosity contrast of the vesicles, which can no longer be efficiently resolved with existing algorithms. In this paper we describe the algorithms needed to handle flows with viscosity contrast accurately and efficiently. We show that a globally semi-implicit method does not have any time-step stability constraint for flows with single and multiple vesicles with moderate viscosity contrast and the computational cost per simulation unit time is comparable to or less than that of an explicit scheme. Automatic oversampling adaptation enables us to achieve high accuracy with very low spectral resolution. We conduct numerical experiments to investigate the stability, accuracy, and the computational cost of the algorithms. Overall, our method achieves several orders of magnitude speed-up compared to the standard explicit schemes. [ABSTRACT FROM AUTHOR]

Abstract: We consider numerical algorithms for the simulation of hydrodynamics of two-dimensional vesicles suspended in a viscous Stokesian fluid. The motion of vesicles is governed by the interplay between hydrodynamic and elastic forces. Continuum models of vesicles use a two-phase fluid system with interfacial forces that include tension (to maintain local “surface” inextensibility) and bending. Vesicle flows are challenging to simulate. On the one hand, explicit time-stepping schemes suffer from a severe stability constraint due to the stiffness related to high-order spatial derivatives in the bending term. On the other hand, implicit time-stepping schemes can be expensive because they require the solution of a set of nonlinear equations at each time step. Our method is an extension of the work of Veerapaneni et al. [S.K. Veerapaneni, D. Gueyffier, D. Zorin, G. Biros, A boundary integral method for simulating the dynamics of inextensible vesicles suspended in a viscous fluid in 2D, Journal of Computational Physics 228(7) (2009) 2334–2353], in which a semi-implicit time-marching scheme based on a boundary integral formulation of the Stokes problem for vesicles in an unbounded medium was proposed. In this paper, we consider two important generalizations: (i) confined flows within arbitrary-shaped stationary/moving geometries; and (ii) flows in which the interior (to the vesicle) and exterior fluids have different viscosity. In the rest of the paper, we will refer to this as the “viscosity contrast”. These two problems require solving additional integral equations and cause nontrivial modifications to the previous numerical scheme. Our method does not have severe time-step stability constraints and its computational cost-per-time-step is comparable to that of an explicit scheme. The discretization is pseudo-spectral in space, and multistep BDF in time. We conduct numerical experiments to investigate the stability, accuracy and the computational cost of the algorithm. Overall, our method achieves several orders of magnitude speed-up compared to standard explicit schemes. As a preliminary validation of our scheme, we study the dependence of the inclination angle of a single vesicle in shear flow on the viscosity contrast and the reduced area of the vesicle, the lateral migration of vesicles in shear flow, the dispersion of two vesicles, and the effective viscosity of a dilute suspension of vesicles. [Copyright &y& Elsevier]

We present a new derivation of a boundary integral equation (BIE) for simulating the three-dimensional dynamics of arbitrarily-shaped rigid particles of genus zero immersed in a Stokes fluid, on which are prescribed forces and torques. Our method is based on a single-layer representation and leads to a simple second-kind integral equation. It avoids the use of auxiliary sources within each particle that play a role in some classical formulations. We use a spectrally accurate quadrature scheme to evaluate the corresponding layer potentials, so that only a small number of spatial discretization points per particle are required. The resulting discrete sums are computed in O ( n ) time, where n denotes the number of particles, using the fast multipole method (FMM). The particle positions and orientations are updated by a high-order time-stepping scheme. We illustrate the accuracy, conditioning and scaling of our solvers with several numerical examples. [ABSTRACT FROM AUTHOR]

• Collision resolution by convex quadratic programming. • Scalable and efficient parallel algorithm and implementation. • Accurate second-kind boundary integral formulation. We describe a computational framework for simulating suspensions of rigid particles in Newtonian Stokes flow. One central building block is a collision-resolution algorithm that overcomes the numerical constraints arising from particle collisions. This algorithm extends the well-known complementarity method for non-smooth multi-body dynamics to resolve collisions in dense rigid body suspensions. This approach formulates the collision resolution problem as a linear complementarity problem with geometric 'non-overlapping' constraints imposed at each time-step. It is then reformulated as a constrained quadratic programming problem and the Barzilai-Borwein projected gradient descent method is applied for its solution. This framework is designed to be applicable for any convex particle shape, e.g., spheres and spherocylinders, and applicable to any Stokes mobility solver, including the Rotne-Prager-Yamakawa approximation, Stokesian Dynamics, and PDE solvers (e.g., boundary integral and immersed boundary methods). In particular, this method imposes Newton's Third Law and records the entire contact network. Further, we describe a fast, parallel, and spectrally-accurate boundary integral method tailored for spherical particles, capable of resolving lubrication effects. We show weak and strong parallel scalings up to 8 × 10 4 particles with approximately 4 × 10 7 degrees of freedom on 1792 cores. We demonstrate the versatility of this framework with several examples, including sedimentation of particle clusters, and active matter systems composed of ensembles of particles driven to rotate. [ABSTRACT FROM AUTHOR]

• A spectrally-accurate close evaluation scheme for Stokes boundary integral operators. • Adaptive panel refinement for arbitrarily shaped boundaries. • Graded meshes to treat corners. • Example problems from microfluidic chip design and vascular network flows. We present a fast, high-order accurate and adaptive boundary integral scheme for solving the Stokes equations in complex—possibly nonsmooth—geometries in two dimensions. We apply the panel-based quadratures of Helsing and coworkers to evaluate to high accuracy the weakly-singular, hyper-singular, and super-singular integrals arising in the Nyström discretization, and also the near-singular integrals needed for flow and traction evaluation close to boundaries. The resulting linear system is solved iteratively via calls to a Stokes fast multipole method. We include an automatic algorithm to "panelize" a given geometry, and choose a panel order, which will efficiently approximate the density (and hence solution) to a user-prescribed tolerance. We show that this adaptive panel refinement procedure works well in practice even in the case of complex geometries with large number of corners, or close-to-touching smooth curves. In one example, for instance, a model 2D vascular network with 378 corners required less than 200K discretization points to obtain a 9-digit solution accuracy. [ABSTRACT FROM AUTHOR]